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Sample records for a-proteobacterium rhodobacter sphaeroides

  1. The architecture of Rhodobacter sphaeroides chromatophores.

    Science.gov (United States)

    Scheuring, Simon; Nevo, Reinat; Liu, Lu-Ning; Mangenot, Stéphanie; Charuvi, Dana; Boudier, Thomas; Prima, Valerie; Hubert, Pierre; Sturgis, James N; Reich, Ziv

    2014-08-01

    The chromatophores of Rhodobacter (Rb.) sphaeroides represent a minimal bio-energetic system, which efficiently converts light energy into usable chemical energy. Despite extensive studies, several issues pertaining to the morphology and molecular architecture of this elemental energy conversion system remain controversial or unknown. To tackle these issues, we combined electron microscope tomography, immuno-electron microscopy and atomic force microscopy. We found that the intracellular Rb. sphaeroides chromatophores form a continuous reticulum rather than existing as discrete vesicles. We also found that the cytochrome bc1 complex localizes to fragile chromatophore regions, which most likely constitute the tubular structures that interconnect the vesicles in the reticulum. In contrast, the peripheral light-harvesting complex 2 (LH2) is preferentially hexagonally packed within the convex vesicular regions of the membrane network. Based on these observations, we propose that the bc1 complexes are in the inter-vesicular regions and surrounded by reaction center (RC) core complexes, which in turn are bounded by arrays of peripheral antenna complexes. This arrangement affords rapid cycling of electrons between the core and bc1 complexes while maintaining efficient excitation energy transfer from LH2 domains to the RCs.

  2. Bioremediation of lead contaminated soil with Rhodobacter sphaeroides.

    Science.gov (United States)

    Li, Xiaomin; Peng, Weihua; Jia, Yingying; Lu, Lin; Fan, Wenhong

    2016-08-01

    Bioremediation with microorganisms is a promising technique for heavy metal contaminated soil. Rhodobacter sphaeroides was previously isolated from oil field injection water and used for bioremediation of lead (Pb) contaminated soil in the present study. Based on the investigation of the optimum culturing conditions and the tolerance to Pb, we employed the microorganism for the remediation of Pb contaminated soil simulated at different contamination levels. It was found that the optimum temperature, pH, and inoculum size for R. sphaeroides is 30-35 °C, 7, and 2 × 10(8) mL(-1), respectively. Rhodobacter sphaeroides did not remove the Pb from soil but did change its speciation. During the bioremediation process, more available fractions were transformed to less accessible and inert fractions; in particular, the exchangeable phase was dramatically decreased while the residual phase was substantially increased. A wheat seedling growing experiment showed that Pb phytoavailability was reduced in amended soils. Results inferred that the main mechanism by which R. sphaeroides treats Pb contaminated soil is the precipitation formation of inert compounds, including lead sulfate and lead sulfide. Although the Pb bioremediation efficiency on wheat was not very high (14.78% root and 24.01% in leaf), R. sphaeroides remains a promising alternative for Pb remediation in contaminated soil. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Hydrogen production by Rhodobacter sphaeroides DSM 158 under intense irradiation.

    Science.gov (United States)

    Krujatz, Felix; Härtel, Paul; Helbig, Karsten; Haufe, Nora; Thierfelder, Simone; Bley, Thomas; Weber, Jost

    2015-01-01

    To identify optimal hydrogen production conditions using growing cultures of Rhodobacter sphaeroides DSM 158 the effects of varying the reactor's volumetric power input (0.01-1.4kWm(-3)) and irradiation intensity (5-2500Wm(-2)) were investigated in batch and continuous production modes. Irradiation intensity had a greater effect on hydrogen production than volumetric power input. Hydrogen production and photofermentative biomass formation were maximized by irradiation at 2250Wm(-2) with a volumetric power input of 0.55kWm(-3). The bacterial dry weight (2.64gL(-1)) and rate of hydrogen production (195mLL(-1)h(-1)) achieved under these conditions were greater than any that have previously been reported for batch-mode hydrogen production by R. sphaeroides. Continuous mode experiments (D=0.1h(-1)) yielded a bacterial dry weight, hydrogen production rate, productivity and hydrogen yield of 2.35±0.18gL(-1), 165±6.2mLL(-1)h(-1), 3.96LL(-1)d(-1) and 36.6%, respectively.

  4. SPECTRAL IDENTIFICATION OF THE ELECTROCHROMICALLY ACTIVE CAROTENOIDS OF RHODOBACTER-SPHAEROIDES IN CHROMATOPHORES AND RECONSTITUTED LIPOSOMES

    NARCIS (Netherlands)

    CRIELAARD, W; VANMOURIK, F; VANGRONDELLE, R; KONINGS, WN; HELLINGWERF, KJ

    1992-01-01

    Reaction centers with both light harvesting complexes I and II (B875 and B800/850; i.e., RCLH(I)LH(II) complexes) have been isolated from Rhodobacter sphaeroides. These complexes have been incorporated into liposomes made from lipids purified from Escherichia coli. The electrochromic bandshift of ca

  5. Hydrogen production by co-cultures of Lactobacillus and a photosynthetic bacterium, Rhodobacter sphaeroides RV

    Energy Technology Data Exchange (ETDEWEB)

    Asada, Yasuo; Ishimi, Katsuhiro [Department of General Education, College of Science and Technology, Nihon University, Narashinodai, Chiba 274-8501 (Japan); Tokumoto, Masaru; Aihara, Yasuyuki; Oku, Masayo; Kohno, Hideki [Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, Izumi-cho, Chiba 275-8575 (Japan); Wakayama, Tatsuki; Miyake, Jun [Research Institute for Cell Engineering, National Institute of Advanced Industrial Science and Technology, Nakoji, Amagasaki, Hyogo 661-0974 (Japan); Tomiyama, Masamitsu [Genetic Diversity Department, National Institute of Agrobiological Science, Tsukuba, Ibaraki 305-8602 (Japan)

    2006-09-15

    Hydrogen production with glucose by using co-immobilized cultures of a lactic acid bacterium, Lactobacillus delbrueckii NBRC13953, and a photosynthetic bacterium, Rhodobacter sphaeroides RV, in agar gels was studied. Glucose was converted to hydrogen gas in a yield of 7.1mol of hydrogen per mole of glucose at a maximum under illuminated conditions. (author)

  6. CHARACTERIZATION OF A BINDING PROTEIN-DEPENDENT GLUTAMATE TRANSPORT-SYSTEM OF RHODOBACTER-SPHAEROIDES

    NARCIS (Netherlands)

    Jacobs, M.H J; Driessen, A.J.M.; Konings, W.N

    1995-01-01

    The mechanism of L-glutamate uptake was studied in Rhodobacter sphaeroides. Uptake of L-glutamate is mediated by a high-affinity (K-t of 1.2 mu M), shock-sensitive transport system that is inhibited by vanadate and dependent on the internal pH. From the shock fluid, an L-glutamate-binding protein wa

  7. Characterization of a Binding Protein-Dependent Glutamate Transport System of Rhodobacter sphaeroides

    NARCIS (Netherlands)

    Jacobs, Mariken H.J.; Driessen, Arnold J.M.; Konings, Wil N.

    1995-01-01

    The mechanism of L-glutamate uptake was studied in Rhodobacter sphaeroides. Uptake of L-glutamate is mediated by a high-affinity (Kt of 1.2 µM), shock-sensitive transport system that is inhibited by vanadate and dependent on the internal pH. From the shock fluid, an L-glutamate-binding protein was i

  8. Hydrogen Production by Co-cultures of Rhizopus oryzae and a Photosynthetic Bacterium, Rhodobacter sphaeroides RV

    Science.gov (United States)

    Asada, Yasuo; Ishimi, Katsuhiro; Nagata, Yoko; Wakayama, Tatsuki; Miyake, Jun; Kohno, Hideki

    Hydrogen production with glucose by using co-immobilized cultures of a fungus, Rhizopus oryzae NBRC5384, and a photosynthetic bacterium, Rhodobacter sphaeroides RV, in agar gels was studied. The co-immobilized cultures converted glucose to hydrogen via lactate in a high molar yield of about 8moles of hydrogen per glucose at a maximum under illuminated conditions.

  9. The Rhodobacter sphaeroides flagellar motor is a variable-speed rotor.

    Science.gov (United States)

    Packer, H L; Lawther, H; Armitage, J P

    1997-06-02

    The rotation rate of the unidirectional stop/start motor of Rhodobacter sphaeroides was investigated using computerised motion analysis of tethered cells. The R. sphaeroides motor was found to have a variable rotation rate compared to the virtually constant-speed motor of wild-type and CheR mutant (smooth swimming) Escherichia coli. In addition, the dynamics of the R. sphaeroides motor during stopping was analysed with no consistent correlation behaviour. The motor could go from full rotation to stop, or stop to full rotation within one video frame, i.e. 0.02 s, but it could also slow down into a stop or restart slowly, taking up to 0.25 s. The R. sphaeroides motor under chemokinetic stimulation was also analysed and was found to show increased torque generation and reduced variation in rotation rate.

  10. Color-Sensitive Motility and Methanol Release Responses in Rhodobacter sphaeroides

    OpenAIRE

    Kort, Remco; Crielaard, Wim; Spudich, John L.; Hellingwerf, Klaas J.

    2000-01-01

    Blue-light-induced repellent and demethylation responses, characteristic of behavioral adaptation, were observed in Rhodobacter sphaeroides. They were analyzed by computer-assisted motion analysis and through the release of volatile tritiated compounds from [methyl-3H]methionine-labeled cells, respectively. Increases in the stop frequency and the rate of methanol release were induced by exposure of cells to repellent light signals, such as an increase in blue- and a decrease in infrared-light...

  11. Feasibility of biohydrogen production from tofu wastewater with glutamine auxotrophic mutant of Rhodobacter sphaeroides

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, G.H.; Wang, L.; Kang, Z.H. [School of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, 1239 Siping road, Shanghai 200092 (China)

    2010-12-15

    NH{sub 4}{sup +}, which is normally the integrant in organic wastewater, such as Tofu wastewater, is an inhibitor to hydrogen production by anoxygenic phototrophic bacterium. In order to release inhibition of NH{sub 4}{sup +} to biohydrogen generation by Rhodobacter sphaeroides, a glutamine auxotrophic mutant R. sphaeroides TJ-0803 was obtained by mutagenizing with ethyl methane sulfonate. The mutant could generate biohydrogen efficiently in the medium with high NH{sub 4}{sup +} concentration, because the inhibition of NH{sub 4}{sup +} to nitrogenase was released. Under suitable conditions, TJ-0803 could effectively produce biohydrogen from tofu wastewater, which commonly containing 50-60 mg L{sup -1} NH{sub 4}{sup +}, and the generation rate was increased by more than 100% compared with that from wild-type R. sphaeroides. (author)

  12. Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides

    Energy Technology Data Exchange (ETDEWEB)

    Pena-Castillo, Lourdes; Mercer, Ryan; Gurinovich, Anastasia; Callister, Stephen J.; Wright, Aaron T.; Westbye, Alexander; Beatty, J. T.; Lang, Andrew S.

    2014-08-28

    The genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of two Rhodobacter species, R. capsulatus and R. sphaeroides, have had their genomes fully sequenced and both have been the subject of transcriptional profiling studies. Gene co-expression networks can be used to identify modules of genes with similar expression profiles. Functional analysis of gene modules can then associate co-expressed genes with biological pathways, and network statistics can determine the degree of module preservation in related networks. In this paper, we constructed an R. capsulatus gene co-expression network, performed functional analysis of identified gene modules, and investigated preservation of these modules in R. capsulatus proteomics data and in R. sphaeroides transcriptomics data. Results: The analysis identified 40 gene co-expression modules in R. capsulatus. Investigation of the module gene contents and expression profiles revealed patterns that were validated based on previous studies supporting the biological relevance of these modules. We identified two R. capsulatus gene modules preserved in the protein abundance data. We also identified several gene modules preserved between both Rhodobacter species, which indicate that these cellular processes are conserved between the species and are candidates for functional information transfer between species. Many gene modules were non-preserved, providing insight into processes that differentiate the two species. In addition, using Local Network Similarity (LNS), a recently proposed metric for expression divergence, we assessed the expression conservation of between-species pairs of orthologs, and within-species gene-protein expression profiles. Conclusions: Our analyses provide new sources of information for functional annotation in R. capsulatus because uncharacterized genes in modules are now connected with groups of genes that constitute a joint functional

  13. Isolation, Identification of Bacillus Thuringiensis/Cereus and Its Enhancement on Protein Wastewater Treatment by Rhodobacter Sphaeroides

    Institute of Scientific and Technical Information of China (English)

    Shuli Liu; Guangming Zhang; Jie Zhang

    2016-01-01

    In order to enhance the degrading protein capability of purple non⁃sulfur bacteria ( PNSB), an effective strain, L2, was used to co⁃culture with Rhodobacter sphaeroides ATCC17023. The effects of added strain on protein removal of R. sphaeroides were investigated. Results showed that strain L2, being identified as Bacillus thuringiensis/cereus, had a high potential for producing protease with a production of 295 U/mL. The optimal B. thuringiensis/cereus ( 40 μL ) could significantly increase protein degradation of R. sphaeroides. Protein removal and biomass production were improved by 483% and 67%, respectively. R. sphaeroides/total biomass production was more than 95%. Theoretical analysis revealed that R. sphaeroides syntrophically interacted with B. thuringiensis/cereus. Protein degradation of B. thuringiensis/cereus provided small molecule substrates ( VFAs) for R. sphaeroides growth and cells materials synthesis.

  14. Oxygen-insensitive synthesis of the photosynthetic membranes of Rhodobacter sphaeroides: a mutant histidine kinase.

    OpenAIRE

    Eraso, J M; Kaplan, S

    1995-01-01

    Two new loci, prrB and prrC, involved in the positive regulation of photosynthesis gene expression in response to anaerobiosis, have been identified in Rhodobacter sphaeroides. prrB encodes a sensor histidine kinase that is responsive to the removal of oxygen and functions through the response regulator PrrA. Inactivation of prrB results in a substantial reduction of photosynthetic spectral complexes as well as in the inability of cells to grow photosynthetically at low to medium light intens...

  15. Brominated lipids identify lipid binding sites on the surface of the reaction center from Rhodobacter sphaeroides.

    Science.gov (United States)

    Roszak, Aleksander W; Gardiner, Alastair T; Isaacs, Neil W; Cogdell, Richard J

    2007-03-20

    This study describes the use of brominated phospholipids to distinguish between lipid and detergent binding sites on the surface of a typical alpha-helical membrane protein. Reaction centers isolated from Rhodobacter sphaeroides were cocrystallized with added brominated phospholipids. X-ray structural analysis of these crystals has revealed the presence of two lipid binding sites from the characteristic strong X-ray scattering from the bromine atoms. These results demonstrate the usefulness of this approach to mapping lipid binding sites at the surface of membrane proteins.

  16. Effect of Photo-Oxidation on Energy Transfer in Light Harvesting Complex (LH2) from Rhodobacter Sphaeroides 601

    Institute of Scientific and Technical Information of China (English)

    LIU Kang-Jun; LIU Wei-Min; YAN Yong-Li; DONG Zhi-Wei; LIU Yuan; XU Chun-He; QIAN Shi-Xiong

    2006-01-01

    @@ We study the photo-oxidation of bacteriochlorophylls (BChls) in peripheral light harvesting complexes (LH2) from rhodobacter sphaeroides by using the steady absorption and the femtosecond pump-probe measurement, to realize the detailed dynamics of LH2 in the presence of photo-oxidation.

  17. Glutamate transport in Rhodobacter sphaeroides is mediated by a novel binding protein-dependent secondary transport system

    NARCIS (Netherlands)

    Jacobs, Mariken H.J.; Heide, Tiemen van der; Driessen, Arnold J.M.; Konings, Wil N.

    1996-01-01

    Growth of a glutamate transport-deficient mutant of Rhodobacter sphaeroides on glutamate as sole carbon and nitrogen source can be restored by the addition of millimolar amounts of Na+. Uptake of glutamate (Kt of 0.2 µM) by the mutant strictly requires Na+ (Km of 25 mM) and is inhibited by

  18. Transient dynamic phenotypes as criteria for model discrimination: fold-change detection in Rhodobacter sphaeroides chemotaxis.

    Science.gov (United States)

    Hamadeh, Abdullah; Ingalls, Brian; Sontag, Eduardo

    2013-03-01

    The chemotaxis pathway of the bacterium Rhodobacter sphaeroides shares many similarities with that of Escherichia coli. It exhibits robust adaptation and has several homologues of the latter's chemotaxis proteins. Recent theoretical results have correctly predicted that the E. coli output behaviour is unchanged under scaling of its ligand input signal; this property is known as fold-change detection (FCD). In the light of recent experimental results suggesting that R. sphaeroides may also show FCD, we present theoretical assumptions on the R. sphaeroides chemosensory dynamics that can be shown to yield FCD behaviour. Furthermore, it is shown that these assumptions make FCD a property of this system that is robust to structural and parametric variations in the chemotaxis pathway, in agreement with experimental results. We construct and examine models of the full chemotaxis pathway that satisfy these assumptions and reproduce experimental time-series data from earlier studies. We then propose experiments in which models satisfying our theoretical assumptions predict robust FCD behaviour where earlier models do not. In this way, we illustrate how transient dynamic phenotypes such as FCD can be used for the purposes of discriminating between models that reproduce the same experimental time-series data.

  19. Advancing Rhodobacter sphaeroides as a platform for expression of functional membrane proteins.

    Science.gov (United States)

    Erbakan, Mustafa; Curtis, Brandon S; Nixon, B Tracy; Kumar, Manish; Curtis, Wayne R

    2015-11-01

    Membrane protein overexpression is often hindered by toxic effects on the expression host, limiting achievable volumetric productivity. Moreover, protein structure and function may be impaired due to inclusion body formation and proteolytic degradation. To address these challenges, we employed the photosynthetic bacterium, Rhodobacter sphaeroides for expression of challenging membrane proteins including human aquaporin 9 (hAQP9), human tight junction protein occludin (Occ), Escherichia coli toxin peptide GhoT, cellulose synthase enzyme complex (BcsAB) of R. sphaeroides and cytochrome-cy (Cyt-cy) from Rhodobacter capsulatus. Titers of 47 mg/L for Cyt-cy, 7.5 mg/L for Occ, 1.5 mg/L for BcsAB and 0.5 mg/L for hAQP9 were achieved from affinity purification. While purification of GhoT was not successful, transformants displayed a distinct growth phenotype that correlated with GhoT expression. We also evaluated the functionality of these proteins by performing water transport studies for hAQP9, peroxidase activity for cytochrome-cy, and in vitro cellulose synthesis activity assay for BcsAB. While previous studies with Rhodobacter have utilized oxygen-limited semi-aerobic growth for membrane protein expression, substantial titer improvements are achieved as a result of a 3-fold increase in biomass yield using the anaerobic photoheterotrophic growth regime, which utilizes the strong native puc promoter. This versatile platform is shown to enable recovery of a wide variety of difficult-to-express membrane proteins in functional form.

  20. Effect of changes in the composition of cellular fatty acids on membrane fluidity of Rhodobacter sphaeroides.

    Science.gov (United States)

    Kim, Eui-Jin; Lee, Jeong K

    2015-02-01

    The cellular fatty acid composition is important for metabolic plasticity in Rhodobacter sphaeroides. We explored the effects of changing the cellular ratio of unsaturated fatty acids (UFAs) to saturated fatty acids (SFAs) in R. sphaeroides by overexpressing several key fatty acid biosynthetic enzymes through the use of expression plasmid pRK415. Bacteria containing the plasmid pRKfabI1 with the fabI1 gene that encodes enoyl-acyl carrier protein (ACP) reductase showed a reduction in the cellular UFA to SFA ratio from 4 (80% UFA) to 2 (65% UFA) and had decreased membrane fluidity and reduced cell growth. Additionally, the ratio of UFA to SFA of the chromatophore vesicles from pRKfabI1 -containing cells was similarly lowered, and the cell had decreased levels of light-harvesting complexes, but no change in intracytoplasmic membrane (ICM) content or photosynthetic (PS) gene expression. Both inhibition of enoyl- ACP reductase with diazaborine and addition of exogenous UFA restored membrane fluidity, cell growth, and the UFA to SFA ratio to wild-type levels in this strain. R. sphaeroides containing the pRKfabB plasmid with the fabB gene that encodes the enzyme β-ketoacyl-ACP synthase I exhibited an increased UFA to SFA ratio from 4 (80% UFA) to 9 (90% UFA), but showed no change in membrane fluidity or growth rate relative to control cells. Thus, membrane fluidity in R. sphaeroides remains fairly unchanged when membrane UFA levels are between 80% and 90%, whereas membrane fluidity, cell growth, and cellular composition are affected when UFA levels are below 80%.

  1. Expression of the gltP gene of Escherichia coli in a glutamate transport-deficient mutant of Rhodobacter sphaeroides restores chemotaxis to glutamate

    NARCIS (Netherlands)

    Jacobs, M.H J; van der Heide, T.; Tolner, B; Driessen, A.J.M.; Konings, W.N

    1995-01-01

    Rhodobacter sphaeroides is chemotactic to glutamate and most other amino acids. In Escherichia coli, chemotaxis involves a membrane-bound sensor that either binds the amino acid directly or interacts with the binding protein loaded with the amino acid. In R. sphaeroides, chemotaxis is thought to req

  2. Hydrogen production from tofu wastewater by Rhodobacter sphaeroides immobilized in agar gels

    Energy Technology Data Exchange (ETDEWEB)

    Zuh, H. [Utsunomiya Univ., Tochigi (Japan). Agricultural Faculty; National Inst. of Bioscience and Human Technology, Ibaraki (Japan); Suzuki, Tomoo; Tsygankov, A.A.; Asada, Yasuo; Miyake, Jun [National Inst. of Bioscience and Human Technology, Ibaraki (Japan)

    1999-04-01

    Hydrogen production from the wastewater of tofu factory was examined by using anoxygenic phototrophic bacterium Rhodobacter sphaeroides immobilized in agar gels. The maximum rate of hydrogen production observed from the wastewater was 2.l l h(-1) m(2) gel which was even slightly higher than that from a glucose medium (as control). The hydrogen production lasted up to 50 h. The yield of hydrogen was 1.9 ml/ml wastewater or 0.24 ml/mg carbohydrates contained in the wastewater. This yield corresponds to 53% or 65% of that from the glucose medium, according to the different expressions of the yield The TOC (total organic carbon) removal ratio in 85 h reached 41% which was comparable to that from the glucose medium. The immobilization protected the bacterium from the inhibitory effect of ammonium ion. (Author)

  3. Kinetics of biological hydrogen production by the photosynthetic bacterium Rhodobacter sphaeroides O.U. 001

    Energy Technology Data Exchange (ETDEWEB)

    Koku, Harun; Eroglu, I. [Middle East Technical Univ., Ankara (Turkey). Dept. of Chemical Engineering; Gunduz, U.; Yucel, M. [Middle East Technical Univ., Ankara (Turkey). Dept. of Biology; Turker, L. [Middle East Technical Univ., Ankara (Turkey). Dept. of Chemistry

    2003-04-01

    The kinetics and the effects of various parameters on hydrogen production by Rhodobacter sphaeroides O.U. 001 were investigated in a batch column photobioreactor. In particular, the effect of the inoculum age and the implementation of a light-dark cycle illumination scheme for emulating natural sunlight have been investigated in detail. The possibility of using yeast extract to replace the rather expensive vitamin mixture in the medium was also studied. The results show that hydrogen production is decreased when the initially inoculated bacteria have a high culture age. Exposure of the bacterial culture to light-dark cycles increased the amount of hydrogen compared to continuous illumination, all other parameters remaining the same. Similarly, the use of yeast extract to replace the vitamins increased the growth and hydrogen production rates, however, with a slight reduction in the total amount of gas produced and the hydrogen fraction in the evolved gas. (Author)

  4. Phosphoribulokinase mediates nitrogenase-induced carbon dioxide fixation gene repression in Rhodobacter sphaeroides

    Science.gov (United States)

    Farmer, Ryan M.

    2015-01-01

    In many organisms there is a balance between carbon and nitrogen metabolism. These observations extend to the nitrogen-fixing, nonsulfur purple bacteria, which have the classic family of P(II) regulators that coordinate signals of carbon and nitrogen status to regulate nitrogen metabolism. Curiously, these organisms also possess a reverse mechanism to regulate carbon metabolism based on cellular nitrogen status. In this work, studies in Rhodobacter sphaeroides firmly established that the activity of the enzyme that catalyses nitrogen fixation, nitrogenase, induces a signal that leads to repression of genes encoding enzymes of the Calvin–Benson–Bassham (CBB) CO2 fixation pathway. Additionally, genetic and metabolomic experiments revealed that NADH-activated phosphoribulokinase is an intermediate in the signalling pathway. Thus, nitrogenase activity appears to be linked to cbb gene repression through phosphoribulokinase. PMID:26306848

  5. Influence of pigment substitution on the electrochemical properties of Rhodobacter sphaeroides 601 reaction centers

    Institute of Scientific and Technical Information of China (English)

    ZOU; YOnglong(

    2001-01-01

    [1]Deisenhofer. J., Epp, O.. Miki, K. et al., Structure of the protein subunits in the photosynthetic reaction center of Rhodopseudomonas viridis at 3A resolution, Nature, 1985, 318: 618-624.[2]Marcus, R. A., Election transfer reaction in chemistry: Theory and experiment (Nobel lecture), Angewandte Chemie, 1993,32: 1111-1121.[3]Woodbury, N. W., Becker, M., Middendorf, D. et al., Picosecond kinetics of the initial photochemical electron-transfer reaction in bacterial photosynthetic reaction centers, Biochemistry, 1985, 24 (26): 7516-7521.[4]Scheer, H., Struck, A., Bacterial reaction centers with modified tetrapyrrole chromophores, in The Photosynthetic Reaction Center (Ⅰ) (eds. Deisenhofer, J., Norris, J.), San Diego: Academic Press, 1993, 157-192.[5]Meyer, M., Scheer, H., Reaction centers of Rhodobacter sphaeroides R26 containing C-3 acetyl and vinyl (bacterio)pheophytines at sites HA,B, Photosynth. Res., 1995, 44: 55-65.[6]Schmidt, S., Arlt, T., Hamm, P. et al., Energetics of the primary electron transfer reaction revealed by ultrafast spectroscopy on modified bacterial reaction centers, Chem. Phys. Lett., 1994, 223: 116-120.[7]Kennis, J. T. M., Shkuropatov, A. Y., Van Stokkum, I. H. M. et al., Formation of a long-lived P+BA- state in plant pheophytin-exchanged reaction centers of Rhodobacter sphaeroides R26 at low temperature, Biochemistry, 1997, 36:16231-16238.[8]Tasayco, M. L., Carey, J., Ordered self-assembly of polypeptide fragments to form native like dimeric trp repressor, Science. 1992, 255: 594-597.[9]Kong, J. L., Lu, Z. Q., Lvov, Y. M. et al., Direct electrochemistry of cofactor redox sites in a bacterial photosynthetic reaction center protein, J. Am. Chem. Soc., 1998, 120 (29): 7371-7372.[10]Nassar, A. E. F., Bobbitt, J. M., Stuart, J. M. et al., Catalytic reduction of organohalide pollutants by myoglobin in a biomembrane-like surfactant film, J. Am. Chem. Soc., 1995, 117: 10986-10993.[11]Zeng, X. H., Wu, Y

  6. Proteomic characterization of the Rhodobacter sphaeroides 2.4.1 photosynthetic membrane: Identification of New Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Xiaohua; Roh, Jung Hyeob; Callister, Stephen J.; Tavano, Christine; Donohue, Timothy; Lipton, Mary S.; Kaplan, Samuel

    2007-10-01

    The intracytoplasmic membrane (ICM) system develops, upon induction, as a structure dedicated to the major events of bacterial photosynthesis, including harvesting light energy, primary charge separation, and electron transport. In this study, multi-chromatographic methods coupled with fourier transform ion cyclotron resonance (FTICR) mass spectrometer, combined with subcellular fractionation, was applied to an investigation of the supramolecular composition of the native photosynthetic membrane of Rhodobacter sphaeroides 2.4.1. A complete proteomic profile of the intracytoplasmic membranes was obtained and the results showed that the intracytoplasmic membranes are mainly composed of four photosynthetic membrane protein complexes, including light harvesting complexes I and II, the reaction center and cytochrome bc1, as well as two new membrane protein components, an unknown protein (RSP1760) and a possible alkane hydroxylase. Proteins necessary for various cellular functions, such as ATP synthesis, respiratory components, ABC transporters, protein translocation, and other proteins with unknown functions were also identified in association with the intracytoplasmic membranes. This study opens a new perspective on the characterization and understanding of the photosynthetic supramolecular complexes of R. sphaeroides, and their internal interactions as well as interactions with other proteins inside or outside the intracytoplasmic membranes.

  7. Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Callister, Stephen J.; Nicora, Carrie D.; Zeng, Xiaohua; Roh, Jung Hyeob; Dominguez, Migual; Tavano, Christine; Monroe, Matthew E.; Kaplan, Samuel; Donohue, Timothy; Smith, Richard D.; Lipton, Mary S.

    2006-07-05

    Proteomes from aerobic and photosynthetic grown Rhodobacter sphaeroides 2.4.1 cell cultures were characterized using liquid chromatography-mass spectrometry in conjunction with an accurate mass and elution time (AMT) tag approach. Roughly 8000 high quality peptides were detected that represented 1,445 gene products and 34% of the predicted proteins. The identified proteins corresponded primarily to open reading frames (ORFs) contained within the two chromosomal elements of this bacterium, but a significant number were also observed from ORFs associated with 5 naturally occurring plasmids. Data mining of peptides revealed a number of proteins uniquely detected within the photosynthetic cell culture. Proteins observed in both aerobic respiratory and photosynthetic grown cultures were analyzed semi-quantitatively by comparing their estimated abundances to provide insights into bioenergetic models for aerobic respiration and photosynthesis. Additional emphasis was placed on gene products annotated as hypothetical to gain information as to their potential roles within these two growth conditions. Where possible, transcriptome data for R. sphaeroides obtained under the same culture conditions were compared with these results. This comparative study demonstrated the applicability of the AMT tag approach for high-throughput proteomic analyses of pathways associated with the photosynthetic lifestyle.

  8. Role of the Irr protein in the regulation of iron metabolism in Rhodobacter sphaeroides.

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    Verena Peuser

    Full Text Available In Rhizobia the Irr protein is an important regulator for iron-dependent gene expression. We studied the role of the Irr homolog RSP_3179 in the photosynthetic alpha-proteobacterium Rhodobacter sphaeroides. While Irr had little effect on growth under iron-limiting or non-limiting conditions its deletion resulted in increased resistance to hydrogen peroxide and singlet oxygen. This correlates with an elevated expression of katE for catalase in the Irr mutant compared to the wild type under non-stress conditions. Transcriptome studies revealed that Irr affects the expression of genes for iron metabolism, but also has some influence on genes involved in stress response, citric acid cycle, oxidative phosphorylation, transport, and photosynthesis. Most genes showed higher expression levels in the wild type than in the mutant under normal growth conditions indicating an activator function of Irr. Irr was however not required to activate genes of the iron metabolism in response to iron limitation, which showed even stronger induction in the absence of Irr. This was also true for genes mbfA and ccpA, which were verified as direct targets for Irr. Our results suggest that in R. sphaeroides Irr diminishes the strong induction of genes for iron metabolism under iron starvation.

  9. Assembly of functional photosystem complexes in Rhodobacter sphaeroides incorporating carotenoids from the spirilloxanthin pathway.

    Science.gov (United States)

    Chi, Shuang C; Mothersole, David J; Dilbeck, Preston; Niedzwiedzki, Dariusz M; Zhang, Hao; Qian, Pu; Vasilev, Cvetelin; Grayson, Katie J; Jackson, Philip J; Martin, Elizabeth C; Li, Ying; Holten, Dewey; Neil Hunter, C

    2015-02-01

    Carotenoids protect the photosynthetic apparatus against harmful radicals arising from the presence of both light and oxygen. They also act as accessory pigments for harvesting solar energy, and are required for stable assembly of many light-harvesting complexes. In the phototrophic bacterium Rhodobacter (Rba.) sphaeroides phytoene desaturase (CrtI) catalyses three sequential desaturations of the colourless carotenoid phytoene, extending the number of conjugated carbon-carbon double bonds, N, from three to nine and producing the yellow carotenoid neurosporene; subsequent modifications produce the yellow/red carotenoids spheroidene/spheroidenone (N=10/11). Genomic crtI replacements were used to swap the native three-step Rba. sphaeroides CrtI for the four-step Pantoea agglomerans enzyme, which re-routed carotenoid biosynthesis and culminated in the production of 2,2'-diketo-spirilloxanthin under semi-aerobic conditions. The new carotenoid pathway was elucidated using a combination of HPLC and mass spectrometry. Premature termination of this new pathway by inactivating crtC or crtD produced strains with lycopene or rhodopin as major carotenoids. All of the spirilloxanthin series carotenoids are accepted by the assembly pathways for LH2 and RC-LH1-PufX complexes. The efficiency of carotenoid-to-bacteriochlorophyll energy transfer for 2,2'-diketo-spirilloxanthin (15 conjugated CC bonds; N=15) in LH2 complexes is low, at 35%. High energy transfer efficiencies were obtained for neurosporene (N=9; 94%), spheroidene (N=10; 96%) and spheroidenone (N=11; 95%), whereas intermediate values were measured for lycopene (N=11; 64%), rhodopin (N=11; 62%) and spirilloxanthin (N=13; 39%). The variety and stability of these novel Rba. sphaeroides antenna complexes make them useful experimental models for investigating the energy transfer dynamics of carotenoids in bacterial photosynthesis.

  10. Skin Anti-Aging Activities of Bacteriochlorophyll a from Photosynthetic Bacteria, Rhodobacter sphaeroides.

    Science.gov (United States)

    Kim, Nam Young; Yim, Tae Bin; Lee, Hyeon Yong

    2015-10-01

    In this work, the anti-aging skin effects of bacteriochlorophyll a isolated from Rhodobacter sphaeroides are first reported, with notably low cytotoxicity in the range of 1% to 14% in adding 0.00078 (% (w/w)) of the extracts, compared with the normal growth of both human dermal fibroblast and keratinocyte cells without any treatment as a control. The highest production of procollagen from human fibroblast cells (CCD-986sk) was observed as 221.7 ng/ml with 0.001 (% (w/w)) of bacteriochlorophyll a, whereas 150 and 200 ng/ml of procollagen production resulted from addition of 0.001 (% (w/w)) of the photosynthetic bacteria. The bacteriochlorophylla- induced TNF-α production increased to 63.8%, which was lower secretion from HaCaT cells than that from addition of 0.00005 (% (w/w)) of bacteriochlorophyll a. Additionally, bacteriochlorophyll a upregulated the expression of genes related to skin anti-aging (i.e., keratin 10, involucrin, transglutaminase-1, and MMPs), by up to 4-15 times those of the control. However, crude extracts from R. sphaeroides did not enhance the expression level of these genes. Bacteriochlorophyll a showed higher antioxidant activity of 63.8% in DPPH free radical scavenging than those of water, ethanol, and 70% ethanol extracts (14.0%, 57.2%, and 12.6%, respectively). It was also shown that the high antioxidant activity could be attributed to the skin anti-aging effect of bacteriochlorophyll a, although R. sphaeroides itself would not exhibit significant anti-aging activities.

  11. Extract from a mutant Rhodobacter sphaeroides as an enriched carotenoid source

    Directory of Open Access Journals (Sweden)

    Chih-Chiang Wang

    2016-03-01

    Full Text Available Background: The extract Lycogen™ from the phototrophic bacterium Rhodobacter sphaeroides (WL-APD911 has attracted significant attention because of its promising potential as a bioactive mixture, attributed in part to its anti-inflammatory properties and anti-oxidative activity. Objective: This study aims to investigate the components of Lycogen™ and its anti-inflammatory properties and anti-oxidative activity. Design and results: The mutant strain R. sphaeroides (WL-APD911 whose carotenoid 1,2-hydratase gene has been altered by chemical mutagenesis was used for the production of a new carotenoid. The strain was grown at 30°C on Luria–Bertani (LB agar plates. After a 4-day culture period, the mutant strain displayed a 3.5-fold increase in carotenoid content, relative to the wild type. In the DPPH test, Lycogen™ showed more potent anti-oxidative activity than lycopene from the wild-type strain. Primary skin irritation test with hamsters showed no irritation response in hamster skins after 30 days of treatment with 0.2% Lycogen™. Chemical investigations of Lycogen™ using nuclear magnetic resonance (NMR 1H, 13C, and COSY/DQCOSY spectra have identified spheroidenone and methoxyneurosporene. Quantitative analysis of these identified compounds based on spectral intensities indicates that spheroidenone and methoxyneurosporene are major components (approximately 1:1; very small quantities of other derivatives are also present in the sample. Conclusions: In this study, we identified the major carotenoid compounds contained in Lycogen™, including spheroidenone and methoxyneurosporene by high-resolution NMR spectroscopy analysis. The carotenoid content of this mutant strain of R. sphaeroides was 3.5-fold higher than that in normal strain. Furthermore, Lycogen™ from the mutant strain is more potent than lycopene from the wild-type strain and does not cause irritation in hamster skins. These findings suggest that this mutant strain has the

  12. Augmenting light coverage for photosynthesis through YFP-enhanced charge separation at the Rhodobacter sphaeroides reaction centre

    OpenAIRE

    Grayson, K.J.; Faries, K.M.; Huang, X.; Qian, P.; Dilbeck, P.; Martin, E.C.; Hitchcock, A; Vasilev, C.; Yuen, J.M.; Niedzwiedzki, D.M.; Leggett, G.J; Holten, D; Kirmaier, C; Hunter, C N

    2017-01-01

    Photosynthesis uses a limited range of the solar spectrum, so enhancing spectral coverage could improve the efficiency of light capture. Here, we show that a hybrid reaction centre (RC)/yellow fluorescent protein (YFP) complex accelerates photosynthetic growth in the bacterium Rhodobacter sphaeroides. The structure of the RC/YFP-light-harvesting 1 (LH1) complex shows the position of YFP attachment to the RC-H subunit, on the cytoplasmic side of the RC complex. Fluorescence lifetime microscopy...

  13. Hydrogen gas production by combined systems of Rhodobacter sphaeroides O.U.001 and Halobacterium salinarum in a photobioreactor

    Energy Technology Data Exchange (ETDEWEB)

    Zabut, Baker; El-Kahlout, Kamal [Department of Biochemistry, School of Science, IUG, Gaza (PS); Yuecel, Meral [Department of Biology, Middle East Technical University, 06531 Ankara (Turkey); Guenduez, Ufuk; Tuerker, Lemi [Department of Chemistry, Middle East Technical University, 06531 Ankara (Turkey); Eroglu, Inci [Department of Chemical Engineering, Middle East Technical University, 06531 Ankara (Turkey)

    2006-09-15

    Rhodobacter sphaeroides O.U.001 is a photosynthetic non-sulfur bacterium which produces hydrogen from organic compounds under anaerobic conditions. Halobacterium salinarum is an archaeon and lives under extremely halophilic conditions (4M NaCl). H. salinarum contains a retinal protein bacteriorhodopsin in its purple membrane which acts as a light-driven proton pump. In this study the Rhodobacter sphaeroides O.U.001 culture was combined with different amounts of packed cells of H. salinarum S9 or isolated purple membrane fragments in order to increase the photofermentative hydrogen gas production. The packed cells of H. salinarum have the ability to pump protons upon illumination due to the presence of bacteriorhodopsin. The proton gradient produced may be used for the formation of ATP or protons may be used for H{sub 2} production by R. sphaeroides. Similar to intact cells purple membrane fragments may also form vesicles around certain ions and may act like closed systems. The hydrogen production experiments were carried out using 400ml water-jacketed-glass column stirred photobioreactors. In combined systems 10-200nmol of bacteriorhodopsin was used. Hydrogen gas production was enhanced by four- to sixfold in combined systems of H. salinarum packed cells with R. sphaeroides O.U.001 cell. Stirring both increased the total gas produced and enhanced the rate of hydrogen production. The light energy conversion efficiency was increased from 0.6% to 2.25% in combined systems. (author)

  14. 5-Aminolevulinate production by Escherichia coli containing the Rhodobacter sphaeroides hemA gene

    Energy Technology Data Exchange (ETDEWEB)

    Van Der Werf, M.J. [Michigan State Univ., East Lansing, MI (United States); Zeikus, J.G. [Michigan State Univ., East Lansing, MI (United States)]|[MBI International, Lansing, MI (United States)

    1996-10-01

    The Rhodobacter sphaeroides hemA gene codes for 5-aminolevulinate (ALA) synthase. This enzyme catalyzes the pyridoxal phosphate-dependent condensation of succinyl coenzyme A and glycine-forming ALA. The R. sphaeroides hemA gene in the pUC18/19 vector system was transformed into Escherichia coli. The effects of both genetic and physiological factors on the expression of ALA synthase and the production of ALA were studied. ALA synthase activity levels were maximal when hemA had the same transcription direction as the lac promoter. The distance between the lac promoter and hemA affected the expression of ALA synthase on different growth substrates. The E. coli host strain used had an enormous effect on the ALA synthase activity level and on the production of ALA, with E. coli DH1 being best suited. The ALA synthase activity level was also dependent on the carbon source. Succinate, L-malate, fumarate, and L-aspartate gave the highest levels of ALA synthase activity, while the use of lactose as a carbon source resulted in a repression of ALA synthase. After growth on succinate, ALA synthase represented {approx}5% of total cellular protein. The ALA synthase activity level was also dependent on the pH of the medium, with maximal activity occurring at pH 6.5. ALA production by whole cells was limited by the availability of glycine, and the addition of 2 g of glycine per liter to the growth medium increased the production of ALA fivefold, to 2.25 mM. In recombinant E. coli extracts, up to 22 mM ALA was produced from succinate, glycine, and ATP. 58 refs., 4 figs., 7 tabs.

  15. In vitro assessment of gastrointestinal viability of two photosynthetic bacteria, Rhodopseudomonas palustris and Rhodobacter sphaeroides

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The objectives of this study were to assess the potential of two photosynthetic bacteria (PSB), Rhodopseudomonas palustris HZ0301 and Rhodobacter sphaeroides HZ0302, as probiotics in aquaculture. The viability of HZ0301 and HZ0302 in simulated gastric transit conditions (pH 2.0, pH 3.0 and pH 4.0 gastric juices) and in simulated small intestinal transit conditions (pH 8.0, with or without 0.3% bile salts) was tested. The effects of HZ0301 and HZ0302 on the viability and permeability of intestinal epithelial cell in primary culture of tilapias, Oreochromis nilotica, were also detected. All the treatments were determined with three replicates. The simulated gastric transit tolerance of HZ0301 and HZ0302 strains was pH-dependent and correspondingly showed lower viability at pH 2.0 after 180 min compared with pH 3.0 and pH 4.0. Both HZ0301 and HZ0302 were tolerant to simulated small intestine transit with or without bile salts in our research. Moreover, there was no significant difference (P>0.05) among three treatments including the control and the groups treated with HZ0301 or HZ0302 both in intestinal epithelial cell viability and membrane permeability, showing no cell damage. In summary, this study demonstrated that HZ0301 and HZ0302 had high capacity of upper gastrointestinal transit tolerance and were relatively safe for intestinal epithelial cells of tilapias.

  16. Influence of pigment substitution on the electrochemical properties of Rhodobacter sphaeroides 601 reaction centers

    Institute of Scientific and Technical Information of China (English)

    邹永龙; 赵杰权; 陈志龙; 孔继烈; 曾小华; 徐春和

    2001-01-01

    With the help of pigment substitution, self-assembled monolayer film and square wave voltammetry, the influence of pigment substitution on the electrochemical properties of Rhodobacter sphaeroides 601 reaction centers was investigated. Results showed that the charge separation could also be driven by externally electric field, similar to the primary photochemical reaction in purple bacterial reaction center. On the surface of Au electrode, a self-assembled monolayer film (the RC-PDDA-DMSA film) was made up of 2,3-dimercaptosuccinic acid (DMSA), poly-dimeth-yldiallylammonium chloride (PDDA) and reaction center (RC). When square wave voltammetry was used to study the RC-PDDA-DMSA film, four redox pairs in the photochemical reaction of RC were observed by changing frequency. With nonlinear fitting, the standard potential of P/P+ and the corresponding electrode reaction rate constant were determined to be 0.522 V and 13.04 S-1, respectively. It was found that the redox peak at -0.02 V changed greatly when bacteriopheophytin was substituted by plant pheophytin in the reaction center. Further studies indicated that this change resulted from the decrease in electron transfer rate between Bphe-/Bphe (Phe-/Phe) and QA-/QA after pigment substitution. After investigations of spectra and electrochemical properties of different RCs and comparisons of different function groups of pigments, it was indicated that the phytyl tail, similar to other substituted groups of pheophytin, affected the efficiencies of pigment substitution.

  17. Replacement of bacteriopheophytin in reaction centers from Rhodobacter sphaeroides RS601 with plant pheophytin

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    In the presence of acetone and an excess of exogenous plant pheophytins,bacteriopheophytins in the reaction centers from Rhodobacter sphaeroides RS601 were replaced by pheophytins at sites HA and HB,when incubated at 43.5℃ for more than 15 min.The substitution of bacteriopheophytins in the reaction centers was 50% and 71% with incubation of 15 and 60 min,respectively.In the absorption spectra of pheophytin-replaced reaction centers (Phe RCs),bands assigned to the transition moments QX (537 nm) and QY (758 nm) of bacteriopheophytin disappeared,and three distinct bands assigned to the transition moments QX (509/542 nm) and QY (674 nm) of pheophytin appeared instead.Compared to that of the control reaction centers,the photochemical activities of Phe RCs are 78% and 71% of control,with the incubation time of 15 and 60 min.Differences might exist between the redox properties of Phe RC and of native reaction centers,but the substitution is significant,and the new system is available for further studies.

  18. Replacement of bacteriopheophytin in reaction centers from Rhodobacter sphaeroides RS601 with plant pheophytin

    Institute of Scientific and Technical Information of China (English)

    曾小华; 吴永强; 沈允钢; 徐春和

    2000-01-01

    In the presence of acetone and an excess of exogenous plant pheophytins, bacterio-pheophytins in the reaction centers from Rhodobacter sphaeroides RS601 were replaced by pheophytins at sites HA and HB, when incubated at 43.5℃ for more than 15 min. The substitution of bacteriopheophytins in the reaction centers was 50% and 71% with incubation of 15 and 60 min, respectively. In the absorption spectra of pheophytin-replaced reaction centers (Phe RCs), bands assigned to the transition moments Qx (537 nm) and QY (758 nm) of bacteriopheophytin disappeared, and three distinct bands assigned to the transition moments Qx (509/542 nm) and QY (674 nm) of pheophytin appeared instead. Compared to that of the control reaction centers, the photochemical activities of Phe RCs are 78% and 71% of control, with the incubation time of 15 and 60 min. Differences might exist between the redox properties of Phe RC and of native reaction centers, but the substitution is significant, and the new system is available for further

  19. Acquirement and characterization of a carotenoid mutant (GM309) of Rhodobacter sphaeroides 601

    Institute of Scientific and Technical Information of China (English)

    LIU Yuan; ZHANG Wei; WU Yongqiang; XU Chunhe

    2004-01-01

    A green mutant was obtained among the chemically induced mutants of Rhodobacter sphaeroides 601 (RS601) and named GM309. A blue shift of 20 nm of the carotenoid absorption spectrum was found in the light-harvesting complex II (LH2) of GM309. Different from LH2 of RS601, it was found that the carotenoids in GM309-LH2 changed to be neurosporene by mutation. Neurosporene lacks a conjugate double bond, compared with the spheroidene in RS601-LH2 which has ten conjugate double bonds. As shown by absorption and circular dichroism spectroscopy, the overall structure of GM309-LH2 is little affected by this change. From fluorescence emission spectra, it is found that GM309-LH2 can transfer energy from carotenoids to Bchl-B850 without any change in efficiency. But the efficiency of energy transfer from B800 to B850 in GM309-LH2 is decreased to be 42% of that of the native. This work would provide a novel method to investigate the mechanism of excitation energy transfer in LH2.

  20. An Extract of Rhodobacter sphaeroides Reduces Cisplatin-Induced Nephrotoxicity in Mice

    Directory of Open Access Journals (Sweden)

    Wen-Wei Chang

    2013-11-01

    Full Text Available Cisplatin is used as a treatment for various types of solid tumors. Renal injury severely limits the use of cisplatin. Renal cell apoptosis, oxidative stress, and inflammation contribute to cisplatin-induced nephrotoxicity. Previously, we found that an extract of Rhodobacter sphaeroides (Lycogen™ inhibited proinflammatory cytokines and the production of nitric oxide in activated macrophages in a dextran sodium sulfate (DSS-induced colitis model. Here, we evaluated the effect of Lycogen™, a potent anti-inflammatory agent, in mice with cisplatin-induced renal injury. We found that attenuated renal injury correlated with decreased apoptosis due to a reduction in caspase-3 expression in renal cells. Oral administration of Lycogen™ significantly reduced the expression of tumor necrosis factor-α and interleukin-1β in mice with renal injury. Lycogen™ reduces renal dysfunction in mice with cisplatin-induced renal injury. The protective effects of the treatment included blockage of the cisplatin-induced elevation in serum urea nitrogen and creatinine. Meanwhile, Lycogen™ attenuated body weight loss and significantly prolonged the survival of mice with renal injury. We propose that Lycogen™ exerts anti-inflammatory activities that represent a promising strategy for the treatment of cisplatin-induced renal injury.

  1. Modification of galactitol dehydrogenase from Rhodobacter sphaeroides D for immobilization on polycrystalline gold surfaces.

    Science.gov (United States)

    Kornberger, P; Gajdzik, J; Natter, H; Wenz, G; Giffhorn, F; Kohring, G W; Hempelmann, R

    2009-10-20

    Galactitol dehydrogenase (GatDH) from Rhodobacter sphaeroides is a multifunctional enzyme that catalyzes in the presence of oxidized beta-nicotinamide adenine dinucleotide (NAD(+)) the interconversion of various multivalent aliphatic alcohols to the corresponding ketones. The recombinant GatDH was provided with an N-terminal His(6)-tag to which distally up to three cysteine residues were attached. This protein construct maintained nearly full enzymatic activity, and it could be covalently immobilized via thiol bonds onto the surface of a gold electrode. Binding of GatDH onto the gold electrode was verified by SPR measurements, and residual enzyme activity was measured by cyclic voltammetry using 1,2-hexanediol as substrate, the cofactor NAD(+) and the redox mediator CTFM (4-carboxy-2,5,7-trinitrofluorenyliden-malonnitrile) in solute form. The results demonstrate the possibility of a directed functional immobilization of proteins on gold surfaces, which represents a proof-of-concept for the development of reactors for electrochemical synthon preparation using dehydrogenases.

  2. Brewery wastewaters in photobiological hydrogen generation in presence of Rhodobacter sphaeroides O.U. 001

    Energy Technology Data Exchange (ETDEWEB)

    Seifert, K.; Waligorska, M.; Laniecki, M. [Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan (Poland)

    2010-05-15

    Rhodobacter sphaeroides O.U. 001 (concentration of inoculum-0.36 g dry wt/l) and brewery wastewaters were applied in photobiogeneration of hydrogen under illumination of 116 W/m{sup 2}. The best results were obtained with filtered wastewaters sterilized at 120 C for 20 min and maximal concentration of waste in medium equal 10% v/v. The main product in generated biogas was hydrogen (90%). After sterilization the amount of generated hydrogen was tripled (from 0.76 to 2.2 l H{sub 2}/l medium), whereas waste concentration of 10% v/v resulted in the best substrate yield (0.22 l H{sub 2}/l of waste). Under these conditions the amount of generated hydrogen was 2.24 l H{sub 2}/l medium and light conversion efficiency reached value of 1.7%. The modified Gompertz equations served in modeling of the kinetics of the studied process. (author)

  3. ChrR positively regulates transcription of the Rhodobacter sphaeroides cytochrome c2 gene.

    Science.gov (United States)

    Schilke, B A; Donohue, T J

    1995-04-01

    Transcription of the Rhodobacter sphaeroides cytochrome c2 gene (cycA) is negatively regulated by both the presence of oxygen and intermediates in tetrapyrrole biosynthesis. A mutation responsible for uncoupling cycA transcription from tetrapyrrole availability was localized to a gene (chrR) that encodes a 357-amino-acid protein. Analysis of a defined chrR null mutation indicated that this protein positively regulated cycA transcription. From this and other results, it appeared that the positive action of ChrR on cycA transcription is blocked by altering the availability of either heme or some intermediate in tetrapyrrole biosynthesis. A single missense mutation which substitutes an Arg for a Cys at residue 182 of ChrR (C182R) was shown to be necessary and sufficient for the increased cycA transcription seen in the mutant strain Chr4. Thus, it appears that this C182R substitution generated an altered-function form of ChrR. In addition, by analyzing cycA transcription in delta ChrR strains, we showed that ChrR was not required for increased cycA transcription under anaerobic conditions. Instead, our results indicated that ChrR and the response regulator PrrA (J. M. Eraso and S. Kaplan, J. Bacteriol. 176:32-43, 1994) functioned independently at the upstream cycA promoter that is activated under anaerobic conditions.

  4. Transient grating spectroscopy in photosynthetic purple bacteria Rhodobacter sphaeroides 2.4.1

    Energy Technology Data Exchange (ETDEWEB)

    Sugisaki, Mitsuru, E-mail: mitsuru@sci.osaka-cu.ac.j [CREST-JST and Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585 (Japan); Fujiwara, Masazumi; Fujii, Ritsuko [CREST-JST and Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585 (Japan); Nakagawa, Katsunori; Nango, Mamoru [CREST-JST and Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555 (Japan); Cogdell, Richard J. [Glasgow Biomedical Research Centre, IBLS, University of Glasgow, 126 University Place, Glasgow G12 8TA, Scotland (United Kingdom); Hashimoto, Hideki [CREST-JST and Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585 (Japan)

    2009-12-15

    The vibronic coherence of photosynthetic pigment-protein complexes has been investigated by means of transient grating spectroscopy using sub 20 fs optical pulses. In the present work, we focus our attention on the LH2 antenna complexes from Rhodobacter sphaeroides 2.4.1 because the information about their structure investigated by the electron and atomic force microscopy is available and the electric levels of pigments are well resolved, resulting in clear absorption spectrum. The vibronic coherent oscillations with a period of a few tens of femtoseconds have been clearly observed. We found that the temporal change of the coherent oscillations reflects the vibrational relaxation in the ground state. Calculations based on the Brownian oscillator model were performed under the impulsive excitation limit. The spectral density has been determined from the Raman measurement of spheroidene. Good agreement between the calculation and the experimental results has been achieved in the linear absorption spectrum and transient grating signal, which strongly supports the validity of our model.

  5. Hydrogen production by Rhodobacter sphaeroides O.U.001 in a flat plate solar bioreactor

    Energy Technology Data Exchange (ETDEWEB)

    Eroglu, Inci; Tabanoglu, Altan; Eroglu, Ela [Department of Chemical Engineering, Middle East Technical University, 06531 Ankara (Turkey); Guenduez, Ufuk; Yuecel, Meral [Department of Biology, Middle East Technical University, 06531 Ankara (Turkey)

    2008-01-15

    Rhodobacter sphaeroides O.U.001 can produce hydrogen under anaerobic conditions and illumination. The objective of this study was to investigate the performance of an 8 l flat plate solar bioreactor operating in outdoor conditions. Different organic acids were used as carbon sources (malate, lactate and acetate) and olive mill waste water was used as a sole substrate source. The consumption and the production of the organic acids were determined by HPLC. The accumulation of by-products, such as poly-{beta}-hydroxybutyrate (PHB) and carotenoid, throughout the course of hydrogen production was determined. The hydrogen production rate was highest (0.01 l/l/h) when malate was the carbon source. Formate was observed as the fermentation end product. Acetate resulted in low hydrogen gas production and high PHB accumulation. When acetate was used as the carbon source, butyrate was produced as a result of fermentation. Promising amounts of PHB and caretenoid were accumulated during hydrogen production from diluted olive mill wastewater. (author)

  6. The Extract of Rhodobacter sphaeroides Inhibits Melanogenesis through the MEK/ERK Signaling Pathway

    Directory of Open Access Journals (Sweden)

    Chen-Hsun Liu

    2013-06-01

    Full Text Available Reducing hyperpigmentation has been a big issue for years. Even though pigmentation is a normal mechanism protecting skin from UV-causing DNA damage and oxidative stress, it is still an aesthetic problem for many people. Bacteria can produce some compounds in response to their environment. These compounds are widely used in cosmetic and pharmaceutical applications. Some probiotics have immunomodulatory activities and modulate the symptoms of several diseases. Previously, we found that the extracts of Rhodobacter sphaeroides (Lycogen™ inhibited nitric oxide production and inducible nitric-oxide synthase expression in activated macrophages. In this study, we sought to investigate an anti-melanogenic signaling pathway in α-melanocyte stimulating hormone (α-MSH-treated B16F10 melanoma cells and zebrafish. Treatment with Lycogen™ inhibited the cellular melanin contents and expression of melanogenesis-related protein, including microphthalmia-associated transcription factor (MITF and tyrosinase in B16F10 cells. Moreover, Lycogen™ reduced phosphorylation of MEK/ERK without affecting phosphorylation of p38. Meanwhile, Lycogen™ decreased zebrafish melanin expression in a dose-dependent manner. These findings establish Lycogen™ as a new target in melanogenesis and suggest a mechanism of action through the ERK signaling pathway. Our results suggested that Lycogen™ may have potential cosmetic usage in the future.

  7. Bioremediation of petroleum hydrocarbon contaminated soil by Rhodobacter sphaeroides biofertilizer and plants.

    Science.gov (United States)

    Jiao, Haihua; Luo, Jinxue; Zhang, Yiming; Xu, Shengjun; Bai, Zhihui; Huang, Zhanbin

    2015-09-01

    Bio-augmentation is a promising technique for remediation of polluted soils. This study aimed to evaluate the bio-augmentation effect of Rhodobacter sphaeroides biofertilizer (RBF) on the bioremediation of total petroleum hydrocarbons (TPH) contaminated soil. A greenhouse pot experiment was conducted over a period of 120 days, three methods for enhancing bio-augmentation were tested on TPH contaminated soils, including single addition RBF, planting, and combining of RBF and three crop species, such as wheat (W), cabbage (C) and spinach (S), respectively. The results demonstrated that the best removal of TPH from contaminated soil in the RBF bio-augmentation rhizosphere soils was found to be 46.2%, 65.4%, 67.5% for W+RBF, C+RBF, S+RBF rhizosphere soils respectively. RBF supply impacted on the microbial community diversity (phospholipid fatty acids, PLFA) and the activity of soil enzymes, such as dehydrogenase (DH), alkaline phosphatase (AP) and urease (UR). There were significant difference among the soil only containing crude oil (CK), W, C and S rhizosphere soils and RBF bio-augmentation soils. Moreover, the changes were significantly distinct depended on crops species. It was concluded that the RBF is a valuable material for improving effect of remediation of TPH polluted soils.

  8. Transcriptional Activation of the Rhodobacter sphaeroides Cytochrome c2 Gene P2 Promoter by the Response Regulator PrrA

    OpenAIRE

    Comolli, James C; Carl, Audrey J.; Hall, Christine; Donohue, Timothy

    2002-01-01

    Anoxygenic photosynthetic growth of Rhodobacter sphaeroides, a member of the α subclass of the class Proteobacteria, requires the response regulator PrrA. PrrA and the sensor kinase PrrB are part of a two-component signaling pathway that influences a wide range of processes under oxygen-limited conditions. In this work we characterized the pathway of transcription activation by PrrB and PrrA by purifying these proteins, analyzing them in vitro, and characterizing a mutant PrrA protein in vivo...

  9. Mutational analysis of the C-terminal domain of the Rhodobacter sphaeroides response regulator PrrA

    OpenAIRE

    Jones, Denise F.; Stenzel, Rachelle A.; Donohue, Timothy J.

    2005-01-01

    The Rhodobacter sphaeroides response regulator PrrA directly activates transcription of genes necessary for energy conservation at low O2 tensions and under anaerobic conditions. It is proposed that PrrA homologues contain a C-terminal DNA-binding domain (PrrA-CTD) that lacks significant amino acid sequence similarity to those found in other response regulators. To test this hypothesis, single amino acid substitutions were created at 12 residues in the PrrA-CTD. These mutant PrrA proteins wer...

  10. Multi-PAS domain-mediated protein oligomerization of PpsR from Rhodobacter sphaeroides

    Energy Technology Data Exchange (ETDEWEB)

    Heintz, Udo; Meinhart, Anton; Winkler, Andreas, E-mail: andreas.winkler@mpimf-heidelberg.mpg.de [Max Planck Institute for Medical Research, Heidelberg (Germany)

    2014-03-01

    Crystal structures of two truncated variants of the transcription factor PpsR from R. sphaeroides are presented that enabled the phasing of a triple PAS domain construct. Together, these structures reveal the importance of α-helical PAS extensions for multi-PAS domain-mediated protein oligomerization and function. Per–ARNT–Sim (PAS) domains are essential modules of many multi-domain signalling proteins that mediate protein interaction and/or sense environmental stimuli. Frequently, multiple PAS domains are present within single polypeptide chains, where their interplay is required for protein function. Although many isolated PAS domain structures have been reported over the last decades, only a few structures of multi-PAS proteins are known. Therefore, the molecular mechanism of multi-PAS domain-mediated protein oligomerization and function is poorly understood. The transcription factor PpsR from Rhodobacter sphaeroides is such a multi-PAS domain protein that, in addition to its three PAS domains, contains a glutamine-rich linker and a C-terminal helix–turn–helix DNA-binding motif. Here, crystal structures of two N-terminally and C-terminally truncated PpsR variants that comprise a single (PpsR{sub Q-PAS1}) and two (PpsR{sub N-Q-PAS1}) PAS domains, respectively, are presented and the multi-step strategy required for the phasing of a triple PAS domain construct (PpsR{sub ΔHTH}) is illustrated. While parts of the biologically relevant dimerization interface can already be observed in the two shorter constructs, the PpsR{sub ΔHTH} structure reveals how three PAS domains enable the formation of multiple oligomeric states (dimer, tetramer and octamer), highlighting that not only the PAS cores but also their α-helical extensions are essential for protein oligomerization. The results demonstrate that the long helical glutamine-rich linker of PpsR results from a direct fusion of the N-cap of the PAS1 domain with the C-terminal extension of the N-domain that

  11. Transient grating spectroscopy and the calorimetry of photosynthesis in Rhodobacter sphaeroides

    Science.gov (United States)

    McCauley, Micah John

    2001-07-01

    Enormous numbers and varieties of experiments have been performed to elucidate the mechanisms of photosynthesis. Within the last twenty years, a host of new studies were enabled by the techniques of ultrafast laser spectroscopy. This work continues to explore the exchange of energy on the picosecond and even the femtosecond regime. Yet in even the relatively simple and determined structure of the photosynthetic centers in the bacteria Rhodobacter sphaeroides, the mechanisms and energetics are unclear. The early events in photosynthesis allow energy trapping through resonance energy transfer and charge separation, in what appears to be a mixture of classical and quantum mechanical motion with strong interactions with the surrounding environment. The technique of transient thermal grating spectroscopy offers unique insight into the mechanisms of energy relaxation in photosynthesis. A pair of laser pulse are tuned to the excitation wavelength and crossed inside the sample. The resulting pattern of interference drives excitation and the subsequent relaxation forms a density grating which diffracts a time-delayed third beam. Thus the energies and the rates of motion may be discerned. The peripheral light harvesting antenna (LH2) is composed of polypeptides that coordinate rings of bacteriochlorophyll. Upon excitation, energy migrates around the ring until intra-ring transfer may take place. Samples of LH2 were purified and studied. While characteristic times of energy release were determined, a volume change due to solvent interaction was found as well. In the membrane spanning protein known as the reaction center, the energy of the light harvesting rings is ultimately transferred to a pair of chlorophyll. From here, the energy is localized onto an electron, which rapidly (picoseconds) transfers to other active pigments. Samples of wild-type and the mutated (M)214H reaction centers were purified and examined. By studying the temperature dependence of the signals, the

  12. Structural characterization of the B800-850 and B875 light-harvesting antenna complexes from Rhodobacter sphaeroides by electron microscopy

    NARCIS (Netherlands)

    Boonstra, Arjen F.; Visschers, Ronald W.; Calkoen, Florentine; Grondelle, Rienk van; Bruggen, Ernst F.J. van; Boekema, Egbert J.

    1993-01-01

    The structure and aggregation behavior of B800-850 (LHII) and B875 (LHI) antenna complexes of Rhodobacter sphaeroides were studied by electron microscopy. Single molecular projections (top views and side views) of isolated particles were analyzed. The B800-850 complexes, isolated as 150 kDa particle

  13. Identification of key residues that confer Rhodobacter sphaeroides LPS activity at horse TLR4/MD-2.

    Directory of Open Access Journals (Sweden)

    Katherine L Irvine

    Full Text Available The molecular determinants underpinning how hexaacylated lipid A and tetraacylated precursor lipid IVa activate Toll-like receptor 4 (TLR4 are well understood, but how activation is induced by other lipid A species is less clear. Species specificity studies have clarified how TLR4/MD-2 recognises different lipid A structures, for example tetraacylated lipid IVa requires direct electrostatic interactions for agonism. In this study, we examine how pentaacylated lipopolysaccharide from Rhodobacter sphaeroides (RSLPS antagonises human TLR4/MD-2 and activates the horse receptor complex using a computational approach and cross-species mutagenesis. At a functional level, we show that RSLPS is a partial agonist at horse TLR4/MD-2 with greater efficacy than lipid IVa. These data suggest the importance of the additional acyl chain in RSLPS signalling. Based on docking analysis, we propose a model for positioning of the RSLPS lipid A moiety (RSLA within the MD-2 cavity at the TLR4 dimer interface, which allows activity at the horse receptor complex. As for lipid IVa, RSLPS agonism requires species-specific contacts with MD-2 and TLR4, but the R2 chain of RSLA protrudes from the MD-2 pocket to contact the TLR4 dimer in the vicinity of proline 442. Our model explains why RSLPS is only partially dependent on horse TLR4 residue R385, unlike lipid IVa. Mutagenesis of proline 442 into a serine residue, as found in human TLR4, uncovers the importance of this site in RSLPS signalling; horse TLR4 R385G/P442S double mutation completely abolishes RSLPS activity without its counterpart, human TLR4 G384R/S441P, being able to restore it. Our data highlight the importance of subtle changes in ligand positioning, and suggest that TLR4 and MD-2 residues that may not participate directly in ligand binding can determine the signalling outcome of a given ligand. This indicates a cooperative binding mechanism within the receptor complex, which is becoming increasingly

  14. Biocontrol activity and patulin-removal effects of Bacillus subtilis, Rhodobacter sphaeroides and Agrobacterium tumefaciens against Penicillium expansum.

    Science.gov (United States)

    Wang, Y; Yuan, Y; Liu, B; Zhang, Z; Yue, T

    2016-11-01

    This study was conducted to evaluate the biocontrol potential of Bacillus subtilis CICC 10034, Rhodobacter sphaeroides CGMCC 1.2182 and Agrobacterium tumefaciens CGMCC 1.2554 against patulin (PAT)-producer Penicillium expansum and their ability to remove PAT. Bacillus subtilis effectively inhibited P. expansum both on apples and in in vitro experiments, which reduced the rot diameter on apples by 38% compared with the control. The reduction was followed by those induced by A. tumefaciens (27·63%) and R. sphaeroides (23·67%). None of the cell-free supernatant (CFS) was able to prevent pathogen growth. Three antagonists could suppress PAT production by P. expansum on apples by 98·5, 93·7 and 94·99% after treatment with B. subtilis, R. sphaeroides and A. tumefaciens respectively. In addition, the three strains led to a 0·56-1·47 log CFU g(-1) reduction in colony number of P. expansum on apples. Survival of antagonists on apple wounds revealed their tolerance to PAT. Furthermore, both live and autoclaved cells of three strains efficiently adsorbed artificially spiked PAT from medium. The selected antagonists could be applied before harvesting to control apple infection by PAT-producing fungi and also during processing to act as PAT detoxifiers. Since little information related to the capability of R. sphaeroides and A. tumefaciens to inhibit P. expansum is currently available, the results of this study provide some new perspectives to the biocontrol field. © 2016 The Society for Applied Microbiology.

  15. A KDP-LIKE, HIGH-AFFINITY, K+-TRANSLOCATING ATPASE IS EXPRESSED DURING GROWTH OF RHODOBACTER-SPHAEROIDES IN LOW POTASSIUM MEDIA - DISTRIBUTION OF THIS K+-ATPASE AMONG PURPLE NONSULFUR PHOTOTROPHIC BACTERIA

    NARCIS (Netherlands)

    ABEE, T; HELLINGWERF, KJ; BAKKER, EP; SIEBERS, A; KONINGS, WN

    1992-01-01

    Cells of the purple non-sulphur bacterium Rhodobacter sphaeroides express a high-affinity K+ uptake system when grown in media with low K+ concentrations. Antibodies against the catalytic KdpB protein or the whole KdpABC complex of Escherichia coli cross-react with a 70.0 kDa R. sphaeroides protein

  16. Direct Visualization of Exciton Reequilibration in the LH1 and LH2 Complexes of Rhodobacter sphaeroides by Multipulse Spectroscopy

    Science.gov (United States)

    Cohen Stuart, Thomas A.; Vengris, Mikas; Novoderezhkin, Vladimir I.; Cogdell, Richard J.; Hunter, C. Neil; van Grondelle, Rienk

    2011-01-01

    The dynamics of the excited states of the light-harvesting complexes LH1 and LH2 of Rhodobacter sphaeroides are governed, mainly, by the excitonic nature of these ring-systems. In a pump-dump-probe experiment, the first pulse promotes LH1 or LH2 to its excited state and the second pulse dumps a portion of the excited state. By selective dumping, we can disentangle the dynamics normally hidden in the excited-state manifold. We find that by using this multiple-excitation technique we can visualize a 400-fs reequilibration reflecting relaxation between the two lowest exciton states that cannot be directly explored by conventional pump-probe. An oscillatory feature is observed within the exciton reequilibration, which is attributed to a coherent motion of a vibrational wavepacket with a period of ∼150 fs. Our disordered exciton model allows a quantitative interpretation of the observed reequilibration processes occurring in these antennas. PMID:21539791

  17. Direct Visualization of Exciton Reequilibration in the LH1 and LH2 Complexes of Rhodobacter sphaeroides by Multipulse Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Stuart, Thomas A. Cohen [Free Univ. of Amsterdam (Netherlands); Vengris, Mikas [Vilnius Univ. (Lithuania); Novoderezhkin, Vladimir I. [A.N. Belozersky Inst. of Physico-Chemical Biology, Moscow State Univ. (Russia); Cogdell, Richard J. [Microbial Photosynthesis Laboratory, Glasgow Biomedical Research Centre, Univ. of Glasgow (United Kingdom); Hunter, C. Neil [Department of Molecular Biology and Biotechnology, Univ. of Sheffield, (United Kingdom); van Grondelle, Rienk [Free Univ. of Amsterdam (Netherlands)

    2011-01-01

    The dynamics of the excited states of the light-harvesting complexes LH1 and LH2 of Rhodobacter sphaeroides are governed, mainly, by the excitonic nature of these ring-systems. In a pump-dump-probe experiment, the first pulse promotes LH1 or LH2 to its excited state and the second pulse dumps a portion of the excited state. By selective dumping, we can disentangle the dynamics normally hidden in the excited-state manifold. We find that by using this multiple-excitation technique we can visualize a 400-fs reequilibration reflecting relaxation between the two lowest exciton states that cannot be directly explored by conventional pump-probe. An oscillatory feature is observed within the exciton reequilibration, which is attributed to a coherent motion of a vibrational wavepacket with a period of ~150 fs. Our disordered exciton model allows a quantitative interpretation of the observed reequilibration processes occurring in these antennas.

  18. Biohydrogen and polyhydroxyalkanoate co-production by Enterobacter aerogenes and Rhodobacter sphaeroides from Calophyllum inophyllum oil cake.

    Science.gov (United States)

    Arumugam, A; Sandhya, M; Ponnusami, V

    2014-07-01

    The feasibility of coupled biohydrogen and polyhydroxyalkanoate production by Enterobacter aerogenes and Rhodobacter sphaeroides using Calophyllum inophyllum oil cake was studied under dark and photo fermentation conditions. The utilization of a non-edible acidic oil cake (C. inophyllum), and exploitation of a modified minimal salt media led to reduction in the cost of media. Cost of fermentation is reduced by implementation of alternate dark-photo fermentative periods and through the use of a co-culture consisting of a dark fermentative (E. aerogenes) and a photo fermentative (R. sphaeroides) bacterium. The biohydrogen and polyhydroxyalkanoate produced were 7.95 L H2/L media and 10.73 g/L media, respectively, under alternate dark and photo fermentation and were 3.23 L H2/L media and 5.6g/L media, respectively under complete dark fermentation. The characteristics of the oil cake and alternate dark (16 h) and photo (8h) fermentative conditions were found to be supportive in producing high biohydrogen and polyhydroxyalkanoate (PHA) yield.

  19. Experimental measurements of the radiation characteristics of Anabaena variabilis ATCC 29413-U and Rhodobacter sphaeroides ATCC 49419

    Energy Technology Data Exchange (ETDEWEB)

    Berberoglu, Halil; Pilon, Laurent [Mechanical and Aerospace Engineering Department, Henry Samueli School of Engineering and Applied Science, University of California Los Angeles, Los Angeles, CA 90095 (United States)

    2007-12-15

    The objective of this study is to experimentally measure the radiation characteristics of hydrogen producing microorganisms. Special attention is paid to the filamentous cyanobacteria Anabaena variabilis ATCC 29413-U and the unicellular purple bacteria Rhodobacter sphaeroides ATCC 49419 two of the widely studied photobiological hydrogen producers. The extinction and absorption coefficients are measured in the spectral range from 300 to 1300 nm using a spectrophotometer with and without an integrating sphere. Moreover, a nephelometer has been constructed to measure the scattering phase function of the microorganisms at 632.8 nm. The data are used to recover the mass specific absorption, scattering, and extinction cross-sections, the single scattering albedo, and the scattering phase function of the microorganisms. The scattering phase functions of both microorganisms were peaked strongly in the forward direction as expected from their size parameter and shape. The results reported in this study can be used with the radiative transport equation (RTE) to accurately predict and optimize light transport in photobioreactors for photobiological hydrogen production. Finally, the results show that absorption cross-sections of A. variabilis and R. sphaeroides have peaks that do not overlap but rather enlarge the spectral width of the absorption cross-section of a potential symbiotic culture promising more efficient utilization of solar radiation from light transfer point of view. (author)

  20. Photobiological transformation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) using Rhodobacter sphaeroides.

    Science.gov (United States)

    Millerick, Kayleigh A; Johnston, Juliet T; Finneran, Kevin T

    2016-09-01

    Pump-and-treat strategies for groundwater containing explosives may be necessary when the contaminated water approaches sensitive receptors. This project investigated bacterial photosynthesis as a strategy for ex situ treatment, using light as the primary energy source to facilitate RDX transformation. The objective was to characterize the ability of photosynthetic Rhodobacter sphaeroides (strain ATCC(®) 17023 ™) to transform the high-energy explosive RDX. R. sphaeroides transformed 30 μM RDX within 40 h under light conditions; RDX was not fully transformed in the dark (non-photosynthetic conditions), suggesting that photosynthetic electron transfer was the primary mechanism. Experiments with RDX demonstrated that succinate and malate were the most effective electron donors for photosynthesis, but glycerol was also utilized as a photosynthetic electron donor. RDX was transformed irrespective of the presence of carbon dioxide. The electron shuttling compound anthraquinone-2,6-disulfonate (AQDS) increased transformation kinetics in the absence of CO2, when the cells had excess NADPH that needed to be re-oxidized because there was limited CO2 for carbon fixation. When CO2 was added, the cells generated more biomass, and AQDS had no stimulatory effect. End products indicated that RDX carbon became CO2, biomass, and a soluble, uncharacterized aqueous metabolite, determined using (14)C-labeled RDX. These data are the first to suggest that photobiological explosives transformation is possible and will provide a framework for which phototrophy can be used in environmental restoration of explosives contaminated water. Copyright © 2016. Published by Elsevier Ltd.

  1. Local electrostatic field induced by the carotenoid bound to the reaction center of the purple photosynthetic bacterium Rhodobacter sphaeroides.

    Science.gov (United States)

    Yanagi, Kazuhiro; Shimizu, Madoka; Hashimoto, Hideki; Gardiner, Alastair T; Roszak, Aleksander W; Cogdell, Richard J

    2005-01-20

    Electroabsorption (EA) spectra were recorded in the region of the reaction center (RC) Qy absorption bands of bacteriochlorophyll (Bchl) and bacteriopheophytin, to investigate the effect of carotenoid (Car) on the electrostatic environment of the RCs of the purple bacterium Rhodobacter (Rb.) sphaeroides. Two different RCs were prepared from Rb. sphaeroides strain R26.1 (R26.1-RC); R26.1 RC lacking Car and a reconstituted RC (R26.1-RC+ Car) prepared by incorporating a synthetic Car (3,4-dihydrospheroidene). Although there were no detectable differences between these two RCs in their near infrared (NIR) absorption spectra at 79 and 293 K, or in their EA spectra at 79 K, significant differences were detected in their EA spectra at 293 K. Three nonlinear optical parameters of each RC were determined in order to evaluate quantitatively these differences; transition dipole-moment polarizability and hyperpolarizability (D factor), the change in polarizability upon photoexcitation (Deltaalpha), and the change in dipole-moment upon photoexcitation (Deltamu). The value of D or Deltaalpha determined for each absorption band of the two RC samples showed similar values at 77 or 293 K. However, the Deltamu values of the special pair Bchls (P) and the monomer Bchls absorption bands showed significant differences between the two RCs at 293 K. X-ray crystallography of the two RCs has revealed that a single molecule of the solubilizing detergent LDAO occupies part of the carotenoid binding site in the absence of a carotenoid. The difference in the value of Deltamu therefore represents the differential effect of the detergent LDAO and the carotenoid on P. The change of electrostatic field around P induced by the presence of Car was determined to be 1.7 x 10(5) [V/cm], corresponding to a approximately 10% change in the electrostatic field around P.

  2. Coenzyme Q10 production in a 150-l reactor by a mutant strain of Rhodobacter sphaeroides.

    Science.gov (United States)

    Kien, Nguyen Ba; Kong, In-Soo; Lee, Min-Gyu; Kim, Joong Kyun

    2010-05-01

    For the commercial production of CoQ(10), batch-type fermentations were attempted in a 150-l fermenter using a mutant strain of R. sphaeroides. Optimum temperature and initial aeration rate were found to be 30 degrees C and 2 vvm, respectively. Under optimum fermentation conditions, the maximum value of specific CoQ(10) content was achieved reproducibly as 6.34 mg/g DCW after 24 h, with 3.02 g/l of DCW. During the fermentation, aeration shift (from the adequate aeration at the early growth phase to the limited aeration in active cellular metabolism) was a key factor in CoQ(10) production for scale-up. A higher value of the specific CoQ(10) content (8.12 mg/g DCW) was achieved in fed-batch fermentation and comparable to those produced by the pilot-scale fed-batch fermentations of A. tumefaciens, which indicated that the mutant strain of R. sphaeroides used in this study was a potential high CoQ(10) producer. This is the first detailed study to demonstrate a pilot-scale production of CoQ(10) using a mutant strain of R. sphaeroides.

  3. Augmenting light coverage for photosynthesis through YFP-enhanced charge separation at the Rhodobacter sphaeroides reaction centre

    Science.gov (United States)

    Grayson, Katie J.; Faries, Kaitlyn M.; Huang, Xia; Qian, Pu; Dilbeck, Preston; Martin, Elizabeth C.; Hitchcock, Andrew; Vasilev, Cvetelin; Yuen, Jonathan M.; Niedzwiedzki, Dariusz M.; Leggett, Graham J.; Holten, Dewey; Kirmaier, Christine; Neil Hunter, C.

    2017-01-01

    Photosynthesis uses a limited range of the solar spectrum, so enhancing spectral coverage could improve the efficiency of light capture. Here, we show that a hybrid reaction centre (RC)/yellow fluorescent protein (YFP) complex accelerates photosynthetic growth in the bacterium Rhodobacter sphaeroides. The structure of the RC/YFP-light-harvesting 1 (LH1) complex shows the position of YFP attachment to the RC-H subunit, on the cytoplasmic side of the RC complex. Fluorescence lifetime microscopy of whole cells and ultrafast transient absorption spectroscopy of purified RC/YFP complexes show that the YFP-RC intermolecular distance and spectral overlap between the emission of YFP and the visible-region (QX) absorption bands of the RC allow energy transfer via a Förster mechanism, with an efficiency of 40+/-10%. This proof-of-principle study demonstrates the feasibility of increasing spectral coverage for harvesting light using non-native genetically-encoded light-absorbers, thereby augmenting energy transfer and trapping in photosynthesis.

  4. Modeling the light- and redox-dependent interaction of PpsR/AppA in Rhodobacter sphaeroides.

    Science.gov (United States)

    Pandey, Rakesh; Flockerzi, Dietrich; Hauser, Marcus J B; Straube, Ronny

    2011-05-18

    Facultative photosynthetic bacteria switch their energy generation mechanism from respiration to photosynthesis depending on oxygen tension and light. Part of this transition is mediated by the aerobic transcriptional repressor PpsR. In Rhodobacter sphaeroides, the repressive action of PpsR is antagonized by the redox- and blue-light-sensitive flavoprotein AppA which results in a unique phenotype: the repression of photosynthesis genes at intermediate oxygen levels and high light intensity, which is believed to reduce the risk of photooxidative stress. To analyze the underlying mechanism we developed a simple mathematical model based on the AppA-dependent reduction of a disulfide bond in PpsR and the light-sensitive complex formation between the reduced forms of AppA and PpsR. A steady-state analysis shows that high light repression can indeed occur at intermediate oxygen levels if PpsR is reduced on a faster timescale than AppA and if the electron transfer from AppA to PpsR is effectively irreversible. The model further predicts that if AppA copy numbers exceed those of PpsR by at least a factor of two, the transition from aerobic to anaerobic growth mode can occur via a bistable regime. We provide necessary conditions for the emergence of bistability and discuss possible experimental verifications.

