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Sample records for hungatei haloarcula marismortui

  1. Characterization of the proteasome from the extremely halophilic archaeon Haloarcula marismortui

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    B. Franzetti

    2002-01-01

    Full Text Available A 20S proteasome, comprising two subunits α and β, was purified from the extreme halophilic archaeon Haloarcula marismortui, which grows only in saturated salt conditions. The three-dimensional reconstruction of the H. marismortui proteasome (Hm proteasome, obtained from negatively stained electron micrographs, is virtually identical to the structure of a thermophilic proteasome filtered to the same resolution. The stability of the Hm proteasome was found to be less salt-dependent than that of other halophilic enzymes previously described. The proteolytic activity of the Hm proteasome was investigated using the malate dehydrogenase from H. marismortui (HmMalDH as a model substrate. The HmMalDH denatures when the salt concentration is decreased below 2 M. Under these conditions, the proteasome efficiently cleaves HmMalDH during its denaturation process, but the fully denatured HmMalDH is poorly degraded. These in vitro experiments show that, at low salt concentrations, the 20S proteasome from halophilic archaea eliminates a misfolded protein.

  2. Effect Of Substrates On The Fractionation Of Hydrogen Isotopes During Lipid-Biosynthesis By Haloarcula marismortui

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    Dirghangi, S. S.; Pagani, M.

    2010-12-01

    Lipids form an important class of proxies for paleoclimatological research, and hydrogen isotope ratios of lipids are being increasingly used for understanding changes in the hydrological system. Proper understanding of hydrogen isotope fractionation during lipid biosynthesis is therefore important and attention has been directed toward understanding the magnitude of hydrogen isotope fractionation that occurs during lipid biosynthesis in various organisms. Hydrogen isotope ratios of lipids depend on the hydrogen isotopic composition of the ambient water, hydrogen isotopic composition of NADPH used during biosynthesis, growth conditions, pathways of lipid biosynthesis, and substrates in the case of heterotrophic organisms. Recently it has been observed that NADPH contributes a significant part of the hydrogen in fatty acids synthesized by bacteria during heterotrophic growth (Zhang et al, 2009). As NADPH is formed by reduction of NADP+ during metabolism of substrates, different metabolic pathways form NADPH with different D/H ratios, which in turn results in variation in D/H ratios of lipids (Zhang et al, 2009). Therefore, substrates play a significant role in hydrogen isotopic compositions of lipids. For this study, we are investigating the effects of substrates on hydrogen isotope fractionation during biosynthesis of isoprenoidal lipids by heterotrophically growing halophilic archaea. Haloarcula marismortui is a halophilic archaea which synthesizes Archaeol (a diether lipid) and other isoprenoidal lipids. We have grown Haloarcula marismortui in pure cultures on three different substrates and are in the process of evaluating isotopic variability of Archaeol and other lipids associated with substrate and the D/H composition of ambient water. Our results will be helpful for a better understanding of hydrogen isotope fractionations during lipid synthesis by archaea. Also, halophilic archaea are the only source of archaeol in hypersaline environments. Therefore, our

  3. Modeling of the structure of ribosomal protein L1 from the archaeon Haloarcula marismortui

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    Nevskaya, N. A.; Kljashtorny, V. G.; Vakhrusheva, A. V.; Garber, M. B.; Nikonov, S. V.

    2017-07-01

    The halophilic archaeon Haloarcula marismortui proliferates in the Dead Sea at extremely high salt concentrations (higher than 3 M). This is the only archaeon, for which the crystal structure of the ribosomal 50S subunit was determined. However, the structure of the functionally important side protuberance containing the abnormally negatively charged protein L1 (HmaL1) was not visualized. Attempts to crystallize HmaL1 in the isolated state or as its complex with RNA using normal salt concentrations (≤500 mM) failed. A theoretical model of HmaL1 was built based on the structural data for homologs of the protein L1 from other organisms, and this model was refined by molecular dynamics methods. Analysis of this model showed that the protein HmaL1 can undergo aggregation due to the presence of a cluster of positive charges unique for proteins L1. This cluster is located at the RNA-protein interface, which interferes with the crystallization of HmaL1 and the binding of the latter to RNA.

  4. Crystal Structure of the 23S rRNA Fragment Specific to r-Protein L1 and Designed Model of the Ribosomal L1 Stalk from Haloarcula marismortui

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    Azat Gabdulkhakov

    2017-02-01

    Full Text Available The crystal structure of the 92-nucleotide L1-specific fragment of 23S rRNA from Haloarcula marismortui (Hma has been determined at 3.3 Å resolution. Similar to the corresponding bacterial rRNA fragments, this structure contains joined helix 76-77 topped by an approximately globular structure formed by the residual part of the L1 stalk rRNA. The position of HmaL1 relative to the rRNA was found by its docking to the rRNA fragment using the L1-rRNA complex from Thermus thermophilus as a guide model. In spite of the anomalous negative charge of the halophilic archaeal protein, the conformation of the HmaL1-rRNA interface appeared to be very close to that observed in all known L1-rRNA complexes. The designed structure of the L1 stalk was incorporated into the H. marismortui 50S ribosomal subunit. Comparison of relative positions of L1 stalks in 50S subunits from H. marismortui and T. thermophilus made it possible to reveal the site of inflection of rRNA during the ribosome function.

  5. Reclassification of Bacillus marismortui as Salibacillus marismortui comb. nov.

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    Arahal, D R; Márquez, M C; Volcani, B E; Schleifer, K H; Ventosa, A

    2000-07-01

    Recently, the features of a group of strains isolated from Dead Sea enrichments obtained in 1936 by one of us (B. E. Volcani) were described. They were gram-positive, moderately halophilic, spore-forming rods, and were placed in a new species, Bacillus marismortui. At the same time, the new genus Salibacillus was proposed for the halophilic species Bacillus salexigens. B. marismortui and Salibacillus salexigens have similar phenotypic characteristics and the same peptidoglycan type. Phylogenetic analysis based on 16S rRNA sequence comparisons showed that they are sufficiently closely related (96.6% similarity) as to warrant placement in the same genus. However, DNA-DNA hybridization experiments showed that they constitute two separate species (41% DNA similarity). Therefore the reclassification of Bacillus marismortui as Salibacillus marismortui comb. nov. is proposed.

  6. Identification of cross-linked amino acids in the protein pair HmaL23-HmaL29 from the 50S ribosomal subunit of the archaebacterium Haloarcula marismortui.

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    Bergmann, U; Wittmann-Liebold, B

    1993-03-23

    50S ribosomal subunits from the extreme halophilic archaebacterium Haloarcula marismortui were treated with the homobifunctional protein-protein cross-linking reagents diepoxybutane (4 A) and dithiobis(succinimidyl propionate) (12 A). The dominant product with both cross-linking reagents was identified on the protein level as HmaL23-HmaL29, which is homologous to the protein pair L23-L29 from Escherichia coli [Walleczek, J., Martin, T., Redl, B., Stöffler-Meilicke, M., & Stöffler, G. (1989) Biochemistry 28, 4099-4105] and from Bacillus stearothermophilus [Brockmöller, J., & Kamp, R. M. (1986) Biol. Chem. Hoppe-Seyler 367, 925-935]. To reveal the exact cross-linking site in HmaL23-HmaL29, the cross-linked complex was purified on a preparative scale by conventional and high-performance liquid chromatography. After endoproteolytic fragmentation of the protein pair, the amino acids engaged in cross-link formation were unambiguously identified by N-terminal sequence analysis and mass spectrometry of the cross-linked peptides. The cross-link is formed between lysine-57 in the C-terminal region of HmaL29 and the alpha-amino group of the N-terminal serine in protein HmaL23, irrespective of the cross-linking reagent. This result demonstrates that the N-terminal region of protein HmaL23 and the C-terminal domain of HmaL29 are highly flexible so that the distance between the two polypeptide chains can vary by at least 8 A. Comparison of our cross-linking results with those obtained with B. stearothermophilus revealed that the fine structure within this ribosomal domain is at least partially conserved.