  5. Orientation of the Q{sub y} optical transition moment of bacteriopheophytin in Rhodobacter sphaeroides reaction centers

    Energy Technology Data Exchange (ETDEWEB)

    Klenina, I.B.; Borovykh, I.V.; Shkuropatov, A.Ya.; Gast, P.; Proskuryakov, I.I

    2003-11-01

    Time-resolved cw EPR measurements of the Rhodobacter (Rb) sphaeroides R-26 reaction center primary donor triplet state excited with plane-polarised light are reported. The pigment composition of the reaction center was chemically modified, so that the bacteriopheophytin molecule in the cofactor branch which is inactive towards electron transfer was replaced by plant pheophytin a. This enabled selective excitation of the bacteriopheophytin and pheophytin molecules, and provided conditions for a high-quality magnetophotoselection study. For the first time, orientation of the Q{sub y} optical transition dipole moment relative to the molecular frame of the bacteriopheophytin in the active cofactor branch is determined. Of the four orientations allowed by magnetophotoselection, one was chosen as the most plausible. The corresponding Q{sub y} vector is tilted from the bacteriopheophytin tetrapyrrole plane by 15 deg. , and projects onto this plane almost on the y-molecular axis. It is suggested that the deviation of the vector from the molecular plane results from an interaction of bacteriopheophytin with the neighbouring molecule of accessory bacteriochlorophyll.

  6. Concomitant biohydrogen and poly-β-hydroxybutyrate production from dark fermentation effluents by adapted Rhodobacter sphaeroides and mixed photofermentative cultures.

    Science.gov (United States)

    Ghimire, Anish; Valentino, Serena; Frunzo, Luigi; Pirozzi, Francesco; Lens, Piet N L; Esposito, Giovanni

    2016-10-01

    This work aimed at investigating concomitant production of biohydrogen and poly-β-hydroxybutyrate (PHB) by photofermentation (PF) using dark fermentation effluents (DFE). An adapted culture of Rhodobacter sphaeroides AV1b (pH 6.5, 24±2°C) achieved H2 and PHB yields of 256 (±2) NmLH2/g Chemical Oxygen Demand (COD) and 273.8mgPHB/gCOD (32.5±3% of the dry cells weight (DCW)), respectively. When a diluted (1:2) DFE medium was applied to the adapted pure and mixed photofermentative culture, the respective H2 yields were 164.0 (±12) and 71.3 (±6) NmLH2/gCOD and the PHB yields were 212.1 (±105.2) and 50.7 (±2.7) mgPHB/gCOD added, corresponding to 24 (±0.7) and 6.3 (±0) % DCW, respectively. The concomitant H2 and PHB production from the PF process gave a good DFE post treatment achieving up to 80% COD removal from the initial DFE.

  7. Optimization of Biomass and 5-Aminolevulinic Acid Production by Rhodobacter sphaeroides ATCC17023 via Response Surface Methodology.

    Science.gov (United States)

    Liu, Shuli; Zhang, Guangming; Li, Jianzheng; Li, Xiangkun; Zhang, Jie

    2016-06-01

    Microbial 5-aminolevulinic acid (ALA) produced from wastewater is considered as potential renewable energy. However, many hurdles are needed to be overcome such as the regulation of key influencing factors on ALA yield. Biomass and ALA production by Rhodobacter sphaeroides was optimized using response surface methodology. The culturing medium was artificial volatile fatty acids wastewater. Three additives were optimized, namely succinate and glycine that are precursors of ALA biosynthesis, and D-glucose that is an inhibitor of ALA dehydratase. The optimal conditions were achieved by analyzing the response surface plots. Statistical analysis showed that succinate at 8.56 mmol/L, glycine at 5.06 mmol/L, and D-glucose at 7.82 mmol/L were the best conditions. Under these optimal conditions, the highest biomass production and ALA yield of 3.55 g/L and 5.49 mg/g-biomass were achieved. Subsequent verification experiments at optimal values had the maximum biomass production of 3.41 ± 0.002 g/L and ALA yield of 5.78 ± 0.08 mg/g-biomass.

  8. Probing energy transfer events in the light harvesting complex 2 (LH2) of Rhodobacter sphaeroides with two-dimensional spectroscopy.

    Science.gov (United States)

    Fidler, Andrew F; Singh, Ved P; Long, Phillip D; Dahlberg, Peter D; Engel, Gregory S

    2013-10-21

    Excitation energy transfer events in the photosynthetic light harvesting complex 2 (LH2) of Rhodobacter sphaeroides are investigated with polarization controlled two-dimensional electronic spectroscopy. A spectrally broadened pulse allows simultaneous measurement of the energy transfer within and between the two absorption bands at 800 nm and 850 nm. The phased all-parallel polarization two-dimensional spectra resolve the initial events of energy transfer by separating the intra-band and inter-band relaxation processes across the two-dimensional map. The internal dynamics of the 800 nm region of the spectra are resolved as a cross peak that grows in on an ultrafast time scale, reflecting energy transfer between higher lying excitations of the B850 chromophores into the B800 states. We utilize a polarization sequence designed to highlight the initial excited state dynamics which uncovers an ultrafast transfer component between the two bands that was not observed in the all-parallel polarization data. We attribute the ultrafast transfer component to energy transfer from higher energy exciton states to lower energy states of the strongly coupled B850 chromophores. Connecting the spectroscopic signature to the molecular structure, we reveal multiple relaxation pathways including a cyclic transfer of energy between the two rings of the complex.

  9. Characterization of ‘Pinky’ Strain Grown in Culture of Rhodobacter sphaeroides R26.1

    Institute of Scientific and Technical Information of China (English)

    PAN Yan; XIE Jing; KOYAMA Yasushi; LI Shi-hao; WANG En-si; HOU A-li

    2013-01-01

    In the process of cultivating Rhodobater sphaeroides R26.1,some of which turned from blue to pink due to the irradiation of a beam of leaking white light.The mutant strains were named ‘pinky’ strains,which were cultivated in the red light and in the dark for a comparative study.It turned out that the strains did not grow in the dark,so they might be photosynthetic bacteria.The electronic absorption spectrum of the ‘pinky’ strains was measured,which shows they contained two main photosynthetic pigments,carotenoids(Cars) and bacteriochlorophylls(BChls).And then they were extracted and analyzed.It proves that Bchls included Bchl a and Bchl a'.Nuclear magnetic resonance (NMR) spectra were exploited to determine the chemical structure of Cars.The results indicate that there were seven kinds of Cars,including lycopene,rhodopin,anhydrorhodovibrin,3,4-dihydroanhydrorhodovibrin,3,3,4-dihydrospirilloxanthin,3,4,3',4'-tetrahydrospirilloxanthin and spirilloxanthin.Based on the above results,it was found that most identified Cars formed via spirilloxanthin biosynthesis pathway.The analyzed results of 16S rRNA gene show that the homology of ‘pinky’ strains with Rhodopseudomonas palusteris was 99%.Rhodopseudomonas palusteris has been cultivated in our laboratory.Because of its strong vitality,it did not become extinct with so many years passing.When Rhodobater sphaeroides R26.1 was cultivated,it got rejuvenated under the appropriate conditions and caused Rhodobater sphaeroides R26.1 to be contaminated.

  10. Acetate-dependent photoheterotrophic growth and the differential requirement for the Calvin-Benson-Bassham reductive pentose phosphate cycle in Rhodobacter sphaeroides and Rhodopseudomonas palustris.

    Science.gov (United States)

    Laguna, Rick; Tabita, F Robert; Alber, Birgit E

    2011-02-01

    Rhodobacter sphaeroides ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-deletion strain 16 was capable of photoheterotrophic growth with acetate, while Rhodopseudomonas palustris RubisCO-deletion strain 2040 could not grow under these conditions. The reason for this difference lies in the fact that Rba. sphaeroides and Rps. palustris use different pathways for acetate assimilation, the ethylmalonyl-CoA pathway, and glyoxylate-bypass cycle, respectively. The ethylmalonyl-CoA pathway is distinct from the glyoxylate cycle as one molecule of CO(2) and one molecule of HCO(3) (-) per three molecules of acetyl-CoA are co-assimilated to form two malate molecules. The glyoxylate cycle directly converts two acetyl-CoA molecules to malate. Each pathway, therefore, also dictates at what point, CO(2) and reductant are consumed, thereby determining the requirement for the Calvin-Benson-Bassham reductive pentose phosphate cycle.

  11. Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4. 1 and its use for whole-genome shotgun sequence assembly

    Energy Technology Data Exchange (ETDEWEB)

    Shou, S. [Univ. Wisc.-Madison; Kvikstad, E. [Univ. Wisc.-Madison; Kile, A. [Univ. Wisc.-Madison; Severin, J. [Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4. 1 and its use for whole-genome shotgun sequence assembly; Forrest, D. [Univ. Wisc.-Madison; Runnheim, R. [Univ. Wisc.-Madison; Churas, C. [Univ. Wisc.-Madison; Hickman, J. W. [Univ. Wisc.-Madison; Mackenzie, C. [University of Texas–Houston Medical School; Choudhary, M. [University of Texas–Houston Medical School; Donohue, T. [Univ. Wisc.-Madison; Kaplan, S. [University of Texas–Houston Medical School; Schwartz, D. C. [Univ. Wisc.-Madison

    2003-09-01

    Rhodobacter sphaeroides 2.4.1 is a facultative photoheterotrophic bacterium with tremendous metabolic diversity, which has significantly contributed to our understanding of the molecular genetics of photosynthesis, photoheterotrophy, nitrogen fixation, hydrogen metabolism, carbon dioxide fixation, taxis, and tetrapyrrole biosynthesis. To further understand this remarkable bacterium, and to accelerate an ongoing sequencing project, two whole-genome restriction maps (EcoRI and HindIII) of R. sphaeroides strain 2.4.1 were constructed using shotgun optical mapping. The approach directly mapped genomic DNA by the random mapping of single molecules. The two maps were used to facilitate sequence assembly by providing an optical scaffold for high-resolution alignment and verification of sequence contigs. Our results show that such maps facilitated the closure of sequence gaps by the early detection of nascent sequence contigs during the course of the whole-genome shotgun sequencing process.

  12. Effect of the mutation of carotenoids on the dynamics of energy transfer in light- harvesting complexes (LH2) from Rhodobacter sphaeroides 601 at room temperature

    Institute of Scientific and Technical Information of China (English)

    Liu Wei-Min; Liu Yuan; Liu Rang-Jun; Yan Yong-Li; Guo Li-Jun; Xu Chun-He; Qian Shi-Xiong

    2006-01-01

    Energy transfers in two kinds of peripheral light-harvesting complexes (LH2) of Rhodobacter sphaeroides (RS) 601 are studied by using femtosecond pump-probe spectroscopy with tunable laser wavelength at room temperature. These two complexes are native LH2 (RS601) and green carotenoid mutated LH2 (GM309). The obtained results demonstrate that, compared with spheroidenes with ten conjugated double bonds in native RS601, carotenoid in GM309 containing neurosporenes with nine conjugated double bonds can lead to a reduction in energy transfer rate in the B800-to-B850 band and the disturbance in the energy relaxation processes within the excitonic B850 band.

  13. Chemotactic Control of the Two Flagellar Systems of Rhodobacter sphaeroides Is Mediated by Different Sets of CheY and FliM Proteins▿ †

    Science.gov (United States)

    del Campo, Ana Martínez; Ballado, Teresa; de la Mora, Javier; Poggio, Sebastian; Camarena, Laura; Dreyfus, Georges

    2007-01-01

    Rhodobacter sphaeroides expresses two different flagellar systems, a subpolar flagellum (fla1) and multiple polar flagella (fla2). These structures are encoded by different sets of flagellar genes. The chemotactic control of the subpolar flagellum (fla1) is mediated by three of the six different CheY proteins (CheY6, CheY4, or CheY3). We show evidence that CheY1, CheY2, and CheY5 control the chemotactic behavior mediated by fla2 flagella and that RSP6099 encodes the fla2 FliM protein. PMID:17890312

  14. PucC and LhaA direct efficient assembly of the light-harvesting complexes in Rhodobacter sphaeroides

    DEFF Research Database (Denmark)

    Mothersole, David; Jackson, Philip J.; Vasilev, Cvetelin

    2016-01-01

    interactions between pigments newly arriving from BchG and nascent proteins within the SecYEG-SecDF-YajC-YidC assembly machinery, thereby co-ordinating pigment delivery, the co-translational insertion of LH polypeptides and their folding and assembly to form photosynthetic complexes.......The mature architecture of the photosynthetic membrane of the purple phototroph Rhodobacter sphaeroides has been characterised to a level where an atomic-level membrane model is available, but the roles of the putative assembly proteins LhaA and PucC in establishing this architecture are unknown...

  15. Complementation of a reaction center-deficient Rhodobacter sphaeroides pufLMX deletion strain in trans with pufBALM does not restore the photosynthesis-positive phenotype.

    OpenAIRE

    Farchaus, J W; Gruenberg, H.; Oesterhelt, D.

    1990-01-01

    The puf operon in Rhodobacter sphaeroides is composed of the genes for the photosynthetic reaction center L and M subunits, light-harvesting antenna complex I, and one other open reading frame termed pufX. Complementation of a reaction center-deficient, photosynthetically incompetent pufLMX deletion strain in trans with a fragment containing the entire puf operon, including pufX and an additional 1,100 base pairs of DNA downstream of pufX, restored the reaction center and the photosynthesis-p...

  16. New insights into the photochemistry of carotenoid spheroidenone in light-harvesting complex 2 from the purple bacterium Rhodobacter sphaeroides.

    Science.gov (United States)

    Niedzwiedzki, Dariusz M; Dilbeck, Preston L; Tang, Qun; Martin, Elizabeth C; Bocian, David F; Hunter, C Neil; Holten, Dewey

    2017-03-01

    Light-harvesting complex 2 (LH2) from the semi-aerobically grown purple phototrophic bacterium Rhodobacter sphaeroides was studied using optical (static and time-resolved) and resonance Raman spectroscopies. This antenna complex comprises bacteriochlorophyll (BChl) a and the carotenoid spheroidenone, a ketolated derivative of spheroidene. The results indicate that the spheroidenone-LH2 complex contains two spectral forms of the carotenoid: (1) a minor, "blue" form with an S2 (1(1)B u(+) ) spectral origin band at 522 nm, shifted from the position in organic media simply by the high polarizability of the binding site, and (2) the major, "red" form with the origin band at 562 nm that is associated with a pool of pigments that more strongly interact with protein residues, most likely via hydrogen bonding. Application of targeted modeling of excited-state decay pathways after carotenoid excitation suggests that the high (92%) carotenoid-to-BChl energy transfer efficiency in this LH2 system, relative to LH2 complexes binding carotenoids with comparable double-bond conjugation lengths, derives mainly from resonance energy transfer from spheroidenone S2 (1(1)B u(+) ) state to BChl a via the Qx state of the latter, accounting for 60% of the total transfer. The elevated S2 (1(1)B u(+) ) → Qx transfer efficiency is apparently associated with substantially decreased energy gap (increased spectral overlap) between the virtual S2 (1(1)B u(+) ) → S0 (1(1)A g(-) ) carotenoid emission and Qx absorption of BChl a. This reduced energetic gap is the ultimate consequence of strong carotenoid-protein interactions, including the inferred hydrogen bonding.

  17. Role of phospholipids of subunit III in the regulation of structural rearrangements in cytochrome c oxidase of Rhodobacter sphaeroides.

    Science.gov (United States)

    Alnajjar, Khadijeh S; Cvetkov, Teresa; Prochaska, Lawrence

    2015-02-03

    Subunit III of cytochrome c oxidase possesses structural domains that contain conserved phospholipid binding sites. Mutations within these domains induce a loss of phospholipid binding, coinciding with decreased electron transfer activity. Functional and structural roles for phospholipids in the enzyme from Rhodobacter sphaeroides have been investigated. Upon the removal of intrinsic lipids using phospholipase A2, electron transfer activity was decreased 30-50%. Moreover, the delipidated enzyme exhibited turnover-induced, suicide inactivation, which was reversed by the addition of exogenous lipids, most specifically by cardiolipin. Cardiolipin exhibited two sites of interaction with the delipidated enzyme, a high-affinity site (Km = 0.14 μM) and a low-affinity site (Km = 26 μM). Subunit I of the delipidated enzyme exhibited a faster digestion rate when it was treated with α-chymotrypsin compared to that of the wild-type enzyme, suggesting that lipid removal induces a conformational change to expose the digestion sites further. Upon reaction of subunit III of the enzyme with a fluorophore (AEDANS), fluorescence anisotropy showed an increased rotational rate of the fluorophore in the absence of lipids, indicating increased flexibility of subunit III within the enzyme's tertiary structure. Additionally, Förster resonance energy transfer between AEDANS and a fluorescently labeled cardiolipin revealed that cardiolipin binds in the v-shaped cleft of subunit III in the delipidated enzyme and that it moves closer to the active site in subunit I upon a change in the redox state of the enzyme. In conclusion, these results show that the phospholipids regulate events occurring during electron transfer activity by maintaining the structural integrity of the enzyme at the active site.

  18. Genome-enabled analysis of the utilization of taurine as sole source of carbon or of nitrogen by Rhodobacter sphaeroides 2.4.1.

    Science.gov (United States)

    Denger, Karin; Smits, Theo H M; Cook, Alasdair M

    2006-11-01

    A degradative pathway for taurine (2-aminoethanesulfonate) in Rhodobacter sphaeroides 2.4.1 was proposed by Brüggemann et al. (2004) (Microbiology 150, 805-816) on the basis of a partial genome sequence. In the present study, R. sphaeroides 2.4.1 was found to grow exponentially with taurine as the sole source of carbon and energy for growth. When taurine was the sole source of nitrogen in succinate-salts medium, the taurine was rapidly degraded, and most of the organic nitrogen was excreted as the ammonium ion, which was then utilized for growth. Most of the enzymes involved in dissimilation, taurine dehydrogenase (TDH), sulfoacetaldehyde acetyltransferase (Xsc) and phosphate acetyltransferase (Pta), were found to be inducible, and evidence for transcription of the corresponding genes (tauXY, xsc and pta), as well as of tauKLM, encoding the postulated TRAP transporter for taurine, and of tauZ, encoding the sulfate exporter, was obtained by reverse-transcription PCR. An additional branch of the pathway, observed by Novak et al. (2004) (Microbiology 150, 1881-1891) in R. sphaeroides TAU3, involves taurine : pyruvate aminotransferase (Tpa) and a presumptive ABC transporter (NsbABC). No evidence for a significant role of this pathway, or of the corresponding alanine dehydrogenase (Ald), was obtained for R. sphaeroides 2.4.1. The anaplerotic pathway needed under these conditions in R. sphaeroides 2.4.1 seems to involve malyl-CoA lyase, which was synthesized inducibly, and not malate synthase (GlcB), whose presumed gene was not transcribed under these conditions.

  19. The cobinamide amidohydrolase (cobyric acid-forming) CbiZ enzyme: A critical activity of the cobamide remodeling system of Rhodobacter sphaeroides

    Science.gov (United States)

    Gray, Michael J.; Escalante-Semerena, Jorge C.

    2010-01-01

    SUMMARY The chemical structures of cobamides (cobalamin [Cbl]-like compounds) are the same, except for the lower ligand, which in adenosylcobalamin (AdoCbl) is 5,6-dimethylbenzimidazole (DMB), and in adenosylpseudocobalamin (AdopseudoCbl) is adenine. Why the lower ligand of cobamides varies and what the mechanism of lower ligand replacement is are long-standing questions in the field of B12 biosynthesis. Work reported here uncovers the strategy used by the photosynthetic α-proteobacterium Rhodobacter sphaeroides to procure the cobamide it needs to grow on acetate as a carbon and energy source. On the basis of genetic and biochemical evidence we conclude that, in R. sphaeroides, the activity of the cobyric acid-producing amidohydrolase CbiZ enzyme is essential for the conversion of AdopseudoCbl into AdoCbl, the cobamide needed for the catabolism of acetate. The CbiZ enzyme uses AdopseudoCbl as a substrate, but not AdoCbl. Implications of these findings for cobamide remodeling in R. sphaeroides and in other CbiZ-containing microorganisms are discussed. PMID:19889098

  20. The cobinamide amidohydrolase (cobyric acid-forming) CbiZ enzyme: a critical activity of the cobamide remodelling system of Rhodobacter sphaeroides.

    Science.gov (United States)

    Gray, Michael J; Escalante-Semerena, Jorge C

    2009-12-01

    The chemical structures of cobamides [cobalamin (Cbl)-like compounds] are the same, except for the lower ligand, which in adenosylcobalamin (AdoCbl) is 5,6-dimethylbenzimidazole, and in adenosylpseudocobalamin (AdopseudoCbl) is adenine. Why the lower ligand of cobamides varies and what the mechanism of lower ligand replacement is are long-standing questions in the field of B(12) biosynthesis. Work reported here uncovers the strategy used by the photosynthetic alpha-proteobacterium Rhodobacter sphaeroides to procure the cobamide it needs to grow on acetate as a carbon and energy source. On the basis of genetic and biochemical evidence we conclude that, in R. sphaeroides, the activity of the cobyric acid-producing amidohydrolase CbiZ enzyme is essential for the conversion of AdopseudoCbl into AdoCbl, the cobamide needed for the catabolism of acetate. The CbiZ enzyme uses AdopseudoCbl as a substrate, but not AdoCbl. Implications of these findings for cobamide remodelling in R. sphaeroides and in other CbiZ-containing microorganisms are discussed.

  1. Cardiolipin Deficiency in Rhodobacter sphaeroides Alters the Lipid Profile of Membranes and of Crystallized Cytochrome Oxidase, but Structure and Function Are Maintained

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xi; Tamot, Banita; Hiser, Carrie; Reid, Gavin E.; Benning, Christoph; Ferguson-Miller, Shelagh (MSU)

    2012-05-08

    Many recent studies highlight the importance of lipids in membrane proteins, including in the formation of well-ordered crystals. To examine the effect of changes in one lipid, cardiolipin, on the lipid profile and the production, function, and crystallization of an intrinsic membrane protein, cytochrome c oxidase, we mutated the cardiolipin synthase (cls) gene of Rhodobacter sphaeroides, causing a >90% reduction in cardiolipin content in vivo and selective changes in the abundances of other lipids. Under these conditions, a fully native cytochrome c oxidase (CcO) was produced, as indicated by its activity, spectral properties, and crystal characteristics. Analysis by MALDI tandem mass spectrometry (MS/MS) revealed that the cardiolipin level in CcO crystals, as in the membranes, was greatly decreased. Lipid species present in the crystals were directly analyzed for the first time using MS/MS, documenting their identities and fatty acid chain composition. The fatty acid content of cardiolipin in R. sphaeroides CcO (predominantly 18:1) differs from that in mammalian CcO (18:2). In contrast to the cardiolipin dependence of mammalian CcO activity, major depletion of cardiolipin in R. sphaeroides did not impact any aspect of CcO structure or behavior, suggesting a greater tolerance of interchange of cardiolipin with other lipids in this bacterial system.

  2. Quenching Capabilities of Long-Chain Carotenoids in Light-Harvesting-2 Complexes from Rhodobacter sphaeroides with an Engineered Carotenoid Synthesis Pathway.

    Science.gov (United States)

    Dilbeck, Preston L; Tang, Qun; Mothersole, David J; Martin, Elizabeth C; Hunter, C Neil; Bocian, David F; Holten, Dewey; Niedzwiedzki, Dariusz M

    2016-06-23

    Six light-harvesting-2 complexes (LH2) from genetically modified strains of the purple photosynthetic bacterium Rhodobacter (Rb.) sphaeroides were studied using static and ultrafast optical methods and resonance Raman spectroscopy. These strains were engineered to incorporate carotenoids for which the number of conjugated groups (N = NC═C + NC═O) varies from 9 to 15. The Rb. sphaeroides strains incorporate their native carotenoids spheroidene (N = 10) and spheroidenone (N = 11), as well as longer-chain analogues including spirilloxanthin (N = 13) and diketospirilloxantion (N = 15) normally found in Rhodospirillum rubrum. Measurements of the properties of the carotenoid first singlet excited state (S1) in antennas from the Rb. sphaeroides set show that carotenoid-bacteriochlorophyll a (BChl a) interactions are similar to those in LH2 complexes from various other bacterial species and thus are not significantly impacted by differences in polypeptide composition. Instead, variations in carotenoid-to-BChl a energy transfer are primarily regulated by the N-determined energy of the carotenoid S1 excited state, which for long-chain (N ≥ 13) carotenoids is not involved in energy transfer. Furthermore, the role of the long-chain carotenoids switches from a light-harvesting supporter (via energy transfer to BChl a) to a quencher of the BChl a S1 excited state B850*. This quenching is manifested as a substantial (∼2-fold) reduction of the B850* lifetime and the B850* fluorescence quantum yield for LH2 housing the longest carotenoids.

  3. Growth characteristics and hydrogen production by Rhodobacter sphaeroides using various amino acids as nitrogen sources and their combinations with carbon sources

    Energy Technology Data Exchange (ETDEWEB)

    Gabrielyan, Lilit; Torgomyan, Heghine; Trchounian, Armen [Department of Biophysics, Biological Faculty, Yerevan State University, 0025 Yerevan (Armenia)

    2010-11-15

    Some amino acids (alanine, asparagine, glutamate, glycine, proline, and tyrosine) were used as nitrogen sources in combination with carbon sources (succinate and malate) to study growth properties and H{sub 2} production by purple non-sulfur bacterium Rhodobacter sphaeroides strains A-10 and D-3. Both strains produced H{sub 2} in succinate-glutamate and malate-glutamate media. Succinate was a better carbon source than malate. In comparison with strain D-3, strain A-10 was able to utilize proline, alanine or tyrosine as nitrogen sources in succinate medium and to produce H{sub 2}. Both strains were unable to produce H{sub 2} in the presence of asparagine or glycine as nitrogen sources. N,N'-dicyclohexylcarbodiimide, the F{sub 0}F{sub 1}-ATPase inhibitor, led to marked inhibition of H{sub 2} production activity of R. sphaeroides. The results suggest that the R. sphaeroides cells growth can be achieved by the use of a large diversity of substrates but only some of them can increase the H{sub 2} production rate. (author)

  4. Light-harvesting complex 1 stabilizes P+QB- charge separation in reaction centers of Rhodobacter sphaeroides.

    Science.gov (United States)

    Francia, Francesco; Dezi, Manuela; Rebecchi, Alberto; Mallardi, Antonia; Palazzo, Gerardo; Melandri, Bruno Andrea; Venturoli, Giovanni

    2004-11-09

    The kinetics of charge recombination following photoexcitation by a laser pulse have been analyzed in the reaction center-light harvesting complex 1 (RC-LH1) purified from the photosynthetic bacterium Rhodobacter sphaeroides. In RC-LH1 core complexes isolated from photosynthetically grown cells P(+)Q(B)(-) recombines with an average rate constant, k approximately 0.3 s(-1), more than three times smaller than that measured in RC deprived of the LH1 (k approximately 1 s(-1)). A comparable, slowed recombination kinetics is observed in RC-LH1 complexes purified from a pufX-deleted strain. Slowing of the charge recombination kinetics is even more pronounced in RC-LH1 complexes isolated from wild-type semiaerobically grown cells (k approximately 0.2 s(-1)). Since the kinetics of P(+)Q(A)(-) recombination is unaffected by the presence of the antenna, the P(+)Q(B)(-) state appears to be energetically stabilized in core complexes. Determinations of the ubiquinone-10 (UQ(10)) complement associated with the purified RC-LH1 complexes always yield UQ(10)/RC ratios larger than 10. These quinone molecules are functionally coupled to the RC-LH1 complex, as judged from the extent of exogenous cytochrome c(2) rapidly oxidized under continuous light excitation. Analysis of P(+)Q(B)(-) recombination, based on a kinetic model which considers fast quinone equilibrium at the Q(B) binding site, indicates that the slowing down of charge recombination kinetics observed in RC-LH1 complexes cannot be explained solely by a quinone concentration effect and suggests that stabilization of the light-induced charge separation is predominantly due to interaction of the Q(B) site with the LH1 complex. The high UQ(10) complements detected in RC-LH1 core complexes, but not in purified light-harvesting complex 2 and in RC, are proposed to reflect an in vivo heterogeneity in the distribution of the quinone pool within the chromatophore bilayer.

  5. Use of new strains of Rhodobacter sphaeroides and a modified simple culture medium to increase yield and facilitate purification of the reaction centre.

    Science.gov (United States)

    Jun, D; Saer, R G; Madden, J D; Beatty, J T

    2014-05-01

    A new gene expression system was developed in Rhodobacter sphaeroides, replacing a pRK415-based system used previously. The broad host-range IPTG-inducible plasmid pIND4 was used to create the plasmid pIND4-RC1 for expression of the puhA and pufQBALMX genes, encoding the reaction centre (RC) and light-harvesting complex 1 (LH1) proteins. The strain R. sphaeroides ΔRCLH was used to make a knockout of the rshI restriction endonuclease gene, enabling electroporation of DNA into the bacterium; a subsequent knockout of ppsR was made, creating the strain R. sphaeroides RCx lacking this oxygen-sensing repressor of the photosynthesis gene cluster. Using pIND4-RC1, LH1 levels were increased by a factor of about 8 over pRS1 per cell in cultures grown semi-aerobically. In addition, the ppsR knockout allowed for photosynthetic pigment-protein complex synthesis in the presence of high concentrations of molecular oxygen; here, LH1 levels per cell increased by 20 % when grown under high aeration conditions. A new medium (called RLB) is the E. coli medium LB supplemented with MgCl2 and CaCl2, which was found to increase growth rates and final cell culture densities, with an increase of 30 % of LH1 per cell detected in R. sphaeroides RCx(pIND4-RC1) grown in RLB versus LB medium. Furthermore, cell density was about three times greater in RLB compared to semi-aerobic conditions. The combination of all the modifications resulted in an increase of LH1 and RC per mL of culture volume by approximately 35-fold, and a decrease in the length of culture incubation time from about 5 days to ~36 h.

  6. Femtosecond Dynamics of Energy Transfer in Native B800-B850 and B800-Released LH2 Complexes of Rhodobacter Sphaeroides

    Institute of Scientific and Technical Information of China (English)

    刘伟民; 朱荣毅; 夏辰安; 刘源; 徐春和; 钱士雄

    2003-01-01

    Two kinds of antenna complexes LH2 of Rhodobacter sphaeroides, wild type RS601 and the removal of B800 pigments (B800-released), were used in our experiment. These two LH2 complexes show quite different behaviour in absorption and femtosecond dynamics. By using the femtosecond pump-probe technique, the energy transfer processes occurring in two complexes were studied. Because of removing the B800 pigment from the LH2 in B800-released LH2 complex, the energy transfer between the B800 to B850 pigment was completely eliminated,while the pure internal energy transfer within the exciton states of B850 pigment could be carefully investigated.The results show that, at B800 absorption band, B800-released LH2 obviously shows a dominated transient absorption different from the photobleaching observed in RS601; while at the B850 band, these two complexes show similar photobleaching behaviour.

  7. Structural and preliminary molecular dynamics studies of the Rhodobacter sphaeroides reaction center and its mutant form L(M196)H + H(M202)L

    Science.gov (United States)

    Klyashtorny, V. G.; Fufina, T. Yu.; Vasilieva, L. G.; Shuvalov, V. A.; Gabdulkhakov, A. G.

    2014-07-01

    Pigment-protein interactions are responsible for the high efficiency of the light-energy transfer and conversion in photosynthesis. The reaction center (RC) from the purple bacterium Rhodobacter sphaeroides is the most convenient model for studying the mechanisms of primary processes of photosynthesis. Site-directed mutagenesis can be used to study the effect of the protein environment of electron-transfer cofactors on the optical properties, stability, pigment composition, and functional activity of RC. The preliminary analysis of RC was performed by computer simulation of the amino acid substitutions L(M196)H + H(M202)L at the pigment-protein interface and by estimating the stability of the threedimensional structure of the mutant RC by the molecular dynamics method. The doubly mutated reaction center was overexpressed, purified, and crystallized. The three-dimensional structure of this mutant was determined by X-ray crystallography and compared with the molecular dynamics model.

  8. The nature of the lower excited state of the special pair of bacterial photosynthetic reaction center of Rhodobacter Sphaeroides and the dynamics of primary charge separation

    Science.gov (United States)

    Ivashin, N. V.; Shchupak, E. E.

    2016-08-01

    Quantum-chemical calculations of the structure in the ground and lower singlet excited states and the vibrations (in the ground state) of special pair P of photosynthetic reaction center of purple bacteria (RCPb) Rhodobacter Sphaeroides, consisting of two bacteriochlorophyll molecules PA and PB, have been carried out. It is shown that excitation of the special pair is followed by fast relaxation dynamics, accompanied by the transformation of the initial P* state into the P A δ+ P B δ- state (δ ~ 0.5) with charge separation. This behavior is due to the presence of several nonplanar vibrations with participation of the acetyl group of macrocycle PB in the nuclear wave packet on the potential surface of the P* state; these vibrations facilitate destabilization of the lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO) of the macrocycle PA and formation of the P A δ+ P B δ- state. The structural transformations in the P* state are due to its linking character in the contact region of the acetyl group-containing pyrrole rings of PA and PB. The transition from the P* state to specifically the P A δ+ P B δ- state is related to the fact that the acetyl group PA is involved in the intermolecular hydrogen bond with amino acid residue HisL168; for this reason, this group and the pyrrole ring linked with it can hardly participate in structural transformations. The electronic matrix element H12 of the electron transfer from the special pair in the P A δ+ P B δ- state to a molecule of accessory bacteriochlorophyll BA greatly exceeds that for the transfer to BB. This circumstance and the fact that the P A δ+ P B δ- state is energetically more favorable than the P* state facilitate the preferred directionality of the electron transfer in RCPb Rhodobacter Sphaeroides with participation of the cofactors located in its subunit L.

  9. Enhancement of phototrophic hydrogen production by Rhodobacter sphaeroides ZX-5 using a novel strategy - shaking and extra-light supplementation approach

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xu; Wang, Yong-Hong; Zhang, Si-Liang; Chu, Ju; Zhang, Ming; Huang, Ming-Zhi; Zhuang, Ying-Ping [State Key Laboratory of Bioreactor Engineering, P.O. Box 329, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237 (China)

    2009-12-15

    Biohydrogen has gained attention due to its potential as a sustainable alternative to conventional methods for hydrogen production. In this study, the effect of light intensity as well as cultivation method (standing- and shaking-culture) on the cell growth and hydrogen production of Rhodobacter sphaeroides ZX-5 were investigated in 38-ml anaerobic photobioreactor with RCVBN medium. Thus, a novel shaking and extra-light supplementation (SELS) approach was developed to enhance the phototrophic H{sub 2} production by R. sphaeroides ZX-5 using malate as the sole carbon source. The optimum illumination condition for shaking-culture by strain ZX-5 increased to 7000-8000 lux, markedly higher than that for standing-culture (4000-5000 lux). Under shaking and elevated illumination (7000-8000 lux), the culture was effective in promoting photo-H{sub 2} production, resulting in a 59% and 56% increase of the maximum and average hydrogen production rate, respectively, in comparison with the culture under standing and 4000-5000 lux conditions. The highest hydrogen-producing rate of 165.9 ml H{sub 2}/l h was observed under the application of SELS approach. To our knowledge, this record is currently the highest hydrogen production rate of non-immobilized purple non-sulphur (PNS) bacteria. This optimal performance of photo-H{sub 2} production using SELS approach is a favorable choice of sustainable and economically feasible strategy to improve phototrophic H{sub 2} production efficiency. (author)

  10. Functional importance of a pair of conserved glutamic acid residues and of Ca(2+) binding in the cbb(3)-type oxygen reductases from Rhodobacter sphaeroides and Vibrio cholerae.

    Science.gov (United States)

    Ouyang, Hanlin; Han, Huazhi; Roh, Jung H; Hemp, James; Hosler, Jonathan P; Gennis, Robert B

    2012-09-18

    The cbb(3)-type cytochrome c oxidases are members of the family of heme-copper proton pumping respiratory oxygen reductases. The structure of the cbb(3)-type oxidase from Pseudomonas stutzeri reveals that, in addition to the six redox-active metal centers (two b-type hemes, three c-type hemes, and Cu(B)), the enzyme also contains at least one Ca(2+). The calcium bridges two propionate carboxyls at the interface between the low-spin heme b and the active-site heme b(3) and, in addition, is ligated to a serine in subunit CcoO and by a glutamate in subunit CcoN. The glutamate that is ligated to Ca(2+) is one of a pair of glutamic acid residues that has previously been suggested to be part of a proton exit pathway for pumped protons. In this work, mutations of these glutamates are investigated in the cbb(3)-type oxidases from Vibrio cholerae and Rhodobacter sphaeroides. Metal analysis shows that each of these wild-type enzymes contains Ca(2+). Mutations of the glutamate expected to ligate the Ca(2+) in each of these enzymes (E126 in V. cholerae and E180 in R. sphaeroides) result in a loss of activity as well as a loss of Ca(2+). Mutations of the nearby glutamate (E129 in V. cholerae and E183 in R. sphaeroides) also resulted in a loss of oxidase activity and a loss of Ca(2+). It is concluded that the Ca(2+) is essential for assembly of the fully functional enzyme and that neither of the glutamates is likely to be part of a pathway for pumped protons within the cbb(3)-type oxygen reductases. A more likely role for these glutamates is the maintenance of the structural integrity of the active conformation of the enzyme.

  11. Functional characteristics of spirilloxanthin and keto-bearing Analogues in light-harvesting LH2 complexes from Rhodobacter sphaeroides with a genetically modified carotenoid synthesis pathway.

    Science.gov (United States)

    Niedzwiedzki, Dariusz M; Dilbeck, Preston L; Tang, Qun; Mothersole, David J; Martin, Elizabeth C; Bocian, David F; Holten, Dewey; Hunter, C Neil

    2015-01-01

    Light-harvesting 2 (LH2) complexes from a genetically modified strain of the purple photosynthetic bacterium Rhodobacter (Rba.) sphaeroides were studied using static and ultrafast optical methods and resonance Raman spectroscopy. Carotenoid synthesis in the Rba. sphaeroides strain was engineered to redirect carotenoid production away from spheroidene into the spirilloxanthin synthesis pathway. The strain assembles LH2 antennas with substantial amounts of spirilloxanthin (total double-bond conjugation length N=13) if grown anaerobically and of keto-bearing long-chain analogs [2-ketoanhydrorhodovibrin (N=13), 2-ketospirilloxanthin (N=14) and 2,2'-diketospirilloxanthin (N=15)] if grown semi-aerobically (with ratios that depend on growth conditions). We present the photophysical, electronic, and vibrational properties of these carotenoids, both isolated in organic media and assembled within LH2 complexes. Measurements of excited-state energy transfer to the array of excitonically coupled bacteriochlorophyll a molecules (B850) show that the mean lifetime of the first singlet excited state (S1) of the long-chain (N≥13) carotenoids does not change appreciably between organic media and the protein environment. In each case, the S1 state appears to lie lower in energy than that of B850. The energy-transfer yield is ~0.4 in LH2 (from the strain grown aerobically or semi-aerobically), which is less than half that achieved for LH2 that contains short-chain (N≤11) analogues. Collectively, the results suggest that the S1 excited state of the long-chain (N≥13) carotenoids participates little if at all in carotenoid-to-BChl a energy transfer, which occurs predominantly via the carotenoid S2 excited state in these antennas.

  12. Functional assembly of the foreign carotenoid lycopene into the photosynthetic apparatus of Rhodobacter sphaeroides, achieved by replacement of the native 3-step phytoene desaturase with its 4-step counterpart from Erwinia herbicola.

    Science.gov (United States)

    Garcia-Asua, Guillermo; Cogdell, Richard J; Hunter, C Neil

    2002-04-01

    Photosynthetic organisms synthesize a diverse range of carotenoids. These pigments are important for the assembly, function and stability of photosynthetic pigment-protein complexes, and they are used to quench harmful radicals. The photosynthetic bacterium Rhodobacter sphaeroides was used as a model system to explore the origin of carotenoid diversity. Replacing the native 3-step phytoene desaturase (CrtI) with the 4-step enzyme from Erwinia herbicola results in significant flux down the spirilloxanthin pathway for the first time in Rb. sphaeroides. In Rb. sphaeroides, the completion of four desaturations to lycopene by the Erwinia CrtI appears to require the absence of CrtC and, in a crtC background, even the native 3-step enzyme can synthesize a significant amount (13%) of lycopene, in addition to the expected neurosporene. We suggest that the CrtC hydroxylase can intervene in the sequence of reactions catalyzed by phytoene desaturase. We investigated the properties of the lycopene-synthesizing strain of Rb. sphaeroides. In the LH2 light-harvesting complex, lycopene transfers absorbed light energy to the bacteriochlorophylls with an efficiency of 54%, which compares favourably with other LH2 complexes that contain carotenoids with 11 conjugated double bonds. Thus, lycopene can join the assembly pathway for photosynthetic complexes in Rb. sphaeroides, and can perform its role as an energy donor to bacteriochlorophylls.

  13. Chronic Exposure to Rhodobacter Sphaeroides Extract Lycogen™ Prevents UVA-Induced Malondialdehyde Accumulation and Procollagen I Down-Regulation in Human Dermal Fibroblasts

    Directory of Open Access Journals (Sweden)

    Tsai-Hsiu Yang

    2014-01-01

    Full Text Available UVA contributes to the pathogenesis of skin aging by downregulation of procollagen I content and induction of matrix metalloproteinase (MMP-associated responses. Application of antioxidants such as lycopene has been demonstrated as a convenient way to achieve protection against skin aging. Lycogen™, derived from the extracts of Rhodobacter sphaeroides, exerts several biological effects similar to that of lycopene whereas most of its anti-aging efficacy remains uncertain. In this study, we attempted to examine whether Lycogen™ could suppress malondialdehyde (MDA accumulation and restore downregulated procollagen I expression induced by UVA exposure. In human dermal fibroblasts Hs68 cells, UVA repressed cell viability and decreased procollagen I protein content accompanied with the induction of MMP-1 and MDA accumulation. Remarkably, incubation with 50 µM Lycogen™ for 24 h ameliorated UVA-induced cell death and restored UVA-induced downregulation of procollagen in a dose-related manner. Lycogen™ treatment also prevented the UVA-induced MMP-1 upregulation and intracellular MDA generation in Hs68 cells. Activation of NFκB levels, one of the downstream events induced by UVA irradiation and MMP-1 induction, were also prevented by Lycogen™ administration. Taken together, our findings demonstrate that Lycogen™ may be an alternative agent that prevents UVA-induced skin aging and could be used in cosmetic and pharmaceutical applications.

  14. Effects of the cryptochrome CryB from Rhodobacter sphaeroides on global gene expression in the dark or blue light or in the presence of singlet oxygen.

    Science.gov (United States)

    Frühwirth, Sebastian; Teich, Kristin; Klug, Gabriele

    2012-01-01

    Several regulators are controlling the formation of the photosynthetic apparatus in the facultatively photosynthetic bacterium Rhodobacter sphaeroides. Among the proteins affecting photosynthesis gene expression is the blue light photoreceptor cryptochrome CryB. This study addresses the effect of CryB on global gene expression. The data reveal that CryB does not only influence photosynthesis gene expression but also genes for the non-photosynthetic energy metabolism like citric acid cycle and oxidative phosphorylation. In addition several genes involved in RNA processing and in transcriptional regulation are affected by a cryB deletion. Although CryB was shown to undergo a photocycle it does not only affect gene expression in response to blue light illumination but also in response to singlet oxygen stress conditions. While there is a large overlap in these responses, some CryB-dependent effects are specific for blue-light or photooxidative stress. In addition to protein-coding genes some genes for sRNAs show CryB-dependent expression. These findings give new insight into the function of bacterial cryptochromes and demonstrate for the first time a function in the oxidative stress response.

  15. Eukaryotic behaviour of a prokaryotic energy-transducing membrane: fully detached vesicular organelles arise by budding from the Rhodobacter sphaeroides intracytoplasmic photosynthetic membrane.

    Science.gov (United States)

    Niederman, Robert A

    2010-05-01

    A major feature that distinguishes prokaryotic organisms from eukaryotes is their less complex internal structure, in which all membrane-associated functions are thought to be present within a continuous lipid-protein bilayer, rather than with distinct organelles. Contrary to this notion, as described by Tucker and co-workers in this issue of Molecular Microbiology, the application of cryo-electron tomography to the purple bacterium Rhodobacter sphaeroides has demonstrated a heretofore unrecognized ultrastructural complexity within the intracytoplasmic membrane (ICM) housing the photosynthetic apparatus. In addition to distinguishing invaginations of the cytoplasmic membrane (CM) and interconnected vesicular structures still attached to the CM, a eukaryote-like ICM budding process was revealed, which results in the formation of fully detached vesicular structures. These bacterial organelles are able to carry out both the light-harvesting and light-driven energy transduction activities necessary for the cells to assume a photosynthetic lifestyle. Their formation is shown to represent the final stage in a membrane invagination and growth process, originating with small CM indentations, which after cell disruption give rise to a membrane fraction that can be separated from mature ICM vesicles by rate-zone sedimentation.

  16. Light induced EPR spectra of reaction centers from Rhodobacter sphaeroides at 80K: Evidence for reduction of QB by B-branch electron transfer in native reaction centers.

    Science.gov (United States)

    Paddock, M. L; Isaacson, R. A.; Abresch, E. C.; Okamura, M. Y.

    2006-01-01

    Photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides capture solar energy by electron transfer from primary donor, D, to quinone acceptor, QB, through the active A-branch of electron acceptors, but not the inactive B-branch. The light induced EPR spectrum from native RCs that had Fe2+ replaced by Zn2+ was investigated at cryogenic temperature (80K, 35 GHz). In addition to the light induced signal due to formation of D+•QA−• observed previously, a small fraction (~5%) of the signal displayed very different characteristics: (1) The signal was absent in RCs in which the QB was displaced by the inhibitor stigmatellin. (2) Its decay time (τ=6 s) was the same as observed for D+•QB−• in mutant RCs lacking QA, which is significantly slower than for D+•QA−• (τ=30 ms). (3) Its EPR spectrum was identical to that of D+•QB−•. (4) The quantum efficiency for forming the major component of the signal was the same as that found for mutant RCs lacking QA (Φ =0.2%) and was temperature independent. These results are explained by direct photochemical reduction of QB via B-branch electron transfer in a small fraction of native RCs. PMID:18163156

  17. Comparison of H{sub 2} accumulation by Rhodobacter sphaeroides KD131 and its uptake hydrogenase and PHB synthase deficient mutant

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Mi-Sun; Baek, Jin-Sook [Biomass Research Center, Korea Institute of Energy Research, 71-2 Jang-dong, Yuseong-gu, Daejeon 305-343 (Korea, Republic of); Lee, Jeong K. [Department of Life Science, Sogang University, Shinsu-dong, Mapo-gu, Seoul 121-742 (Korea, Republic of)

    2006-01-15

    Rhodobacter sphaeroides KD131 and its mutant strain lacking uptake hydrogenase (Hup{sup -}) and PHB synthase (Phb{sup -}) have been studied on H{sub 2} production and cell growth under different culture conditions. Both strains started producing H{sub 2} from the middle of the logarithmic growth phase and continued until the cell concentration leveled out. The rates of H{sub 2} production were 1.32 and 3.34ml H{sub 2}/mg-dcw for the wild-type and Hup{sup -}/Phb{sup -} mutant strain, respectively, at the optimum conditions. Malate and lactate were better carbon sources than starch, sucrose or glycerol. Approximately 60% of acetic acid was degraded in 48h by the wild-type strain and pH increased to 9.4. However, the Hup{sup -}/Phb{sup -} mutant strain did not grow well and degraded only 19% of acetic acid. The pH ranges of 7.0 were the optimum for the cell growth and pH 7.5 for the H{sub 2} production. Both strains grew and produced hydrogen under the irradiance of 12-120W/m{sup 2}, but cell growth was inhibited over 400W/m{sup 2}. (author)

  18. The Photoheterotrophic Growth of Bacteriochlorophyll Synthase-Deficient Mutant of Rhodobacter sphaeroides Is Restored by I44F Mutant Chlorophyll Synthase of Synechocystis sp. PCC 6803.

    Science.gov (United States)

    Kim, Eui-Jin; Kim, Hyeonjun; Lee, Jeong K

    2016-05-28

    Chlorophyll synthase (ChlG) and bacteriochlorophyll synthase (BchG) have a high degree of substrate specificity. The BchG mutant of Rhodobacter sphaeroides, BG1 strain, is photosynthetically incompetent. When BG1 harboring chlG of Synechocystis sp. PCC 6803 was cultured photoheterotrophically, colonies arose at a frequency of approximately 10(-8). All the suppressor mutants were determined to have the same mutational change, ChlGI44F. The mutated enzyme ChlGI44F showed BchG activity. Remarkably, BchGF28I, which has the substitution of F at the corresponding 28(th) residue to I, showed ChlG activity. The Km values of ChlGI44F and BchGF28I for their original substrates, chlorophyllide (Chlide) a and bacteriochlorophyllide (Bchlide) a, respectively, were not affected by the mutations, but the Km values of ChlGI44F and BchGF28I for the new substrates Bchlide a and Chlide a, respectively, were more than 10-fold larger than those for their original substrates, suggesting the lower affinities for new substrates. Taken together, I44 and F28 are important for the substrate specificities of ChlG and BchG, respectively. The BchG activity of ChlGI44F and the ChlG activity of BchGF28I further suggest that ChlG and BchG are evolutionarily related enzymes.

  19. Effects of ammonium ion, acetate and aerobic conditions on hydrogen production and expression levels of nitrogenase genes in Rhodobacter sphaeroides O.U.001

    Energy Technology Data Exchange (ETDEWEB)

    Akkoese, Sevilay; Guenduez, Ufuk; Yuecel, Meral [Middle East Technical University, Department of Biological Sciences, 06531 Ankara (Turkey); Eroglu, Inci [Middle East Technical University, Department of Chemical Engineering, 06531 Ankara (Turkey)

    2009-11-15

    In the present study, expression levels of nitrogenase encoding nifH and control genes nifA and prrA were examined at different physiological conditions in Rhodobacter sphaeroides O.U.001. In addition to variations in expression levels, changes in hydrogen production and growth were also investigated in response to different concentrations of ammonium source, acetate and aerobic conditions. In the present study, increasing concentration of ammonium chloride was found to be caused decrease in hydrogen production. Glutamate containing medium had the capacity for higher hydrogen production. Hydrogen production was observed even in aerobic conditions. The expression levels of nifH and nifA genes decreased with the increasing concentrations of ammonium chloride. Although the expression of nifA was present in the highest concentrations of NH{sub 4}Cl under anaerobic conditions, no expression was observed under aerobic conditions of the same culture conditions. This was likely due to transcriptional level inhibition of nitrogenase in the presence of ammonium ion. Negative correlation was observed between the expression levels of prrA gene and its target, nifA gene. (author)

  20. Effects of the cryptochrome CryB from Rhodobacter sphaeroides on global gene expression in the dark or blue light or in the presence of singlet oxygen.

    Directory of Open Access Journals (Sweden)

    Sebastian Frühwirth

    Full Text Available Several regulators are controlling the formation of the photosynthetic apparatus in the facultatively photosynthetic bacterium Rhodobacter sphaeroides. Among the proteins affecting photosynthesis gene expression is the blue light photoreceptor cryptochrome CryB. This study addresses the effect of CryB on global gene expression. The data reveal that CryB does not only influence photosynthesis gene expression but also genes for the non-photosynthetic energy metabolism like citric acid cycle and oxidative phosphorylation. In addition several genes involved in RNA processing and in transcriptional regulation are affected by a cryB deletion. Although CryB was shown to undergo a photocycle it does not only affect gene expression in response to blue light illumination but also in response to singlet oxygen stress conditions. While there is a large overlap in these responses, some CryB-dependent effects are specific for blue-light or photooxidative stress. In addition to protein-coding genes some genes for sRNAs show CryB-dependent expression. These findings give new insight into the function of bacterial cryptochromes and demonstrate for the first time a function in the oxidative stress response.

  1. Coproporphyrin Excretion and Low Thiol Levels Caused by Point Mutation in the Rhodobacter sphaeroides S-Adenosylmethionine Synthetase Gene ▿ †

    Science.gov (United States)

    Sabaty, Monique; Adryanczyk, Géraldine; Roustan, Chloë; Cuiné, Stephan; Lamouroux, Christine; Pignol, David

    2010-01-01

    A spontaneous mutant of Rhodobacter sphaeroides f. sp. denitrificans IL-106 was found to excrete a large amount of a red compound identified as coproporphyrin III, an intermediate in bacteriochlorophyll and heme synthesis. The mutant, named PORF, is able to grow under phototrophic conditions but has low levels of intracellular cysteine and glutathione and overexpresses the cysteine synthase CysK. The expression of molybdoenzymes such as dimethyl sulfoxide (DMSO) and nitrate reductases is also affected under certain growth conditions. Excretion of coproporphyrin and overexpression of CysK are not directly related but were both found to be consequences of a diminished synthesis of the key metabolite S-adenosylmethionine (SAM). The wild-type phenotype is restored when the gene metK encoding SAM synthetase is supplied in trans. The metK gene in the mutant strain has a mutation leading to a single amino acid change (H145Y) in the encoded protein. This point mutation is responsible for a 70% decrease in intracellular SAM content which probably affects the activities of numerous SAM-dependent enzymes such as coproporphyrinogen oxidase (HemN); uroporphyrinogen III methyltransferase (CobA), which is involved in siroheme synthesis; and molybdenum cofactor biosynthesis protein A (MoaA). We propose a model showing that the attenuation of the activities of SAM-dependent enzymes in the mutant could be responsible for the coproporphyrin excretion, the low cysteine and glutathione contents, and the decrease in DMSO and nitrate reductase activities. PMID:20038586

  2. Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: combined transcriptome and proteome analysis

    Energy Technology Data Exchange (ETDEWEB)

    Eraso, Jesus M.; Roh, Jung Hyeob; Zeng, Xiaohua; Callister, Stephen J.; Lipton, Mary S.; Kaplan, Samuel

    2008-07-01

    The PrrBA two-component regulatory system is a major global regulator in Rhodobacter sphaeroides 2.4.1. In this study we have compared the transcriptome and proteome profiles of the wild type (WT) and mutant PrrA2 cells grown anaerobically, in the dark, with DMSO as electron acceptor. Approximately 25% of the genes present in the genome are PrrA-regulated, at the transcriptional level, either directly or indirectly, by ≥ 2-fold relative to wild type. The genes affected are widespread throughout all COG functional categories, with previously unsuspected “metabolic” genes affected when in the PrrA mutant background. PrrA was found to act both as an activator and a repressor of transcription, with more genes being repressed in the presence of PrrA (9:5 ratio). An analysis of the genes encoding the 1,536 peptides detected through our chromatographic study, which corresponds to 36% coverage of the genome, revealed that approximately 20% of the genes encoding these proteins were positively regulated, whereas approximately 32% were negatively regulated by PrrA, which is in excellent agreement with the percentages obtained for the whole genomic transcriptome profile. In addition, comparison of the transcriptome and proteome mean parameter values chosen between WT and PrrA2 showed good qualitative agreement, indicating that transcript regulation paralleled the corresponding protein abundance, although not one for one. The microarray analysis was validated by direct mRNA measurement of randomly selected, both positively and negatively regulated genes. lacZ transcriptional and kan translational fusions enabled us to map putative PrrA binding sites, as well as revealing potential gene targets for indirect regulation by PrrA.

  3. Quinone (QB) reduction by B-branch electron transfer in mutant bacterial reaction centers from Rhodobacter sphaeroides: quantum efficiency and X-ray structure.

    Science.gov (United States)

    Paddock, M L; Chang, C; Xu, Q; Abresch, E C; Axelrod, H L; Feher, G; Okamura, M Y

    2005-05-10

    The photosynthetic reaction center (RC) from purple bacteria converts light into chemical energy. Although the RC shows two nearly structurally symmetric branches, A and B, light-induced electron transfer in the native RC occurs almost exclusively along the A-branch to a primary quinone electron acceptor Q(A). Subsequent electron and proton transfer to a mobile quinone molecule Q(B) converts it to a quinol, Q(B)H(2). We report the construction and characterization of a series of mutants in Rhodobacter sphaeroides designed to reduce Q(B) via the B-branch. The quantum efficiency to Q(B) via the B-branch Phi(B) ranged from 0.4% in an RC containing the single mutation Ala-M260 --> Trp to 5% in a quintuple mutant which includes in addition three mutations to inhibit transfer along the A-branch (Gly-M203 --> Asp, Tyr-M210 --> Phe, Leu-M214 --> His) and one to promote transfer along the B-branch (Phe-L181 --> Tyr). Comparing the value of 0.4% for Phi(B) obtained in the AW(M260) mutant, which lacks Q(A), to the 100% quantum efficiency for Phi(A) along the A-branch in the native RC, we obtain a ratio for A-branch to B-branch electron transfer of 250:1. We determined the structure of the most effective (quintuple) mutant RC at 2.25 A (R-factor = 19.6%). The Q(A) site did not contain a quinone but was occupied by the side chain of Trp-M260 and a Cl(-). In this structure a nonfunctional quinone was found to occupy a new site near M258 and M268. The implications of this work to trap intermediate states are discussed.

  4. Trapped Conformational States of Semiquinone (D+•QB−•) Formed by B-Branch Electron Transfer at Low Temperature in Rhodobacter sphaeroides Reaction Centers‡

    Science.gov (United States)

    Paddock, M. L.; Flores, M.; Isaacson, R.; Chang, C.; Abresch, E. C.; Selvaduray, P.; Okamura, M.Y.

    2006-01-01

    The reaction center (RC) from Rhodobacter sphaeroides captures light energy by electron transfer between quinones QA and QB, involving a conformational gating step. In this work, conformational states of D+•QB−• were trapped (80K) and studied using EPR spectroscopy in mutant RCs that lack QA in which QB was reduced by the bacteriopheophytin along the B-branch. In mutant RCs frozen in the dark, a light induced EPR signal due to D+•QB−• formed in 30% of the sample with low quantum yield (0.2%–20%) and decayed in 6 s. A small signal with similar characteristics was also observed in native RCs. In contrast, the EPR signal due to D+QB− in mutant RCs illuminated while freezing formed in ~ 95% of the sample that did not decay (τ >107s) at 80K. In all samples, the observed g-values were the same (g=2.0026) indicating that all active QB−• was located in a proximal conformation coupled with the non-heme Fe2+. We propose that before electron transfer at 80K, the majority (~70%) of QB, structurally located in the distal site, cannot be stably reduced, while the minor (~30%) active configurations are in the proximal site. The large difference in the lifetimes of the un-relaxed and relaxed D+•QB−• states is attributed to relaxation of protein residues and internal water molecules that stabilize D+•QB−•. These results demonstrate energetically significant conformational changes involved in stabilizing the D+•QB−• state. The unrelaxed and relaxed states can be considered to be the initial and final states along the reaction coordinate for conformationally-gated electron transfer. PMID:17115698

  5. An isotope-edited FTIR investigation of the role of Ser-L223 in binding quinone (QB) and semiquinone (QB-) in the reaction center from Rhodobacter sphaeroides.

    Science.gov (United States)

    Nabedryk, Eliane; Paddock, Mark L; Okamura, Melvin Y; Breton, Jacques

    2005-11-08

    In the photosynthetic reaction center (RC) from the purple bacterium Rhodobacter sphaeroides, proton-coupled electron-transfer reactions occur at the secondary quinone (Q(B)) site. Several nearby residues are important for both binding and redox chemistry involved in the light-induced conversion from Q(B) to quinol Q(B)H(2). Ser-L223 is one of the functionally important residues located near Q(B). To obtain information on the interaction between Ser-L223 and Q(B) and Q(B)(-), isotope-edited Q(B)(-)/Q(B) FTIR difference spectra were measured in a mutant RC in which Ser-L223 is replaced with Ala and compared to the native RC. The isotope-edited IR fingerprint spectra for the C=O [see text] and C=C [see text] modes of Q(B) (Q(B)(-)) in the mutant are essentially the same as those of the native RC. These findings indicate that highly equivalent interactions of Q(B) and Q(B)(-) with the protein occur in both native and mutant RCs. The simplest explanation of these results is that Ser-L223 is not hydrogen bonded to Q(B) or Q(B)(-) but presumably forms a hydrogen bond to a nearby acid group, preferentially Asp-L213. The rotation of the Ser OH proton from Asp-L213 to Q(B)(-) is expected to be an important step in the proton transfer to the reduced quinone. In addition, the reduced quinone remains firmly bound, indicating that other distinct hydrogen bonds are more important for stabilizing Q(B)(-). Implications on the design features of the Q(B) binding site are discussed.

  6. Conformational gating of the electron transfer reaction QA−⋅QB → QAQB−⋅ in bacterial reaction centers of Rhodobacter sphaeroides determined by a driving force assay

    Science.gov (United States)

    Graige, M. S.; Feher, G.; Okamura, M. Y.

    1998-01-01

    The mechanism of the electron transfer reaction, QA−⋅QB → QAQB−⋅, was studied in isolated reaction centers from the photosynthetic bacterium Rhodobacter sphaeroides by replacing the native Q10 in the QA binding site with quinones having different redox potentials. These substitutions are expected to change the intrinsic electron transfer rate by changing the redox free energy (i.e., driving force) for electron transfer without affecting other events that may be associated with the electron transfer (e.g., protein dynamics or protonation). The electron transfer from QA−⋅ to QB was measured by three independent methods: a functional assay involving cytochrome c2 to measure the rate of QA−⋅ oxidation, optical kinetic spectroscopy to measure changes in semiquinone absorption, and kinetic near-IR spectroscopy to measure electrochromic shifts that occur in response to electron transfer. The results show that the rate of the observed electron transfer from QA−⋅ to QB does not change as the redox free energy for electron transfer is varied over a range of 150 meV. The strong temperature dependence of the observed rate rules out the possibility that the reaction is activationless. We conclude, therefore, that the independence of the observed rate on the driving force for electron transfer is due to conformational gating, that is, the rate limiting step is a conformational change required before electron transfer. This change is proposed to be the movement, controlled kinetically either by protein dynamics or intermolecular interactions, of QB by ≈5 Å as observed in the x-ray studies of Stowell et al. [Stowell, M. H. B., McPhillips, T. M., Rees, D. C., Soltis, S. M., Abresch, E. & Feher, G. (1997) Science 276, 812–816]. PMID:9751725

  7. Trapped conformational states of semiquinone (D+*QB-*) formed by B-branch electron transfer at low temperature in Rhodobacter sphaeroides reaction centers.

    Science.gov (United States)

    Paddock, M L; Flores, M; Isaacson, R; Chang, C; Abresch, E C; Selvaduray, P; Okamura, M Y

    2006-11-28

    The reaction center (RC) from Rhodobacter sphaeroides captures light energy by electron transfer between quinones QA and QB, involving a conformational gating step. In this work, conformational states of D+*QB-* were trapped (80 K) and studied using EPR spectroscopy in native and mutant RCs that lack QA in which QB was reduced by the bacteriopheophytin along the B-branch. In mutant RCs frozen in the dark, a light induced EPR signal due to D+*QB-* formed in 30% of the sample with low quantum yield (0.2%-20%) and decayed in 6 s. A small signal with similar characteristics was also observed in native RCs. In contrast, the EPR signal due to D+*QB-* in mutant RCs illuminated while freezing formed in approximately 95% of the sample did not decay (tau >107 s) at 80 K (also observed in the native RC). In all samples, the observed g-values were the same (g = 2.0026), indicating that all active QB-*'s were located in a proximal conformation coupled with the nonheme Fe2+. We propose that before electron transfer at 80 K, the majority (approximately 70%) of QB, structurally located in the distal site, was not stably reducible, whereas the minority (approximately 30%) of active configurations was in the proximal site. The large difference in the lifetimes of the unrelaxed and relaxed D+*QB-* states is attributed to the relaxation of protein residues and internal water molecules that stabilize D+*QB-*. These results demonstrate energetically significant conformational changes involved in stabilizing the D+*QB-* state. The unrelaxed and relaxed states can be considered to be the initial and final states along the reaction coordinate for conformationally gated electron transfer.

  8. Electron-Transfer Secondary Reaction Matrices for MALDI MS Analysis of Bacteriochlorophyll a in Rhodobacter sphaeroides and Its Zinc and Copper Analogue Pigments.

    Science.gov (United States)

    Calvano, Cosima Damiana; Ventura, Giovanni; Trotta, Massimo; Bianco, Giuliana; Cataldi, Tommaso R I; Palmisano, Francesco

    2017-01-01

    Bacteriochlorophyll a (BChl a), a photosynthetic pigment performing the same functions of chlorophylls in plants, features a bacteriochlorin macrocycle ring (18 π electrons) with two reduced pyrrole rings along with a hydrophobic terpenoid side chain (i.e., the phytol residue). Chlorophylls analysis by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is not so straightforward since pheophytinization (i.e., release of the central metal ion) and cleavage of the phytol-ester linkage are invariably observed by employing protonating matrices such as 2,5-dihydroxybenzoic acid, sinapinic acid, and α-cyano-4-hydroxycinnamic acid. Using BChl a from Rhodobacter sphaeroides R26 strain as a model system, different electron-transfer (ET) secondary reaction matrices, leading to the formation of almost stable radical ions in both positive ([M](+•)) and negative ([M](-•)) ionization modes at m/z 910.55, were evaluated. Compared with ET matrices such as trans-2-[3-(4-t-butyl-phenyl)-2-methyl-2-propenylidene]malononitrile (DCTB), 2,2':5',2''-terthiophene (TER), anthracene (ANT), and 9,10-diphenylanthracene (DP-ANT), 1,5-diaminonaphthalene (DAN) was found to provide the highest ionization yield with a negligible fragmentation. DAN also displayed excellent ionization properties for two metal ion-substituted bacteriochlorophylls, (i.e., Zn- and Cu-BChl a at m/z 950.49 and 949.49), respectively. MALDI MS/MS of both radical charged molecular species provide complementary information, thus making analyte identification more straightforward. Graphical Abstract ᅟ.

  9. Electron-Transfer Secondary Reaction Matrices for MALDI MS Analysis of Bacteriochlorophyll a in Rhodobacter sphaeroides and Its Zinc and Copper Analogue Pigments

    Science.gov (United States)

    Calvano, Cosima Damiana; Ventura, Giovanni; Trotta, Massimo; Bianco, Giuliana; Cataldi, Tommaso R. I.; Palmisano, Francesco

    2017-01-01

    Bacteriochlorophyll a ( BChl a), a photosynthetic pigment performing the same functions of chlorophylls in plants, features a bacteriochlorin macrocycle ring (18 π electrons) with two reduced pyrrole rings along with a hydrophobic terpenoid side chain (i.e., the phytol residue). Chlorophylls analysis by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is not so straightforward since pheophytinization (i.e., release of the central metal ion) and cleavage of the phytol-ester linkage are invariably observed by employing protonating matrices such as 2,5-dihydroxybenzoic acid, sinapinic acid, and α-cyano-4-hydroxycinnamic acid. Using BChl a from Rhodobacter sphaeroides R26 strain as a model system, different electron-transfer (ET) secondary reaction matrices, leading to the formation of almost stable radical ions in both positive ([M]+•) and negative ([M]-•) ionization modes at m/z 910.55, were evaluated. Compared with ET matrices such as trans-2-[3-(4-t-butyl-phenyl)-2-methyl-2-propenylidene]malononitrile (DCTB), 2,2':5',2''-terthiophene (TER), anthracene (ANT), and 9,10-diphenylanthracene (DP-ANT), 1,5-diaminonaphthalene (DAN) was found to provide the highest ionization yield with a negligible fragmentation. DAN also displayed excellent ionization properties for two metal ion-substituted bacteriochlorophylls, (i.e., Zn- and Cu-BChl a at m/z 950.49 and 949.49), respectively. MALDI MS/MS of both radical charged molecular species provide complementary information, thus making analyte identification more straightforward.

  10. Partial steps of charge translocation in the nonpumping N139L mutant of Rhodobacter sphaeroides cytochrome c oxidase with a blocked D-channel.

    Science.gov (United States)

    Siletsky, Sergey A; Zhu, Jiapeng; Gennis, Robert B; Konstantinov, Alexander A

    2010-04-13

    The N139L substitution in the D-channel of cytochrome oxidase from Rhodobacter sphaeroides results in an approximately 15-fold decrease in the turnover number and a loss of proton pumping. Time-resolved absorption and electrometric assays of the F --> O transition in the N139L mutant oxidase result in three major findings. (1) Oxidation of the reduced enzyme by O(2) shows approximately 200-fold inhibition of the F --> O step (k approximately 2 s(-1) at pH 8) which is not compatible with enzyme turnover ( approximately 30 s(-1)). Presumably, an abnormal intermediate F(deprotonated) is formed under these conditions, one proton-deficient relative to a normal F state. In contrast, the F --> O transition in N139L oxidase induced by single-electron photoreduction of intermediate F, generated by reaction of the oxidized enzyme with H(2)O(2), decelerates to an extent compatible with enzyme turnover. (2) In the N139L mutant, the protonic phase of Deltapsi generation coupled to the flash-induced F --> O transition greatly decreases in rate and magnitude and can be assigned to the movement of a proton from E286 to the binuclear site, required for reduction of heme a(3) from the Fe(4+) horizontal lineO(2-) state to the Fe(3+)-OH(-) state. Electrogenic reprotonation of E286 from the inner aqueous phase is missing from the F --> O step in the mutant. (3) In the N139L mutant, the KCN-insensitive rapid electrogenic phase may be composed of two components with lifetimes of approximately 10 and approximately 40 mus and a magnitude ratio of approximately 3:2. The 10 mus phase matches vectorial electron transfer from Cu(A) to heme a, whereas the 40 mus component is assigned to intraprotein proton displacement across approximately 20% of the membrane dielectric thickness. This proton displacement might be triggered by rotation of the charged K362 side chain coupled to heme a reduction. The two components of the rapid electrogenic phase have been resolved subsequently with other D

  11. Heterologous Production of the Photosynthetic Reaction Center and Light Harvesting 1 Complexes of the Thermophile Thermochromatium tepidum in the Mesophile Rhodobacter sphaeroides and Thermal Stability of a Hybrid Core Complex.

    Science.gov (United States)

    Jun, D; Huang, V; Beatty, J T

    2017-10-15

    The photosynthetic complexes of the thermophile Thermochromatium tepidum are of considerable interest in biohybrid solar cell applications because of the ability of thermophilic proteins to tolerate elevated temperatures. Synthetic operons encoding reaction center (RC) and light harvesting 1 (LH1) pigment-protein complexes of T. tepidum were expressed in the mesophile Rhodobacter sphaeroides The T. tepidum RC (TRC) was assembled and was found to be functional with the addition of menadione to populate the QA pocket. The production of T. tepidum LH1 (TLH1) was increased by selection of a phototrophy-capable mutant after UV irradiation mutagenesis, which yielded a hybrid RC-TLH1 core complex consisting of the R. sphaeroides RC and T. tepidum TLH1, confirmed by the absorbance peak of TLH1 at 915 nm. Affinity chromatography partial purification and subsequent sucrose gradient analysis of the hybrid RC-TLH1 core complex indicated that this core complex assembled as a monomer. Furthermore, the RC-TLH1 hybrid core complex was more tolerant of a temperature of 70°C than the R. sphaeroides RC-LH1 core complexes in both the dimeric and monomeric forms; after 1 h, the hybrid complex retained 58% of the initial starting value, compared to values of 11% and 53% for the R. sphaeroides RC-LH1 dimer and monomer forms, respectively.IMPORTANCE This work is important because it is a new approach to bioengineering of photosynthesis proteins for potential use in biophotovoltaic solar energy capture. The work establishes a proof of principle for future biohybrid solar cell applications. Copyright © 2017 American Society for Microbiology.

  12. 浑球红细菌(Rhodobacter sphaeroides)中氢化酶正调节基因hupR的克隆及功能分析%Isolation and Analysis of hupR Gene Required for the Expression of Hydrogenase in Rhodobacter sphaeroides

    Institute of Scientific and Technical Information of China (English)

    徐冬青; 吴永强

    2001-01-01

    Cosmid 1 containing the hup genes isolated from the photosynthetic b acterium Rhodobacter sphaeroides was studied. The hupR gene from cosmid 1 was cl oned and sequenced (EMBL accession number AJ243734). It encoded a 54.031 kD prot ein homologous to transcriptional regulators belonging to the superfamily of two -component regulatory systems. The HupR protein was overexpressed in Escheric hia coli in the form of His6-tagged HupR. The cloned hupR gene could res tore hydrog enase activity in R. Sphaeroides hupR mutants and activate hupSL gene transcription.%从光合细菌Rhodobacter sphaeroides基因文库中分离出含有氢化酶基因簇(hup)的粘粒cosmid 1后, 亚克隆了R. sphaeroides的氢化酶调节基因hupR, 测定了hupR的核苷酸序列, 并完成了氢化酶基因簇的部分物理图谱. 实验结果表明, hupR基因全长1 476 bp, 编码的HupR蛋白分子量约为54.031 kD (EMBL接受号: AJ243734). 与R. capsulatus中HupR相比, 同源性高达73%. 同源性比较结果表明, 它属于双组分调节系统中受体蛋白. hupR基因在E. coli中进行了体外表达, 纯化后测定得到的HupR蛋白的分子量大小与hupR基因推测的分子量大小一致. 通过双交换, 将卡那霉素抗性基因插入hupR基因, 获得丧失氢化酶活性的hupR-的突变株, KR5和KR7. hupS∷lacZ融合基因在野生型中的转录表达量是在该突变株中的7~9倍. 将hupR基因置于弱启动子pfru下游, 构建了质粒pNRC3, 并将其导入hupR-的突变株, 可使突变株重新获得氢化酶活性. 以上结果说明, HupR蛋白对氢化酶的转录表达起着正调节作用. 在HupR蛋白的磷酸化区域进行定点和缺失突变, 不影响HupR激活氢化酶基因的表达, 推测HupR蛋白是在非磷酸化的状态下起调节作用的.

  13. Formation of charge separated state P+OA- and triplet state 3P at low temperature in Rhodobacter sphaeroides (R-26) reaction centers in which bacteriopheophytin a is replaced by plant pheophytin a.

    Science.gov (United States)

    Shkuropatov Aya; Proskuryakov, I I; Shkuropatova, V A; Zvereva, M G; Shuvalov, V A

    1994-09-05

    Low temperature optical and photochemical properties of Rhodobacter sphaeroides (R-26) reaction centers, in which bacteriopheophytin a has been replaced by plant pheophytin a, are reported. Modified reaction centers preserve the ability for photoinduced electron transfer from the primary electron donor P to the primary quinone acceptor QA at 80K. The triplet state ESR signal of modified reaction centers with prereduced QA at 10K shows an electron spin polarization pattern and ZFS parameters analogous to those for the triplet state 3P in non-treated reaction centers. It was found that at low temperature both P+QA- and 3P states are formed via a precursor radical pair P+I- in which I is the introduced plant pheophytin molecule. This shows that acceptor systems of bacterial and plant (photosystem II) reaction centers are mutually replacable in structural and functional aspects.

  14. Relationship of proton motive force and the F(0)F (1)-ATPase with bio-hydrogen production activity of Rhodobacter sphaeroides: effects of diphenylene iodonium, hydrogenase inhibitor, and its solvent dimethylsulphoxide.

    Science.gov (United States)

    Hakobyan, Lilit; Gabrielyan, Lilit; Trchounian, Armen

    2012-08-01

    Rhodobacter sphaeroides MDC 6521 was able to produce bio-hydrogen (H(2)) in anaerobic conditions under illumination. In this study the effects of the hydrogenase inhibitor-diphenylene iodonium (Ph(2)I) and its solvent dimethylsulphoxide (DMSO) on growth characteristics and H(2) production by R. sphaeroides were investigated. The results point out the concentration dependent DMSO effect: in the presence of 10 mM DMSO H(2) yield was ~6 fold lower than that of the control. The bacterium was unable to produce H(2) in the presence of Ph(2)I. In order to examine the mediatory role of proton motive force (∆p) or the F(0)F(1)-ATPase in H(2) production by R. sphaeroides, the effects of Ph(2)I and DMSO on ∆p and its components (membrane potential (∆ψ) and transmembrane pH gradient), and ATPase activity were determined. In these conditions ∆ψ was of -98 mV and the reversed ∆pH was +30 mV, resulting in ∆p of -68 mV. Ph(2)I decreased ∆ψ in concentrations of 20 μM and higher; lower concentrations of Ph(2)I as DMSO had no valuable effect on ∆ψ. The R. sphaeroides membrane vesicles demonstrated significant ATPase activity sensitive to N,N'-dicyclohexylcarbodiimide. The 10-20 μM Ph(2)I did not affect the ATPase activity, whereas 40 μM Ph(2)I caused a marked inhibition (~2 fold) in ATPase activity. The obtained results provide novel evidence on the involvement of hydrogenase and the F(0)F(1)-ATPase in H(2) production by R. sphaeroides. Moreover, these data indicate the role of hydrogenase and the F(0)F(1)-ATPase in ∆p generation. In addition, DMSO might increase an interaction of nitrogenase with CO(2), decreasing nitrogenase activity and affecting H(2) production.

  15. Effect of co-substrate on production of poly-β- hydroxybutyrate (PHB and copolymer PHBV from newly identified mutant Rhodobacter sphaeroides U7 cultivated under aerobic-dark condition

    Directory of Open Access Journals (Sweden)

    Kemarajt Kemavongse

    2007-07-01

    Full Text Available Photosynthetic bacterial mutant strain U7 was identified using both classical and molecular (16S rDNA techniques to be Rhodobacter sphaeroides. The glutamate-acetate (GA medium containing sodium acetate and sodium glutamate as carbon and nitrogen sources was used for production of poly-β-hydroxybutyrate (PHB from R. sphaeroides U7 cultivated under aerobic-dark condition (200 rpm at 37oC. Effect of auxiliary carbon sources (propionate and valerate and concentrations (molar ratio of 40/0, 40/20, 40/40 and 40/80 on copolymer production were studied. Both combinations of acetate with valerate and acetate with propionate were found to induce the accumulation of poly-β-hydroxybutyrate-co-β-hydroxyvalerate (PHBV within the cell. Acetate with propionate in the molar ratio of 40/40 gave the highest poly-β-hydroxyalkanoates (PHA content (77.68%, followed by acetate with valerate at the same molar ratio (77.42%. Although their polymer contents were similar, the presence of 40 mM valerate gave more than 4 times higher hydroxyvalerate (HV fraction (84.77% than in the presence of 40 mM propionate (19.12% HV fraction.

  16. The functional importance of a pair of conserved glutamic acid residues and of Ca2+ binding in the cbb3–type oxygen reductases from Rhodobacter sphaeroides and Vibrio cholerae

    Science.gov (United States)

    Ouyang, Hanlin; Han, Huazhi; Roh, Jung H.; Hemp, James; Hosler, Jonathan P.; Gennis, Robert B.

    2012-01-01

    The cbb3-type cytochrome c oxidases are members of the heme-copper proton pumping respiratory oxygen reductases. The structure of the cbb3-type oxidase from Pseudomonas stutzeri reveals that, in addition to the six redox-active metal centers (two hemes b, three hemes c and CuB), the enzyme also contains at least one Ca2+. The calcium bridges two propionate carboxyls at the interface between the low-spin heme b and the active-site heme b3 and, in addition, is ligated to a serine in subunit CcoO and by a glutamate in CcoN. The glutamate that is ligated to Ca2+ is one of a pair of glutamic acid residues that has previously been suggested to be part of a proton exit pathway for pumped protons. In the current work, mutants in these glutamates are investigated in the cbb3-type oxidases from Vibrio cholerae and from Rhodobacter sphaeroides. Metal analysis shows that each of these wild type enzymes contains Ca2+. Mutations of the glutamate expected to ligate the Ca2+ in each of these enzymes (E126 in V. cholerae; E180 in R. sphaeroides) result in the loss of activity as well as loss of Ca2+. Mutations in the nearby glutamate (E129 in V. cholerae; E183 in R. sphaeroides) also resulted in loss of oxidase activity and loss of Ca2+. It is concluded that the Ca2+ is essential for assembly of the fully functional enzyme and that neither of the glutamates is likely to be part of a pathway for pumped protons within the cbb3-type oxygen reductases. A more likely role for these glutamates is the maintenance of the structural integrity of the active conformation of the enzyme. PMID:22913716

  17. Application of the Accurate Mass and Time Tag Approach to the Proteome Analysis of Sub-cellular Fractions Obtained from Rhodobacter sphaeroides 2.4.1 Aerobic and Photosynthetic Cell Cultures

    Energy Technology Data Exchange (ETDEWEB)

    Callister, Stephen J.; Dominguez, Migual; Nicora, Carrie D.; Zeng, Xiaohua; Tavano, Christine; Kaplan, Samuel; Donohue, Timothy; Smith, Richard D.; Lipton, Mary S.

    2006-08-04

    Abstract The high-throughput accurate mass and time tag (AMT) proteomic approach was utilized to characterize the proteomes for cytoplasm, cytoplasmic membrane, periplasm, and outer membrane fractions from aerobic and photosynthetic cultures of the gram-nagtive bacterium Rhodobacter sphaeroides 2.4.1. In addition, we analyzed the proteins within purified chromatophore fractions that house the photosynthetic apparatus from photosynthetically grown cells. In total, 8300 peptides were identified with high confidence from at least one sub-cellular fraction from either cell culture. These peptides were derived from 1514 genes or 35% percent of proteins predicted to be encoded by the genome. A significant number of these proteins were detected within a single sub-cellular fraction and their localization was compared to in-silico predictions. However, the majority of proteins were observed in multiple sub-cellular fractions, and the most likely sub-cellular localization for these proteins was investigated using a Z-score analysis of peptide abundance along with clustering techniques. Good (81%) agreement was observed between the experimental results and in-silico predictions. The AMT tag approach provides localization evidence for those proteins that have no predicted localization information, those annotated as putative proteins, and/or for those proteins annotated as hypothetical and conserved hypothetical.

  18. Oligomerization and enzyme activity analysis on inorganic pyrophosphatase from Rhodobacter sphaeroides%球形红细菌无机焦磷酸酶的寡聚化及酶活性分析

    Institute of Scientific and Technical Information of China (English)

    陈果果; 孙梅好

    2016-01-01

    球形红细菌(Rhodobacter sphaeroides)是一种重要的微生物资源,其无机焦磷酸酶(PPase)属于Ⅱ型可溶性焦磷酸酶.通过原核表达和纯化,得到了正常型RsPPase和突变型RsPPasemono,进一步进行了寡聚化和酶活性分析.结果表明:突变型RsPPasemono为单聚体,在钴离子存在条件下会导致谷胱甘肽S-转移酶(glutathione sulfotransferase,GST)标签进行蛋白酶切,且去标签后的RsPPasemono催化效率较高(Kcat/Km(PPi)=12.64L·μmol-1·min-1),相对于RsPPase-GST提高了12倍;在无钴离子存在条件下仍能进行蛋白酶切,且保持催化效率(Kcat/Km(PPi) =0.34 L·μmol-1·min-1).

  19. Application of the Accurate Mass and Time Tag Approach to the Proteome Analysis of Sub-cellular Fractions Obtained from Rhodobacter sphaeroides 2.4.1. Aerobic and Photosynthetic Cell Cultures

    Science.gov (United States)

    Callister, Stephen J.; Dominguez, Miguel A.; Nicora, Carrie D.; Zeng, Xiaohua; Tavano, Christine L.; Kaplan, Samuel; Donohue, Timothy J.; Smith, Richard D.; Lipton, Mary S.

    2009-01-01

    The high-throughput accurate mass and time (AMT) tag proteomic approach was utilized to characterize the proteomes for cytoplasm, cytoplasmic membrane, periplasm, and outer membrane fractions from aerobic and photosynthetic cultures of the gram-nagtive bacterium Rhodobacter sphaeroides 2.4.1. In addition, we analyzed the proteins within purified chromatophore fractions that house the photosynthetic apparatus from photosynthetically grown cells. In total, 8300 peptides were identified with high confidence from at least one subcellular fraction from either cell culture. These peptides were derived from 1514 genes or 35% percent of proteins predicted to be encoded by the genome. A significant number of these proteins were detected within a single subcellular fraction and their localization was compared to in silico predictions. However, the majority of proteins were observed in multiple subcellular fractions, and the most likely subcellular localization for these proteins was investigated using a Z-score analysis of estimated protein abundance along with clustering techniques. Good (81%) agreement was observed between the experimental results and in silico predictions. The AMT tag approach provides localization evidence for those proteins that have no predicted localization information, those annotated as putative proteins, and/or for those proteins annotated as hypothetical and conserved hypothetical. PMID:16889416

  20. Catalytically-relevant electron transfer between two hemes bL in the hybrid cytochrome bc1-like complex containing a fusion of Rhodobacter sphaeroides and capsulatus cytochromes b.

    Science.gov (United States)

    Czapla, Monika; Cieluch, Ewelina; Borek, Arkadiusz; Sarewicz, Marcin; Osyczka, Artur

    2013-06-01

    To address mechanistic questions about the functioning of dimeric cytochrome bc1 new genetic approaches have recently been developed. They were specifically designed to enable construction of asymmetrically-mutated variants suitable for functional studies. One approach exploited a fusion of two cytochromes b that replaced the separate subunits in the dimer. The fusion protein, built from two copies of the same cytochrome b of purple bacterium Rhodobacter capsulatus, served as a template to create a series of asymmetrically-mutated cytochrome bc1-like complexes (B-B) which, through kinetic studies, disclosed several important principles of dimer engineering. Here, we report on construction of another fusion protein complex that adds a new tool to investigate dimeric function of the enzyme through the asymmetrically mutated forms of the protein. This complex (BS-B) contains a hybrid protein that combines two different cytochromes b: one coming from R. capsulatus and the other - from a closely related species, R. sphaeroides. With this new fusion we addressed a still controversial issue of electron transfer between the two hemes bL in the core of dimer. Kinetic data obtained with a series of BS-B variants provided new evidence confirming the previously reported observations that electron transfer between those two hemes occurs on a millisecond timescale, thus is a catalytically-relevant event. Both types of the fusion complexes (B-B and BS-B) consistently implicate that the heme-bL-bL bridge forms an electronic connection available for inter-monomer electron transfer in cytochrome bc1. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Steady-state FTIR spectra of the photoreduction of QA and QB in Rhodobacter sphaeroides reaction centers provide evidence against the presence of a proposed transient electron acceptor X between the two quinones.

    Science.gov (United States)

    Breton, Jacques

    2007-04-17

    In the reaction center (RC) of the photosynthetic bacterium Rhodobacter sphaeroides, two ubiquinone molecules, QA and QB, play a pivotal role in the conversion of light energy into chemical free energy by coupling electron transfer to proton uptake. In native RCs, the transfer of an electron from QA to QB takes place in the time range of 5-200 micros. On the basis of time-resolved FTIR step-scan measurements in native RCs, a new and unconventional mechanism has been proposed in which QB- formation precedes QA- oxidation [Remy, A., and Gerwert, K. (2003) Nat. Struct. Biol. 10, 637-644]. The IR signature of the proposed transient intermediary electron acceptor (denoted X) operating between QA and QB has been recently measured by the rapid-scan technique in the DN(L210) mutant RCs, in which the QA to QB electron transfer is slowed 8-fold compared to that in native RCs. This IR signature has been reported as a difference spectrum involving states X+, X, QA, and QA- [Hermes, S., et al. (2006) Biochemistry 45, 13741-13749]. Here, we report the steady-state FTIR difference spectra of the photoreduction of either QA or QB measured in both native and DN(L210) mutant RCs in the presence of potassium ferrocyanide. In these spectra, the CN stretching marker modes of ferrocyanide and ferricyanide allow the extent of the redox reactions to be quantitatively compared and are used for a precise normalization of the QA-/QA and QB-/QB difference spectra. The calculated QA- QB/QA QB- double-difference spectrum in DN(L210) mutant RCs is closely equivalent to the reported QA- X+/QA X spectrum in the rapid-scan measurement. We therefore conclude that species X+ and X are spectrally indistinguishable from QB and QB-, respectively. Further comparison of the QA- QB/QA QB- double-difference spectra in native and DN(L210) RCs also allows the possibility that QB- formation precedes QA- reoxidation to be ruled out for native RCs.

  2. Prokaryotic Expression, Purification and Preliminary Analysis on Inorganic Pyrophosphatase from Rhodobacter sphaeroides%球形红细菌无机焦磷酸酶的原核表达、纯化及初步分析

    Institute of Scientific and Technical Information of China (English)

    黄园波; 王艳兴; 戴梦瑶; 马建辉; 孙梅好

    2013-01-01

    无机焦磷酸酶(inorganic pyrophosphatase,PPase)水解在许多生物大分子的生物合成过程中产生焦磷酸并释放能量,形成的热力学拉力可促进合成反应的进行.球形红细菌(Rhodobacter sphaeroides 2.4.1)无机焦磷酸酶(RsPPase)属于Ⅱ型可溶性焦磷酸酶,钴离子对于其活性的维持具有重要的功能,而其活性调控及其表达对细菌生长的影响尚未报道.研究克隆、原核表达纯化RsPPase.结果发现,钴离子会导致谷胱甘肽S-转移酶(glutathione sulfotransferase,GST)标签不能进行蛋白酶切,且融合蛋白GST-PPase水解焦磷酸的催化效率较低(Km/kcat=2.0×104 mol/(L·s));在球形红细菌胞内表达大肠杆菌焦磷酸酶(Km/kcat=5.5×107 mol/(L·s))没有影响细菌的生长,暗示球形红细菌胞内PPase活性足够高.通过对其结构的模拟推测,在钴离子存在的情况下为闭合构象,GST标签的存在可能影响PPase羧基端结构域的运动,而影响其结合底物和释放产物的能力;在钴离子不存在的情况下为开放构象,GST标签具有较大的自由度,可暴露蛋白酶识别位点酶切产生无标签RsPPase.

  3. Electron spin echo envelope modulation spectroscopy supports the suggested coordination of two histidine ligands to the Rieske Fe-S centers of the cytochrome b sub 6 f complex of spinach and the cytochrome bc sub 1 complexes of Rhodospirillum rubrum, Rhodobacter sphaeroides R-26, and bovine heart mitochondria

    Energy Technology Data Exchange (ETDEWEB)

    Britt, R.D.; Sauer, K.; Klein, M.P. (Lawrence Berkeley Lab., CA (USA)); Knaff, D.B.; Kriauciunas, A. (Texas Tech Univ., Lubbock (USA)); Yu, Changan; Yu, Linda (Oklahoma State Univ., Stillwater (USA)); Malkin, R. (Univ. of California, Berkeley (USA))

    1991-02-19

    Electron spin echo envelope modulation (ESEEM) experiments performed on the Rieske Fe-S clusters of the cytochrome b{sub 6}f complex of spinach chloroplasts and of the cytochrome bc{sub 1} complexes of Rhodospirillum rubrum, Rhodobacter sphaeroides R-26, and bovine heart mitochondria show modulation components resulting from two distinct classes of {sup 14}N ligands. At the g = 1.92 region of the Rieske EPR spectrum of the cytochrome b{sub 6}f complex, the measured hyperfine couplings for the two classes of coupled nitrogens are A{sub 1} = 4.6 MHz and A{sub 2} = 3.8 MHz. Similar couplings are observed for the Rieske centers in the three cytochrome bc{sub 1} complexes. These ESEEM results indicate a nitrogen coordination environment for these Rieske Fe-S centers that is similar to that of the Fe-S cluster of a bacterial dioxygenase enzyme with two coordinated histidine ligands. The Rieske Fe-S cluster lacks modulation components from a weakly coupled peptide nitrogen observed in water-soluble spinach ferredoxin. Treatment with the quinone analogue inhibitor DBMIB causes a shift in the Rieske EPR spectrum to g = 1.95 with no alteration in the magnetic couplings to the two nitrogen atoms. However, the ESEEM pattern of the DBMIB-altered Rieske EPR signal shows evidence of an additional weakly coupled nitrogen similar to that observed in the spinach ferrodoxin ESEEM patterns.

  4. Spin-torch experiment on reaction centers of Rhodobacter sphaeroides

    NARCIS (Netherlands)

    Sai Sankar Gupta, Karthick Babu

    2011-01-01

    Photosynthesis is the physico-chemical process by which plants, algae and photosynthetic bacteria use light energy to drive the synthesis of organic compounds. Light-induced electron transfer in photosynthetic reaction centers (RCs) is highly efficient, having a quantum yield close to unity. In RCs

  5. Rhodobacter megalophilus sp. nov., a phototroph from the Indian Himalayas possessing a wide temperature range for growth.

    Science.gov (United States)

    Arunasri, K; Venkata Ramana, V; Spröer, C; Sasikala, Ch; Ramana, Ch V

    2008-08-01

    Two strains of phototrophic, purple non-sulfur bacteria capable of growing at low temperatures (5 degrees C) were isolated from the Himalayas. The two strains showed positive phototaxis and grew over a relatively wide temperature range (5-40 degrees C). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA194T clustered with members of the genus Rhodobacter. Strain JA194T showed highest 16S rRNA gene sequence similarity with Rhodobacter sphaeroides DSM 158T (99 %). However, DNA-DNA hybridization experiments between Rba. sphaeroides DSM 158T and strain JA194T revealed a level of relatedness of only 67 %. The DNA base composition of strain JA194T was 66.67 mol% G+C (by HPLC). Based on 16S rRNA gene sequence analysis, morphological, physiological, Fourier transform infrared fingerprinting and DNA-DNA hybridization studies, strain JA194T (=KCTC 5602T =JCM 14598T) is sufficiently different from other Rhodobacter species to merit its description as the type strain of a novel species, for which the name Rhodobacter megalophilus sp. nov. is proposed.

  6. Kinetics of cytochrome c oxidase from R. sphaeroides initiated by direct electron transfer followed by tr-SEIRAS.

    Science.gov (United States)

    Steininger, Christoph; Reiner-Rozman, Ciril; Schwaighofer, Andreas; Knoll, Wolfgang; Naumann, Renate L C

    2016-12-01

    Time-resolved surface-enhanced IR-absorption spectroscopy (tr-SEIRAS) has been performed on cytochrome c oxidase from Rhodobacter sphaeroides. The enzyme was converted electrochemically into the fully reduced state. Thereafter, in the presence of oxygen, the potential was switched to open circuit potential (OCP). Under these conditions, the enzyme is free to undergo enzymatic oxidation in the absence of an external electric field. Tr-SEIRAS was performed using the step-scan technique, triggered by periodic potential pulses switching between - 800mV and OCP. Single bands were resolved in a broad band in the amide I region using phase sensitive detection. Amplitudes of these bands were analyzed as a function of time. Time constants in the ms time scale were considered in terms of conformational changes of the protein secondary structures associated with the enzymatic turnover of the protein.

  7. Paepalanthus sphaeroides, a new species of Eriocaulaceae from the Atlantic Forest, Brazil

    NARCIS (Netherlands)

    Trovó, M.; Echternacht, L.; Sano, P.T.

    2012-01-01

    We describe and illustrate Paepalanthus sphaeroides (Eriocaulaceae, Paepalanthoideae) from the Mantiqueira Range in South-eastern Brazil and compare it with the morphologically most similar species: Paepalanthus aequalis and Paepalanthus eriophaeus. Paepalanthus sphaeroides has unique membranaceous

  8. Complete Genome Sequences of Five Bacteriophages That Infect Rhodobacter capsulatus.

    Science.gov (United States)

    Bollivar, David W; Bernardoni, Brooke; Bockman, Matthew R; Miller, Brenda M; Russell, Daniel A; Delesalle, Veronique A; Krukonis, Gregory P; Hatfull, Graham F; Cross, Madeline R; Szewczyk, Marlena M; Eppurath, Atul

    2016-05-26

    Five bacteriophages that infect the Rhodobacter capsulatus strain YW1 were isolated from stream water near Bloomington, Illinois, USA. Two distinct genome types are represented in the newly isolated bacteriophages. These genomes are different from other bacteriophage genomes previously described.

  9. The Conserved Dcw Gene Cluster of R. sphaeroides Is Preceded by an Uncommonly Extended 5' Leader Featuring the sRNA UpsM.

    Science.gov (United States)

    Weber, Lennart; Thoelken, Clemens; Volk, Marcel; Remes, Bernhard; Lechner, Marcus; Klug, Gabriele

    2016-01-01

    Cell division and cell wall synthesis mechanisms are similarly conserved among bacteria. Consequently some bacterial species have comparable sets of genes organized in the dcw (division and cell wall) gene cluster. Dcw genes, their regulation and their relative order within the cluster are outstandingly conserved among rod shaped and gram negative bacteria to ensure an efficient coordination of growth and division. A well studied representative is the dcw gene cluster of E. coli. The first promoter of the gene cluster (mraZ1p) gives rise to polycistronic transcripts containing a 38 nt long 5' UTR followed by the first gene mraZ. Despite reported conservation we present evidence for a much longer 5' UTR in the gram negative and rod shaped bacterium Rhodobacter sphaeroides and in the family of Rhodobacteraceae. This extended 268 nt long 5' UTR comprises a Rho independent terminator, which in case of termination gives rise to a non-coding RNA (UpsM). This sRNA is conditionally cleaved by RNase E under stress conditions in an Hfq- and very likely target mRNA-dependent manner, implying its function in trans. These results raise the question for the regulatory function of this extended 5' UTR. It might represent the rarely described case of a trans acting sRNA derived from a riboswitch with exclusive presence in the family of Rhodobacteraceae.

  10. The Conserved Dcw Gene Cluster of R. sphaeroides Is Preceded by an Uncommonly Extended 5’ Leader Featuring the sRNA UpsM

    Science.gov (United States)

    Weber, Lennart; Thoelken, Clemens; Volk, Marcel; Remes, Bernhard; Lechner, Marcus; Klug, Gabriele

    2016-01-01

    Cell division and cell wall synthesis mechanisms are similarly conserved among bacteria. Consequently some bacterial species have comparable sets of genes organized in the dcw (division and cell wall) gene cluster. Dcw genes, their regulation and their relative order within the cluster are outstandingly conserved among rod shaped and gram negative bacteria to ensure an efficient coordination of growth and division. A well studied representative is the dcw gene cluster of E. coli. The first promoter of the gene cluster (mraZ1p) gives rise to polycistronic transcripts containing a 38 nt long 5’ UTR followed by the first gene mraZ. Despite reported conservation we present evidence for a much longer 5’ UTR in the gram negative and rod shaped bacterium Rhodobacter sphaeroides and in the family of Rhodobacteraceae. This extended 268 nt long 5’ UTR comprises a Rho independent terminator, which in case of termination gives rise to a non-coding RNA (UpsM). This sRNA is conditionally cleaved by RNase E under stress conditions in an Hfq- and very likely target mRNA-dependent manner, implying its function in trans. These results raise the question for the regulatory function of this extended 5’ UTR. It might represent the rarely described case of a trans acting sRNA derived from a riboswitch with exclusive presence in the family of Rhodobacteraceae. PMID:27802301

  11. Cytochrome c2-independent respiratory growth of Rhodobacter capsulatus.

    OpenAIRE

    Daldal, F

    1988-01-01

    To assess the role of cytochrome c2 as a respiratory electron carrier, we obtained a double mutant of Rhodobacter capsulatus defective in cytochrome c2 and in the quinol oxidase260. This mutant was able to grow chemoheterotrophically, indicating that an electron pathway independent of cytochrome c2 was functional between the ubiquinol:cytochrome c2 oxidoreductase and the cytochrome oxidase410.

  12. Photomixotrophic growth of Rhodobacter capsulatus SB1003 on ferrous iron

    OpenAIRE

    Kopf, Sebastian H.; Newman, Dianne K.

    2011-01-01

    This study investigates the role iron oxidation plays in the purple non-sulfur bacterium Rhodobacter capsulatus SB1003. This organism is unable to grow photoautotrophically on unchelated ferrous iron [Fe(II)] despite its ability to oxidize chelated Fe(II). This apparent paradox was partly resolved by the discovery that SB1003 can grow photoheterotrophically on the photochemical breakdown products of certain ferric iron–ligand complexes, yet whether it could concomitantly benefit from the oxid...

  13. The phosphoenolpyruvate-dependent fructose-specific phosphotransferase system in Rhodopseudomonas sphaeroides : Distribution of EIIFru over the membranes of phototrophically grown Rps. sphaeroides

    NARCIS (Netherlands)

    Lolkema, Juke S.; Hoeve-Duurkens, Ria H. ten; Robillard, George T.

    1986-01-01

    The distribution of the fructose carrier over the membranes of Rhodopseudomonas sphaeroides was studied in cells grown under light saturation and light limitation. Three types of membranes were isolated after disruption of the cells in a French press. All three types were present in the cells grown

  14. Proton transfer from the bulk to the bound ubiquinone QB of the reaction center in chromatophores of Rhodobacter sphaeroides: Retarded conveyance by neutral water

    Science.gov (United States)

    Gopta, Oksana A.; Cherepanov, Dmitry A.; Junge, Wolfgang; Mulkidjanian, Armen Y.

    1999-01-01

    The mechanism of proton transfer from the bulk into the membrane protein interior was studied. The light-induced reduction of a bound ubiquinone molecule QB by the photosynthetic reaction center is accompanied by proton trapping. We used kinetic spectroscopy to measure (i) the electron transfer to QB (at 450 nm), (ii) the electrogenic proton delivery from the surface to the QB site (by electrochromic carotenoid response at 524 nm), and (iii) the disappearance of protons from the bulk solution (by pH indicators). The electron transfer to QB− and the proton-related electrogenesis proceeded with the same time constant of ≈100 μs (at pH 6.2), whereas the alkalinization in the bulk was distinctly delayed (τ ≈ 400 μs). We investigated the latter reaction as a function of the pH indicator concentration, the added pH buffers, and the temperature. The results led us to the following conclusions: (i) proton transfer from the surface-located acidic groups into the QB site followed the reduction of QB without measurable delay; (ii) the reprotonation of these surface groups by pH indicators and hydronium ions was impeded, supposedly, because of their slow diffusion in the surface water layer; and (iii) as a result, the protons were slowly donated by neutral water to refill the proton vacancies at the surface. It is conceivable that the same mechanism accounts for the delayed relaxation of the surface pH changes into the bulk observed previously with bacteriorhodopsin membranes and thylakoids. Concerning the coupling between proton pumps in bioenergetic membranes, our results imply a tendency for the transient confinement of protons at the membrane surface. PMID:10557290

  15. Hydrogen production from starch by co-culture of Clostridium acetobutylicum and Rhodobacter sphaeroides in one step hybrid dark- and photofermentation in repeated fed-batch reactor.

    Science.gov (United States)

    Zagrodnik, R; Łaniecki, M

    2017-01-01

    Hydrogen production from starch by a co-culture hybrid dark and photofermentation under repeated fed-batch conditions at different organic loading rates (OLR) was studied. Effective cooperation between bacteria in co-culture during initial days was observed at controlled pH 7.0. However, at pH above 6.5 dark fermentation phase was redirected from H2 formation towards production of formic acid, lactic acid and ethanol (which are not coupled with hydrogen production) with simultaneous lower starch removal efficiency. This resulted in decrease in the hydrogen production rate. The highest H2 production in co-culture process (3.23LH2/Lmedium - after 11days) was achieved at OLR of 1.5gstarch/L/day, and it was twofold higher than for dark fermentation process (1.59LH2/Lmedium). The highest H2 yield in the co-culture (2.62molH2/molhexose) was obtained at the OLR of 0.375gstarch/L/day. Different pH requirements of bacteria were proven to be a key limitation in co-culture system. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Effects of the Medium Composition on the Components of the Electrochemical Proton Gradient in Rhodopseudomonas sphaeroides

    NARCIS (Netherlands)

    Michels, Paul A.M.; Hellingwerf, K; Lolkema, Juke S.; Friedberg, Ilan; Konings, Wilhelmus

    1981-01-01

    The magnitude and composition of the proton motive force (Δµ~H+) has been measured in chromatophores and whole cells of Rhodopseudomonas sphaeroides as a function of the ionic composition of the buffer in which the energy-transducing membranes are suspended. Measurements with the flow-dialysis techn

  17. Energy Coupling of Facilitated Transport of Inorganic Ions in Rhodopseudomonas sphaeroides

    NARCIS (Netherlands)

    Hellingwerf, K; Friedberg, Ilan; Lolkema, Juke S.; Michels, Paul A.M.; Konings, Wilhelmus

    1982-01-01

    Within the scope of a study on the effects of changes in medium composition on the proton motive force in Rhodopseudomonas sphaeroides, the energy coupling of sodium, phosphate, and potassium (rubidium) transport was investigated. Sodium was transported via an electroneutral exchange system against

  18. Effects of the Medium Composition on the Components of the Electrochemical Proton Gradient in Rhodopseudomonas sphaeroides

    NARCIS (Netherlands)

    Michels, Paul A.M.; Hellingwerf, K; Lolkema, Juke S.; Friedberg, Ilan; Konings, Wilhelmus

    1981-01-01

    The magnitude and composition of the proton motive force (Δµ~H+) has been measured in chromatophores and whole cells of Rhodopseudomonas sphaeroides as a function of the ionic composition of the buffer in which the energy-transducing membranes are suspended. Measurements with the flow-dialysis techn

  19. Analysis of the puc Operon Promoter from Rhodobacter capsulatus

    Science.gov (United States)

    Nickens, David G.; Bauer, Carl E.

    1998-01-01

    Expression of the Rhodobacter capsulatus puc operon, which codes for structural polypeptides of the light-harvesting-II peripheral antenna complex, is highly regulated in response to alterations in oxygen tension and light intensity. To obtain an understanding of the puc promoter region we report the high-resolution 5′ mapping of the puc mRNA transcriptional start site and DNA sequence analysis of the puc upstream regulatory sequence (pucURS). A ς70-type promoter sequence was identified (pucP1) which has a high degree of sequence similarity with carotenoid and bacteriochlorophyll biosynthesis promoters. Inspection of the DNA sequence also indicated the presence of two CrtJ and four integration host factor (IHF) binding sites. Transcriptional fusions of the pucURS fused to lacZ also confirmed that puc promoter activity is regulated by the transcriptional regulators IHF, CrtJ, and RegA. Gel retardation analysis using cell extracts indicates that mutations in IHF and RegA disrupt protein binding to DNA fragments containing the pucURS. PMID:9696778

  20. Photomixotrophic growth of Rhodobacter capsulatus SB1003 on ferrous iron.

    Science.gov (United States)

    Kopf, S H; Newman, D K

    2012-05-01

    This study investigates the role iron oxidation plays in the purple non-sulfur bacterium Rhodobacter capsulatus SB1003. This organism is unable to grow photoautotrophically on unchelated ferrous iron [Fe(II)] despite its ability to oxidize chelated Fe(II). This apparent paradox was partly resolved by the discovery that SB1003 can grow photoheterotrophically on the photochemical breakdown products of certain ferric iron-ligand complexes, yet whether it could concomitantly benefit from the oxidation of Fe(II) to fix CO(2) was unknown. Here, we examine carbon fixation by stable isotope labeling of the inorganic carbon pool in cultures growing phototrophically on acetate with and without Fe(II). We show that R. capsulatus SB1003, an organism formally thought incapable of phototrophic growth on Fe(II), can actually harness the reducing power of this substrate and grow photomixotrophically, deriving carbon both from organic sources and from fixation of inorganic carbon. This suggests the possibility of a wider occurrence of photoferrotrophy than previously assumed. © 2011 Blackwell Publishing Ltd.

  1. Nostoc sphaeroides Kützing, an excellent candidate producer for CELSS

    Science.gov (United States)

    Hao, Zongjie; Li, Dunhai; Li, Yanhui; Wang, Zhicong; Xiao, Yuan; Wang, Gaohong; Liu, Yongding; Hu, Chunxiang; Liu, Qifang

    2011-11-01

    Some phytoplankton can be regarded as possible candidates in the establishment of Controlled Ecological Life Support System (CELSS) for some intrinsic characteristics, the first characteristic is that they should grow rapidly, secondly, they should be able to endure some stress factors and develop some corresponding adaptive strategies; also it is very important that they could provide food rich in nutritious protein and vitamins for the crew; the last but not the least is they can also fulfill the other main functions of CELSS, including supplying oxygen, removing carbon dioxide and recycling the metabolic waste. According to these characteristics, Nostoc sphaeroides, a potential healthy food in China, was selected as the potential producer in CELSS. It was found that the oxygen average evolution rate of this algae is about 150 μmol O 2 mg -1 h -1, and the size of them are ranged from 2 to 20 mm. Also it can be cultured with high population density, which indicated that the potential productivity of Nostoc sphaeroides is higher than other algae in limited volume. We measured the nutrient contents of the cyanobacterium and concluded it was a good food for the crew. Based on above advantages, Nostoc sphaeroides was assumed to a suitable phytoplankton for the establishment of Controlled Ecological Life Support System. We plan to develop suitable bioreactor with the cyanobacterium for supplying oxygen and food in future space missions.

  2. Colony development and physiological characterization of the edible blue-green alga, Nostoc sphaeroides (Nostocaceae, Cyanophyta)

    Institute of Scientific and Technical Information of China (English)

    Zhongyang Deng; Qiang Hu; Fan Lu; Guoxiang Liu; Zhengyu Hu

    2008-01-01

    The edible blue-green alga,Nostoc sphaeroides Kützing,is able to form microcolorties and spherical macrocolonies.It has been used as a potent herbal medicine and dietary supplement for centuries because of its nutraceutical and pharmacological benefits.However,lim-ited information is available on the development of the spherical macrocolonies and the environmental factors that affect their structure.This report described the morphogenesis of N.Sphaeroides from single trichomes to macrocolonies.During the process,most structural features of macrocolonies of various sizes were dense maculas,rings,the compact core and the formation of liquid core;and the filaments within the macrocolonies showed different lengths and arrays depending on the sizes of macrocolonies.Meanwhile temperature and light intensity also strongly affected the internal structure of macrocolonies.As microcolonies further increased in size to form 30 mm mac-rocolonies,the colonies differentiated into distinct outer,middle and inner layers.The filaments of the outer layer showed higher max-imum photosynthetic rates,higher light saturation point,and higher photosynthetic efficiency than those of the inner layer;whereas the filaments of the inner layer had a higher content of chlorophyll a and phycobiliproteins than those of the outer layer.The results obtained in this study were important for the mass cultivation of N.Sphaeroides as a nutraceutical product.

  3. Inactivation of Mg Chelatase during Transition from Anaerobic to Aerobic Growth in Rhodobacter capsulatus

    OpenAIRE

    Willows, Robert D.; Lake, Vanessa; Roberts, Thomas Hugh; Beale, Samuel I.

    2003-01-01

    The facultative photosynthetic bacterium Rhodobacter capsulatus can adapt from an anaerobic photosynthetic mode of growth to aerobic heterotrophic metabolism. As this adaptation occurs, the cells must rapidly halt bacteriochlorophyll synthesis to prevent phototoxic tetrapyrroles from accumulating, while still allowing heme synthesis to continue. A likely control point is Mg chelatase, the enzyme that diverts protoporphyrin IX from heme biosynthesis toward the bacteriochlorophyll biosynthetic ...

  4. Electrochemical determination of hydrogen peroxide using Rhodobacter capsulatus cytochrome c peroxidase at a gold electrode

    NARCIS (Netherlands)

    De Wael, K.; Buschop, H.; Heering, H.A.; De Smet, L.; Van Beeumen, J.; Devreese, B.; Adriaens, A.

    2007-01-01

    We describe the redox behaviour of horse heart cytochrome c (HHC) and Rhodobacter capsulatus cytochrome c peroxidase (RcCCP) at a gold electrode modified with 4,4′-bipyridyl. RcCCP shows no additional oxidation or reduction peaks compared to the electrochemistry of only HHC, which indicates that it

  5. Effects of light intensity and quality on phycobiliprotein accumulation in the cyanobacterium Nostoc sphaeroides Kützing.

    Science.gov (United States)

    Ma, Rui; Lu, Fan; Bi, Yonghong; Hu, Zhengyu

    2015-08-01

    To assess the effects of light intensity and quality on the growth and phycobiliproteins (PBP) accumulation in Nostoc sphaeroides Kützing (N. sphaeroides). Dry weights, dry matter, protein, chlorophyll and PBP contents were higher under 90 μmol m(-2) s(-1) than under other intensities (both higher and lower). Phycocyanin and allophycocyanin increased with light intensity while phycoerythrin decreased. Fresh weights, protein and PBP contents increased at the highest rates under blue light. Red light resulted in higher values of dry matter, phycocyanin and chlorophyll a. White light at 90 μmol m(-2) s(-1) or blue light 30 μmol m(-2) s(-1) were optimal for the growth and phycobiliprotein accumulation in N. sphaeroides.

  6. 葛仙米表层结构的扫描电子显微镜观察%Obsevation for Epidermal Ultrastructure of Nostoc sphaeroides Kutzing under Scanning Electron Microscope

    Institute of Scientific and Technical Information of China (English)

    李莉

    2009-01-01

    [Objective]The experiment aimed to explore a new way for observing surface structure of Nostoc sphaeroides Kutzing. [Method] The scanning electron microscope was used to observe the epidermal ultrastructure of wild and cultured Nostoc sphaeroides Kutzing. [Result] The epidermis of wild and cultured Nostoc sphaeroides Kutzing showed mixture structure of fibril colloid which was reticular arranged. The difference between wild and cultured Nostoc sphaeroides Kutzing was that the outer epidermis of cultured Nostoc sphaeroides Kutzing had trichome distribution but the wild Nostoc sphaeroides Kutzing did not has such distribution. The obsevation results of under smaller than 10 μm by scanning electron microscope was touched thick and showed many folds and distortions.[Conclusion] The scanning electron microscope was an effective way to study development of Nostoc sphaeroides Kutzing colony and it was worth popularizing.

  7. Embryonic, Larval, and Early Juvenile Development of the Tropical Sea Urchin, Salmacis sphaeroides (Echinodermata: Echinoidea

    Directory of Open Access Journals (Sweden)

    M. Aminur Rahman

    2012-01-01

    Full Text Available Salmacis sphaeroides (Linnaeus, 1758 is one of the regular echinoids, occuring in the warm Indo-West Pacific, including Johor Straits, between Malaysia and Singapore. In order to investigate the developmental basis of morphological changes in embryos and larvae, we documented the ontogeny of S. sphaeroides in laboratory condition. Gametes were obtained from adult individuals by 0.5 M KCl injection into the coelomic cavity. Fertilization rate at limited sperm concentration (10−5 dilution was 96.6±1.4% and the resulting embryos were reared at 24°C. First cleavage (2-cell, 4-cell, 8-cell, 16-cell, 32-cell, and multicell (Morulla stages were achieved 01.12, 02.03, 02.28, 02.51, 03.12, and 03.32 h postfertilization. Ciliated blastulae with a mean length of 174.72±4.43 μm hatched 08.45 h after sperm entry. The gastrulae formed 16.15 h postfertilization and the archenteron elongated constantly while ectodermal red-pigmented cells migrated synchronously to the apical plate. Pluteus larva started to feed unicellular algae in 2 d, grew continuously, and finally attained metamorphic competence in 35 d after fertilization. Metamorphosis took approximately 1 h 30 min from attachment to the complete resorption of larval tissues and the development of complete juvenile structure with adult spines, extended tubefeet and well-developed pedicellaria, the whole event of which usually took place within 1 d postsettlement. This study represents the first successful investigation on embryonic, larval, and early juvenile development of S. sphaeroides. The findings would greatly be helpful towards the understanding of ontogeny and life-history strategies, which will facilitate us to develop the breeding, seed production, and culture techniques of sea urchins in captive condition.

  8. First Insights into the Genome Sequence of the Strictly Anaerobic Homoacetogenic Sporomusa sphaeroides Strain E (DSM 2875)

    Science.gov (United States)

    Villamizar, Genis Andrés Castillo; Daniel, Rolf

    2017-01-01

    ABSTRACT Here, we report the draft genome sequence of Sporomusa sphaeroides strain E (DSM 2875), a strict anaerobic homoacetogenic bacterium. It is able to grow autotrophically on different one-carbon compounds. The strain possesses several genes of the Wood-Ljungdahl pathway. The genome consists of a single chromosome (4.98 Mb). PMID:28336590

  9. Isolation of a Rhodobacter capsulatus mutant that lacks c-type cytochromes and excretes porphyrins.

    OpenAIRE

    Biel, S W; Biel, A J

    1990-01-01

    A Rhodobacter capsulatus mutant lacking cytochrome oxidase activity was isolated by Tn5 mutagenesis. Difference spectroscopy of crude extracts and extracted c-type cytochromes demonstrated that this mutant completely lacked all c-type cytochromes. The strain did, however, synthesize normal amounts of b-type cytochromes and nonheme iron. This mutant also excreted large amounts of coproporphyrin and protoporphyrin and synthesized reduced amounts of bacteriochlorophyll, suggesting a link between...

  10. Nostoc sphaeroides Kütz, a candidate producer par excellence for CELSS

    Science.gov (United States)

    Wang, Gaohong; Hao, Zongjie; Liu, Yongding

    A lot of aquatic organisms could be regarded as suitable candidates par excellence in the establishment of CELSS, since they are relatively easy and fast to grow and resistant to changes in environmental condition as well as providing nutritious, protein-and vitamin-rich foods for the crew, which can fulfill the main functions of CELSS, including supplying oxygen, water and food, removing carbon dioxide and making daily life waste reusable. Our labotory has developed mass culture of Nostoc sphaeroides Kütz, which is one of traditional healthy food in China and. The oxygen evolution rate of the cyanobacterium is about 150 molO2.mg-1.h-1, and it usually grows into colony with size between 2-20mm, which is easy to be harvested. It also can be cultured with high density, which show that the productivity of the cyanobacterium in limited volume is higher than other microalgae. We had measured the nutrient content of the cyanobacterium and developed some Chinese Dishes and Soups with Nostoc sphaeroides Kütz, which showed that it was a good food for crew. Using remote sensing technique, we also investigated its growth in Closed System under microgravity by SHENZHOU-2 spacecraft in January 2001. We plan to develop suitable bioreactor with the cyanobacterium for supplying oxygen and food to crew in future.

  11. Photoregulated or Energy Dependent Process of Hormogonia Differentiation in Nostoc sphaeroides Kützing (Cyanobacterium)

    Institute of Scientific and Technical Information of China (English)

    Dun-Hai LI; Lan-Zhou CHEN; Gen-Bao LI; Gao-Hong WANG; Li-Rong SONG; Yong-Ding LIU

    2005-01-01

    Hormogonium, which was thought to play an important role in the dispersal and survival of these microorganisms in their natural habitats, is a distinguishable developmental stage of heterocystous cyanobacteria. The present study examined the effects of different light conditions and sugars on the of hormogonia was light dependent in the absence of sugar, but that close to 100% of cyanobacteria differentiated to hormogonia in the presence of glucose or sucrose, irrespective of the light conditions. This differentiation was inhibited, even in the presence of sugars, upon application of an inhibitor of respiration.Following the testing of different sugars, the effects of different lights were examined. It was found that 5-10 μmol.m-2.s-1 photon flux density was optimal for hormogonia differentiation. One hundred percent differentiation was obtained with white light irradiation, in contrast with irradiation with green light (80%differentiation) and red light (0-10% differentiation). Although they showed different efficiencies in induc ing hormogonia differentiation in N. sphaeroides, the green and red radiation did not display antagonistic effects. When the additional aspect of time dependence was investigated through the application of different light radiations and an inhibitor of protein synthesis, it was found that the initial 6 h of the differentiation process was crucial for hormogonia differentiation. Taken together, these results show that hormogonia differentiation in N. sphaeroides is either a photoregulated or an energy dependent process.

  12. Rhodobacter changlensis sp. nov., a psychrotolerant, phototrophic alphaproteobacterium from the Himalayas of India.

    Science.gov (United States)

    Anil Kumar, P; Srinivas, T N R; Sasikala, Ch; Ramana, Ch V

    2007-11-01

    A Gram-negative, non-motile, oval to rod-shaped, psychrotolerant, phototrophic, purple non-sulfur bacterium (designated strain JA139T) was isolated from a snow sample from Changla Pass in the Indian Himalayas. Strain JA139T had vesicular-type intracytoplasmic membrane structures and contained bacteriochlorophyll a and most probably spheroidene-like carotenoids. Biotin, niacin and thiamine were required for growth of strain JA139T. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that the strain clustered with species of the genus Rhodobacter but was distinctly separate from all recognized members of the family Rhodobacteraceae. Based on the genotypic and phenotypic differences observed between strain JA139T and recognized Rhodobacter species, strain JA139T is considered to represent a novel species of the genus, for which the name Rhodobacter changlensis sp. nov. is proposed. The type strain is JA139T (=DSM 18774T=CCUG 53722T=JCM 14338T).

  13. The mechanisms of protection of antioxidants on Nostoc sphaeroides against UV-B radiation

    Science.gov (United States)

    Wang, G. H.

    UV radiation is one of space harmful factor for earth organisms in space exploration In the present work we studied on the role of antioxidant system in Nostoc sphaeroides K u tz Cyanobacteria and the effects of exogenous antioxidant molecules on its photosynthetic rate under UV-B radiation It was found that UV-B radiation decreased the photosynthetic activity of cyanobacterium but promoted the activity of antioxidant system to protect photosystem II PSII and exogenous antioxidant sodium nitroprusside SNP N-acetylcysteine NAC had an obvious protection on PSII activity under UV-B radiation The activity of SOD Superoxide Dismutase EC 1 15 1 1 CAT Catalase EC 1 11 1 6 POD Peroxidase EC 1 11 1 7 and content of MDA and ASC were improved by 0 5mM and 1mM SNP but 0 1mM SNP decreased the activity of antioxide system Exogenous NAC addition decreased the activity of SOD POD CAT and the content MDA and ASC but exogenous NAC addition increased the content of GSH The results suggested that exogenous SNP and NAC may protect algae by different mechanisms in which SNP maybe play double roles as sources of reactive free radicals or ROS scavengers in formation of algae s protection of PSII under UV-B radiation while NAC does function as antioxidant reagent or precursor of glutathione which could protect PSII directly from UV-B radiation Keyword antioxidant system exogenous or endogenous antioxidant Nostoc sphaeroides photosynthesis UV-B radiation

  14. The effect of temperature and light intensity on hydrogen production by Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Eroglu, Inci [Middle East Technical Univ., Ankara (Turkey). Dept. of Chemical Engineering; Sevinc, Pelin [Middle East Technical Univ., Ankara (Turkey). Dept. of Biotechnology; Guenduez, Ufuk; Yucel, Meral [Middle East Technical Univ., Ankara (Turkey). Dept. of Biological Sciences

    2010-07-01

    Rhodobacter capsulatus is a purple non-sulfur photosynthetic bacterium which can produce hydrogen by photofermentation on acetate and lactate. Hydrogen productivity depends on several parameters such as medium composition, pH, light intensity and temperature. In the present study, the effects of temperature and light intensity on hydrogen production were investigated. The cell growth curve has been fitted to the logistic model and hydrogen productivity was interpreted by Modified Gompertz Equation. The maximum productivity was obtained at 30 C and light intensity of 4000 lux. (orig.)

  15. Microbial photodegradation of aminoarenes. Metabolism of 2-amino-4-nitrophenol by Rhodobacter capsulatus.

    Science.gov (United States)

    Witte, C P; Blasco, R; Castillo, F

    1998-03-01

    The phototrophic bacterium Rhodobacter capsulatus photoreduces 2,4-dinitrophenol to 2-amino-4-nitrophenol, which is further metabolized by an aerobic pathway that is also light-dependent. The catabolism of 2-amino-4-nitrophenol requires O2 and the presence of alternative carbon (C) and nitrogen (N) sources, preferably acetate and ammonium. Rhodobacter capsulatus B10, a bacterium unable to assimilate nitrate, releases negligible amounts of nitrite when growing with 2-amino-4-nitrophenol, thus suggesting that an oxygenase, nitrite-producing activity is not involved in the metabolization of the compound. The diazotrophic growth of R. capsulatus increases in the presence of 2-amino-4-nitrophenol, but growth with ammonium is clearly inhibited by the compound. Mutant strains of R. capsulatus B10, which are affected in nifHDK, nifR1, or nifR4 genes, unable to fix dinitrogen, do not grow with 2-amino-4-nitrophenol as the sole N source. This indicates that the compound cannot be used as a N source. The nif mutants degrade 2-amino-4-nitrophenol to the same extent as the wild-type in the presence of ammonium. The compound is not used as a C source by the bacterium, either. Aromatic stable intermediates, such as 2,4-diaminophenol or 4-nitrocatechol, are not detectable in microaerobic cultures of R. capsulatus growing with 2,4-dinitrophenol or 2-amino-4-nitrophenol.

  16. Ultrafast excitation relaxation in light-harvesting complex LH2 from Rb.sphaeroides 601

    Institute of Scientific and Technical Information of China (English)

    GUO Lijun; LIU Yuan; LIU Weimin; GUO Junhua; XU Chunhe; QIAN Shixiong

    2004-01-01

    The energy relaxation and kinetic evolution of transient spectra of bacteriochloro- phylls (BChls) in light-harvesting complex LH2 from Rb. Sphaeroides 601 were investigated using femtosecond pump-probe technique. Upon 783 nm excitation, the energy at B800 BChls experiences an intramolecular redistribution with 0.35 ps time constant before transferring to B850 BChls. With tuning the excitation wavelength, the dynamical evolution of excited BChls was clearly observed, which indicates an obvious competition between the ground state bleaching and excited state absorption (ESA) of BChls involved and an isosbestic point near 818 nm, and also demonstrates that from the lower electronic excited state of B800 BChls to the higher excitonic state of B850 BChls is an efficient routine for energy transfer. The excitation energy in higher excitonic states of B850 BChls relaxes rapidly to the next lowest excitonic state by interconversion, delocalization to adjacent molecular, populating the lowest excitonic state and the change of molecular conformation.

  17. Ultrafast excitation relaxation in light-harvesting complex LH2 from Rb. sphaeroides 601

    Institute of Scientific and Technical Information of China (English)

    GUO; Lijun; LIU; Yuan; LIU; Weimin; GUO; Junhua; XU; Chunhe

    2004-01-01

    The energy relaxation and kinetic evolution of transient spectra of bacteriochloro- phylls (BChls) in light-harvesting complex LH2 from Rb. Sphaeroides 601 were investigated using femtosecond pump-probe technique. Upon 783 nm excitation, the energy at B800 BChls experiences an intramolecular redistribution with 0.35 ps time constant before transferring to B850 BChls. With tuning the excitation wavelength, the dynamical evolution of excited BChls was clearly observed, which indicates an obvious competition between the ground state bleaching and excited state absorption (ESA) of BChls involved and an isosbestic point near 818 nm, and also demonstrates that from the lower electronic excited state of B800 BChls to the higher excitonic state of B850 BChls is an efficient routine for energy transfer. The excitation energy in higher excitonic states of B850 BChls relaxes rapidly to the next lowest excitonic state by interconversion, delocalization to adjacent molecular, populating the lowest excitonic state and the change of molecular conformation.

  18. ENDOR Spectroscopy Reveals A Light Induced Movement of the H-Bond from Ser-L223 Upon Forming the Semiquinone (QB−•) in Reaction Centers from Rhodobacter sphaeroides

    Science.gov (United States)

    Paddock, M. L.; Flores, M.; Isaacson, R.; Chang, C.; Abresch, E. C.; Okamura, M.Y.

    2008-01-01

    Proton ENDOR spectroscopy was used to monitor local conformational changes in bacterial reaction centers (RC) associated with the electron transfer reaction DQB → D+•QB−• using mutant RCs capable of photo-reducing QB at cryogenic temperatures. The charge separated state D+•QB−• was studied in mutant RCs formed by either (i) illuminating at low temperature (77K) a sample frozen in the dark (ground state protein conformation) or (ii) illuminating at room temperature prior to and during the freezing (charge separated state protein conformation). The charge recombination rates from the two states differed greatly (>106 fold) as shown previously, indicating a structural change (Paddock et al (2006) Biochemistry 45, 14032 - 14042). ENDOR spectra of QB−• from both samples (35 GHz, 77K) showed three nearly identical sets of hyperfine couplings due to exchangeable protons that were similar to those for QB−• in native RCs indicating that in all RCs, QB−• was located at the proximal position near the metal site. In contrast, one set of H-bond couplings was observed only in the sample frozen under illumination in which the protein can relax prior to freezing. This H-bond was assigned to an interaction between the Ser-L223 hydroxyl and QB−• based on its absence in Ser L223 → Ala mutant RCs. The Ser-L223 hydroxyl H-bond was also observed in the native RCs frozen under illumination. Thus, part of the protein relaxation in response to light induced charge separation involves the formation of an H-bond between the OH group of Ser-L223 and the anionic semiquinone QB−•. This proton movement serves to stabilize the charge separated state and facilitate proton transfer to reduced QB. PMID:17590017

  19. Effects of Rhodobacter sphaeroides on Cadmiun Accumulations of Wheat Seedlligs under Cadmium Stress%球形红细菌对镉胁迫下小麦幼苗镉积累的影响

    Institute of Scientific and Technical Information of China (English)

    郭凌; 张肇铭; 张峰; 芦冬涛

    2007-01-01

    为了研究光合细菌球形红细菌菌悬液对镉胁迫下小麦幼苗镉积累的影响.运用三因素交叉分组随机设计,通过水培试验,研究了球形红细菌菌悬液对小麦幼苗生长过程中培养液Cd2+浓度的影响,以及球形红细菌菌悬液与Cd2+复合处理对小麦幼苗茎叶和根系镉积累量的影响.培养液中Cd2+浓度随培养时间的延长而降低,在小麦幼苗生长初期降低幅度较大;茎叶和根系镉积累量既随培养液Cd2+浓度增加而增加,也随培养时间的延长而增加,在第7~10天镉积累量的增长幅度最大,且根系镉积累量>茎叶镉积累量;施用球形红细菌菌悬液后培养液Cd2+浓度以及小麦幼苗茎叶和根系中镉积累量比对照分别降低了1.9%~49.9%、12.3%~58.1%和8.3%~53.9%.该研究为光合细菌的进一步开发利用提供了理论基础.

  20. Bioproduction of hydrogen by Rhodobacter capsulatus KU002 isolated from leather industry effluents

    Energy Technology Data Exchange (ETDEWEB)

    Merugu, Ramchander; Girisham, S.; Reddy, S.M. [Department of Biochemistry and Microbiology, Kakatiya University, Warangal (India)

    2010-09-15

    A preliminary study on photoproduction of hydrogen by Rhodobacter capsulatus KU002 isolated from leather industry effluents under different cultural conditions with various carbon and nitrogen sources was investigated. Hydrogen production was measured using a Gas chromatograph. Lactate promoted more amounts of hydrogen production under anaerobic light conditions and aerobic light conditions. Cumulative hydrogen production by the organism was recorded at various time intervals. Incubation period of 120 h was optimum for production of hydrogen. pH 7.0 {+-} 0.2 was optimum for production of hydrogen by growing cells, while pH 7.5 {+-} 0.26 for resting cells. L-cystine was a good nitrogen source for production of hydrogen. Growing cells produced more amount of hydrogen than resting cells. Glutamine was a poor nitrogen source for hydrogen production by Rb. capsulatus. Significance of the above results in the presence of existing literature is discussed. (author)

  1. State estimation of a batch hydrogen production process using the photosynthetic bacteria Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Obeid, Jamila; Magnin, Jean-Pierre [Grenoble University, LEPMI, UMR 5631 (CNRS-INPG-UJF), Laboratoire d' Electrochimie et de Physico chimie des Materiaux et Interfaces, BP 75, 38402 St. Martin d' Heres (France); Flaus, Jean-Marie; Adrot, Olivier [Grenoble University, G-SCOP UMR 272 (CNRS-INPG-UJF), Laboratoire des Sciences pour la Conception, l' Optimisation et la Production, 46, avenue Felix Viallet, 38031 Grenoble (France); Willison, John C. [Laboratoire de Chimie et Biologie des Metaux (UMR 5249 CEA-CNRS-UJF), iRTSV/LCBM, CEA-Grenoble, 38054 Grenoble (France)

    2010-10-15

    This paper addresses the problem of estimating the states of an anaerobic photosynthetic process used for biohydrogen production by the photosynthetic bacterium Rhodobacter capsulatus. The process is described by a non-linear, time-discrete model and the state estimation is solved using an observer based on the Moving-Horizon State Estimation Method (MHSE). This approach is based on the minimization of a criterion (a non-linear function), in this case, the difference between the estimated output and the measured output of the system over a considered time horizon, where the solution is computed by using a numerical interval method. The observer was successfully applied to hydrogen production by R. capsulatus strain B10 in a batch process. (author)

  2. A structural role of the carotenoid in the light-harvesting II protein of Rhodobacter capsulatus.

    Science.gov (United States)

    Zurdo, J; Fernandez-Cabrera, C; Ramirez, J M

    1993-03-01

    The membrane-linked light-harvesting II protein (LHII) of Rhodobacter capsulatus was partly depleted of carotenoids by selective extraction with light petroleum. Carotenoid removal was accompanied by bleaching of the Qy(S1<--S0) absorption band of bacteriochlorophyll (Bchl) a near 800 nm, by a bathochromic shift and a broadening of the other Bchl Qy band at 850 nm, and by the formation of a weak Qy band of dissociated Bchl near 770 nm. The changes in the 800 and 850 nm bands seemed to reflect alterations in only those Bchl molecules that had lost their associated carotenoids, firstly, because the extent of the changes was closely correlated to the degree of carotenoid extraction, and, secondly, because the residual fraction of carotenoid-containing LHII, which could be almost quantitatively recovered from the membrane after detergent solubilization and ion-exchange chromatography, showed an unmodified LHII absorption spectrum. The Bchl responsible for the shifted 850 nm band remained bound to protein, since its visible (Qx) transition seemed to retain the induced optical activity of the native bound pigment. Besides, the shifted Bchl could act as an efficient acceptor of singlet excitation energy from the pigments of the intact LHII fraction. The close similarity between the spectroscopic Bchl changes that accompany carotenoid extraction and the differential spectral features of carotenoidless LHII of Rhodobacter mutants, previously reported, strongly suggests that the direct cause of the spectral modifications is the absence of carotenoid and not any independent effect of the experimental manipulation of the membrane. Several interpretations of the structural changes that underlie the observed spectral changes are possible. The simplest one is to assume that carotenoid removal elicits an alteration in the angle between the Qy transition moments of two strongly interacting Bchl molecules.

  3. Structural and phylogenetic analysis of Rhodobacter capsulatus NifF: uncovering general features of nitrogen-fixation (nif)-flavodoxins.

    Science.gov (United States)

    Pérez-Dorado, Inmaculada; Bortolotti, Ana; Cortez, Néstor; Hermoso, Juan A

    2013-01-09

    Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50's loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as "short-chain" with the firmicutes flavodoxins and the "long-chain" with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

  4. Structural and Phylogenetic Analysis of Rhodobacter capsulatus NifF: Uncovering General Features of Nitrogen-fixation (nif-Flavodoxins

    Directory of Open Access Journals (Sweden)

    Inmaculada Pérez-Dorado

    2013-01-01

    Full Text Available Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50’s loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as “short-chain” with the firmicutes flavodoxins and the “long-chain” with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

  5. Hypocholesterolemic effect of Nostoc commune var. sphaeroides Kützing, an edible blue-green alga.

    Science.gov (United States)

    Rasmussen, Heather E; Blobaum, Kara R; Jesch, Elliot D; Ku, Chai Siah; Park, Young-Ki; Lu, Fan; Carr, Timothy P; Lee, Ji-Young

    2009-10-01

    Intake of an edible blue-green alga Nostoc commune var. sphaeroides Kützing (N. Commune) has been shown to lower plasma total cholesterol concentration, but the mechanisms behind the hypocholesterolemic effect have not been elucidated. To elucidate the mechanisms underlying the cholesterol-lowering effect of N. commune in mice. Male C57BL/6J mice were fed the AIN-93 M diet supplemented with 0 or 5% (wt/wt) dried N. Commune for 4 weeks. Lipid levels in the plasma and liver, intestinal cholesterol absorption and fecal sterol excretion were measured. Expression of hepatic and intestinal genes involved in cholesterol metabolism was evaluated by quantitative realtime PCR. N. commune supplementation significantly reduced total plasma cholesterol and triglyceride concentrations by approximately 20% compared to controls. Intestinal cholesterol absorption was significantly decreased, while fecal neutral sterol output was significantly increased in N. commune-fed mice. mRNA levels of the cholesterol transporters such as Niemann Pick C1 Like 1, scavenger receptor class B type 1, ATP-binding cassette transporters G5 and A1 in small intestine were not significantly different between two groups. Hepatic lipid contents including total cholesterol, triglyceride and free cholesterol in N. commune-fed mice were not significantly altered. However, the expression of cholesterol modulating genes including sterol regulatory element binding protein-2 and 3-hydroxy-3-methylglutaryl coenzyme A reductase were significantly increased in mice fed N. commune. N. commune supplementation exerted a hypocholesterolemic effect in mice, largely in part, by reducing intestinal cholesterol absorption and promoting fecal neutral sterol excretion.

  6. The phosphoenolpyruvate-dependent fructose-specific phosphotransferase system in Rhodopseudomonas sphaeroides : Energetics of the phosphoryl group transfer from phosphoenolpyruvate to fructose

    NARCIS (Netherlands)

    Lolkema, Juke S.; Hoeve-Duurkens, Ria H. ten; Robillard, George T.

    1986-01-01

    Energy coupling to fructose transport in Rhodopseudomonas sphaeroides is achieved by phosphorylation of the membrane-spanning fructose-specific carrier protein, EIIFru. The phosphoryl group of phosphoenolpyruvate is transferred to EIIFru via the cytoplasmic component SF (soluble factor). The standar

  7. The Transmembrane Electrical Potential in Rhodopseudomonas sphaeroides Determined from the Distribution of Tetraphenylphosphonium after Correction for Its Binding to Cell Components

    NARCIS (Netherlands)

    Lolkema, Juke S.; Abbing, Arend; Hellingwerf, K; Konings, Wilhelmus

    1983-01-01

    The membrane potential was determined in intact cells of Rhodopseudomonas sphaeroides from the distribution of the lipophilic cation tetraphenylphosphonium (Ph4P+) after correction for probe binding to cell components. The concentration of Ph4P+ in the external medium of the cells was recorded with

  8. Dynamics of Antagonistic Potency of Rhodobacter capsulatus PG Lipopolysaccharide against Endotoxin-Induced Effects.

    Science.gov (United States)

    Kabanov, D S; Serov, D A; Zubova, S V; Grachev, S V; Prokhorenko, I R

    2016-03-01

    The dynamics of antagonistic potency of lipopolysaccharide (LPS) isolated from Rhodobacter capsulatus PG on the synthesis of proinflammatory (TNF-α, IL-1β, IL-8, IL-6, IFN-γ) and antiinflammatory (IL-10, IL-1Ra) cytokines induced by highly stimulatory endotoxins from Escherichia coli or Salmonella enterica have been studied. Using human whole blood, we have shown that R. capsulatus PG LPS inhibited most pronouncedly the endotoxin-induced synthesis of TNF-α, IL-1β, IL-8, and IL-6 during the first 6 h after endotoxin challenge. Similarly, the endotoxin-induced release of IFN-γ was abolished by R. capsulatus PG LPS as well (24 h). In contrast to the above-mentioned cytokines, the relatively weak antagonistic activity of R. capsulatus PG LPS against endotoxin-triggered production of IL-6 and IL-8 was revealed. Since R. capsulatus PG LPS displays more potent antagonistic activity against deleterious effects of S. enterica LPS than those of E. coli LPS in the cases of such cytokines as IL-1β (6 and 24 h), IL-6 and IL-8 (4 h), we conclude that the effectiveness of protective action of antagonist is mostly determined by the primary lipid A structure of the employed agonist.

  9. Transcriptional Profiling of Hydrogen Production Metabolism of Rhodobacter capsulatus under Temperature Stress by Microarray Analysis

    Directory of Open Access Journals (Sweden)

    Muazzez Gürgan

    2015-06-01

    Full Text Available Biohydrogen is a clean and renewable form of hydrogen, which can be produced by photosynthetic bacteria in outdoor large-scale photobioreactors using sunlight. In this study, the transcriptional response of Rhodobacter capsulatus to cold (4 °C and heat (42 °C stress was studied using microarrays. Bacteria were grown in 30/2 acetate/glutamate medium at 30 °C for 48 h under continuous illumination. Then, cold and heat stresses were applied for two and six hours. Growth and hydrogen production were impaired under both stress conditions. Microarray chips for R. capsulatus were custom designed by Affymetrix (GeneChip®. TR_RCH2a520699F. The numbers of significantly changed genes were 328 and 293 out of 3685 genes under cold and heat stress, respectively. Our results indicate that temperature stress greatly affects the hydrogen production metabolisms of R. capsulatus. Specifically, the expression of genes that participate in nitrogen metabolism, photosynthesis and the electron transport system were induced by cold stress, while decreased by heat stress. Heat stress also resulted in down regulation of genes related to cell envelope, transporter and binding proteins. Transcriptome analysis and physiological results were consistent with each other. The results presented here may aid clarification of the genetic mechanisms for hydrogen production in purple non-sulfur (PNS bacteria under temperature stress.

  10. Potential use of thermophilic dark fermentation effluents in photofermentative hydrogen production by Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Ozgura, E.; Afsar, N.; Eroglu, I. [Middle East Technical University, Department of Chemical Engineering, 06531 Ankara (Turkey); De Vrije, T.; Claassen, P.A.M. [Wageningen UR, Agrotechnology and Food Sciences Group, Wageningen UR, P.O. Box 17, 6700 AA Wageningen (Netherlands); Yucel, M.; Gunduz, U. [Middle East Technical University, Department of Biology, 06531 Ankara (Turkey)

    2010-12-15

    Biological hydrogen production by a sequential operation of dark and photofermentation is a promising route to produce hydrogen. The possibility of using renewable resources, like biomass and agro-industrial wastes, provides a dual effect of sustainability in biohydrogen production and simultaneous waste removal. In this study, photofermentative hydrogen production on effluents of thermophilic dark fermentations on glucose, potato steam peels (PSP) hydrolysate and molasses was investigated in indoor, batch operated bioreactors. An extreme thermophile Caldicellulosiruptor saccharolyticus was used in the dark fermentation step, and Rhodobacter capsulatus (DSM1710) was used in the photofermentation step. Addition of buffer, Fe and Mo to dark fermentor effluents (DFEs) improved the overall efficiency of hydrogen production. The initial acetate concentration in the DFE needed to be adjusted to 30-40 mM by dilution to increase the yield of hydrogen in batch light-supported fermentations. The thermophilic DFEs are suitable for photofermentative hydrogen production, provided that they are supplemented with buffer and nutrients. The overall hydrogen yield of the two-step fermentations was higher than the yield of single step dark fermentations.

  11. Long-term biological hydrogen production by agar immobilized Rhodobacter capsulatus in a sequential batch photobioreactor.

    Science.gov (United States)

    Elkahlout, Kamal; Alipour, Siamak; Eroglu, Inci; Gunduz, Ufuk; Yucel, Meral

    2017-04-01

    In this study, agar immobilization technique was employed for biological hydrogen production using Rhodobacter capsulatus DSM 1710 (wild type) and YO3 (hup-mutant) strains in sequential batch process. Different agar and glutamate concentrations were tested with defined nutrient medium. Agar concentration 4% (w/v) and 4 mM glutamate were selected for bacterial immobilization in terms of rate and longevity of hydrogen production. Acetate concentration was increased from 40 to 60-100 and 60 mM gave best results with both bacterial strains immobilized in 4% (w/v) agar. Cell concentration was increased from 2.5 to 5 mg dcw mL(-1) agar and it was found that increasing cell concentration of wild-type strain caused decrease in yield and productivity while these parameters improved by increasing cell concentration of mutant strain. Also, the hydrogen production time has extended from 17 days up to 60 days according to the process conditions and parameters. Hydrogen production by immobilized photosynthetic bacteria is a convenient technology for hydrogen production as it enables to produce hydrogen with high organic acid concentrations comparing to suspended cultures. Besides, immobilization increases the stability of the system and allowed sequential batch operation for long-term application.

  12. A Rhodobacter capsulatus member of a universal permease family imports molybdate and other oxyanions.

    Science.gov (United States)

    Gisin, Jonathan; Müller, Alexandra; Pfänder, Yvonne; Leimkühler, Silke; Narberhaus, Franz; Masepohl, Bernd

    2010-11-01

    Molybdenum (Mo) is an important trace element that is toxic at high concentrations. To resolve the mechanisms underlying Mo toxicity, Rhodobacter capsulatus mutants tolerant to high Mo concentrations were isolated by random transposon Tn5 mutagenesis. The insertion sites of six independent isolates mapped within the same gene predicted to code for a permease of unknown function located in the cytoplasmic membrane. During growth under Mo-replete conditions, the wild-type strain accumulated considerably more Mo than the permease mutant. For mutants defective for the permease, the high-affinity molybdate importer ModABC, or both transporters, in vivo Mo-dependent nitrogenase (Mo-nitrogenase) activities at different Mo concentrations suggested that ModABC and the permease import molybdate in nanomolar and micromolar ranges, respectively. Like the permease mutants, a mutant defective for ATP sulfurylase tolerated high Mo concentrations, suggesting that ATP sulfurylase is the main target of Mo inhibition in R. capsulatus. Sulfate-dependent growth of a double mutant defective for the permease and the high-affinity sulfate importer CysTWA was reduced compared to those of the single mutants, implying that the permease plays an important role in sulfate uptake. In addition, permease mutants tolerated higher tungstate and vanadate concentrations than the wild type, suggesting that the permease acts as a general oxyanion importer. We propose to call this permease PerO (for oxyanion permease). It is the first reported bacterial molybdate transporter outside the ABC transporter family.

  13. Coenzyme binding and hydride transfer in Rhodobacter capsulatus ferredoxin/flavodoxin NADP(H) oxidoreductase.

    Science.gov (United States)

    Bortolotti, Ana; Pérez-Dorado, Inmaculada; Goñi, Guillermina; Medina, Milagros; Hermoso, Juan A; Carrillo, Néstor; Cortez, Néstor

    2009-02-01

    Ferredoxin-NADP(H) reductases catalyse the reversible hydride/electron exchange between NADP(H) and ferredoxin/flavodoxin, comprising a structurally defined family of flavoenzymes with two distinct subclasses. Those present in Gram-negative bacteria (FPRs) display turnover numbers of 1-5 s(-1) while the homologues of cyanobacteria and plants (FNRs) developed a 100-fold activity increase. We investigated nucleotide interactions and hydride transfer in Rhodobacter capsulatus FPR comparing them to those reported for FNRs. NADP(H) binding proceeds as in FNRs with stacking of the nicotinamide on the flavin, which resulted in formation of charge-transfer complexes prior to hydride exchange. The affinity of FPR for both NADP(H) and 2'-P-AMP was 100-fold lower than that of FNRs. The crystal structure of FPR in complex with 2'-P-AMP and NADP(+) allowed modelling of the adenosine ring system bound to the protein, whereas the nicotinamide portion was either not visible or protruding toward solvent in different obtained crystals. Stabilising contacts with the active site residues are different in the two reductase classes. We conclude that evolution to higher activities in FNRs was partially favoured by modification of NADP(H) binding in the initial complexes through changes in the active site residues involved in stabilisation of the adenosine portion of the nucleotide and in the mobile C-terminus of FPR.

  14. Purification and activities of the Rhodobacter capsulatus RpoN (sigma N) protein.

    Science.gov (United States)

    Cannon, W; Missailidis, S; Austin, S; Moore, M; Drake, A; Buck, M

    1996-07-01

    The rpoN-encoded sigma factors (sigma N) are a distinct class of bacterial sigma factors, with no obvious homology to the major sigma 70 class. The sigma N-containing RNA polymerase holoenzyme functions in enhancer-dependent transcription to allow expression of positively controlled genes. We have purified the Rhodobacter capsulatus sigma N protein, which is distinctive in lacking an acidic region implicated in the melting of promoter DNA by the Escherichia coll sigma N holoenzyme, and may represent a minor subclass of sigma N proteins. Assays of promoter recognition and holoenzyme formation and function showed that the purified R. capsulatus sigma N protein is distinct in activity compared to the enteric proteins, but retains the broad functions described for these proteins. As first described for the Klebsiella pneumoniae protein, promoter recognition in the absence of core RNA polymerase was detected, but contact of certain promoter bases by the R. capsulatus sigma N protein and its response to core RNA polymerase was clearly different from that determined for the K. pneumoniae and E. coli proteins. Results are discussed in the context of a requirement to modulate the activity of the DNA-binding surfaces of sigma N to regulate sigma N function. Circular dichroism was used to evaluate the structure of the R. capsulatus protein and revealed differences in the tertiary signals as compared to the K. pneumoniae protein, some of which are attributable to the DNA-binding domain of sigma N.

  15. Modelling of hydrogen production in batch cultures of the photosynthetic bacterium Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Obeid, Jamila; Magnin, Jean-Pierre [Grenoble Institute of Technology, LEPMI, UMR 5631 (CNRS-INPG-UJF), BP 75, 38402 St Martin d' Heres (France); Flaus, Jean-Marie; Adrot, Olivier [Grenoble Institute of Technology, Laboratoire des sciences pour la conception, l' optimisation et la production, 46, avenue Felix Viallet, 38031 Grenoble (France); Willison, John C. [Laboratoire de Chimie et Biologie des Metaux (UMR 5249 CEA-CNRS-UJF), iRTSV/LCBM, CEA-Grenoble, 38054 Grenoble (France); Zlatev, Roumen [Autonomous University of Baja California, Institute of Engineering, Mexicali, Baja California (Mexico)

    2009-01-15

    The photosynthetic bacterium, Rhodobacter capsulatus, produces hydrogen under nitrogen-limited, anaerobic, photosynthetic culture conditions, using various carbon substrates. In the present study, the relationship between light intensity and hydrogen production has been modelled in order to predict both the rate of hydrogen production and the amount of hydrogen produced at a given time during batch cultures of R. capsulatus. The experimental data were obtained by investigating the effect of different light intensities (6000-50,000 lux) on hydrogen-producing cultures of R. capsulatus grown in a batch photobioreactor, using lactate as carbon and hydrogen source. The rate of hydrogen production increased with increasing light intensity in a manner that was described by a static Baly model, modified to include the square of the light intensity. In agreement with previous studies, the kinetics of substrate utilization and growth of R. capsulatus was represented by the classical Monod or Michaelis-Menten model. When combined with a dynamic Leudekong-Piret model, the amount of hydrogen produced as a function of time was effectively predicted. These results will be useful for the automatization and control of bioprocesses for the photoproduction of hydrogen. (author)

  16. Improving the hydrogen production capacity of Rhodobacter capsulatus by genetically modifying redox balancing pathways

    Energy Technology Data Exchange (ETDEWEB)

    Oeztuerk, Yavuz [TUEBITAK Research Institute for Genetic Engineering and Biotechnology, Gebze Kocaeli (Turkey); Goekce, Abdulmecit [Istanbul Technical Univ. (Turkey). Dept. of Molecular Biology and Genetics; Guergan, Muazzez; Yuecel, Meral [Middle East Technical Univ., Ankara (Turkey). Dept. of Biology

    2010-07-01

    In Rhodobacter capsulatus, balancing the oxidation-reduction potential (redox-balance) is maintained via a number of inter-dependent regulatory mechanisms that enable these organisms to accommodate divergent growth modes. In order to maintain redox homeostasis, this bacterium possesses regulatory mechanisms functioning as electron sinks affecting the oxidation-reduction state of the ubiquinone pool. Under the photoheterotrophic growth conditions with reduced carbon sources, the excess reducing equivalents are primarily consumed via the reduction of CO{sub 2} through the Calvin-Benson-Bassham (CBB) pathway or by the reduction of protons into hydrogen with the use of dinitrogenase enzyme system. In this study, our aim was to develop strategies to funnel the excess reducing equivalents to nitrogenase-dependent hydrogen production by blocking the carbon-fixation pathway. To realize this purpose, CO{sub 2} fixation was blocked by inactivating the Phosphoribulokinase (PRK) of CBB pathway in wild type (MT1131), uptake-hydrogenase (YO3) and cyt cbb{sub 3} oxidase deficient (YO4) strains. The hydrogen production capacity of newly generated strains deficient in the Calvin-Benson-Bassham pathway were analyzed and compared with wild type strains. The results indicated that, the hydrogen production efficiency and capacity of R. capsulatus was further improved by directing the excess reducing equivalents to dinitrogenase-dependent hydrogen production. (orig.)

  17. Field evidence for the potential of Rhodobacter capsulatus as Biofertilizer for flooded rice.

    Science.gov (United States)

    Gamal-Eldin, Hosny; Elbanna, Khaled

    2011-02-01

    In a previous study, we evaluated the effects of inoculating rice plants with the phototrophic purple nonsulfur bacterium Rhodobacter capsulatus (Rc) on growth and yield of rice in pots and lysimeter experiments and the results obtained have been highly encouraging. In this study, we carried out two field experiments: one in the experimental farm of the Faculty of Agriculture, Fayoum University, and the second in a farmer's field in Kafr El-sheikh, to assess the effects of Rc on growth and yield of rice in comparison and in combination with chemical nitrogen fertilizer (CNF) and farmyard manure. The results indicated that both biological and grain yields in all the Rc inoculated treatments were significantly higher than those in the uninoculated corresponding treatments in both fields. With regard to grain yield, the major factor for determining the effectiveness of any agricultural treatment, inoculation with Rc in combination with 50% of the recommended CNF rate gave a grain yield that was statistically equivalent to that obtained with 100% of the recommended CNF rate. These results provide a clear evidence for the potential of Rc as biofertilizer for flooded rice under field conditions.

  18. Structural and Phylogenetic Analysis of Rhodobacter capsulatus NifF: Uncovering General Features of Nitrogen-fixation (nif)-Flavodoxins

    OpenAIRE

    Inmaculada Pérez-Dorado; Ana Bortolotti; Néstor Cortez; Hermoso, Juan A.

    2013-01-01

    Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50’s loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including...

  19. A [2Fe-2S] ferredoxin (FdVI) is essential for growth of the photosynthetic bacterium Rhodobacter capsulatus.

    OpenAIRE

    Armengaud, J.; Meyer, C.; Jouanneau, Y

    1997-01-01

    The physiological function of Rhodobacter capsulatus FdVI, a [2Fe-2S] ferredoxin, was investigated by the cloning, sequence analysis, and mutagenesis of its structural gene, called fdxE. The DNA region surrounding fdxE was mapped, and the nucleotide sequence of a 4.2-kb fragment was determined. fdxE is preceded by a sequence that is very similar to a sigma54 recognition site and is followed by a putative transcription stop signal, suggesting that fdxE forms a separate cistron. Two open readin...

  20. Identification and mapping of nitrogen fixation genes of Rhodobacter capsulatus: duplication of a nifA-nifB region.

    OpenAIRE

    Klipp, W; Masepohl, B; Pühler, A.

    1988-01-01

    Rhodobacter capsulatus mutants unable to fix nitrogen were isolated by random transposon Tn5 mutagenesis. The Tn5 insertion sites of 30 Nif- mutants were mapped within three unlinked chromosomal regions designated A, B, and C. The majority of Tn5 insertions (21 mutants) map within nif region A, characterized by two ClaI fragments of 2.5 and 25 kilobases (kb). The 17-kb ClaI fragment of nif region B contains six nif::Tn5 insertions, and the three remaining mutations are located on a 32-kb ClaI...

  1. Optimizing multi-step B-side charge separation in photosynthetic reaction centers from Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Faries, Kaitlyn M. [Washington Univ., St. Louis, MO (United States); Kressel, Lucas L. [Argonne National Lab. (ANL), Argonne, IL (United States); Dylla, Nicholas P. [Argonne National Lab. (ANL), Argonne, IL (United States); Wander, Marc J. [Argonne National Lab. (ANL), Argonne, IL (United States); Hanson, Deborah K. [Argonne National Lab. (ANL), Argonne, IL (United States); Holten, Dewey [Washington Univ., St. Louis, MO (United States); Laible, Philip D. [Argonne National Lab. (ANL), Argonne, IL (United States); Kirmaier, Christine [Washington Univ., St. Louis, MO (United States)

    2016-02-01

    Using high-throughput methods for mutagenesis, protein isolation and charge-separation functionality, we have assayed 40 Rhodobacter capsulatus reaction center (RC) mutants for their P+ QB- yield (P is a dimer of bacteriochlorophylls and Q is a ubiquinone) as produced using the normally inactive B-side cofactors BB and HB (where B is a bacteriochlorophyll and H is a bacteriopheophytin). Two sets of mutants explore all possible residues at M131 (M polypeptide, native residue Val near HB) in tandem with either a fixed His or a fixed Asn at L181 (L polypeptide, native residue Phe near BB). A third set of mutants explores all possible residues at L181 with a fixed Glu at M131 that can form a hydrogen bond to HB. For each set of mutants, the results of a rapid millisecond screening assay that probes the yield of P+ QB- are compared among that set and to the other mutants reported here or previously. For a subset of eight mutants, the rate constants and yields of the individual B-side electron transfer processes are determined via transient absorption measurements spanning 100 fs to 50 μs. The resulting ranking of mutants for their yield of P+ QB- from ultrafast experiments is in good agreement with that obtained from the millisecond screening assay, further validating the efficient, high-throughput screen for B-side transmembrane charge separation. Results from mutants that individually show progress toward optimization of P+ HB- → P+ QB- electron transfer or initial P* → P+ HB- conversion highlight unmet challenges of optimizing both processes simultaneously.

  2. Extracellular production of tellurium nanoparticles by the photosynthetic bacterium Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Borghese, Roberto, E-mail: roberto.borghese@unibo.it [Dept. of Pharmacy and Biotechnology, University of Bologna (Italy); Brucale, Marco [Institute for the Study of Nanostructured Materials (CNR-ISMN), Rome (Italy); Fortunato, Gianuario [Dept. of Pharmacy and Biotechnology, University of Bologna (Italy); Lanzi, Massimiliano [Dept. of Industrial Chemistry “Toso Montanari”, University of Bologna (Italy); Mezzi, Alessio [Institute for the Study of Nanostructured Materials (CNR-ISMN), Rome (Italy); Valle, Francesco; Cavallini, Massimiliano [Institute for the Study of Nanostructured Materials (CNR-ISMN), Bologna (Italy); Zannoni, Davide [Dept. of Pharmacy and Biotechnology, University of Bologna (Italy)

    2016-05-15

    Highlights: • Tellurite is reduced by R. capsulatus as cytosolic tellurium nanoprecipitates TeNPs. • Lawsone allows R. capsulatus to produce extracellular TeNPs. • Extracellular TeNPs production depends on the carbon source used for cells growth. • Both lawsone concentration and the incubation time determine the TeNPs size. • Extracellular TeNPs are coated with extracellular polymeric substances (EPS). - Abstract: The toxic oxyanion tellurite (TeO{sub 3}{sup 2−}) is acquired by cells of Rhodobacter capsulatus grown anaerobically in the light, via acetate permease ActP2 and then reduced to Te{sup 0} in the cytoplasm as needle-like black precipitates. Interestingly, photosynthetic cultures of R. capsulatus can also generate Te{sup 0} nanoprecipitates (TeNPs) outside the cells upon addition of the redox mediator lawsone (2-hydroxy-1,4-naphtoquinone). TeNPs generation kinetics were monitored to define the optimal conditions to produce TeNPs as a function of various carbon sources and lawsone concentration. We report that growing cultures over a 10 days period with daily additions of 1 mM tellurite led to the accumulation in the growth medium of TeNPs with dimensions from 200 up to 600–700 nm in length as determined by atomic force microscopy (AFM). This result suggests that nucleation of TeNPs takes place over the entire cell growth period although the addition of new tellurium Te{sup 0} to pre-formed TeNPs is the main strategy used by R. capsulatus to generate TeNPs outside the cells. Finally, X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FT-IR) analysis of TeNPs indicate they are coated with an organic material which keeps the particles in solution in aqueous solvents.

  3. Coordinated, long-range, solid substrate movement of the purple photosynthetic bacterium Rhodobacter capsulatus.

    Directory of Open Access Journals (Sweden)

    Kristopher John Shelswell

    Full Text Available The long-range movement of Rhodobacter capsulatus cells in the glass-agar interstitial region of borosilicate Petri plates was found to be due to a subset of the cells inoculated into plates. The macroscopic appearance of plates indicated that a small group of cells moved in a coordinated manner to form a visible satellite cluster of cells. Satellite clusters were initially separated from the point of inoculation by the absence of visible cell density, but after 20 to 24 hours this space was colonized by cells apparently shed from a group of cells moving away from the point of inoculation. Cell movements consisted of flagellum-independent and flagellum-dependent motility contributions. Flagellum-independent movement occurred at an early stage, such that satellite clusters formed after 12 to 24 hours. Subsequently, after 24 to 32 hours, a flagellum-dependent dispersal of cells became visible, extending laterally outward from a line of flagellum-independent motility. These modes of taxis were found in several environmental isolates and in a variety of mutants, including a strain deficient in the production of the R. capsulatus acyl-homoserine lactone quorum-sensing signal. Although there was great variability in the direction of movement in illuminated plates, cells were predisposed to move toward broad spectrum white light. This predisposition was increased by the use of square plates, and a statistical analysis indicated that R. capsulatus is capable of genuine phototaxis. Therefore, the variability in the direction of cell movement was attributed to optical effects on light waves passing through the plate material and agar medium.

  4. Degradation of p-nitrophenol by the phototrophic bacterium Rhodobacter capsulatus.

    Science.gov (United States)

    Roldán, M D; Blasco, R; Caballero, F J; Castillo, F

    1998-01-01

    The phototrophic bacterium Rhodobacter capsulatus detoxified p-nitrophenol and 4-nitrocatechol. The bacterium tolerated moderate concentrations of p-nitrophenol (up to 0.5 mM) and degraded it under light at an optimal O2 pressure of 20 kPa. The bacterium did not metabolize the xenobiotic in the dark or under strictly anoxic conditions or high O2 pressure. Bacterial growth with acetate in the presence of p-nitrophenol took place with the simultaneous release of nonstoichiometric amounts of 4-nitrocatechol, which can also be degraded by the bacterium. Crude extracts from R. capsulatus produced 4-nitrocatechol from p-nitrophenol upon the addition of NAD(P)H, although at a very low rate. A constitutive catechol 1, 2-dioxygenase activity yielding cis,cis-muconate was also detected in crude extracts of R. capsulatus. Further degradation of 4-nitrocatechol included both nitrite- and CO2-releasing steps since: (1) a strain of R. capsulatus (B10) unable to assimilate nitrate and nitrite released nitrite into the medium when grown with p-nitrophenol or 4-nitrocatechol, and the nitrite concentration was stoichiometric with the 4-nitrocatechol degraded, and (2) cultures of R. capsulatus growing microaerobically produced low amounts of 14CO2 from radiolabeled p-nitrophenol. The radioactivity was also incorporated into cellular compounds from cells grown with uniformly labeled 14C-p-nitrophenol. From these results we concluded that the xenobiotic is used as a carbon source by R. capsulatus, but that only the strain able to assimilate nitrite (E1F1) can use p-nitrophenol as a nitrogen source.