  7. ORF Alignment: NC_006395 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_006395 gi|55376664 >1v7zA 1 249 5 243 8e-44 ... ref|YP_134515.1| creatinine amidoh...ydrolase [Haloarcula marismortui ATCC 43049] ... gb|AAV44809.1| creatinine amidohydrolase [Haloarcula

  8. ORF Alignment: NC_006396 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... [Haloarcula marismortui ATCC 43049] ... Length = 295 ... Query: 8 ... GEQPLVLIWEVTQACELACKHCRADA...QPRRHPDELSTAEGKALLDQASEFGDGQLVVLSG 67 ... GEQPLVLIWEVTQACELACKHCRADAQPRRHP...DELSTAEGKALLDQASEFGDGQLVVLSG Sbjct: 1 ... GEQPLVLIWEVTQACELACKHCRADAQPRRHPDELSTAEGKALLDQASEFGDGQLVVLSG 60 ... Que

  9. ORF Alignment: NC_006396 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available porter ... permease protein [Haloarcula marismortui ATCC 43049] ... Length = 228 ... Query: 33 ... GDSQTLTAGTAPGFPPFEM...KQDGELVGFDVELLEAVVAATEYELSGWEELEFKSLIPALN 92 ... GDSQTLTAGTAPGFPPFEM...KQDGELVGFDVELLEAVVAATEYELSGWEELEFKSLIPALN Sbjct: 1 ... GDSQTLTAGTAPGFPPFEMKQDGELVGFDVELLEAVVAATEYE

  10. ORF Alignment: NC_006394 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... factor IIB 5 [Haloarcula marismortui ATCC 43049] ... Length = 54 ... Query: 16 DEDVQTESSATQCPECDGRVTTNAVETICE...DCGLVIEEQRIDHGPEWRAYDADE 69 ... DEDVQTESSATQCPECDGRVTTNAVETICE...DCGLVIEEQRIDHGPEWRAYDADE Sbjct: 1 ... DEDVQTESSATQCPECDGRVTTNAVETICEDCGLVIEEQRIDHGPEWRAYDADE 54

  11. ORF Alignment: NC_004369 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... [Haloarcula marismortui ATCC 43049] ... Length = 295 ... Query: 17 ... KPFIAIWEVTRACQLVCRHCRADAQH...EPAPGQLSTEEGFALLDSLATYDHPRPLVVLTGG 76 ... +P++ IWEVT+AC+L C+HCRADAQ ... P +...LST EG ALLD ... + + ... + LVVL+GG Sbjct: 3 ... QPLVLIWEVTQACELACKHCRADAQPRRHPDELSTAEGKALLDQASEFGDGQ-LVVLSGG 61 ... Que

  12. ORF Alignment: NC_002935 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... [Haloarcula marismortui ATCC 43049] ... Length = 295 ... Query: 24 ... KPFIAIWEVTRACGLVCQHCRADAQH...EPHPEQLTTEQGKQLLSDLASYERPKPLVVLTGG 83 ... +P++ IWEVT+AC L C+HCRADAQ ... HP++...L+T +GK LL D AS ... LVVL+GG Sbjct: 3 ... QPLVLIWEVTQACELACKHCRADAQPRRHPDELSTAEGKALL-DQASEFGDGQLVVLSGG 61 ... Que

  13. ORF Alignment: NC_006395 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_006395 gi|55376890 >1v7zA 5 250 13 257 5e-37 ... ref|YP_134741.1| creatinine amido...hydrolase [Haloarcula marismortui ATCC 43049] ... gb|AAV45035.1| creatinine amidohydrolase [Haloarcul

  14. Enzymatic activity of a novel halotolerant lipase from Haloarcula hispanica 2TK2

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    Ozgen Melis

    2016-06-01

    Full Text Available A strain of Haloarcula hispanica isolated from Tuzkoy salt mine, Turkey exhibited extracellular lipolytic activity. Important parameters such as carbon sources and salt concentration for lipase production were investigated. Optimal conditions for the enzyme production from Haloarcula hispanica 2TK2 were determined. It was observed that the lipolytic activity of Haloarcula hispanica was stimulated by some of the carbon sources. The high lipase acitivity values were obtained in the presence of 2% (v/v walnut oil (6.16 U/ml, 1% (v/v fish oil (5.07 U/ml, 1% (v/v olive oil (4.52 U/ml and 1% (w/v stearic acid (4.88 U/ml at 4M NaCl concentration. Lipase was partially purified by ammonium sulfate precipitation and ultrafiltration. Optimal temperature and pH values were determined as 45°C and 8.0, respectively. Lipase activity decreased with the increasing salt concentration, but 85% activity of the enzyme was maintained at 5M NaCl concentration. The enzyme preserved 41% of its relative activity at 90°C. The partially purified lipase maintained its activity in the presence of surfactants such as Triton X-100 and SDS. Therefore, the lipase which is an extremozyme may have potential applications especially in detergent industry.

  15. Amorphous Ca-phosphate precursors for Ca-carbonate biominerals mediated by Chromohalobacter marismortui

    NARCIS (Netherlands)

    Rivadeneyra, María Angustias; Martín-Algarra, Agustín; Sánchez-Román, Mónica; Sánchez-Navas, Antonio; Martín-Ramos, José Daniel

    Although diverse microbial metabolisms are known to induce the precipitation of carbonate minerals, the mechanisms involved in the bacterial mediation, in particular nucleation, are still debated. The study of aragonite precipitation by Chromohalobacter marismortui during the early stages (3-7 days)

  16. Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria.

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    Hansen, M A; Kirpekar, F; Ritterbusch, W; Vester, B

    2002-01-01

    Posttranscriptional modifications were mapped in helices 90-92 of 23S rRNA from the following phylogenetically diverse organisms: Haloarcula marismortui, Sulfolobus acidocaldarius, Bacillus subtilis, and Bacillus stearothermophilus. Helix 92 is a component of the ribosomal A-site, which contacts the aminoacyl-tRNA during protein synthesis, implying that posttranscriptional modifications in helices 90-92 may be important for ribosome function. RNA fragments were isolated from 23S rRNA by site-...

  17. GenBank blastx search result: AK104368 [KOME

    Lifescience Database Archive (English)

    Full Text Available , ureE, ureF genes for urease beta subunit UreB, urease alpha subunit UreC, urease gamma subunit UreA, urease... accessory protein UreG, urease accessory protein UreD, urease accessory protein UreE, urease accessory protein UreF, complete cds.|BCT BCT 1e-46 +1 ... ...AK104368 001-035-E04 AB119092.1 Haloarcula marismortui ureB, ureC, ureA, ureG, ureD

  18. Crystal Structure of the Oxazolidinone Antibiotic Linezolid Bound to the 50S Ribosomal Subunit

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    Ippolito,J.; Kanyo, Z.; Wang, D.; Franceschi, F.; Moore, P.; Steitz, T.; Duffy, E.

    2008-01-01

    The oxazolidinone antibacterials target the 50S subunit of prokaryotic ribosomes. To gain insight into their mechanism of action, the crystal structure of the canonical oxazolidinone, linezolid, has been determined bound to the Haloarcula marismortui 50S subunit. Linezolid binds the 50S A-site, near the catalytic center, which suggests that inhibition involves competition with incoming A-site substrates. These results provide a structural basis for the discovery of improved oxazolidinones active against emerging drug-resistant clinical strains.

  19. Draft genome of Haloarcula rubripromontorii strain SL3, a novel halophilic archaeon isolated from the solar salterns of Cabo Rojo, Puerto Rico.

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    Sánchez-Nieves, Rubén; Facciotti, Marc; Saavedra-Collado, Sofía; Dávila-Santiago, Lizbeth; Rodríguez-Carrero, Roy; Montalvo-Rodríguez, Rafael

    2016-03-01

    The genus Haloarcula belongs to the family Halobacteriaceae which currently has 10 valid species. Here we report the draft genome sequence of strain SL3, a new species within this genus, isolated from the Solar Salterns of Cabo Rojo, Puerto Rico. Genome assembly performed using NGEN Assembler resulted in 18 contigs (N50 = 601,911 bp), the largest of which contains 1,023,775 bp. The genome consists of 3.97 MB and has a GC content of 61.97%. Like all species of Haloarcula, the genome encodes heterogeneous copies of the small subunit ribosomal RNA. In addition, the genome includes 6 rRNAs, 48 tRNAs, and 3797 protein coding sequences. Several carbohydrate-active enzymes genes were found, as well as enzymes involved in the dihydroxyacetone processing pathway which are not found in other Haloarcula species. The NCBI accession number for this genome is LIUF00000000 and the strain deposit number is CECT9001.