  5. Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Burke-Agueero, D.H.

    1992-08-01

    Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight bch'' genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.

  6. Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Burke-Agueero, D.H.

    1992-08-01

    Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight ``bch`` genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.

  7. Reprint of “Extracellular production of tellurium nanoparticles by the photosynthetic bacterium Rhodobacter capsulatus”

    Energy Technology Data Exchange (ETDEWEB)

    Borghese, Roberto, E-mail: roberto.borghese@unibo.it [Dept. of Pharmacy and Biotechnology, University of Bologna (Italy); Brucale, Marco [Institute for the Study of Nanostructured Materials (CNR-ISMN), Rome (Italy); Fortunato, Gianuario [Dept. of Pharmacy and Biotechnology, University of Bologna (Italy); Lanzi, Massimiliano [Dept. of Industrial Chemistry “Toso Montanari”, University of Bologna (Italy); Mezzi, Alessio [Institute for the Study of Nanostructured Materials (CNR-ISMN), Rome (Italy); Valle, Francesco; Cavallini, Massimiliano [Institute for the Study of Nanostructured Materials (CNR-ISMN), Bologna (Italy); Zannoni, Davide [Dept. of Pharmacy and Biotechnology, University of Bologna (Italy)

    2017-02-15

    Highlights: • Tellurite is reduced by R. capsulatus as cytosolic tellurium nanoprecipitates TeNPs. • Lawsone allows R. capsulatus to produce extracellular TeNPs. • Extracellular TeNPs production depends on the carbon source used for cells growth. • Both lawsone concentration and the incubation time determine the TeNPs size. • Extracellular TeNPs are coated with extracellular polymeric substances (EPS). - Abstract: The toxic oxyanion tellurite (TeO{sub 3}{sup 2−}) is acquired by cells of Rhodobacter capsulatus grown anaerobically in the light, via acetate permease ActP2 and then reduced to Te{sup 0} in the cytoplasm as needle-like black precipitates. Interestingly, photosynthetic cultures of R. capsulatus can also generate Te{sup 0} nanoprecipitates (TeNPs) outside the cells upon addition of the redox mediator lawsone (2-hydroxy-1,4-naphtoquinone). TeNPs generation kinetics were monitored to define the optimal conditions to produce TeNPs as a function of various carbon sources and lawsone concentration. We report that growing cultures over a 10 days period with daily additions of 1 mM tellurite led to the accumulation in the growth medium of TeNPs with dimensions from 200 up to 600–700 nm in length as determined by atomic force microscopy (AFM). This result suggests that nucleation of TeNPs takes place over the entire cell growth period although the addition of new tellurium Te{sup 0} to pre-formed TeNPs is the main strategy used by R. capsulatus to generate TeNPs outside the cells. Finally, X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FT-IR) analysis of TeNPs indicate they are coated with an organic material which keeps the particles in solution in aqueous solvents.

  8. Reduction of chalcogen oxyanions and generation of nanoprecipitates by the photosynthetic bacterium Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Borghese, Roberto, E-mail: roberto.borghese@unibo.it [Department of Pharmacy and Biotechnology, University of Bologna (Italy); Baccolini, Chiara; Francia, Francesco [Department of Pharmacy and Biotechnology, University of Bologna (Italy); Sabatino, Piera [Department of Chemistry G. Ciamician, University of Bologna (Italy); Turner, Raymond J. [Department of Biological Sciences, University of Calgary, Calgary, Alberta (Canada); Zannoni, Davide, E-mail: davide.zannoni@unibo.it [Department of Pharmacy and Biotechnology, University of Bologna (Italy)

    2014-03-01

    Graphical abstract: - Highlights: • R. capsulatus cells produce extracellular chalcogens nanoprecipitates when lawsone is present. • Lawsone acts as a redox mediator from reducing equivalents to tellurite and selenite. • Nanoprecipitates production depends on carbon source and requires metabolically active cells. • Te{sup 0} and Se{sup 0} nanoprecipitates are identified by X-ray diffraction (XRD) spectroscopy. - Abstract: The facultative photosynthetic bacterium Rhodobacter capsulatus is characterized in its interaction with the toxic oxyanions tellurite (Te{sup IV}) and selenite (Se{sup IV}) by a highly variable level of resistance that is dependent on the growth mode making this bacterium an ideal organism for the study of the microbial interaction with chalcogens. As we have reported in the past, while the oxyanion tellurite is taken up by R. capsulatus cells via acetate permease and it is reduced to Te{sup 0} in the cytoplasm in the form of splinter-like black intracellular deposits no clear mechanism was described for Se{sup 0} precipitation. Here, we present the first report on the biotransformation of tellurium and selenium oxyanions into extracellular Te{sup 0} and Se{sup 0}nanoprecipitates (NPs) by anaerobic photosynthetically growing cultures of R. capsulatus as a function of exogenously added redox-mediator lawsone, i.e. 2-hydroxy-1,4-naphthoquinone. The NPs formation was dependent on the carbon source used for the bacterial growth and the rate of chalcogen reduction was constant at different lawsone concentrations, in line with a catalytic role for the redox mediator. X-ray diffraction (XRD) analysis demonstrated the Te{sup 0} and Se{sup 0} nature of the nanoparticles.

  9. Exploration of the hydrogen producing potential of Rhodobacter capsulatus chemostat cultures: The application of deceleration-stat and gradient-stat methodology

    NARCIS (Netherlands)

    Hoekema, S.; Breukelen, van F.R.; Janssen, M.G.J.; Tramper, J.; Wijffels, R.H.

    2009-01-01

    In this work, the dependency of the volumetric hydrogen production rate of ammonium-limited Rhodobacter capsulatus chemostat cultures on their imposed biomass concentration and dilution rate was investigated. A deceleration-stat experiment was performed by lowering the dilution rate from 1.0 d-1 to

  10. Exploration of the hydrogen producing potential of Rhodobacter capsulatus chemostat cultures: The application of deceleration-stat and gradient-stat methodology

    NARCIS (Netherlands)

    Hoekema, S.; Breukelen, van F.R.; Janssen, M.G.J.; Tramper, J.; Wijffels, R.H.

    2009-01-01

    In this work, the dependency of the volumetric hydrogen production rate of ammonium-limited Rhodobacter capsulatus chemostat cultures on their imposed biomass concentration and dilution rate was investigated. A deceleration-stat experiment was performed by lowering the dilution rate from 1.0 d-1 to

  11. Draft Genome Sequences of Two Heat-Resistant Mutant Strains (A52 and B41) of the Photosynthetic Hydrogen-Producing Bacterium Rhodobacter capsulatus

    Science.gov (United States)

    Gokce, Abdulmecit; Cakar, Zeynep Petek; Yucel, Meral; Ozcan, Orhan; Sencan, Sevde; Sertdemir, Ibrahim; Erguner, Bekir; Yuceturk, Betul; Sarac, Aydan; Yuksel, Bayram

    2016-01-01

    The draft genome sequences of two heat-resistant mutant strains, A52 and B41, derived from Rhodobacter capsulatus DSM 1710, and with different hydrogen production levels, are reported here. These sequences may help understand the molecular basis of heat resistance and hydrogen production in R. capsulatus. PMID:27284151

  12. Genetic and biochemical characterization of carotenoid biosynthesis mutants of Rhodobacter capsulatus.

    Science.gov (United States)

    Armstrong, G A; Schmidt, A; Sandmann, G; Hearst, J E

    1990-05-15

    We have used genetic and biochemical techniques to study carotenoid biosynthesis (crt) mutants of Rhodobacter capsulatus, a purple non-sulfur photosynthetic bacterium. All nine identified crt genes are located within the 46-kilobase pair photosynthesis gene cluster, and eight of the crt genes form a subcluster. We have studied the operon structure of the crt gene cluster using transposon Tn5.7 mutants. The Tn5.7 insertion sites in 10 mutants have been mapped to high resolution (25-267 base pairs) by Southern hybridization. Two insertions each map within the coding regions of the crtA, crtC, crtE, and crtF genes, and one insertion lies within the crtI gene. The insertion in crtI is not polar on the downstream crtB gene, suggesting that crtI and crtB may form two separate operons. Another insertion located in the 5' noncoding region between the divergent crtA and crtI genes has no effect on wild-type pigmentation and apparently lies between the promoters for these operons. A Tn5.7 mutation in the 3' region of crtA yields a bacteriochlorophyll-minus phenotype, while a 5' insertion affects only carotenoid biosynthesis. Regulatory signals for transcription of a downstream operon required for bacteriochlorophyll biosynthesis may thus overlap the coding region of crtA. We also present the first evidence for the functions of the crtB, crtE, and crtJ gene products using a new in vitro assay for the incorporation of [14C]isopentenyl pyrophosphate into carotenoid precursors and phytoene in cell-free extracts. Extracts from a crtE mutant accumulate [14C]prephytoene pyrophosphate, while those from crtB and crtJ mutants accumulate [14C]geranylgeranyl pyrophosphate. We therefore propose that CrtE is the phytoene synthetase and that CrtB, and possibly CrtJ, are components of the prephytoene pyrophosphate synthetase.

  13. Effect of uncoupler on assembly pathway for pigment-binding protein of bacterial photosynthetic membranes. [Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Dierstein, R.; Drews, G.

    1986-10-01

    The uncoupler carbonylcyanide m-chlorophenylhydrazone (CCCP) was used to investigate membrane protein assembly in the phototrophic bacterium Rhodobacter capsulatus. As found for Escherichia coli and mitochondrial proteins, assembly across the bacterial photosynthetic membranes was sensitive to CCCP. At uncoupler concentrations which were sufficient to block the export of the periplasmic cytochrome c/sub 2/ and an outer membrane protein, the integration of pigment-binding protein into the photosynthetic apparatus was abolished. The unassembled protein was detected on the inner surface of the intracytoplasmic membrane. After inactivation of CCCP, accumulated protein continued insertion into the membrane. The data suggest that after binding to the cytoplasmic face of the membrane (i), translocation of protein into a transmembrane orientation takes place (ii), which is a prerequisite for the formation of a functional pigment-protein complex (iii).

  14. Loss of the Response Regulator CtrA Causes Pleiotropic Effects on Gene Expression but Does Not Affect Growth Phase Regulation in Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Mercer, Ryan; Callister, Stephen J.; Lipton, Mary S.; Pasa-Tolic, Ljiljana; Strnad, Hynek; Paces, Vaclav; Beatty, J. T.; Lang, Andrew S.

    2010-06-01

    The purple non-sulfur bacterium Rhodobacter capsulatus has been extensively studied for its diverse metabolic capabilities, as well as for its production of a Gene Transfer Agent (RcGTA). Production of RcGTA requires the response regulator protein CtrA. We have used whole genome transcript and whole cell proteome analyses of wild type and ctrA mutant cultures to completely characterize the regulatory role of CtrA in R. capsulatus.

  15. The response of antioxidant systems in Nostoc sphaeroides against UV-B radiation and the protective effects of exogenous antioxidants

    Science.gov (United States)

    Wang, Gaohong; Hu, Chunxiang; Li, Dunhai; Zhang, Delu; Li, Xiaoyan; Chen, Kun; Liu, Yongding

    UV radiation is one of many harmful factors found in space that are detrimental to organisms on earth in space exploration. In the present work, we examined the role of antioxidant system in Nostoc sphaeroides Kütz (Cyanobacterium) and the effects of exogenously applied antioxidant molecules on its photosynthetic rate under UV-B radiation. It was found that UV-B radiation promoted the activity of antioxidant system to protect photosystem II (PSII) and exogenously applied antioxidant: sodium nitroprusside (SNP) and N-acetylcysteine (NAC) had an obvious protection on PSII activity under UV-B radiation. The activity of superoxide dismutase (SOD, EC 1.15.1.1), catalase (CAT, EC 1.11.1.6), peroxidase (POD, EC 1.11.1.7) and content of MDA (malondialdehyde) and ASC (ascorbate) were improved by 0.5 mM and 1 mM SNP, but 0.1 mM SNP decreased the activity of antioxidant system. Addition of exogenous NAC decreased the activity of SOD, POD, CAT and the content MDA and ASC. In contrast, exogenously applied NAC increased GSH content. The results suggest that exogenous SNP and NAC may protect algae by different mechanisms: SNP may play double roles as both sources of reactive free radicals as well as ROS scavengers in mediating the protective role of PSII on algae under UV-B radiation. On the other hand, NAC functions as an antioxidant or precursor of glutathione, which could protect PSII directly from UV-B radiation.

  16. Uniform designation for genes of the Calvin-Benson-Bassham reductive pentose phosphate pathway of bacteria

    NARCIS (Netherlands)

    Tabita, F. Robert; Gibson, Janet L.; Bowien, Botho; Dijkhuizen, Lubbert; Meijer, Wilhelmus

    1992-01-01

    Structural and regulatory genes encoding enzymes and proteins of the reductive pentose phosphate pathway have been isolated from a number of bacteria recently. In the phototroph Rhodobacter sphaeroides, and in two chemoautotrophic bacteria, Alcaligenes eutrophus and Xanthobacter flavus, these genes

  17. Carotenogenesis gene cluster and phytoene desaturase catalyzing both three- and four-step desaturations from Rhodobacter azotoformans.

    Science.gov (United States)

    Zhang, Jinhua; Lu, Lili; Yin, Lijie; Xie, Shen; Xiao, Min

    2012-08-01

    A carotenogenesis gene cluster from the purple nonsulfur photosynthetic bacterium Rhodobacter azotoformans CGMCC 6086 was cloned. A total of eight carotenogenesis genes ( crtA , crtI , crtB , tspO , crtC , crtD , crtE , and crtF ) were located in two separate regions within the genome, a 4.9 kb region containing four clustered genes of crtAIB - tspO and a 5.3 kb region containing four clustered genes of crtCDEF . The organization was unusual for a carotenogenesis gene cluster in purple photosynthetic bacteria. A gene encoding phytoene desaturase ( CrtI ) from Rba. azotoformans was expressed in Escherichia coli. The recombinant CrtI could catalyze both three- and four-step desaturations of phytoene to produce neurosporene and lycopene, and the relative contents of neurosporene and lycopene formed by CrtI were approximately 23% and 75%, respectively. Even small amounts of five-step desaturated 3,4-didehydrolycopene could be produced by CrtI . This product pattern was novel because CrtI produced only neurosporene leading to spheroidene pathway in the cells of Rba. azotoformans. In the in vitro reaction, the relative content of lycopene in desaturated products increased from 19.6% to 62.5% when phytoene reduced from 2.6 to 0.13 μM. The results revealed that the product pattern of CrtI might be affected by the kinetics.

  18. Hydrogen production by photosynthetic bacteria Rhodobacter capsulatus Hup{sup -} strain on acetate in continuous panel photobioreactors

    Energy Technology Data Exchange (ETDEWEB)

    Deo Androga, Dominic; Ozgur, Ebru; Eroglu, Inci [Middle East Technical Univ., Ankara (Turkey). Dept. of Chemical Engineering; Guenduez, Ufuk [Middle East Technical Univ., Ankara (Turkey). Dept. of Biology

    2010-07-01

    Photobiological hydrogen production from organic acids occurs in the presence of light and under anaerobic conditions. Stable and optimized operation of the photobioreactors is the most challenging task in the photofermentation process. The aim of this study was to achieve a stable and high hydrogen production on acetate, using the photosynthetic bacteria Rhodobacter capsulatus Hup{sup -} (uptake hydrogenase deleted strain) in continuous panel photobioreactors. An indoor experiment with continuous illumination (1500-2500 lux, corresponding to 101-169 W/m{sup 2}) and controlled temperature was carried out in a 8 L panel photobioreactor. A modified form of basal culture media containing 40 mM of acetate and 2 mM of glutamate with a feeding rate of 0.8 L/day was used. Stable hydrogen productivity of 0.7 mmol H{sub 2}/l{sub c}.h was obtained, however, biomass decreased during the continuous operation. Further indoor experiments with a biomass recycle and different feed compositions were carried out to optimise the feed composition for a stable biomass and hydrogen production. The highest hydrogen productivity of 0.8 mmol H{sub 2}/l{sub c}.h and yield of 88% was obtained in the 40 mM/ 4 mM acetate/glutamate continuously fed photobioreactor for a period of 21 days. (orig.)

  19. Purification and assays of Rhodobacter capsulatus RegB-RegA two-component signal transduction system.

    Science.gov (United States)

    Swem, Lee R; Swem, Danielle L; Wu, Jiang; Bauer, Carl E

    2007-01-01

    Two-component signal-transduction systems, composed of a histidine-sensor kinase and a DNA-binding response regulator, allow bacteria to detect environmental changes and adjust cellular physiology to live more efficiently in a broad distribution of niches. Although many two-component signal-transduction systems are known, a limited number of signals that stimulate these systems have been discovered. This chapter describes the purification and characterization of the predominant two-component signal-transduction system utilized by Rhodobacter capsulatus, a nonsulfur purple photosynthetic bacterium. Specifically, we explain the overexpression, detergent solubilization, and purification of the full-length membrane-spanning histidine-sensor kinase RegB. We also provide a method to measure autophosphorylation of RegB and discern the effect of its signal molecule, ubiquinone, on autophosphorylation levels. In addition we describe the overexpression and purification of the cognate response regulator RegA and a technique used to visualize the phosphotransfer reaction from RegB to RegA.

  20. Continuous Cultivation of Photosynthetic Bacteria for Fatty Acids Production

    DEFF Research Database (Denmark)

    Kim, Dong-Hoon; Lee, Ji-Hye; Hwang, Yuhoon

    2013-01-01

    In the present work, we introduced a novel approach for microbial fatty acids (FA) production. Photosynthetic bacteria, Rhodobacter sphaeroides KD131, were cultivated in a continuous-flow, stirred-tank reactor (CFSTR) at various substrate (lactate) concentrations.At hydraulic retention time (HRT) 4....... sphaeroides was around 35% of dry cell weight, mainly composed of vaccenic acid (C18:1, omega-7)....

  1. Rhodobacter capsulatus nifA1 Promoter: High-GC −10 Regions in High-GC Bacteria and the Basis for Their Transcription

    OpenAIRE

    Richard, Cynthia L.; Tandon, Animesh; Kranz, Robert G.

    2004-01-01

    It was previously shown that the Rhodobacter capsulatus NtrC enhancer-binding protein activates the R. capsulatus housekeeping RNA polymerase but not the Escherichia coli RNA polymerase at the nifA1 promoter. We have tested the hypothesis that this activity is due to the high G+C content of the −10 sequence. A comparative analysis of R. capsulatus and other α-proteobacterial promoters with known transcription start sites suggests that the G+C content of the −10 region is higher than that for ...

  2. Yeast Two-Hybrid Studies on Interaction of Proteins Involved in Regulation of Nitrogen Fixation in the Phototrophic Bacterium Rhodobacter capsulatus

    OpenAIRE

    Pawlowski, Alice; Riedel, Kai-Uwe; Klipp, Werner; Dreiskemper, Petra; Groß, Silke; Bierhoff, Holger; Drepper, Thomas; Masepohl, Bernd

    2003-01-01

    Rhodobacter capsulatus contains two PII-like proteins, GlnB and GlnK, which play central roles in controlling the synthesis and activity of nitrogenase in response to ammonium availability. Here we used the yeast two-hybrid system to probe interactions between these PII-like proteins and proteins known to be involved in regulating nitrogen fixation. Analysis of defined protein pairs demonstrated the following interactions: GlnB-NtrB, GlnB-NifA1, GlnB-NifA2, GlnB-DraT, GlnK-NifA1, GlnK-NifA2, ...

  3. Die Rolle der P II -Proteine GlnB und GlnK bei der Regulation des Stickstoff-Metabolismus in dem phototrophen Purpurbakterium Rhodobacter capsulatus

    OpenAIRE

    2002-01-01

    Das phototrophe Purpurbakterium Rhodobacter capsulatus ist in der Lage über eine Molybdän-Nitrogenase (nif-codiert) oder eine alternative Heterometall-freie Nitrogenase (anf-codiert) atmosphärischen Stickstoff zu fixieren. Die Expression und die Aktivität beider Nitrogenase-Systeme wird über die Stickstoffverfügbarkeit auf drei Ebenen reguliert. 1. die Regulation der Transkription der nif- und anf-spezifischen Transkriptionsaktivatoren NifA1, NifA2 und AnfA. 2. die Regulation i...

  4. Hydrogen gas production by fermentation from various organic wastewater using Clostridium butyricum NCIB 9576 and Rhodopseudomonas sphaeroides E15-1

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Young Sue; Kim, Hyun Kyung; Rye, Hye Yeon; Lee, In Gu; Kim, Mi Sun [Biomass Research Team, Korea Institute of Energy Research, Taejeon (Korea)

    2000-03-01

    Anaerobic fermentation using Clostidium butyricum NCIB 9576, and phto-fermentation using Rhodopseudomonas sphaeroides E15-1 were studied for the production of hydrogen from Makkoli, fruits (orange and apple, watermelon and melon) and Tofu wastewaters. From the Makkoli wastewater, which contained 0.94 g/liter sugars and 2.74 g/liter solubel starch, approximately 49 mM H{sub 2}/liter wastewater was produced during the initial 18h of the anaerobic fermentation with pH control between 6.5-7.0. Several organic acids such as butyric acid, acetic acid, propionic acid, lactic acid and ethanol were also produced. From watermelon and melon wastewater, which contained 43 g/liter sugars, generated about approximately 71 mM H{sub 2}/liter wastewater was produced during the initial 24h of the anaerobic fermentation. Tofu wastewater, pH 6.5, containing 12.6 g/liter soluble starch and 0.74 g/liter sugars, generated about 30mM H{sub 2}/liter wastewater, along with some organic acids, during the initial 24 h of anaerobic fermentation. Makkoli and Tofu wastewaters as substrates for the photo-fermentation by Rhodopseudomonas sphaeroides E15-1 produced approximately 37.9 and 22.2 {mu}M H{sub 2}/ml wastewaters, respectively for 9 days of incubation under the average of 9,000010,000 lux illumination at the surface of reactor using tungsten halogen lamps. Orange and apple wastewater, which contained 93.4 g/l produced approximately 13.1 {mu}M H{sub 2}/ml wastewater only for 2 days of photo-fermentation and the growth of Rhodopseudomonas spnaeroides E15-1 and hydrogen production were stopped. 22 refs, 4 figs., 2 tabs.

  5. The reductive half-reaction of xanthine dehydrogenase from Rhodobacter capsulatus: the role of Glu232 in catalysis.

    Science.gov (United States)

    Hall, James; Reschke, Stefan; Cao, Hongnan; Leimkühler, Silke; Hille, Russ

    2014-11-14

    The kinetic properties of an E232Q variant of the xanthine dehydrogenase from Rhodobacter capsulatus have been examined to ascertain whether Glu(232) in wild-type enzyme is protonated or unprotonated in the course of catalysis at neutral pH. We find that kred, the limiting rate constant for reduction at high [xanthine], is significantly compromised in the variant, a result that is inconsistent with Glu(232) being neutral in the active site of the wild-type enzyme. A comparison of the pH dependence of both kred and kred/Kd from reductive half-reaction experiments between wild-type and enzyme and the E232Q variant suggests that the ionized Glu(232) of wild-type enzyme plays an important role in catalysis by discriminating against the monoanionic form of substrate, effectively increasing the pKa of substrate by two pH units and ensuring that at physiological pH the neutral form of substrate predominates in the Michaelis complex. A kinetic isotope study of the wild-type R. capsulatus enzyme indicates that, as previously determined for the bovine and chicken enzymes, product release is principally rate-limiting in catalysis. The disparity in rate constants for the chemical step of the reaction and product release, however, is not as great in the bacterial enzyme as compared with the vertebrate forms. The results indicate that the bacterial and bovine enzymes catalyze the chemical step of the reaction to the same degree and that the faster turnover observed with the bacterial enzyme is due to a faster rate constant for product release than is seen with the vertebrate enzyme.

  6. The SOS Response Master Regulator LexA Regulates the Gene Transfer Agent of Rhodobacter capsulatus and Represses Transcription of the Signal Transduction Protein CckA

    Science.gov (United States)

    Kuchinski, Kevin S.; Brimacombe, Cedric A.; Westbye, Alexander B.; Ding, Hao

    2016-01-01

    ABSTRACT The gene transfer agent of Rhodobacter capsulatus (RcGTA) is a genetic exchange element that combines central aspects of bacteriophage-mediated transduction and natural transformation. RcGTA particles resemble a small double-stranded DNA bacteriophage, package random ∼4-kb fragments of the producing cell genome, and are released from a subpopulation (5-fold in the lexA mutant, and a lexA cckA double mutant was found to have the same phenotype as a ΔcckA single mutant in terms of RcGTA production. The data indicate that LexA is required for RcGTA production and maximal recipient capability and that the RcGTA-deficient phenotype of the lexA mutant is largely due to the overexpression of cckA. IMPORTANCE This work describes an unusual phenotype of a lexA mutant of the alphaproteobacterium Rhodobacter capsulatus in respect to the phage transduction-like genetic exchange carried out by the R. capsulatus gene transfer agent (RcGTA). Instead of the expected SOS response characteristic of prophage induction, this lexA mutation not only abolishes the production of RcGTA particles but also impairs the ability of cells to receive RcGTA-borne genes. The data show that, despite an apparent evolutionary relationship to lambdoid phages, the regulation of RcGTA gene expression differs radically. PMID:26833411

  7. Spectral Diffusion and Electron-Phonon Coupling of the B800 BChl a Molecules in LH2 Complexes from Three Different Species of Purple Bacteria

    Science.gov (United States)

    Baier, J.; Gabrielsen, M.; Oellerich, S.; Michel, H.; van Heel, M.; Cogdell, R.J.; Köhler, J.

    2009-01-01

    We have investigated the spectral diffusion and the electron-phonon coupling of B800 bacteriochlorophyll a molecules in the peripheral light-harvesting complex LH2 for three different species of purple bacteria, Rhodobacter sphaeroides, Rhodospirillum molischianum, and Rhodopseudomonas acidophila. We come to the conclusion that B800 binding pockets for Rhodobacter sphaeroides and Rhodopseudomonas acidophila are rather similar with respect to the polarity of the protein environment but that the packaging of the αβ-polypeptides seems to be less tight in Rb. sphaeroides with respect to the other two species. PMID:19883604

  8. 硫酸酯化修饰葛仙米多糖工艺研究%Sulfation Modification of Polysaccharide Extracted from Nostoc sphaeroides Ktzing

    Institute of Scientific and Technical Information of China (English)

    朱玉婷; 谭姚; 莫开菊

    2011-01-01

    The orthogonal array design method was used to optimize three reaction conditions,including esterification reagent,temperature and reaction time,for the sulfation of crude polysaccharides extracted from Nostoc sphaeroides Ku..tzing by water extraction and subsequent alcohol precipitation.Besides,FTIR spectroscopic analysis was carried out to identify the structural difference of Nostoc sphaeroides Ku..tzing polysaccharides as a result of the sulfation reaction,and a correlation analysis was done between FTIR A1261/A1418 and degree of substitution(DS) of sulfated polysaccharides,as determined by the barium chloride-gelation method.The optimal sulfation reaction conditions were found to be: 1:4 chlorosulfonic acid-pyridine as esterification reagent for 6 h reaction at 70 ℃.Under the optimal sulfation conditions,the DS of the final products was 1.042.Meanwhile,the sulfated polysaccharide obtained revealed typical sulfated functional groups.The correlation coefficient between FTIR A1261/A1418 and DS of sulfated Nostoc sphaeroides Ku..tzing polysaccharides was 0.974.Therefore,infrared spectroscopy can be used to characterize the structural difference of sulfated polysaccharides and quantify the DS of sulfate groups.%采用氯磺酸-吡啶法合成硫酸酯化葛仙米多糖,利用正交设计对酯化试剂比例、反应温度及反应时间进行优化。通过傅里叶红外光谱分析酯化前后的结构差异,氯化钡-明胶比浊法测定取代度,并分析红外光谱法与取代度之间的相关性。结果表明:葛仙米多糖硫酸酯化修饰的最佳条件为V(氯磺酸)与V(吡啶)比例1:4、反应温度70℃、反应时间6h,此条件下取代度达到1.042;红外光谱分析表明,硫酸酯化后的葛仙米多糖具有硫酸酯键的特征吸收峰,其吸光度比值A1261/A1418与化学方法所测得的硫酸酯化取代度的相关系数达到0.974。红外光谱不仅可以表征硫酸酯化多

  9. In vitro and in vivo safety assessment of edible blue-green algae, Nostoc commune var. sphaeroides Kützing and Spirulina plantensis

    Science.gov (United States)

    Yang, Yue; Park, Youngki; Cassada, David A.; Snow, Daniel D.; Rogers, Douglas G.; Lee, Jiyoung

    2011-01-01

    Blue-green algae (BGA) have been consumed as food and herbal medicine for centuries. However, safety for their consumption has not been well investigated. This study was undertaken to evaluate in vitro and in vivo toxicity of cultivated Nostoc commune var. sphaeroides Kützing (NO) and Spirulina platensis (SP). Neither NO nor SP contained detectable levels of microcystin (MC)-LA, MC-RR, MC-LW and MC-LR by LC/MS/MS. Cell viability remained ~70-80% when HepG2 cells were incubated with 0-500 μg/ml of hexane, chloroform, methanol and water-extractable fractions of NO and SP. Four-week-old male and female C57BL/6J mice were fed an AIN-93G/M diet supplemented with 0, 2.5% or 5% of NO and SP (wt/wt) for 6 months. For both genders, BGA-rich diets did not induce noticeable abnormality in weight gain and plasma alanine aminotransferase (ALT) and aspartate aminotransferase concentrations except a significant increase in plasma ALT levels by 2.5% NO supplementation in male mice at 6 month. Histopathological analysis of livers, however, indicated that BGA did not cause significant liver damage compared with controls. In conclusion, our results suggest that NO and SP are free of MC and the long-term dietary supplementation of up to 5% of the BGA may be consumed without evident toxic side-effects. PMID:21473896

  10. Lipid extract of Nostoc commune var. sphaeroides Kutzing, a blue-green alga, inhibits the activation of sterol regulatory element binding proteins in HepG2 cells.

    Science.gov (United States)

    Rasmussen, Heather E; Blobaum, Kara R; Park, Young-Ki; Ehlers, Sarah J; Lu, Fan; Lee, Ji-Young

    2008-03-01

    Nostoc commune var. sphaeroides Kützing (N. commune), a blue-green alga, has been used as both a food ingredient and in medicine for centuries. To determine the effect of N. commune on cholesterol metabolism, N. commune lipid extract was incubated at increasing concentrations (25-100 mg/L) with HepG2 cells, a human hepatoma cell line. The addition of N. commune lipid extract markedly reduced mRNA abundance of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) and LDL receptor (LDLR) (P commune lipid extract confirmed the inhibitory role of N. commune in cholesterol synthesis (P commune lipid extract, expression of sterol regulatory element binding protein 2 (SREBP-2) was assessed. Whereas mRNA for SREBP-2 remained unchanged, SREBP-2 mature protein was reduced by N. commune (P commune lipid extract also decreased SREBP-1 mature protein by approximately 30% (P commune lipid extract inhibits the maturation process of both SREBP-1 and -2, resulting in a decrease in expression of genes involved in cholesterol and fatty acid metabolism.

  11. Hydrogen production by hup(-) mutant and wild-type strains of Rhodobacter capsulatus from dark fermentation effluent of sugar beet thick juice in batch and continuous photobioreactors.

    Science.gov (United States)

    Uyar, Basar; Gürgan, Muazzez; Özgür, Ebru; Gündüz, Ufuk; Yücel, Meral; Eroglu, Inci

    2015-10-01

    Photofermentative production of hydrogen is a promising and sustainable process; however, it should be coupled to dark fermentation to become cost effective. In order to integrate dark fermentation and photofermentation, the suitability of dark fermenter effluents for the photofermentative hydrogen production must be demonstrated. In this study, thermophilic dark fermenter effluent (DFE) of sugar beet thick juice was used as a substrate in photofermentation process to compare wild-type and uptake hydrogenase-deficient (hup (-)) mutant strains of Rhodobacter capsulatus by means of hydrogen production and biomass growth. The tests were conducted in small-scale (50 mL) batch and large-scale (4 L) continuous photobioreactors in indoor conditions under continuous illumination. In small scale batch conditions, maximum cell concentrations were 0.92 gdcw/L c and 1.50 gdcw/L c, hydrogen yields were 34 % and 31 %, hydrogen productivities were 0.49 mmol/(L c·h) and 0.26 mmol/(Lc·h), for hup (-) and wild-type cells, respectively. In large-scale continuous conditions, maximum cell concentrations were 1.44 gdcw/L c and 1.87 gdcw/L c, hydrogen yields were 48 and 46 %, and hydrogen productivities were 1.01 mmol/(L c·h) and 1.05 mmol/(L c·h), for hup (-) and wild-type cells, respectively. Our results showed that Rhodobacter capsulatus hup (-) cells reached to a lower maximum cell concentration but their hydrogen yield and productivity were in the same range or superior compared to the wild-type cells in both batch and continuous operating modes. The maximum biomass concentration, yield and productivity of hydrogen were higher in continuous mode compared to the batch mode with both bacterial strains.

  12. Synergistic dark and photo-fermentation continuous system for hydrogen production from molasses by Clostridium acetobutylicum ATCC 824 and Rhodobacter capsulatus DSM 1710.

    Science.gov (United States)

    Morsy, Fatthy Mohamed

    2017-04-01

    This study investigated synergistic dark and photo-fermentation using continuous fermentation system (CFS). The system relies on connecting several fermenters from bottom of one to top culture level of the next in a manner that allows for delaying movement of the substrate and thus for its full consumption. While H2 was collected, CFS allowed for moving liquid byproducts toward the outlet and hence continuous productivity. CFS could be efficiently used for: (1) Continuous dark and photo-fermentation H2 production by Clostridium acetobutylicum and Rhodobacter capsulatus producing 5.65moleH2mole(-1) hexose; (2) Continuous dark-fermentation synergistic H2, acetone, butanol and ethanol (ABE) production by C. acetobutylicum which produced per mole hexose, 2.43mol H2 along with 73.08g ABE (3) Continuous H2 and methane production by C. acetobutylicum and bacterial sludge producing, per mole hexose, 1.64mol pure H2 and 2.56mol CH4 mixed with 0.37mol H2·The hydraulic retention time (HRT) for whole system was short where organic acids produced in dark-fermentation in first fermenter were synergistically utilized for H2 production by R. capsulatus in subsequent fermenters. CFS is suitable for fast-digestible sugars but not lignocelluloses or other hard-digestible organics, requiring prolonged HRT, unless such polymeric organics were hydrolyzed prior to fermentation. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Removal of the effect of ammonium on the regulation of nitrogenase enzyme in Rhodobacter capsulatus DSM1710 for improved hydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Pekgoez, Guelsah; Guenduez, Ufuk [Middle East Technical Univ. (Turkey). Dept. of Biology; Eroglu, Inci [Middle East Technical Univ. (Turkey). Dept. of Chemical Engineering; Rakhely, Gabor [Szeged Univ. (Hungary). Dept. of Biotechnology

    2010-07-01

    Photofermentative biohydrogen production by purple non-sulfur (PNS) bacteria is a renewable and clean way of producing hydrogen. Hydrogen production by PNS bacteria, Rhodobacter capsulatus, is mediated mainly by nitrogenases, which primarily fix molecular nitrogen to ammonium and produce hydrogen as byproduct. The reaction catalyzed by nitrogenases requires a lot of energy. Hence, there is a complex regulation on nitrogenase enzyme complex, consequently, on hydrogen production. Whenever ammonium, which is the end product of nitrogen fixation reaction, is found in the environment, hydrogen production stops. GlnB and GlnK proteins are the critical regulatory proteins in ammonium dependent regulation of the nitrogenase gene expression. In this study, the aim is to release the ammonium regulation on nitrogenase enzyme by inactivating glnB and glnK genes. For this purpose, relevant recombinant vectors were constructed; R.capsulatus glnB- strain was obtained. The double R.capsulatus glnB{sup -}glnK{sup -} strain, able to produce hydrogen independent of ammonium concentration of the environment is to be obtained. (orig.)

  14. Dietary Karaya Saponin and Rhodobacter capsulatus Exert Hypocholesterolemic Effects by Suppression of Hepatic Cholesterol Synthesis and Promotion of Bile Acid Synthesis in Laying Hens

    Directory of Open Access Journals (Sweden)

    Sadia Afrose

    2010-01-01

    Full Text Available This study was conducted to elucidate the mechanism underlying the hypolipidemic action of karaya saponin or Rhodobacter (R. capsulatus. A total of 40 laying hens (20-week-old were assigned into four dietary treatment groups and fed a basal diet (as a control or basal diets supplemented with either karaya saponin, R. capsulatus, or both for 60 days. The level of serum low-density-lipoprotein cholesterol and the levels of cholesterol and triglycerides in the serum, liver, and egg yolk were reduced by all the supplementations (<.05. Liver bile acid concentration and fecal concentrations of cholesterol, triacylglycerol, and bile acid were simultaneously increased by the supplementation of karaya saponin, R. capsulatus, and the combination of karaya saponin and R. capsulatus (<.05. The supplementation of karaya saponin, R. capsulatus, and the combination of karaya saponin and R. capsulatus suppressed the incorporation of 14C from 1-14C-palmitic acid into the fractions of total lipids, phospholipids, triacylglycerol, and cholesterol in the liver in vitro (<.05. These findings suggest that the hypocholesterolemic effects of karaya saponin and R. capsulatus are caused by the suppression of the cholesterol synthesis and the promotion of cholesterol catabolism in the liver.

  15. The ccoNOQP gene cluster codes for a cb-type cytochrome oxidase that functions in aerobic respiration of Rhodobacter capsulatus.

    Science.gov (United States)

    Thöny-Meyer, L; Beck, C; Preisig, O; Hennecke, H

    1994-11-01

    The genes for a new type of a haem-copper cytochrome oxidase were cloned from Rhodobacter capsulatus strain 37b4, using the Bradyrhizobium japonicum fixNOQP gene region as a hybridizing probe. Four genes, probably organized in an operon (ccoNOQP), were identified; their products share extensive amino acid sequence similarity with the FixN, O, Q and P proteins that have recently been shown to be the subunits of a cb-type oxidase. CcoN is a b-type cytochrome, CcoO and CcoP are membrane-bound mono- and dihaem c-type cytochromes and CcoQ is a small membrane protein of unknown function. Genes for a similar oxidase are also present in other non-rhizobial bacterial species such as Azotobacter vinelandii, Agrobacterium tumefaciens and Pseudomonas aeruginosa, as revealed by polymerase chain reaction analysis. A ccoN mutant was constructed whose phenotype, in combination with the structural information on the gene products, provides evidence that the CcoNOQP oxidase is a cytochrome c oxidase of the cb type, which supports aerobic respiration in R. capsulatus and which is probably identical to the cbb3-type oxidase that was recently purified from a different strain of the same species. Mutant analysis also showed that this oxidase has no influence on photosynthetic growth and nitrogen-fixation activity.

  16. Effect of light-dark cycles on hydrogen and poly-β-hydroxybutyrate production by a photoheterotrophic culture and Rhodobacter capsulatus using a dark fermentation effluent as substrate.

    Science.gov (United States)

    Montiel Corona, Virginia; Le Borgne, Sylvie; Revah, Sergio; Morales, Marcia

    2017-02-01

    A Rhodobacter capsulatus strain and a photoheterotrophic culture (IZT) were cultivated to produce hydrogen under different light-dark cycles. A dark fermentation effluent (DFE) was used as substrate. It was found that IZT culture had an average cumulative hydrogen production (Paccum H2) of 1300±43mLH2L(-1) under continuous illumination and light-dark cycles of 30 or 60min. In contrast, R. capsulatus reduced its Paccum H2 by 20% under 30:30min light-dark cycles, but tripled its poly-β-hydroxybutyrate (PHB) content (308±2mgPHB gdw(-1)) compared to continuous illumination. The highest PHB content by IZT culture was 178±10mgPHB gdw(-1) under 15:15min light-dark cycles. PCR-DGGE analysis revealed that the IZT culture was mainly composed of Rhodopseudomonas palustris identified with high nucleotide similarity (99%). The evaluated cultures might be used for hydrogen and PHB production. They might provide energy savings by using light-dark cycles and DFE valorization.

  17. Potential of Rhodobacter capsulatus Grown in Anaerobic-Light or Aerobic-Dark Conditions as Bioremediation Agent for Biological Wastewater Treatments

    Directory of Open Access Journals (Sweden)

    Stefania Costa

    2017-02-01

    Full Text Available The use of microorganisms to clean up wastewater provides a cheaper alternative to the conventional treatment plant. The efficiency of this method can be improved by the choice of microorganism with the potential of removing contaminants. One such group is photosynthetic bacteria. Rhodobacter capsulatus is a purple non-sulfur bacterium (PNSB found to be capable of different metabolic activities depending on the environmental conditions. Cell growth in different media and conditions was tested, obtaining a concentration of about 108 CFU/mL under aerobic-dark and 109 CFU/mL under anaerobic-light conditions. The biomass was then used as a bioremediation agent for denitrification and nitrification of municipal wastewater to evaluate the potential to be employed as an additive in biological wastewater treatment. Inoculating a sample of mixed liquor withdrawn from the municipal wastewater treatment plant with R. capsulatus grown in aerobic-dark and anaerobic-light conditions caused a significant decrease of N-NO3 (>95%, N-NH3 (70% and SCOD (soluble chemical oxygen demand (>69%, independent of the growth conditions. A preliminary evaluation of costs indicated that R. capsulatus grown in aerobic-dark conditions could be more convenient for industrial application.

  18. Heterologous production of two unusual acyclic carotenoids, 1,1'-dihydroxy-3,4-didehydrolycopene and 1-hydroxy-3,4,3',4'-tetradehydrolycopene by combination of the crtC and crtD genes from Rhodobacter and Rubrivivax.

    Science.gov (United States)

    Steiger, Sabine; Takaichi, Shinichi; Sandmann, Gerhard

    2002-07-17

    Acyclic hydroxy carotenoids were produced from lycopene and 3,4-didehydrolycopene in Escherichia coli by combining different carotenogenic genes including the carotene hydratase gene crtC and the carotene 3,4-desaturase gene crtD. The genes originated either from Rhodobacter species or Rubrivivax gelatinosus. It was shown that the product of crtD from Rubrivivax unlike the one from Rhodobacter is able to convert 1-HO-3,4-didehydrolycopene to 1-HO-3,4,3',4'-tetradehydrolycopene (=3,4,3',4'-tetradehydro-1,2-dihydro-psi,psi-caroten-1-ol). Thus, only when the desaturase from Rubrivivax is expressed can this novel carotenoid be obtained. In the presence of crtC from Rubrivivax, another carotenoid 1,1'-(HO)(2)-3,4-didehydrolycopene (=3,4-didehydrolycopene-1,2,1',2'-tetrahydro-psi,psi-caroten-1,1'-diol) not found in a non-transgenic organism before is formed in E. coli. Its accumulation under these conditions and its absence when crtC from Rubrivivax is replaced by the corresponding gene from Rhodobacter is discussed. The function of the different crtC and crtD genes in the pathway leading to the individual carotenoids is outlined. Since 1,1'-(HO)(2)-3,4-didehydrolycopene could not be produced in substantial amounts and 1-HO-3,4,3',4'-tetradehydrolycopene has not been described before, their structural characteristics were determined for the definite assignment of their identity. This included spectral properties, determination of relative molecular mass as well as the number of hydroxy groups by mass spectroscopy and NMR spectroscopy for 1,1'-(HO)(2)-3,4-didehydrolycopene.

  19. Open reading frame 5 (ORF5), encoding a ferredoxinlike protein, and nifQ are cotranscribed with nifE, nifN, nifX, and ORF4 in Rhodobacter capsulatus.

    OpenAIRE

    Moreno-Vivian, C; Hennecke, S; Pühler, A.; Klipp, W

    1989-01-01

    DNA sequence analysis of a 1,600-base-pair fragment located downstream of nifENX in nif region A of Rhodobacter capsulatus revealed two additional open reading frames (ORFs): ORF5, encoding a ferredoxinlike protein, and nifQ. The ferredoxinlike gene product contained two cysteine motifs, typical of ferredoxins coordinating two 4Fe-4S clusters, but the distance between these two motifs was unusual for low-molecular-weight ferredoxins. The R. capsulatus nifQ gene product shared a high degree of...

  20. The Effects of Rhodobacter capsulatus KCTC-2583 on Cholesterol Metabolism, Egg Production and Quality Parameters during the Late Laying Periods in Hens.

    Science.gov (United States)

    Lokhande, Anushka; Ingale, S L; Lee, S H; Kim, J S; Lohakare, J D; Chae, B J; Kwon, I K

    2013-06-01

    An experiment was conducted to investigate the effects of dietary supplementation of Rhodobacter capsulatus KCTC-2583 on egg-yolk and serum cholesterol, egg production and quality parameters during the late laying periods in hens. A total of 160 Hy-Line Brown layers (54 wk-old) were randomly allotted to 4 treatment groups on the basis of laying performance. Each treatment had 4 replicates with 10 birds each (40 birds per treatment). Two hens were confined individually with cage size 35×35×40 cm and each 10 birds (5 cages) shared a common feed trough between them forming one experimental unit. Dietary treatments were; basal diet supplemented with 0 (control), 0.05, 0.10 and 0.15% R. capsulatus KCTC-2583. Experimental diets were fed in meal form for 56 d. Dietary supplementation of increasing levels of R. capsulatus KCTC-2583 reduced (linear, phens fed a diet supplemented with increasing levels of R. capsulatus KCTC-2583 had increased (linear; p0.05) on feed intake of laying hens. At d 28 and 56, breaking strength and yolk colour of eggs were linearly improved (phens fed dietary increasing levels of R. capsulatus KCTC-2583. Dietary treatment had no effects (linear or quadratic; p>0.05) on albumin height, shell thickness and shell weight at any period of experiment. These results indicate that dietary supplementation of R. capsulatus KCTC-2583 has the potential to improve the laying hen performance and lead to the development of low cholesterol eggs during late laying period in Hy-Line Brown hens.

  1. Functional assignment of gene AAC16202.1 from Rhodobacter capsulatus SB1003: new insights into the bacterial SDR sorbitol dehydrogenases family.

    Science.gov (United States)

    Sola-Carvajal, Agustín; García-García, María Inmaculada; Sánchez-Carrón, Guiomar; García-Carmona, Francisco; Sánchez-Ferrer, Alvaro

    2012-11-01

    Short-chain dehydrogenases/reductases (SDR) constitute one of the largest enzyme superfamilies with over 60,000 non-redundant sequences in the database, many of which need a correct functional assignment. Among them, the gene AAC16202.1 (NCBI) from Rhodobacter capsulatus SB1003 has been assigned in Uniprot both as a sorbitol dehydrogenase (#D5AUY1) and, as an N-acetyl-d-mannosamine dehydrogenase (#O66112), both enzymes being of biotechnological interest. When the gene was overexpressed in Escherichia coli Rosetta (DE3)pLys, the purified enzyme was not active toward N-acetyl-d-mannosamine, whereas it was active toward d-sorbitol and d-fructose. However, the relative activities toward xylitol and l-iditol (0.45 and 6.9%, respectively) were low compared with that toward d-sorbitol. Thus, the enzyme could be considered sorbitol dehydrogenase (SDH) with very low activity toward xylitol, which could increase its biotechnological interest for determining sorbitol without the unspecific cross-determination of added xylitol in food and pharma compositions. The tetrameric enzyme (120 kDa) showed similar catalytic efficiency (2.2 × 10(3) M(-1) s(-1)) to other sorbitol dehydrogenases for d-sorbitol, with an optimum pH of 9.0 and an optimum temperature of 37 °C. The enzyme was also more thermostable than other reported SDH, ammonium sulfate being the best stabilizer in this respect, increasing the melting temperature (T(m)) up to 52.9 °C. The enzyme can also be considered as a new member of the Zn(2+) independent SDH family since no effect on activity was detected in the presence of divalent cations or chelating agents. Finally, its in silico analysis enabled the specific conserved sequence blocks that are the fingerprints of bacterial sorbitol dehydrogenases and mainly located at C-terminal of the protein, to be determined for the first time. This knowledge will facilitate future data curation of present databases and a better functional assignment of newly described

  2. Dynamics of Rhodobacter capsulatus [2Fe-2S] Ferredoxin VI and Aquifex aeolicus Ferredoxin 5 Via Nuclear Resonance Vibrational Spectroscopy (NRVS) and Resonance Raman Spectroscopy.

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Yuming; Tan, Ming-Liang; Ichiye, Toshiko; Wang, Hongxin; Guo, Yisong; Smith, Matt C.; Meyer, Jacques; Sturhahn, Wolfgang; Alp, E. E.; Zhao, Jiyong; Yoda, Yoshitaka; Cramer, Stephen P.

    2008-06-24

    We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe(2)S(2)(Cys)(4) sites in oxidized and reduced [2Fe-2S] ferredoxins from Rhodobacter capsulatus (Rc FdVI) and Aquifex aeolicus (Aa Fd5). In the oxidized forms, nearly identical NRVS patterns are observed, with strong bands from Fe-S stretching modes peaking around 335 cm(-1), and additional features observed as high as the B(2u) mode at approximately 421 cm(-1). Both forms of Rc FdVI have also been investigated by resonance Raman (RR) spectroscopy. There is good correspondence between NRVS and Raman frequencies, but because of different selection rules, intensities vary dramatically between the two kinds of spectra. For example, the B(3u) mode at approximately 288 cm(-1), attributed to an asymmetric combination of the two FeS(4) breathing modes, is often the strongest resonance Raman feature. In contrast, it is nearly invisible in the NRVS, as there is almost no Fe motion in such FeS(4) breathing. NRVS and RR analysis of isotope shifts with (36)S-substituted into bridging S(2-) ions in Rc FdVI allowed quantitation of S(2-) motion in different normal modes. We observed the symmetric Fe-Fe stretching mode at approximately 190 cm(-1) in both NRVS and RR spectra. At still lower energies, the NRVS presents a complex envelope of bending, torsion, and protein modes, with a maximum at 78 cm(-1). The (57)Fe partial vibrational densities of states (PVDOS) were interpreted by normal-mode analysis with optimization of Urey-Bradley force fields. Progressively more complex D(2h) Fe(2)S(2)S'(4), C(2h) Fe(2)S(2)(SCC)(4), and C(1) Fe(2)S(2)(Cys)(4) models were optimized by comparison with the experimental spectra. After modification of the CHARMM22 all-atom force field by the addition of refined Fe-S force constants, a simulation employing the complete protein structure was used to reproduce the PVDOS, with better results in the low frequency protein mode region. This process was then repeated

  3. Characterization of a nif-regulated flavoprotein (FprA) from Rhodobacter capsulatus. Redox properties and molecular interaction with a [2Fe-2S] ferredoxin.

    Science.gov (United States)

    Jouanneau, Y; Meyer, C; Asso, M; Guigliarelli, B; Willison, J C

    2000-02-01

    A flavoprotein from Rhodobacter capsulatus was purified as a recombinant (His)6-tag fusion from an Escherichia coli clone over-expressing the fprA structural gene. The FprA protein is a homodimer containing one molecule of FMN per 48-kDa monomer. Reduction of the flavoprotein by dithionite showed biphasic kinetics, starting with a fast step of semiquinone (SQ) formation, and followed by a slow reduction of the SQ. This SQ was in the anionic form as shown by EPR and optical spectroscopies. Spectrophotometric titration gave a midpoint redox potential for the oxidized/SQ couple of Em1 = +20 mV (pH 8.0), whereas the SQ/hydroquinone couple could not be titrated due to the thermodynamic instability of SQ associated with its slow reduction process. The inability to detect the intermediate form, SQ, upon oxidative titration confirmed this instability and led to an estimate of Em2 - Em1 of > 80 mV. The reduction of SQ by dithionite was significantly accelerated when the [2Fe-2S] ferredoxin FdIV was used as redox mediator. The midpoint redox potential of this ferredoxin was determined to be -275 +/- 2 mV at pH 7.5, consistent with FdIV serving as electron donor to FprA in vivo. FdIV and FprA were found to cross-react when incubated together with the 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide, giving a covalent complex with an Mr of approximately 60 000. Formation of this complex was unaffected by the redox states of the two proteins. Other [2Fe-2S] ferredoxins, including FdV and FdVI from R. capsulatus, were ineffective as electron carriers to FprA, and cross-reacted poorly with the flavoprotein. The possible function of FprA with regard to nitrogen fixation was investigated using an fprA-deleted mutant. Although nitrogenase activity was significantly reduced in the mutant compared with the wild-type strain, nitrogen fixation was apparently unaffected by the fprA deletion even under iron limitation or microaerobic conditions.

  4. Effect of Spray Freeze Drying on Antioxidant Activity of Phycocyprotein from Nostoc sphaeroides KUting%喷雾冷冻干燥对葛仙米藻胆蛋白抗氧化特性的影响

    Institute of Scientific and Technical Information of China (English)

    程超; 朱玉婷; 田瑞; 汪兴平; 潘思轶

    2012-01-01

    研究喷雾冷冻干燥对葛仙米藻胆蛋白抗氧化特性的影响,并与冷冻干燥技术进行比较。主要测定ABTS+·、铁还原抗氧化能力(FRAP)、对羟自由基(·OH)清除作用和H2O2诱导的脂质过氧化的抑制作用,结果发现,喷雾冷冻干燥(SFD)对葛仙米藻胆蛋白的抗氧化特性有一定的影响,在基于电子转移和氢原子转移的抗氧化测定方法中,SFD与冷冻干燥(FD)制备的样品差异不明显,但在基于活性氧自由基清除的测定方法中,SFD显著优于FD。表明SFD非常适合于高活性成分的干燥。%In this study, the effect of spray freeze drying on the antioxidant activity of phycobiliprotein fromNostoc sphaeroides KUting was studied and compared with that of common freeze drying. The scavenging effect of phycobiliprotein on ABTS+· and hydroxyl radicals (·OH), H2O2-induced lipid peroxidation and ferric-ion reducing power (FRAP) were evaluated. The results indicated that spray freeze drying method had obvious effect on antioxidant activity of phycobiliprotein from Nostoc sphaeroides Kuting. The samples dried by two different methods showed no significant difference in the antioxidant activity determined based on electron transfer and hydrogen atom transfer. The free radical scavenging activity of the sample dried by spray freeze drying method was markedly higher than that of the sample dried by common freeze drying method. These data suggest that spray freeze drying is more suitable for drying active substances.

  5. Development of a Rhodobacter capsulatus self-reporting model system for optimizing light-dependent, [FeFe]-hydrogenase-driven H 2 production: A Model System for Optimizing H 2 Production

    Energy Technology Data Exchange (ETDEWEB)

    Wecker, Matt S. A. [GeneBiologics, LLC, Boulder Colorado; Beaton, Stephen E. [United States Air Force Academy, Department of Chemistry, Colorado Springs Colorado; Chado, Robert A. [United States Air Force Academy, Department of Chemistry, Colorado Springs Colorado; Ghirardi, Maria L. [National Renewable Energy Laboratory, MS 3313, 15013 Denver West Parkway Golden Colorado 80401

    2016-08-23

    The photosynthetic bacterium Rhodobacter capsulatus normally photoproduces H2 as a by-product of its nitrogenase-catalyzed nitrogen-fixing activity. Such H2 production, however, is expensive from a metabolic perspective, requiring nearly four times as many photons as the equivalent algal hydrogenase-based system (Ghirardi et al. 2009). Here we report the insertion of a Clostridium acetobutylicum [FeFe]-hydrogenase and its three attendant hydrogenase assembly proteins into an R. capsulatus strain lacking its native uptake hydrogenase. Further, this strain is modified to fluoresce upon sensing H2. The resulting strain photoproduces H2 and self-reports its own H2 production through fluorescence. This model system represents a unique method of developing hydrogenase-based H2 production in R. capsulatus, may serve as a powerful system for in vivo directed evolution of hydrogenases and hydrogenase-associated genes, and provides a means of screening for increased metabolic production of H2.

  6. GenBank blastx search result: AK061856 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK061856 001-040-G03 AF018073.1 Rhodobacter sphaeroides operon regulator (smoC), periplasmic sorbitol...-binding protein (smoE), sorbitol/mannitol transport inner membrane protein (smoF), sorbitol.../mannitol transport inner membrane protein (smoG), sorbitol/mannitol transport ATP-binding transport protein (smoK), sorbitol

  7. GenBank blastx search result: AK243491 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK243491 J100073O14 M86823.1 RCANIFA Rhodobacter sphaeroides ORF1, complete cds; nif...U gene, complete cds; nifS gene, complete cds; nifV gene, complete cds; nifW gene, complete cds; rponN gene, partial cds. BCT 2e-36 1 ...

  8. GenBank blastx search result: AK287500 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287500 J043034C21 M86823.1 RCANIFA Rhodobacter sphaeroides ORF1, complete cds; nif...U gene, complete cds; nifS gene, complete cds; nifV gene, complete cds; nifW gene, complete cds; rponN gene, partial cds. BCT 7e-11 0 ...

  9. Atomic force microscopy of bacterial photosynthetic systems: a new model for native membrane organization

    NARCIS (Netherlands)

    Bahatyrova, Svetlana

    2005-01-01

    The main goal of this thesis was to investigate the supramolecular architecture of a photosynthetic membrane from Rhodobacter sphaeroides purple bacteria cells. This is extremely timely, since we now know all of the structures of photosynthetic pigment-protein LH and RC complexes, ATP-synthase and b

  10. Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA

    NARCIS (Netherlands)

    Swarts, D.C.; Hegge, J.W.; Hinojo, Ismael; Shiimori, Masami; Ellis, Michael A.; Dumrongkulraksa, Justin; Terns, Rebecca M.; Terns, Michael P.; Oost, Van Der John

    2015-01-01

    Functions of prokaryotic Argonautes (pAgo) have long remained elusive. Recently, Argonautes of the bacteria Rhodobacter sphaeroides and Thermus thermophilus were demonstrated to be involved in host defense. The Argonaute of the archaeon Pyrococcus furiosus (PfAgo) belongs to a different branch in

  11. On the signaling mechanism and the absence of photoreversibility in the AppA BLUF domain

    NARCIS (Netherlands)

    Toh, K.C.; van Stokkum, I.H.M.; Hendriks, J.; Alexandre, M.T.A.; Arents, J.C.; Avila Perez, M.; van Grondelle, R.; Hellingwerf, K.J.; Kennis, J.T.M.

    2008-01-01

    The flavoprotein AppA from Rhodobacter sphaeroides contains an N-terminal, FAD-binding BLUF photoreceptor domain. Upon illumination, the AppA BLUF domain forms a signaling state that is characterized by red-shifted absorbance by 10 nm, a state known as AppA(RED). We have applied ultrafast spectrosco

  12. Conformational regulation of charge recombination reactions in a photosynthetic bacterial reaction center

    DEFF Research Database (Denmark)

    Katona, Gergely; Snijder, Arjan; Gourdon, Pontus Emanuel;

    2005-01-01

    In bright light the photosynthetic reaction center (RC) of Rhodobacter sphaeroides stabilizes the P(+)(870).Q(-)(A) charge-separated state and thereby minimizes the potentially harmful effects of light saturation. Using X-ray diffraction we report a conformational change that occurs within the cy...

  13. GenBank blastx search result: AK111944 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK111944 001-022-C09 AF016236.1 Rhodobacter sphaeroides DMSO/TMAO-sensor kinase (dorS), DMSO.../TMAO-response regulator (dorR), DMSO/TMAO-cytochrome c-containing subunit (dorC), DMSO-membrane protein (dorB), and DMSO

  14. GenBank blastx search result: AK058791 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK058791 001-002-F06 M86823.1 Rhodobacter sphaeroides ORF1, complete cds; nifU gene, complete... cds; nifS gene, complete cds; nifV gene, complete cds; nifW gene, complete cds; rponN gene, partial cds.|BCT BCT 3e-13 +3 ...

  15. GenBank blastx search result: AK059171 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK059171 001-023-F01 M86823.1 Rhodobacter sphaeroides ORF1, complete cds; nifU gene, complete... cds; nifS gene, complete cds; nifV gene, complete cds; nifW gene, complete cds; rponN gene, partial cds.|BCT BCT 2e-66 +3 ...

  16. On the Role of Aromatic Side Chains in the Photoactivation of BLUF Domains

    NARCIS (Netherlands)

    Gauden, M.; Grinstead, J.S.; Laan, W.; Stokkum, I.H.M.; Avila-Perez, M.; Toh, K.C.; Boelens, R.; Kaptein, R.; van Grondelle, R.; Hellingwerf, K.J.; Kennis, J.T.M.

    2007-01-01

    BLUF (blue-light sensing using FAD) domain proteins are a novel group of blue-light sensing receptors found in many microorganisms. The role of the aromatic side chains Y21 and W104, which are in close vicinity to the FAD cofactor in the AppA BLUF domain from Rhodobacter sphaeroides, is investigated

  17. 草甘膦对可食用蓝藻葛仙米生长和生理的影响%EFFECTS OF ACUTE GLYPHOSATE EXPOSURE ON THE GROWTH AND PHYSIOLOGY OF NOSTOC SPHAEROIDES, AN EDIBLE CYANOBACTERIUM OF PADDY RICE FIELDS

    Institute of Scientific and Technical Information of China (English)

    阮祚禧; Murray T.Brown

    2008-01-01

    The productivity of Nostoc sphaeroides,an edible cyanobacterium found in paddy rice fields has declined in recent years. It may relate to the increased application of agricultural herbicides. To assess the impact of glyphosate exposure(0.15,0.30,0.45 and 0.6 mmol/L Gly acid) ,the effects on colony size,dry biomass accumulation,chlorophyll a fluorescence (Fv/Fm) and chlorophyll a biosynthesis were investigated over an 8d period. All parameters were significantly inhibited in a concentration used and time dependent way. After 2d exposure to 0. 15 mmol/L Gly colonies were approximately 15% smaller than the controls. After 4d exposure,chlorophyll a content and Fv/Fm were affected by the highest concentration used(0.6 mmol/L Gly). By the 8d, chlorophyll biosynthesis and Fv/Fm were significantly inhibited by concentrations greater than 0.15 and 0.3 mmol/L Gly, respectively. The 8d relative growth rates ( RGRs), calculated for dry biomass, were significantly affected by all glyphosate treatments,there was a 60% reduction at 0.15 mmol/L Gly and negative RGRs at higher concentrations indicate a loss of biomass. Exposure to 0. 6 mmol/L Gly was lethal with loss of colony integrity,bleaching of pigments and no photosynthetic activity by 8d. These results are discussed in terms of the mechanisms of toxicity and the potential implications for the long term sustainability of the N. sphaeroides resource.%葛仙米(N.sphaeroides)的产量和产地面积逐年减少,这可能与当地广泛使用除草剂草甘膦有关.为此,本文测定了不同浓度(0.15、0.30、0.45、0.6mmol/L)的草甘膦处理的葛仙米的颗粒大小、干重、叶绿素荧光、叶绿素浓度.所有测量参数与浓度和时间显著相关:0.15mmol/L处理组的颗粒直径较对照组小15%(2d后);叶绿素a浓度和最大量子产率(Fv/Fm)在最高浓度组(0.6mmol/L)4d后开始受到影响;第8天,相对生长速率(以干重计算,大于0.15mmol/L)、光合作用活性(大于0.3mmol

  18. Molecular Regulation of Photosynthetic Carbon Dioxide Fixation in Nonsulfur Purple Bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Tabita, Fred Robert [The Ohio State Univ., Columbus, OH (United States)

    2015-12-01

    The overall objective of this project is to determine the mechanism by which a transcriptional activator protein affects CO2 fixation (cbb) gene expression in nonsulfur purple photosynthetic bacteria, with special emphasis to Rhodobacter sphaeroides and with comparison to Rhodopseudomonas palustris. These studies culminated in several publications which indicated that additional regulators interact with the master regulator CbbR in both R. sphaeroides and R. palustris. In addition, the interactive control of the carbon and nitrogen assimilatory pathways was studied and unique regulatory signals were discovered.

  19. GenBank blastx search result: AK243680 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK243680 J100090I20 AF018073.1 AF018073 Rhodobacter sphaeroides operon regulator (smoC), periplasmic sorbito...l-binding protein (smoE), sorbitol/mannitol transport inner membrane protein (smoF), sorbitol.../mannitol transport inner membrane protein (smoG), sorbitol/mannitol transport ATP-binding transport protein (smoK), sorbit...ol dehydrogenase (smoS), mannitol dehydrogenase (mtlK),

  20. GenBank blastx search result: AK240874 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK240874 J065025K09 AF018073.1 AF018073 Rhodobacter sphaeroides operon regulator (smoC), periplasmic sorbito...l-binding protein (smoE), sorbitol/mannitol transport inner membrane protein (smoF), sorbitol.../mannitol transport inner membrane protein (smoG), sorbitol/mannitol transport ATP-binding transport protein (smoK), sorbit...ol dehydrogenase (smoS), mannitol dehydrogenase (mtlK),

  1. GenBank blastx search result: AK241729 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241729 J065199L10 AF018073.1 AF018073 Rhodobacter sphaeroides operon regulator (smoC), periplasmic sorbito...l-binding protein (smoE), sorbitol/mannitol transport inner membrane protein (smoF), sorbitol.../mannitol transport inner membrane protein (smoG), sorbitol/mannitol transport ATP-binding transport protein (smoK), sorbit...ol dehydrogenase (smoS), mannitol dehydrogenase (mtlK),

  2. Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine

    OpenAIRE

    Kumar, Ritesh; Zhao, Suwen; Vetting, Matthew W.; Wood, B. McKay; Sakai, Ayano; Cho, Kyuil; Solbiati, José; Steven C Almo; Jonathan V Sweedler; Matthew P Jacobson; Gerlt, John A.; Cronan, John E.

    2014-01-01

    ABSTRACT Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catab...

  3. GenBank blastx search result: AK289073 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK289073 J090094I16 AF016236.1 AF016236 Rhodobacter sphaeroides DMSO/TMAO-sensor kinase (dorS), DMSO.../TMAO-response regulator (dorR), DMSO/TMAO-cytochrome c-containing subunit (dorC), DMSO-mem...brane protein (dorB), and DMSO/TMAO-reductase (dorA) genes, complete cds. BCT 0.0 0 ...

  4. Mapping lipid and detergent molecules at the surface of membrane proteins.

    Science.gov (United States)

    Cogdell, Richard J; Gardiner, Alastair T; Roszak, Aleksander W; Stončius, Sigitas; Kočovský, Pavel; Isaacs, Neil W

    2011-06-01

    Electron-density maps for the crystal structures of membrane proteins often show features suggesting binding of lipids and/or detergent molecules on the hydrophobic surface, but usually it is difficult to identify the bound molecules. In our studies, heavy-atom-labelled phospholipids and detergents have been used to unequivocally identify these binding sites at the surfaces of test membrane proteins, the reaction centres from Rhodobacter sphaeroides and Blastochloris viridis. The generality of this method is discussed in the present article.

  5. Photobiological hydrogen production.

    Science.gov (United States)

    Asada, Y; Miyake, J

    1999-01-01

    The principles and recent progress in the research and development of photobiological hydrogen production are reviewed. Cyanobacteria produce hydrogen gas using nitrogenase and/or hydrogenase. Hydrogen production mediated by native hydrogenases in cyanobacteria occurs under in the dark under anaerobic conditions by degradation of intracellular glycogen. In vitro and in vivo coupling of the cyanobacterial photosynthetic system with a clostridial hydrogenase via cyanobacterial ferredoxin was demonstrated in the presence of light. Genetic transformation of Synechococcus PCC7942 with the hydrogenase gene from Clostridium pasteurianum was successful; the active enzyme was expressed in PCC7942. The strong hydrogen producers among photosynthetic bacteria were isolated and characterized. Coculture of Rhodobacter and Clostriudium was applied for hydrogen production from glucose. A mutant strain of Rhodobacter sphaeroides RV whose light-harvesting proteins were altered was obtained by UV irradiation. Hydrogen productivity by the mutant was improved when irradiated with monochromatic light of some wavelengths. The development of photobioreactors for hydrogen production is also reviewed.

  6. The study of photo-induced ultrafast dynamics in light-harvesting complex LH2 of purple bacteria

    Institute of Scientific and Technical Information of China (English)

    LIU Wei-min; YAN Yong-li; LIU Kang-jun; XU Chun-he; QIAN Shi-xiong

    2006-01-01

    In this paper,we introduce the photo-induced ultrafast dynamics taking place in the peripheral light harvesting antenna LH2 from purple bacteria Rhodobacter sphaeroides by using absorption,fluorescence emission and ultrafast spectroscopic techniques.Three kinds of LH2 sampies,pH treated LH2 (complete removal of B800 pigments),carotenoid mutated LH2 (GM 309) and electrochemical oxidation treated LH2 were used in comparison with native LH2 to investigate the mechanism of photo-induced ultrafast energy transfer within the LH2 complex.

  7. AcEST: DK956327 [AcEST

    Lifescience Database Archive (English)

    Full Text Available tr|Q470H5|Q470H5_RALEJ Probable proline-rich protein OS=Ralstoni... 35 4.3 tr|A4WX08|A4WX08_RHOS5 Antenna co...ell division protein OS=Bacillus thuring... 33 9.5 tr|A3PG62|A3PG62_RHOS1 Antenna complex, alpha/beta subuni...tr|A4WX08|A4WX08_RHOS5 Antenna complex, alpha/beta subunit OS=Rhodobacter sphaeroides (strain ATCC 17025 / A... E A S Sbjct: 68 PVTEALPVSPSKAPAQASAPATEDSNLFSLYAMRRVEAPAAQAPVAALSPASEDAVHS 125 >

  8. Biodegradation of azo dyes by genetically engineered azoreductase

    Institute of Scientific and Technical Information of China (English)

    WANG Jing; YAN Bin; ZHOU Ji-ti; BAO Yong-ming; LU Hong; YUAN Xiao-dong

    2005-01-01

    A azoreductase gene with 537 bp was obtained by PGR amplification from Rhodobacter sphaeroides AS1.1737. The enzyme,with a molecular weight of 18.7 kD, was efficiently expressed in Escherichia coli and its biodegradation characteristics for azo dyes were investigated. Furthermore, the reaction kinetics and mechanism of azo dyes catalyzed by the genetically engineered azoreductase were studied in detail. The presence of a hydrazo-intermediate was identified, which provided a convincing evidence for the assumption that azo dyes were degraded via an incomplete reduction stage.

  9. A Conserved Steroid Binding Site in Cytochrome c Oxidase

    Energy Technology Data Exchange (ETDEWEB)

    Qin, Ling; Mills, Denise A.; Buhrow, Leann; Hiser, Carrie; Ferguson-Miller, Shelagh (Michigan)

    2010-09-02

    Micromolar concentrations of the bile salt deoxycholate are shown to rescue the activity of an inactive mutant, E101A, in the K proton pathway of Rhodobacter sphaeroides cytochrome c oxidase. A crystal structure of the wild-type enzyme reveals, as predicted, deoxycholate bound with its carboxyl group at the entrance of the K path. Since cholate is a known potent inhibitor of bovine oxidase and is seen in a similar position in the bovine structure, the crystallographically defined, conserved steroid binding site could reveal a regulatory site for steroids or structurally related molecules that act on the essential K proton path.

  10. A Computational Strategy to Analyze Label-Free Temporal Bottom-Up Proteomics Data§

    Science.gov (United States)

    Du, Xiuxia; Callister, Stephen J.; Manes, Nathan P.; Adkins, Joshua N.; Alexandridis, Roxana A.; Zeng, Xiaohua; Roh, Jung Hyeob; Smith, William E.; Donohue, Timothy J.; Kaplan, Samuel; Smith, Richard D.; Lipton, Mary S.

    2008-01-01

    Biological systems are in a continual state of flux, which necessitates an understanding of the dynamic nature of protein abundances. The study of protein abundance dynamics has become feasible with recent improvements in mass spectrometry-based quantitative proteomics. However, a number of challenges still remain related to how best to extract biological information from dynamic proteomics data, for example, challenges related to extraneous variability, missing abundance values, and the identification of significant temporal patterns. This paper describes a strategy that addresses these issues and demonstrates its values for analyzing temporal bottom-up proteomics data using data from a Rhodobacter sphaeroides 2.4.1 time-course study. PMID:18442284

  11. Continuous Cultivation of Photosynthetic Bacteria for Fatty Acids Production

    OpenAIRE

    Kim, Dong-Hoon; Lee, Ji-Hye; Hwang, Yuhoon; Kang, Seoktae; Kim, Mi-Sun

    2013-01-01

    In the present work, we introduced a novel approach for microbial fatty acids (FA) production. Photosynthetic bacteria, Rhodobacter sphaeroides KD131, were cultivated in a continuous-flow, stirred-tank reactor (CFSTR) at various substrate (lactate) concentrations.At hydraulic retention time (HRT) 4 d, cell concentration continuously increased from 0.97 g dcw/L to 2.05 g dcw/L as lactate concentration increased from 30 mM to 60 mM. At 70 mM, however, cell concentration fluctuated with incomple...

  12. Reverse micelles as suitable microreactor for increased biohydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Pandey, Anjana [Nanotechnology and Molecular Biology Laboratory, Centre of Biotechnology, University of Allahabad, Allahabad 211002 (India); Pandey, Ashutosh [Centre of Energy Studies, MNNIT, Allahabad 211004 (India)

    2008-01-15

    Reverse micelles have been shown to act as efficient microreactors for enzymic reactions and whole cell entrapment in organic (non-aqueous) media wherein the reactants are protected from denaturation by the surrounding organic solvent. These micelles are thermodynamically stable, micrometer sized water droplets dispersed in an organic phase by a surfactant. It has been observed that when whole cells of photosynthetic bacteria (Rhodopseudomonas sphaeroides or Rhodobacter sphaeroides 2.4.1) are entrapped inside these reverse micelles, the H{sub 2} production enhanced from 25 to 35 folds. That is, 1.71mmol(mgprotein){sup -1}h{sup -1} in case of R. sphaeroides which is 25 fold higher in benzene-sodium lauryl sulfate reverse micelles. Whereas, in case of R. sphaeroides 2.4.1 the H{sub 2} production was increased by 35 fold within AOT-isooctane reverse micelles i.e. 11.5mmol(mgprotein){sup -1}h{sup -1}. The observations indicate that the entrapment of whole cells of microbes within reverse micelles provides a novel and efficient technique to produce hydrogen by the inexhaustible biological route. The two microorganisms R. sphaeroides 2.4.1 (a photosynthetic bacteria) and Citrobacter Y19 (a facultative anaerobic bacteria) together are also entrapped within AOT-isooctane and H{sub 2} production was measured i.e. 69mmol(mgprotein){sup -1}h{sup -1}. The nitrogenase enzyme responsible for hydrogen production by R. sphaeroides/R. sphaeroides 2.4.1 cells is oxygen sensitive, and very well protected within reverse micelles by the use of combined approach of two cells (R. sphaeroides 2.4.1 and Citrobacter Y19). In this case glucose present in the medium of Citrobacter Y19 serves double roles in enhancing the sustained production rate of hydrogen. Firstly, it quenches the free O{sub 2}liberated as a side product of reaction catalyzed by nitrogenase, which is O{sub 2} labile. Secondly, organic acid produced by this reaction is utilized by the Citrobacter Y19 as organic substrate in

  13. Organization and Evolution of the Biological Response to Singlet Oxygen Stress

    Science.gov (United States)

    Dufour, Yann S.; Landick, Robert; Donohue, Timothy J.

    2008-01-01

    The appearance of atmospheric oxygen from photosynthetic activity led to the evolution of aerobic respiration and responses to the resulting reactive oxygen species. In Rhodobacter sphaeroides, a photosynthetic α-proteobacterium, a transcriptional response to the reactive oxygen species singlet oxygen (1O2) is controlled by the group IV σ factor σE and the anti-σ factor ChrR. In this study, we integrated various large datasets to identify genes within the 1O2 stress response that contain σE-dependent promoters both within R. sphaeroides and across the bacterial phylogeny. Transcript pattern clustering and a σE-binding sequence model were used to predict candidate promoters that respond to 1O2 stress in R. sphaeroides. These candidate promoters were experimentally validated to nine R. sphaeroides σE-dependent promoters that control the transcription of 15 1O2-activated genes. Knowledge of the R. sphaeroides response to 1O2 and its regulator σE–ChrR was combined with large-scale phylogenetic and sequence analyses to predict the existence of a core set of approximately eight conserved σE-dependent genes in α-proteobacteria and γ-proteobacteria. The bacteria predicted to contain this conserved response to 1O2 include photosynthetic species, as well as free-living and symbiotic/pathogenic nonphotosynthetic species. Our analysis also predicts that the response to 1O2 evolved within the time frame of the accumulation of atmospheric molecular oxygen on this planet. PMID:18723027

  14. Communication: Coherences observed in vivo in photosynthetic bacteria using two-dimensional electronic spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Dahlberg, Peter D. [Graduate Program in the Biophysical Sciences, Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States); Norris, Graham J.; Wang, Cheng; Viswanathan, Subha; Singh, Ved P.; Engel, Gregory S., E-mail: gsengel@uchicago.edu [Department of Chemistry, Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States)

    2015-09-14

    Energy transfer through large disordered antenna networks in photosynthetic organisms can occur with a quantum efficiency of nearly 100%. This energy transfer is facilitated by the electronic structure of the photosynthetic antennae as well as interactions between electronic states and the surrounding environment. Coherences in time-domain spectroscopy provide a fine probe of how a system interacts with its surroundings. In two-dimensional electronic spectroscopy, coherences can appear on both the ground and excited state surfaces revealing detailed information regarding electronic structure, system-bath coupling, energy transfer, and energetic coupling in complex chemical systems. Numerous studies have revealed coherences in isolated photosynthetic pigment-protein complexes, but these coherences have not been observed in vivo due to the small amplitude of these signals and the intense scatter from whole cells. Here, we present data acquired using ultrafast video-acquisition gradient-assisted photon echo spectroscopy to observe quantum beating signals from coherences in vivo. Experiments were conducted on isolated light harvesting complex II (LH2) from Rhodobacter sphaeroides, whole cells of R. sphaeroides, and whole cells of R. sphaeroides grown in 30% deuterated media. A vibronic coherence was observed following laser excitation at ambient temperature between the B850 and the B850{sup ∗} states of LH2 in each of the 3 samples with a lifetime of ∼40-60 fs.

  15. Communication: Coherences observed in vivo in photosynthetic bacteria using two-dimensional electronic spectroscopy

    Science.gov (United States)

    Dahlberg, Peter D.; Norris, Graham J.; Wang, Cheng; Viswanathan, Subha; Singh, Ved P.; Engel, Gregory S.

    2015-01-01

    Energy transfer through large disordered antenna networks in photosynthetic organisms can occur with a quantum efficiency of nearly 100%. This energy transfer is facilitated by the electronic structure of the photosynthetic antennae as well as interactions between electronic states and the surrounding environment. Coherences in time-domain spectroscopy provide a fine probe of how a system interacts with its surroundings. In two-dimensional electronic spectroscopy, coherences can appear on both the ground and excited state surfaces revealing detailed information regarding electronic structure, system-bath coupling, energy transfer, and energetic coupling in complex chemical systems. Numerous studies have revealed coherences in isolated photosynthetic pigment-protein complexes, but these coherences have not been observed in vivo due to the small amplitude of these signals and the intense scatter from whole cells. Here, we present data acquired using ultrafast video-acquisition gradient-assisted photon echo spectroscopy to observe quantum beating signals from coherences in vivo. Experiments were conducted on isolated light harvesting complex II (LH2) from Rhodobacter sphaeroides, whole cells of R. sphaeroides, and whole cells of R. sphaeroides grown in 30% deuterated media. A vibronic coherence was observed following laser excitation at ambient temperature between the B850 and the B850∗ states of LH2 in each of the 3 samples with a lifetime of ∼40-60 fs. PMID:26373989

  16. Thermal Adaptability of the Light-Harvesting Complex 2 from Thermochromatium tepidum: Temperature-Dependent Excitation Transfer Dynamics.

    Science.gov (United States)

    Shi, Ying; Zhao, Ning-Jiu; Wang, Peng; Fu, Li-Min; Yu, Long-Jiang; Zhang, Jian-Ping; Wang-Otomo, Zheng-Yu

    2015-11-25

    The photosynthetic purple bacterium Thermochromatium (Tch.) tepidum is a thermophile that grows at an optimal temperature of ∼50 °C. We have investigated, by means of steady-state and time-resolved optical spectroscopies, the effects of temperature on the near-infrared light absorption and the excitation energy transfer (EET) dynamics of its light-harvesting complex 2 (LH2), for which the mesophilic counterpart of Rhodobacter (Rba.) sphaeroides 2.4.1 (∼30 °C) was examined in comparison. In a limited range around the physiological temperature (10-55 °C), the B800-to-B850 EET process of the Tch. tepidum LH2, but not the Rba. sphaeroides LH2, was found to be characteristically temperature-dependent, mainly because of a temperature-tunable spectral overlap. At 55 °C, the LH2 complex from Tch. tepidum maintained efficient near-infrared light harvesting and B800-to-B850 EET dynamics, whereas this EET process was disrupted in the case of Rba. sphaeroides 2.4.1 owing to the structural distortion of the LH2 complex. Our results reveal a remarkable thermal adaptability of the light-harvesting function of Tch. tepidum, which could enhance our understanding of the survival strategy of this thermophile in response to environmental challenges.

  17. Mechanisms for hydrogen production by different bacteria during mixed-acid and photo-fermentation and perspectives of hydrogen production biotechnology.

    Science.gov (United States)

    Trchounian, Armen

    2015-03-01

    H2 has a great potential as an ecologically-clean, renewable and capable fuel. It can be mainly produced via hydrogenases (Hyd) by different bacteria, especially Escherichia coli and Rhodobacter sphaeroides. The operation direction and activity of multiple Hyd enzymes in E. coli during mixed-acid fermentation might determine H2 production; some metabolic cross-talk between Hyd enzymes is proposed. Manipulating the activity of different Hyd enzymes is an effective way to enhance H2 production by E. coli in biotechnology. Moreover, a novel approach would be the use of glycerol as feedstock in fermentation processes leading to H2 production. Mixed carbon (sugar and glycerol) utilization studies enlarge the kind of organic wastes used in biotechnology. During photo-fermentation under limited nitrogen conditions, H2 production by Rh. sphaeroides is observed when carbon and nitrogen sources are supplemented. The relationship of H2 production with H(+) transport across the membrane and membrane-associated ATPase activity is shown. On the other hand, combination of carbon sources (succinate, malate) with different nitrogen sources (yeast extract, glutamate, glycine) as well as different metal (Fe, Ni, Mg) ions might regulate H2 production. All these can enhance H2 production yield by Rh. sphaeroides in biotechnology Finally, two of these bacteria might be combined to develop and consequently to optimize two stages of H2 production biotechnology with high efficiency transformation of different organic sources.

  18. 4-Vinylphenol biosynthesis from cellulose as the sole carbon source using phenolic acid decarboxylase- and tyrosine ammonia lyase-expressing Streptomyces lividans.

    Science.gov (United States)

    Noda, Shuhei; Kawai, Yoshifumi; Tanaka, Tsutomu; Kondo, Akihiko

    2015-03-01

    Streptomyces lividans was adopted as a host strain for 4-vinylphenol (4VPh) production directly from cellulose. In order to obtain novel phenolic acid decarboxylase (PAD) expressed in S. lividans, PADs distributed among Streptomyces species were screened. Three novel PADs, derived from Streptomycessviceus, Streptomyceshygroscopicus, and Streptomycescattleya, were successfully obtained and expressed in S. lividans. S. sviceus PAD (SsPAD) could convert p-hydroxycinnamic acid (pHCA) to 4VPh more efficiently than the others both in vitro and in vivo. For 4VPh production directly from cellulose, l-tyrosine ammonia lyase derived from Rhodobacter sphaeroides and SsPAD were introduced into endoglucanase-secreting S. lividans, and the 4VPh biosynthetic pathway was constructed therein. The created transformants successfully produced 4VPh directly from cellulose.

  19. Ultrafast Structural Dynamics of BlsA, a Photoreceptor from the Pathogenic Bacterium Acinetobacter baumannii

    Science.gov (United States)

    2013-01-01

    Acinetobacter baumannii is an important human pathogen that can form biofilms and persist under harsh environmental conditions. Biofilm formation and virulence are modulated by blue light, which is thought to be regulated by a BLUF protein, BlsA. To understand the molecular mechanism of light sensing, we have used steady-state and ultrafast vibrational spectroscopy to compare the photoactivation mechanism of BlsA to the BLUF photosensor AppA from Rhodobacter sphaeroides. Although similar photocycles are observed, vibrational data together with homology modeling identify significant differences in the β5 strand in BlsA caused by photoactivation, which are proposed to be directly linked to downstream signaling. PMID:24723998

  20. Light-induced structural changes in photosynthetic reaction centres studied by ESEEM of spin-correlated D+QA- radical pairs.

    Science.gov (United States)

    Borovykh, I V; Dzuba, S A; Proskuryakov, I I; Gast, P; Hoff, A J

    1998-03-25

    Zn-substituted Rhodobacter sphaeroides R26 reaction centres (RCs) frozen in the dark and under illumination exhibit quite different recombination kinetics of the D+QA- radical pairs [Kleinfeld et al., Biochemistry, 23 (1984) 5780]. We have applied electron spin echo envelope modulation (ESEEM) of the spin-correlated D+QA- radical pairs to assess a possible light-induced change in the distance between the D and QA cofactors. The recombination kinetics and the field-swept spin-polarized EPR signal for the two preparations have been monitored by time-resolved EPR spectroscopy. For the samples frozen under illumination, a slight increase in the distance, 0.4+/-0.2 A, has been detected.

  1. Fabrication of biomolecule copolymer hybrid nanovesicles as energy conversion systems

    Science.gov (United States)

    Ho, Dean; Chu, Benjamin; Lee, Hyeseung; Brooks, Evan K.; Kuo, Karen; Montemagno, Carlo D.

    2005-12-01

    This work demonstrates the integration of the energy-transducing proteins bacteriorhodopsin (BR) from Halobacterium halobium and cytochrome c oxidase (COX) from Rhodobacter sphaeroides into block copolymeric vesicles towards the demonstration of coupled protein functionality. An ABA triblock copolymer-based biomimetic membrane possessing UV-curable acrylate endgroups was synthesized to serve as a robust matrix for protein reconstitution. BR-functionalized polymers were shown to generate light-driven transmembrane pH gradients while pH gradient-induced electron release was observed from COX-functionalized polymers. Cooperative behaviour observed from composite membrane functionalized by both proteins revealed the generation of microamp-range currents with no applied voltage. As such, it has been shown that the fruition of technologies based upon bio-functionalizing abiotic materials may contribute to the realization of high power density devices inspired by nature.

  2. Comparison of different mixed cultures for bio-hydrogen production from ground wheat starch by combined dark and light fermentation.

    Science.gov (United States)

    Ozmihci, Serpil; Kargi, Fikret

    2010-04-01

    Composition of the mixed culture was varied in combined dark-light fermentation of wheat powder starch in order to improve hydrogen gas formation rate and yield. Heat-treated anaerobic sludge and pure culture of Clostridium beijerinckii (DSMZ 791T) were combined with two different light fermentation bacteria of Rhodobacter sphaeroides (RS-NRRL and RS-RV) in order to select a more suitable mixture resulting in high hydrogen yield and formation rate. A combination of the anaerobic sludge and RS-NRRL yielded the highest cumulative hydrogen (CHF = 140 ml), the highest yield (0.36 mol H2 mol(-1) glucose) and specific hydrogen formation rate (2.5 ml H2 g(-1) biomass h(-1)). During dark fermentation (70 h) hydrogen was produced simultaneously by the dark and light fermentation bacteria using glucose from hydrolyzed starch. However, only light fermentation bacteria produced hydrogen from VFA's derived from dark fermentation after a long adaptation period.

  3. Photoprotection Mechanism of Light-Harvesting Antenna Complex from Purple Bacteria.

    Science.gov (United States)

    Kosumi, Daisuke; Horibe, Tomoko; Sugisaki, Mitsuru; Cogdell, Richard J; Hashimoto, Hideki

    2016-02-11

    Photosynthetic light-harvesting apparatus efficiently capture sunlight and transfer the energy to reaction centers, while they safely dissipate excess energy to surrounding environments for a protection of their organisms. In this study, we performed pump-probe spectroscopic measurements with a temporal window ranging from femtosecond to submillisecond on the purple bacterial antenna complex LH2 from Rhodobacter sphaeroides 2.4.1 to clarify its photoprotection functions. The observed excited state dynamics in the time range from subnanosecond to microsecond exhibits that the triplet-triplet excitation energy transfer from bacteriochlorophyll a to carotenoid takes place with a time constant of 16.7 ns. Furthermore, ultrafast spectroscopic data suggests that a molecular assembly of bacteriochlorophyll a in LH2 efficiently suppresses a generation of triple bacteriochlorophyll a.

  4. Breeding of Coenzyme Q10 High Yield Strain%发酵生产辅酶Q10高产菌株的选育

    Institute of Scientific and Technical Information of China (English)

    陈金卿

    2016-01-01

    以实验室保存的类球红细菌(Rhodobacter sphaeroides)JDW61为出发菌株,考察了紫外、紫外结合氯化锂和亚硝基胍对菌株产生辅酶Q10能力的诱变效应,并结合辅酶Q10的合成途径设计了快速筛选辅酶Q10高产菌株的模型,获得一株辅酶Q10产量提高的突变株CP222,该菌株摇瓶发酵的辅酶Q10产量为276.14 mg·L-1,较出发菌株提高了190%,并且遗传性能稳定.

  5. Synthetic Antenna Functioning As Light Harvester in the Whole Visible Region for Enhanced Hybrid Photosynthetic Reaction Centers.

    Science.gov (United States)

    Hassan Omar, Omar; la Gatta, Simona; Tangorra, Rocco Roberto; Milano, Francesco; Ragni, Roberta; Operamolla, Alessandra; Argazzi, Roberto; Chiorboli, Claudio; Agostiano, Angela; Trotta, Massimo; Farinola, Gianluca M

    2016-07-20

    The photosynthetic reaction center (RC) from the Rhodobacter sphaeroides bacterium has been covalently bioconjugated with a NIR-emitting fluorophore (AE800) whose synthesis was specifically tailored to act as artificial antenna harvesting light in the entire visible region. AE800 has a broad absorption spectrum with peaks centered in the absorption gaps of the RC and its emission overlaps the most intense RC absorption bands, ensuring a consistent increase of the protein optical cross section. The covalent hybrid AE800-RC is stable and fully functional. The energy collected by the artificial antenna is transferred to the protein via FRET mechanism, and the hybrid system outperforms by a noteworthy 30% the overall photochemical activity of the native protein under the entire range of visible light. This improvement in the optical characteristic of the photoenzyme demonstrates the effectiveness of the bioconjugation approach as a suitable route to new biohybrid materials for energy conversion, photocatalysis, and biosensing.

  6. 光合细菌对土壤中呋喃丹的生物降解%Characterization of Biodegradation for Carbofuran Pesticides in Soils by Photosynthetic Bacteria

    Institute of Scientific and Technical Information of China (English)

    白红娟; 肖根林; 贾万利

    2013-01-01

    以一株降解呋喃丹的光合细菌球形红细菌(Rhodobacter sphaeroides)H菌株为材料,考察了其在实验室模拟条件下降解土壤中呋喃丹的影响因素及其动力学过程.结果表明,该菌降解呋喃丹的最适条件为:温度30℃,pH=7.0,接种量107个/g.在最适条件下,H菌株对初始质量浓度为5.0~25 mg/kg呋喃丹的降解反应均符合一级动力学特征.可以将其应用于呋喃丹污染土壤的生物修复.

  7. A Computational Strategy to Analyze Label-Free Temporal Bottom-up Proteomics Data

    Energy Technology Data Exchange (ETDEWEB)

    Du, Xiuxia; Callister, Stephen J.; Manes, Nathan P.; Adkins, Joshua N.; Alexandridis, Roxana A.; Zeng, Xiaohua; Roh, Jung Hyeob; Smith, William E.; Donohue, Timothy J.; Kaplan, Samuel; Smith, Richard D.; Lipton, Mary S.

    2008-07-01

    Motivation: Biological systems are in a continual state of flux, which necessitates an understanding of the dynamic nature of protein abundances. The study of protein abundance dynamics has become feasible with recent improvements in mass spectrometry-based quantitative proteomics. However, a number of challenges still re-main related to how best to extract biological information from dy-namic proteomics data; for example, challenges related to extrane-ous variability, missing abundance values, and the identification of significant temporal patterns. Results: This article describes a strategy that addresses the afore-mentioned issues for the analysis of temporal bottom-up proteomics data. The core strategy for the data analysis algorithms and subse-quent data interpretation was formulated to take advantage of the temporal properties of the data. The analysis procedure presented herein was applied to data from a Rhodobacter sphaeroides 2.4.1 time-course study. The results were in close agreement with existing knowledge about R. sphaeroides, therefore demonstrating the utility of this analytical strategy.

  8. Enhanced Hydrogen Production by Co-cultures of Hydrogenase and Nitrogenase in Escherichia coli.

    Science.gov (United States)

    Lee, Hyun Jeong; Sekhon, Simranjeet Singh; Kim, Young Su; Park, Ju-Yong; Kim, Yang-Hoon; Min, Jiho

    2016-03-01

    Rhodobacter sphaeroides is a bacterium that can produce hydrogen by interaction with hydrogenase and nitrogenase. We report a hydrogen production system using co-cultivation of hydrogenase in liquid medium and immobilized nitrogenase in Escherichia coli. The recombinant plasmid has been constructed to analyze the effect of hydrogen production on the expression of hupSL hydrogenase and nifHDK nitrogenase isolated from R. sphaeroides. All recombinant E. coli strains were cultured anaerobically, and cells for nitrogenase were immobilized in agar gel, whereas cells for hydrogenase were supplemented on the nitrogenase agar gel. The hupSL hydrogenase has been observed to enhance hydrogen production and hydrogenase activity under co-culture with nifHDK nitrogenase. The maximum hydrogen production has been obtained at an agar gel concentration and a cell concentration for co-culture of 2 % and 6.4 × 10(8) CFU. Thus, co-culture of hupSL hydrogenase and nifHDK nitrogenase provides a promising route for enhancing the hydrogen production and hydrogenase activity.

  9. Mutations That Alter the Bacterial Cell Envelope Increase Lipid Production

    Directory of Open Access Journals (Sweden)

    Kimberly C. Lemmer

    2017-05-01

    Full Text Available Lipids from microbes offer a promising source of renewable alternatives to petroleum-derived compounds. In particular, oleaginous microbes are of interest because they accumulate a large fraction of their biomass as lipids. In this study, we analyzed genetic changes that alter lipid accumulation in Rhodobacter sphaeroides. By screening an R. sphaeroides Tn5 mutant library for insertions that increased fatty acid content, we identified 10 high-lipid (HL mutants for further characterization. These HL mutants exhibited increased sensitivity to drugs that target the bacterial cell envelope and changes in shape, and some had the ability to secrete lipids, with two HL mutants accumulating ~60% of their total lipids extracellularly. When one of the highest-lipid-secreting strains was grown in a fed-batch bioreactor, its lipid content was comparable to that of oleaginous microbes, with the majority of the lipids secreted into the medium. Based on the properties of these HL mutants, we conclude that alterations of the cell envelope are a previously unreported approach to increase microbial lipid production. We also propose that this approach may be combined with knowledge about biosynthetic pathways, in this or other microbes, to increase production of lipids and other chemicals.

  10. Improved hydrogen production by coupled systems of hydrogenase negative photosynthetic bacteria and fermentative bacteria in reverse micelles

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Anita [Centre for Biotechnology, University of Allahabad, Allahabad 211002 (India); Misra, Krishna [Indo-Russian Center for Bioinformatics, Indian Institute of Information Technology, Allahabad 211011 (India)

    2008-11-15

    Significant improvement in biological hydrogen production is achieved by the use of coupled bacterial cells in reverse micellar systems. Two coupled systems (a) Rhodopseudomonas palustris CGA009/Citrobacter Y19, and (b) Rhodobacter sphaeroides 2.4.1/Citrobacter Y19 bacteria have been immobilized separately in aqueous pool of the reverse micelles fabricated by various surfactants (AOT, CBAC and SDS) and apolar organic solvents (benzene and isooctane). The gene for uptake hydrogenase enzyme has been manipulated further for hydrogen generation. Mutants deficient in uptake hydrogenase (Hup{sup -}) were obtained from R. palustris CGA009 and R. sphaeroides 2.4.1, and entrapped with Citrobacter Y19 in the reverse micellar systems. More than two fold increase in hydrogen production was obtained by the use of Hup{sup -} mutants instead of wild-type photosynthetic bacteria together with Citrobacter Y19. Addition of sodium dithionite, a reducing agent to AOT/H{sub 2}O/isooctane reverse micellar system with the coupled systems of wild-type photosynthetic bacteria and fermentative bacterium Y19 effected similar increase in hydrogen production rate as it is obtained by the use of mutants. CBAC/H{sub 2}O/isooctane reverse micellar system is used for the first time for hydrogen production and is as promising as AOT/H{sub 2}O/isooctane reverse micellar system. All reverse micellar systems of coupled bacterial cultures gave encouraging hydrogen production (rate as well as yield) compared to uncoupled bacterial culture. (author)

  11. Continuous cultivation of photosynthetic bacteria for fatty acids production.

    Science.gov (United States)

    Kim, Dong-Hoon; Lee, Ji-Hye; Hwang, Yuhoon; Kang, Seoktae; Kim, Mi-Sun

    2013-11-01

    In the present work, we introduced a novel approach for microbial fatty acids (FA) production. Photosynthetic bacteria, Rhodobacter sphaeroides KD131, were cultivated in a continuous-flow, stirred-tank reactor (CFSTR) at various substrate (lactate) concentrations. At hydraulic retention time (HRT) 4d, cell concentration continuously increased from 0.97 g dcw/L to 2.05 g dcw/L as lactate concentration increased from 30 mM to 60mM. At 70 mM, however, cell concentration fluctuated with incomplete substrate degradation. By installing a membrane unit to CFSTR, a stable performance was observed under much higher substrate loading (lactate 100mM and HRT 1.5d). A maximum cell concentration of 16.2g dcw/L, cell productivity of 1.9 g dcw/L/d, and FA productivity of 665 mg FA/L/d were attained, and these values were comparable with those achieved using microalgae. The FA content of R. sphaeroides was around 35% of dry cell weight, mainly composed of vaccenic acid (C18:1, omega-7).

  12. Redox-Dependent Conformational Changes in Cytochrome c Oxidase Suggest a Gating Mechanism for Proton Uptake

    Energy Technology Data Exchange (ETDEWEB)

    Qin, Ling; Liu, Jian; Mills, Denise A.; Proshlyakov, Denis A.; Hiser, Carrie; Ferguson-Miller, Shelagh; (MSU)

    2009-08-05

    A role for conformational change in the coupling mechanism of cytochrome c oxidase is the subject of controversy. Relatively small conformational changes have been reported in comparisons of reduced and oxidized crystal structures of bovine oxidase but none in bacterial oxidases. Comparing the X-ray crystal structures of the reduced (at 2.15 {angstrom} resolution) and oxidized forms of cytochrome c oxidase from Rhodobacter sphaeroides, we observe a displacement of heme a3 involving both the porphyrin ring and the hydroxyl farnesyl tail, accompanied by protein movements in nearby regions, including the mid part of helix VIII of subunit I which harbors key residues of the K proton uptake path, K362 and T359. The conformational changes in the reduced form are reversible upon reoxidation. They result in an opening of the top of the K pathway and more ordered waters being resolved in that region, suggesting an access path for protons into the active site. In all high-resolution structures of oxidized R. sphaeroides cytochrome c oxidase, a water molecule is observed in the hydrophobic region above the top of the D path, strategically positioned to facilitate the connection of residue E286 of subunit I to the active site or to the proton pumping exit path. In the reduced and reduced plus cyanide structures, this water molecule disappears, implying disruption of proton conduction from the D path under conditions when the K path is open, thus providing a mechanism for alternating access to the active site.

  13. Modeling chemotaxis reveals the role of reversed phosphotransfer and a bi-functional kinase-phosphatase.

    Directory of Open Access Journals (Sweden)

    Marcus J Tindall

    2010-08-01

    Full Text Available Understanding how multiple signals are integrated in living cells to produce a balanced response is a major challenge in biology. Two-component signal transduction pathways, such as bacterial chemotaxis, comprise histidine protein kinases (HPKs and response regulators (RRs. These are used to sense and respond to changes in the environment. Rhodobacter sphaeroides has a complex chemosensory network with two signaling clusters, each containing a HPK, CheA. Here we demonstrate, using a mathematical model, how the outputs of the two signaling clusters may be integrated. We use our mathematical model supported by experimental data to predict that: (1 the main RR controlling flagellar rotation, CheY(6, aided by its specific phosphatase, the bifunctional kinase CheA(3, acts as a phosphate sink for the other RRs; and (2 a phosphorelay pathway involving CheB(2 connects the cytoplasmic cluster kinase CheA(3 with the polar localised kinase CheA(2, and allows CheA(3-P to phosphorylate non-cognate chemotaxis RRs. These two mechanisms enable the bifunctional kinase/phosphatase activity of CheA(3 to integrate and tune the sensory output of each signaling cluster to produce a balanced response. The signal integration mechanisms identified here may be widely used by other bacteria, since like R. sphaeroides, over 50% of chemotactic bacteria have multiple cheA homologues and need to integrate signals from different sources.

  14. Light-field-characterization in a continuous hydrogen-producing photobioreactor by optical simulation and computational fluid dynamics.

    Science.gov (United States)

    Krujatz, Felix; Illing, Rico; Krautwer, Tobias; Liao, Jing; Helbig, Karsten; Goy, Katharina; Opitz, Jörg; Cuniberti, Gianaurelio; Bley, Thomas; Weber, Jost

    2015-12-01

    Externally illuminated photobioreactors (PBRs) are widely used in studies on the use of phototrophic microorganisms as sources of bioenergy and other photobiotechnology research. In this work, straightforward simulation techniques were used to describe effects of varying fluid flow conditions in a continuous hydrogen-producing PBR on the rate of photofermentative hydrogen production (rH2 ) by Rhodobacter sphaeroides DSM 158. A ZEMAX optical ray tracing simulation was performed to quantify the illumination intensity reaching the interior of the cylindrical PBR vessel. 24.2% of the emitted energy was lost through optical effects, or did not reach the PBR surface. In a dense culture of continuously producing bacteria during chemostatic cultivation, the illumination intensity became completely attenuated within the first centimeter of the PBR radius as described by an empirical three-parametric model implemented in Mathcad. The bacterial movement in chemostatic steady-state conditions was influenced by varying the fluid Reynolds number. The "Computational Fluid Dynamics" and "Particle Tracing" tools of COMSOL Multiphysics were used to visualize the fluid flow pattern and cellular trajectories through well-illuminated zones near the PBR periphery and dark zones in the center of the PBR. A moderate turbulence (Reynolds number = 12,600) and fluctuating illumination of 1.5 Hz were found to yield the highest continuous rH2 by R. sphaeroides DSM 158 (170.5 mL L(-1) h(-1) ) in this study.

  15. Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ.

    Science.gov (United States)

    Mank, Nils N; Berghoff, Bork A; Hermanns, Yannick N; Klug, Gabriele

    2012-10-02

    The small RNA PcrZ (photosynthesis control RNA Z) of the facultative phototrophic bacterium Rhodobacter sphaeroides is induced upon a drop of oxygen tension with similar kinetics to those of genes for components of photosynthetic complexes. High expression of PcrZ depends on PrrA, the response regulator of the PrrB/PrrA two-component system with a central role in redox regulation in R. sphaeroides. In addition the FnrL protein, an activator of some photosynthesis genes at low oxygen tension, is involved in redox-dependent expression of this small (s)RNA. Overexpression of full-length PcrZ in R. sphaeroides affects expression of a small subset of genes, most of them with a function in photosynthesis. Some mRNAs from the photosynthetic gene cluster were predicted to be putative PcrZ targets and results from an in vivo reporter system support these predictions. Our data reveal a negative effect of PcrZ on expression of its target mRNAs. Thus, PcrZ counteracts the redox-dependent induction of photosynthesis genes, which is mediated by protein regulators. Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this is one of the rare cases of an incoherent feed-forward loop including an sRNA. Our data identified PcrZ as a trans acting sRNA with a direct regulatory function in formation of photosynthetic complexes and provide a model for the control of photosynthesis gene expression by a regulatory network consisting of proteins and a small noncoding RNA.

  16. The phylogenetic relationships of Caulobacter, Asticcacaulis and Brevundimonas species and their taxonomic implications.

    Science.gov (United States)

    Sly, L I; Cox, T L; Beckenham, T B

    1999-04-01

    The phylogenetic relationships among the species of Caulobacter, Asticcacaulis and Brevundimonas were studied by comparison of their 16S rDNA sequences. The analysis of almost complete sequences confirmed the early evolutionary divergence of the freshwater and marine species of Caulobacter reported previously [Stahl, D. A., Key, R., Flesher, B. & Smit, J. (1992). J Bacteriol 174, 2193-2198]. The freshwater species formed two distinct clusters. One cluster contained the species Caulobacter bacteroides, Caulobacter crescentus, Caulobacter fusiformis and Caulobacter henricii. C. bacteroides and C. fusiformis are very closely related (sequence identity 99.8%). The second cluster was not exclusive and contained the specis Caulobacter intermedius, Caulobacter subvibrioides and Caulobacter variabilis, as well as Brevundimonas diminuta and Brevundimonas vesicularis. The marine species Caulobacter halobacteroides and Caulobacter maris were very closely related, with a sequence identity of 99.7%. These two species were most closely but distantly related to the marine hyphal/budding bacteria Hyphomonas jannaschiana and Hirschia baltica, which formed a deep phylogenetic line with Rhodobacter sphaeroides and Rhodobacter capsulatus. Caulobacter leidyia is unrelated to the other species of Caulobacter and belongs to the alpha-4 subclass of the Proteobacteria, forming a distinct cluster with Asticcacaulis excentricus and Asticcacaulis biprosthecium. The taxonomic implications of the polyphyletic nature of the genus Caulobacter and the absence of a type culture for the type species of the genus Caulobacter vibrioides, are discussed.

  17. Comparison of the Photosynthetic Characteristics of Two Developmental Stages in Nostoc sphaeroides Kützing(Cyanophyta)

    Institute of Scientific and Technical Information of China (English)

    LI Dun-hai; CHEN Lan-zhou; LI Gen-bao; WANG Gao-hong; LIU Yong-ding

    2005-01-01

    The photosynthetic activities between two main developmental stages, colony and hormogonium, of the edible cyanobacterium Nostoc sphaephyll than that of colonies. It showed that the ratios of phycocyain (PC), allophycocyain (APC) and phycoerythrocyanin (PEC) in hormogonia and colonies were different. The room temperature chlorophyll fluorescence, 77 K chlorophyll fluorescence, measurements of PS Ⅰ and PS Ⅱ activities all showed that colony has higher photosynthetic competence than hormogonia. Hormogonia had a higher respiration rate than colony, while their maximum photosynthetic oxygen evolution rates were very close. The responses of hormogonia and colonies to high light illuminations also were different. Both of their oxygen evolution rates decreased quickly with the prolonged high light illumination, but hormogonia can keep relatively higher PS Ⅱ activity (Fv/Fm ) than that of colonies.The results suggested that colony was photosynthetically more competent than hormogonia, while the ability of hormogonia to tolerate high light illumination was higher than that of colony.

  18. Molecular Mechanism of Solar Energy Harvesting by Purple Photosynthetic Bacteria%紫色光合细菌捕获太阳能的分子机理

    Institute of Scientific and Technical Information of China (English)

    王万能; 陈国平; 胡宗利; 李尽哲; 何帅

    2011-01-01

    光合作用是地球上最重要的化学反应,生物体通过它捕获太阳能,转为化学能供生长繁殖需要.光合细菌是地球上最早出现的具有原始光能合成体系的微生物,其光合反应中心是一个由多种色素分子与蛋白质以非共价键方式结合的、具有特定构象的色素-蛋白复合体-光反应中心RC(Reaction center)和LH(Light Harvesting),光能通过电荷分离及电子转移反应转化为化学能,其效率是当前人工模拟远远不能及的.本文综述了紫色光合细菌捕获太阳能的分子结构、作用机理的研究进展,并结合作者在R.sphaeroides LHII蛋白组份同源及异源基因表达方面的研究结果进行相应的分析,明确了Rhodobacter sphaeroides基因组中同源基因puc2BA的表达特点和功能,Rhodovulum sulfidophilum pucsBA与R.sphaeroides pufBA能够同时在R.sphaeroides中表达,能同时形成LHII和LHI,并具有能量传递功能.%Photosynthesis is arguably the most important biological process, by it organisms harvest solar energy and transfer it into chemical energy for growth and reproduction.The photosynthetic bacteria are the earliest microbe with photosynthesis found on earth.The photosynthetic apparatus of purple bacteria is a nanometric assembly in the intracytoplasmic membranes and consists of pigment-protein complexes, the photosynthetic RC (Reaction center) and LH (Light harvesting).The primary processes of photosynthesis involve absorption of photons by LH complexes, transfer of excitation energy from the LH complexes to the photosynthetic RC, where the primary energy conversion takes place.The researches on molecular structure and mechanism of purple photosynthetic bacteria harvesting solar energy were summarized.Molecular biology techniques and spectroscopic analysis were applied to research the expression and function of puc2BA and pucsBA by the authors, and it was concluded that the puc2BA gene was normally expressed in Rhodobacter

  19. Stoichiometry of ATP hydrolysis and chlorophyllide formation of dark-operative protochlorophyllide oxidoreductase from Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Nomata, Jiro [Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 (Japan); Terauchi, Kazuki [Department of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577 (Japan); Fujita, Yuichi, E-mail: fujita@agr.nagoya-u.ac.jp [Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 (Japan)

    2016-02-12

    Dark-operative protochlorophyllide (Pchlide) oxidoreductase (DPOR) is a nitrogenase-like enzyme catalyzing a reduction of the C17 = C18 double bond of Pchlide to form chlorophyllide a (Chlide) in bacteriochlorophyll biosynthesis. DPOR consists of an ATP-dependent reductase component, L-protein (a BchL dimer), and a catalytic component, NB-protein (a BchN–BchB heterotetramer). The L-protein transfers electrons to the NB-protein to reduce Pchlide, which is coupled with ATP hydrolysis. Here we determined the stoichiometry of ATP hydrolysis and the Chlide formation of DPOR. The minimal ratio of ATP to Chlide (ATP/2e{sup –}) was 4, which coincides with that of nitrogenase. The ratio increases with increasing molar ratio of L-protein to NB-protein. This profile differs from that of nitrogenase. These results suggest that DPOR has a specific intrinsic property, while retaining the common features shared with nitrogenase. - Highlights: • The stoichiometry of nitrogenase-like protochlorophyllide reductase was determined. • The minimal ATP/2e{sup –} ratio was 4, which coincides with that of nitrogenase. • The ATP/2e{sup –} ratio increases with increasing L-protein/NB-protein molar ratio. • DPOR has an intrinsic property, but retains features shared with nitrogenase.

  20. Potential use of thermophilic dark fermentation effluents in photofermentative hydrogen production by Rhodobacter capsulatus

    NARCIS (Netherlands)

    Ozgur, E.; Afsar, N.; Vrije, de G.J.; Yucel, M.; Gunduz, U.; Claassen, P.A.M.; Eroglu, I.

    2010-01-01

    Biological hydrogen production by a sequential operation of dark and photofermentation is a promising route to produce hydrogen. The possibility of using renewable resources, like biomass and agro-industrial wastes, provides a dual effect of sustainability in biohydrogen production and simultaneous

  1. Biological hydrogen production from olive mill wastewater with two-stage processes

    Energy Technology Data Exchange (ETDEWEB)

    Eroglu, Ela; Eroglu, Inci [Department of Chemical Engineering, Middle East Technical University, 06531, Ankara (Turkey); Guenduez, Ufuk; Yuecel, Meral [Department of Biology, Middle East Technical University, 06531, Ankara (Turkey); Tuerker, Lemi [Department of Chemistry, Middle East Technical University, 06531, Ankara (Turkey)

    2006-09-15

    In the present work two novel two-stage hydrogen production processes from olive mill wastewater (OMW) have been introduced. The first two-stage process involved dark-fermentation followed by a photofermentation process. Dark-fermentation by activated sludge cultures and photofermentation by Rhodobacter sphaeroides O.U.001 were both performed in 55ml glass vessels, under anaerobic conditions. In some cases of dark-fermentation, activated sludge was initially acclimatized to the OMW to provide the adaptation of microorganisms to the extreme conditions of OMW. The highest hydrogen production potential obtained was 29l{sub H{sub 2}}/l{sub OMW} after photofermentation with 50% (v/v) effluent of dark fermentation with activated sludge. Photofermentation with 50% (v/v) effluent of dark fermentation with acclimated activated sludge had the highest hydrogen production rate (0.008ll{sup -1}h{sup -1}). The second two-stage process involved a clay treatment step followed by photofermentation by R. sphaeroides O.U.001. Photofermentation with the effluent of the clay pretreatment process (4% (v/v)) gives the highest hydrogen production potential (35l{sub H{sub 2}}/l{sub OMW}), light conversion efficiency (0.42%) and COD conversion efficiency (52%). It was concluded that both pretreatment processes enhanced the photofermentative hydrogen production process. Moreover, hydrogen could be produced with highly concentrated OMW. Two-stage processes developed in the present investigation have a high potential for solving the environmental problems caused by OMW. (author)

  2. Temperature dependent LH1→RC energy transfer in purple bacteria Tch. tepidum with shiftable LH1-Qy band: A natural system to investigate thermally activated energy transfer in photosynthesis.

    Science.gov (United States)

    Ma, Fei; Yu, Long-Jiang; Wang-Otomo, Zheng-Yu; van Grondelle, Rienk

    2016-04-01

    The native LH1-RC complex of the purple bacterium Thermochromatium (Tch.) tepidum has an ultra-red LH1-Qy absorption at 915nm, which can shift to 893 and 882nm by means of chemical modifications. These unique complexes are a good natural system to investigate the thermally activated energy transfer process, with the donor energies different while the other factors (such as the acceptor energy, special pair at 890nm, and the distance/relative orientation between the donor and acceptor) remain the same. The native B915-RC, B893-RC and B882-RC complexes, as well as the LH1-RC complex of Rhodobacter (Rba.) sphaeroides were studied by temperature-dependent time-resolved absorption spectroscopy. The energy transfer time constants, kET(-1), are 65, 45, 46 and 45ps at room temperature while 225, 58, 85, 33ps at 77K for the B915-RC, B893-RC, B882-RC and Rba. sphaeroides LH1-RC, respectively. The dependences of kET on temperature have different trends. The reorganization energies are determined to be 70, 290, 200 and 45cm(-1), respectively, by fitting kET vs temperature using Marcus equation. The activation energies are 200, 60, 115 and 20cm(-1), respectively. The influences of the structure (the arrangement of the 32 BChl a molecules) on kET are discussed based on these results, to reveal how the B915-RC complex accomplishes its energy transfer function with a large uphill energy of 290cm(-1).

  3. Production of bioplastics and hydrogen gas by photosynthetic microorganisms

    Science.gov (United States)

    Yasuo, Asada; Masato, Miyake; Jun, Miyake

    1998-03-01

    Our efforts have been aimed at the technological basis of photosynthetic-microbial production of materials and an energy carrier. We report here accumulation of poly-(3-hydroxybutyrate) (PHB), a raw material of biodegradable plastics and for production of hydrogen gas, and a renewable energy carrier by photosynthetic microorganisms (tentatively defined as cyanobacteria plus photosynthetic bateria, in this report). A thermophilic cyanobacterium, Synechococcus sp. MA19 that accumulates PHB at more than 20% of cell dry wt under nitrogen-starved conditions was isolated and microbiologically identified. The mechanism of PHB accumulation was studied. A mesophilic Synechococcus PCC7942 was transformed with the genes encoding PHB-synthesizing enzymes from Alcaligenes eutrophus. The transformant accumulated PHB under nitrogen-starved conditions. The optimal conditions for PHB accumulation by a photosynthetic bacterium grown on acetate were studied. Hydrogen production by photosynthetic microorganisms was studied. Cyanobacteria can produce hydrogen gas by nitrogenase or hydrogenase. Hydrogen production mediated by native hydrogenase in cyanobacteria was revealed to be in the dark anaerobic degradation of intracellular glycogen. A new system for light-dependent hydrogen production was targeted. In vitro and in vivo coupling of cyanobacterial ferredoxin with a heterologous hydrogenase was shown to produce hydrogen under light conditions. A trial for genetic trasformation of Synechococcus PCC7942 with the hydrogenase gene from Clostridium pasteurianum is going on. The strong hydrogen producers among photosynthetic bacteria were isolated and characterized. Co-culture of Rhodobacter and Clostriumdium was applied to produce hydrogen from glucose. Conversely in the case of cyanobacteria, genetic regulation of photosynthetic proteins was intended to improve conversion efficiency in hydrogen production by the photosynthetic bacterium, Rhodobacter sphaeroides RV. A mutant acquired by

  4. Studies of Structure and Dynamics of Light Harvesting Complex 1 of R. Sphaeroides by Solid State NMR

    Energy Technology Data Exchange (ETDEWEB)

    McDermott, Ann E [Columbia Univ., New York, NY (United States)

    2014-11-14

    Studies of the structure and dynamics of a light harvesting complex from photosynthetic bacteria are described. Using Nuclear Magnetic Resonance methods, we explored the idea that optical properties are modulated via a conformational switch in the BChl chromophores, in a way that provides benefits for the efficiency of energy conversion.

  5. Hydrogen production as a novel process of wastewater treatment - studies on tofu wastewater with entrapped R. sphaeroides and mutagenesis

    Energy Technology Data Exchange (ETDEWEB)

    Heguang Zhu [Tongji Univ., Shanghai (China). Inst. of Environmental Science; Ueda, Shunsaku [Utsunomiya Univ. (Japan). Dept. of Biological Productive Science; Asada, Yasio [Nihon Univ., Chiba (Japan). College of Science and Technology; Miyake, Jun [National Inst. for Advanced Interdisciplinary Research, Ibaraki (Japan)

    2002-12-01

    Attention is focusing on hydrogen production from wastewater, not only because hydrogen is a clean energy but also because it can be a process for wastewater treatment. In this paper, the characteristics of biological hydrogen production as a process of wastewater treatment is discussed by a comparison with methane production. The hydrogen production from tofu wastewater by anoxygenic phototrophic bacteria and its potential for wastewater treatment are reported. The possibility of co-cultivation with heterotrophic anaerobic bacteria was also investigated. As a solution to overcome the repressive effect of NH{sub 4}{sup +} on hydrogen production by anoxygenic phototrophic bacteria, a study was done using glutamine auxotroph which was obtained by chemical mutagenesis. To confirm that the mutation had occurred in DNA molecular level, the glutamine synthetase gene was cloned and sequenced. (Author)

  6. Structural Changes of Water Molecules Upon the Reduction of Quinones in The Reaction Center from Rhodobactery Sphaeroides

    Institute of Scientific and Technical Information of China (English)

    T.Iwata; M.L.Paddock; M.Y.Okamura; H.Kandori

    2007-01-01

    1 Results The photosynthetic bacterial reaction center (RC) is a membrane protein complex.The RC is composed of three protein subunits and redox components such as bacteriochlorophylls, bacteriopheophytins,and quinones.The RC performs the photochemical electron transfer from the bacteriochlorophyll dimer through a series of electron donor and acceptor molecules to a secondary quinone,QB.QB accepts electrons from a primary quinone,QA,in two sequential electron transfer reactions.The second electron trans...

  7. Pleiotropic effects of puf interposon mutagenesis on carotenoid biosynthesis in Rubrivivax gelatinosus. A new gene organization in purple bacteria.

    Science.gov (United States)

    Ouchane, S; Picaud, M; Vernotte, C; Reiss-Husson, F; Astier, C

    1997-01-17

    Rubrivivax gelatinosus mutants affected in the carotenoid biosynthesis pathways were created by interposon mutagenesis within the puf operon. Genetic and biochemical analysis of several constructed mutants suggest that at least crtC is localized downstream of the puf operon and that it is cotranscribed with this operon. Sequence analysis confirmed the genetic data and showed the presence of crtD and crtC genes downstream of the puf operon, a localization different from that known for other purple bacteria. Inactivation of the crtD gene indicated that the two crt genes are cotranscribed and that they are involved not only in the hydroxyspheroidene biosynthesis pathway as in Rhodobacter sphaeroides and R. capsulatus, but also in the spirilloxanthin biosynthesis pathway. Carotenoid genes implicated in the spirilloxanthin biosynthesis pathway were thus identified for the first time. Furthermore, analysis of carotenoid synthesis in the mutants gave genetic evidence that crtD and crtC genes are cotranscribed with the puf operon using the oxygen-regulated puf promoter.

  8. A time-resolved iron-specific X-ray absorption experiment yields no evidence for an Fe2+ --> Fe3+ transition during QA- --> QB electron transfer in the photosynthetic reaction center.

    Science.gov (United States)

    Hermes, Sabine; Bremm, Oliver; Garczarek, Florian; Derrien, Valerie; Liebisch, Peter; Loja, Paola; Sebban, Pierre; Gerwert, Klaus; Haumann, Michael

    2006-01-17

    Previous time-resolved FTIR measurements suggested the involvement of an intermediary component in the electron transfer step Q(A)- --> Q(B) in the photosynthetic reaction center (RC) from Rhodobacter sphaeroides [Remy and Gerwert (2003) Nat. Struct. Biol. 10, 637]. By a kinetic X-ray absorption experiment at the Fe K-edge we investigated whether oxidation occurs at the ferric non-heme iron located between the two quinones. In isolated reaction centers with a high content of functional Q(B), at a time resolution of 30 micros and at room temperature, no evidence for transient oxidation of Fe was obtained. However, small X-ray transients occurred, in a similar micro- to millisecond time range as in the IR experiments, which may point to changes in the Fe ligand environment due to the charges on Q(A)- and Q(B)-. In addition, VIS measurements agree with the IR data and do not exclude an intermediate in the Q(A)- --> Q(B) transition.

  9. Proton transfer in ba(3) cytochrome c oxidase from Thermus thermophilus.

    Science.gov (United States)

    von Ballmoos, Christoph; Adelroth, Pia; Gennis, Robert B; Brzezinski, Peter

    2012-04-01

    The respiratory heme-copper oxidases catalyze reduction of O(2) to H(2)O, linking this process to transmembrane proton pumping. These oxidases have been classified according to the architecture, location and number of proton pathways. Most structural and functional studies to date have been performed on the A-class oxidases, which includes those that are found in the inner mitochondrial membrane and bacteria such as Rhodobacter sphaeroides and Paracoccus denitrificans (aa(3)-type oxidases in these bacteria). These oxidases pump protons with a stoichiometry of one proton per electron transferred to the catalytic site. The bacterial A-class oxidases use two proton pathways (denoted by letters D and K, respectively), for the transfer of protons to the catalytic site, and protons that are pumped across the membrane. The B-type oxidases such as, for example, the ba(3) oxidase from Thermus thermophilus, pump protons with a lower stoichiometry of 0.5 H(+)/electron and use only one proton pathway for the transfer of all protons. This pathway overlaps in space with the K pathway in the A class oxidases without showing any sequence homology though. Here, we review the functional properties of the A- and the B-class ba(3) oxidases with a focus on mechanisms of proton transfer and pumping. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Global analysis of photosynthesis transcriptional regulatory networks.

    Science.gov (United States)

    Imam, Saheed; Noguera, Daniel R; Donohue, Timothy J

    2014-12-01

    Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888), which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis.

  11. Final Technical Report for USDOE Grant No. DE-FG02-96ER14675 Supermolecular Photosynthetic Arrays: Construction, Characterization, Exploration and Utilization

    Energy Technology Data Exchange (ETDEWEB)

    Norris, James

    2009-12-13

    Biological processes provide paradigms for the development of solar energy devices of practical utility. In nature, the light harvesting -complexes (LHCs) are not chemically active. However, with unnatural chemical oxidation by potassium ferricyanide, cation free radicals of bacteriochlorophyll (BChl) can be formed in the light harvesting complex 1 (LH1) of Rhodobacter sphaeroides. Based on EPR studies, the site of the BChl{sup +} cations move rather freely about the LH1 complex as in a molecular wire. These molecular wires function in the frozen, solid state. This work seeks to understand better how nature controls electron transfer in some of its molecular wires. To investigate the nature of electron-hole transfer we have e.onducted both electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) experiments on oxidized LH1 complexes. Progress has been achieved in two main areas: EPR studies of the role of ferricyanide in the molecular wire nature of oxidized LH1; and ENDOR studies of oxidized LH1 at 80K.

  12. Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism.

    Science.gov (United States)

    Fuhrer, Tobias; Sauer, Uwe

    2009-04-01

    To sustain growth, the catabolic formation of the redox equivalent NADPH must be balanced with the anabolic demand. The mechanisms that ensure such network-wide balancing, however, are presently not understood. Based on 13C-detected intracellular fluxes, metabolite concentrations, and cofactor specificities for all relevant central metabolic enzymes, we have quantified catabolic NADPH production in Agrobacterium tumefaciens, Bacillus subtilis, Escherichia coli, Paracoccus versutus, Pseudomonas fluorescens, Rhodobacter sphaeroides, Sinorhizobium meliloti, and Zymomonas mobilis. For six species, the estimated NADPH production from glucose catabolism exceeded the requirements for biomass synthesis. Exceptions were P. fluorescens, with balanced rates, and E. coli, with insufficient catabolic production, in which about one-third of the NADPH is supplied via the membrane-bound transhydrogenase PntAB. P. versutus and B. subtilis were the only species that appear to rely on transhydrogenases for balancing NADPH overproduction during growth on glucose. In the other four species, the main but not exclusive redox-balancing mechanism appears to be the dual cofactor specificities of several catabolic enzymes and/or the existence of isoenzymes with distinct cofactor specificities, in particular glucose 6-phosphate dehydrogenase. An unexpected key finding for all species, except E. coli and B. subtilis, was the lack of cofactor specificity in the oxidative pentose phosphate pathway, which contrasts with the textbook view of the pentose phosphate pathway dehydrogenases as being NADP+ dependent.

  13. Solvation effect of bacteriochlorophyll excitons in light-harvesting complex LH2.

    Science.gov (United States)

    Urboniene, V; Vrublevskaja, O; Trinkunas, G; Gall, A; Robert, B; Valkunas, L

    2007-09-15

    We have characterized the influence of the protein environment on the spectral properties of the bacteriochlorophyll (Bchl) molecules of the peripheral light-harvesting (or LH2) complex from Rhodobacter sphaeroides. The spectral density functions of the pigments responsible for the 800 and 850 nm electronic transitions were determined from the temperature dependence of the Bchl absorption spectra in different environments (detergent micelles and native membranes). The spectral density function is virtually independent of the hydrophobic support that the protein experiences. The reorganization energy for the B850 Bchls is 220 cm(-1), which is almost twice that of the B800 Bchls, and its Huang-Rhys factor reaches 8.4. Around the transition point temperature, and at higher temperatures, both the static spectral inhomogeneity and the resonance interactions become temperature-dependent. The inhomogeneous distribution function of the transitions exhibits less temperature dependence when LH2 is embedded in membranes, suggesting that the lipid phase protects the protein. However, the temperature dependence of the fluorescence spectra of LH2 cannot be fitted using the same parameters determined from the analysis of the absorption spectra. Correct fitting requires the lowest exciton states to be additionally shifted to the red, suggesting the reorganization of the exciton spectrum.

  14. Architecture of the native photosynthetic apparatus of Phaeospirillum molischianum.

    Science.gov (United States)

    Gonçalves, Rui Pedro; Bernadac, Alain; Sturgis, James N; Scheuring, Simon

    2005-12-01

    The ubiquity and importance of photosynthetic organisms in nature has made the molecular mechanisms of photosynthesis a widely studied subject at both structural and functional levels. A current challenge is to understand the supramolecular assembly of the proteins involved in photosynthesis in native membranes. We have used atomic force microscopy to study the architecture of the photosynthetic apparatus and analyze the structure of single molecules in chromatophores of Phaeospirillum molischianum. Core complexes are formed by the reaction center enclosed by an elliptical light harvesting complex 1. LH2 are octameric rings, assembled either with cores or in hexagonally packed LH2 antenna domains. The symmetry mismatch caused by octameric LH2 packing in a hexagonal lattice, that could be avoided in a square lattice, suggests lipophobic effects rather than specific inter-molecular interactions drive protein organization. The core and LH2 complexes are organized to form a supramolecular assembly reminiscent to that found in Rhodospirillum photometricum, and very different from that observed in Rhodobacter sphaeroides, Rb. blasticus, and Blastochloris viridis.

  15. Evidence for high-pressure-induced rupture of hydrogen bonds in LH2 photosynthetic antenna pigment-protein complexes

    Energy Technology Data Exchange (ETDEWEB)

    Kangur, L; Leiger, K; Freiberg, A [Institute of Physics, University of Tartu, Riia 142, Tartu 51014 (Estonia)

    2008-07-15

    The bacteriochlorophyll a-containing LH2 light harvesting complex is an integral membrane protein that catalyzes the photosynthetic process in purple photosynthetic bacteria. The LH2 complexes from Rhodobacter sphaeroides show characteristic strong absorbance at 800 and 850 nm due to the bacteriochlorophyll a molecules confined in two separate areas of the protein. Using these cofactors as intrinsic probes to monitor changes in membrane protein structure, we investigate the response to high hydrostatic pressure up to 2.1 GPa of LH2 complexes embedded into natural membrane environment or extracted with detergent. We demonstrate that high pressure does induce significant alterations to the tertiary structure of the protein in proximity of the protein-bound bacteriochlorophyll a molecules, including breakage of the hydrogen bond they are involved in. The membrane-embedded complexes appear more resilient to damaging effects of the compression than the complexes extracted into detergent environment. This difference has tentatively been explained by more compact structure of the membrane-embedded complexes.

  16. The kinetic model for slow photoinduced electron transport in the reaction centers of purple bacteria

    Science.gov (United States)

    Serdenko, T. V.; Barabash, Y. M.; Knox, P. P.; Seifullina, N. Kh.

    2016-06-01

    The present work is related to the investigation of slow kinetics of electron transport in the reaction centers (RCs) of Rhodobacter sphaeroides. Experimental data on the absorption kinetics of aqueous solutions of reaction centers at different modes of photoexcitation are given. It is shown that the kinetics of oxidation and reduction of RCs are well described by the sum of three exponential functions. This allows to suggest a two-level kinetic model for electron transport in the RC as a system of four electron-conformational states which correspond to three balance differential equations combined with state equation. The solution of inverse problem made it possible to obtain the rate constant values in kinetic equations for different times and intensities of exciting light. Analysis of rate constant values in different modes of RC excitation allowed to suggest that two mechanisms of structural changes are involved in RC photo-oxidation. One mechanism leads to the increment of the rate of electron return, another one—to its drop. Structural changes were found out to occur in the RCs under incident light. After light was turned off, the reduction of RCs was determined by the second mechanism.

  17. Long term stabilization of reaction center protein photochemistry by carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Magyar, Melinda; Hajdu, Kata; Szabo, Tibor; Nagy, Laszlo [Department of Medical Physics and Informatics, University of Szeged, 6720 Szeged (Hungary); Hernadi, Klara [Department of Applied and Environmental Chemistry, University of Szeged, 6720 Szeged (Hungary); Dombi, Andras [Institute of Material Sciences and Engineering, University of Szeged, 6701 Szeged (Hungary); Horvath, Endre; Magrez, Arnaud; Forro, Laszlo [Institute of Physics of Complex Matter, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne (Switzerland)

    2011-11-15

    The long term stability and the redox interaction between single walled carbon nanotubes (SWNTs) and photosynthetic reaction center proteins (RCs) purified from purple bacterium Rhodobacter sphaeroides R-26 in the SWNT/RC complex has been investigated. The binding of SWNT to RC results in an accumulation of positive (the oxidized primary electron donor, P{sup +}) and negative (semiquinone forms, Q{sup -}{sub A} and Q{sup -}{sub B}, the reduced primary and secondary quinones, respectively) charges followed by slow reorganization of the protein structure after excitation. The photochemical activity of the SWNT/RC complexes remains stable for several weeks even in dried form. In the absence of SWNT the secondary quinone activity decays quickly as a function of time after drying the RC onto a glass surface. Polarography measurements substantiate the idea that there is an electronic interaction between the RCs and SWNTs after light excitation, which was suggested earlier by optical measurements. The special electronic properties of the SWNT/protein complexes open the possibility for several applications, e.g., in microelectronics, analytics, or energy conversion and storage. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  18. Quantitative affinity chromatographic studies of mitochondrial cytochrome c binding to bacterial photosynthetic reaction center, reconstituted in liposome membranes and immobilized by detergent dialysis and avidin--biotin binding.

    Science.gov (United States)

    Yang, Q; Liu, X Y; Hara, M; Lundahl, P; Miyake, J

    2000-04-10

    In order to study the affinity binding of c-type cytochromes to the photosynthetic reaction center (RC) by quantitative affinity chromatography (QAC), RC from Rhodobacter sphaeroides was reconstituted into liposomes composed of egg phosphatidylcholine (EPC) and 2 mol% of biotinyl phosphatidylethanolamine simultaneously as the liposomes were formed and immobilized in (strept)avidin-coupled gel beads by rotary detergent dialysis. The immobilized amount was up to 80 nmol of RC and 33 micromol of lipid/g of moist gel in streptavidin-coupled Sephacryl S-1000 gel. By QAC frontal runs, retardation of mitochondrial cyt c on immobilized RC liposome columns was demonstrated. The dissociation constant for the RC-cyt c interaction was determined to be 0.20-0.57 microM. QAC studies also allowed evaluation of the orientation of reconstituted RC in immobilized liposomes by comparison of the total amount of cyt c binding sites with the amount of available binding sites obtained by QAC. It seems that the RC proteoliposomes immobilized in Sephacryl S-1000 gel exposed the cyt c binding sites on the outer surface of the liposomes due to effects of the gel network pore size and the resulting liposomal size.

  19. Excited state dynamics in photosynthetic reaction center and light harvesting complex 1

    Science.gov (United States)

    Strümpfer, Johan; Schulten, Klaus

    2012-08-01

    Key to efficient harvesting of sunlight in photosynthesis is the first energy conversion process in which electronic excitation establishes a trans-membrane charge gradient. This conversion is accomplished by the photosynthetic reaction center (RC) that is, in case of the purple photosynthetic bacterium Rhodobacter sphaeroides studied here, surrounded by light harvesting complex 1 (LH1). The RC employs six pigment molecules to initiate the conversion: four bacteriochlorophylls and two bacteriopheophytins. The excited states of these pigments interact very strongly and are simultaneously influenced by the surrounding thermal protein environment. Likewise, LH1 employs 32 bacteriochlorophylls influenced in their excited state dynamics by strong interaction between the pigments and by interaction with the protein environment. Modeling the excited state dynamics in the RC as well as in LH1 requires theoretical methods, which account for both pigment-pigment interaction and pigment-environment interaction. In the present study we describe the excitation dynamics within a RC and excitation transfer between light harvesting complex 1 (LH1) and RC, employing the hierarchical equation of motion method. For this purpose a set of model parameters that reproduce RC as well as LH1 spectra and observed oscillatory excitation dynamics in the RC is suggested. We find that the environment has a significant effect on LH1-RC excitation transfer and that excitation transfers incoherently between LH1 and RC.

  20. Efficiency of light harvesting in a photosynthetic bacterium adapted to different levels of light.

    Science.gov (United States)

    Timpmann, Kõu; Chenchiliyan, Manoop; Jalviste, Erko; Timney, John A; Hunter, C Neil; Freiberg, Arvi

    2014-10-01

    In this study, we use the photosynthetic purple bacterium Rhodobacter sphaeroides to find out how the acclimation of photosynthetic apparatus to growth conditions influences the rates of energy migration toward the reaction center traps and the efficiency of charge separation at the reaction centers. To answer these questions we measured the spectral and picosecond kinetic fluorescence responses as a function of excitation intensity in membranes prepared from cells grown under different illumination conditions. A kinetic model analysis yielded the microscopic rate constants that characterize the energy transfer and trapping inside the photosynthetic unit as well as the dependence of exciton trapping efficiency on the ratio of the peripheral LH2 and core LH1 antenna complexes, and on the wavelength of the excitation light. A high quantum efficiency of trapping over 80% was observed in most cases, which decreased toward shorter excitation wavelengths within the near infrared absorption band. At a fixed excitation wavelength the efficiency declines with the LH2/LH1 ratio. From the perspective of the ecological habitat of the bacteria the higher population of peripheral antenna facilitates growth under dim light even though the energy trapping is slower in low light adapted membranes. The similar values for the trapping efficiencies in all samples imply a robust photosynthetic apparatus that functions effectively at a variety of light intensities. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. The PufX quinone channel enables the light-harvesting 1 antenna to bind more carotenoids for light collection and photoprotection.

    Science.gov (United States)

    Olsen, John D; Martin, Elizabeth C; Hunter, C Neil

    2017-02-01

    Photosynthesis in some phototrophic bacteria requires the PufX component of the reaction centre-light-harvesting 1-PufX (RC-LH1-PufX) complex, which creates a pore for quinone/quinol (Q/QH2 ) exchange across the LH1 barrier surrounding the RC. However, photosynthetic bacteria such as Thermochromatium (T.) tepidum do not require PufX because there are fewer carotenoid binding sites, which creates multiple pores in the LH1 ring for Q/QH2 exchange. We show that an αTrp-24 →Phe alteration of the Rhodobacter (Rba.) sphaeroides LH1 antenna impairs carotenoid binding and allows photosynthetic growth in the absence of PufX. We propose that acquisition of PufX and confining Q/QH2 traffic to a pore adjacent to the RC QB site is an evolutionary upgrade that allows increased LH1 carotenoid content for enhanced light absorption and photoprotection. © 2017 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

  2. Overall energy conversion efficiency of a photosynthetic vesicle.

    Science.gov (United States)

    Sener, Melih; Strumpfer, Johan; Singharoy, Abhishek; Hunter, C Neil; Schulten, Klaus

    2016-08-26

    The chromatophore of purple bacteria is an intracellular spherical vesicle that exists in numerous copies in the cell and that efficiently converts sunlight into ATP synthesis, operating typically under low light conditions. Building on an atomic-level structural model of a low-light-adapted chromatophore vesicle from Rhodobacter sphaeroides, we investigate the cooperation between more than a hundred protein complexes in the vesicle. The steady-state ATP production rate as a function of incident light intensity is determined after identifying quinol turnover at the cytochrome bc1 complex (cytb⁢c1) as rate limiting and assuming that the quinone/quinol pool of about 900 molecules acts in a quasi-stationary state. For an illumination condition equivalent to 1% of full sunlight, the vesicle exhibits an ATP production rate of 82 ATP molecules/s. The energy conversion efficiency of ATP synthesis at illuminations corresponding to 1%-5% of full sunlight is calculated to be 0.12-0.04, respectively. The vesicle stoichiometry, evolutionarily adapted to the low light intensities in the habitat of purple bacteria, is suboptimal for steady-state ATP turnover for the benefit of protection against over-illumination.

  3. Ionic liquids effects on the permeability of photosynthetic membranes probed by the electrochromic shift of endogenous carotenoids.

    Science.gov (United States)

    Malferrari, Marco; Malferrari, Danilo; Francia, Francesco; Galletti, Paola; Tagliavini, Emilio; Venturoli, Giovanni

    2015-11-01

    Ionic liquids (ILs) are promising materials exploited as solvents and media in many innovative applications, some already used at the industrial scale. The chemical structure and physicochemical properties of ILs can differ significantly according to the specific applications for which they have been synthesized. As a consequence, their interaction with biological entities and toxicity can vary substantially. To select highly effective and minimally harmful ILs, these properties need to be investigated. Here we use the so called chromatophores--protein-phospholipid membrane vesicles obtained from the photosynthetic bacterium Rhodobacter sphaeroides--to assess the effects of imidazolinium and pyrrolidinium ILs, with chloride or dicyanamide as counter anions, on the ionic permeability of a native biological membrane. The extent and modalities by which these ILs affect the ionic conductivity can be studied in chromatophores by analyzing the electrochromic response of endogenous carotenoids, acting as an intramembrane voltmeter at the molecular level. We show that chromatophores represent an in vitro experimental model suitable to probe permeability changes induced in cell membranes by ILs differing in chemical nature, degree of oxygenation of the cationic moiety and counter anion.

  4. Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle.

    Science.gov (United States)

    Sener, Melih K; Olsen, John D; Hunter, C Neil; Schulten, Klaus

    2007-10-02

    The photosynthetic unit (PSU) of purple photosynthetic bacteria consists of a network of bacteriochlorophyll-protein complexes that absorb solar energy for eventual conversion to ATP. Because of its remarkable simplicity, the PSU can serve as a prototype for studies of cellular organelles. In the purple bacterium Rhodobacter sphaeroides the PSU forms spherical invaginations of the inner membrane, approximately 70 nm in diameter, composed mostly of light-harvesting complexes, LH1 and LH2, and reaction centers (RCs). Atomic force microscopy studies of the intracytoplasmic membrane have revealed the overall spatial organization of the PSU. In the present study these atomic force microscopy data were used to construct three-dimensional models of an entire membrane vesicle at the atomic level by using the known structure of the LH2 complex and a structural model of the dimeric RC-LH1 complex. Two models depict vesicles consisting of 9 or 18 dimeric RC-LH1 complexes and 144 or 101 LH2 complexes, representing a total of 3,879 or 4,464 bacteriochlorophylls, respectively. The in silico reconstructions permit a detailed description of light absorption and electronic excitation migration, including computation of a 50-ps excitation lifetime and a 95% quantum efficiency for one of the model membranes, and demonstration of excitation sharing within the closely packed RC-LH1 dimer arrays.

  5. Effects of starch loading rate on performance of combined fed-batch fermentation of ground wheat for bio-hydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Ozmihci, Serpil; Kargi, Fikret [Department of Environmental Engineering, Dokuz Eylul University, 35160 Buca, Izmir (Turkey)

    2010-02-15

    Ground wheat powder solution (10 g L{sup -1}) was subjected to combined dark and light fermentations for bio-hydrogen production by fed-batch operation. A mixture of heat treated anaerobic sludge (AN) and Rhodobacter sphaeroides-NRRL (RS-NRRL) were used as the mixed culture of dark and light fermentation bacteria with an initial dark/light biomass ratio of 1/2. Effects of wheat starch loading rate on the rate and yield of bio-hydrogen formation were investigated. The highest cumulative hydrogen formation (CHF = 3460 ml), hydrogen yield (201 ml H{sub 2} g{sup -1} starch) and formation rate (18.1 ml h{sup -1}) were obtained with a starch loading rate of 80.4 mg S h{sup -1}. Complete starch hydrolysis and glucose fermentation were achieved within 96 h of fed-batch operation producing volatile fatty acids (VFA) and H{sub 2}. Fermentation of VFAs by photo-fermentation for bio-hydrogen production was most effective at starch loading rate of 80.4 mg S h{sup -1}. Hydrogen formation by combined fermentation took place by a fast dark fermentation followed by a rather slow light fermentation after a lag period. (author)

  6. Construction and validation of an atomic model for bacterial TSPO from electron microscopy density, evolutionary constraints, and biochemical and biophysical data.

    Science.gov (United States)

    Hinsen, Konrad; Vaitinadapoule, Aurore; Ostuni, Mariano A; Etchebest, Catherine; Lacapere, Jean-Jacques

    2015-02-01

    The 18 kDa protein TSPO is a highly conserved transmembrane protein found in bacteria, yeast, animals and plants. TSPO is involved in a wide range of physiological functions, among which the transport of several molecules. The atomic structure of monomeric ligand-bound mouse TSPO in detergent has been published recently. A previously published low-resolution structure of Rhodobacter sphaeroides TSPO, obtained from tubular crystals with lipids and observed in cryo-electron microscopy, revealed an oligomeric structure without any ligand. We analyze this electron microscopy density in view of available biochemical and biophysical data, building a matching atomic model for the monomer and then the entire crystal. We compare its intra- and inter-molecular contacts with those predicted by amino acid covariation in TSPO proteins from evolutionary sequence analysis. The arrangement of the five transmembrane helices in a monomer of our model is different from that observed for the mouse TSPO. We analyze possible ligand binding sites for protoporphyrin, for the high-affinity ligand PK 11195, and for cholesterol in TSPO monomers and/or oligomers, and we discuss possible functional implications.

  7. Culture Studies of Nitrogen and Oxygen Isotope Effects Associated with Nitrate Assimilation and Denitrification

    Science.gov (United States)

    Sigman, D. M.; Granger, J.; Lehmann, M. F.; Difiore, P. J.; Tortell, P. D.

    2007-12-01

    The isotope effects of nitrate-consuming reactions such as nitrate assimilation and denitrification are potential indicators of the physiological state of the organisms carrying out these reactions. Moreover, an understanding of these isotope effects is needed to use the stable isotopes to investigate the fluxes associated with these reactions in modern and ancient environments. We have used batch cultures to investigate the nitrogen (N) and oxygen (O) isotope effects of (1) nitrate assimilation by eukaryotic and prokaryotic algae and by heterotrophic bacteria, and (2) nitrate reduction by denitrifying bacteria. We observe intra- and inter-specific variation in isotope effect amplitudes and, in the case of denitrifiers, indications of isotope effect decreases during individual nitrate drawdown experiments. However, the measured N and O isotope effect ratio is close to 1 for all studied organisms, with the exception of an unusual denitrifier (Rhodobacter sphaeroides) that possesses only periplasmic (non-respiratory) nitrate reductase. This observation and other findings are consistent with nitrate reductase being the predominant source of isotope fractionation and with most isotope effect amplitude variability arising from variable degrees to which nitrate imported into the cell is reduced versus effluxed back into the environment; the more efflux, the more complete the expression of the fractionation imparted by nitrate reduction. If this is the case, then isotope effect amplitudes in the field should be related to physiological conditions in the environment, a prediction that, we argue, is supported by recent studies of (1) nitrate assimilation in the polar ocean and (2) denitrification in sediment porewaters.

  8. Prokaryotic phototaxis.

    Science.gov (United States)

    Hoff, Wouter D; van der Horst, Michael A; Nudel, Clara B; Hellingwerf, Klaas J

    2009-01-01

    Microorganisms have various mechanisms at their disposal to react to (changes in) their ambient light climate (i.e., intensity, color, direction, and degree of polarization). Of these, one of the best studied mechanisms is the process of phototaxis. This process can be described as a behavioral migration-response of an organism toward a change in illumination regime. In this chapter we discuss three of these migration responses, based on swimming, swarming, and twitching motility, respectively. Swimming motility has been studied using a wide range of techniques, usually microscopy based. We present a detailed description of the assays used to study phototaxis in liquid cultures of the phototrophic organisms Halobacterium salinarum, Halorhodospira halophila, and Rhodobacter sphaeroides and briefly describe the molecular basis of these responses. Swarming and twitching motility are processes taking place at the interface between a solid phase and a liquid or gas phase. Although assays to study these processes are relatively straightforward, they are accompanied by technical complications, which we describe. Furthermore, we discuss the molecular processes underlying these forms of motility in Rhodocista centenaria and Synechocystis PCC6803. Recently, it has become clear that also chemotrophic organisms contain photoreceptor proteins that allow them to respond to their ambient light climate. Surprisingly, light-modulated motility responses can also be observed in the chemotrophic organisms Escherichia coli and Acinetobacter calcoaceticus. In the light-modulated surface migration not only "che-like" signal transduction reactions may play a role, but in addition processes as modulation of gene expression and even intermediary metabolism.

  9. Kinetic study approach of remazol black-B use for the development of two-stage anoxic-oxic reactor for decolorization/biodegradation of azo dyes by activated bacterial consortium.

    Science.gov (United States)

    Dafale, Nishant; Wate, Satish; Meshram, Sudhir; Nandy, Tapas

    2008-11-30

    The laboratory-isolated strains Pseudomonas aeruginosa, Rhodobacter sphaeroides, Proteus mirabilis, Bacillus circulance, NAD 1 and NAD 6 were observed to be predominant in the bacterial consortium responsible for effective decolorization of the azo dyes. The kinetic characteristics of azo dye decolorization by bacterial consortium were determined quantitatively using reactive vinyl sulfonated diazo dye, remazol black-B (RB-B) as a model substrate. Effects of substrate (RB-B) concentration as well as different substrates (azo dyes), environmental parameters (temperature and pH), glucose and other electron donor/co-substrate on the rate of decolorization were investigated to reveal the key factor that determines the performance of dye decolorization. The activation energy (E(a)) and frequency factor (K(0)) based on the Arrhenius equation was calculated as 11.67 kcal mol(-1) and 1.57 x 10(7)mg lg MLSS(-1)h(-1), respectively. The Double-reciprocal or Lineweaver-Burk plot was used to evaluate V(max), 15.97 h(-1) and K(m), 85.66 mg l(-1). The two-stage anoxic-oxic reactor system has proved to be successful in achieving significant decolorization and degradation of azo dyes by specific developed bacterial consortium with a removal of 84% color and 80% COD for real textile effluents vis-à-vis >or=90% color and COD removal for synthetic dye solution.

  10. Electrostatics of the photosynthetic bacterial reaction center. Protonation of Glu L 212 and Asp L 213 - A new method of calculation.

    Science.gov (United States)

    Ptushenko, Vasily V; Cherepanov, Dmitry A; Krishtalik, Lev I

    2015-12-01

    Continuum electrostatic calculation of the transfer energies of anions from water into aprotic solvents gives the figures erroneous by order of magnitude. This is due to the hydrogen bond disruption that suggests the necessity to reconsider the traditional approach of the purely electrostatic calculation of the transfer energy from water into protein. In this paper, the method combining the experimental estimates of the transfer energies from water into aprotic solvent and the electrostatic calculation of the transfer energies from aprotic solvent into protein is proposed. Hydrogen bonds between aprotic solvent and solute are taken into account by introducing an imaginary aprotic medium incapable to form hydrogen bonds with the solute. Besides, a new treatment of the heterogeneous intraprotein dielectric permittivity based on the microscopic protein structure and electrometric measurements is elaborated. The method accounts semi-quantitatively for the electrostatic effect of diverse charged amino acid substitutions in the donor and acceptor parts of the photosynthetic bacterial reaction center from Rhodobacter sphaeroides. Analysis of the volatile secondary acceptor site QB revealed that in the conformation with a minimal distance between quinone QB and Glu L 212 the proton uptake upon the reduction of QB is prompted by Glu L 212 in alkaline and by Asp L 213 in slightly acidic regions. This agrees with the pH dependences of protonation degrees and the proton uptake. The method of pK calculation was applied successfully also for dissociation of Asp 26 in bacterial thioredoxin.

  11. RpoH2 sigma factor controls the photooxidative stress response in a non-photosynthetic rhizobacterium, Azospirillum brasilense Sp7.

    Science.gov (United States)

    Kumar, Santosh; Rai, Ashutosh Kumar; Mishra, Mukti Nath; Shukla, Mansi; Singh, Pradhyumna Kumar; Tripathi, Anil Kumar

    2012-12-01

    Bacteria belonging to the Alphaproteobacteria normally harbour multiple copies of the heat shock sigma factor (known as σ(32), σ(H) or RpoH). Azospirillum brasilense, a non-photosynthetic rhizobacterium, harbours five copies of rpoH genes, one of which is an rpoH2 homologue. The genes around the rpoH2 locus in A. brasilense show synteny with that found in rhizobia. The rpoH2 of A. brasilense was able to complement the temperature-sensitive phenotype of the Escherichia coli rpoH mutant. Inactivation of rpoH2 in A. brasilense results in increased sensitivity to methylene blue and to triphenyl tetrazolium chloride (TTC). Exposure of A. brasilense to TTC and the singlet oxygen-generating agent methylene blue induced several-fold higher expression of rpoH2. Comparison of the proteome of A. brasilense with its rpoH2 deletion mutant and with an A. brasilense strain overexpressing rpoH2 revealed chaperone GroEL, elongation factors (Ef-Tu and EF-G), peptidyl prolyl isomerase, and peptide methionine sulfoxide reductase as the major proteins whose expression was controlled by RpoH2. Here, we show that the RpoH2 sigma factor-controlled photooxidative stress response in A. brasilense is similar to that in the photosynthetic bacterium Rhodobacter sphaeroides, but that RpoH2 is not involved in the detoxification of methylglyoxal in A. brasilense.

  12. Bacterial bioremediation of selenium oxyanions using a dynamic flow bioreactor and headspace analysis

    Energy Technology Data Exchange (ETDEWEB)

    McCarty, S.L.; Chasteen, T.G. [Sam Houston State Univ., Huntsville, TX (United States). Dept. of Chemistry; Stalder, V.; Bachofen, R. [Univ. of Zuerich (Switzerland). Inst. of Plant Biology

    1995-12-31

    The volatile products of the biological reduction and methylation of selenium`s most common oxyanions, selenate and selenite, were determined using capillary gas chromatography and fluorine-induced chemiluminescence detection. Dimethyl selenide and dimethyl diselenide were detected in the headspace above cultures of bacteria resistant to this metalloid using static and dynamic headspace sampling techniques. Fluorine-induced chemiluminescence detection was applied to determine the relative concentrations of the organosulfur and organoselenium species released over many days of culture growth at a controlled temperature and purge rate. A selenium-resistant bacterium, Pseudomonas fluorescens K27, and a phototrophic bacterium Rhodobacter sphaeroides 2.4.1 were exposed to SeO{sub 4}{sup 2{minus}}, and the cultures` headspaces were examined over a period of several days for volatile selenium-containing products. The results show that the relative production of the volatile species over time depicts a pattern generally independent of the growth phase in the case of the phototrophic bacterium; the concentrations of metabolic dimethyl sulfide and dimethyl selenide determined in static headspace were highest after the microbe had been in stationary phase for 4 days.

  13. The role of pH control on biohydrogen production by single stage hybrid dark- and photo-fermentation.

    Science.gov (United States)

    Zagrodnik, R; Laniecki, M

    2015-10-01

    The role of pH control on biohydrogen production by co-culture of dark-fermentative Clostridium acetobutylicum and photofermentative Rhodobacter sphaeroides was studied. Single stage dark fermentation, photofermentation and hybrid co-culture systems were studied at different values of controlled and uncontrolled pH. Increasing pH during dark fermentation resulted in lower hydrogen production rate (HPR) and longer lag time for both controlled and uncontrolled conditions. However, it only slightly affected cumulative H2 volume. Results have shown that pH control at pH 7.5 increased photofermentative hydrogen production from 0.966 to 2.502 L H2/L(medium) when compared to uncontrolled process. Fixed pH value has proven to be an important control strategy also for the hybrid process and resulted in obtaining balanced co-culture of dark and photofermentative bacteria. Control of pH at 7.0 was found optimum for bacteria cooperation in the co-culture what resulted in obtaining 2.533 L H2/L(medium) and H2 yield of 6.22 mol H2/mol glucose.

  14. Overall energy conversion efficiency of a photosynthetic vesicle

    Science.gov (United States)

    Sener, Melih; Strumpfer, Johan; Singharoy, Abhishek; Hunter, C Neil; Schulten, Klaus

    2016-01-01

    The chromatophore of purple bacteria is an intracellular spherical vesicle that exists in numerous copies in the cell and that efficiently converts sunlight into ATP synthesis, operating typically under low light conditions. Building on an atomic-level structural model of a low-light-adapted chromatophore vesicle from Rhodobacter sphaeroides, we investigate the cooperation between more than a hundred protein complexes in the vesicle. The steady-state ATP production rate as a function of incident light intensity is determined after identifying quinol turnover at the cytochrome bc1 complex (cytb⁢c1) as rate limiting and assuming that the quinone/quinol pool of about 900 molecules acts in a quasi-stationary state. For an illumination condition equivalent to 1% of full sunlight, the vesicle exhibits an ATP production rate of 82 ATP molecules/s. The energy conversion efficiency of ATP synthesis at illuminations corresponding to 1%–5% of full sunlight is calculated to be 0.12–0.04, respectively. The vesicle stoichiometry, evolutionarily adapted to the low light intensities in the habitat of purple bacteria, is suboptimal for steady-state ATP turnover for the benefit of protection against over-illumination. DOI: http://dx.doi.org/10.7554/eLife.09541.001 PMID:27564854

  15. Analysis of the Electronic Structure of the Special Pair of a Bacterial Photosynthetic Reaction Center by (13) C Photochemically Induced Dynamic Nuclear Polarization Magic-Angle Spinning NMR Using a Double-Quantum Axis.

    Science.gov (United States)

    Najdanova, Marija; Gräsing, Daniel; Alia, A; Matysik, Jörg

    2017-07-26

    The origin of the functional symmetry break in bacterial photosynthesis challenges since several decades. Although structurally very similar, the two branches of cofactors in the reaction center (RC) protein complex act very differently. Upon photochemical excitation, an electron is transported along one branch, while the other remains inactive. Photochemically induced dynamic nuclear polarization (photo-CIDNP) magic-angle spinning (MAS) (13) C NMR revealed that the two bacteriochlorophyll cofactors forming the "Special Pair" donor dimer are already well distinguished in the electronic ground state. These previous studies are relying solely on (13) C-(13) C correlation experiments as radio-frequency-driven recoupling (RFDR) and dipolar-assisted rotational resonance (DARR). Obviously, the chemical-shift assignment is difficult in a dimer of tetrapyrrole macrocycles, having eight pyrrole rings of similar chemical shifts. To overcome this problem, an INADEQUATE type of experiment using a POST C7 symmetry-based approach is applied to selectively isotope-labeled bacterial RC of Rhodobacter (R.) sphaeroides wild type (WT). We, therefore, were able to distinguish unresolved sites of the macromolecular dimer. The obtained chemical-shift pattern is in-line with a concentric assembly of negative charge within the common center of the Special Pair supermolecule in the electronic ground state. © 2017 The American Society of Photobiology.

  16. A molecular genetic analysis of carotenoid biosynthesis and the effects of carotenoid mutations on other photosynthetic genes in Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, G.A.

    1989-04-01

    The nine known R. capsulatus carotenoid genes are contained within the 46 kilobase (kb) photosynthesis gene cluster. An 11 kb subcluster containing eight of these genes has been cloned and its nucleotide sequence determined. A new gene, crtK, has been located in the middle of the subcluster. The carotenoid gene cluster contains sequences homologous to Escherichia coli ..omega../sup 70/ promoters, rho-independent transcription terminators, and prokaryotic transcriptional factor binding sites. The phenotypes and genotypes of ten transposon Tn5.7 insertion mutations within the carotenoid gene cluster have been analyzed, by characterization of the carotenoids accumulated and high resolution mapping of the Tn5.7 insertions. The enzymatic blockages in previously uncharacterized early carotenoid mutants have been determined using a new in vitro synthesis system, suggesting specific roles for the CrtB and CrtE gene products. The expression of six of the eight carotenoid genes in the cluster is induced upon the shift from dark chemoheterotrophic to anaerobic photosynthetic growth. The magnitude of the induction is equivalent to that of genes encoding structural photosynthesis polypeptides, although the carotenoid genes are induced earlier after the growth shift. Different means of regulating photosynthesis genes in R. capsulatus are discussed, and a rationale for the temporal pattern of expression of the carotenoid genes during photosynthetic adaptation is presented. Comparison of the deduced amino acid sequences of the two dehydrogenases of the R. capsulatus carotenoid biosynthesis pathway reveals two regions of strong similarity. The effect of carotenoid mutations on the photosynthetic phenotype has been studied by examining growth rates, pigments, pigment-protein complexes and gene expression for a complete set of carotenoid mutants. 161 refs.

  17. Photo-fermentational hydrogen production of Rhodobacter sp. KKU-PS1 isolated from an UASB reactor

    Directory of Open Access Journals (Sweden)

    Thitirut Assawamongkholsiri

    2015-05-01

    Conclusions: KKU-PS1 can produce hydrogen from at least 8 types of organic acids. By optimizing pH and temperature, a maximal hydrogen production by this strain was obtained. Additionally, by optimizing the light intensity, Rm was increased by approximately two fold and the lag phase of hydrogen production was shortened.

  18. Mutations That Alter the Bacterial Cell Envelope Increase Lipid Production.

    Science.gov (United States)

    Lemmer, Kimberly C; Zhang, Weiping; Langer, Samantha J; Dohnalkova, Alice C; Hu, Dehong; Lemke, Rachelle A; Piotrowski, Jeff S; Orr, Galya; Noguera, Daniel R; Donohue, Timothy J

    2017-05-23

    Lipids from microbes offer a promising source of renewable alternatives to petroleum-derived compounds. In particular, oleaginous microbes are of interest because they accumulate a large fraction of their biomass as lipids. In this study, we analyzed genetic changes that alter lipid accumulation in Rhodobacter sphaeroides By screening an R. sphaeroides Tn5 mutant library for insertions that increased fatty acid content, we identified 10 high-lipid (HL) mutants for further characterization. These HL mutants exhibited increased sensitivity to drugs that target the bacterial cell envelope and changes in shape, and some had the ability to secrete lipids, with two HL mutants accumulating ~60% of their total lipids extracellularly. When one of the highest-lipid-secreting strains was grown in a fed-batch bioreactor, its lipid content was comparable to that of oleaginous microbes, with the majority of the lipids secreted into the medium. Based on the properties of these HL mutants, we conclude that alterations of the cell envelope are a previously unreported approach to increase microbial lipid production. We also propose that this approach may be combined with knowledge about biosynthetic pathways, in this or other microbes, to increase production of lipids and other chemicals.IMPORTANCE This paper reports on experiments to understand how to increase microbial lipid production. Microbial lipids are often cited as one renewable replacement for petroleum-based fuels and chemicals, but strategies to increase the yield of these compounds are needed to achieve this goal. While lipid biosynthesis is often well understood, increasing yields of these compounds to industrially relevant levels is a challenge, especially since genetic, synthetic biology, or engineering approaches are not feasible in many microbes. We show that altering the bacterial cell envelope can be used to increase microbial lipid production. We also find that the utility of some of these alterations can be

  19. Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria

    Directory of Open Access Journals (Sweden)

    Grammel Hartmut

    2011-09-01

    Full Text Available Abstract Background Purple nonsulfur bacteria (PNSB are facultative photosynthetic bacteria and exhibit an extremely versatile metabolism. A central focus of research on PNSB dealt with the elucidation of mechanisms by which they manage to balance cellular redox under diverse conditions, in particular under photoheterotrophic growth. Results Given the complexity of the central metabolism of PNSB, metabolic modeling becomes crucial for an integrated analysis of the accumulated biological knowledge. We reconstructed a stoichiometric model capturing the central metabolism of three important representatives of PNSB (Rhodospirillum rubrum, Rhodobacter sphaeroides and Rhodopseudomonas palustris. Using flux variability analysis, the model reveals key metabolic constraints related to redox homeostasis in these bacteria. With the help of the model we can (i give quantitative explanations for non-intuitive, partially species-specific phenomena of photoheterotrophic growth of PNSB, (ii reproduce various quantitative experimental data, and (iii formulate several new hypotheses. For example, model analysis of photoheterotrophic growth reveals that - despite a large number of utilizable catabolic pathways - substrate-specific biomass and CO2 yields are fixed constraints, irrespective of the assumption of optimal growth. Furthermore, our model explains quantitatively why a CO2 fixing pathway such as the Calvin cycle is required by PNSB for many substrates (even if CO2 is released. We also analyze the role of other pathways potentially involved in redox metabolism and how they affect quantitatively the required capacity of the Calvin cycle. Our model also enables us to discriminate between different acetate assimilation pathways that were proposed recently for R. sphaeroides and R. rubrum, both lacking the isocitrate lyase. Finally, we demonstrate the value of the metabolic model also for potential biotechnological applications: we examine the theoretical

  20. Mutations That Alter the Bacterial Cell Envelope Increase Lipid Production

    Energy Technology Data Exchange (ETDEWEB)

    Lemmer, Kimberly C.; Zhang, Weiping; Langer, Samantha J.; Dohnalkova, Alice C.; Hu, Dehong; Lemke, Rachelle A.; Piotrowski, Jeff S.; Orr, Galya; Noguera, Daniel R.; Donohue, Timothy J.; Ruby, Edward G.