  20. Primary structures of ribosomal proteins from the archaebacterium Halobacterium marismortui and the eubacterium Bacillus stearothermophilus.

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    Arndt, E; Scholzen, T; Krömer, W; Hatakeyama, T; Kimura, M

    1991-06-01

    Approximately 40 ribosomal proteins from each Halobacterium marismortui and Bacillus stearothermophilus have been sequenced either by direct protein sequence analysis or by DNA sequence analysis of the appropriate genes. The comparison of the amino acid sequences from the archaebacterium H marismortui with the available ribosomal proteins from the eubacterial and eukaryotic kingdoms revealed four different groups of proteins: 24 proteins are related to both eubacterial as well as eukaryotic proteins. Eleven proteins are exclusively related to eukaryotic counterparts. For three proteins only eubacterial relatives-and for another three proteins no counterpart-could be found. The similarities of the halobacterial ribosomal proteins are in general somewhat higher to their eukaryotic than to their eubacterial counterparts. The comparison of B stearothermophilus proteins with their E coli homologues showed that the proteins evolved at different rates. Some proteins are highly conserved with 64-76% identity, others are poorly conserved with only 25-34% identical amino acid residues.

  1. Draft genome of Haloarcula rubripromontorii strain SL3, a novel halophilic archaeon isolated from the solar salterns of Cabo Rojo, Puerto Rico

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    Rubén Sánchez-Nieves

    2016-03-01

    Full Text Available The genus Haloarcula belongs to the family Halobacteriaceae which currently has 10 valid species. Here we report the draft genome sequence of strain SL3, a new species within this genus, isolated from the Solar Salterns of Cabo Rojo, Puerto Rico. Genome assembly performed using NGEN Assembler resulted in 18 contigs (N50 = 601,911 bp, the largest of which contains 1,023,775 bp. The genome consists of 3.97 MB and has a GC content of 61.97%. Like all species of Haloarcula, the genome encodes heterogeneous copies of the small subunit ribosomal RNA. In addition, the genome includes 6 rRNAs, 48 tRNAs, and 3797 protein coding sequences. Several carbohydrate-active enzymes genes were found, as well as enzymes involved in the dihydroxyacetone processing pathway which are not found in other Haloarcula species. The NCBI accession number for this genome is LIUF00000000 and the strain deposit number is CECT9001. Keywords: Halophilic archaea, Henome sequence, Puerto Rico

  2. Differential Gene Expression in Response to Salinity and Temperature in a Haloarcula Strain from Great Salt Lake, Utah

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    Swati Almeida-Dalmet

    2018-01-01

    Full Text Available Haloarchaea that inhabit Great Salt Lake (GSL, a thalassohaline terminal lake, must respond to the fluctuating climate conditions of the elevated desert of Utah. We investigated how shifting environmental factors, specifically salinity and temperature, affected gene expression in the GSL haloarchaea, NA6-27, which we isolated from the hypersaline north arm of the lake. Combined data from cultivation, microscopy, lipid analysis, antibiotic sensitivity, and 16S rRNA gene alignment, suggest that NA6-27 is a member of the Haloarcula genus. Our prior study demonstrated that archaea in the Haloarcula genus were stable in the GSL microbial community over seasons and years. In this study, RNA arbitrarily primed PCR (RAP-PCR was used to determine the transcriptional responses of NA6-27 grown under suboptimal salinity and temperature conditions. We observed alteration of the expression of genes related to general stress responses, such as transcription, translation, replication, signal transduction, and energy metabolism. Of the ten genes that were expressed differentially under stress, eight of these genes responded in both conditions, highlighting this general response. We also noted gene regulation specific to salinity and temperature conditions, such as osmoregulation and transport. Taken together, these data indicate that the GSL Haloarcula strain, NA6-27, demonstrates both general and specific responses to salinity and/or temperature stress, and suggest a mechanistic model for homeostasis that may explain the stable presence of this genus in the community as environmental conditions shift.

  3. Ultrastructure, inferred porosity, and gram-staining character of Methanospirillum hungatei filament termini describe a unique cell permeability for this archaeobacterium

    International Nuclear Information System (INIS)

    Beveridge, T.J.; Sprott, G.D.; Whippey, P.

    1991-01-01

    By light microscopy, Methanospirillum hungatei GP1 stains gram positive at the terminal ends of each multicellular filament and gram negative at all regions in between. This phenomenon was studied further by electron microscopy and energy-dispersive X-ray spectroscopy of Gram-stained cells, using a platinum compound to replace Gram's iodine. Crystal violet-platinum precipitates could be found only in the terminal cells of each filament, which suggested that the multilamellar plugs at the filament ends were involved with stain penetration. When sheaths were isolated by sodium dodecyl sulfate-dithiothreitol treatment, the end plugs could be ejected and their layers could be separated from one another by 0.1 M NaOH treatment. Each plug consisted of at least three individual layers; two were particulate and possessed 14.0-nm particles hexagonally arranged on their surfaces with a spacing of a = b = 18.0 nm, whereas the other was a netting of 12.5-nm holes with spacings and symmetry identical to those of the particulate layers. Optical diffraction and computer image reconstruction were used to clarify the structures of each layer in an intact plug and to provide a high-resolution image of their interdigitated structures. The holes through this composite were three to six times larger than those through the sheath. Accordingly, we propose that the terminal plugs of M. hungatei allow the access of larger solutes than does the sheath and that this is the reason why the end cells of each filament stain gram positive whereas more internal cells are gram negative. Intuitively, since the cell spacers which partition the cells from one another along the filament contain plugs identical in structure to terminal plugs, the diffusion of large solutes for these cells would be unidirectional along the filament-cell axis

  4. Characterization of a novel chitinase from a moderately halophilic bacterium, Virgibacillus marismortui strain M3-23

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    Essghaier, Badiaa; Hedi, Abdeljabbar; Bajji, Mohammed; Jijakli, Haissam; Boudabous, Abdellatif; Sadfi-Zouaoui, Najla

    2012-01-01

    A new chitinase produced by the moderately halophilic bacterium Virgibacillus marismortui strain M3- 23 was identified and characterized. Distinguishable characteristics of high activity and stability at different pH, temperatures and salinity of M3-23 chitinase are reported. Analysis of the catalytic domain sequence from the enzyme highlighted its relationship to glycosyl hydrolase family 18. Comparison of the deduced chitinase sequence from strain M3-23 to known chitinases from Bacillus spe...

  5. Perchlorate and halophilic prokaryotes: implications for possible halophilic life on Mars.

    Science.gov (United States)

    Oren, Aharon; Elevi Bardavid, Rahel; Mana, Lily

    2014-01-01

    In view of the finding of perchlorate among the salts detected by the Phoenix Lander on Mars, we investigated the relationships of halophilic heterotrophic microorganisms (archaea of the family Halobacteriaceae and the bacterium Halomonas elongata) toward perchlorate. All strains tested grew well in NaCl-based media containing 0.4 M perchlorate, but at the highest perchlorate concentrations, tested cells were swollen or distorted. Some species (Haloferax mediterranei, Haloferax denitrificans, Haloferax gibbonsii, Haloarcula marismortui, Haloarcula vallismortis) could use perchlorate as an electron acceptor for anaerobic growth. Although perchlorate is highly oxidizing, its presence at a concentration of 0.2 M for up to 2 weeks did not negatively affect the ability of a yeast extract-based medium to support growth of the archaeon Halobacterium salinarum. These findings show that presence of perchlorate among the salts on Mars does not preclude the possibility of halophilic life. If indeed the liquid brines that may exist on Mars are inhabited by salt-requiring or salt-tolerant microorganisms similar to the halophiles on Earth, presence of perchlorate may even be stimulatory when it can serve as an electron acceptor for respiratory activity in the anaerobic Martian environment.

  6. Complete amino acid sequences of the ribosomal proteins L25, L29 and L31 from the archaebacterium Halobacterium marismortui.