    2017-05-23

    ABSTRACT

    Lipids from microbes offer a promising source of renewable alternatives to petroleum-derived compounds. In particular, oleaginous microbes are of interest because they accumulate a large fraction of their biomass as lipids. In this study, we analyzed genetic changes that alter lipid accumulation inRhodobacter sphaeroides. By screening anR. sphaeroidesTn5mutant library for insertions that increased fatty acid content, we identified 10 high-lipid (HL) mutants for further characterization. These HL mutants exhibited increased sensitivity to drugs that target the bacterial cell envelope and changes in shape, and some had the ability to secrete lipids, with two HL mutants accumulating ~60% of their total lipids extracellularly. When one of the highest-lipid-secreting strains was grown in a fed-batch bioreactor, its lipid content was comparable to that of oleaginous microbes, with the majority of the lipids secreted into the medium. Based on the properties of these HL mutants, we conclude that alterations of the cell envelope are a previously unreported approach to increase microbial lipid production. We also propose that this approach may be combined with knowledge about biosynthetic pathways, in this or other microbes, to increase production of lipids and other chemicals.

    IMPORTANCEThis paper reports on experiments to understand how to increase microbial lipid production. Microbial lipids are often cited as one renewable replacement for petroleum-based fuels and chemicals, but strategies to increase the yield of these compounds are needed to achieve this goal. While lipid biosynthesis is often well understood, increasing yields of these compounds to industrially relevant levels is a challenge, especially since genetic, synthetic biology, or engineering approaches are not feasible in many microbes. We show that altering the bacterial cell envelope can be used to increase

  1. Study on the prescription simplification of the compound Danshen transformed by the mixed photosynthetic bacteria%简化混合光合细菌转化复方丹参制剂处方

    Institute of Scientific and Technical Information of China (English)

    秦娟; 杨飞; 赵建滨; 杨官娥; 王慧敏; 张肇铭

    2011-01-01

    目的:研究简化混合光合细菌转化复方丹参制剂(Ⅳ)处方.方法:用高脂饲料建立高脂血症大鼠模型,以血脂康为阳性对照,比较丹参提取液(Ⅰ)、球形红细菌转化丹参制剂(Ⅱ)、球形红细菌(Ⅲ)及Ⅳ血脂、抗氧化能力和血液流变学指标.结果:Ⅰ、Ⅱ、Ⅳ组能显著降低高脂血症大鼠血清总胆固醇、甘油三脂、低密度脂蛋白水平( P<0.01,P<0.05),Ⅱ、Ⅲ组能显著提高高密度脂蛋白水平(P<0.05);Ⅱ、Ⅲ、Ⅳ能显著提高高脂血症大鼠谷胱甘肽过氧化物酶活力(P<0.01),Ⅰ-Ⅲ组能显著提高超氧化物歧化酶活力(P<0.01),Ⅰ、Ⅱ、Ⅳ组能显著降低丙二醛水平( P<0.01,P<0.05);Ⅰ-Ⅲ组能显著降低不同切变率下全血黏度(P<0.01),Ⅱ-Ⅳ组能有效降低血浆黏度(P<0.01),Ⅰ-Ⅳ组能有效降低红细胞压积(P<0.01).结论:Ⅱ综合降脂作用优于Ⅰ、Ⅲ、Ⅳ,可以作为混合光合细菌转化复方丹参制剂(Ⅳ)的简化处方.%Objective: To simplify the preparation prescription of the compound Danshen transformed by the mixed photosynthetic bacteria. Method: High-fat rat model was set up by feeding the high fat fodder. Xuezhikang as positive control, to compare the blood lipids, antioxidant capacity and hemorheology of Danshen extract liquid (I), Danshen transformed by Rhodobacter sphaeroides preparation (II), Rhodobacter sphaeroides culture solution (DI) and the compound Danshen transformed by the mixed photosynthetic bacteria preparation (IV) between them. Result: I, II, IV could significantly reduce the serum TC, TG, LDL-C levels (/><0.01), I-IV could significantly reduce the hematocrit (P<0.01). Conclusion: Comprehensive lowering lipids efficiency of II was superior to the other I, III, IV. II could be used as the simplified preparation of the IV.

  2. Bacterial ortholog of mammalian translocator protein (TSPO with virulence regulating activity.

    Directory of Open Access Journals (Sweden)

    Annelise Chapalain

    Full Text Available The translocator protein (TSPO, previously designated as peripheral-type benzodiazepine receptor, is a protein mainly located in the outer mitochondrial membrane of eukaryotic cells. TSPO is implicated in major physiological functions and functionally associated with other proteins such as the voltage-dependent anionic channel, also designated as mitochondrial porin. Surprisingly, a TSPO-related protein was identified in the photosynthetic bacterium Rhodobacter sphaeroides but it was initially considered as a relict of evolution. In the present study we cloned a tspO gene in Pseudomonas fluorescens MF37, a non-photosynthetic eubacterium and we used bioinformatics tools to identify TSPO in the genome of 97 other bacteria. P. fluorescens TSPO was recognized by antibodies against mouse protein and by PK 11195, an artificial ligand of mitochondrial TSPO. As in eukaryotes, bacterial TSPO appears functionally organized as a dimer and the apparent Kd for PK 11195 is in the same range than for its eukaryotic counterpart. When P. fluorescens MF37 was treated with PK 11195 (10(-5 M adhesion to living or artificial surfaces and biofilm formation activity were increased. Conversely, the apoptotic potential of bacteria on eukaryotic cells was significantly reduced. This effect of PK11195 was abolished in a mutant of P. fluorescens MF37 deficient for its major outer membrane porin, OprF. The present results demonstrate the existence of a bacterial TSPO that shares common structural and functional characteristics with its mammalian counterpart. This protein, apparently involved in adhesion and virulence, reveals the existence of a possible new inter kingdom signalling system and suggests that the human microbiome should be involuntarily exposed to the evolutionary pressure of benzodiazepines and related molecules. This discovery also represents a promising opportunity for the development of alternative antibacterial strategies.

  3. Metabolic engineering of the Stevia rebaudiana ent-kaurene biosynthetic pathway in recombinant Escherichia coli.

    Science.gov (United States)

    Kong, Min Kyung; Kang, Hyun-Jun; Kim, Jin Ho; Oh, Soon Hwan; Lee, Pyung Cheon

    2015-11-20

    The ent-kaurene is a dedicated precursor pool and is responsible for synthesizing natural sweeteners such as steviol glycosides. In this study, to produce ent-kaurene in Escherichia coli, we modularly constructed and expressed two ent-kaurene genes encoding ent-copalyl diphosphate synthase (CPPS) and ent-kaurene synthase (KS) from Stevia rebaudiana known as a typical plant producing steviol glycoside. The CPPS and KS from S. rebaudiana were functionally expressed in a heterologous host E. coli. Furthermore, in order to enhance ent-kaurene production in E. coli, six geranylgeranyl diphosphate synthases (GGPPS) from various microorganisms and eight strains of E. coli as host were compared by measuring ent-kaurene production. The highest ent-kaurene production of approximately 41.1mg/L was demonstrated in E. coli strain MG1655 co-expressing synthetic CPPS-KS module and GGPPS from Rhodobacter sphaeroides. The ent-kaurene production was further increased up to 179.6 mg/L by overexpression of the three key enzymes for isoprenoid precursor, 1-deoxyxylulose-5-phosphate synthase (DXS), farnesyl diphosphate synthase (IspA) and isopentenyl diphosphate isomerase (IDI) from E. coli. Finally, the highest titer of ent-kaurene (578 mg/L) with a specific yield of ent-kaurene of 143.5mg/g dry cell weight was obtained by culturing E. coli strain MG1655 co-expressing the ent-kaurene module, DXS, IDI and IspA in 1L bioreactor containing 20 g/L glycerol.

  4. Hydrogen bonds between nitrogen donors and the semiquinone in the QB-site of bacterial reaction centers

    Science.gov (United States)

    Martin, Erik; Samoilova, Rimma I.; Narasimhulu, Kupala V.; Wraight, Colin A.; Dikanov, Sergei A.

    2010-01-01

    Photosynthetic reaction centers from Rhodobacter sphaeroides have identical ubiquinone-10 molecules functioning as primary (QA) and secondary (QB) electron acceptors. X-band 2D pulsed EPR spectroscopy, called HYSCORE, was applied to study the interaction of the QB site semiquinone with nitrogens from the local protein environment in natural and 15N uniformly labeled reactions centers. 14N and 15N HYSCORE spectra of the QB semiquinone show the interaction with two nitrogens carrying transferred unpaired spin density. Quadrupole coupling constants estimated from 14N HYSCORE spectra indicate them to be a protonated nitrogen of an imidazole residue and amide nitrogen of a peptide group. 15N HYSCORE spectra allowed estimation of the isotropic and anisotropic couplings with these nitrogens. From these data, we calculated the unpaired spin density transferred onto 2s and 2p orbitals of nitrogen, and analyzed the contribution of different factors to the anisotropic hyperfine tensors. The hyperfine coupling of other protein nitrogens with the semiquinone is weak (<0.1 MHz). These results clearly indicate that the QB semiquinone forms hydrogen bonds with two nitrogens, and provide quantitative characteristics of the hyperfine couplings with these nitrogens, which can be used in theoretical modeling of the QB site. Based on the quadrupole coupling constant, one nitrogen can only be assigned to Nδ of His-L190, consistent with all existing structures. However, we cannot specify between two candidates the residue corresponding to the second nitrogen. Further work employing multifrequency spectroscopic approaches or selective isotope labeling would be desirable for unambiguous assignment of this nitrogen. PMID:20672818

  5. Nuclear Hyperfine and Quadrupole Tensor Characterization of the Nitrogen Hydrogen Bond Donors to the Semiquinone of the QB Site in Bacterial Reaction Centers: A Combined X- and S-Band 14,15N ESEEM and DFT Study

    Science.gov (United States)

    2015-01-01

    The secondary quinone anion radical QB– (SQB) in reaction centers of Rhodobacter sphaeroides interacts with Nδ of His-L190 and Np (peptide nitrogen) of Gly-L225 involved in hydrogen bonds to the QB carbonyls. In this work, S-band (∼3.6 GHz) ESEEM was used with the aim of obtaining a complete characterization of the nuclear quadrupole interaction (nqi) tensors for both nitrogens by approaching the cancelation condition between the isotropic hyperfine coupling and 14N Zeeman frequency at lower microwave frequencies than traditional X-band (9.5 GHz). By performing measurements at S-band, we found a dominating contribution of Nδ in the form of a zero-field nqi triplet at 0.55, 0.92, and 1.47 MHz, defining the quadrupole coupling constant K = e2qQ/4h = 0.4 MHz and associated asymmetry parameter η = 0.69. Estimates of the hyperfine interaction (hfi) tensors for Nδ and Np were obtained from simulations of 1D and 2D 14,15N X-band and three-pulse 14N S-band spectra with all nuclear tensors defined in the SQB g-tensor coordinate system. From simulations, we conclude that the contribution of Np to the S-band spectrum is suppressed by its strong nqi and weak isotropic hfi comparable to the level of hyperfine anisotropy, despite the near-cancelation condition for Np at S-band. The excellent agreement between our EPR simulations and DFT calculations of the nitrogen hfi and nqi tensors to SQB is promising for the future application of powder ESEEM to full tensor characterizations. PMID:24437652

  6. The binding of quinone to the photosynthetic reaction centers: kinetics and thermodynamics of reactions occurring at the QB-site in zwitterionic and anionic liposomes.

    Science.gov (United States)

    Mavelli, Fabio; Trotta, Massimo; Ciriaco, Fulvio; Agostiano, Angela; Giotta, Livia; Italiano, Francesca; Milano, Francesco

    2014-07-01

    Liposomes represent a versatile biomimetic environment for studying the interaction between integral membrane proteins and hydrophobic ligands. In this paper, the quinone binding to the QB-site of the photosynthetic reaction centers (RC) from Rhodobacter sphaeroides has been investigated in liposomes prepared with either the zwitterionic phosphatidylcholine (PC) or the negatively charged phosphatidylglycerol (PG) to highlight the role of the different phospholipid polar heads. Quinone binding (K Q) and interquinone electron transfer (L AB) equilibrium constants in the two type of liposomes were obtained by charge recombination reaction of QB-depleted RC in the presence of increasing amounts of ubiquinone-10 over the temperature interval 6-35 °C. The kinetic of the charge recombination reactions has been fitted by numerically solving the ordinary differential equations set associated with a detailed kinetic scheme involving electron transfer reactions coupled with quinone release and uptake. The entire set of traces at each temperature was accurately fitted using the sole quinone release constants (both in a neutral and a charge separated state) as adjustable parameters. The temperature dependence of the quinone exchange rate at the QB-site was, hence, obtained. It was found that the quinone exchange regime was always fast for PC while it switched from slow to fast in PG as the temperature rose above 20 °C. A new method was introduced in this paper for the evaluation of constant K Q using the area underneath the charge recombination traces as the indicator of the amount of quinone bound to the QB-site.

  7. Residual Water Modulates QA−-to-QB Electron Transfer in Bacterial Reaction Centers Embedded in Trehalose Amorphous Matrices

    Science.gov (United States)

    Francia, Francesco; Palazzo, Gerardo; Mallardi, Antonia; Cordone, Lorenzo; Venturoli, Giovanni

    2003-01-01

    The role of protein dynamics in the electron transfer from the reduced primary quinone, QA−, to the secondary quinone, QB, was studied at room temperature in isolated reaction centers (RC) from the photosynthetic bacterium Rhodobacter sphaeroides by incorporating the protein in trehalose water systems of different trehalose/water ratios. The effects of dehydration on the reaction kinetics were examined by analyzing charge recombination after different regimes of RC photoexcitation (single laser pulse, double flash, and continuous light) as well as by monitoring flash-induced electrochromic effects in the near infrared spectral region. Independent approaches show that dehydration of RC-containing matrices causes reversible, inhomogeneous inhibition of QA−-to-QB electron transfer, involving two subpopulations of RCs. In one of these populations (i.e., active), the electron transfer to QB is slowed but still successfully competing with P+QA− recombination, even in the driest samples; in the other (i.e., inactive), electron transfer to QB after a laser pulse is hindered, inasmuch as only recombination of the P+QA− state is observed. Small residual water variations (∼7 wt %) modulate fully the relative fraction of the two populations, with the active one decreasing to zero in the driest samples. Analysis of charge recombination after continuous illumination indicates that, in the inactive subpopulation, the conformational changes that rate-limit electron transfer can be slowed by >4 orders of magnitude. The reported effects are consistent with conformational gating of the reaction and demonstrate that the conformational dynamics controlling electron transfer to QB is strongly enslaved to the structure and dynamics of the surrounding medium. Comparing the effects of dehydration on P+QA−→PQA recombination and QA−QB→QAQB− electron transfer suggests that conformational changes gating the latter process are distinct from those stabilizing the primary

  8. Nuclear hyperfine and quadrupole tensor characterization of the nitrogen hydrogen bond donors to the semiquinone of the QB site in bacterial reaction centers: a combined X- and S-band (14,15)N ESEEM and DFT study.

    Science.gov (United States)

    Taguchi, Alexander T; O'Malley, Patrick J; Wraight, Colin A; Dikanov, Sergei A

    2014-02-13

    The secondary quinone anion radical QB(-) (SQB) in reaction centers of Rhodobacter sphaeroides interacts with Nδ of His-L190 and Np (peptide nitrogen) of Gly-L225 involved in hydrogen bonds to the QB carbonyls. In this work, S-band (∼3.6 GHz) ESEEM was used with the aim of obtaining a complete characterization of the nuclear quadrupole interaction (nqi) tensors for both nitrogens by approaching the cancelation condition between the isotropic hyperfine coupling and (14)N Zeeman frequency at lower microwave frequencies than traditional X-band (9.5 GHz). By performing measurements at S-band, we found a dominating contribution of Nδ in the form of a zero-field nqi triplet at 0.55, 0.92, and 1.47 MHz, defining the quadrupole coupling constant K = e(2)qQ/4h = 0.4 MHz and associated asymmetry parameter η = 0.69. Estimates of the hyperfine interaction (hfi) tensors for Nδ and Np were obtained from simulations of 1D and 2D (14,15)N X-band and three-pulse (14)N S-band spectra with all nuclear tensors defined in the SQB g-tensor coordinate system. From simulations, we conclude that the contribution of Np to the S-band spectrum is suppressed by its strong nqi and weak isotropic hfi comparable to the level of hyperfine anisotropy, despite the near-cancelation condition for Np at S-band. The excellent agreement between our EPR simulations and DFT calculations of the nitrogen hfi and nqi tensors to SQB is promising for the future application of powder ESEEM to full tensor characterizations.

  9. High-pressure modulation of the structure of the bacterial photochemical reaction center at physiological and cryogenic temperatures

    Science.gov (United States)

    Timpmann, Kõu; Kangur, Liina; Lõhmus, Ants; Freiberg, Arvi

    2017-07-01

    The optical absorption and fluorescence response to external high pressure of the reaction center membrane chromoprotein complex from the wild-type non-sulfur photosynthetic bacterium Rhodobacter sphaeroides was investigated using the native pigment cofactors as local molecular probes of the reaction center structure at physiological (ambient) and cryogenic (79 K) temperatures. In detergent-purified complexes at ambient temperature, abrupt blue shift and accompanied broadening of the special pair band was observed at about 265 MPa. These reversible in pressure features were assigned to a pressure-induced rupture of a lone hydrogen bond that binds the photo-chemically active L-branch primary electron donor bacteriochlorophyll cofactor to the surrounding protein scaffold. In native membrane-protected complexes the hydrogen bond rupture appeared significantly restricted and occurred close to about 500 MPa. The free energy change associated with the rupture of the special pair hydrogen bond in isolate complexes was estimated to be equal to about 12 kJ mol-1. In frozen samples at cryogenic temperatures the hydrogen bond remained apparently intact up to the maximum utilized pressure of 600 MPa. In this case, however, heterogeneous spectral response of the cofactors from the L-and M-branches was observed due to anisotropic build-up of the protein structure. While in solid phase, the special pair fluorescence as a function of pressure exactly followed the respective absorption spectrum at a constant Stokes shift, at ambient temperature, the two paths began to deviate strongly from one other at the hydrogen bond rupture pressure. This effect was tentatively interpreted by different emission properties of hydrogen-bound and hydrogen-unbound special pair exciton states.

  10. Photosynthetic reaction centers/ITO hybrid nanostructure

    Energy Technology Data Exchange (ETDEWEB)

    Szabo, Tibor [Department of Medical Physics and Informatics, University of Szeged, Szeged (Hungary); Bencsik, Gabor [Department of Physical Chemistry and Materials Science, University of Szeged, Szeged (Hungary); Magyar, Melinda [Department of Medical Physics and Informatics, University of Szeged, Szeged (Hungary); Visy, Csaba [Department of Physical Chemistry and Materials Science, University of Szeged, Szeged (Hungary); Gingl, Zoltan [Department of Technical Informatics, University of Szeged, Szeged (Hungary); Nagy, Krisztina; Varo, Gyoergy [Institute of Biophysics, Hungarian Academy of Sciences, Biological Research Center, Szeged (Hungary); Hajdu, Kata; Kozak, Gabor [Department of Medical Physics and Informatics, University of Szeged, Szeged (Hungary); Nagy, Laszlo, E-mail: lnagy@sol.cc.u-szeged.hu [Department of Medical Physics and Informatics, University of Szeged, Szeged (Hungary)

    2013-03-01

    Photosynthetic reaction center proteins purified from Rhodobacter sphaeroides purple bacterium were deposited on the surface of indium tin oxide (ITO), a transparent conductive oxide, and the photochemical/-physical properties of the composite were investigated. The kinetics of the light induced absorption change indicated that the RC was active in the composite and there was an interaction between the protein cofactors and the ITO. The electrochromic response of the bacteriopheophytine absorption at 771 nm showed an increased electric field perturbation around this chromophore on the surface of ITO compared to the one measured in solution. This absorption change is associated with the charge-compensating relaxation events inside the protein. Similar life time, but smaller magnitude of this absorption change was measured on the surface of borosilicate glass. The light induced change in the conductivity of the composite as a function of the concentration showed the typical sigmoid saturation characteristics unlike if the photochemically inactive chlorophyll was layered on the ITO. In this later case the light induced change in the conductivity was oppositely proportional to the chlorophyll concentration due to the thermal dissipation of the excitation energy. The sensitivity of the measurement is very high; few picomole RC can change the light induced resistance of the composite. - Highlights: Black-Right-Pointing-Pointer Photosynthetic reaction center/ITO nanocomposite has been fabricated. Black-Right-Pointing-Pointer The composite showed photochemical/-physical activity with very high sensitivity. Black-Right-Pointing-Pointer This new type of material can be a good model of optoelectronic devices.

  11. The effectiveness of styrene-maleic acid (SMA) copolymers for solubilisation of integral membrane proteins from SMA-accessible and SMA-resistant membranes.

    Science.gov (United States)

    Swainsbury, David J K; Scheidelaar, Stefan; Foster, Nicholas; van Grondelle, Rienk; Killian, J Antoinette; Jones, Michael R

    2017-10-01

    Solubilisation of biological lipid bilayer membranes for analysis of their protein complement has traditionally been carried out using detergents, but there is increasing interest in the use of amphiphilic copolymers such as styrene maleic acid (SMA) for the solubilisation, purification and characterisation of integral membrane proteins in the form of protein/lipid nanodiscs. Here we survey the effectiveness of various commercially-available formulations of the SMA copolymer in solubilising Rhodobacter sphaeroides reaction centres (RCs) from photosynthetic membranes. We find that formulations of SMA with a 2:1 or 3:1 ratio of styrene to maleic acid are almost as effective as detergent in solubilising RCs, with the best solubilisation by short chain variants (SMA to solubilise RCs gradually declined when genetically-encoded coiled-coil bundles were used to artificially tether normally monomeric RCs into dimeric, trimeric and tetrameric multimers. The ability of SMA to solubilise reaction centre-light harvesting 1 (RC-LH1) complexes from densely packed and highly ordered photosynthetic membranes was uniformly low, but could be increased through a variety of treatments to increase the lipid:protein ratio. However, proteins isolated from such membranes comprised clusters of complexes in small membrane patches rather than individual proteins. We conclude that short-chain 2:1 and 3:1 formulations of SMA are the most effective in solubilising integral membrane proteins, but that solubilisation efficiencies are strongly influenced by the size of the target protein and the density of packing of proteins in the membrane. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  12. A unified description of the electrochemical, charge distribution, and spectroscopic properties of the special-pair radical cation in bacterial photosynthesis.

    Science.gov (United States)

    Reimers, Jeffrey R; Hush, Noel S

    2004-04-01

    We apply our four-state 70-vibration vibronic-coupling model for the properties of the photosynthetic special-pair radical cation to: (1) interpret the observed correlations between the midpoint potential and the distribution of spin density between the two bacteriochlorophylls for 30 mutants of Rhodobacter sphaeroides, (2) interpret the observed average intervalence hole-transfer absorption energies as a function of spin density for six mutants, and (3) simulate the recently obtained intervalence electroabsorption Stark spectrum of the wild-type reaction center. While three new parameters describing the location of the sites of mutation with respect to the special pair are required to describe the midpoint-potential data, a priori predictions are made for the transition energies and the Stark spectrum. In general, excellent predictions are made of the observed quantities, with deviations being typically of the order of twice the experimental uncertainties. A unified description of many chemical and spectroscopic properties of the bacterial reaction center is thus provided. Central to the analysis is the assumption that the perturbations made to the reaction center, either via mutations of protein residues or by application of an external electric field, act only to independently modify the oxidation potentials of the two halves of the special pair and hence the redox asymmetry E0. While this appears to be a good approximation, clear evidence is presented that effects of mutation can be more extensive than what is allowed for. A thorough set of analytical equations describing the observed properties is obtained using the Born-Oppenheimer adiabatic approximation. These equations are generally appropriate for intervalence charge-transfer problems and include, for the first time, full treatment of both symmetric and antisymmetric vibrational motions. The limits of validity of the adiabatic approach to the full nonadiabatic problem are obtained.

  13. Static and dynamic protein impact on electronic properties of light-harvesting complex LH2.

    Science.gov (United States)

    Zerlauskiene, O; Trinkunas, G; Gall, A; Robert, B; Urboniene, V; Valkunas, L

    2008-12-11

    A comparative analysis of the temperature dependence of the absorption spectra of the LH2 complexes from different species of photosynthetic bacteria, i.e., Rhodobacter sphaeroides, Rhodoblastus acidophilus, and Phaeospirillum molischianum, was performed in the temperature range from 4 to 300 K. Qualitatively, the temperature dependence is similar for all of the species studied. The spectral bandwidths of both B800 and B850 bands increases with temperature while the band positions shift in opposite directions: the B800 band shifts slightly to the red while the B850 band to the blue. These results were analyzed using the modified Redfield theory based on the exciton model. The main conclusion drawn from the analysis was that the spectral density function (SDF) is the main factor underlying the strength of the temperature dependence of the bandwidths for the B800 and B850 electronic transitions, while the bandwidths themselves are defined by the corresponding inhomogeneous distribution function (IDF). Slight variation of the slope of the temperature dependence of the bandwidths between species can be attributed to the changes of the values of the reorganization energies and characteristic frequencies determining the SDF. To explain the shift of the B850 band position with temperature, which is unusual for the conventional exciton model, a temperature dependence of the IDF must be postulated. This dependence can be achieved within the framework of the modified (dichotomous) exciton model. The slope of the temperature dependence of the B850 bandwidth is then defined by the value of the reorganization energy and by the difference between the transition energies of the dichotomous states of the pigment molecules. The equilibration factor between these dichotomous states mainly determines the temperature dependence of the peak shift.

  14. A high-throughput strategy to screen 2D crystallization trials of membrane proteins.

    Science.gov (United States)

    Vink, Martin; Derr, Kd; Love, James; Stokes, David L; Ubarretxena-Belandia, Iban

    2007-12-01

    Electron microscopy of two-dimensional (2D) crystals has demonstrated potential for structure determination of membrane proteins. Technical limitations in large-scale crystallization screens have, however, prevented a major breakthrough in the routine application of this technology. Dialysis is generally used for detergent removal and reconstitution of the protein into a lipid bilayer, and devices for testing numerous conditions in parallel are not readily available. Furthermore, the small size of resulting 2D crystals requires electron microscopy to evaluate the results and automation of the necessary steps is essential to achieve a reasonable throughput. We have designed a crystallization block, using standard microplate dimensions, by which 96 unique samples can be dialyzed simultaneously against 96 different buffers and have demonstrated that the rate of detergent dialysis is comparable to those obtained with conventional dialysis devices. A liquid-handling robot was employed to set up 2D crystallization trials with the membrane proteins CopA from Archaeoglobus fulgidus and light-harvesting complex II (LH2) from Rhodobacter sphaeroides. For CopA, 1 week of dialysis yielded tubular crystals and, for LH2, large and well-ordered vesicular 2D crystals were obtained after 24 h, illustrating the feasibility of this approach. Combined with a high-throughput procedure for preparation of EM-grids and automation of the subsequent negative staining step, the crystallization block offers a novel pipeline that promises to speed up large-scale screening of 2D crystallization and to increase the likelihood of producing well-ordered crystals for analysis by electron crystallography.

  15. Toll-Like Receptor 4 Inhibition Improves Oxidative Stress and Mitochondrial Health in Isoproterenol-Induced Cardiac Hypertrophy in Rats

    Directory of Open Access Journals (Sweden)

    Parmeshwar B. Katare

    2017-06-01

    Full Text Available BackgroundInflammation remains a crucial factor for progression of cardiac diseases and cardiac hypertrophy remains an important cause of cardiac failure over all age groups. As a key regulator of inflammation, toll-like receptor 4 (TLR4 plays an important role in pathogenesis of cardiac diseases. Being an important regulator of innate immunity, the precise pathway of TLR4-mediated cardiac complications is yet to be established. Therefore, the primary objective of the present study was to find the role of TLR4 in cardiac hypertrophy and the molecular mechanism thereof.MethodsCardiac hypertrophy was induced with administration of isoproterenol (5 mg/kg/day, sc. TLR4 receptor inhibitor RS-LPS (lipopolysaccharide from the photosynthetic bacterium Rhodobacter sphaeroides; 5 μg/day and agonist lipopolysaccharide (LPS (from Escherichia coli; 3.12 μg/day were administered through osmotic pump along with isoproterenol. Cardiac hypertrophy as well as oxidative stress and mitochondrial parameters were evaluated.ResultsCardiac hypertrophy was confirmed with increased heart weight/body weight ratio as well as assessment of hypertrophic markers in heart. There was a marked increase in the TLR4 expression and oxidative stress along with mitochondrial dysfunction in ISO group. TLR4 inhibition significantly decreased heart weight/body weight ratio and ANP, collagen, and β-MHC expression and restored the disturbed cellular antioxidant flux. The mitochondrial perturbations that were observed in hypertrophy heart was normalized after administration of TLR4 inhibitor but not with the agonist. TLR4 agonism further exaggerated the oxidative stress in heart and hence accelerated the disease development and progression.ConclusionOur data show that increased TLR4 ligand pool in cardiac hypertrophy may exaggerate the disease progression. However, inhibition of TLR4 attenuated cardiac hypertrophy through reduced cardiac redox imbalance and mitochondrial

  16. [Improving Agricultural Safety of Soils Contaminated with Polycyclic Aromatic Hydrocarbons by In Situ Bioremediation].

    Science.gov (United States)

    Jiao, Hai-huan; Pan, Jian-gang; Xu, Shena-jun; Bai, Zhi-hui; Wang, Dong; Huang, Zhan-bin

    2015-08-01

    In order to reduce the risk of enrichment of polycyclic aromatic hydrocarbons (PAHs) in crops, reduce the potential hazards of food-sourced PAHs to human and increase the agricultural safety of PAHs contaminated soils, the bio-augmented removal of polycyclic aromatic hydrocarbons (PAHs) was investigated through in situ remediation by introducing Rhodobacter sphaeroides (RS) into the agricultural soil contaminated by PAHs. The 50-times diluted RS was sprayed on leaf surface (in area B) or irrigated to roots (in area D). The treatment of spraying water of the equal amount was taken as the control (A) and the wheat field without any treatment as the blank (CK). Treatments were conducted since wheat seeding. Soil and wheat samples were collected in the mature period to analyze the changes of community structure of the soil microorganisms and the concentration of PAHs in soils and investigate the strengthening and restoration effects of RS on PAHs contaminated soils. Compared to the CK Area, the areas B and D revealed that the variation ratio of phospholipid fatty acids (PLFAs) that were the biomarker of soil microorganisms was 29.6%, and the ratio of total PAHs removed was increased 1.59 times and 1.68 times, respectively. The dry weight of wheat grain of 50 spikes was increased by 8.95% and 12.5%, respectively, and the enrichment factor of total PAHs was decreased by 58.9% and 62.2% respectively in the wheat grains. All the results suggested that RS reduced enrichment of PAHs in wheat grains and increased wheat yield, which had great exploitation and utilization potentiality in repairing and improving the agricultural safety of the soils contaminated with PHAs.

  17. Versatile design of biohybrid light-harvesting architectures to tune location, density, and spectral coverage of attached synthetic chromophores for enhanced energy capture.

    Science.gov (United States)

    Harris, Michelle A; Jiang, Jianbing; Niedzwiedzki, Dariusz M; Jiao, Jieying; Taniguchi, Masahiko; Kirmaier, Christine; Loach, Paul A; Bocian, David F; Lindsey, Jonathan S; Holten, Dewey; Parkes-Loach, Pamela S

    2014-07-01

    Biohybrid antennas built upon chromophore-polypeptide conjugates show promise for the design of efficient light-capturing modules for specific purposes. Three new designs, each of which employs analogs of the β-polypeptide from Rhodobacter sphaeroides, have been investigated. In the first design, amino acids at seven different positions on the polypeptide were individually substituted with cysteine, to which a synthetic chromophore (bacteriochlorin or Oregon Green) was covalently attached. The polypeptide positions are at -2, -6, -10, -14, -17, -21, and -34 relative to the 0-position of the histidine that coordinates bacteriochlorophyll a (BChl a). All chromophore-polypeptides readily formed LH1-type complexes upon combination with the α-polypeptide and BChl a. Efficient energy transfer occurs from the attached chromophore to the circular array of 875 nm absorbing BChl a molecules (denoted B875). In the second design, use of two attachment sites (positions -10 and -21) on the polypeptide affords (1) double the density of chromophores per polypeptide and (2) a highly efficient energy-transfer relay from the chromophore at -21 to that at -10 and on to B875. In the third design, three spectrally distinct bacteriochlorin-polypeptides were prepared (each attached to cysteine at the -14 position) and combined in an ~1:1:1 mixture to form a heterogeneous mixture of LH1-type complexes with increased solar coverage and nearly quantitative energy transfer from each bacteriochlorin to B875. Collectively, the results illustrate the great latitude of the biohybrid approach for the design of diverse light-harvesting systems.

  18. The rate of second electron transfer to QB(-) in bacterial reaction center of impaired proton delivery shows hydrogen-isotope effect.

    Science.gov (United States)

    Maróti, Ágnes; Wraight, Colin A; Maróti, Péter

    2015-02-01

    The 2nd electron transfer in reaction center of photosynthetic bacterium Rhodobacter sphaeroides is a two step process in which protonation of QB(-) precedes interquinone electron transfer. The thermal activation and pH dependence of the overall rate constants of different RC variants were measured and compared in solvents of water (H2O) and heavy water (D2O). The electron transfer variants where the electron transfer is rate limiting (wild type and M17DN, L210DN and H173EQ mutants) do not show solvent isotope effect and the significant decrease of the rate constant of the second electron transfer in these mutants is due to lowering the operational pKa of QB(-)/QBH: 4.5 (native), 3.9 (L210DN), 3.7 (M17DN) and 3.1 (H173EQ) at pH7. On the other hand, the proton transfer variants where the proton transfer is rate limiting demonstrate solvent isotope effect of pH-independent moderate magnitude (2.11±0.26 (WT+Ni(2+)), 2.16±0.35 (WT+Cd(2+)) and 2.34±0.44 (L210DN/M17DN)) or pH-dependent large magnitude (5.7 at pH4 (L213DN)). Upon deuteration, the free energy and the enthalpy of activation increase in all proton transfer variants by about 1 kcal/mol and the entropy of activation becomes negligible in L210DN/M17DN mutant. The results are interpreted as manifestation of equilibrium and kinetic solvent isotope effects and the structural, energetic and kinetic possibility of alternate proton delivery pathways are discussed.

  19. Characterizing the proton loading site in cytochrome c oxidase.

    Science.gov (United States)

    Lu, Jianxun; Gunner, M R

    2014-08-26

    Cytochrome c oxidase (CcO) uses the energy released by reduction of O2 to H2O to drive eight charges from the high pH to low pH side of the membrane, increasing the electrochemical gradient. Four electrons and protons are used for chemistry, while four more protons are pumped. Proton pumping requires that residues on a pathway change proton affinity through the reaction cycle to load and then release protons. The protonation states of all residues in CcO are determined in MultiConformational Continuum Electrostatics simulations with the protonation and redox states of heme a, a3, Cu(B), Y288, and E286 used to define the catalytic cycle. One proton is found to be loaded and released from residues identified as the proton loading site (PLS) on the P-side of the protein in each of the four CcO redox states. Thus, the same proton pumping mechanism can be used each time CcO is reduced. Calculations with structures of Rhodobacter sphaeroides, Paracoccus denitrificans, and bovine CcO derived by crystallography and molecular dynamics show the PLS functions similarly in different CcO species. The PLS is a cluster rather than a single residue, as different structures show 1-4 residues load and release protons. However, the proton affinity of the heme a3 propionic acids primarily determines the number of protons loaded into the PLS; if their proton affinity is too low, less than one proton is loaded.

  20. [Production of coenzyme Q10 by metabolically engineered Escherichia coli].

    Science.gov (United States)

    Dai, Guanping; Miao, Liangtian; Sun, Tao; Li, Qingyan; Xiao, Dongguang; Zhang, Xueli

    2015-02-01

    Coenzyme Q10 (CoQ10) is a lipophilic antioxidant that improves human immunity, delays senility and enhances the vitality of the human body and has wide applications in pharmaceutical and cosmetic industries. Microbial fermentation is a sustainable way to produce CoQ10, and attracts increased interest. In this work, the native CoQ8 synthetic pathway of Escherichia coli was replaced by the CoQ10 synthetic pathway through integrating decaprenyl diphosphate synthase gene (dps) from Rhodobacter sphaeroides into chromosome of E. coli ATCC 8739, followed by deletion of the native octaprenyl diphosphate synthase gene (ispB). The resulting strain GD-14 produced 0.68 mg/L CoQ10 with a yield of 0.54 mg/g DCW. Modulation of dxs and idi genes of the MEP pathway and ubiCA genes in combination led to 2.46-fold increase of CoQ10 production (from 0.54 to 1.87 mg/g DCW). Recruiting glucose facilitator protein of Zymomonas mobilis to replace the native phosphoenolpyruvate: carbohydrate phosphotransferase systems (PTS) further led to a 16% increase of CoQ10 yield. Finally, fed-batch fermentation of the best strain GD-51 was performed, which produced 433 mg/L CoQ10 with a yield of 11.7 mg/g DCW. To the best of our knowledge, this was the highest CoQ10 titer and yield obtained for engineered E. coli.

  1. High-Field EPR Spectroscopy on Transfer Proteins in Biological Action

    Science.gov (United States)

    Möbius, K.; Schnegg, A.; Plato, M.; Fuchs, M. R.; Savitsky, A.

    2006-08-01

    In the last decade joint efforts of biologists, chemists, and physicists were made to understand the dominant factors determining specificity and directionality of transmembrane transfer processes in proteins. Characteristic examples of such factors are time varying specific H-bonding patterns and/or polarity effects of the microenvironment. In this overview, a few large paradigm biosystems are surveyed which have been explored lately in our laboratory. Taking advantage of the improved spectral and temporal resolution of high-frequency/high-field EPR at 95 GHz/3.4 T and 360 GHz/12.9 T, as compared to conventional X-band EPR (9.5 GHz/0.34 T), three transfer proteins in action are characterized with respect to structure and dynamics: (1) light-induced electron-transfer intermediates in wild-type and mutant reaction-centre proteins from photosynthetic bacteria Rhodobacter sphaeroides, (2) light-driven proton-transfer intermediates of site-specifically nitroxide spin-labelled mutants of bacteriorhodopsin proteins from Halobacterium salinarium, (3) refolding intermediates of site-specifically nitroxide spin-labelled mutants of the channel-forming protein domain of Colicin A bacterial toxin produced in Escherichia coli. The information obtained is complementary to that of protein crystallography, solid-state NMR, infrared and optical spectroscopy techniques. A unique strength of high-field EPR is particularly noteworthy: it can provide detailed information on transient intermediates of proteins in biological action. They can be observed and characterized while staying in their working states on biologically relevant time scales.

  2. Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis

    Directory of Open Access Journals (Sweden)

    McGuire Abigail

    2012-03-01

    Full Text Available Abstract Background The sequence of the pathogen Mycobacterium tuberculosis (Mtb strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to understand the evolution of Mtb pathogenesis. We conducted a comparative analysis using 31 genomes from the Tuberculosis Database (TBDB.org, including 8 strains of Mtb and M. bovis, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes, and Bifidobacterium longum. Results Our results highlight the functional importance of lipid metabolism and its regulation, and reveal variation between the evolutionary profiles of genes implicated in saturated and unsaturated fatty acid metabolism. It also suggests that DNA repair and molybdopterin cofactors are important in pathogenic Mycobacteria. By analyzing sequence conservation and gene expression data, we identify nearly 400 conserved noncoding regions. These include 37 predicted promoter regulatory motifs, of which 14 correspond to previously validated motifs, as well as 50 potential noncoding RNAs, of which we experimentally confirm the expression of four. Conclusions Our analysis of protein evolution highlights gene families that are associated with the adaptation of environmental Mycobacteria to obligate pathogenesis. These families include fatty acid metabolism, DNA repair, and molybdopterin biosynthesis. Our analysis reinforces recent findings suggesting that small noncoding RNAs are more common in Mycobacteria than previously expected. Our data provide a foundation for understanding the genome and biology of Mtb in a comparative context, and are available online and through TBDB.org.

  3. The electronic behavior of a photosynthetic reaction center monitored by conductive atomic force microscopy.

    Science.gov (United States)

    Mikayama, Takeshi; Iida, Kouji; Suemori, Yoshiharu; Dewa, Takehisa; Miyashita, Tokuji; Nango, Mamoru; Gardiner, Alastair T; Cogdell, Richard J

    2009-01-01

    The conductivity of a photosynthetic reaction center (RC) from Rhodobacter sphaeroides was measured with conductive atomic force microscopy (CAFM) on SAM-modified Au(111) substrates. 2-mercaptoethanol (2ME), 2-mercaptoacetic acid (MAC), 2-mercaptopyridine (2MP) and 4-mercaptopyridine (4MP) were prepared as SAM materials to investigate the stability and morphology of RCs on the substrate by using near-IR absorption spectroscopy and AFM, respectively. The clear presence of the three well known RC near-IR absorption peaks indicates that the RCs were native on the SAM-modified Au(111). Dense grains with various diameters of 5-20 nm, which corresponded to mixtures of single RCs up to aggregates of 10, were observed in topographs of RCs adsorbed on all the different SAM-modified Au(111) substrates. The size of currents obtained from the RC using a bare conductive cantilever were produced in the following order for SAM molecules: 2MP > 2ME > 4MP > MAC. A clear rectification of this current was observed for the modification of the Au(111) substrate with the pi-conjugated thiol, 2MP, indicating that 2MP was effective in both promoting the specific orientation of the RCs on the electrode and electron injection into the RC. Cyclic voltammetry measurements indicate that the 2MP is better mediator for the electron transfer between a quinone and substrate. The current with 2MP-modified cantilever was twice as high as that obtained with the Au-coated one alone, indicating that 2MP has an important role in lowering the electron injection barrier between special pair side of RC and gold electrode.

  4. Interaction and Synergism of Microbial Fuel Cell Bacteria within Methanogenesis

    Science.gov (United States)

    Klaus, David

    2004-01-01

    Biological hydrogen production from waste biomass has both terrestrial and Martian advanced life support applications. On earth, biological hydrogen production is being explored as a greenhouse neutral form of clean and efficient energy. In a permanently enclosed space habitat, carbon loop closure is required to reduce mission costs. Plants are grown to revitalize oxygen supply and are consumed by habitat inhabitants. Unharvested portions must then be recycled for reuse in the habitat. Several biological degradation techniques exist, but one process, biophotolysis, can be used to produce hydrogen from inedible plant biomass. This process is two-stage, with one stage using dark fermentation to convert plant wastes into organic acids. The second stage, photofermentation, uses photoheterotrophic purple non-sulfur bacteria with the addition of light to turn the organic acids into hydrogen and carbon dioxide. Such a system can prove useful as a co-generation scheme, providing some of the energy needed to power a larger primary carbon recovery system, such as composting. Since butyrate is expected as one of the major inputs into photofermentation, a characterization study was conducted with the bacterium Rhodobacter sphaeroides SCJ, a novel photoheterotrophic non-sulfur purple bacteria, to examine hydrogen production performance at 10 mM-100 mM butyrate concentrations. As butyrate levels increased, hydrogen production increased up to 25 mM, and then decreased and ceased by 100 mM. Additionally, lag phase increased with butyrate concentration, possibly indicating some product inhibition. Maximal substrate conversion efficiency was 8.0%; maximal light efficiency was 0.89%; and maximal hydrogen production rate was 7.7 Umol/mg/cdw/hr (173 ul/mg cdw/hr). These values were either consistent or lower than expected from literature.

  5. Reconstruction of the core and extended regulons of global transcription factors.

    Directory of Open Access Journals (Sweden)

    Yann S Dufour

    2010-07-01

    Full Text Available The processes underlying the evolution of regulatory networks are unclear. To address this question, we used a comparative genomics approach that takes advantage of the large number of sequenced bacterial genomes to predict conserved and variable members of transcriptional regulatory networks across phylogenetically related organisms. Specifically, we developed a computational method to predict the conserved regulons of transcription factors across alpha-proteobacteria. We focused on the CRP/FNR super-family of transcription factors because it contains several well-characterized members, such as FNR, FixK, and DNR. While FNR, FixK, and DNR are each proposed to regulate different aspects of anaerobic metabolism, they are predicted to recognize very similar DNA target sequences, and they occur in various combinations among individual alpha-proteobacterial species. In this study, the composition of the respective FNR, FixK, or DNR conserved regulons across 87 alpha-proteobacterial species was predicted by comparing the phylogenetic profiles of the regulators with the profiles of putative target genes. The utility of our predictions was evaluated by experimentally characterizing the FnrL regulon (a FNR-type regulator in the alpha-proteobacterium Rhodobacter sphaeroides. Our results show that this approach correctly predicted many regulon members, provided new insights into the biological functions of the respective regulons for these regulators, and suggested models for the evolution of the corresponding transcriptional networks. Our findings also predict that, at least for the FNR-type regulators, there is a core set of target genes conserved across many species. In addition, the members of the so-called extended regulons for the FNR-type regulators vary even among closely related species, possibly reflecting species-specific adaptation to environmental and other factors. The comparative genomics approach we developed is readily applicable to other

  6. Protein-matrix coupling/uncoupling in "dry" systems of photosynthetic reaction center embedded in trehalose/sucrose: the origin of trehalose peculiarity.

    Science.gov (United States)

    Francia, Francesco; Dezi, Manuela; Mallardi, Antonia; Palazzo, Gerardo; Cordone, Lorenzo; Venturoli, Giovanni

    2008-08-06

    Trehalose is a nonreducing disaccharide of glucose found in organisms, which can survive adverse conditions such as extreme drought and high temperatures. Furthermore, isolated structures, as enzymes or liposomes, embedded in trehalose are preserved against stressing conditions [see, e.g., Crowe, L. M. Comp. Biochem. Physiol. A 2002, 131, 505-513]. Among other hypotheses, such protective effect has been suggested to stem, in the case of proteins, from the formation of a water-mediated, hydrogen bond network, which anchors the protein surface to the water-sugar matrix, thus coupling the internal degrees of freedom of the biomolecule to those of the surroundings [Giuffrida, S.; et al. J. Phys. Chem. B 2003, 107, 13211-13217]. Analogous protective effect is also accomplished by other saccharides, although with a lower efficiency. Here, we studied the recombination kinetics of the primary, light-induced charge separated state (P(+)Q(A)(-)) and the thermal stability of the photosynthetic reaction center (RC) of Rhodobacter sphaeroides in trehalose-water and in sucrose-water matrixes of decreasing water content. Our data show that, in sucrose, at variance with trehalose, the system undergoes a "nanophase separation" when the water/sugar mole fraction is lower than the threshold level approximately 0.8. We rationalize this result assuming that the hydrogen bond network, which anchors the RC surface to its surrounding, is formed in trehalose but not in sucrose. We suggest that both the couplings, in the case of trehalose, and the nanophase separation, in the case of sucrose, start at low water content when the components of the system enter in competition for the residual water.

  7. Charge recombination kinetics and protein dynamics in wild type and carotenoid-less bacterial reaction centers: studies in trehalose glasses.

    Science.gov (United States)

    Francia, Francesco; Malferrari, Marco; Sacquin-Mora, Sophie; Venturoli, Giovanni

    2009-07-30

    The coupling between electron transfer and protein dynamics has been investigated in reaction centers (RCs) from the wild type (wt) and the carotenoid-less strain R26 of the photosynthetic bacterium Rhodobacter sphaeroides. Recombination kinetics between the primary photoreduced quinone acceptor (QA-) and photoxidized donor (P+) have been analyzed at room temperature in RCs incorporated into glassy trehalose matrices of different water/sugar ratios. As previously found in R26 RCs, also in the wt RC, upon matrix dehydration, P+QA- recombination accelerates and becomes broadly distributed, reflecting the inhibition of protein relaxation from the dark-adapted to the light-adapted conformation and the hindrance of interconversion between conformational substates. While in wet trehalose matrices (down to approximately one water per trehalose molecule) P+QA- recombination kinetics are essentially coincident in wt and R26 RCs, more extensive dehydration leads to two-times faster and more distributed kinetics in the carotenoid-containing RC, indicating a stronger inhibition of the internal protein dynamics in the wt RC. Coarse-grained Brownian dynamics simulations performed on the two RC structures reveal a markedly larger flexibility of the R26 RC, showing that a rigid core of residues, close to the quinone acceptors, is specifically softened in the absence of the carotenoid. These experimental and computational results concur to indicate that removal of the carotenoid molecule has long-range effects on protein dynamics and that the structural/dynamical coupling between the protein and the glassy matrix depends strongly upon the local mechanical properties of the protein interior. The data also suggest that the conformational change stabilizing P+QA- is localized around the QA binding pocket.

  8. Purple-bacterial photosynthetic reaction centers and quantum-dot hybrid-assemblies in lecithin liposomes and thin films.

    Science.gov (United States)

    Lukashev, Eugeny P; Knox, Petr P; Gorokhov, Vladimir V; Grishanova, Nadezda P; Seifullina, Nuranija Kh; Krikunova, Maria; Lokstein, Heiko; Paschenko, Vladimir Z

    2016-11-01

    Quantum dots (QDs) absorb ultraviolet and long-wavelength visible light energy much more efficiently than natural bacterial light-harvesting proteins and can transfer the excitation energy to photosynthetic reaction centers (RCs). Inclusion of RCs combined with QDs as antennae into liposomes opens new opportunities for using such hybrid systems as a basis for artificial energy-transforming devices that potentially can operate with greater efficiency and stability than devices based only on biological components or inorganic components alone. RCs from Rhodobacter sphaeroides and QDs (CdSe/ZnS with hydrophilic covering) were embedded in lecithin liposomes by extrusion of a solution of multilayer lipid vesicles through a polycarbonate membrane or by dialysis of lipids and proteins dispersed with excess detergent. The efficiency of RC and QD interaction within the liposomes was estimated using fluorescence excitation spectra of the photoactive bacteriochlorophyll of the RCs and by measuring the fluorescence decay kinetics of the QDs. The functional activity of the RCs in hybrid complexes was fully maintained, and their stability was even increased. The efficiency of energy transfer between QDs and RCs and conditions of long-term stability of function of such hybrid complexes in film preparations were investigated as well. It was found that dry films containing RCs and QDs, maintained at atmospheric humidity, are capable of maintaining their functional activity for at least some months as judged by measurements of their spectral characteristics, efficiency of energy transfer from QDs to RCs and RC electron transport activity. Addition of trehalose to the films increases the stability further, especially for films maintained at low humidity. These stable hybrid film structures are promising for further studies towards developing new phototransformation devices for biotechnological applications. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Protein dynamics modulated electron transfer kinetics in early stage photosynthesis.

    Science.gov (United States)

    Kundu, Prasanta; Dua, Arti

    2013-01-28

    A recent experiment has probed the electron transfer kinetics in the early stage of photosynthesis in Rhodobacter sphaeroides for the reaction center of wild type and different mutants [Science 316, 747 (2007)]. By monitoring the changes in the transient absorption of the donor-acceptor pair at 280 and 930 nm, both of which show non-exponential temporal decay, the experiment has provided a strong evidence that the initial electron transfer kinetics is modulated by the dynamics of protein backbone. In this work, we present a model where the electron transfer kinetics of the donor-acceptor pair is described along the reaction coordinate associated with the distance fluctuations in a protein backbone. The stochastic evolution of the reaction coordinate is described in terms of a non-Markovian generalized Langevin equation with a memory kernel and Gaussian colored noise, both of which are completely described in terms of the microscopics of the protein normal modes. This model provides excellent fits to the transient absorption signals at 280 and 930 nm associated with protein distance fluctuations and protein dynamics modulated electron transfer reaction, respectively. In contrast to previous models, the present work explains the microscopic origins of the non-exponential decay of the transient absorption curve at 280 nm in terms of multiple time scales of relaxation of the protein normal modes. Dynamic disorder in the reaction pathway due to protein conformational fluctuations which occur on time scales slower than or comparable to the electron transfer kinetics explains the microscopic origin of the non-exponential nature of the transient absorption decay at 930 nm. The theoretical estimates for the relative driving force for five different mutants are in close agreement with the experimental estimates obtained using electrochemical measurements.

  10. Membrane development in purple photosynthetic bacteria in response to alterations in light intensity and oxygen tension.

    Science.gov (United States)

    Niederman, Robert A

    2013-10-01

    Studies on membrane development in purple bacteria during adaptation to alterations in light intensity and oxygen tension are reviewed. Anoxygenic phototrophic such as the purple α-proteobacterium Rhodobacter sphaeroides have served as simple, dynamic, and experimentally accessible model organisms for studies of the photosynthetic apparatus. A major landmark in photosynthesis research, which dramatically illustrates this point, was provided by the determination of the X-ray structure of the reaction center (RC) in Blastochloris viridis (Deisenhofer and Michel, EMBO J 8:2149-2170, 1989), once it was realized that this represented the general structure for the photosystem II RC present in all oxygenic phototrophs. This seminal advance, together with a considerable body of subsequent research on the light-harvesting (LH) and electron transfer components of the photosynthetic apparatus has provided a firm basis for the current understanding of how phototrophs acclimate to alterations in light intensity and quality. Oxygenic phototrophs adapt to these changes by extensive thylakoid membrane remodeling, which results in a dramatic supramolecular reordering to assure that an appropriate flow of quinone redox species occurs within the membrane bilayer for efficient and rapid electron transfer. Despite the high level of photosynthetic unit organization in Rba. sphaeroides as observed by atomic force microscopy (AFM), fluorescence induction/relaxation measurements have demonstrated that the addition of the peripheral LH2 antenna complex in cells adapting to low-intensity illumination results in a slowing of the rate of electron transfer turnover by the RC of up to an order of magnitude. This is ascribed to constraints in quinone redox species diffusion between the RC and cytochrome bc1 complexes arising from the increased packing density as the intracytoplasmic membrane (ICM) bilayer becomes crowded with LH2 rings. In addition to downshifts in light intensity as a paradigm

  11. Fusing two cytochromes b of Rhodobacter capsulatus cytochrome bc1 using various linkers defines a set of protein templates for asymmetric mutagenesis.

    Science.gov (United States)

    Czapla, Monika; Borek, Arkadiusz; Sarewicz, Marcin; Osyczka, Artur

    2012-01-01

    Cytochrome bc(1) (mitochondrial complex III), one of the key enzymes of biological energy conversion, is a functional homodimer in which each monomer contains three catalytic subunits: cytochrome c(1), the iron-sulfur subunit and cytochrome b. The latter is composed of eight transmembrane α-helices which, in duplicate, form a hydrophobic core of a dimer. We show that two cytochromes b can be fused into one 16-helical subunit using a number of different peptide linkers that vary in length but all connect the C-terminus of one cytochrome with the N-terminus of the other. The fusion proteins replace two cytochromes b in the dimer defining a set of available protein templates for introducing mutations that allow breaking symmetry of a dimer. A more detailed comparison of the form with the shortest, 3 amino acid, linker to the form with 12 amino acid linker established that both forms display similar level of structural plasticity to accommodate several, but not all, asymmetric patterns of mutations that knock out individual segments of cofactor chains. While the system based on a fused gene does not allow for the assessments of the functionality of electron-transfer paths in vivo, the family of proteins with fused cytochrome b offers attractive model for detailed investigations of molecular mechanism of catalysis at in vitro/reconstitution level.

  12. Expression of Uptake Hydrogenase and Molybdenum Nitrogenase in Rhodobacter capsulatus Is Coregulated by the RegB-RegA Two-Component Regulatory System

    OpenAIRE

    2000-01-01

    Purple photosynthetic bacteria are capable of generating cellular energy from several sources, including photosynthesis, respiration, and H2 oxidation. Under nutrient-limiting conditions, cellular energy can be used to assimilate carbon and nitrogen. This study provides the first evidence of a molecular link for the coregulation of nitrogenase and hydrogenase biosynthesis in an anoxygenic photosynthetic bacterium. We demonstrated that molybdenum nitrogenase biosynthesis is under the control o...

  13. Isolation and in vitro phosphorylation of sensory transduction components controlling anaerobic induction of light harvesting and reaction center gene expression in Rhodobacter capsulatus.

    Science.gov (United States)

    Inoue, K; Kouadio, J L; Mosley, C S; Bauer, C E

    1995-01-17

    Anaerobic induction of light harvesting and reaction center gene expression involves two transacting factors termed RegA and RegB. Sequence and mutational analysis has indicated that RegA and RegB constitute cognate components of a prokaryotic sensory transduction cascade with RegB comprising a membrane-spanning sensor kinase and RegA a cytosolic response regulator. In this study we have purified RegA, as well as a truncated portion of RegB (RegB') and undertaken an in vitro analysis of autophosphorylation and phosphotransfer activities. Incubation of RegB' with [gamma-32P]ATP and MgCl2 resulted in phosphorylation of RegB' (RegB' approximately P) over a 20-min incubation period. Incubation of RegB' approximately P with RegA resulted in rapid transfer of the phosphate from RegB' to RegA. In analogy to other characterized prokaryotic sensory transduction components, mutational and chemical stability studies also indicate that RegB' is autophosphorylated at a conserved histidine and that RegA accepts the phosphate from RegB at a conserved aspartate.

  14. Carotenoid biosynthesis in bacteria: In vitro studies of a crt/bch transcription factor from Rhodobacter capsulatus and carotenoid enzymes from Erwinia herbicola

    Energy Technology Data Exchange (ETDEWEB)

    O' Brien, D.A.

    1992-11-01

    A putative transcription factor in Rhodobactor capsulatus which binds upstream of the crt and bch pigment biosynthesis operons and appears to play a role in the adaptation of the organism from the aerobic to the anaerobic-photosynthetic growth mode was characterized. Chapter 2 describes the identification of this factor through an in vitro mobility shift assay, as well as the determination of its binding properties and sequence specificity. Chapter 3 focuses on the isolation of this factor. Biochemistry of later carotenoid biosynthesis enzymes derived from the non-photosynthetic bacterium, Erwinia herbicola. Chapter 4 describes the separate overexpression and in vitro analysis of two enzymes involved in the main sequence of the carotenoid biosynthesis pathway, lycopene cyclase and 5-carotene hydroxylase. Chapter 5 examines the overexpression and enzymology of functionally active zeaxanthin glucosyltransferase, an enzyme which carries out a more unusual transformation, converting a carotenoid into its more hydrophilic mono- and diglucoside derivatives. In addition, amino acid homology with other glucosyltransferases suggests a putative binding site for the UDP-activated glucose substrate.

  15. Carotenoid biosynthesis in bacteria: In vitro studies of a crt/bch transcription factor from Rhodobacter capsulatus and carotenoid enzymes from Erwinia herbicola

    Energy Technology Data Exchange (ETDEWEB)

    O`Brien, David Allen [Univ. of California, Berkeley, CA (United States)

    1992-11-01

    A putative transcription factor in Rhodobactor capsulatus which binds upstream of the crt and bch pigment biosynthesis operons and appears to play a role in the adaptation of the organism from the aerobic to the anaerobic-photosynthetic growth mode was characterized. Chapter 2 describes the identification of this factor through an in vitro mobility shift assay, as well as the determination of its binding properties and sequence specificity. Chapter 3 focuses on the isolation of this factor. Biochemistry of later carotenoid biosynthesis enzymes derived from the non-photosynthetic bacterium, Erwinia herbicola. Chapter 4 describes the separate overexpression and in vitro analysis of two enzymes involved in the main sequence of the carotenoid biosynthesis pathway, lycopene cyclase and 5-carotene hydroxylase. Chapter 5 examines the overexpression and enzymology of functionally active zeaxanthin glucosyltransferase, an enzyme which carries out a more unusual transformation, converting a carotenoid into its more hydrophilic mono- and diglucoside derivatives. In addition, amino acid homology with other glucosyltransferases suggests a putative binding site for the UDP-activated glucose substrate.

  16. The influence of quorum sensing in compartment II of the MELiSSA loop

    Science.gov (United States)

    Condori, Sandra; Mastroleo, Felice; Wattiez, Ruddy; Leys, Natalie

    MELiSSA (Micro-Ecological Life Support System Alternative) has been conceived as a 5 compartments microorganisms and higher plants recycling system for long haul space flights. Rhodospirillum rubrum S1H colonizes compartment II. Previous work reported that continuous culture of the bacterium in a photobioreactor could lead to thick biofilm formation, leading to bioreactor arrest. Our aim is to investigate the unknown quorum sensing (QS) system of R. rubrum S1H, specifically under MELiSSA relevant culture conditions meaning light anaerobic (LAN) and using acetate as carbon source. In that purpose an autoinducer synthase gene (Rru_A3396) knockout mutant was constructed by allelic exchange generating strain M68. In addition phenotypic comparison between wild type (WT) and M68 was performed. Results of thin layer chromatography assay where Agrobacterium tumefaciens NT1 have been used as reporter strain showed that WT produces acyl-homoserine lactones (AHLs) from C4 to C12 acyl carbon chain length; however, in M68 no AHLs were detected confirming that gene Rru_A3396 (named rruI) encodes an autoinducer synthase. Interestingly under a low shear or static environment M68 showed cell aggregation similar as reported in a closely related bacterium Rhodobacter sphaeroides (cerI mutant). In contrast to WT, M68 did not form biofilm and exhibited a decreased motility and pigment content. M68 vs wild type transcriptomics results showed that 326 genes were statistically significant differentially expressed. Downregulation of genes related to photosynthesis e.g., reaction center subunits, light harvesting complex and photosynthetic assembly proteins was observed. Similar results were obtained for preliminary proteomic analysis. Results obtained showed that in R. rubrum S1H the AHL-based QS system regulates almost 8% of the genome which is linked to biofilm formation among other biological processes described above. Since strain M68 could not be used in compartment II due to its less

  17. Identification of the proton pathway in bacterial reaction centers: Both protons associated with reduction of QB to QBH2 share a common entry point

    Science.gov (United States)

    Ädelroth, Pia; Paddock, Mark L.; Sagle, Laura B.; Feher, George; Okamura, Melvin Y.

    2000-01-01

    The reaction center from Rhodobacter sphaeroides uses light energy for the reduction and protonation of a quinone molecule, QB. This process involves the transfer of two protons from the aqueous solution to the protein-bound QB molecule. The second proton, H+(2), is supplied to QB by Glu-L212, an internal residue protonated in response to formation of QA− and QB−. In this work, the pathway for H+(2) to Glu-L212 was studied by measuring the effects of divalent metal ion binding on the protonation of Glu-L212, which was assayed by two types of processes. One was proton uptake from solution after the one-electron reduction of QA (DQA→D+QA−) and QB (DQB→D+QB−), studied by using pH-sensitive dyes. The other was the electron transfer kAB(1) (QA−QB→QAQB−). At pH 8.5, binding of Zn2+, Cd2+, or Ni2+ reduced the rates of proton uptake upon QA− and QB− formation as well as kAB(1) by ≈an order of magnitude, resulting in similar final values, indicating that there is a common rate-limiting step. Because D+QA− is formed 105-fold faster than the induced proton uptake, the observed rate decrease must be caused by an inhibition of the proton transfer. The Glu-L212→Gln mutant reaction centers displayed greatly reduced amplitudes of proton uptake and exhibited no changes in rates of proton uptake or electron transfer upon Zn2+ binding. Therefore, metal binding specifically decreased the rate of proton transfer to Glu-L212, because the observed rates were decreased only when proton uptake by Glu-L212 was required. The entry point for the second proton H+(2) was thus identified to be the same as for the first proton H+(1), close to the metal binding region Asp-H124, His-H126, and His-H128. PMID:11078513

  18. Hydrogen bonding and spin density distribution in the Qb semiquinone of bacterial reaction centers and comparison with the Qa site.

    Science.gov (United States)

    Martin, Erik; Samoilova, Rimma I; Narasimhulu, Kupala V; Lin, Tzu-Jen; O'Malley, Patrick J; Wraight, Colin A; Dikanov, Sergei A

    2011-04-13

    In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (Q(A)) and secondary (Q(B)) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the Q(A) and Q(B) sites, using samples of (15)N-labeled reaction centers, with the native high spin Fe(2+) exchanged for diamagnetic Zn(2+), prepared in (1)H(2)O and (2)H(2)O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the Q(A) SQ by Flores et al. (Biophys. J.2007, 92, 671-682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6-5.4 MHz. HYSCORE was then applied to the Q(B) SQ where we found proton lines corresponding to T ≈ 5.2, 3.7 MHz and T ≈ 1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the Q(B) site, were used to assign the observed couplings to specific hydrogen bonding interactions with the Q(B) SQ. These calculations allow us to assign the T = 5.2 MHz proton to the His-L190 N(δ)H···O(4) (carbonyl) hydrogen bonding interaction. The T = 3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the Q(B) site show less asymmetric distribution of unpaired spin density over the SQ than seen for the Q(A) site, consistent with available experimental data for (13)C and (17)O carbonyl hyperfine couplings. The implications of these interactions for Q

  19. Hydrogen bonding and spin density distribution in the QB semiquinone of bacterial reaction centers and comparison with the QA site

    Science.gov (United States)

    Martin, Erik; Samoilova, Rimma I.; Narasimhulu, Kupala V.; Lin, Tzu-Jen; O’Malley, Patrick J.; Wraight, Colin A.; Dikanov, Sergei A.

    2011-01-01

    In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (QA) and secondary (QB) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the QA and QB sites, using samples of 15N-labeled reaction centers, with the native high spin Fe2+ exchanged for diamagnetic Zn2+, prepared in 1H2O and 2H2O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the QA SQ by Flores et al. (Biophys. J. 2007, 92, 671–682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6–5.4 MHz. HYSCORE was then applied to the QB SQ where we found proton lines corresponding to T~5.2, 3.7 MHz and T~1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the QB site, were used to assign the observed couplings to specific hydrogen bonding interactions with the QB SQ. These calculations allow us to assign the T=5.2 MHz proton to the His-L190 NδH…O4 (carbonyl) hydrogen bonding interaction. The T =3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the QB site show less asymmetric distribution of unpaired spin density over the SQ than seen for the QA site, consistent with available experimental data for 13C and 17O carbonyl hyperfine couplings. The implications of these interactions for QB function and comparisons with the QA site are discussed

  20. Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems.

    Science.gov (United States)

    Huo, Pengfei; Coker, David F

    2012-03-21

    Two-dimensional photon-echo experiments indicate that excitation energy transfer between chromophores near the reaction center of the photosynthetic purple bacterium Rhodobacter sphaeroides occurs coherently with decoherence times of hundreds of femtoseconds, comparable to the energy transfer time scale in these systems. The original explanation of this observation suggested that correlated fluctuations in chromophore excitation energies, driven by large scale protein motions could result in long lived coherent energy transfer dynamics. However, no significant site energy correlation has been found in recent molecular dynamics simulations of several model light harvesting systems. Instead, there is evidence of correlated fluctuations in site energy-electronic coupling and electronic coupling-electronic coupling. The roles of these different types of correlations in excitation energy transfer dynamics are not yet thoroughly understood, though the effects of site energy correlations have been well studied. In this paper, we introduce several general models that can realistically describe the effects of various types of correlated fluctuations in chromophore properties and systematically study the behavior of these models using general methods for treating dissipative quantum dynamics in complex multi-chromophore systems. The effects of correlation between site energy and inter-site electronic couplings are explored in a two state model of excitation energy transfer between the accessory bacteriochlorophyll and bacteriopheophytin in a reaction center system and we find that these types of correlated fluctuations can enhance or suppress coherence and transfer rate simultaneously. In contrast, models for correlated fluctuations in chromophore excitation energies show enhanced coherent dynamics but necessarily show decrease in excitation energy transfer rate accompanying such coherence enhancement. Finally, for a three state model of the Fenna-Matthews-Olsen light

  1. Kinetics of H+ ion binding by the P+QA-state of bacterial photosynthetic reaction centers: rate limitation within the protein.

    Science.gov (United States)

    Maróti, P; Wraight, C A

    1997-07-01

    The kinetics of flash-induced H+ ion binding by isolated reaction centers (RCs) of Rhodobacter sphaeroides, strain R-26, were measured, using pH indicators and conductimetry, in the presence of terbutryn to block electron transfer between the primary and secondary quinones (QA and QB), and in the absence of exogenous electron donors to the oxidized primary donor, P+, i.e., the P+QA-state. Under these conditions, proton binding by RCs is to the protein rather than to any of the cofactors. After light activation to form P+QA-, the kinetics of proton binding were monoexponential at all pH values studied. At neutral pH, the apparent bimolecular rate constant was close to the diffusional limit for proton transfer in aqueous solution (approximately 10(11) M-1 s-1), but increased significantly in the alkaline pH range (e.g., 2 x 10(13) M-1 s-1 at pH 10). The average slope of the pH dependence was -0.4 instead of -1.0, as might be expected for a H+ diffusion-controlled process. High activation energy (0.54 eV at pH 8.0) and weak viscosity dependence showed that H+ ion uptake by RCs is not limited by diffusion. The salt dependence of the H+ ion binding rate and the pK values of the protonatable amino acid residues of the reaction center implicated surface charge influences, and Gouy-Chapman theory provided a workable description of the ionic effects as arising from modulation of the pH at the surface of the RC. Incubation in D2O caused small increases in the pKs of the protonatable groups and a small, pH (pD)-dependent slowing of the binding rate. The salt, pH, temperature, viscosity, and D2O dependences of the proton uptake by RCs in the P+QA- state were accounted for by three considerations: 1) parallel pathways of H+ delivery to the RC, contributing to the observed (net) H+ disappearance; 2) rate limitation of the protonation of target groups within the protein by conformational dynamics; and 3) electrostatic influences of charged groups in the protein, via the surface pH.

  2. Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups

    Directory of Open Access Journals (Sweden)

    Mok Amy

    2007-11-01

    Full Text Available Abstract Background Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major subgroups (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales, very few or no distinctive molecular or biochemical characteristics are known. Results We have carried out comprehensive phylogenomic analyses by means of Blastp and PSI-Blast searches on the open reading frames in the genomes of several α-proteobacteria (viz. Bradyrhizobium japonicum, Brucella suis, Caulobacter crescentus, Gluconobacter oxydans, Mesorhizobium loti, Nitrobacter winogradskyi, Novosphingobium aromaticivorans, Rhodobacter sphaeroides 2.4.1, Silicibacter sp. TM1040, Rhodospirillum rubrum and Wolbachia (Drosophila endosymbiont. These studies have identified several proteins that are distinctive characteristics of all α-proteobacteria, as well as numerous proteins that are unique repertoires of all of its main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales and many families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae. Many other proteins that are present at different phylogenetic depths in α-proteobacteria provide important information regarding their evolution. The evolutionary relationships among α-proteobacteria as deduced from these studies are in excellent agreement with their branching pattern in the phylogenetic trees and character compatibility cliques based on concatenated sequences for many conserved proteins. These studies provide evidence that the major groups within α-proteobacteria have diverged in the following order: (Rickettsiales(Rhodospirillales (Sphingomonadales (Rhodobacterales (Caulobacterales-Parvularculales (Rhizobiales. We also describe two conserved inserts in DNA

  3. Structure of the Cellulose Synthase Complex of Gluconacetobacter hansenii at 23.4 A Resolution.

    Directory of Open Access Journals (Sweden)

    Juan Du

    Full Text Available Bacterial crystalline cellulose is used in biomedical and industrial applications, but the molecular mechanisms of synthesis are unclear. Unlike most bacteria, which make non-crystalline cellulose, Gluconacetobacter hansenii extrudes profuse amounts of crystalline cellulose. Its cellulose synthase (AcsA exists as a complex with accessory protein AcsB, forming a 'terminal complex' (TC that has been visualized by freeze-fracture TEM at the base of ribbons of crystalline cellulose. The catalytic AcsAB complex is embedded in the cytoplasmic membrane. The C-terminal portion of AcsC is predicted to form a translocation channel in the outer membrane, with the rest of AcsC possibly interacting with AcsD in the periplasm. It is thus believed that synthesis from an organized array of TCs coordinated with extrusion by AcsC and AcsD enable this bacterium to make crystalline cellulose. The only structural data that exist for this system are the above mentioned freeze-fracture TEM images, fluorescence microscopy images revealing that TCs align in a row, a crystal structure of AcsD bound to cellopentaose, and a crystal structure of PilZ domain of AcsA. Here we advance our understanding of the structural basis for crystalline cellulose production by bacterial cellulose synthase by determining a negative stain structure resolved to 23.4 Å for highly purified AcsAB complex that catalyzed incorporation of UDP-glucose into β-1,4-glucan chains, and responded to the presence of allosteric activator cyclic diguanylate. Although the AcsAB complex was functional in vitro, the synthesized cellulose was not visible in TEM. The negative stain structure revealed that AcsAB is very similar to that of the BcsAB synthase of Rhodobacter sphaeroides, a non-crystalline cellulose producing bacterium. The results indicate that the crystalline cellulose producing and non-crystalline cellulose producing bacteria share conserved catalytic and membrane translocation components, and

  4. Structure of the Cellulose Synthase Complex of Gluconacetobacter hansenii at 23.4 Å Resolution

    Science.gov (United States)

    Du, Juan; Vepachedu, Venkata; Cho, Sung Hyun; Kumar, Manish; Nixon, B. Tracy

    2016-01-01

    Bacterial crystalline cellulose is used in biomedical and industrial applications, but the molecular mechanisms of synthesis are unclear. Unlike most bacteria, which make non-crystalline cellulose, Gluconacetobacter hansenii extrudes profuse amounts of crystalline cellulose. Its cellulose synthase (AcsA) exists as a complex with accessory protein AcsB, forming a 'terminal complex' (TC) that has been visualized by freeze-fracture TEM at the base of ribbons of crystalline cellulose. The catalytic AcsAB complex is embedded in the cytoplasmic membrane. The C-terminal portion of AcsC is predicted to form a translocation channel in the outer membrane, with the rest of AcsC possibly interacting with AcsD in the periplasm. It is thus believed that synthesis from an organized array of TCs coordinated with extrusion by AcsC and AcsD enable this bacterium to make crystalline cellulose. The only structural data that exist for this system are the above mentioned freeze-fracture TEM images, fluorescence microscopy images revealing that TCs align in a row, a crystal structure of AcsD bound to cellopentaose, and a crystal structure of PilZ domain of AcsA. Here we advance our understanding of the structural basis for crystalline cellulose production by bacterial cellulose synthase by determining a negative stain structure resolved to 23.4 Å for highly purified AcsAB complex that catalyzed incorporation of UDP-glucose into β-1,4-glucan chains, and responded to the presence of allosteric activator cyclic diguanylate. Although the AcsAB complex was functional in vitro, the synthesized cellulose was not visible in TEM. The negative stain structure revealed that AcsAB is very similar to that of the BcsAB synthase of Rhodobacter sphaeroides, a non-crystalline cellulose producing bacterium. The results indicate that the crystalline cellulose producing and non-crystalline cellulose producing bacteria share conserved catalytic and membrane translocation components, and support the

  5. Stigmatellin probes the electrostatic potential in the QB site of the photosynthetic reaction center.

    Science.gov (United States)

    Gerencsér, László; Boros, Bogáta; Derrien, Valerie; Hanson, Deborah K; Wraight, Colin A; Sebban, Pierre; Maróti, Péter

    2015-01-20

    The electrostatic potential in the secondary quinone (QB) binding site of the reaction center (RC) of the photosynthetic bacterium Rhodobacter sphaeroides determines the rate and free energy change (driving force) of electron transfer to QB. It is controlled by the ionization states of residues in a strongly interacting cluster around the QB site. Reduction of the QB induces change of the ionization states of residues and binding of protons from the bulk. Stigmatellin, an inhibitor of the mitochondrial and photosynthetic respiratory chain, has been proven to be a unique voltage probe of the QB binding pocket. It binds to the QB site with high affinity, and the pK value of its phenolic group monitors the local electrostatic potential with high sensitivity. Investigations with different types of detergent as a model system of isolated RC revealed that the pK of stigmatellin was controlled overwhelmingly by electrostatic and slightly by hydrophobic interactions. Measurements showed a high pK value (>11) of stigmatellin in the QB pocket of the dark-state wild-type RC, indicating substantial negative potential. When the local electrostatics of the QB site was modulated by a single mutation, L213Asp → Ala, or double mutations, L213Asp-L212Glu → Ala-Ala (AA), the pK of stigmatellin dropped to 7.5 and 7.4, respectively, which corresponds to a >210 mV increase in the electrostatic potential relative to the wild-type RC. This significant pK drop (ΔpK > 3.5) decreased dramatically to (ΔpK > 0.75) in the RC of the compensatory mutant (AA+M44Asn → AA+M44Asp). Our results indicate that the L213Asp is the most important actor in the control of the electrostatic potential in the QB site of the dark-state wild-type RC, in good accordance with conclusions of former studies using theoretical calculations or light-induced charge recombination assay.

  6. HMGB1 Contributes to the Expression of P-Glycoprotein in Mouse Epileptic Brain through Toll-Like Receptor 4 and Receptor for Advanced Glycation End Products.

    Directory of Open Access Journals (Sweden)

    Yan Chen

    Full Text Available The objective of the present study was to investigate the role of high-mobility group box-1 (HMGB1 in the seizure-induced P-glycoprotein (P-gp overexpression and the underlying mechanism. Kainic acid (KA-induced mouse seizure model was used for in vivo experiments. Male C57BL/6 mice were divided into four groups: normal saline control (NS group, KA-induced epileptic seizure (EP group, and EP group pretreated with HMGB1 (EP+HMGB1 group or BoxA (HMGB1 antagonist, EP+BoxA group. Compared to the NS group, increased levels of HMGB1 and P-gp in the brain were observed in the EP group. Injection of HMGB1 before the induction of KA further increased the expression of P-gp while pre-treatment with BoxA abolished this up-regulation. Next, the regulatory role of HMGB1 and its potential involved signal pathways were investigated in mouse microvascular endothelial bEnd.3 cells in vitro. Cells were treated with HMGB1, HMGB1 plus lipopolysaccharide from Rhodobacter sphaeroides (LPS-RS [toll-like receptor 4 (TLR4 antagonist], HMGB1 plus FPS-ZM1 [receptor for advanced glycation end products (RAGE inhibitor], HMGB1 plus SN50 [nuclear factor-kappa B (NF-κB inhibitor], or vehicle. Treatment with HMGB1 increased the expression levels of P-gp, TLR4, RAGE and the activation of NF-κB in bEnd.3 cells. These effects were inhibited by the pre-treatment with either LPS-RS or FPS-ZM1, and were abolished by the pre-treatment of SN50 or a combination treatment of both LPS-RS and FPS-ZM1. Luciferase reporter assays showed that exogenous expression of NF-κB p65 increased the promoter activity of multidrug resistance 1a (P-gp-encoding gene in endothelial cells. These data indicate that HMGB1 contributes to the overexpression of P-gp in mouse epileptic brain tissues via activation of TLR4/RAGE receptors and the downstream transcription factor NF-κB in brain microvascular endothelial cells.

  7. Crystallographic Location and Mutational Analysis of Zn and Cd Inhibitory Sites and Role of Lipidic Carboxylates in Rescuing Proton Path Mutants in Cytochrome c Oxidase

    Energy Technology Data Exchange (ETDEWEB)

    Qin, Ling; Mills, Denise A.; Hiser, Carrie; Murphree, Anna; Garavito, R. Michael; Ferguson-Miller, Shelagh; Hosler, Jonathan (MSU); (UMMC)

    2009-01-15

    Cytochrome c oxidase (CcO) transfers protons from the inner surface of the enzyme to the buried O{sub 2} reduction site through two different pathways, termed K and D, and from the outer surface via an undefined route. These proton paths can be inhibited by metals such as zinc or cadmium, but the sites of inhibition have not been established. Anomalous difference Fourier analyses of Rhodobacter sphaeroides CcO crystals, with cadmium added, reveal metal binding sites that include the proposed initial proton donor/acceptor of the K pathway, Glu-101 of subunit II. Mutant forms of CcO that lack Glu-101{sub II} (E101A and E101A/H96A) exhibit low activity and eliminate metal binding at this site. Significant activity is restored to E101A and E101A/H96A by adding the lipophilic carboxylic compounds, arachidonic acid and cholic acid, but not by their non-carboxylic analogues. These amphipathic acids likely provide their carboxylic groups as substitute proton donors/acceptors in the absence of Glu-101{sub II}, as previously observed for arachidonic acid in mutants that alter Asp-132{sub I} of the D pathway. The activity of E101A/H96A is still inhibited by zinc, but this remaining inhibition is nearly eliminated by removal of subunit III, which is known to alter the D pathway. The results identify the Glu-101/His-96 site of subunit II as the site of metal binding that inhibits the uptake of protons into the K pathway and indicate that subunit III contributes to zinc binding and/or inhibition of the D pathway. By removing subunit III from E101A/H96A, thereby eliminating zinc inhibition of the uptake of protons from the inner surface of CcO, we confirm that an external zinc binding site is involved in inhibiting the backflow of protons to the active site.

  8. Kinetics of H+ ion binding by the P+QA-state of bacterial photosynthetic reaction centers: rate limitation within the protein.

    Science.gov (United States)

    Maróti, P; Wraight, C A

    1997-01-01

    The kinetics of flash-induced H+ ion binding by isolated reaction centers (RCs) of Rhodobacter sphaeroides, strain R-26, were measured, using pH indicators and conductimetry, in the presence of terbutryn to block electron transfer between the primary and secondary quinones (QA and QB), and in the absence of exogenous electron donors to the oxidized primary donor, P+, i.e., the P+QA-state. Under these conditions, proton binding by RCs is to the protein rather than to any of the cofactors. After light activation to form P+QA-, the kinetics of proton binding were monoexponential at all pH values studied. At neutral pH, the apparent bimolecular rate constant was close to the diffusional limit for proton transfer in aqueous solution (approximately 10(11) M-1 s-1), but increased significantly in the alkaline pH range (e.g., 2 x 10(13) M-1 s-1 at pH 10). The average slope of the pH dependence was -0.4 instead of -1.0, as might be expected for a H+ diffusion-controlled process. High activation energy (0.54 eV at pH 8.0) and weak viscosity dependence showed that H+ ion uptake by RCs is not limited by diffusion. The salt dependence of the H+ ion binding rate and the pK values of the protonatable amino acid residues of the reaction center implicated surface charge influences, and Gouy-Chapman theory provided a workable description of the ionic effects as arising from modulation of the pH at the surface of the RC. Incubation in D2O caused small increases in the pKs of the protonatable groups and a small, pH (pD)-dependent slowing of the binding rate. The salt, pH, temperature, viscosity, and D2O dependences of the proton uptake by RCs in the P+QA- state were accounted for by three considerations: 1) parallel pathways of H+ delivery to the RC, contributing to the observed (net) H+ disappearance; 2) rate limitation of the protonation of target groups within the protein by conformational dynamics; and 3) electrostatic influences of charged groups in the protein, via the surface p

  9. Photobiological hydrogen production and carbon dioxide sequestration

    Science.gov (United States)

    Berberoglu, Halil

    Photobiological hydrogen production is an alternative to thermochemical and electrolytic technologies with the advantage of carbon dioxide sequestration. However, it suffers from low solar to hydrogen energy conversion efficiency due to limited light transfer, mass transfer, and nutrient medium composition. The present study aims at addressing these limitations and can be divided in three parts: (1) experimental measurements of the radiation characteristics of hydrogen producing and carbon dioxide consuming microorganisms, (2) solar radiation transfer modeling and simulation in photobioreactors, and (3) parametric experiments of photobiological hydrogen production and carbon dioxide sequestration. First, solar radiation transfer in photobioreactors containing microorganisms and bubbles was modeled using the radiative transport equation (RTE) and solved using the modified method of characteristics. The study concluded that Beer-Lambert's law gives inaccurate results and anisotropic scattering must be accounted for to predict the local irradiance inside a photobioreactor. The need for accurate measurement of the complete set of radiation characteristics of microorganisms was established. Then, experimental setup and analysis methods for measuring the complete set of radiation characteristics of microorganisms have been developed and successfully validated experimentally. A database of the radiation characteristics of representative microorganisms have been created including the cyanobacteria Anabaena variabilis, the purple non-sulfur bacteria Rhodobacter sphaeroides and the green algae Chlamydomonas reinhardtii along with its three genetically engineered strains. This enabled, for the first time, quantitative assessment of the effect of genetic engineering on the radiation characteristics of microorganisms. In addition, a parametric experimental study has been performed to model the growth, CO2 consumption, and H 2 production of Anabaena variabilis as functions of

  10. A light-harvesting antenna protein retains its folded conformation in the absence of protein-lipid and protein-pigment interactions.

    Science.gov (United States)

    Kikuchi, J; Asakura, T; Loach, P A; Parkes-Loach, P S; Shimada, K; Hunter, C N; Conroy, M J; Williamson, M P

    1999-04-15

    The first study by nmr of the integral membrane protein, the bacterial light-harvesting (LH) antenna protein LH1 beta, is reported. The photosynthetic apparatus of purple bacteria contains two different kinds of antenna complexes (LH1 and LH2), which consist of two small integral membrane proteins alpha and beta, each of approximately 6 kDa, and bacteriochlorophyll and carotenoid pigments. We have purified the antenna polypeptide LH1 beta from Rhodobacter sphaeroides, and have recorded CD spectra and a series of two-dimensional nmr spectra. A comparison of CD spectra of LH1 beta observed in organic solvents and detergent micelles shows that the helical character of the peptide does not change appreciably between the two milieus. A significantly high-field shifted methyl signal was observed both in organic solvents and in detergent micelles, implying that a similar three-dimensional structure is present in each case. However, the 1H-nmr signals observed in organic solvents had a narrower line width and better resolution, and it is shown that in this case organic solvents provide a better medium for nmr studies than detergent micelles. A sequential assignment has been carried out on the C-terminal transmembrane region, which is the region in which the pigment is bound. The region is shown to have a helical structure by the chemical shift values of the alpha-CH protons and the presence of nuclear Overhauser effects characteristic of helices. An analysis of the amide proton chemical shifts of the residues surrounding the histidine chlorophyll ligand suggests that the local structure is well ordered even in the absence of protein-lipid and protein-pigment interactions. Its structure was determined from 348 nmr-derived constraints by using distance geometry calculations. The polypeptide contains an alpha-helix extending from Leu19 (position of cytoplasmic surface) to Trp44 (position of periplasmic surface). The helix is bent, as expected from the amide proton chemical

  11. Evolution of taxis responses in virtual bacteria: non-adaptive dynamics.

    Directory of Open Access Journals (Sweden)

    Richard A Goldstein

    2008-05-01

    mediating taxis responses provide an explanation for experimental observations made in mutant strains of E. coli and in wild-type Rhodobacter sphaeroides that could not be explained with standard models. We speculate that such dynamics exist in other bacteria as well and play a role linking the metabolic state of the cell and the taxis response. The simplicity of mechanisms mediating such dynamics makes them a candidate precursor of more complex taxis responses involving adaptation. This study suggests a strong link between stimulus conditions during evolution and evolved pathway dynamics. When evolution was simulated under conditions of scarce and fluctuating stimulus conditions, the evolved pathway contained features of both adaptive and non-adaptive dynamics, suggesting that these two types of dynamics can have different advantages under distinct environmental circumstances.

  12. Repression of proinflammatory gene expression by lipid extract of Nostoc commune var sphaeroides Kützing, a blue-green alga, via inhibition of nuclear factor-kappaB in RAW 264.7 macrophages.

    Science.gov (United States)

    Park, Young-Ki; Rasmussen, Heather E; Ehlers, Sarah J; Blobaum, Kara R; Lu, Fan; Schlegal, Vicki L; Carr, Timothy P; Lee, Ji-Young

    2008-02-01

    We investigated whether lipid extract from a blue-green alga, N commune, modulates proinflammatory gene expression in RAW 264.7 macrophages. The cells were incubated with N commune lipid extract (0-100 microg/mL) and subsequently activated by LPS (100 ng/mL). Quantitative real-time PCR analysis showed that mRNA abundance of proinflammatory mediators, including TNF-alpha, COX-2, IL-1beta, IL-6, and iNOS, was significantly reduced by N commune lipid extract in a dose-dependent manner. Secretion of TNF-alpha and IL-1beta into cell culture medium was also significantly decreased by N commune lipid extract. Thin-layer chromatography-densitometry analysis showed that N commune lipid extract contained approximately 15% of fatty acids. To determine whether the inhibition of proinflammatory mediator production by N commune lipid extract is primarily conferred by fatty acids in the lipid extract, macrophages were incubated with 100 microg/mL of N commune lipid extract or 15 microg/mL of a fatty acid mixture, which was formulated to reflect the fatty acid composition of N commune lipid extract. The fatty acid mixture significantly reduced RNA abundance of TNF-alpha and COX-2, but to a lesser extent than did the N commune lipid extract, suggesting the presence of additional bioactive compounds with an antiinflammatory property in the lipid extract. As NF-kappaB is a major regulator for the proinflammatory gene expression, we measured its DNA-binding activity. DNA-binding activity of NF-kappaB was significantly reduced by N commune lipid extract. In conclusion, our study suggests that N commune lipid extract represses the expression of proinflammatory genes in RAW 264.7 macrophages, at least in part, by inhibiting the activation of NF-kappaB pathway.

  13. Content determination of the Metal Elements in the Edible Algae Spirulina and Nostoc sphaeroides%食用蓝藻螺旋藻和葛仙米中金属元素的分析

    Institute of Scientific and Technical Information of China (English)

    方倩; 马军国; 李效宇

    2015-01-01

    采用硝酸和高氯酸(4∶1)混合酸消化2种可食用蓝藻螺旋藻和葛仙米,原子吸收光谱法检测螺旋藻和葛仙米中的K、Na、Mg、Ca、Zn、Fe、Cu、Mn、Cr、Pb和Cd共11种金属元素含量.结果表明,2种蓝藻中矿质元素含量均较高,特别是Ca含量高达61 905.132 mg· kg-1;而有害重金属Cr,Po和Cd含量均远低于国家规定标准,表明这2种食用蓝藻均无重金属富集或污染.本结果显示,螺旋藻和葛仙米是极好的天然富钙营养食品,可作为人体矿质元素和微量元素缺乏症的补给品.

  14. 原位生物修复提高多环芳烃污染土壤农用安全性%Improving Agricultural Safety of Soils Contaminated with Polycyclic Aromatic Hydrocarbons by In Situ Bioremediation

    Institute of Scientific and Technical Information of China (English)

    焦海华; 潘建刚; 徐圣君; 白志辉; 王栋; 黄占斌

    2015-01-01

    In order to reduce the risk of enrichment of polycyclic aromatic hydrocarbons (PAHs) in crops, reduce the potential hazards of food-sourced PAHs to human and increase the agricultural safety of PAHs contaminated soils, the bio-augmented removal of polycyclic aromatic hydrocarbons (PAHs) was investigated through in situ remediation by introducing Rhodobacter sphaeroides (RS) into the agricultural soil contaminated by PAHs. The 50-times diluted RS was sprayed on leaf surface (in area B) or irrigated to roots (in area D). The treatment of spraying water of the equal amount was taken as the control ( A) and the wheat field without any treatment as the blank (CK). Treatments were conducted since wheat seeding. Soil and wheat samples were collected in the mature period to analyze the changes of community structure of the soil microorganisms and the concentration of PAHs in soils and investigate the strengthening and restoration effects of RS on PAHs contaminated soils. Compared to the CK area, the areas B and D revealed that the variation ratio of phospholipid fatty acids (PLFAs) that were the biomarker of soil microorganisms was 29. 6% , and the ratio of total PAHs removed was increased 1. 59 times and 1. 68 times, respectively. The dry weight of wheat grain of 50 spikes was increased by 8. 95% and 12. 5% , respectively, and the enrichment factor of total PAHs was decreased by 58. 9% and 62. 2% respectively in the wheat grains. All the results suggested that RS reduced enrichment of PAHs in wheat grains and increased wheat yield, which had great exploitation and utilization potentiality in repairing and improving the agricultural safety of the soils contaminated with PHAs.%为了减少多环芳烃(polycyclic aromatic hydrocarbons, PAHs)在作物体内的富集,降低食源性 PAHs 对人类的潜在风险,提高 PAHs 污染土壤的农用安全性,在受到 PAHs 污染的麦田中施用类球红细菌(Rhodobacter sphaeroide)菌剂(RS)进行原位修复.以叶

  15. NCBI nr-aa BLAST: CBRC-CJAC-01-1468 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CJAC-01-1468 ref|ZP_01615828.1| hypothetical protein GP2143_16686 [marine gamm...a proteobacterium HTCC2143] gb|EAW32911.1| hypothetical protein GP2143_16686 [marine gamma proteobacterium HTCC2143] ZP_01615828.1 2e-05 27% ...

  16. NCBI nr-aa BLAST: CBRC-DRER-05-0036 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DRER-05-0036 ref|ZP_01615828.1| hypothetical protein GP2143_16686 [marine gamm...a proteobacterium HTCC2143] gb|EAW32911.1| hypothetical protein GP2143_16686 [marine gamma proteobacterium HTCC2143] ZP_01615828.1 9e-08 40% ...

  17. NCBI nr-aa BLAST: CBRC-XTRO-01-2327 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-XTRO-01-2327 ref|ZP_01615828.1| hypothetical protein GP2143_16686 [marine gamm...a proteobacterium HTCC2143] gb|EAW32911.1| hypothetical protein GP2143_16686 [marine gamma proteobacterium HTCC2143] ZP_01615828.1 4e-05 28% ...

  18. NCBI nr-aa BLAST: CBRC-XTRO-01-3128 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-XTRO-01-3128 ref|ZP_01615828.1| hypothetical protein GP2143_16686 [marine gamm...a proteobacterium HTCC2143] gb|EAW32911.1| hypothetical protein GP2143_16686 [marine gamma proteobacterium HTCC2143] ZP_01615828.1 9e-06 43% ...

  19. NCBI nr-aa BLAST: CBRC-CREM-01-1347 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CREM-01-1347 ref|ZP_01225472.1| hypothetical protein GB2207_07756 [marine gamm...a proteobacterium HTCC2207] gb|EAS45933.1| hypothetical protein GB2207_07756 [marine gamma proteobacterium HTCC2207] ZP_01225472.1 4e-20 35% ...

  20. NCBI nr-aa BLAST: CBRC-XTRO-01-3110 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-XTRO-01-3110 ref|ZP_01615828.1| hypothetical protein GP2143_16686 [marine gamm...a proteobacterium HTCC2143] gb|EAW32911.1| hypothetical protein GP2143_16686 [marine gamma proteobacterium HTCC2143] ZP_01615828.1 0.003 30% ...

  1. NCBI nr-aa BLAST: CBRC-PTRO-27-0032 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PTRO-27-0032 ref|ZP_01618027.1| hypothetical protein GP2143_02145 [marine gamm...a proteobacterium HTCC2143] gb|EAW30306.1| hypothetical protein GP2143_02145 [marine gamma proteobacterium HTCC2143] ZP_01618027.1 5.3 26% ...

  2. NCBI nr-aa BLAST: CBRC-XTRO-01-1662 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-XTRO-01-1662 ref|ZP_01615828.1| hypothetical protein GP2143_16686 [marine gamm...a proteobacterium HTCC2143] gb|EAW32911.1| hypothetical protein GP2143_16686 [marine gamma proteobacterium HTCC2143] ZP_01615828.1 1e-08 32% ...

  3. Two “Candidatus Liberibacter asiaticus” strains recently found in California harbor different prophages

    Science.gov (United States)

    “Candidatus Liberibacter asiaticus” (CLas), an a-proteobacterium, is associated with citrus Huanglongbing (HLB; yellow shoot disease). In California, CLas was first detected in the residential neighborhoods in Los Angeles County of Hacienda Heights (HH) in 2012 and in San Gabriel (SG) in 2015. Altho...

  4. Whole genome sequence analyses revealed that strains of “Candidatus Liberibacter asiaticus” recently found in two California locations were different

    Science.gov (United States)

    ‘Candidatus Liberibacter asiaticus’ (CLas), an a-proteobacterium, is associated with citrus Huanglongbing (HLB; yellow shoot disease). In California, CLas was first detected in residential neighborhoods of Hacienda Heights (HH) in 2012 and San Gabriel (SG) in 2015. Although all infected trees were d...

  5. A single prophage carrying a CRISPR/cas system in ‘Candidatus Liberibacter asiaticus’ strain A4 from Guangdong, China

    Science.gov (United States)

    “Candidatus Liberibacter asiaticus” (CLas) is an unculturable a-proteobacterium associated with citrus huanglongbing (HLB, yellow shoot disease), a highly destructive disease that affects citrus production worldwide. HLB was observed in Guangdong Province of China over a hundred years ago and remain...

  6. Engineering and Coordination of Regulatory Networks and Intracellular Complexes to Maximize Hydrogen Production by Phototrophic Microorganisms

    Energy Technology Data Exchange (ETDEWEB)

    James C. Liao

    2012-05-22

    reductive pentose phosphate pathway, whose key enzyme is ribulose 1,5-biphosphate carboxylase/oxygenase (RubisCO). In addition to providing virtually all cellular carbon during autotrophic metabolism, RubisCO-mediated CO{sub 2} assimilation is also very important for nonsulfur purple photosynthetic bacteria under photoheterotrophic growth conditions since CO{sub 2} becomes the major electron sink under these conditions. In this work, Ensemble Modeling (EM) was developed to examine the behavior of CBB-compromised RubisCO knockout mutant strains of the nonsulfur purple photosynthetic bacterium Rhodobacter sphaeroides. Mathematical models of metabolism can be a great aid in studying the effects of large perturbations to the system, such as the inactivation of RubisCO. Due to the complex and highly-interconnected nature of these networks, it is not a trivial process to understand what the effect of perturbations to the metabolic network will be, or vice versa, what enzymatic perturbations are necessary to yield a desired effect. Flux distribution is controlled by multiple enzymes in the network, often indirectly linked to the pathways of interest. Further, depending on the state of the cell and the environmental conditions, the effect of a perturbation may center around how it effects the carbon flow in the network, the balancing of cofactors, or both. Thus, it is desirable to develop mathematical models to describe, understand, and predict network behavior. Through the development of such models, one may gain the ability to generate a set of testable hypotheses for system behavior.

  7. Bio-Photoelectrochemical Solar Cells Incorporating Reaction Center and Reaction Center Plus Light Harvesting Complexes

    Science.gov (United States)

    Yaghoubi, Houman

    onto Au electrodes via surface exposed cysteine residues. This resulted in photocurrent densities as large as ~600 nA cm-2 while still the incident photon to generated electron quantum efficiency was as low as %3 x 10-4. 2- The second approach is to immobilize wild type RCs of Rhodobacter sphaeroides on the surface of a Au underlying electrode using self-assembled monolayers of carboxylic acid terminated oligomers and cytochrome c charge mediating layers, with a preferential orientation from the primary electron donor site. This approach resulted in EQE of up to 0.06%, which showed 200 times efficiency improvement comparing to the first approach. In the third approach, instead of isolated protein complexes, RCs plus light harvesting (LH) complexes were employed for a better photon absorption. Direct attachment of RC-LH1 complexes on Au working electrodes, resulted in 0.21% EQE which showed 3.5 times efficiency improvement over the second approach (700 times higher than the first approach). The main impact of this work is the harnessing of biological RCs for efficient energy harvesting in man-made structures. Specifically, the results in this work will advance the application of RCs in devices for energy harvesting and will enable a better understanding of bio and nanomaterial interfaces, thereby advancing the application of biological materials in electronic devices. At the end, this work offers general guidelines that can serve to improve the performance of bio-hybrid solar cells.

  8. Structural and Functional Proteomic Analysis of a Developing Energy Transducing Membrane

    Energy Technology Data Exchange (ETDEWEB)

    Niederman, Robert A

    2012-06-04

    While much is known about the light reactions of photosynthesis in purple bacteria, comparatively little information is available on how the requisite integral membrane proteins are assembled, their patterns of cellular localization are established or their apoproteins cooperate with numerous assembly factors in their insertion into the growing intracytoplasmic membrane (ICM). This problem was approached through a detailed structural and functional proteomic analysis of ICM assembly process in the well-characterized purple bacterium Rhodobacter sphaeroides. Proteomic approaches have focused upon identification of membrane proteins temporally expressed during ICM development and spatially localized in both membrane growth initiation sites and in mature ICM vesicles. Protocols were established for ICM induction under reduced aeration and ICM remodeling in cells adapting to low intensity illumination, which permitted isolation, in sucrose density gradients, of ICM growth initiation sites as an upper pigmented band (UPB) and mature ICM vesicles as the main (chromatophore) band. Non-denaturing clear native gel electrophoresis (CNE) of these isolated membrane fractions gave rise to pigmented bands containing the peripheral light-harvesting 2 (LH2) antenna and the reaction center-light-harvesting 1 (RC-LH1) core complex, together with a full array of other ICM proteins, which were subjected to proteomic analysis. Proteomic analysis of the gel bands from chromatophores revealed developmental changes including increasing levels of the LH2 complex as ICM development proceeded, as well as a large array of other associated proteins including high spectral counts for the F1FO ATP synthase subunits, given the inability to detect this coupling factor, as well as the more abundant cytochrome bc1 complex by atomic force microscopy (AFM). Significant levels of general membrane assembly factors were encountered, as well as high counts for RSP6124, a protein of unknown function

  9. ACTIVATION OF HUMAN BLOOD MONONUCLEARS BY LIPOPOLYSACCHARIDE OF DIFFERENT COMPOSITION

    Directory of Open Access Journals (Sweden)

    S. V. Zubova

    2010-01-01

    Full Text Available Influence of lipopolysaccharide (LPS composition upon activation of human blood mononuclears was investigated, by measuring levels of pro-inflammatory TNFα and IL-6 cytokines released by the cells. It is shown that LPS from Rhodobacter capsulatus PG, in contrast to E. coli LPS, did not activate the target cells for synthesis of the cytokines.

  10. GenBank blastx search result: AK103974 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK103974 001-016-F05 U23145.1 Rhodobacter capsulatus Calvin cycle carbon dioxide fi...ose-1,5-bisphosphate carboxylase/oxygenase (cbbM) gene, complete cds, and Calvin cycle operon: pentose-5-pho

  11. GenBank blastx search result: AK062574 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK062574 001-047-A01 U23145.1 Rhodobacter capsulatus Calvin cycle carbon dioxide fi...ose-1,5-bisphosphate carboxylase/oxygenase (cbbM) gene, complete cds, and Calvin cycle operon: pentose-5-pho

  12. GenBank blastx search result: AK061772 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK061772 001-039-C12 U23145.1 Rhodobacter capsulatus Calvin cycle carbon dioxide fi...ose-1,5-bisphosphate carboxylase/oxygenase (cbbM) gene, complete cds, and Calvin cycle operon: pentose-5-pho

  13. GenBank blastx search result: AK288454 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288454 J090035A12 U23145.1 RCU23145 Rhodobacter capsulatus Calvin cycle carbon di...II ribulose-1,5-bisphosphate carboxylase/oxygenase (cbbM) gene, complete cds, and Calvin cycle operon: pento

  14. GenBank blastx search result: AK110716 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK110716 002-170-D07 U23145.1 Rhodobacter capsulatus Calvin cycle carbon dioxide fi...ose-1,5-bisphosphate carboxylase/oxygenase (cbbM) gene, complete cds, and Calvin cycle operon: pentose-5-pho

  15. AcEST: DK958462 [AcEST

    Lifescience Database Archive (English)

    Full Text Available nyl hydrogenase OS=Rhodobacter c... 33 0.34 sp|O87875|BCRB_THAAR Benzoyl-CoA reductase subunit B OS=Thauera ...R Benzoyl-CoA reductase subunit B OS=Thauera aromatica GN=bcrB PE=1 SV=1 Length =

  16. AcEST: BP915350 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 3286|CCMF_ARATH Putative cytochrome c biogenesis ccmF-like ... 30 3.2 sp|O68032|SBCC_RHOCA Nuclease sbcCD su...-----LHWWMKNRKHNNFWL 360 >sp|O68032|SBCC_RHOCA Nuclease sbcCD subunit C OS=Rhodobacter capsulatus GN=sbcC PE

  17. Visualizing tributyltin (TBT) in bacterial aggregates by specific rhodamine-based fluorescent probes.

    Science.gov (United States)

    Jin, Xilang; Hao, Likai; She, Mengyao; Obst, Martin; Kappler, Andreas; Yin, Bing; Liu, Ping; Li, Jianli; Wang, Lanying; Shi, Zhen

    2015-01-01

    Here we present the first examples of fluorescent and colorimetric probes for microscopic TBT imaging. The fluorescent probes are highly selective and sensitive to TBT and have successfully been applied for imaging of TBT in bacterial Rhodobacter ferrooxidans sp. strain SW2 cell-EPS-mineral aggregates and in cell suspensions of the marine cyanobacterium Synechococcus PCC 7002 by using confocal laser scanning microscopy.

  18. "Paraffin wax-overlay of pour plate", a method for the isolation and enumeration of purple non-sulfur bacteria.

    Science.gov (United States)

    Archana, A; Sasikala, Ch; Ramana, Ch V; Arunasri, K

    2004-12-01

    A modification of pour plate technique with an overlay of wax was used for isolation and enumeration of purple non-sulfur bacteria (PNSB) with equal efficiency as that of agar shake culture. The total count of PNSB ranged from 10(5)-10(8) CFU g dry soil(-1) and belonged to the genera of Rhodobacter, Rhodopseudomonas, Rhodocista and Rubrivivax.

  19. Effect of a magnetic field on recombination fluorescence of a number of photosynthesizing bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Voznyak, V.M.; Elfimov, E.I.; Proskuryakov, I.I.

    1978-10-01

    A brief survey is initially presented of the transformation of the energy of an electron exitant into chemical energy of separated charges in a photosynthesing body, a transformation which occurs in the reaction centers (RC) of that body. The RC consists of 3 protein units, 4 molecules of bacteriochlorophyl (BCh), 2 molecules of bacteriotheophite (BTh) and an Fe-quinone complex. The primary reaction of photoinduced separators of charges occurs between BCh and BTh. Products formed have been discussed by several authors and the effect of a magnetic field has already been demonstrated. This present article studies photosynthesizing bacteria and the effect of a magnetic field on the yield of fluorescin. Bacteria studied include Rhodopseudomonas sphaeroides (a wild strain); Rhodospirillum rubrum; and Rhodopseudomonas sphaeroides R-26. Changes in the strength of a magnetic field are portrayed graphically, and a discussion is presented of the physical chemistry of the reactions involved.

  20. Malate dehydrogenase in phototrophic purple bacteria: purification, molecular weight, and quaternary structure.

    OpenAIRE

    1987-01-01

    The citric acid cycle enzyme malate dehydrogenase was purified to homogeneity from the nonsulfur purple bacteria Rhodobacter capsulatus, Rhodospirillum rubrum, Rhodomicrobium vannielii, and Rhodocyclus purpureus. Malate dehydrogenase was purified from each species by either a single- or a two-step protocol: triazine dye affinity chromatography was the key step in purification of malate dehydrogenase in all cases. Purification of malate dehydrogenase resulted in a 130- to 240-fold increase in ...

  1. Microbiological Hydrogen Production by Anaerobic Fermentation and Photosynthetic Process

    Energy Technology Data Exchange (ETDEWEB)

    Asada, Y.; Ohsawa, M.; Nagai, Y.; Fukatsu, M.; Ishimi, K.; Ichi-ishi, S.

    2009-07-01

    Hydrogen gas is a clean and renewable energy carrier. Microbiological hydrogen production from glucose or starch by combination used of an anaerobic fermenter and a photosynthetic bacterium, Rhodobacter spheroides RV was studied. In 1984, the co-culture of Clostridium butyricum and RV strain to convert glucose to hydrogen was demonstrated by Miyake et al. Recently, we studied anaerobic fermentation of starch by a thermophilic archaea. (Author)

  2. Microbial production of hydrogen from starch-manufacturing wastes

    Energy Technology Data Exchange (ETDEWEB)

    Yokoi, H.; Maki, R.; Hirose, J.; Hayashi, S. [Miyazaki Univ. (Japan). Dept. of Applied Chemistry

    2002-05-01

    Effective hydrogen production from starch-manufacturing wastes by microorganisms was investigated. Continuous hydrogen production in high yield of 2.7 mol H{sub 2} mol{sup -1} glucose was attained by a mixed culture of Clostridium butyricum and Enterobacter aerogenes HO-39 in the starch waste medium consisting of sweet potato starch residue as a carbon source and corn steep liquor as a nitrogen source in a repeated batch culture. Rhodobacter sp. M-19 could produce hydrogen from the supernatant of the culture broth obtained in the repeated batch culture of C. butyricum and E. aerogenes HO-39. Hydrogen yield of 4.5 mol H{sub 2} mol{sup -1} glucose was obtained by culturing Rhodobacter sp. M-19 in the supernatant supplemented with 20{mu}gl{sup -1} Na{sub 2}MoO{sub 4} 2H{sub 2}O and 10mgl{sup -1} EDTA in a repeated batch culture with pH control at 7.5. Therefore, continuous hydrogen production with total hydrogen yield of 7.2 mol H{sub 2} mol{sup -1} glucose from the starch remaining in the starch residue was attained by the repeated batch culture with C. butyricum and E. aerogenes HO-39 and by the successive repeated batch culture with Rhodobacter sp. M-19. (Author)

  3. Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis.

    Directory of Open Access Journals (Sweden)

    Kay Hamacher

    Full Text Available Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K(+ channels. To determine if these viral K(+ channels are the product of molecular piracy from their hosts, we compared the sequences of the K(+ channel pore modules from seven phycodnaviruses to the K(+ channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K(+ channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K(+ channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K(+ channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K(+ channels in algae and perhaps even all cellular organisms.

  4. Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis.

    Science.gov (United States)

    Hamacher, Kay; Greiner, Timo; Ogata, Hiroyuki; Van Etten, James L; Gebhardt, Manuela; Villarreal, Luis P; Cosentino, Cristian; Moroni, Anna; Thiel, Gerhard

    2012-01-01

    Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K(+) channels. To determine if these viral K(+) channels are the product of molecular piracy from their hosts, we compared the sequences of the K(+) channel pore modules from seven phycodnaviruses to the K(+) channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K(+) channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K(+) channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K(+) channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K(+) channels in algae and perhaps even all cellular organisms.

  5. Rhodobaca bogoriensis gen. nov. and sp. nov., an alkaliphilic purple nonsulfur bacterium from African Rift Valley soda lakes.

    Science.gov (United States)

    Milford, A D; Achenbach, L A; Jung, D O; Madigan, M T

    2000-01-01

    From enrichment cultures established for purple nonsulfur bacteria using water and sediment samples from Lake Bogoria and Crater Lake, two soda lakes in the African Rift Valley, three strains of purple nonsulfur bacteria were isolated; strain LBB1 was studied in detail. Cells of strain LBB1 were motile and spherical to rod-shaped, suggesting a relationship to Rhodobacter or Rhodovulum species, and the organism was capable of both phototrophic and chemotrophic growth on a wide variety of organic compounds. Phototrophically grown cultures were yellow to yellow-brown in color and grew optimally at pH 9 (pH range 7.5-10) and 1% NaCl (range 0-10%). In physiological studies of strain LBB1, neither photoautotrophy (H2- or sulfide-dependent) nor nitrogen fixation was observed. Absorption spectra revealed that all three strains contained bacteriochlorophyll a and carotenoids of the spheroidene pathway and synthesized only a light-harvesting (LH) I-type photosynthetic antenna complex. Electron microscopy of cells of strain LBB1 revealed a vesicular intracytoplasmic membrane system, although only a few vesicles were observed per cell. The G+C content of strain LBB1 DNA was 59 mol%, significantly lower than that of known Rhodobacter and Rhodovulum species, and its phylogeny as determined by ribosomal RNA gene sequencing placed it within the Rhodobacter/Rhodovulum clade yet distinct from all described species of either of these genera. The unique assemblage of properties observed in strain LBB1 warrants its inclusion in a new genus of purple nonsulfur bacteria and the name Rhodobaca bogoriensis is proposed herein, the genus name reflecting morphological characteristics and the species epithet referring to the habitat.

  6. Characterization of a major cluster of nif, fix, and associated genes in a sugarcane endophyte, Acetobacter diazotrophicus.

    Science.gov (United States)

    Lee, S; Reth, A; Meletzus, D; Sevilla, M; Kennedy, C

    2000-12-01

    A major 30.5-kb cluster of nif and associated genes of Acetobacter diazotrophicus (syn. Gluconacetobacter diazotrophicus), a nitrogen-fixing endophyte of sugarcane, was sequenced and analyzed. This cluster represents the largest assembly of contiguous nif-fix and associated genes so far characterized in any diazotrophic bacterial species. Northern blots and promoter sequence analysis indicated that the genes are organized into eight transcriptional units. The overall arrangement of genes is most like that of the nif-fix cluster in Azospirillum brasilense, while the individual gene products are more similar to those in species of Rhizobiaceae or in Rhodobacter capsulatus.

  7. Biomimetic Membranes for Multi-Redox Center Proteins

    Directory of Open Access Journals (Sweden)

    Renate L. C. Naumann

    2016-03-01

    Full Text Available His-tag technology was applied for biosensing purposes involving multi-redox center proteins (MRPs. An overview is presented on various surfaces ranging from flat to spherical and modified with linker molecules with nitrile-tri-acetic acid (NTA terminal groups to bind his-tagged proteins in a strict orientation. The bound proteins are submitted to in situ dialysis in the presence of lipid micelles to form a so-called protein-tethered bilayer lipid membrane (ptBLM. MRPs, such as the cytochrome c oxidase (CcO from R. sphaeroides and P. denitrificans, as well as photosynthetic reactions centers (RCs from R. sphaeroides, were thus investigated. Electrochemical and surface-sensitive optical techniques, such as surface plasmon resonance, surface plasmon-enhanced fluorescence, surface-enhanced infrared absorption spectroscopy (SEIRAS and surface-enhanced resonance Raman spectroscopy (SERRS, were employed in the case of the ptBLM structure on flat surfaces. Spherical particles ranging from µm size agarose gel beads to nm size nanoparticles modified in a similar fashion were called proteo-lipobeads (PLBs. The particles were investigated by laser-scanning confocal fluorescence microscopy (LSM and UV/Vis spectroscopy. Electron and proton transfer through the proteins were demonstrated to take place, which was strongly affected by the membrane potential. MRPs can thus be used for biosensing purposes under quasi-physiological conditions.

  8. Microbial diversity in Los Azufres geothermal field (Michoacán, Mexico) and isolation of representative sulfate and sulfur reducers.

    Science.gov (United States)

    Brito, Elcia M S; Villegas-Negrete, Norberto; Sotelo-González, Irene A; Caretta, César A; Goñi-Urriza, Marisol; Gassie, Claire; Hakil, Florence; Colin, Yannick; Duran, Robert; Gutiérrez-Corona, Felix; Piñón-Castillo, Hilda A; Cuevas-Rodríguez, Germán; Malm, Olaf; Torres, João P M; Fahy, Anne; Reyna-López, Georgina E; Guyoneaud, Rémy

    2014-03-01

    Los Azufres spa consists of a hydrothermal spring system in the Mexican Volcanic Axis. Five samples (two microbial mats, two mud pools and one cenote water), characterized by high acidity (pH between 1 and 3) and temperatures varying from 27 to 87 °C, were investigated for their microbial diversity by Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and 16S rRNA gene library analyses. These data are the first to describe microbial diversity from Los Azufres geothermal belt. The data obtained from both approaches suggested a low bacterial diversity in all five samples. Despite their proximity, the sampling points differed by their physico-chemical conditions (mainly temperature and matrix type) and thus exhibited different dominant bacterial populations: anoxygenic phototrophs related to the genus Rhodobacter in the biomats, colorless sulfur oxidizers Acidithiobacillus sp. in the warm mud and water samples, and Lyzobacter sp.-related populations in the hot mud sample (87 °C). Molecular data also allowed the detection of sulfate and sulfur reducers related to Thermodesulfobium and Desulfurella genera. Several strains affiliated to both genera were enriched or isolated from the mesophilic mud sample. A feature common to all samples was the dominance of bacteria involved in sulfur and iron biogeochemical cycles (Rhodobacter, Acidithiobacillus, Thiomonas, Desulfurella and Thermodesulfobium genera).

  9. Biodegradation of Various Aromatic Compounds by Enriched Bacterial Cultures: Part A-Monocyclic and Polycyclic Aromatic Hydrocarbons.

    Science.gov (United States)

    Oberoi, Akashdeep Singh; Philip, Ligy; Bhallamudi, S Murty

    2015-08-01

    Present study focused on the screening of bacterial consortium for biodegradation of monocyclic aromatic hydrocarbon (MAH) and polycyclic aromatic hydrocarbons (PAHs). Target compounds in the present study were naphthalene, acenaphthene, phenanthrene (PAHs), and benzene (MAH). Microbial consortia enriched with the above target compounds were used in screening experiments. Naphthalene-enriched consortium was found to be the most efficient consortium, based on its substrate degradation rate and its ability to degrade other aromatic pollutants with significantly high efficiency. Substrate degradation rate with naphthalene-enriched culture followed the order benzene > naphthalene > acenaphthene > phenanthrene. Chryseobacterium and Rhodobacter were discerned as the predominant species in naphthalene-enriched culture. They are closely associated to the type strain Chryseobacterium arthrosphaerae and Rhodobacter maris, respectively. Single substrate biodegradation studies with naphthalene (PAH) and benzene (MAH) were carried out using naphthalene-enriched microbial consortium (NAPH). Phenol and 2-hydroxybenzaldehyde were identified as the predominant intermediates during benzene and naphthalene degradation, respectively. Biodegradation of toluene, ethyl benzene, xylene, phenol, and indole by NAPH was also investigated. Monod inhibition model was able to simulate biodegradation kinetics for benzene, whereas multiple substrate biodegradation model was able to simulate biodegradation kinetics for naphthalene.

  10. The genome of obligately intracellular Ehrlichia canis revealsthemes of complex membrane structure and immune evasion strategies

    Energy Technology Data Exchange (ETDEWEB)

    Mavromatis, K.; Kuyler Doyle, C.; Lykidis, A.; Ivanova, N.; Francino, P.; Chain, P.; Shin, M.; Malfatti, S.; Larimer, F.; Copeland,A.; Detter, J.C.; Land, M.; Richardson, P.M.; Yu, X.J.; Walker, D.H.; McBride, J.W.; Kyrpides, N.C.

    2005-09-01

    Ehrlichia canis, a small obligately intracellular, tick-transmitted, gram-negative, a-proteobacterium is the primary etiologic agent of globally distributed canine monocytic ehrlichiosis. Complete genome sequencing revealed that the E. canis genome consists of a single circular chromosome of 1,315,030 bp predicted to encode 925 proteins, 40 stable RNA species, and 17 putative pseudogenes, and a substantial proportion of non-coding sequence (27 percent). Interesting genome features include a large set of proteins with transmembrane helices and/or signal sequences, and a unique serine-threonine bias associated with the potential for O-glycosylation that was prominent in proteins associated with pathogen-host interactions. Furthermore, two paralogous protein families associated with immune evasion were identified, one of which contains poly G:C tracts, suggesting that they may play a role in phase variation and facilitation of persistent infections. Proteins associated with pathogen-host interactions were identified including a small group of proteins (12) with tandem repeats and another with eukaryotic-like ankyrin domains (7).

  11. Decoding the genomic tree of life.

    Science.gov (United States)

    Simonson, Anne B; Servin, Jacqueline A; Skophammer, Ryan G; Herbold, Craig W; Rivera, Maria C; Lake, James A

    2005-05-03

    Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer (HGT) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. HGT among prokaryotes is not random, however. Some genes (informational genes) are more difficult to transfer than others (operational genes). Furthermore, environmental, metabolic, and genetic differences among organisms restrict HGT, so that prokaryotes preferentially share genes with other prokaryotes having properties in common, including genome size, genome G+C composition, carbon utilization, oxygen utilization/sensitivity, and temperature optima, further complicating attempts to reconstruct the tree of life. A new method of phylogenetic reconstruction based on gene presence and absence, called conditioned reconstruction, has improved our prospects for reconstructing prokaryotic evolution. It is also able to detect past genome fusions, such as the fusion that appears to have created the first eukaryote. This genome fusion between a deep branching eubacterium, possibly an ancestor of the cyanobacterium and a proteobacterium, with an archaeal eocyte (crenarchaea), appears to be the result of an early symbiosis. Given new tools and new genes from relevant organisms, it should soon be possible to test current and future fusion theories for the origin of eukaryotes and to discover the general outlines of the prokaryotic tree of life.

  12. Population Genetic Baseline of the First Plataspid Stink Bug Symbiosis (Hemiptera: Heteroptera: Plataspidae Reported in North America

    Directory of Open Access Journals (Sweden)

    Tyler D. Eaton

    2011-06-01

    Full Text Available The stink bug, Megacopta cribraria, has an obligate relationship with a bacterial endosymbiont which allows it to feed on legumes. The insect is a pest of soybeans in Asia and was first reported in the Western Hemisphere in October 2009 on kudzu vine, Pueraria montana, in North Georgia, USA. By October 2010 M. cribraria had been confirmed in 80 counties in Georgia actively feeding on kudzu vine and soybean plants. Since the symbiosis may support the bug’s ecological expansions, a population genetic baseline for the symbiosis was developed from mitochondrial DNA (mtDNA and nuclear DNA (nuDNA gene sequence collected from each insect and its primary g- proteobacterium and secondary a -proteobacterium endosymbionts. A single mitochondrial DNA haplotype was found in all insects sampled in Georgia and South Carolina identified as GA1. The GAI haplotype appears to be rapidly dispersing across Georgia and into contiguous states. Primary and secondary endosymbiont gene sequences from M. cribraria in Georgia were the same as those found in recently collected Megacopta samples from Japan. The implications of these data are discussed.

  13. Tuning cofactor redox potentials: the 2-methoxy dihedral angle generates a redox potential difference greater than 160 mV between the primary (QA) and secondary (QB) quinones of the photosynthetic reaction center

    Science.gov (United States)

    Taguchi, Alexander T.; Mattis, Aidas J.; O'Malley, Patrick J.; Dikanov, Sergei A.; Wraight, Colin A.

    2013-01-01

    Only quinones with a 2-methoxy group can act simultaneously as the primary (QA) and secondary (QB) electron acceptors in photosynthetic reaction centers from Rb. sphaeroides. 13C HYSCORE measurements of the 2-methoxy in the semiquinone states, SQA and SQB, were compared with QM calculations of the 13C couplings as a function of dihedral angle. X-ray structures support dihedral angle assignments corresponding to a redox potential gap (ΔEm) between QA and QB of ~180 mV. This is consistent with the failure of a ubiquinone analog lacking the 2-methoxy to function as QB in mutant reaction centers with a ΔEm ≈ 160–195 mV. PMID:24079813

  14. Selection and Determination of Some Photosynthetic Bacteria (PSB) Applied to Refine Sewage%几株光合细菌的分离鉴定及用于水质净化的初步研究

    Institute of Scientific and Technical Information of China (English)

    邓晓皋; 唐斌

    2001-01-01

    Five strains were selected from sludge of bean curd factory. Theywere determinated fringely RP. Palustris、Rp. acidophila、Rp.sphaeroides. The sewage of slaughterhouse and breeding turtle in glasshouse was applied to culture mixed PSB and its content of N、BOD、COD were declined ,but transparency was increased. So,the sewage was refined distinctly.%从南充市豆制品厂污泥中,分离到五株光合细菌。经初步鉴定分别为沼泽红假单胞菌、球形红假单胞菌、嗜酸红假单胞菌;将其混合培养处理屠宰场污水和温室养鳖场污水,其氨氮量。BOD,COD均下降,而透明度增加。水质得到明显净化。

  15. Final technical report for award NO. DE-FG02-95ER20206

    Energy Technology Data Exchange (ETDEWEB)

    James P. Shapleigh

    2010-02-23

    ABSTRACT Initial work focused on the regulation of nitrite reductase, the defining reaction of denitrification as well as nitric oxide (NO) reductase. Expression of the genes encoding both proteins was controlled by NnrR. This regulator was shown to be responsive to NO. More recent work has shown NnrR function is also likely inhibited by oxygen. Therefore, it is this protein that sets the oxygen level at which nitrate respiration takes over from aerobic respiration. The gene encoding NO reductase appears to only require NnrR for expression. Expression of the gene encoding nitrite reductase is more complex. In addition to NnrR, a two component sensor regulator complex termed PrrA and PrrB is also required for expression. These proteins are global regulators and serve to link denitrification with other bioenergetic processes in the cell. They also provide an additional layer of oxygen dependent regulation. The sequencing of the R. sphaeroides 2.4.3 genome allowed us to identify several other genes regulated by NnrR. Surprisingly, most of the genes were not essential for denitrification. Their high level of conservation in related denitrifiers suggests they do provide a selectable benefit to the bacterium, however. We also examined the role of nitrate reductase in contributing to denitrification in R. sphaeroides. Strain 2.4.3 is unusual in having two distinct, but related clusters of genes encoding nitrate reductase. One of these genes clusters is expressed under high oxygen conditions but is repressed, likely by PrrB-PrrA, under low oxygen conditions. The other cluster is expressed only under low oxygen conditions. This cluster expresses the nitrate reductase used during denitrification. The high oxygen expressed cluster encodes a protein used for redox homeostasis. Surprisingly, both clusters are fully expressed even in the absence of nitrate. During the course of this work we found that the type strain of R. sphaeroides, 2.4.1, is a partial denitrifier because it

  16. Seeded Growth Route to Noble Calcium Carbonate Nanocrystal.

    Directory of Open Access Journals (Sweden)

    Aminul Islam

    Full Text Available A solution-phase route has been considered as the most promising route to synthesize noble nanostructures. A majority of their synthesis approaches of calcium carbonate (CaCO3 are based on either using fungi or the CO2 bubbling methods. Here, we approached the preparation of nano-precipitated calcium carbonate single crystal from salmacis sphaeroides in the presence of zwitterionic or cationic biosurfactants without external source of CO2. The calcium carbonate crystals were rhombohedron structure and regularly shaped with side dimension ranging from 33-41 nm. The high degree of morphological control of CaCO3 nanocrystals suggested that surfactants are capable of strongly interacting with the CaCO3 surface and control the nucleation and growth direction of calcium carbonate nanocrystals. Finally, the mechanism of formation of nanocrystals in light of proposed routes was also discussed.

  17. Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers

    Energy Technology Data Exchange (ETDEWEB)

    Reppert, Mike; Kell, Adam; Pruitt, Thomas [Department of Chemistry, Kansas State University, Manhattan, Kansas 66506 (United States); Jankowiak, Ryszard, E-mail: ryszard@ksu.edu [Department of Chemistry, Kansas State University, Manhattan, Kansas 66506 (United States); Department of Physics, Kansas State University, Manhattan, Kansas 66506 (United States)

    2015-03-07

    The vibrational spectral density is an important physical parameter needed to describe both linear and non-linear spectra of multi-chromophore systems such as photosynthetic complexes. Low-temperature techniques such as hole burning (HB) and fluorescence line narrowing are commonly used to extract the spectral density for a given electronic transition from experimental data. We report here that the lineshape function formula reported by Hayes et al. [J. Phys. Chem. 98, 7337 (1994)] in the mean-phonon approximation and frequently applied to analyzing HB data contains inconsistencies in notation, leading to essentially incorrect expressions in cases of moderate and strong electron-phonon (el-ph) coupling strengths. A corrected lineshape function L(ω) is given that retains the computational and intuitive advantages of the expression of Hayes et al. [J. Phys. Chem. 98, 7337 (1994)]. Although the corrected lineshape function could be used in modeling studies of various optical spectra, we suggest that it is better to calculate the lineshape function numerically, without introducing the mean-phonon approximation. New theoretical fits of the P870 and P960 absorption bands and frequency-dependent resonant HB spectra of Rb. sphaeroides and Rps. viridis reaction centers are provided as examples to demonstrate the importance of correct lineshape expressions. Comparison with the previously determined el-ph coupling parameters [Johnson et al., J. Phys. Chem. 94, 5849 (1990); Lyle et al., ibid. 97, 6924 (1993); Reddy et al., ibid. 97, 6934 (1993)] is also provided. The new fits lead to modified el-ph coupling strengths and different frequencies of the special pair marker mode, ω{sub sp}, for Rb. sphaeroides that could be used in the future for more advanced calculations of absorption and HB spectra obtained for various bacterial reaction centers.

  18. Heterologous expression, purification, and enzymatic characterization of the acyclic carotenoid 1,2-hydratase from Rubrivivax gelatinosus.

    Science.gov (United States)

    Steiger, Sabine; Mazet, Andreas; Sandmann, Gerhard

    2003-06-01

    The carotenoid 1,2-hydratase CrtC from Rubrivivax gelatinosus has been expressed in Escherichia coli in an active form and purified by affinity chromatography. The enzyme catalyzes the conversion of various acyclic carotenes including 1-hydroxy derivatives. This broad substrate specificity reflects the participation of CrtC in 1'-HO-spheroidene and in spirilloxanthin biosynthesis. Enzyme kinetic studies including the determination of substrate specificity constants indicate that among the alternative biosynthetic routes to 1'-HO-spheroidene the one via spheroidene is the dominating pathway. In contrast to CrtC from Rvi. gelatinosus, the equivalent enzyme from Rhodobacter capsulatus, a closely related bacterium which lacks the biosynthetic branch to spirilloxanthin and accumulates spheroidene instead of substantial amounts of 1'-HO-spheroidene, is extremely poor in converting 1-HO-carotenoids. The individual catalytic properties of both carotenoid 1,2-hydratases reflect the in situ carotenogenic pathways in both purple photosynthetic bacteria.

  19. Tracking bio-hydrogen-mediated production of commodity chemicals from carbon dioxide and renewable electricity.

    Science.gov (United States)

    Puig, Sebastià; Ganigué, Ramon; Batlle-Vilanova, Pau; Balaguer, M Dolors; Bañeras, Lluís; Colprim, Jesús

    2017-03-01

    This study reveals that reduction of carbon dioxide (CO2) to commodity chemicals can be functionally compartmentalized in bioelectrochemical systems. In the present example, a syntrophic consortium composed by H2-producers (Rhodobacter sp.) in the biofilm is combined with carboxidotrophic Clostridium species, mainly found in the bulk liquid. The performance of these H2-mediated electricity-driven systems could be tracked by the activity of a biological H2 sensory protein identified at cathode potentials between -0.2V and -0.3V vs SHE. This seems to point out that such signal is not strain specific, but could be detected in any organism containing hydrogenases. Thus, the findings of this work open the door to the development of a biosensor application or soft sensors for monitoring such systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Parameterization of the prosthetic redox centers of the bacterial cytochrome bc(1) complex for atomistic molecular dynamics simulations

    DEFF Research Database (Denmark)

    Kaszuba, K.; Postila, P. A.; Cramariuc, O.

    2013-01-01

    -molecular interactions at different redox stages of the cyt bc(1) complex. Accordingly, here we present high-precision atomic point charges for the metal centers of the cyt bc(1) complex of Rhodobacter capsulatus derived from extensive density functional theory calculations, fitted using the restrained electrostatic......Cytochrome (cyt) bc(1) is a multi-subunit membrane protein complex that is a vital component of the respiratory and photosynthetic electron transfer chains both in bacteria and eukaryotes. Although the complex's dimer structure has been solved using X-ray crystallography, it has not yet been...... studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex's prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter...

  1. Identification of the chlE gene encoding oxygen-independent Mg-protoporphyrin IX monomethyl ester cyclase in cyanobacteria.

    Science.gov (United States)

    Yamanashi, Kaori; Minamizaki, Kei; Fujita, Yuichi

    2015-08-07

    The fifth ring (E-ring) of chlorophyll (Chl) a is produced by Mg-protoporphyrin IX monomethyl ester (MPE) cyclase. There are two evolutionarily unrelated MPE cyclases: oxygen-independent (BchE) and oxygen-dependent (ChlA/AcsF) MPE cyclases. Although ChlA is the sole MPE cyclase in Synechocystis PCC 6803, it is yet unclear whether BchE exists in cyanobacteria. A BLAST search suggests that only few cyanobacteria possess bchE. Here, we report that two bchE candidate genes from Cyanothece strains PCC 7425 and PCC 7822 restore the photosynthetic growth and bacteriochlorophyll production in a bchE-lacking mutant of Rhodobacter capsulatus. We termed these cyanobacterial bchE orthologs "chlE."

  2. The legacy of Hans Molisch (1856-1937), photosynthesis savant.

    Science.gov (United States)

    Gest, H

    1991-10-01

    Hans Molisch (1856-1937) was an exceptionally gifted and productive researcher who had broad interests in plant biology, physiology and biochemistry. In addition, he pioneered in isolating a number of species of purple photosynthetic bacteria in pure culture (including Rhodobacter capsulatus), which facilitated his discovery of basic aspects of bacterial photosynthesis. Molisch demonstrated conclusively that molecular oxygen is not produced by photosynthetic bacteria, and discovered the photoheterotrophic growth mode. The range of Molisch's research accomplishments was impressive, and he emerges as a major figure in the history of photosynthesis research. This essay reviews the numerous research contributions made by Molisch, particularly in regard to advancing knowledge of the several forms of photosynthetic metabolism. An English translation of his 1914 paper on the photosynthetic creation of visual images on leaves is included as an Appendix.

  3. Highly ordered crystals of channel-forming membrane proteins, of nucleoside-monophosphate kinases, of FAD-containing oxidoreductases and of sugar-processing enzymes and their mutants

    Science.gov (United States)

    Schulz, G. E.; Dreyer, M.; Klein, C.; Kreusch, A.; Mittl, P.; Mu¨ller, C. W.; Mu¨ller-Dieckmann, J.; Muller, Y. A.; Proba, K.; Schlauderer, G.; Spu¨rgin, P.; Stehle, T.; Weiss, M. S.

    1992-08-01

    Preparation and crystallization procedures as well as crystal properties are reported for 12 proteins plus numerous site-directed mutants. The proteins are: the integral membrane protein porin from Rhodobacter capsulatus which diffracts to at least 1.8A˚resolution, porin from Rhodopseudomonas blastica which diffracts to at least 2.0A˚resolution, adenylate kinase from yeast and mutants, adenylate kinase from Escherichia coli and mutants, bovine liver mitochondrial adenylate kinase, guanylate kinase from yeast, uridylate kinase from yeast, glutathione reductase from E. coli and mutants, NADH peroxidase from Streptococcus faecalis containing a sulfenic acid as redox-center, pyruvate oxidase from Lactobacillus plantarum containing FAD and TPP, cyclodextrin glycosyltransferase from Bacillus circulans and mutants, and a fuculose aldolase from E. coli.

  4. Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp. Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B

    Directory of Open Access Journals (Sweden)

    Caroline Chénard

    2016-06-01

    Full Text Available Here we present the first genomic characterization of viruses infecting Nostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infect Nostoc sp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids of Cyanothece sp. strain PCC 7424, Nostoc sp. strain PCC 7120, and Anabaena variabilis ATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome of Nostoc sp. strain PCC 7524. The Nostoc cyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages.

  5. Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B

    Science.gov (United States)

    Chénard, Caroline; Wirth, Jennifer F.

    2016-01-01

    ABSTRACT   Here we present the first genomic characterization of viruses infecting Nostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infect Nostoc sp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids of Cyanothece sp. strain PCC 7424, Nostoc sp. strain PCC 7120, and Anabaena variabilis ATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome of Nostoc sp. strain PCC 7524. The Nostoc cyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages. PMID:27302758

  6. Transcriptome-based analysis of the Pantoea stewartii quorum-sensing regulon and identification of EsaR direct targets.

    Science.gov (United States)

    Ramachandran, Revathy; Burke, Alison Kernell; Cormier, Guy; Jensen, Roderick V; Stevens, Ann M

    2014-09-01

    Pantoea stewartii subsp. stewartii is a proteobacterium that causes Stewart's wilt disease in corn plants. The bacteria form a biofilm in the xylem of infected plants and produce capsule that blocks water transport, eventually causing wilt. At low cell densities, the quorum-sensing (QS) regulatory protein EsaR is known to directly repress expression of esaR itself as well as the genes for the capsular synthesis operon transcription regulator, rcsA, and a 2,5-diketogluconate reductase, dkgA. It simultaneously directly activates expression of genes for a putative small RNA, esaS, the glycerol utilization operon, glpFKX, and another transcriptional regulator, lrhA. At high bacterial cell densities, all of this regulation is relieved when EsaR binds an acylated homoserine lactone signal, which is synthesized constitutively over growth. QS-dependent gene expression is critical for the establishment of disease in the plant. However, the identity of the full set of genes controlled by EsaR/QS is unknown. A proteomic approach previously identified around 30 proteins in the QS regulon. In this study, a whole-transcriptome, next-generation sequencing analysis of rRNA-depleted RNA from QS-proficient and -deficient P. stewartii strains was performed to identify additional targets of EsaR. EsaR-dependent transcriptional regulation of a subset of differentially expressed genes was confirmed by quantitative reverse transcription-PCR (qRT-PCR). Electrophoretic mobility shift assays demonstrated that EsaR directly bound 10 newly identified target promoters. Overall, the QS regulon of P. stewartii orchestrates three major physiological responses: capsule and cell envelope biosynthesis, surface motility and adhesion, and stress response. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  7. A Phylogenetic Analysis of the Globins in Fungi

    Science.gov (United States)

    Hoogewijs, David; Dewilde, Sylvia; Vierstraete, Andy; Moens, Luc; Vinogradov, Serge N.

    2012-01-01

    Background All globins belong to one of three families: the F (flavohemoglobin) and S (sensor) families that exhibit the canonical 3/3 α-helical fold, and the T (truncated 3/3 fold) globins characterized by a shortened 2/2 α-helical fold. All eukaryote 3/3 hemoglobins are related to the bacterial single domain F globins. It is known that Fungi contain flavohemoglobins and single domain S globins. Our aims are to provide a census of fungal globins and to examine their relationships to bacterial globins. Results Examination of 165 genomes revealed that globins are present in >90% of Ascomycota and ∼60% of Basidiomycota genomes. The S globins occur in Blastocladiomycota and Chytridiomycota in addition to the phyla that have FHbs. Unexpectedly, group 1 T globins were found in one Blastocladiomycota and one Chytridiomycota genome. Phylogenetic analyses were carried out on the fungal globins, alone and aligned with representative bacterial globins. The Saccharomycetes and Sordariomycetes with two FHbs form two widely divergent clusters separated by the remaining fungal sequences. One of the Saccharomycete groups represents a new subfamily of FHbs, comprising a previously unknown N-terminal and a FHb missing the C-terminal moiety of its reductase domain. The two Saccharomycete groups also form two clusters in the presence of bacterial FHbs; the surrounding bacterial sequences are dominated by Proteobacteria and Bacilli (Firmicutes). The remaining fungal FHbs cluster with Proteobacteria and Actinobacteria. The Sgbs cluster separately from their bacterial counterparts, except for the intercalation of two Planctomycetes and a Proteobacterium between the Fungi incertae sedis and the Blastocladiomycota and Chytridiomycota. Conclusion Our results are compatible with a model of globin evolution put forward earlier, which proposed that eukaryote F, S and T globins originated via horizontal gene transfer of their bacterial counterparts to the eukaryote ancestor, resulting from

  8. A phylogenetic analysis of the globins in fungi.

    Directory of Open Access Journals (Sweden)

    David Hoogewijs

    Full Text Available BACKGROUND: All globins belong to one of three families: the F (flavohemoglobin and S (sensor families that exhibit the canonical 3/3 α-helical fold, and the T (truncated 3/3 fold globins characterized by a shortened 2/2 α-helical fold. All eukaryote 3/3 hemoglobins are related to the bacterial single domain F globins. It is known that Fungi contain flavohemoglobins and single domain S globins. Our aims are to provide a census of fungal globins and to examine their relationships to bacterial globins. RESULTS: Examination of 165 genomes revealed that globins are present in >90% of Ascomycota and ~60% of Basidiomycota genomes. The S globins occur in Blastocladiomycota and Chytridiomycota in addition to the phyla that have FHbs. Unexpectedly, group 1 T globins were found in one Blastocladiomycota and one Chytridiomycota genome. Phylogenetic analyses were carried out on the fungal globins, alone and aligned with representative bacterial globins. The Saccharomycetes and Sordariomycetes with two FHbs form two widely divergent clusters separated by the remaining fungal sequences. One of the Saccharomycete groups represents a new subfamily of FHbs, comprising a previously unknown N-terminal and a FHb missing the C-terminal moiety of its reductase domain. The two Saccharomycete groups also form two clusters in the presence of bacterial FHbs; the surrounding bacterial sequences are dominated by Proteobacteria and Bacilli (Firmicutes. The remaining fungal FHbs cluster with Proteobacteria and Actinobacteria. The Sgbs cluster separately from their bacterial counterparts, except for the intercalation of two Planctomycetes and a Proteobacterium between the Fungi incertae sedis and the Blastocladiomycota and Chytridiomycota. CONCLUSION: Our results are compatible with a model of globin evolution put forward earlier, which proposed that eukaryote F, S and T globins originated via horizontal gene transfer of their bacterial counterparts to the eukaryote

  9. Screening and Identification of Microorganisms for Degrading Essence and Spice%香精香料废水降解微生物的筛选及鉴定

    Institute of Scientific and Technical Information of China (English)

    王亮; 蔡家利; 段云霞; 吕晶华

    2012-01-01

    It is aromatic compound which is mainly organic pollution that essence and spice industry wastewater in Shan dong, para-tertiary butyl phenol is very difficult degradation. In order to screen biodegradation microbiology in essence and spice industry wastewater, a strain it existing in para-tertiary butyl phenol was isolated from activated flavors and fragrances industry wastewater with mixed organic compounds as sample. According to thxonomic outline of the prokaryotes Bergey's Manual of Systematic Bacteriology (the 8th version) and the Routine Germ Authenticates a Manual( Edited by Dong Xiu-zhu, et al. ) that it was identified according to morphological, physiological and biochemical and the 16S rDNA gene sequence was blasted from www. Ncbi. Nlm. Nih. Gov/genbank/. As a result, it was bacterial of Rhodobacter sp.. It was adapted to plant wastewater of slanting salt and phenol. It was able to biodegradation para-tertiary butyl phenol in the wastewater. In this study, this discovers laying foundation is going to contribute the microorganism of solving the waste water share.%山东省某家香精香料厂废水中主要有机污染物是芳香族化合物,以叔丁基苯酚最难降解.为了筛选香精香料废水降解微生物,实验采集上述香精香料厂好氧曝气池的活性污泥为样本,以叔丁基苯酚为唯一碳源,进行筛选并分离出一株能降解废水的微生物.对该微生物的形态、生理生化特征进行鉴定,并对它的16S rDNA基因序列进行分析比对.结果表明,该菌株属于类球红细菌属(Rhodobacter sp.),适应偏盐性和适当芳香有机物的废水环境中生长并能有力地降解废水中的叔丁基苯酚.研究认为该菌株在有关废水处理方面的贡献难以估量.

  10. The 2-Methoxy Group Orientation Regulates the Redox Potential Difference between the Primary (QA) and Secondary (QB) Quinones of Type II Bacterial Photosynthetic Reaction Centers

    Science.gov (United States)

    2015-01-01

    Recent studies have shown that only quinones with a 2-methoxy group can act simultaneously as the primary (QA) and secondary (QB) electron acceptors in photosynthetic reaction centers from purple bacteria such as Rb. sphaeroides. 13C HYSCORE measurements of the 2-methoxy group in the semiquinone states, SQA and SQB, were compared with DFT calculations of the 13C hyperfine couplings as a function of the 2-methoxy dihedral angle. X-ray structure comparisons support 2-methoxy dihedral angle assignments corresponding to a redox potential gap (ΔEm) between QA and QB of 175–193 mV. A model having a methyl group substituted for the 2-methoxy group exhibits no electron affinity difference. This is consistent with the failure of a 2-methyl ubiquinone analogue to function as QB in mutant reaction centers with a ΔEm of ∼160–195 mV. The conclusion reached is that the 2-methoxy group is the principal determinant of electron transfer from QA to QB in type II photosynthetic reaction centers with ubiquinone serving as both acceptor quinones. PMID:25126386

  11. The 2-Methoxy Group Orientation Regulates the Redox Potential Difference between the Primary (QA) and Secondary (QB) Quinones of Type II Bacterial Photosynthetic Reaction Centers.

    Science.gov (United States)

    de Almeida, Wagner B; Taguchi, Alexander T; Dikanov, Sergei A; Wraight, Colin A; O'Malley, Patrick J

    2014-08-07

    Recent studies have shown that only quinones with a 2-methoxy group can act simultaneously as the primary (QA) and secondary (QB) electron acceptors in photosynthetic reaction centers from purple bacteria such as Rb. sphaeroides. (13)C HYSCORE measurements of the 2-methoxy group in the semiquinone states, SQA and SQB, were compared with DFT calculations of the (13)C hyperfine couplings as a function of the 2-methoxy dihedral angle. X-ray structure comparisons support 2-methoxy dihedral angle assignments corresponding to a redox potential gap (ΔEm) between QA and QB of 175-193 mV. A model having a methyl group substituted for the 2-methoxy group exhibits no electron affinity difference. This is consistent with the failure of a 2-methyl ubiquinone analogue to function as QB in mutant reaction centers with a ΔEm of ∼160-195 mV. The conclusion reached is that the 2-methoxy group is the principal determinant of electron transfer from QA to QB in type II photosynthetic reaction centers with ubiquinone serving as both acceptor quinones.

  12. APPLICATIONS OF LASERS AND OTHER TOPICS IN QUANTUM ELECTRONICS: Role of relaxation processes in stabilization of photoinduced charges in a biological membrane

    Science.gov (United States)

    Logunov, S. L.; Pashchenko, V. Z.

    1989-01-01

    Picosecond absorption spectroscopy was used in a study of stabilization of a primary ion-radical pair P +I - in reaction centers of purple bacteria Rb. sphaeroides. Measurements were made on samples with hydrogen bonds modified by isotopic substitution of H2O with D2O and by introduction of cryoprotectors into the structure of the reaction centers. The state P +I -, which appeared as a result of separation of charges in a P *I complex, was stabilized by the interaction of P +I - with charged light groups of the water-protein environment in modified reaction centers after an interval of ~ 1 ns (stabilization in control samples took ~ 100 ps). Moreover, the transport of an electron to the next acceptor Qa was slowed down (by a factor of ~ 5) in modified reaction centers and the probability of recombination of charges increased (by a factor of ~ 3) in the unrelaxed state. Relaxation processes lowered the energy level of P +I - by 0.03-0.05 eV and reduced the energy of the interaction in an ion-radical pair by a factor of 2.

  13. Photoinduced ESR signals from the primary electron donors in deuterated highly /sup 13/C enriched photosynthetic bacteria and algae

    Energy Technology Data Exchange (ETDEWEB)

    Wasielewski, M.R.; Norris, J.R.; Crespi, H.L.; Harper, J.

    1981-12-16

    In purple photosynthetic bacteria such as Rhodopseudomonas sphaeroides the oxidized primary donar P865/sup +/ exhibits a single Gaussian ESR signal posessing a line width that is narrowed by 1/%2 relative to that of monomeric BChl a/sup +/ in vitro. Data show that P700/sup +/ from the green plant photosystem I donor is a single oxidized Chl a type macrocycle. New data confirm that P865/sup +/ is a dimer of a BChl a type macrocycle. A method that accounts for the entire spin is needed in order to count the number of spins per macrocycle. The solution to this problem is to make each carbon atom of the ..pi.. system over which the electron is distributed magnetic resonance active. This requires that each position in the ..pi.. framework be highly enriched in /sup 13/C. Under these conditions the total ESR line width is the sum of the hyperfine lines due to each carbon atom of the ..pi.. system. Data indicate that the spin in P700/sup +/ is located on only one Chl a type macrocycle whereas that of P865/sup +/ is shared between two BChl a type macrocycles. (MWF)

  14. Morphological Research on Indigenous Sambucus Species Pollen

    Directory of Open Access Journals (Sweden)

    Mircea TAMAS

    2009-06-01

    Full Text Available The pollen grains have a definite shape, size, colour, structure for each species, genus and family and these characters are useful for systematical botany. The pollen has nutritive properties due to its content: proteins, lipids, carbohydrates, vitamins, hormones and minerals. In the Romanian flora vegetate three species of Sambucus, but only S. nigra L. (elder or black elder supplies a vegetal medical product, Sambuci flos or elder flowers, whereas the others species S. ebulus L. (dwarf elder and S. racemosa L. (mountain elder or red elder are considered adulterations. The pollen of Sambucus species were already studied using optical microscopy (Tarnavschi et al., but the images are in one single layout, therefore the structure details cannot be easily notice. In this context the pollen grains of the three species already mentioned above were studied by SEM (Scanning Electron Microscopy. The results demonstrated that this pollen have a small-middle size, oblat-sphaeroidal-prolat shape, threecolpat and the exine adornments are of reticulate type, haemitectate with sticks in the meshs of polygonale net. The flavonoids content is lower than in others species (0.146-0.564 %. The SEM analyse of Sambucus pollen allow a reliable identification of the genus but less for the species.

  15. Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B.

    Science.gov (United States)

    Chénard, Caroline; Wirth, Jennifer F; Suttle, Curtis A

    2016-06-14

    Here we present the first genomic characterization of viruses infecting Nostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infect Nostoc sp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids of Cyanothece sp. strain PCC 7424, Nostoc sp. strain PCC 7120, and Anabaena variabilis ATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome of Nostoc sp. strain PCC 7524. The Nostoc cyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages. Filamentous cyanobacteria belonging to the genus Nostoc are widespread and ecologically important in freshwater, yet little is known about the genomic content of their viruses. Here we report the first genomic analysis of cyanophages infecting

  16. A Comprehensive Insight into Tetracycline Resistant Bacteria and Antibiotic Resistance Genes in Activated Sludge Using Next-Generation Sequencing

    Directory of Open Access Journals (Sweden)

    Kailong Huang

    2014-06-01

    Full Text Available In order to comprehensively investigate tetracycline resistance in activated sludge of sewage treatment plants, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential tetracycline resistant bacteria (TRB and antibiotic resistance genes (ARGs in sludge cultured with different concentrations of tetracycline. Pyrosequencing of 16S rRNA gene revealed that tetracycline treatment greatly affected the bacterial community structure of the sludge. Nine genera consisting of Sulfuritalea, Armatimonas, Prosthecobacter, Hyphomicrobium, Azonexus, Longilinea, Paracoccus, Novosphingobium and Rhodobacter were identified as potential TRB in the sludge. Results of qPCR, molecular cloning and metagenomic analysis consistently indicated that tetracycline treatment could increase both the abundance and diversity of the tet genes, but decreased the occurrence and diversity of non-tetracycline ARG, especially sulfonamide resistance gene sul2. Cluster analysis showed that tetracycline treatment at subinhibitory concentrations (5 mg/L was found to pose greater effects on the bacterial community composition, which may be responsible for the variations of the ARGs abundance. This study indicated that joint use of 454 pyrosequencing and Illumina high-throughput sequencing can be effectively used to explore ARB and ARGs in the environment, and future studies should include an in-depth investigation of the relationship between microbial community, ARGs and antibiotics in sewage treatment plant (STP sludge.

  17. Regulation of carotenoid and bacteriochlorophyll biosynthesis genes and identification of an evolutionarily conserved gene required for bacteriochlorophyll accumulation.

    Science.gov (United States)

    Armstrong, G A; Cook, D N; Ma, D; Alberti, M; Burke, D H; Hearst, J E

    1993-05-01

    The temporal expression of ten clustered genes required for carotenoid (crt) and bacteriochlorophyll (bch) biosynthesis was examined during the transition from aerobic respiration to anaerobiosis requisite for the development of the photosynthetic membrane in the bacterium Rhodobacter capsulatus. Accumulation of crtA, crtC, crtD, crtE, crtF, crtK, bchC and bchD mRNAs increased transiently and coordinately, up to 12-fold following removal of oxygen from the growth medium, paralleling increases in mRNAs encoding pigment-binding polypeptides of the photosynthetic apparatus. The crtB and crtI genes, in contrast, were expressed similarly in the presence or absence of oxygen. The regulation patterns of promoters for the crtA and crtI genes and the bchCXYZ operon were characterized using lacZ transcriptional fusion and qualitatively reflected the corresponding mRNA accumulation patterns. We also report that the bchI gene product, encoded by a DNA sequence previously considered to be a portion of crtA, shares 49% sequence identity with the nuclear-encoded Arabidopsis thaliana Cs chloroplast protein required for normal pigmentation in plants.

  18. Vertical Distribution of Bacterial Community Diversity and Water Quality during the Reservoir Thermal Stratification

    Directory of Open Access Journals (Sweden)

    Hai-Han Zhang

    2015-06-01

    Full Text Available Reservoir thermal stratification drives the water temperature and dissolved oxygen gradient, however, the characteristic of vertical water microbial community during thermal stratification is so far poorly understood. In this work, water bacterial community diversity was determined using the Illumina Miseq sequencing technique. The results showed that epilimnion, metalimnion and hypolimnion were formed steadily in the JINPEN drinking water reservoir. Water temperature decreased steadily from the surface (23.11 °C to the bottom (9.17 °C. Total nitrogen ranged from 1.07 to 2.06 mg/L and nitrate nitrogen ranged from 0.8 to 1.84 mg/L. The dissolved oxygen concentration decreased sharply below 50 m, and reached zero at 65 m. The Miseq sequencing revealed a total of 4127 operational taxonomic units (OTUs with 97% similarity, which were affiliated with 15 phyla including Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Caldiserica, Chlamydiae, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria, and Verrucomicrobia. The highest Shannon diversity was 4.41 in 45 m, and the highest Chao 1 diversity was 506 in 5 m. Rhodobacter dominated in 55 m (23.24% and 65 m (12.58%. Prosthecobacter dominated from 0.5 to 50 m. The heat map profile and redundancy analysis (RDA indicated significant difference in vertical water bacterial community composition in the reservoir. Meanwhile, water quality properties including dissolved oxygen, conductivity, nitrate nitrogen and total nitrogen have a dramatic influence on vertical distribution of bacterial communities.

  19. Comparative pyrosequencing analysis of bacterial community change in biofilm formed on seawater reverse osmosis membrane.

    Science.gov (United States)

    Kim, In S; Lee, Jinwook; Kima, Sung-Jo; Yu, Hye-Weon; Jang, Am

    2014-01-01

    The change in bacterial community structure induced by bacterial competition and succession was investigated during seawater reverse osmosis (SWRO) in order to elucidate a possible link between the bacterial consortium on SWRO membranes and biofouling. To date, there has been no definitive characterization of the microbial diversity in SWRO in terms of distinguishing time-dependent changes in the richness or abundance of bacterial species. For bacterial succession within biofilms on the membrane surface, SWRO using a cross-flow filtration membrane test unit was operated for 5 and 100h, respectively. As results of the pyrosequencing analysis, bacterial communities differed considerably among seawater and the 5 and 100 h samples. From a total of 33,876 pyrosequences (using a 95% sequence similarity), there were less than 1% of shared species, confirming the influence of the operational time factor and lack of similarity of these communities. During SWRO operation, the abundance of Pseudomonas stutzeri BBSPN3 (GU594474) belonging to gamma-Proteobacteria suggest that biofouling of SWRO membrane might be driven by the dominant influence of a specific species. In addition, among the bacterial competition of five bacterial species (Pseudomonas aeruginosa, Bacillus sp., Rhodobacter sp., Flavobacterium sp., and Mycobacterium sp.) competing for bacterial colonization on the SWRO membrane surfaces, it was exhibited that Bacillus sp. was the most dominant. The dominant influences ofPseudomonas sp. and Bacillus sp. on biofouling during actual SWRO is decisive depending on higher removal efficiency of the seawater pretreatment.

  20. Trends of bio-hydrogen research and development in Europe. Report for the Research Institute of Innovative Technology for the Earth (RITE), Tokyo, Japan

    Energy Technology Data Exchange (ETDEWEB)

    Huesing, B.

    1997-03-01

    Research into applied aspects of biological hydrogen production is carried out on a much lower level in Europe than basic hydrogenase research. However, the screening for good H{sub 2} producers, their cultivation, and the development of optimised culture and bioreactor systems has never been a strength in Europe. Although there are a few good groups in Europe major contributions in this field traditionally come from countries outside Europe. However, in the nineties a special application-oriented research subfield has begun to evolve in Europe: the use of genetic enginering to rationally optimise H{sub 2} producing organisms. The most important players who focus on green algae, cyanobacteria, and purple bacteria can be found in Germany, France, and Sweden. In European biohydrogen research, a large and diverse variety of organisms is investigated. Among the organisms most thoroughly studied are Alcaligenes eutrophus, Escherichia coli, Rhodobacter capsulatus, sulfate-reducing bacteria, and methanogenic bacteria. Moreover, a leading position has been obtained with respect to molecular genetics of green algae and cyanobacteria, albeit on a low level. The fact that such a broad range of diverse organisms is studied has advantages and disadvantages. A positive aspect is that the multitude of different approaches had led to several unexpected results which had otherwise been overlooked. On the other hand, an obvious link to biohydrogen production is often lacking. Moreover, there are many 'me-too' approaches and results in which previous findings are only reproduced for another organism as well. (orig.)

  1. Ready to use bioinformatics analysis as a tool to predict immobilisation strategies for protein direct electron transfer (DET).

    Science.gov (United States)

    Cazelles, R; Lalaoui, N; Hartmann, T; Leimkühler, S; Wollenberger, U; Antonietti, M; Cosnier, S

    2016-11-15

    Direct electron transfer (DET) to proteins is of considerable interest for the development of biosensors and bioelectrocatalysts. While protein structure is mainly used as a method of attaching the protein to the electrode surface, we employed bioinformatics analysis to predict the suitable orientation of the enzymes to promote DET. Structure similarity and secondary structure prediction were combined underlying localized amino-acids able to direct one of the enzyme's electron relays toward the electrode surface by creating a suitable bioelectrocatalytic nanostructure. The electro-polymerization of pyrene pyrrole onto a fluorine-doped tin oxide (FTO) electrode allowed the targeted orientation of the formate dehydrogenase enzyme from Rhodobacter capsulatus (RcFDH) by means of hydrophobic interactions. Its electron relays were directed to the FTO surface, thus promoting DET. The reduction of nicotinamide adenine dinucleotide (NAD(+)) generating a maximum current density of 1μAcm(-2) with 10mM NAD(+) leads to a turnover number of 0.09electron/s/molRcFDH. This work represents a practical approach to evaluate electrode surface modification strategies in order to create valuable bioelectrocatalysts.

  2. Genetic analysis of photosynthesis in Rhodospirillum centenum.

    Science.gov (United States)

    Yildiz, F H; Gest, H; Bauer, C E

    1991-01-01

    A genetic system has been developed for studying bacterial photosynthesis in the recently described nonsulfur purple photosynthetic bacterium Rhodospirillum centenum. Nonphotosynthetic mutants of R. centenum were obtained by enrichment for spontaneous mutations, by ethyl methanesulfonate mutagenesis coupled to penicillin selection on solid medium, and by Tn5 transposition mutagenesis with an IncP plasmid vector containing a temperature-sensitive origin of replication. In vivo and in vitro characterization of individual strains demonstrated that 38 strains contained mutations that blocked bacteriochlorophyll a biosynthesis at defined steps of the biosynthetic pathway. Collectively, these mutations were shown to block seven of eight steps of the pathway leading from protoporphyrin IX to bacteriochlorophyll a. Three mutants were isolated in which carotenoid biosynthesis was blocked early in the biosynthetic pathway; the mutants also exhibited pleiotropic effects on stability or assembly of the photosynthetic apparatus. Five mutants failed to assemble a functional reaction center complex, and seven mutants contained defects in electron transport as shown by an alteration in cytochromes. In addition, several regulatory mutants were isolated that acquired enhanced repression of bacteriochlorophyll in response to the presence of molecular oxygen. The phenotypes of these mutants are discussed in relation to those of similar mutants of Rhodobacter and other Rhodospirillum species of purple photosynthetic bacteria. Images PMID:1648078

  3. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex

    Science.gov (United States)

    Postila, Pekka A.; Kaszuba, Karol; Kuleta, Patryk; Vattulainen, Ilpo; Sarewicz, Marcin; Osyczka, Artur; Róg, Tomasz

    2016-09-01

    The cytochrome (cyt) bc1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme’s substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Qi-site of the cyt bc1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Qi-site to facilitate binding of half-protonated semiquinone – a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Qi-site.

  4. Early succession of bacterial biofilms in paper machines.

    Science.gov (United States)

    Tiirola, Marja; Lahtinen, Tomi; Vuento, Matti; Oker-Blom, Christian

    2009-07-01

    Formation of biofilms causes severe problems in paper machines, and hence financial costs. It would be preferable to prevent attachment of the primary-colonizing bacteria than to control the growth of secondary communities, which are sheltered by exopolysaccharide slime layers. We have therefore investigated the early succession of paper-machine biofilms by incubating stainless-steel test coupons in the process water-flow lines in two paper machines operating in slightly alkaline conditions in temperatures (45 and 49 degrees C) supporting thermophilic microbes. Microbial succession was profiled using length heterogeneity analysis of PCR-amplified 16S rRNA genes (LH-PCR) and linking the sequence data of the created 16S rRNA gene libraries to the dominant LH-PCR peaks. Although the bacterial fingerprints obtained from the attached surface communities varied slightly in different samples, the biomarker signals of the dominating primary-colonizing bacterial groups remained high over time in each paper machine. Most of the 16S rRNA gene copies in the early biofilms were assigned to the genera Rhodobacter, Tepidimonas, and Cloacibacterium. The dominance of these sequence types decreased in the developing biofilms. Finally, as phylogenetically identical primary-colonizers were detected in the two different paper mills, the machines evidently had similar environmental conditions for bacterial growth and potentially a common source of contamination.

  5. Bacterial symbionts in the hepatopancreas of isopods: diversity and environmental transmission.

    Science.gov (United States)

    Wang, Yongjie; Brune, Andreas; Zimmer, Martin

    2007-07-01

    The midgut glands (hepatopancreas) of terrestrial isopods contain bacterial symbionts. We analysed the phylogenetic diversity of hepatopancreatic bacteria in isopod species from various suborders colonizing marine, semiterrestrial, terrestrial and freshwater habitats. Hepatopancreatic bacteria were absent in the marine isopod Idotea balthica (Valvifera). The symbiotic bacteria present in the midgut glands of the freshwater isopod Asellus aquaticus (Asellota) were closely related to members of the proteobacterial genera Rhodobacter, Burkholderia, Aeromonas or Rickettsiella, but differed markedly between populations. By contrast, species of the suborder Oniscidea were consistently colonized by the same phylotypes of hepatopancreatic bacteria. While symbionts in the semiterrestrial isopod Ligia oceanica (Oniscidea) were close relatives of Pseudomonas sp. (Gammaproteobacteria), individuals of the terrestrial isopod Oniscus asellus (Oniscidea) harboured either 'Candidatus Hepatoplasma crinochetorum' (Mollicutes) or 'Candidatus Hepatincola porcellionum' (Rickettsiales), previously described as symbionts of another terrestrial isopod, Porcellio scaber. These two uncultivated bacterial taxa were consistently present in each population of six and three different species of terrestrial isopods, respectively, collected in different geographical locations. However, infection rates of individuals within a population ranged between 10% and 100%, rendering vertical transmission unlikely. Rather, feeding experiments suggest that 'Candidatus Hepatoplasma crinochetorum' is environmentally transmitted to the progeny.