    Science.gov (United States)

    Hatakeyama, T; Kimura, M

    1988-03-15

    Ribosomal proteins were extracted from 50S ribosomal subunits of the archaebacterium Halobacterium marismortui by decreasing the concentration of Mg2+ and K+, and the proteins were separated and purified by ion-exchange column chromatography on DEAE-cellulose. Ten proteins were purified to homogeneity and three of these proteins were subjected to sequence analysis. The complete amino acid sequences of the ribosomal proteins L25, L29 and L31 were established by analyses of the peptides obtained by enzymatic digestion with trypsin, Staphylococcus aureus protease, chymotrypsin and lysylendopeptidase. Proteins L25, L29 and L31 consist of 84, 115 and 95 amino acid residues with the molecular masses of 9472 Da, 12293 Da and 10418 Da respectively. A comparison of their sequences with those of other large-ribosomal-subunit proteins from other organisms revealed that protein L25 from H. marismortui is homologous to protein L23 from Escherichia coli (34.6%), Bacillus stearothermophilus (41.8%), and tobacco chloroplasts (16.3%) as well as to protein L25 from yeast (38.0%). Proteins L29 and L31 do not appear to be homologous to any other ribosomal proteins whose structures are so far known.

  7. U2504 Determines the Species Specificity of the A-site Cleft Antibiotics: The sStructures of Tiamulin, Homoharringtonine and Bruceantin Bound to the Ribosome

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    Gurel, G.; Blaha, G; Moore, P; Steitz,

    2009-01-01

    Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 {angstrom}. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

  8. U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.

    Science.gov (United States)

    Gürel, Güliz; Blaha, Gregor; Moore, Peter B; Steitz, Thomas A

    2009-05-29

    Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 A. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

  9. U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: The Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome

    Energy Technology Data Exchange (ETDEWEB)

    Gürel, Güliz; Blaha, Gregor; Moore, Peter B.; Steitz, Thomas A.; Yale

    2009-06-30

    Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 {angstrom}. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the Asite cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

  10. Interaction of Extreme Halophilic Archaea With the Evaporites of the Solar Salterns Guerrero Negro Baja California, Mexico

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    Tamez, P.; Lopez-Cortés, A.

    2008-12-01

    morphology. Other strain match, with 99% of similarity, with three sequences Haloarcula: Haloarcula japonica (EF645686), Haloarcula hispanica (DQ089681) and Haloarcula marismortui (X61689), differences among them were only 3 base pairs. We suggest that strain, C205030908, could correspond to Haloarcula californiae previously reported by Javor et al, (1982), from which there is not sequence known. Nested-PCR-DGGE analysis showed a pattern of 11 bands, meaning the archaeal community is more complex than we could detect by culture approach.

  11. Amino acid sequences of the ribosomal proteins HL30 and HmaL5 from the archaebacterium Halobacterium marismortui.

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    Hatakeyama, T; Hatakeyama, T

    1990-07-06

    The complete amino acid sequences of the ribosomal proteins HL30 and HmaL5 from the archaebacterium Halobacterium marismortui were determined. Protein HL30 was found to be acetylated at its N-terminal amino acid and shows homology to the eukaryotic ribosomal proteins YL34 from yeast and RL31 from rat. Protein HmaL5 was homologous to the protein L5 from Escherichia coli and Bacillus stearothermophilus as well as to YL16 from yeast. HmaL5 shows more similarities to its eukaryotic counterpart than to eubacterial ones.

  12. U2504 Determines the Species Specificity of the A-site Cleft Antibiotics. The Structures of Tiamulin, Homoharringtonine and Bruceantin Bound to the Ribosome

    Science.gov (United States)

    Gürel, Güliz; Blaha, Gregor; Moore, Peter B.; Steitz, Thomas A.

    2009-01-01

    Structures have been obtained for the complexes tiamulin, homoharringtonine and bruceatin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.8 to 3.2 Å. They show that these inhibitors all block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl transferase center, which is universally conserved. In addition these structures support the hypothesis that the species-specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (E. coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms. PMID:19362093

  13. New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface

    Science.gov (United States)

    Zorgani, Mohamed Amine; Patron, Kevin; Desvaux, Mickaël

    2014-07-01

    Proteins from halophilic archaea, which live in extreme saline conditions, have evolved to remain folded, active and stable at very high ionic strengths. Understanding the mechanism of haloadaptation is the first step toward engineering of halostable biomolecules. Amylases are one of the main enzymes used in industry. Yet, no three-dimensional structure has been experimentally resolved for α-amylases from halophilic archaea. In this study, homology structure modeling of α-amylases from the halophilic archaea Haloarcula marismortui, Haloarcula hispanica, and Halalkalicoccus jeotgali were performed. The resulting models were subjected to energy minimization, evaluation, and structural analysis. Calculations of the amino acid composition, salt bridges and hydrophobic interactions were also performed and compared to a set of non-halophilic counterparts. It clearly appeared that haloarchaeal α-amylases exhibited lower propensities for helix formation and higher propensities for coil-forming regions. Furthermore, they could maintain a folded and stable conformation in high salt concentration through highly negative charged surface with over representation of acidic residues, especially Asp, and low hydrophobicity with increase of salt bridges and decrease in hydrophobic interactions on the protein surface. This study sheds some light on the stability of α-amylases from halophilic archaea and provides strong basis not only to understand haloadaptation mechanisms of proteins in microorganisms from hypersalines environments but also for biotechnological applications.

  14. Haloarcula hispanica CRISPR authenticates PAM of a target sequence to prime discriminative adaptation.

    Science.gov (United States)

    Li, Ming; Wang, Rui; Xiang, Hua

    2014-06-01

    The prokaryotic immune system CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated genes) adapts to foreign invaders by acquiring their short deoxyribonucleic acid (DNA) fragments as spacers, which guide subsequent interference to foreign nucleic acids based on sequence matching. The adaptation mechanism avoiding acquiring 'self' DNA fragments is poorly understood. In Haloarcula hispanica, we previously showed that CRISPR adaptation requires being primed by a pre-existing spacer partially matching the invader DNA. Here, we further demonstrate that flanking a fully-matched target sequence, a functional PAM (protospacer adjacent motif) is still required to prime adaptation. Interestingly, interference utilizes only four PAM sequences, whereas adaptation-priming tolerates as many as 23 PAM sequences. This relaxed PAM selectivity explains how adaptation-priming maximizes its tolerance of PAM mutations (that escape interference) while avoiding mis-targeting the spacer DNA within CRISPR locus. We propose that the primed adaptation, which hitches and cooperates with the interference pathway, distinguishes target from non-target by CRISPR ribonucleic acid guidance and PAM recognition. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. The primary structures of ribosomal proteins L16, L23 and L33 from the archaebacterium Halobacterium marismortui.

    Science.gov (United States)

    Hatakeyama, T; Hatakeyama, T; Kimura, M

    1988-11-21

    The complete amino acid sequences of ribosomal proteins L16, L23 and L33 from the archaebacterium Halobacterium marismortui were determined. The sequences were established by manual sequencing of peptides produced with several proteases as well as by cleavage with dilute HCl. Proteins L16, L23 and L33 consist of 119, 154 and 69 amino acid residues, and their molecular masses are 13,538, 16,812 and 7620 Da, respectively. The comparison of their sequences with those of ribosomal proteins from other organisms revealed that L23 and L33 are related to eubacterial ribosomal proteins from Escherichia coli and Bacillus stearothermophilus, while protein L16 was found to be homologous to a eukaryotic ribosomal protein from yeast. These results provide information about the special phylogenetic position of archaebacteria.

  16. Bacillus marismortui sp. nov., a new moderately halophilic species from the Dead Sea.

    Science.gov (United States)

    Arahal, D R; Márquez, M C; Volcani, B E; Schleifer, K H; Ventosa, A

    1999-04-01

    A group of 91 moderately halophilic, Gram-positive, rod-shaped strains were isolated from enrichments prepared from Dead Sea water samples collected 57 years ago. These strains were examined for 117 morphological, physiological, biochemical, nutritional and antibiotic susceptibility characteristics. All strains formed endospores and were motile, strictly aerobic and positive for catalase and oxidase. They grew in media containing 5-25% (w/v) total salts, showing optimal growth at 10% (w/v). Eighteen strains were chosen as representative isolates and were studied in more detail. All these strains had mesodiaminopimelic acid in the cell wall and a DNA G + C content of 39.0-42.8 mol%; they constitute a group with levels of DNA-DNA similarity of 70-100%. The sequences of the 16S rRNA genes of three representative strains (strains 123T, 557 and 832) were almost identical (99.9%), and placed the strains in the low G + C content Gram-positive bacteria. On the basis of their features, these isolates should be regarded as members of a new species of the genus Bacillus, for which the name Bacillus marismortui sp. nov. is proposed. The type strain is strain 123T (= DSM 12325T = ATCC 700626T = CIP 105609T = CECT 5066T).

  17. Comparison of four phaC genes from Haloferax mediterranei and their function in different PHBV copolymer biosyntheses in Haloarcula hispanica

    DEFF Research Database (Denmark)

    Han, Jing; Li, Ming; Hou, Jing

    2010-01-01

    , PhaCHme and PhaEHme, has been identified in this strain, and shown to account for the PHBV biosynthesis. RESULTS: With the aid of the genome sequence of Hfx. mediterranei CGMCC 1.2087, three additional phaC genes (designated phaC1, phaC2, and phaC3) were identified, which encoded putative PhaCs. Like......, among the four genes, only phaCHme was transcribed under PHA-accumulating conditions in the wild-type strain. However, heterologous coexpression of phaEHme with each phaC gene in Haloarcula hispanica PHB-1 showed that all PhaCs, except PhaC2, could lead to PHBV accumulation with various 3HV fractions...... meet various application requirements. CONCLUSION: We discover three cryptic phaC genes in Hfx. mediterranei, and demonstrate that genetic engineering of these newly identified phaC genes has biotechnological potential for PHBV production with tailor-made material properties....

  18. Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry.

    Science.gov (United States)

    Kirpekar, F; Douthwaite, S; Roepstorff, P

    2000-02-01

    We present a method to screen RNA for posttranscriptional modifications based on Matrix Assisted Laser Desorption/Ionization mass spectrometry (MALDI-MS). After the RNA is digested to completion with a nucleotide-specific RNase, the fragments are analyzed by mass spectrometry. A comparison of the observed mass data with the data predicted from the gene sequence identifies fragments harboring modified nucleotides. Fragments larger than dinucleotides were valuable for the identification of posttranscriptional modifications. A more refined mapping of RNA modifications can be obtained by using two RNases in parallel combined with further fragmentation by Post Source Decay (PSD). This approach allows fast and sensitive screening of a purified RNA for posttranscriptional modification, and has been applied on 5S rRNA from two thermophilic microorganisms, the bacterium Bacillus stearothermophilus and the archaeon Sulfolobus acidocaldarius, as well as the halophile archaea Halobacterium halobium and Haloarcula marismortui. One S. acidocaldarius posttranscriptional modification was identified and was further characterized by PSD as a methylation of cytidine32. The modified C is located in a region that is clearly conserved with respect to both sequence and position in B. stearothermophilus and H. halobium and to some degree also in H. marismortui. However, no analogous modification was identified in the latter three organisms. We further find that the 5' end of H. halobium 5S rRNA is dephosphorylated, in contrast to the other 5S rRNA species investigated. The method additionally gives an immediate indication of whether the expected RNA sequence is in agreement with the observed fragment masses. Discrepancies with two of the published 5S rRNA sequences were identified and are reported here.

  19. Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs.

    Science.gov (United States)

    Mandal, Debabrata; Köhrer, Caroline; Su, Dan; Babu, I Ramesh; Chan, Clement T Y; Liu, Yuchen; Söll, Dieter; Blum, Paul; Kuwahara, Masayasu; Dedon, Peter C; Rajbhandary, Uttam L

    2014-02-01

    Most archaea and bacteria use a modified C in the anticodon wobble position of isoleucine tRNA to base pair with A but not with G of the mRNA. This allows the tRNA to read the isoleucine codon AUA without also reading the methionine codon AUG. To understand why a modified C, and not U or modified U, is used to base pair with A, we mutated the C34 in the anticodon of Haloarcula marismortui isoleucine tRNA (tRNA2(Ile)) to U, expressed the mutant tRNA in Haloferax volcanii, and purified and analyzed the tRNA. Ribosome binding experiments show that although the wild-type tRNA2(Ile) binds exclusively to the isoleucine codon AUA, the mutant tRNA binds not only to AUA but also to AUU, another isoleucine codon, and to AUG, a methionine codon. The G34 to U mutant in the anticodon of another H. marismortui isoleucine tRNA species showed similar codon binding properties. Binding of the mutant tRNA to AUG could lead to misreading of the AUG codon and insertion of isoleucine in place of methionine. This result would explain why most archaea and bacteria do not normally use U or a modified U in the anticodon wobble position of isoleucine tRNA for reading the codon AUA. Biochemical and mass spectrometric analyses of the mutant tRNAs have led to the discovery of a new modified nucleoside, 5-cyanomethyl U in the anticodon wobble position of the mutant tRNAs. 5-Cyanomethyl U is present in total tRNAs from euryarchaea but not in crenarchaea, eubacteria, or eukaryotes.

  20. Detecting protein-protein interactions in the intact cell of Bacillus subtilis (ATCC 6633).

    Science.gov (United States)

    Winters, Michael S; Day, R A

    2003-07-01

    The salt bridge, paired group-specific reagent cyanogen (ethanedinitrile; C(2)N(2)) converts naturally occurring pairs of functional groups into covalently linked products. Cyanogen readily permeates cell walls and membranes. When the paired groups are shared between associated proteins, isolation of the covalently linked proteins allows their identity to be assigned. Examination of organisms of known genome sequence permits identification of the linked proteins by mass spectrometric techniques applied to peptides derived from them. The cyanogen-linked proteins were isolated by polyacrylamide gel electrophoresis. Digestion of the isolated proteins with proteases of known specificity afforded sets of peptides that could be analyzed by mass spectrometry. These data were compared with those derived theoretically from the Swiss Protein Database by computer-based comparisons (Protein Prospector; http://prospector.ucsf.edu). Identification of associated proteins in the ribosome of Bacillus subtilis strain ATCC 6633 showed that there is an association homology with the association patterns of the ribosomal proteins of Haloarcula marismortui and Thermus thermophilus. In addition, other proteins involved in protein biosynthesis were shown to be associated with ribosomal proteins.

  1. Low-pass sequencing for microbial comparative genomics

    Directory of Open Access Journals (Sweden)

    Kennedy Sean

    2004-01-01

    Full Text Available Abstract Background We studied four extremely halophilic archaea by low-pass shotgun sequencing: (1 the metabolically versatile Haloarcula marismortui; (2 the non-pigmented Natrialba asiatica; (3 the psychrophile Halorubrum lacusprofundi and (4 the Dead Sea isolate Halobaculum gomorrense. Approximately one thousand single pass genomic sequences per genome were obtained. The data were analyzed by comparative genomic analyses using the completed Halobacterium sp. NRC-1 genome as a reference. Low-pass shotgun sequencing is a simple, inexpensive, and rapid approach that can readily be performed on any cultured microbe. Results As expected, the four archaeal halophiles analyzed exhibit both bacterial and eukaryotic characteristics as well as uniquely archaeal traits. All five halophiles exhibit greater than sixty percent GC content and low isoelectric points (pI for their predicted proteins. Multiple insertion sequence (IS elements, often involved in genome rearrangements, were identified in H. lacusprofundi and H. marismortui. The core biological functions that govern cellular and genetic mechanisms of H. sp. NRC-1 appear to be conserved in these four other halophiles. Multiple TATA box binding protein (TBP and transcription factor IIB (TFB homologs were identified from most of the four shotgunned halophiles. The reconstructed molecular tree of all five halophiles shows a large divergence between these species, but with the closest relationship being between H. sp. NRC-1 and H. lacusprofundi. Conclusion Despite the diverse habitats of these species, all five halophiles share (1 high GC content and (2 low protein isoelectric points, which are characteristics associated with environmental exposure to UV radiation and hypersalinity, respectively. Identification of multiple IS elements in the genome of H. lacusprofundi and H. marismortui suggest that genome structure and dynamic genome reorganization might be similar to that previously observed in the

  2. Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui. Comparison of the ribosomal protein S11 family.

    Science.gov (United States)

    Kimura, M; Kimura, J; Hatakeyama, T

    1988-11-21

    The complete amino acid sequences of ribosomal proteins S11 from the Gram-positive eubacterium Bacillus stearothermophilus and of S19 from the archaebacterium Halobacterium marismortui have been determined. A search for homologous sequences of these proteins revealed that they belong to the ribosomal protein S11 family. Homologous proteins have previously been sequenced from Escherichia coli as well as from chloroplast, yeast and mammalian ribosomes. A pairwise comparison of the amino acid sequences showed that Bacillus protein S11 shares 68% identical residues with S11 from Escherichia coli and a slightly lower homology (52%) with the homologous chloroplast protein. The halophilic protein S19 is more related to the eukaryotic (45-49%) than to the eubacterial counterparts (35%).