  6. A process economic assessment of hydrocarbon biofuels production using chemoautotrophic organisms

    Energy Technology Data Exchange (ETDEWEB)

    Khan, NE; Myers, JA; Tuerk, AL; Curtis, WR

    2014-11-01

    Economic analysis of an ARPA-e Electrofuels (http://arpa-e.energy.gov/?q=arpa-e-programs/electrofuels) process is presented, utilizing metabolically engineered Rhodobacter capsulatus or Ralstonia eutropha to produce the C30+ hydrocarbon fuel, botryococcene, from hydrogen, carbon dioxide, and oxygen. The analysis is based on an Aspen plus (R) bioreactor model taking into account experimentally determined Rba. capsulatus and Rls. eutropha growth and maintenance requirements, reactor residence time, correlations for gas-liquid mass-transfer coefficient, gas composition, and specific cellular fuel productivity. Based on reactor simulation results encompassing technically relevant parameter ranges, the capital and operating costs of the process were estimated for 5000 bbl-fuel/day plant and used to predict fuel cost. Under the assumptions used in this analysis and crude oil prices, the Levelized Cost of Electricity (LCOE) required for economic feasibility must be less than 2(sic)/kWh. While not feasible under current market prices and costs, this work identifies key variables impacting process cost and discusses potential alternative paths toward economic feasibility. (C) 2014 Elsevier Ltd. All rights reserved.

  7. Studies of DNA supercoiling in vivo and in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Cook, D.N.

    1990-10-01

    This thesis describes a number of diverse experiments whose common theme is to elaborate some aspect of DNA supercoiling. The torsion elastic constant of DNA is measure as a function of superhelix density using the technique of picosecond Time Resolved Fluorescence Polarization Anisotropy (FPA) of intercalated ethidium bromide. The results agree with theories which predict that the anisotropy decay should vary with the square root of the relative viscosity. This experiment furthermore demonstrates a sensitivity of FPA to a change in torsion elastic constant of less than 10%. A number of covalently closed DNA samples, ranging in superhelix density from = [minus]0.123 to [plus]0.042, are then examined. A novel method for measuring changes in local supercoiling on a large PNA molecule which is sensitive to changes in supercoiling of regions of chromosomal DNA as short as 1 kilobase in length is presented. Study of chromosomal supercoiling regulating anaerobic gene expression in the facultative photosynthetic bacterium, Rhodobacter capsulatus showed that no stable change in chromosomal supercoiling upon a shift from aerobic respiratory growth to anaerobic photosynthetic conditions. Studies to detect transient changes in DNA supercoiling indicate that DNA downstream from heavily transcribed genes for the photosynthetic reaction center are relaxed or perhaps overwound upon the induction of photosynthetic metabolism. These results are interpreted in terms of the twin domain model of transcriptional supercoiling.

  8. Studies of DNA supercoiling in vivo and in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Cook, David Nelson [Univ. of California, Berkeley, CA (United States)

    1990-10-01

    This thesis describes a number of diverse experiments whose common theme is to elaborate some aspect of DNA supercoiling. The torsion elastic constant of DNA is measure as a function of superhelix density using the technique of picosecond Time Resolved Fluorescence Polarization Anisotropy (FPA) of intercalated ethidium bromide. The results agree with theories which predict that the anisotropy decay should vary with the square root of the relative viscosity. This experiment furthermore demonstrates a sensitivity of FPA to a change in torsion elastic constant of less than 10%. A number of covalently closed DNA samples, ranging in superhelix density from = -0.123 to +0.042, are then examined. A novel method for measuring changes in local supercoiling on a large PNA molecule which is sensitive to changes in supercoiling of regions of chromosomal DNA as short as 1 kilobase in length is presented. Study of chromosomal supercoiling regulating anaerobic gene expression in the facultative photosynthetic bacterium, Rhodobacter capsulatus showed that no stable change in chromosomal supercoiling upon a shift from aerobic respiratory growth to anaerobic photosynthetic conditions. Studies to detect transient changes in DNA supercoiling indicate that DNA downstream from heavily transcribed genes for the photosynthetic reaction center are relaxed or perhaps overwound upon the induction of photosynthetic metabolism. These results are interpreted in terms of the twin domain model of transcriptional supercoiling.

  9. Efficient behavior of photosynthetic organelles via Pareto optimality, identifiability, and sensitivity analysis.

    Science.gov (United States)

    Carapezza, Giovanni; Umeton, Renato; Costanza, Jole; Angione, Claudio; Stracquadanio, Giovanni; Papini, Alessio; Lió, Pietro; Nicosia, Giuseppe

    2013-05-17

    In this work, we develop methodologies for analyzing and cross comparing metabolic models. We investigate three important metabolic networks to discuss the complexity of biological organization of organisms, modeling, and system properties. In particular, we analyze these metabolic networks because of their biotechnological and basic science importance: the photosynthetic carbon metabolism in a general leaf, the Rhodobacter spheroides bacterium, and the Chlamydomonas reinhardtii alga. We adopt single- and multi-objective optimization algorithms to maximize the CO 2 uptake rate and the production of metabolites of industrial interest or for ecological purposes. We focus both on the level of genes (e.g., finding genetic manipulations to increase the production of one or more metabolites) and on finding concentration enzymes for improving the CO 2 consumption. We find that R. spheroides is able to absorb an amount of CO 2 until 57.452 mmol h (-1) gDW (-1) , while C. reinhardtii obtains a maximum of 6.7331. We report that the Pareto front analysis proves extremely useful to compare different organisms, as well as providing the possibility to investigate them with the same framework. By using the sensitivity and robustness analysis, our framework identifies the most sensitive and fragile components of the biological systems we take into account, allowing us to compare their models. We adopt the identifiability analysis to detect functional relations among enzymes; we observe that RuBisCO, GAPDH, and FBPase belong to the same functional group, as suggested also by the sensitivity analysis.

  10. Mutational analysis of three bchH paralogs in (bacterio-)chlorophyll biosynthesis in Chlorobaculum tepidum

    DEFF Research Database (Denmark)

    Gomez Maqueo Chew, Aline; Frigaard, Niels-Ulrik; Bryant, Donald A

    2009-01-01

    The first committed step in the biosynthesis of (bacterio-)chlorophyll is the insertion of Mg2+ into protoporphyrin IX by Mg-chelatase. In all known (B)Chl-synthesizing organisms, Mg-chelatase is encoded by three genes that are homologous to bchH, bchD, and bchI of Rhodobacter spp. The genomes...... of all sequenced strains of green sulfur bacteria (Chlorobi) encode multiple bchH paralogs, and in the genome of Chlorobaculum tepidum, there are three bchH paralogs, denoted CT1295 (bchT), CT1955 (bchS), and CT1957 (bchH). Cba. tepidum mutants lacking one or two of these paralogs were constructed...... and characterized. All of the mutants lacking only one of these BchH homologs, as well as bchS bchT and bchH bchT double mutants, which can only produce BchH or BchS, respectively, were viable. However, attempts to construct a bchH bchS double mutant, in which only BchT was functional, were consistently...

  11. Bacterial nitrate assimilation: gene distribution and regulation.

    Science.gov (United States)

    Luque-Almagro, Víctor M; Gates, Andrew J; Moreno-Vivián, Conrado; Ferguson, Stuart J; Richardson, David J; Roldán, M Dolores

    2011-12-01

    In the context of the global nitrogen cycle, the importance of inorganic nitrate for the nutrition and growth of marine and freshwater autotrophic phytoplankton has long been recognized. In contrast, the utilization of nitrate by heterotrophic bacteria has historically received less attention because the primary role of these organisms has classically been considered to be the decomposition and mineralization of dissolved and particulate organic nitrogen. In the pre-genome sequence era, it was known that some, but not all, heterotrophic bacteria were capable of growth on nitrate as a sole nitrogen source. However, examination of currently available prokaryotic genome sequences suggests that assimilatory nitrate reductase (Nas) systems are widespread phylogenetically in bacterial and archaeal heterotrophs. Until now, regulation of nitrate assimilation has been mainly studied in cyanobacteria. In contrast, in heterotrophic bacterial strains, the study of nitrate assimilation regulation has been limited to Rhodobacter capsulatus, Klebsiella oxytoca, Azotobacter vinelandii and Bacillus subtilis. In Gram-negative bacteria, the nas genes are subjected to dual control: ammonia repression by the general nitrogen regulatory (Ntr) system and specific nitrate or nitrite induction. The Ntr system is widely distributed in bacteria, whereas the nitrate/nitrite-specific control is variable depending on the organism.

  12. Metabolic engineering of Escherichia coli cell factory for highly active xanthine dehydrogenase production.

    Science.gov (United States)

    Wang, Cheng-Hua; Zhang, Chong; Xing, Xin-Hui

    2017-05-31

    The aim of this work was to demonstrate the first proof-of-concept for the use of ab initio-aided assembly strategy intensifying in vivo biosynthesis process to construct Escherichia coli cell factory overproducing highly active xanthine dehydrogenase (XDH). Three global regulator (IscS, TusA and NarJ) and four chaperone proteins (DsbA, DsbB, NifS and XdhC) were overexpressed to aid the formation and ordered assembly of three redox center cofactors of Rhodobacter capsulatus XDH in E. coli. The NifS, IscS and DsbB enhanced the specific activity of RcXDH by 30%, 94% and 49%, respectively. The combinatorial expression of NarJ and IscS synergistically increased the specific activity by 129% and enhanced the total enzyme activity by a remarkable 3.9-fold. The crude enzyme showed nearly the same coupling efficiency of electron transfer and product formation as previously purified XDHs, indicating an integrity and efficient assembly of highly active XDH. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Bacillus megaterium has both a functional BluB protein required for DMB synthesis and a related flavoprotein that forms a stable radical species.

    Science.gov (United States)

    Collins, Hannah F; Biedendieck, Rebekka; Leech, Helen K; Gray, Michael; Escalante-Semerena, Jorge C; McLean, Kirsty J; Munro, Andrew W; Rigby, Stephen E J; Warren, Martin J; Lawrence, Andrew D

    2013-01-01

    Despite the extensive study of the biosynthesis of the complex molecule B12 (cobalamin), the mechanism by which the lower ligand 5,6-dimethylbenzimidazole (DMB) is formed has remained something of a mystery. However, recent work has identified and characterized a DMB-synthase (BluB) responsible for the oxygen-dependent, single enzyme conversion of FMN to DMB. In this work, we have identified BluB homologs from the aerobic purple, nonsulfur, photosynthetic bacterium Rhodobacter capsulatus and the aerobic soil bacterium Bacillus megaterium and have demonstrated DMB synthesis by the use of a novel complementation assay in which a B12 deficient strain, substituted with the precursor cobinamide is recovered either by the addition of DMB or by the recombinant expression of a bluB gene. The DMB-synthetic activity of the purified recombinant BluB enzymes was further confirmed in vitro by providing the enzyme with FMNH2 and oxygen and observing the formation of DMB by HPLC. The formation of a 4a-peroxyflavin intermediate, the first step in the oxygen dependent mechanism of DMB biosynthesis, is reported here and is the first intermediate in the enzyme catalysed reaction to be demonstrated experimentally to date. The identification and characterization of an FMN-binding protein found on the cobI operon of B. megaterium, CbiY, is also detailed, revealing an FMN-containing enzyme which is able to stabilize a blue flavin semiquinone upon reduction with a 1-electron donor.

  14. A process economic assessment of hydrocarbon biofuels production using chemoautotrophic organisms.

    Science.gov (United States)

    Khan, Nymul E; Myers, John A; Tuerk, Amalie L; Curtis, Wayne R

    2014-11-01

    Economic analysis of an ARPA-e Electrofuels (http://arpa-e.energy.gov/?q=arpa-e-programs/electrofuels) process is presented, utilizing metabolically engineered Rhodobacter capsulatus or Ralstonia eutropha to produce the C30+ hydrocarbon fuel, botryococcene, from hydrogen, carbon dioxide, and oxygen. The analysis is based on an Aspen plus® bioreactor model taking into account experimentally determined Rba. capsulatus and Rls. eutropha growth and maintenance requirements, reactor residence time, correlations for gas-liquid mass-transfer coefficient, gas composition, and specific cellular fuel productivity. Based on reactor simulation results encompassing technically relevant parameter ranges, the capital and operating costs of the process were estimated for 5000 bbl-fuel/day plant and used to predict fuel cost. Under the assumptions used in this analysis and crude oil prices, the Levelized Cost of Electricity (LCOE) required for economic feasibility must be less than 2¢/kWh. While not feasible under current market prices and costs, this work identifies key variables impacting process cost and discusses potential alternative paths toward economic feasibility.

  15. Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet.

    Science.gov (United States)

    Koo, Hyunmin; Hakim, Joseph A; Powell, Mickie L; Kumar, Ranjit; Eipers, Peter G; Morrow, Casey D; Crowley, Michael; Lefkowitz, Elliot J; Watts, Stephen A; Bej, Asim K

    2017-04-01

    In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using a metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine. The CFD-fed D. rerio exhibited KEGG functional categories of bacteria-mediated cobalamin biosynthesis, which was supported by the presence of cobalamin synthesizers such as Bacteroides and Lactobacillus. Though these bacteria were absent in GFD-fed D. rerio, a comparable level of the cobalamin biosynthesis KEGG functional category was observed, which could be contributed by the compensatory enrichment of Cetobacterium. Based on these results, we conclude D. rerio to be a suitable alternative animal model for the use of a targeted metagenomics approach along with bioinformatics tools to further investigate the relationship between the gluten diet and microbiome profile in the gut ecosystem leading to gastrointestinal diseases and other undesired adverse health effects.

  16. Functional rigidity of a methane biofilter during the temporal microbial succession.

    Science.gov (United States)

    Kim, Tae Gwan; Jeong, So-Yeon; Cho, Kyung-Suk

    2014-04-01

    Temporal microbial succession was investigated in relation to the performance of a methane biofilter. A laboratory-scale biofilter packed with perlite was operated for 108 days, without a deliberate biomass control. The system performance was stable over the period with a mean elimination capacity of 1,563 g m(-3) day(-1), despite a temporal deterioration (45-56 days). Ribosomal-tag pyrosequencing showed that bacterial communities at days 14-28 were distinct from those of days 68-108. The accumulation of nonviable substances strongly coincided with the community change (R (2) > 0.97). Rhodobacter, Hydrogenophaga, and Methylomonas were dominated in the earlier period, while Methylocaldum and Methylococcus were abundant in the later period. The methanotrophic proportion gradually increased to 41 %, and type I methanotrophs became predominant over time. However, community structure and methanotrophic population density stably retained over time, allowing the system to keep the similar performance. Therefore, the perlite biofilter system was functionally rigid against the temporal microbial succession.

  17. Integrated expanded granular sludge bed and sequential batch reactor treating beet sugar industrial wastewater and recovering bioenergy.

    Science.gov (United States)

    Justo, Ambuchi John; Junfeng, Liu; Lili, Shan; Haiman, Wang; Lorivi, Moirana Ruth; Mohammed, Mohammed O A; Xiangtong, Zhou; Yujie, Feng

    2016-10-01

    The exponential rise in energy demand vis-à-vis depletion of mineral oil resources has accelerated recovery of bioenergy from organic waste. In this study, a laboratory-scale anaerobic (An)/aerobic (Ar) system comprising of expanded granular sludge bed (EGSB) reactor coupled to an aerobic sequential batch reactor (SBR) was constructed to treat beet sugar industrial wastewater (BSIW) of chemical oxygen demand (COD) 1665 mg L(-1) while harnessing methane gas. The EGSB reactor generated methane at the rate of 235 mL/g COD added, with considerably higher than previously reported methane content of 86 %. Meanwhile, contaminants were successfully reduced in the combined An/Ar system, realizing a removal rate of more than 71.4, 97.3, 97.7, and 99.3 % of organic matter as total phosphorus, total nitrogen, biological oxygen demand (BOD), and soluble COD, respectively. Microbial community analysis showed that the bacterial genus Clostridium sp. and archaeal genus Methanosaeta sp. dominated the EGSB reactor, while Rhodobacter sp. dominance was observed in the SBR. The obtained experimental results indicate that the integration of expanded granular sludge bed and sequential batch reactor in treating BSIW obtained competitively outstanding performance.

  18. Dimeric carotenoid interaction in the light-harvesting antenna of purple phototrophic bacteria.

    Science.gov (United States)

    Zurdo, J; Lozano, R M; Fernandez-Cabrera, C; Ramirez, J M

    1991-03-15

    The carotenoid content of intracytoplasmic membrane vesicles isolated from purple phototrophic bacteria was reduced to a variable extent by mild extraction with light petroleum. Using preparations obtained from Rhodobacter capsulatus strains that contained the Light Harvesting System I (LHI) complex as the only major photosynthetic holochrome, it was shown that the visible circular dichroism of the carotenoids increased with the square of the membrane carotenoid content, as expected from being caused by dimeric exciton interaction. No chirality resulting from twists of the individual planar chromophore was detected. Therefore the contribution to carotenoid optical activity of non-degenerate interactions with bacteriochlorophyll or the apoprotein does not appear to be significant. The broadening of the absorption band of the bound pigment, caused by the splitting of the monomer transition, was demonstrated in membrane vesicles of both Rb, capsulatus and Rhodospirillum rubrum as a decrease of the fine structure of the band. Furthermore, the dimeric organization of the carotenoid pigments in the bacterial LHI complex accounted for the observed quantitative relationship between the fine structure of the band and the carotenoid content of the membrane.

  19. The structural role of the carotenoid in the bacterial light-harvesting protein 2 (LH2) of Rhodonbacter capsulatus. A Fourier transform Raman spectroscopy and circular dichroism study.

    Science.gov (United States)

    Zurdo, J; Centeno, M A; Odriozola, J A; Fernández-Cabrera, C; Ramírez, J M

    1995-11-01

    In previous work (Zurdo J, Fernández-Cabrera C and Ramírez JM (1993) Biochem J 290: 531-537), it had been shown that selective extraction of the carotenoid from the light-harvesting protein 2 (LH2) of Rhodobacter capsulatus induced the dissociation of 800-nm absorbing bacteriochlorophyll (Bchl), a 10-nm red shift of 854-nm Bchl, and a decrease of the stability of the protein in detergent solution. In the present study, the Fourier transform Raman and near-infrared circular dichroism spectra of native and carotenoid-depleted LH2 membrane preparations were compared. It was found that while the coupled carbonyls of 854-nm Bchl remained specifically H-bonded to the peptides after carotenoid extraction, the optical activity of the near-infrared electronic transition was significantly altered. Given the excitonic origin of such optical activity, our data suggest that carotenoid extraction elicits a rearrengement of the chromophore cluster and of the associated polypeptide subunits. This implies a significant role of the carotenoid in maintaining the native quaternary structure of the protein, which would be consistent with the observed dissociation of 800-nm Bchl and the loss of solubilized LH2 stability that result from carotenoid removal. There is no evidence for a similar role of the carotenoid in the LH1 protein.

  20. Biohydrogen production by isolated halotolerant photosynthetic bacteria using long-wavelength light-emitting diode (LW-LED)

    Energy Technology Data Exchange (ETDEWEB)

    Kawagoshi, Yasunori; Oki, Yukinori; Nakano, Issei; Fujimoto, Aya [Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555 (Japan); Takahashi, Hirokazu [Environmental Business DivisionDaiki Ataka Engineering Co. Ltd., 2-1-9 Nishiku-Urihori, Osaka 550-0012 (Japan)

    2010-12-15

    Biohydrogen is expected as one of the alternative energy to fossil fuel. In this study, halotolerant photosynthetic hydrogen producing bacteria (ht-PHB) were isolated from a sediment of tideland, and hydrogen gas (H{sub 2}) production by isolated ht-PHB from mixed short-chain fatty acids (SFAs) using a long-wavelength light emitting diode (LW-LED) was investigated. The isolated ht-PHB grow on a culture containing three kinds of SFAs (lactic acid, acetic acid, butyric acid) and produced H{sub 2} with their complete consumption at NaCl concentration in the 0-3% range in the light of tungsten lamp. The isolated ht-PHB was phylogenetically identified as Rhodobacter sp. KUPB1. The KUPB1 showed well growth and H{sub 2} production even under LW-LED light irradiation, indicating that LW-LED is quite useful as an energy-saving light source for photosynthetic H{sub 2} production. (author)

  1. Study on the novel producing approach of lycopene%番茄红素的新型生产途径研究

    Institute of Scientific and Technical Information of China (English)

    薛姣; 胡宗利; 陈国平; 赵志平; 陈绪清

    2008-01-01

    研究利用PCR技术扩增出Erwinia herbicola的crtI基因,并连接到含强启动子Puc的表达载体pRKR5上构建表达质粒pRKR5-crtI,通过接合转移的方式将其导入光合细菌Rhodobacter sphaeroides突变株TC72中,调控氧浓度诱导工程菌累积红色色素,经HPLC和吸收光谱分析,工程菌中合成的色素为番茄红素,工程菌的生物量(干重)为2.36g/L,番茄红素含量可达1.52mg/g,与其他生产番茄红素的工程菌如大肠杆菌和产朊假丝酵母相比,番茄红素产量有一定程度的提高.

  2. Genetic probes of structure/function relationships in the Q{sub B} binding site of the photosynthetic reaction center

    Energy Technology Data Exchange (ETDEWEB)

    Hanson, D.K.; Tiede, D.M.; Nance, S.L.; Chang, Chong-Hwan; Schiffer, M.

    1991-06-25

    In photosynthetic reaction centers, a quinone molecule, Q{sub B}, is the terminal acceptor in light-induced electron transfer. The crystal structure of the reaction center implicates the protonatable amiho acid residues L212Glu and L213Asp in the binding of Q{sub B} to the reaction center and in proton transfer to the anionic forms of Q{sub B} generated by electron transfer from Q{sub A}. Here we report the construction of the double mutant L212Ala-L213Ala by site-specific mutagenesis, and the isolation and preliminary biophysical characterization of revertant and suppressor strains that have regained the ability to grow under photosynthetic conditions. Our results show that neither L212Glu nor L213Asp is essential for efficient light-induced electron or proton transfer in Rhodobacter capsulatus and that second-site mutations, located within the QB binding pocket or at a more distant site, can compensate for mutations at L212 and L213. Acquisition of a single negatively charged residue (at position L213, or on the other side of the binding pocket at position L225) or loss of a positively charged residue (at position M231) is sufficient to restore activity to the complex.

  3. Purificación y caracterización de lipopolisacáridos de Eikenella corrodens 23834 y Porphyromonas gingivalis W83

    Directory of Open Access Journals (Sweden)

    Diego Fernando Gualtero Escobar

    2014-06-01

    Full Text Available Título corto: Metodología para el aislamiento e identificación  de LPS de periodonto-patógenosTítulo en inglés: Purification and characterization of lipopolysaccharide from Eikenella corrodens 23834 and Porphyromonas gingivalis W83Resumen: La purificación de lipopolisacáridos (LPS o endotoxinas y su caracterización es un aspecto esencial para estudios que buscan aclarar el papel de estas biomoléculas de bacterias Gram negativas presentes en la cavidad oral y su relación con enfermedades locales periodontales y sistémicas. Este estudio implementa una metodología para la extracción, purificación y caracterización de LPS a partir de bacteria completa de Eikenella corrodens 23834 y Porphyromonas gingivalis W83,  utilizando técnicas previamente descritas. La extracción cruda de LPS se realizó con fenol-agua caliente; la purificación se realizó con tratamiento enzimático con nucleasas y proteasa, seguido de cromatografía de exclusión por tamaño (Sephacryl S-200 HR con deoxicolato de sodio como fase móvil. La caracterización de los extractos purificados se realizó por barrido espectrofotométrico, pruebas bioquímicas de electroforesis SDS-PAGE, ensayo Purpald y la prueba cromogénica de LAL. Como control para la identificación y caracterización de los extractos purificados se utilizaron LPS comerciales de Escherichia coli, Salmonella typhimurium, Rodobacter sphaeroides y Porphyromonas gingivalis. La metodología implementada permitió la obtención de LPS de elevada pureza con la identificación de KDO o heptosas, un quimiotipo de LPS-S (liso para E. corrodens y LPS-SR (semi-rugoso para P. gingivalis W83. Ambos LPS purificados mostraron capacidad endotóxica a bajas concentraciones. La metodología implementada en este estudio para la purificación y caracterización de LPS a partir de bacteria completa  fue eficiente al compararla con los LPS comerciales.Palabras clave: endotoxinas, cromatografía, ácido 2-ceto-3

  4. Heterologous expression of membrane proteins: choosing the appropriate host.

    Directory of Open Access Journals (Sweden)

    Florent Bernaudat

    Full Text Available BACKGROUND: Membrane proteins are the targets of 50% of drugs, although they only represent 1% of total cellular proteins. The first major bottleneck on the route to their functional and structural characterisation is their overexpression; and simply choosing the right system can involve many months of trial and error. This work is intended as a guide to where to start when faced with heterologous expression of a membrane protein. METHODOLOGY/PRINCIPAL FINDINGS: The expression of 20 membrane proteins, both peripheral and integral, in three prokaryotic (E. coli, L. lactis, R. sphaeroides and three eukaryotic (A. thaliana, N. benthamiana, Sf9 insect cells hosts was tested. The proteins tested were of various origins (bacteria, plants and mammals, functions (transporters, receptors, enzymes and topologies (between 0 and 13 transmembrane segments. The Gateway system was used to clone all 20 genes into appropriate vectors for the hosts to be tested. Culture conditions were optimised for each host, and specific strategies were tested, such as the use of Mistic fusions in E. coli. 17 of the 20 proteins were produced at adequate yields for functional and, in some cases, structural studies. We have formulated general recommendations to assist with choosing an appropriate system based on our observations of protein behaviour in the different hosts. CONCLUSIONS/SIGNIFICANCE: Most of the methods presented here can be quite easily implemented in other laboratories. The results highlight certain factors that should be considered when selecting an expression host. The decision aide provided should help both newcomers and old-hands to select the best system for their favourite membrane protein.

  5. Hydrogen bonding between the QB site ubisemiquinone and Ser-L223 in the bacterial reaction centre – a combined spectroscopic and computational perspective^

    Science.gov (United States)

    Martin, Erik; Baldansuren, Amgalanbaatar; Lin, Tzu-Jen; Samoilova, Rimma I.; Wraight, Colin A.; Dikanov, Sergei A.; O’Malley, Patrick J.

    2012-01-01

    In the QB site of the Rba. sphaeroides photosynthetic reaction centre the donation of a hydrogen bond from the hydroxyl group of Ser-L223 to the ubisemiquinone formed after the first flash is debatable. In this study we use a combination of spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations to comprehensively explore this topic. We show that ENDOR, ESEEM and HYSCORE spectroscopic differences between the mutant L223SA and the wild type sample (WT) are negligible, indicating only minor perturbations in the ubisemiquinone spin density for the mutant sample. Qualitatively this suggests that a strong hydrogen bond does not exist in the WT between the Ser-L223 hydroxyl group and the semiquinone O1 atom, as removal of this hydrogen bond in the mutant should cause a significant redistribution of spin density in the semiquinone. We show quantitatively, using QM/MM calculations, that a WT model in which the Ser-L223 hydroxyl group is rotated to prevent hydrogen bond formation with the O1 atom of the semiquinone predicts negligible change for the L223SA mutant. This, together with the better agreement between key QM/MM calculated and experimental hyperfine couplings for the non-hydrogen bonded model, leads us to conclude that no strong hydrogen bond is formed between the Ser-L223 hydroxyl group and the semiquinone O1 atom after the first flash. The implications of this finding for quinone reduction in photosynthetic reaction centres are discussed. PMID:23016832

  6. Affinity and activity of non-native quinones at the QB site of bacterial photosynthetic reaction centers

    Science.gov (United States)

    Zhang, Xinyu; Gunner, M. R.

    2014-01-01

    Purple, photosynthetic reaction centers (RCs) from Rb. sphaeroides bacteria use UQ10 as primary (QA) and secondary (QB) electron acceptors. Many quinones reconstitute QA function, while few will act as QB. Nine quinones were tested for their ability to bind and reconstitute QA and QB function. Only ubiquinone (UQ) reconstitutes both QA and QB function in the same protein. The affinities of the non-native quinones for the QB site were determined by a competitive inhibition assay. The affinities of benzoquinones (BQ), napthoquinone (NQ) and 2-methyl-NQ for the QB site are 7±3 times weaker than for the QA site. However, di-ortho substituted NQs and anthraquinone bind tightly to the QA site (Kd ≤200 nM) and ≥1000 times more weakly to the QB site, perhaps setting a limit on the size of the site. With a low potential electron donor (2-methyl, 3-dimethylamino-1,4-Napthoquinone (Me-diMeAm-NQ)) at QA, QB reduction is 260 meV more favorable than with UQ as QA. Electron transfer from Me-diMeAm-NQ at the QA site to NQ at the QB site can be detected. In the QB site the NQ semiquinone is estimated to be ≈ 60–100 meV higher in energy than the UQ semiquinone, while in the QA site the semiquinone energy level is similar or lower with NQ than with UQ. Thus, the NQ semiquinone is more stable in the QA than QB site. In contrast, the native UQ semiquinone is ≈ 60 meV lower in energy in the QB than the QA site, stabilizing forward electron transfer from QA to QB. PMID:23715773

  7. Neighboring Deschampsia flexuosa and Trientalis europaea harbor contrasting root fungal endophytic communities.

    Science.gov (United States)

    Tejesvi, Mysore V; Sauvola, Tiina; Pirttilä, Anna Maria; Ruotsalainen, Anna Liisa

    2013-01-01

    Fungal endophytic communities and potential host preference of root-inhabiting fungi of boreal forest understory plants are poorly known. The objective of this study was to find out whether two neighboring plant species, Deschampsia flexuosa (Poaceae) and Trientalis europaea (Primulaceae), share similar root fungal endophytic communities and whether the communities differ between two sites. The study was carried out by analysis of pure culture isolates and root fungal colonization percentages. A total of 84 isolates from D. flexuosa and 27 isolates from T. europaea were obtained. The roots of D. flexuosa harbored 16 different isolate types based on macromorphological characteristics, whereas only 4 isolate types were found in T. europaea. The root colonization by dark septate and hyaline septate hyphae correlated with isolate numbers being higher in D. flexuosa compared to T. europaea. The different isolate types were further identified on the basis of internal transcribed spacer sequence and phylogenetic analysis. An isolate type identified as dark septate endophyte Phialocephala fortinii colonized 50 % of the T. europaea and 21 % of the D. flexuosa specimens. In addition, Meliniomyces variabilis, Phialocephala sphaeroides, and Umbelopsis isabellina were found colonizing the grass, D. flexuosa, for the first time and Mycena sp. was confirmed as an endophyte of D. flexuosa. Site-specific differences were observed in the abundance and diversity of endophytic fungi in the roots of both study plants, but the differences were not as predominant as those between plant species. It is concluded that D. flexuosa harbors both higher amount and more diverse community of endophytic fungi in its roots compared to T. europaea.

  8. Theoretical studies of the functional role of the cross-linked histidine-tyrosine copper-B ligand of cytochrome c oxidase

    Science.gov (United States)

    McDonald, William J.

    In the present work density functional theory calculations were performed to explore the vibrational and electronic spectral changes associated with proton and electron transfer from the CuB center at the active site of cytochrome c oxidase that lead to the formation of either the PR or PM intermediates in the catalytic reduction of dioxygen to water. Furthermore, the thermodynamics of proton and electron transfer from the cross-linked histidine-tyrosine Cu B ligand were explored to assess the possible role of this ligand as a proton and/or electron donor during enzymatic turnover. Characteristic calculated cross-linked imidazole-phenolate and imidazole-phenoxyl radical vibrational frequencies and isotope shifts are in good agreement with the vibrational spectra of the PR and PM intermediates of the bo3 quinol oxidase from E. coli and R. sphaeroides and P. denitrificans suggesting that the Y244 (bovine numbering) is deprotonated in the PR intermediate, and is a tyrosyl radical in P M. Furthermore, using isodesmic reactions, the cross-linked phenol is found to be a significantly stronger acid than an unmodified phenol in the gas-phase, and likely in the inhomogeneous low-dielectric environment of the membrane bound enzyme, supporting the conclusion that the cross-linked tyrosine is a proton donor during enzymatic turnover. Time-dependent density functional theory calculations qualitatively reproduce the red-shift in the UV/visible absorption spectrum of a cross-linked imidazole-phenolate anion compared to the imidazole-phenol. Furthermore, the unique ˜500 nm absorption of a cross-linked imidazole-phenoxyl radical is correctly predicted using TDDFT and may be assigned as an imidazole-phenoxyl radical pi-to-pi* transition. Furthermore, this absorption is predicted in the spectrum of a Cu2+-imidazole-phenoxyl biradical model.

  9. Heterologous expression of membrane proteins: choosing the appropriate host.

    Science.gov (United States)

    Bernaudat, Florent; Frelet-Barrand, Annie; Pochon, Nathalie; Dementin, Sébastien; Hivin, Patrick; Boutigny, Sylvain; Rioux, Jean-Baptiste; Salvi, Daniel; Seigneurin-Berny, Daphné; Richaud, Pierre; Joyard, Jacques; Pignol, David; Sabaty, Monique; Desnos, Thierry; Pebay-Peyroula, Eva; Darrouzet, Elisabeth; Vernet, Thierry; Rolland, Norbert

    2011-01-01

    Membrane proteins are the targets of 50% of drugs, although they only represent 1% of total cellular proteins. The first major bottleneck on the route to their functional and structural characterisation is their overexpression; and simply choosing the right system can involve many months of trial and error. This work is intended as a guide to where to start when faced with heterologous expression of a membrane protein. The expression of 20 membrane proteins, both peripheral and integral, in three prokaryotic (E. coli, L. lactis, R. sphaeroides) and three eukaryotic (A. thaliana, N. benthamiana, Sf9 insect cells) hosts was tested. The proteins tested were of various origins (bacteria, plants and mammals), functions (transporters, receptors, enzymes) and topologies (between 0 and 13 transmembrane segments). The Gateway system was used to clone all 20 genes into appropriate vectors for the hosts to be tested. Culture conditions were optimised for each host, and specific strategies were tested, such as the use of Mistic fusions in E. coli. 17 of the 20 proteins were produced at adequate yields for functional and, in some cases, structural studies. We have formulated general recommendations to assist with choosing an appropriate system based on our observations of protein behaviour in the different hosts. Most of the methods presented here can be quite easily implemented in other laboratories. The results highlight certain factors that should be considered when selecting an expression host. The decision aide provided should help both newcomers and old-hands to select the best system for their favourite membrane protein. © 2011 Bernaudat et al.

  10. Non-Growth-Associated Demethylation of Dimethylsulfoniopropionate by (Homo)acetogenic Bacteria

    Science.gov (United States)

    Jansen, Michael; Hansen, Theo A.

    2001-01-01

    The demethylation of the algal osmolyte dimethylsulfoniopropionate (DMSP) to methylthiopropionate (MTPA) by (homo)acetogenic bacteria was studied. Five Eubacterium limosum strains (including the type strain), Sporomusa ovata DSM 2662T, Sporomusa sphaeroides DSM 2875T, and Acetobacterium woodii DSM 1030T were shown to demethylate DMSP stoichiometrically to MTPA. The (homo)acetogenic fermentation based on this demethylation did not result in any significant increase in biomass. The analogous demethylation of glycine betaine to dimethylglycine does support growth of acetogens. In batch cultures of E. limosum PM31 DMSP and glycine betaine were demethylated simultaneously. In mixed substrates experiments with fructose-DMSP or methanol-DMSP, DMSP was used rapidly but only after exhaustion of the fructose or the methanol. In steady-state fructose-limited chemostat cultures (at a dilution rate of 0.03 h−1) with DMSP as a second reservoir substrate, DMSP was biotransformed to MTPA but this did not result in higher biomass values than in cultures without DMSP; cells from such cultures demethylated DMSP at rates of approximately 50 nmol min−1 mg of protein−1, both after growth in the presence of DMSP and after growth in its absence. In cell extracts of glycine betaine-grown strain PM31, DMSP demethylation activities of 21 to 24 nmol min−1 mg of protein−1 were detected with tetrahydrofolate as a methyl acceptor; the activities seen with glycine betaine were approximately 10-fold lower. A speculative explanation for the demethylation of DMSP without an obvious benefit for the organism is that the DMSP-demethylating activity is catalyzed by the glycine betaine-demethylating enzyme and that a transport-related factor, in particular a higher energy demand for DMSP transport across the cytoplasmic membrane than for glycine betaine transport, may reduce the overall ATP yield of the fermentation to virtually zero. PMID:11133459

  11. Mimicking protein-protein electron transfer: voltammetry of Pseudomonas aeruginosa azurin and the Thermus thermophilus Cu(A) domain at omega-derivatized self-assembled-monolayer gold electrodes.

    Science.gov (United States)

    Fujita, Kyoko; Nakamura, Nobufumi; Ohno, Hiroyuki; Leigh, Brian S; Niki, Katsumi; Gray, Harry B; Richards, John H

    2004-11-03

    Well-defined voltammetric responses of redox proteins with acidic-to-neutral pI values have been obtained on pure alkanethiol as well as on mixed self-assembled-monolayer (SAM) omega-derivatized alkanethiol/gold bead electrodes. Both azurin (P. aeruginosa) (pI = 5.6) and subunit II (Cu(A) domain) of ba(3)-type cytochrome c oxidase (T. thermophilus) (pI = 6.0) exhibit optimal voltammetric responses on 1:1 mixtures of [H(3)C(CH(2))(n)()SH + HO(CH(2))(n)()SH] SAMs. The electron transfer (ET) rate vs distance behavior of azurin and Cu(A) is independent of the omega-derivatized alkanethiol SAM headgroups. Strikingly, only wild-type azurin and mutants containing Trp48 give voltammetric responses: based on modeling, we suggest that electronic coupling with the SAM headgroup (H(3)C- and/or HO-) occurs at the Asn47 side chain carbonyl oxygen and that an Asn47-Cys112 hydrogen bond promotes intramolecular ET to the copper. Inspection of models also indicates that the Cu(A) domain of ba(3)-type cytochrome c oxidase is coupled to the SAM headgroup (H(3)C- and/or HO-) near the main chain carbonyl oxygen of Cys153 and that Phe88 (analogous to Trp143 in subunit II of cytochrome c oxidase from R. sphaeroides) is not involved in the dominant tunneling pathway. Our work suggests that hydrogen bonds from hydroxyl or other proton-donor groups to carbonyl oxygens potentially can facilitate intermolecular ET between physiological redox partners.

  12. Transient W-band EPR study of sequential electron transfer in photosynthetic bacterial reaction centers

    Energy Technology Data Exchange (ETDEWEB)

    Tang, J.; Utschig, L.M.; Poluektov, O.; Thurnauer, M.C. [Argonne National Lab., IL (United States). Chemistry Div.

    1999-06-17

    The key reaction of photosynthetic solar energy conversion involves the photoexcitation of a primary donor (P) followed by rapid, sequential electron transfer to a series of acceptors resulting in charge separation. Electron-spin polarized (ESP) EPR spectra at W-band (95 GHz) were obtained for deuterated Fe-removed/Zn-substituted photosynthetic bacterial reaction centers (RCs) to investigate the influence of the rate of charge separation on the observed P{sup +}Q{sub A}{sup {minus}} charge separated state. Temperature dependent ESP EPR spectra for kinetically characterized Zn-substituted RCs from Rb. sphaeroides R-26 having different rates (k{sub Q}) of the electron transfer from the bacteriopheophytin to the quinone acceptor were obtained. The Zn-RCs exhibited either the native fast (200 ps){sup {minus}1} k{sub Q} or a slow (3--6 ns){sup {minus}1} k{sub Q} at 298 K as determined from transient optical measurements. Sequential electron-transfer polarization modeling of the polarized W-band EPR spectra obtained with these samples was used to address the reason for the differences in the electron-transfer rates. Here, the authors report the k{sub Q} rate constant, the temperature dependence of k{sub Q}, and the reorganization energy for the P{sup +}H{sup {minus}}Q{sub A} and P{sup +}HQ{sub A}{sup {minus}} electron-transfer step determined from SETP modeling of the experimental spectra. The reorganization energy for the electron-transfer process between P{sup +}H{sup {minus}}Q{sub A} and P{sup +}HQ{sub A}{sup {minus}}, and not structural changes in the donor or acceptor, was found to be the dominant factor that is altered during Fe-removal procedures.

  13. Blue-Green Algae Inhibit the Development of Atherosclerotic Lesions in Apolipoprotein E Knockout Mice.

    Science.gov (United States)

    Ku, Chai Siah; Kim, Bohkyung; Pham, Tho X; Yang, Yue; Wegner, Casey J; Park, Young-Ki; Balunas, Marcy; Lee, Ji-Young

    2015-12-01

    Hyperlipidemia and inflammation contribute to the development of atherosclerotic lesions. Our objective was to determine antiatherogenic effect of edible blue-green algae (BGA) species, that is, Nostoc commune var. sphaeroides Kützing (NO) and Spirulina platensis (SP), in apolipoprotein E knockout (ApoE(-/-)) mice, a well-established mouse model of atherosclerosis. Male ApoE(-/-) mice were fed a high-fat/high-cholesterol (HF/HC, 15% fat and 0.2% cholesterol by wt) control diet or a HF/HC diet supplemented with 5% (w/w) of NO or SP powder for 12 weeks. Plasma total cholesterol (TC) and triglycerides (TG) were measured, and livers were analyzed for histology and gene expression. Morphometric analysis for lesions and immunohistochemical analysis for CD68 were conducted in the aorta and the aortic root. NO supplementation significantly decreased plasma TC and TG, and liver TC, compared to control and SP groups. In the livers of NO-fed mice, less lipid droplets were present with a concomitant decrease in fatty acid synthase protein levels than the other groups. There was a significant increase in hepatic low-density lipoprotein receptor protein levels in SP-supplemented mice than in control and NO groups. Quantification of aortic lesions by en face analysis demonstrated that both NO and SP decreased aortic lesion development to a similar degree compared with control. While lesions in the aortic root were not significantly different between groups, the CD68-stained area in the aortic root was significantly lowered in BGA-fed mice than controls. In conclusion, both NO and SP supplementation decreased the development of atherosclerotic lesions, suggesting that they may be used as a natural product for atheroprotection.

  14. Hypolipidemic Effect of a Blue-Green Alga (Nostoc commune) Is Attributed to Its Nonlipid Fraction by Decreasing Intestinal Cholesterol Absorption in C57BL/6J Mice.

    Science.gov (United States)

    Ku, Chai Siah; Kim, Bohkyung; Pham, Tho X; Yang, Yue; Weller, Curtis L; Carr, Timothy P; Park, Young-Ki; Lee, Ji-Young

    2015-11-01

    We previously demonstrated that Nostoc commune var. sphaeroids Kützing (NO), a blue-green alga (BGA), exerts a hypolipidemic effect in vivo and its lipid extract regulates the expression of genes involved in cholesterol and lipid metabolism in vitro. The objective of this study was to investigate whether the hypolipidemic effect of NO is attributed to an algal lipid or a delipidated fraction in vivo compared with Spirulina platensis (SP). Male C57BL/6J mice were fed an AIN-93M diet containing 2.5% or 5% of BGA (w/w) or a lipid extract equivalent to 5% of BGA for 4 weeks to measure plasma and liver lipids, hepatic gene expression, intestinal cholesterol absorption, and fecal sterol excretion. Plasma total cholesterol (TC) was significantly lower in 2.5% and 5% NO-fed groups, while plasma triglyceride (TG) levels were decreased in the 5% NO group compared with controls. However, neither NO organic extract (NOE) nor SP-fed groups altered plasma lipids. Hepatic mRNA levels of sterol regulatory element-binding protein 2, 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGR), carnitine palmitoyltransferase-1α, and acyl-CoA oxidase 1 were induced in 5% NO-fed mice, while there were no significant changes in hepatic lipogenic gene expression between groups. NO, but not NOE and SP groups, significantly decreased intestinal cholesterol absorption. When HepG2 cells and primary mouse hepatocytes were incubated with NOE and SP organic extract (SPE), there were marked decreases in protein levels of HMGR, low-density lipoprotein receptor, and fatty acid synthase. In conclusion, the nonlipid fraction of NO exerts TC and TG-lowering effects primarily by inhibiting intestinal cholesterol absorption and by increasing hepatic fatty acid oxidation, respectively.

  15. Isolation of acetogenic bacteria that induce biocorrosion by utilizing metallic iron as the sole electron donor.

    Science.gov (United States)

    Kato, Souichiro; Yumoto, Isao; Kamagata, Yoichi

    2015-01-01

    Corrosion of iron occurring under anoxic conditions, which is termed microbiologically influenced corrosion (MIC) or biocorrosion, is mostly caused by microbial activities. Microbial activity that enhances corrosion via uptake of electrons from metallic iron [Fe(0)] has been regarded as one of the major causative factors. In addition to sulfate-reducing bacteria and methanogenic archaea in marine environments, acetogenic bacteria in freshwater environments have recently been suggested to cause MIC under anoxic conditions. However, no microorganisms that perform acetogenesis-dependent MIC have been isolated or had their MIC-inducing mechanisms characterized. Here, we enriched and isolated acetogenic bacteria that induce iron corrosion by utilizing Fe(0) as the sole electron donor under freshwater, sulfate-free, and anoxic conditions. The enriched communities produced significantly larger amounts of Fe(II) than the abiotic controls and produced acetate coupled with Fe(0) oxidation prior to CH4 production. Microbial community analysis revealed that Sporomusa sp. and Desulfovibrio sp. dominated in the enrichments. Strain GT1, which is closely related to the acetogen Sporomusa sphaeroides, was eventually isolated from the enrichment. Strain GT1 grew acetogenetically with Fe(0) as the sole electron donor and enhanced iron corrosion, which is the first demonstration of MIC mediated by a pure culture of an acetogen. Other well-known acetogenic bacteria, including Sporomusa ovata and Acetobacterium spp., did not grow well on Fe(0). These results indicate that very few species of acetogens have specific mechanisms to efficiently utilize cathodic electrons derived from Fe(0) oxidation and induce iron corrosion.

  16. Arsenic metabolism in purple nonsulfur bacteria%紫色非硫细菌的砷代谢机制

    Institute of Scientific and Technical Information of China (English)

    吕常江; 赵春贵; 杨素萍; 曲音波

    2012-01-01

    arrangement. Some members of PNSB evolved two independently families of arsenate reduction genes (arsC). The cells of Rhodopseudomonas palustris CQV97 , Rhodobacter azotoformans 134K20 and Rhodobacter capsulatus XJ-1 could reduce As ( V ) to As ( M ) , whereas As ( HI) could not be transformed back to As ( V ). Higher concentration phosphate competitively inhibited arsenate toxicity to cells. [Conclusion] Our investigations shed light on the evolution and functional implications in arsenic gene clusters of PNSB, and support the notion that arsenate reduction and arsenite methylation appears to be the dominant process in PNSB.

  17. The Vitamin B12-Dependent Photoreceptor AerR Relieves Photosystem Gene Repression by Extending the Interaction of CrtJ with Photosystem Promoters

    Directory of Open Access Journals (Sweden)

    Mingxu Fang

    2017-03-01

    Full Text Available Purple nonsulfur bacteria adapt their physiology to a wide variety of environmental conditions often through the control of transcription. One of the main transcription factors involved in controlling expression of the Rhodobacter capsulatus photosystem is CrtJ, which functions as an aerobic repressor of photosystem genes. Recently, we reported that a vitamin B12 binding antirepressor of CrtJ called AerR is required for anaerobic expression of the photosystem. However, the mechanism whereby AerR regulates CrtJ activity is unclear. In this study, we used a combination of next-generation sequencing and biochemical methods to globally identify genes under control of CrtJ and the role of AerR in controlling this regulation. Our results indicate that CrtJ has a much larger regulon than previously known, with a surprising regulatory function under both aerobic and anaerobic photosynthetic growth conditions. A combination of in vivo chromatin immunoprecipitation-DNA sequencing (ChIP-seq and ChIP-seq and exonuclease digestion (ChIP-exo studies and in vitro biochemical studies demonstrate that AerR forms a 1:2 complex with CrtJ (AerR-CrtJ2 and that this complex binds to many promoters under photosynthetic conditions. The results of in vitro and in vivo DNA binding studies indicate that AerR-CrtJ2 anaerobically forms an extended interaction with the bacteriochlorophyll bchC promoter to relieve repression by CrtJ. This is contrasted by aerobic growth conditions where CrtJ alone functions as an aerobic repressor of bchC expression. These results indicate that the DNA binding activity of CrtJ is modified by interacting with AerR in a redox-regulated manner and that this interaction alters CrtJ’s function.

  18. Site-specific and compensatory mutations imply unexpected pathways for proton delivery to the QB binding site of the photosynthetic reaction center.

    Science.gov (United States)

    Hanson, D K; Tiede, D M; Nance, S L; Chang, C H; Schiffer, M

    1993-01-01

    In photosynthetic reaction centers, a quinone molecule, QB, is the terminal acceptor in light-induced electron transfer. The protonatable residues Glu-L212 and Asp-L213 have been implicated in the binding of QB and in proton transfer to QB anions generated by electron transfer from the primary quinone QA. Here we report the details of the construction of the Ala-L212/Ala-L213 double mutant strain by site-specific mutagenesis and show that its photosynthetic incompetence is due to an inability to deliver protons to the QB anions. We also report the isolation and biophysical characterization of a collection of revertant and suppressor strains that have regained the photosynthetic phenotype. The compensatory mutations that restore function are diverse and show that neither Glu-L212 nor Asp-L213 is essential for efficient light-induced electron or proton transfer in Rhodobacter capsulatus. Second-site mutations, located within the QB binding pocket or at more distant sites, can compensate for mutations at L212 and L213 to restore photocompetence. Acquisition of a single negatively charged residue (at position L213, across the binding pocket at position L225, or outside the pocket at M43) or loss of a positively charged residue (at position M231) is sufficient to restore proton transfer activity to the complex. The proton transport pathways in the suppressor strains cannot, in principle, be identical to that of the wild type. The apparent mutability of this pathway suggests that the reaction center can serve as a model system to study the structural basis of protein-mediated proton transport. PMID:8105468

  19. The diversity of PAH-degrading bacteria in a deep-sea water column above the Southwest Indian Ridge.

    Science.gov (United States)

    Yuan, Jun; Lai, Qiliang; Sun, Fengqin; Zheng, Tianling; Shao, Zongze

    2015-01-01

    The bacteria involved in organic pollutant degradation in pelagic deep-sea environments are largely unknown. In this report, the diversity of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria was analyzed in deep-sea water on the Southwest Indian Ridge (SWIR). After enrichment with a PAH mixture (phenanthrene, anthracene, fluoranthene, and pyrene), nine bacterial consortia were obtained from depths of 3946-4746 m. While the consortia degraded all four PAHs when supplied in a mixture, when PAHs were tested individually, only phenanthrene supported growth. Thus, degradation of the PAH mixture reflected a cometabolism of anthracene, fluoranthene, and pyrene with phenanthrene. Further, both culture-dependent and independent methods revealed many new bacteria involved in PAH degradation. Specifically, the alpha and gamma subclasses of Proteobacteria were confirmed as the major groups within the communities. Additionally, Actinobacteria, the CFB group and Firmicutes were detected. Denaturing Gradient Gel Electrophoresis (DGGE) analysis showed that bacteria closely affiliated with Alcanivorax, Novosphingobium, and Rhodovulum occurred most frequently in different PAH-degrading consortia. By using general heterotrophic media, 51 bacteria were isolated from the consortia and of these 34 grew with the PAH mixture as a sole carbon source. Of these, isolates most closely related to Alterierythrobacter, Citricella, Erythrobacter, Idiomarina, Lutibacterium, Maricaulis, Marinobacter, Martelella, Pseudidiomarina, Rhodobacter, Roseovarius, Salipiger, Sphingopyxis, and Stappia were found to be PAH degraders. To the best of our knowledge, this is the first time these bacteria have been identified in this context. In summary, this report revealed significant diversity among the PAH-degrading bacteria in the deep-sea water column. These bacteria may play a role in PAH removal in deep-sea environments.

  20. Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module.

    Science.gov (United States)

    Hebbeln, Peter; Rodionov, Dmitry A; Alfandega, Anja; Eitinger, Thomas

    2007-02-20

    BioMNY proteins are considered to constitute tripartite biotin transporters in prokaryotes. Recent comparative genomic and experimental analyses pointed to the similarity of BioMN to homologous modules of prokaryotic transporters mediating uptake of metals, amino acids, and vitamins. These systems resemble ATP-binding cassette-containing transporters and include typical ATPases (e.g., BioM). Absence of extracytoplasmic solute-binding proteins among the members of this group, however, is a distinctive feature. Genome context analyses uncovered that only one-third of the widespread bioY genes are linked to bioMN. Many bioY genes are located at loci encoding biotin biosynthesis, and others are unlinked to biotin metabolic or transport genes. Heterologous expression of the bioMNY operon and of the single bioY of the alpha-proteobacterium Rhodobacter capsulatus conferred biotin-transport activity on recombinant Escherichia coli cells. Kinetic analyses identified BioY as a high-capacity transporter that was converted into a high-affinity system in the presence of BioMN. BioMNY-mediated biotin uptake was severely impaired by replacement of the Walker A lysine residue in BioM, demonstrating dependency of high-affinity transport on a functional ATPase. Biochemical assays revealed that BioM, BioN, and BioY proteins form stable complexes in membranes of the heterologous host. Expression of truncated bio transport operons, each with one gene deleted, resulted in stable BioMN complexes but revealed only low amounts of BioMY and BioNY aggregates in the absence of the respective third partner. The results substantiate our earlier suggestion of a mechanistically novel group of membrane transporters.

  1. 几株光合细菌的分离鉴定及在养殖罗非鱼中的应用%Isolation and Identification of Several Photosynthesis Bacteria and Their Application in the Culture of Tilapia sp.

    Institute of Scientific and Technical Information of China (English)

    黄志勇; 王海胜; 蒋培霞; 宋安东; 刘志培

    2005-01-01

    从渔场底泥样品中分离纯化得到5株紫色非硫光合细菌,根据分离菌株的细胞形态结构、光合内膜结构、活细胞光吸收特征以及生理生化特征,参照伯杰氏细菌分类学手册,5个分离株分别属于沼泽红假单胞菌(Rhodopseudomonas palusteris)和类球红细菌(Rhodobacter spheroides).利用它们的纯培养物及混合培养物进行的水产养殖试验表明,光合细菌可以明显提高养殖鱼的成活率以及生长速度,罗非鱼经过2周的养殖后,加入光合细菌的试验组比没加入光合细菌的对照组(成活率80%)成活率显著提高,最高达100%;平均体长、体重分别提高了3%~5%、20%~30%,效果显著;而同时加入光合细菌纯培养物的试验组和加入混合培养物的试验组,差别不大.

  2. Biodegradation Of Thiocyanate Using Microbial Consortia Cultured From Gold Mine Tailings

    Science.gov (United States)

    Moreau, J. W.; Watts, M. P.; Spurr, L. P.; Vu, H. P.

    2015-12-01

    Some bacteria possess the capability to degrade SCN-; therefore, harnessing this metabolic trait offers a biotechnological remediation strategy for SCN- produced in gold ore processing. A tailings storage facility (TSF) at a gold mine in Victoria, Australia holds large quantities of thiocyanate (SCN-) contaminated mine waste. The surface water in the TSF typically contains SCN- concentrations of >800 mg L-1, and seepage from the facility has contaminated the groundwater at the site. This study aimed to culture SCN-degrading microbes from the TSF, characterize the microbial consortia and test its operational parameters for use in a thiocyanate-degrading bioreactor. Surface samples were obtained from several locations around the TSF facility and used to inoculate medium reflective of the moderately saline and alkaline tailings water at the TSF, in the absence of organic carbon but subject to additions of phosphate and trace metals. Four microbial consortia capable of rapid SCN- degradation were successfully cultured. Sequencing of 16S rRNA genes found that the consortia were dominated by Thiobacillus species, a genus of known SCN- degraders. Lower abundances of other SCN- degraders; Sphingopyxis and Rhodobacter, were also identified. The impact of a number of geochemical conditions, including pH, temperature and SCN- concentration, upon the growth and SCN- degrading capacity of these consortia was determined. These results informed the optimization of a lab-scale thiocyanate degrading bioreactor. In summary, the cultured bacterial consortia proved effective towards SCN- degradation at the prevailing geochemical conditions of the TSF, requiring minimal nutrient additions. These consortia were dominated by genera of known autotrophic SCN- degraders. The comprehensive characterisation of these SCN- degrading consortia will provide the fundamental operational parameters required for deployment of this technique at the field scale.

  3. The Diversity of PAH-degrading bacteria in a deep-sea water column above the Southwest Indian Ridge

    Directory of Open Access Journals (Sweden)

    Zongze eShao

    2015-08-01

    Full Text Available The bacteria involved in organic pollutant degradation in pelagic deep-sea environments are largely unknown. In this report, the diversity of polycyclic aromatic hydrocarbon ( PAH-degrading bacteria was analyzed in deep-sea water on the Southwest Indian Ridge (SWIR. After enrichment with a PAH mixture (phenanthrene, anthracene, fluoranthene and pyrene, 9 nine bacterial consortia were obtained from depths of 3946 m to 4746 m. PAH degradation occurred to all components of the mixture, but when using a single PAH as the sole carbon and energy source, only phenanthrene can be degraded obviously. This indicates the cometabolism of anthracene, fluoranthene and pyrene with phenanthreneWhile the consortia degraded all four PAHs when supplied in a mixture, when PAHs were tested individually, only phenanthrene supported growth. Thus, degradation of the PAH mixture reflected a cometabolism of anthracene, fluoranthene and pyrene with phenanthrene. Further, both culture-dependent and independent methods revealed many new bacteria involved in PAH degradation. Specifically, the alpha and gamma subclasses of Proteobacteria were confirmed as the major groups within the communities. Additionally, Actinobacteria, the CFB group and Firmicutes were detected. Denaturing Gradient Gel Electrophoresis (DGGE analysis showed that bacteria closely affiliated with Alcanivorax, Novosphingobium and Rhodovulum occurred most frequently in different PAH-degrading consortia. More than half of the isolates (34 of 51 isolates were confirmed to have the ability to grow with the PAH mixture By using general heterotrophic media, 51 bacteria were isolated from the consortia and of these 34 grew with the PAH mixture as a sole carbon source. Of these, isolates most closely related to Alterierythrobacter, Citricella, Erythrobacter, Idiomarina, Lutibacterium, Maricaulis, Marinobacter, Martelella, Pseudidiomarina, Rhodobacter, Roseovarius, Salipiger, Sphingopyxis and Stappia were found to

  4. The Vitamin B12-Dependent Photoreceptor AerR Relieves Photosystem Gene Repression by Extending the Interaction of CrtJ with Photosystem Promoters

    Science.gov (United States)

    Fang, Mingxu

    2017-01-01

    ABSTRACT Purple nonsulfur bacteria adapt their physiology to a wide variety of environmental conditions often through the control of transcription. One of the main transcription factors involved in controlling expression of the Rhodobacter capsulatus photosystem is CrtJ, which functions as an aerobic repressor of photosystem genes. Recently, we reported that a vitamin B12 binding antirepressor of CrtJ called AerR is required for anaerobic expression of the photosystem. However, the mechanism whereby AerR regulates CrtJ activity is unclear. In this study, we used a combination of next-generation sequencing and biochemical methods to globally identify genes under control of CrtJ and the role of AerR in controlling this regulation. Our results indicate that CrtJ has a much larger regulon than previously known, with a surprising regulatory function under both aerobic and anaerobic photosynthetic growth conditions. A combination of in vivo chromatin immunoprecipitation-DNA sequencing (ChIP-seq) and ChIP-seq and exonuclease digestion (ChIP-exo) studies and in vitro biochemical studies demonstrate that AerR forms a 1:2 complex with CrtJ (AerR-CrtJ2) and that this complex binds to many promoters under photosynthetic conditions. The results of in vitro and in vivo DNA binding studies indicate that AerR-CrtJ2 anaerobically forms an extended interaction with the bacteriochlorophyll bchC promoter to relieve repression by CrtJ. This is contrasted by aerobic growth conditions where CrtJ alone functions as an aerobic repressor of bchC expression. These results indicate that the DNA binding activity of CrtJ is modified by interacting with AerR in a redox-regulated manner and that this interaction alters CrtJ’s function. PMID:28325764

  5. Uncovering the Transmembrane Metal Binding Site of the Novel Bacterial Major Facilitator Superfamily-Type Copper Importer CcoA

    Directory of Open Access Journals (Sweden)

    Bahia Khalfaoui-Hassani

    2016-01-01

    Full Text Available Uptake and trafficking of metals and their delivery to their respective metalloproteins are important processes. Cells need precise control of each step to avoid exposure to excessive metal concentrations and their harmful consequences. Copper (Cu is a required micronutrient used as a cofactor in proteins. However, in large amounts, it can induce oxidative damage; hence, Cu homeostasis is indispensable for cell survival. Biogenesis of respiratory heme-Cu oxygen (HCO reductases includes insertion of Cu into their catalytic subunits to form heme-Cu binuclear centers. Previously, we had shown that CcoA is a major facilitator superfamily (MFS-type bacterial Cu importer required for biogenesis of cbb3-type cytochrome c oxidase (cbb3-Cox. Here, using Rhodobacter capsulatus, we focused on the import and delivery of Cu to cbb3-Cox. By comparing the CcoA amino acid sequence with its homologues from other bacterial species, we located several well-conserved Met, His, and Tyr residues that might be important for Cu transport. We determined the topology of the transmembrane helices that carry these residues to establish that they are membrane embedded, and substituted for them amino acids that do not ligand metal atoms. Characterization of these mutants for their uptake of radioactive 64Cu and cbb3-Cox activities demonstrated that Met233 and His261 of CcoA are essential and Met237 and Met265 are important, whereas Tyr230 has no role for Cu uptake or cbb3-Cox biogenesis. These findings show for the first time that CcoA-mediated Cu import relies on conserved Met and His residues that could act as metal ligands at the membrane-embedded Cu binding domain of this transporter.

  6. Microbial diversity observed during hemp retting.

    Science.gov (United States)

    Ribeiro, Alexandra; Pochart, Philippe; Day, Arnaud; Mennuni, Sarah; Bono, Pierre; Baret, Jean-Luc; Spadoni, Jean-Louis; Mangin, Irène

    2015-05-01

    Historically used in textile and paper industry, hemp fibres have started to find new applications in composite materials with important economic and ecological advantages. However, their applications are limited since manufacturers have some difficulties to standardise fabrication processes. This study is a first step before selection and isolation of strains that could later be used to optimise microbial retting efficiency and hence fibre quality. We studied six samples harvested on different ground types, at different dates and with different retting durations on field to obtain an exhaustive representation of the process. After DNA extraction, total bacteria and fungi associated with stems during retting were specifically quantified using real-time PCR. Then, using sequence analysis of randomly cloned 16S and 18S ribosomal RNA (rRNA) genes, a phylogenetic characterisation of the dominant microorganisms was carried out. Quantitatively, we showed that there were 8.1-9.5 log₁₀ 16S rRNA gene copies per gram of hemp straw for bacteria and 8.6-9.6 log₁₀ 18S rRNA gene copies per gram for fungi. Qualitatively, we noticed a higher bacterial diversity in comparison to fungi. This work showed that in the different samples, the same species were present but in significantly different proportions according to ground type, harvest dates and retting durations on field. The most frequent bacterial sequences were affiliated to species Escherichia coli, Pantoea agglomerans, Pseudomonas rhizosphaerae, Rhodobacter sp., Pseudomonas fulva, Rhizobium huautlense and Massilia timonae, whereas fungal sequences were principally related to the genera Cladosporium and Cryptococcus.

  7. The single NqrB and NqrC subunits in the Na(+)-translocating NADH: quinone oxidoreductase (Na(+)-NQR) from Vibrio cholerae each carry one covalently attached FMN.

    Science.gov (United States)

    Casutt, Marco S; Schlosser, Andreas; Buckel, Wolfgang; Steuber, Julia

    2012-10-01

    The Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR) is the prototype of a novel class of flavoproteins carrying a riboflavin phosphate bound to serine or threonine by a phosphodiester bond to the ribityl side chain. This membrane-bound, respiratory complex also contains one non-covalently bound FAD, one non-covalently bound riboflavin, ubiquinone-8 and a [2Fe-2S] cluster. Here, we report the quantitative analysis of the full set of flavin cofactors in the Na(+)-NQR and characterize the mode of linkage of the riboflavin phosphate to the membrane-bound NqrB and NqrC subunits. Release of the flavin by β-elimination and analysis of the cofactor demonstrates that the phosphate group is attached at the 5'-position of the ribityl as in authentic FMN and that the Na(+)-NQR contains approximately 1.7mol covalently bound FMN per mol non-covalently bound FAD. Therefore, each of the single NqrB and NqrC subunits in the Na(+)-NQR carries a single FMN. Elimination of the phosphodiester bond yields a dehydro-2-aminobutyrate residue, which is modified with β-mercaptoethanol by Michael addition. Proteolytic digestion followed by mass determination of peptide fragments reveals exclusive modification of threonine residues, which carry FMN in the native enzyme. The described reactions allow quantification and localization of the covalently attached FMNs in the Na(+)-NQR and in related proteins belonging to the Rhodobacter nitrogen fixation (RNF) family of enzymes. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).

  8. The ActP acetate transporter acts prior to the PitA phosphate carrier in tellurite uptake by Escherichia coli.

    Science.gov (United States)

    Elías, Alex; Díaz-Vásquez, Waldo; Abarca-Lagunas, María José; Chasteen, Thomas G; Arenas, Felipe; Vásquez, Claudio C

    2015-08-01

    The tellurium oxyanion tellurite is harmful for most microorganisms. Since its toxicity occurs chiefly once the toxicant reaches the intracellular compartment, unveiling the toxicant uptake process is crucial for understanding the whole phenomenon of tellurium toxicity. While the PitA phosphate transporter is thought to be one of the main paths responsible for toxicant entry into Escherichia coli, genetic and physiological evidence have identified the ActP acetate carrier as the main tellurite importer in Rhodobacter capsulatus. In this work, new background on the role of these transporters in tellurite uptake by E. coli is presented. It was found that, similar to what occurs in R. capsulatus, ActP is able to mediate toxicant entry to this bacterium. Lower reactive oxygen species levels were observed in E. coli lacking the actP gene. Antioxidant enzyme catalase and fumarase C activity was almost unchanged after short exposure of E. coli ΔactP to sublethal tellurite concentrations, suggesting a low antioxidant response. In this strain, tellurite uptake decreased significantly during the first 5 min of exposure and inductively coupled plasma optical emission spectroscopy assays using an actP-overexpressing strain confirmed that this carrier mediates toxicant uptake. Relative gene expression experiments by qPCR showed that actP expression is enhanced at short times of tellurite exposure, while pitA and pitB genes are induced later. Summarizing, the results show that ActP is involved in tellurite entry to E. coli and that its participation occurs mainly at early stages of toxicant exposure.

  9. The CcrM DNA methyltransferase is widespread in the alpha subdivision of proteobacteria, and its essential functions are conserved in Rhizobium meliloti and Caulobacter crescentus.

    Science.gov (United States)

    Wright, R; Stephens, C; Shapiro, L

    1997-09-01

    The Caulobacter crescentus DNA methyltransferase CcrM (M.CcrMI) methylates the adenine residue in the sequence GANTC. The CcrM DNA methyltransferase is essential for viability, but it does not appear to be part of a DNA restriction-modification system. CcrM homologs are widespread in the alpha subdivision of gram-negative bacteria. We have amplified and sequenced a 258-bp region of the cerM gene from several of these bacteria, including Rhizobium meliloti, Brucella abortus, Agrobacterium tumefaciens, and Rhodobacter capsulatus. Alignment of the deduced amino acid sequences revealed that these proteins constitute a highly conserved DNA methyltransferase family. Isolation of the full-length ccrM genes from the aquatic bacterium C. crescentus, the soil bacterium R. meliloti, and the intracellular pathogen B. abortus showed that this sequence conservation extends over the entire protein. In at least two alpha subdivision bacteria, R. meliloti and C. crescentus, CcrM-mediated methylation has important cellular functions. In both organisms, CcrM is essential for viability. Overexpression of CcrM in either bacterium results in defects in cell division and cell morphology and in the initiation of DNA replication. Finally, the C. crescentus and R. meliloti ccrM genes are functionally interchangeable, as the complemented strains are viable and the chromosomes are methylated. Thus, in both R. meliloti and C. crescentus, CcrM methylation is an integral component of the cell cycle. We speculate that CcrM-mediated DNA methylation is likely to have similar roles among alpha subdivision bacteria.

  10. Biohydrogen production from beet molasses by sequential dark and photofermentation

    Energy Technology Data Exchange (ETDEWEB)

    Oezguer, Ebru; Eroglu, Inci [Middle East Technical University, Department of Chemical Engineering, 06531, Ankara (Turkey); Mars, Astrid E.; Louwerse, Annemarie; Claassen, Pieternel A.M. [Wageningen UR, Agrotechnology and Food Sciences Group, Wageningen UR, P.O. Box 17, 6700 AA Wageningen (Netherlands); Peksel, Beguem; Yuecel, Meral; Guenduez, Ufuk [Middle East Technical University, Department of Biology, 06531, Ankara (Turkey)

    2010-01-15

    Biological hydrogen production using renewable resources is a promising possibility to generate hydrogen in a sustainable way. In this study, a sequential dark and photofermentation has been employed for biohydrogen production using sugar beet molasses as a feedstock. An extreme thermophile Caldicellulosiruptor saccharolyticus was used for the dark fermentation, and several photosynthetic bacteria (Rhodobacter capsulatus wild type, R. capsulatus hup{sup -} mutant, and Rhodopseudomonas palustris) were used for the photofermentation. C. saccharolyticus was grown in a pH-controlled bioreactor, in batch mode, on molasses with an initial sucrose concentration of 15 g/L. The influence of additions of NH{sub 4}{sup +} and yeast extract on sucrose consumption and hydrogen production was determined. The highest hydrogen yield (4.2 mol of H{sub 2}/mol sucrose) and maximum volumetric productivity (7.1 mmol H{sub 2}/L{sub c}.h) were obtained in the absence of NH{sub 4}{sup +}. The effluent of the dark fermentation containing no NH{sub 4}{sup +} was fed to a photobioreactor, and hydrogen production was monitored under continuous illumination, in batch mode. Productivity and yield were improved by dilution of the dark fermentor effluent (DFE) and the additions of buffer, iron-citrate and sodium molybdate. The highest hydrogen yield (58% of the theoretical hydrogen yield of the consumed organic acids) and productivity (1.37 mmol H{sub 2}/L{sub c}.h) were attained using the hup{sup -} mutant of R. capsulatus. The overall hydrogen yield from sucrose increased from the maximum of 4.2 mol H{sub 2}/mol sucrose in dark fermentation to 13.7 mol H{sub 2}/mol sucrose (corresponding to 57% of the theoretical yield of 24 mol of H{sub 2}/mole of sucrose) by sequential dark and photofermentation. (author)

  11. The thioreduction component CcmG confers efficiency and the heme ligation component CcmH ensures stereo-specificity during cytochrome c maturation.

    Science.gov (United States)

    Verissimo, Andreia F; Khalfaoui-Hassani, Bahia; Hwang, Josephine; Steimle, Stefan; Selamoglu, Nur; Sanders, Carsten; Khatchikian, Camilo E; Daldal, Fevzi

    2017-08-11

    In many Gram-negative bacteria, including Rhodobacter capsulatus, cytochrome c maturation (Ccm) is carried out by a membrane-integral machinery composed of nine proteins (CcmA to I). During this process, the periplasmic thiol-disulfide oxidoreductase DsbA is thought to catalyze the formation of a disulfide bond between the Cys residues at the apocytochrome c heme-binding site (CXXCH). Subsequently, a Ccm-specific thioreductive pathway involving CcmG and CcmH reduces this disulfide bond to allow covalent heme ligation. Currently, the sequence of thioredox reactions occurring between these components and apocytochrome c and the identity of their active Cys residues are unknown. In this work, we first investigated protein-protein interactions among the apocytochrome c, CcmG, and the heme-ligation components CcmF, CcmH, and CcmI. We found that they all interact with each other, forming a CcmFGHI-apocytochrome c complex. Using purified wild-type CcmG, CcmH, and apocytochrome c, as well as their respective Cys mutant variants, we determined the rates of thiol-disulfide exchange reactions between selected pairs of Cys residues from these proteins. We established that CcmG can efficiently reduce the disulfide bond of apocytochrome c and also resolve a mixed disulfide bond formed between apocytochrome c and CcmH. We further show that Cys-45 of CcmH and Cys-34 of apocytochrome c are most likely to form this mixed disulfide bond, which is consistent with the stereo-specificity of the heme-apocytochrome c ligation reaction. We conclude that CcmG confers efficiency, and CcmH ensures stereo-specificity during Ccm and present a comprehensive model for thioreduction reactions that lead to heme-apocytochrome c ligation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Temperature-induced changes in treatment efficiency and microbial structure of aerobic granules treating landfill leachate.

    Science.gov (United States)

    Mieczkowski, Dorian; Cydzik-Kwiatkowska, Agnieszka; Rusanowska, Paulina; Świątczak, Piotr

    2016-06-01

    This paper investigates the effect of temperature on nitrogen and carbon removal by aerobic granules from landfill leachate with a high ammonium concentration and low concentration of biodegradable organics. The study was conducted in three stages; firstly the operating temperature of the batch reactor with aerobic granules was maintained at 29 °C, then at 25 °C, and finally at 20 °C. It was found that a gradual decrease in operational temperature allowed the nitrogen-converting community in the granules to acclimate, ensuring efficient nitrification even at ambient temperature (20 °C). Ammonium was fully removed from leachate regardless of the temperature, but higher operational temperatures resulted in higher ammonium removal rates [up to 44.2 mg/(L h) at 29 °C]. Lowering the operational temperature from 29 to 20 °C decreased nitrite accumulation in the GSBR cycle. The highest efficiency of total nitrogen removal was achieved at 25 °C (36.8 ± 10.9 %). The COD removal efficiency did not exceed 50 %. Granules constituted 77, 80 and 83 % of the biomass at 29, 25 and 20 °C, respectively. Ammonium was oxidized by both aerobic and anaerobic ammonium-oxidizing bacteria. Accumulibacter sp., Thauera sp., cultured Tetrasphaera PAO and Azoarcus-Thauera cluster occurred in granules independent of the temperature. Lower temperatures favored the occurrence of denitrifiers of Zooglea lineage (not Z. resiniphila), bacteria related to Comamonadaceae, Curvibacter sp., Azoarcus cluster, Rhodobacter sp., Roseobacter sp. and Acidovorax spp. At lower temperatures, the increased abundance of denitrifiers compensated for the lowered enzymatic activity of the biomass and ensured that nitrogen removal at 20 °C was similar to that at 25 °C and significantly higher than removal at 29 °C.

  13. Linking ceragenins to water-treatment membranes to minimize biofouling.

    Energy Technology Data Exchange (ETDEWEB)

    Hibbs, Michael R.; Altman, Susan Jeanne; Feng, Yanshu (Brigham Young University, Provo, Utah); Savage, Paul B. (Brigham Young University, Provo, Utah); Pollard, Jacob (Brigham Young University, Provo, Utah); Branda, Steven S.; Goeres, Darla (Montana State University, Bozeman, MT); Buckingham-Meyer, Kelli (Montana State University, Bozeman, MT); Stafslien, Shane (North Dakota State University, Fargo, ND); Marry, Christopher; Jones, Howland D. T.; Lichtenberger, Alyssa; Kirk, Matthew F.; McGrath, Lucas K. (LMATA, Albuquerque, NM)

    2012-01-01

    Ceragenins were used to create biofouling resistant water-treatment membranes. Ceragenins are synthetically produced antimicrobial peptide mimics that display broad-spectrum bactericidal activity. While ceragenins have been used on bio-medical devices, use of ceragenins on water-treatment membranes is novel. Biofouling impacts membrane separation processes for many industrial applications such as desalination, waste-water treatment, oil and gas extraction, and power generation. Biofouling results in a loss of permeate flux and increase in energy use. Creation of biofouling resistant membranes will assist in creation of clean water with lower energy usage and energy with lower water usage. Five methods of attaching three different ceragenin molecules were conducted and tested. Biofouling reduction was observed in the majority of the tests, indicating the ceragenins are a viable solution to biofouling on water treatment membranes. Silane direct attachment appears to be the most promising attachment method if a high concentration of CSA-121a is used. Additional refinement of the attachment methods are needed in order to achieve our goal of several log-reduction in biofilm cell density without impacting the membrane flux. Concurrently, biofilm forming bacteria were isolated from source waters relevant for water treatment: wastewater, agricultural drainage, river water, seawater, and brackish groundwater. These isolates can be used for future testing of methods to control biofouling. Once isolated, the ability of the isolates to grow biofilms was tested with high-throughput multiwell methods. Based on these tests, the following species were selected for further testing in tube reactors and CDC reactors: Pseudomonas ssp. (wastewater, agricultural drainage, and Colorado River water), Nocardia coeliaca or Rhodococcus spp. (wastewater), Pseudomonas fluorescens and Hydrogenophaga palleronii (agricultural drainage), Sulfitobacter donghicola, Rhodococcus fascians, Rhodobacter

  14. Precipitation of Phosphate Minerals by Microorganisms Isolated from a Fixed-Biofilm Reactor Used for the Treatment of Domestic Wastewater

    Directory of Open Access Journals (Sweden)

    Almudena Rivadeneyra

    2014-04-01

    Full Text Available The ability of bacteria isolated from a fixed-film bioreactor to precipitate phosphate crystals for the treatment of domestic wastewater in both artificial and natural media was studied. When this was demonstrated in artificial solid media for crystal formation, precipitation took place rapidly, and crystal formation began 3 days after inoculation. The percentage of phosphate-forming bacteria was slightly higher than 75%. Twelve major colonies with phosphate precipitation capacity were the dominant heterotrophic platable bacteria growing aerobically in artificial media. According to their taxonomic affiliations (based on partial sequencing of the 16S rRNA, the 12 strains belonged to the following genera of Gram-negative bacteria: Rhodobacter, Pseudoxanthobacter, Escherichia, Alcaligenes, Roseobacter, Ochrobactrum, Agromyce, Sphingomonas and Paracoccus. The phylogenetic tree shows that most of the identified populations were evolutionarily related to the Alphaproteobacteria (91.66% of sequences. The minerals formed were studied by X-ray diffraction, scanning electron microscopy (SEM, and energy dispersive X-ray microanalysis (EDX. All of these strains formed phosphate crystals and precipitated struvite (MgNH4PO4·6H2O, bobierrite [Mg3(PO42·8H2O] and baricite [(MgFe3(PO42·8H2O]. The results obtained in this study show that struvite and spherulite crystals did not show any cell marks. Moreover, phosphate precipitation was observed in the bacterial mass but also near the colonies. Our results suggest that the microbial population contributed to phosphate precipitation by changing the media as a consequence of their metabolic activity. Moreover, the results of this research suggest that bacteria play an active role in the mineral precipitation of soluble phosphate from urban wastewater in submerged fixed-film bioreactors.

  15. Molecular dynamics analysis of the structural and dynamic properties of the functionally enhanced hepta-variant of mouse 5-aminolevulinate synthase.

    Science.gov (United States)

    Na, Insung; DeForte, Shelly; Stojanovski, Bosko M; Ferreira, Gloria C; Uversky, Vladimir N

    2017-01-09

    Heme biosynthesis, a complex, multistage, and tightly controlled process, starts with 5-aminolevulinate (ALA) production, which, in metazoa and certain bacteria, is a reaction catalyzed by 5-aminolevulinate synthase (ALAS), a pyridoxal 5'-phosphate (PLP)-dependent enzyme. Functional aberrations in ALAS are associated with several human diseases. ALAS can adopt open and closed conformations, with segmental rearrangements of a C-terminal, 16-amino acid loop and an α-helix regulating accessibility to the ALAS active site. Of the murine erythroid ALAS (mALAS2) forms previously engineered to assess the role of the flexible C-terminal loop versus mALAS2 function one stood out due to its impressive gain in catalytic power. To elucidate how the simultaneously introduced seven mutations of this activity-enhanced variant affected structural and dynamic properties of mALAS2, we conducted extensive molecular dynamics simulation analysis of the dimeric forms of wild-type mALAS2, hepta-variant and Rhodobacter capsulatus ALAS (aka R. capsulatus HemA). This analysis revealed that the seven simultaneous mutations in the C-terminal loop, which extends over the active site of the enzyme, caused the bacterial and murine proteins to adopt different conformations. Specifically, a new β-strand in the mutated 'loop' led to interaction with two preexisting β-strands and formation of an anti-parallel three-stranded β-sheet, which likely endowed the murine hepta-variant a more 'stable' open conformation than that of wild-type mALAS2, consistent with a kinetic mechanism involving a faster closed-to-open conformation transition and product release for the mutated than wild-type enzyme. Further, the dynamic behavior of the mALAS2 protomers was strikingly different in the two dimeric forms.

  16. Molecular basis of proton uptake in single and double mutants of cytochrome c oxidase

    Energy Technology Data Exchange (ETDEWEB)

    Henry, Rowan M; Caplan, David; Pomes, Regis [Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, M5G 1X8 (Canada); Fadda, Elisa, E-mail: pomes@sickkids.ca [Department of Chemistry, University of Galway (Ireland)

    2011-06-15

    Cytochrome c oxidase, the terminal enzyme of the respiratory chain, utilizes the reduction of dioxygen into water to pump protons across the mitochondrial inner membrane. The principal pathway of proton uptake into the enzyme, the D channel, is a 2.5 nm long channel-like cavity named after a conserved, negatively charged aspartic a