  3. Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria.

    Science.gov (United States)

    Hansen, M A; Kirpekar, F; Ritterbusch, W; Vester, B

    2002-02-01

    Posttranscriptional modifications were mapped in helices 90-92 of 23S rRNA from the following phylogenetically diverse organisms: Haloarcula marismortui, Sulfolobus acidocaldarius, Bacillus subtilis, and Bacillus stearothermophilus. Helix 92 is a component of the ribosomal A-site, which contacts the aminoacyl-tRNA during protein synthesis, implying that posttranscriptional modifications in helices 90-92 may be important for ribosome function. RNA fragments were isolated from 23S rRNA by site-directed RNase H digestion. A novel method of mapping modifications by analysis of short, nucleotide-specific, RNase digestion fragments with Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) was utilized. The MALDI-MS data were complemented by two primer extension techniques using reverse transcriptase. One technique utilizes decreasing concentrations of deoxynucleotide triphosphates to map 2'-O-ribose methylations. In the other, the rRNA is chemically modified, followed by mild alkaline hydrolysis to map pseudouridines (psis). A total of 10 posttranscriptionally methylated nucleotides and 6 psis were detected in the five organisms. Eight of the methylated nucleotides and one psi have not been reported previously. The distribution of modified nucleotides and their locations on the surface of the ribosomal peptidyl transferase cleft suggests functional importance.

  4. Biopan-survival I: exposure of the osmophiles synechococcus sp. (Nageli) and haloarcula sp. to the space environment

    Science.gov (United States)

    Mancinelli, R. L.; White, M. R.; Rothschild, L. J.

    The objective of this study was to determine the survivability of osmophilic microorganisms in space, as well as examine the DNA breakage in osmophilic cells exposed to solar UV-radiation plus vacuum and to vacuum only. The organisms used were an unidentified species of Synechococcus (Nägeli) that inhabits the evaporitic gypsum-halite crusts that form along the marine intertidal, and an unidentified species of the extremely halophilic genus Haloarcula (designated as isolate G) isolated from a evaporitic NaCl crystal. Because these organisms are desiccation resistant and gypsum-halite as well as NaCl attenuate UV-radiation, we hypothesized that these organisms would survive in the space environment, better than most others. The organisms were exposed to the space environment for 2 weeks while in earth orbit aboard the Biopan facility. Ground controls were tested in a space simulation facility. All samples were compared to unexposed samples. Survivability was determined by plate counts and the most probable number technique. DNA breakage was determined by labeling breaks in the DNA with ^32P followed by translation. Results indicate that the osmophilic microbes survived the 2 week exposure. The major cause of cell death was DNA damage. The number of strand breaks in the DNA from vacuum UV exposed cells was greater than the vacuum only exposed cells.

  5. The N-terminal sequence of ribosomal protein L10 from the archaebacterium Halobacterium marismortui and its relationship to eubacterial protein L6 and other ribosomal proteins.

    Science.gov (United States)

    Dijk, J; van den Broek, R; Nasiulas, G; Beck, A; Reinhardt, R; Wittmann-Liebold, B

    1987-08-01

    The amino-terminal sequence of ribosomal protein L10 from Halobacterium marismortui has been determined up to residue 54, using both a liquid- and a gas-phase sequenator. The two sequences are in good agreement. The protein is clearly homologous to protein HcuL10 from the related strain Halobacterium cutirubrum. Furthermore, a weaker but distinct homology to ribosomal protein L6 from Escherichia coli and Bacillus stearothermophilus can be detected. In addition to 7 identical amino acids in the first 36 residues in all four sequences a number of conservative replacements occurs, of mainly hydrophobic amino acids. In this common region the pattern of conserved amino acids suggests the presence of a beta-alpha fold as it occurs in ribosomal proteins L12 and L30. Furthermore, several potential cases of homology to other ribosomal components of the three ur-kingdoms have been found.

  6. Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

    Science.gov (United States)

    Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav

    2002-12-01

    The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.

  7. Solid-state fermentation as a potential technique for esterase/lipase production by halophilic archaea.

    Science.gov (United States)

    Martin del Campo, Martha; Camacho, Rosa M; Mateos-Díaz, Juan C; Müller-Santos, Marcelo; Córdova, Jesus; Rodríguez, Jorge A

    2015-11-01

    Halophilic archaea are extremophiles, adapted to high-salt environments, showing a big biotechnological potential as enzyme, lipids and pigments producers. Four inert supports (perlite, vermiculite, polyurethane foam and glass fiber) were employed for solid-state fermentation (SSF) of the halophilic archaeon Natronococcus sp. TC6 to investigate biomass and esterase production. A very low esterase activity and high water activity were observed when perlite, vermiculite and polyurethane were used as supports. When glass fiber was employed, an important moisture loss was observed (8.6%). Moreover, moisture retention was improved by mixing polyurethane and glass fiber, resulting in maximal biomass and esterase production. Three halophilic archaea: Natronococcus sp. TC6, Halobacterium sp. NRC-1 and Haloarcula marismortui were cultured by submerged fermentation (SmF) and by SSF; an improvement of 1.3- to 6.2-fold was observed in the biomass and esterase production when SSF was used. Growth was not homogeneous in the mixture, but was predominant in the glass fiber thus was probably because the glass fiber provides a holder to the cells, while the polyurethane acts as an impregnation medium reservoir. To the best of our knowledge, this work is the first report on haloarchaea cultivation by SSF aiming biomass and esterase/lipase activity production.

  8. Halophilic mechanism of the enzymatic function of a moderately halophilic dihydrofolate reductase from Haloarcula japonica strain TR-1.

    Science.gov (United States)

    Miyashita, Yurina; Ohmae, Eiji; Ikura, Teikichi; Nakasone, Kaoru; Katayanagi, Katsuo

    2017-05-01

    Dihydrofolate (DHF) reductase coded by a plasmid of the extremely halophilic archaeon Haloarcula japonica strain TR-1 (HjDHFR P1) shows moderate halophilicity on enzymatic activity at pH 6.0, although there is no significant effect of NaCl on its secondary structure. To elucidate the salt-activation and -inactivation mechanisms of this enzyme, we investigated the effects of pH and salt concentration, deuterium isotope effect, steady-state kinetics, and rapid-phase ligand-binding kinetics. Enzyme activity was increased eightfold by the addition of 500 mM NaCl at pH 6.0, fourfold by 250 mM at pH 8.0, and became independent of salt concentration at pH 10.0. Full isotope effects observed at pH 10.0 under 0-1000 mM NaCl indicated that the rate of hydride transfer, which was the rate-determining step at the basic pH region, was independent of salt concentration. Conversely, rapid-phase ligand-binding experiments showed that the amplitude of the DHF-binding reaction increased and the tetrahydrofolate (THF)-releasing rate decreased with increasing NaCl concentration. These results suggested that the salt-activation mechanism of HjDHFR P1 is via the population change of the anion-unbound and anion-bound conformers, which are binding-incompetent and -competent conformations for DHF, respectively, while that of salt inactivation is via deceleration of the THF-releasing rate, which is the rate-determining step at the neutral pH region.

  9. The primary structures of ribosomal proteins S14 and S16 from the archaebacterium Halobacterium marismortui. Comparison with eubacterial and eukaryotic ribosomal proteins.

    Science.gov (United States)

    Kimura, J; Kimura, M

    1987-09-05

    The amino acid sequences of two ribosomal proteins, S14 and S16, from the archaebacterium Halobacterium marismortui have been determined. Sequence data were obtained by the manual and solid-phase sequencing of peptides derived from enzymatic digestions with trypsin, chymotrypsin, pepsin, and Staphylococcus aureus protease as well as by chemical cleavage with cyanogen bromide. Proteins S14 and S16 contain 109 and 126 amino acid residues and have Mr values of 11,964 and 13,515, respectively. Comparison of the sequences with those of ribosomal proteins from other organisms demonstrates that S14 has a significant homology with the rat liver ribosomal protein S11 (36% identity) as well as with the Escherichia coli ribosomal protein S17 (37%), and that S16 is related to the yeast ribosomal protein YS22 (40%) and proteins S8 from E. coli (28%) and Bacillus stearothermophilus (30%). A comparison of the amino acid residues in the homologous regions of halophilic and nonhalophilic ribosomal proteins reveals that halophilic proteins have more glutamic acids, asparatic acids, prolines, and alanines, and less lysines, arginines, and isoleucines than their nonhalophilic counterparts. These amino acid substitutions probably contribute to the structural stability of halophilic ribosomal proteins.

  10. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

    Energy Technology Data Exchange (ETDEWEB)

    Hamdani, Hazrina Yusof, E-mail: hazrina@mfrlab.org [School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi (Malaysia); Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas (Malaysia); Artymiuk, Peter J., E-mail: p.artymiuk@sheffield.ac.uk [Dept. of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 T2N Sheffield (United Kingdom); Firdaus-Raih, Mohd, E-mail: firdaus@mfrlab.org [School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi (Malaysia)

    2015-09-25

    A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods.

  11. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

    International Nuclear Information System (INIS)

    Hamdani, Hazrina Yusof; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2015-01-01

    A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods

  12. Molecular interactions within the halophilic, thermophilic, and mesophilic prokaryotic ribosomal complexes: clues to environmental adaptation.

    Science.gov (United States)

    Mallik, Saurav; Kundu, Sudip

    2015-01-01

    Using the available crystal structures of 50S ribosomal subunits from three prokaryotic species: Escherichia coli (mesophilic), Thermus thermophilus (thermophilic), and Haloarcula marismortui (halophilic), we have analyzed different structural features of ribosomal RNAs (rRNAs), proteins, and of their interfaces. We have correlated these structural features with the environmental adaptation strategies of the corresponding species. While dense intra-rRNA packing is observed in thermophilic, loose intra-rRNA packing is observed in halophilic (both compared to mesophilic). Interestingly, protein-rRNA interfaces of both the extremophiles are densely packed compared to that of the mesophilic. The intersubunit bridge regions are almost devoid of cavities, probably ensuring the proper formation of each bridge (by not allowing any loosely packed region nearby). During rRNA binding, the ribosomal proteins experience some structural transitions. Here, we have analyzed the intrinsically disordered and ordered regions of the ribosomal proteins, which are subjected to such transitions. The intrinsically disordered and disorder-to-order transition sites of the thermophilic and mesophilic ribosomal proteins are simultaneously (i) highly conserved and (ii) slowly evolving compared to rest of the protein structure. Although high conservation is observed at such sites of halophilic ribosomal proteins, but slow rate of evolution is absent. Such differences between thermophilic, mesophilic, and halophilic can be explained from their environmental adaptation strategy. Interestingly, a universal biophysical principle evident by a linear relationship between the free energy of interface formation, interface area, and structural changes of r-proteins during assembly is always maintained, irrespective of the environmental conditions.

  13. Secondary structures of rRNAs from all three domains of life.

    Directory of Open Access Journals (Sweden)

    Anton S Petrov

    Full Text Available Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2° structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU 23S/28S and small subunit (SSU 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only, Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery. Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision.

  14. Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.

    Science.gov (United States)

    Nakashima, T; Yao, M; Kawamura, S; Iwasaki, K; Kimura, M; Tanaka, I

    2001-05-01

    Ribosomal protein L5 is a 5S rRNA binding protein in the large subunit and plays an essential role in the promotion of a particular conformation of 5S rRNA. The crystal structure of the ribosomal protein L5 from Bacillus stearothermophilus has been determined at 1.8 A resolution. The molecule consists of a five-stranded antiparallel beta-sheet and four alpha-helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. The molecular shape and electrostatic representation suggest that the concave surface and loop regions are involved in 5S rRNA binding. To identify amino acid residues responsible for 5S rRNA binding, we made use of Ala-scanning mutagenesis of evolutionarily conserved amino acids occurring in the beta-strands and loop regions. The mutations of Asn37 at the beta1-strand and Gln63 at the loop between helix 2 and beta3-strand as well as that of Phe77 at the tip of the loop structure between the beta2- and beta3-strands caused a significant reduction in 5S rRNA binding. In addition, the mutations of Thr90 on the beta3-strand and Ile141 and Asp144 at the loop between beta4- and beta5-strands moderately reduced the 5S rRNA-binding affinity. Comparison of these results with the more recently analyzed structure of the 50S subunit from Haloarcula marismortui suggests that there are significant differences in the structure at N- and C-terminal regions and probably in the 5S rRNA binding.

  15. Link between capacity for current production and syntrophic growth in Geobacter species

    DEFF Research Database (Denmark)

    Rotaru, Amelia-Elena; Woodard, Trevor; Nevin, Kelly

    2015-01-01

    -culture with Methanosarcina barkeri, which is capable of direct interspecies electron transfer (DIET), but not with Methanospirillium hungatei capable only of H2 or formate transfer. Conductive granular activated carbon (GAC) stimulated metabolism of the G. hydrogenophilus - M. barkeri co-culture, consistent with electron...

  16. ORF Alignment: NC_006396 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available cula ... marismortui ATCC 43049] ... Length = 135 ... Query: 1 ... MTDTPLKFGFVCVQNAGRSQMSAAFAERERTR...RGLEDAVEILTGGTDPADEVHPEVVEAM 60 ... MTDTPLKFGFVCVQNAGRSQMSAAFAERERTRRGLEDA...VEILTGGTDPADEVHPEVVEAM Sbjct: 1 ... MTDTPLKFGFVCVQNAGRSQMSAAFAERERTRRGLEDAVEILTGGTDPADEVHPEVVEAM 60 ... Query: 12

  17. Solution Behavior and Activity of a Halophilic Esterase under High Salt Concentration

    Science.gov (United States)

    Rao, Lang; Zhao, Xiubo; Pan, Fang; Li, Yin; Xue, Yanfen; Ma, Yanhe; Lu, Jian R.

    2009-01-01

    Background Halophiles are extremophiles that thrive in environments with very high concentrations of salt. Although the salt reliance and physiology of these extremophiles have been widely investigated, the molecular working mechanisms of their enzymes under salty conditions have been little explored. Methodology/Principal Findings A halophilic esterolytic enzyme LipC derived from archeaon Haloarcula marismortui was overexpressed from Escherichia coli BL21. The purified enzyme showed a range of hydrolytic activity towards the substrates of p-nitrophenyl esters with different alkyl chains (n = 2−16), with the highest activity being observed for p-nitrophenyl acetate, consistent with the basic character of an esterase. The optimal esterase activities were found to be at pH 9.5 and [NaCl] = 3.4 M or [KCl] = 3.0 M and at around 45°C. Interestingly, the hydrolysis activity showed a clear reversibility against changes in salt concentration. At the ambient temperature of 22°C, enzyme systems working under the optimal salt concentrations were very stable against time. Increase in temperature increased the activity but reduced its stability. Circular dichroism (CD), dynamic light scattering (DLS) and small angle neutron scattering (SANS) were deployed to determine the physical states of LipC in solution. As the salt concentration increased, DLS revealed substantial increase in aggregate sizes, but CD measurements revealed the maximal retention of the α-helical structure at the salt concentration matching the optimal activity. These observations were supported by SANS analysis that revealed the highest proportion of unimers and dimers around the optimal salt concentration, although the coexistent larger aggregates showed a trend of increasing size with salt concentration, consistent with the DLS data. Conclusions/Significance The solution α-helical structure and activity relation also matched the highest proportion of enzyme unimers and dimers. Given that

  18. Presence of sulfate does not inhibit low-temperature dolomite precipitation

    NARCIS (Netherlands)

    Sánchez-Román, Mónica; McKenzie, Judith A.; de Luca Rebello Wagener, Angela; Rivadeneyra, Maria A.; Vasconcelos, Crisógono

    2009-01-01

    The hypothesis that sulfate inhibits dolomite formation evolved from geochemical studies of porewaters from deep-sea sedimentary sequences and has been tested with hydrothermal experiments. We examined the sulfate inhibition factor using aerobic culture experiments with Virgibacillus marismortui and

  19. Evaluation of cell lysis procedures and use of a micro fluidic system for an automated DNA-based cell identification in interplanetary missions

    Science.gov (United States)

    Hall, J. A.; Felnagle, E.; Fries, M.; Spearing, S.; Monaco, L.; Steele, A.

    2006-12-01

    A Modular Assay System for Solar System Exploration (MASSE) is being developed to include sample handling, pre-treatment, separation and analysis of biological target compounds by both DNA and protein microarrays. To better design sensitive and accurate initial upstream sample handling of the MASSE instrument, experiments investigating the sensitivity and potential extraction bias of commercially available DNA extraction kits between classes of environmentally relevant prokaryotes such as gram-negative bacteria ( Escherichia coli), gram-positive bacteria ( Bacillus megatarium), and Archaea ( Haloarcula marismortui) were performed. For extractions of both planktonic cultures and spiked Mars simulated regolith, FTA ® paper demonstrated the highest sensitivity, with detection as low as ˜1×10 1 cells and ˜3.3×10 2 cells, respectively. In addition to the highest sensitivity, custom modified application of FTA ® paper extraction protocol is the simplest in terms of incorporation into MASSE and displayed little bias in sensitivity with respect to prokaryotic cell type. The implementation of FTA paper for environmental microbiology investigations appears to be a viable and effective option potentially negating the need for other pre-concentration steps such as filtration and negating concerns regarding extraction efficiency of cells. In addition to investigations on useful technology for upstream sample handling in MASSE, we have also evaluated the potential for μTAS to be employed in the MASSE instrument by employing proprietary lab-on-a-chip development technology to investigate the potential for microfluidic cell lysis of different prokaryotic cells employing both chemical and biological lysis agents. Real-time bright-field microscopy and quantitative PMT detection indicated that that gram positive, gram negative and archaeal cells were effectively lyzed in a few seconds using the microfluidic chip protocol developed. This included employing a lysis buffer with

  20. The CCA-end of P-tRNA Contacts Both the Human RPL36AL and the A-site Bound Translation Termination Factor eRF1 at the Peptidyl Transferase Center of the Human 80S Ribosome.

    Science.gov (United States)

    Hountondji, Codjo; Bulygin, Konstantin; Créchet, Jean-Bernard; Woisard, Anne; Tuffery, Pierre; Nakayama, Jun-Ichi; Frolova, Ludmila; Nierhaus, Knud H; Karpova, Galina; Baouz, Soria

    2014-01-01

    We have demonstrated previously that the E-site specific protein RPL36AL present in human ribosomes can be crosslinked with the CCA-end of a P-tRNA in situ. Here we report the following: (i) We modeled RPL36AL into the structure of the archaeal ortholog RPL44E extracted from the known X-ray structure of the 50S subunit of Haloarcula marismortui. Superimposing the obtained RPL36AL structure with that of P/E tRNA observed in eukaryotic 80S ribosomes suggested that RPL36AL might in addition to its CCA neighbourhood interact with the inner site of the tRNA elbow similar to an interaction pattern known from tRNA•synthetase pairs. (ii) Accordingly, we detected that the isolated recombinant protein RPL36AL can form a tight binary complex with deacylated tRNA, and even tRNA fragments truncated at their CCA end showed a high affinity in the nanomolar range supporting a strong interaction outside the CCA end. (iii) We constructed programmed 80S complexes containing the termination factor eRF1 (stop codon UAA at the A-site) and a 2',3'-dialdehyde tRNA (tRNAox) analog at the P-site. Surprisingly, we observed a crosslinked ternary complex containing the tRNA, eRF1 and RPL36AL crosslinked both to the aldehyde groups of tRNAox at the 2'- and 3'-positions of the ultimate A. We also demonstrated that, upon binding to the ribosomal A-site, eRF1 induces an alternative conformation of the ribosome and/or the tRNA, leading to a novel crosslink of tRNAox to another large-subunit ribosomal protein (namely L37) rather than to RPL36AL, both ribosomal proteins being labeled in a mutually exclusive fashion. Since the human 80S ribosome in complex with P-site bound tRNAox and A-site bound eRF1 corresponds to the post-termination state of the ribosome, the results represent the first biochemical evidence for the positioning of the CCA-arm of the P-tRNA in close proximity to both RPL36AL and eRF1 at the end of the translation process.

  1. Isolation and Partial Characterization of Bacteria in an Anaerobic Consortium That Mineralizes 3-Chlorobenzoic Acid †

    OpenAIRE

    Shelton, Daniel R.; Tiedje, James M.

    1984-01-01

    A methanogenic consortium able to use 3-chlorobenzoic acid as its sole energy and carbon source was enriched from anaerobic sewage sludge. Seven bacteria were isolated from the consortium in mono- or coculture. They included: one dechlorinating bacterium (strain DCB-1), one benzoate-oxidizing bacterium (strain BZ-2), two butyrate-oxidizing bacteria (strains SF-1 and NSF-2), two H2-consuming methanogens (Methanospirillum hungatei PM-1 and Methanobacterium sp. strain PM-2), and a sulfate-reduci...

  2. Proteomic analysis reveals metabolic and regulatory systems involved the syntrophic and axenic lifestyle of Syntrophomonas wolfei.

    Directory of Open Access Journals (Sweden)

    Jessica Rhea Sieber

    2015-02-01

    Full Text Available Microbial syntrophy is a vital metabolic interaction necessary for the complete oxidation of organic biomass to methane in all-anaerobic ecosystems. However, this process is thermodynamically constrained and represents an ecosystem-level metabolic bottleneck. To gain insight into the physiology of this process, a shotgun proteomic approach was used to quantify the protein landscape of the model syntrophic metabolizer, Syntrophomonas wolfei, grown axenically and syntrophically with Methanospirillum hungatei. Remarkably, the abundance of most proteins as represented by normalized spectral abundance factor (NSAF value changed very little between the pure and coculture growth conditions. Among the most abundant proteins detected were GroEL and GroES chaperonins, a small heat shock protein, and proteins involved in electron transfer, beta-oxidation, and ATP synthesis. Several putative energy conservation enzyme systems that utilize NADH and ferredoxin were present. The abundance of an EtfAB2 and the membrane-bound iron-sulfur oxidoreductase (Swol_0698 gene product delineated a potential conduit for electron transfer between acyl-CoA dehydrogenases and membrane redox carriers. Proteins detected only when S. wolfei was grown with M. hungatei included a zinc-dependent dehydrogenase with a GroES domain, whose gene is present in genomes in many organisms capable of syntrophy, and transcriptional regulators responsive to environmental stimuli or the physiological status of the cell. The proteomic analysis revealed an emphasis macromolecular stability and energy metabolism to S. wolfei and presence of regulatory mechanisms responsive to external stimuli and cellular physiological status.

  3. Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Iain; Ulrich, Luke E.; Lupa, Boguslaw; Susanti, Dwi; Porat, Iris; Hooper, Sean D.; Lykidis, Athanasios; Sieprawska-Lupa, Magdalena; Dharmarajan, Lakshmi; Goltsman, Eugene; Lapidus, Alla; Saunders, Elizabeth; Han, Cliff; Land, Miriam; Lucas, Susan; Mukhopadhyay, Biswarup; Whitman, William B.; Woese, Carl; Bristow, James; Kyrpides, Nikos

    2009-05-01

    Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens. In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales. Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).

  4. Isolation, characterization and phylogenetic analysis of halophilic archaea from a salt mine in central Anatolia (Turkey).

    Science.gov (United States)

    Yildiz, Evrim; Ozcan, Birgul; Caliskan, Mahmut

    2012-01-01

    The haloarchaeal diversity of a salt mine, a natural cave in central Anatolia, was investigated using convential microbiological and molecular biology methods. Eight halophilic archaeal isolates selected based on their colony morphology and whole cell protein profiles were taxonomically classified on the basis of their morphological, physiological, biochemical properties, polar lipid and protein profiles and 16S rDNA sequences. From the 16S rDNA sequences comparisons it was established that the isolates CH2, CH3 and CHC resembled Halorubrum saccharovorum by 98.8%, 98.9% and 99.5%, respectively. There was a 99.7% similarity between the isolate CH11 and Halobacterium noricense and 99.2% between the isolate CHA1 and Haloarcula argentinensis. The isolate CH8K and CH8B revealed a similarity rate of 99.8% and 99.3% to Halococcus dombrowskii, respectively. It was concluded that the isolates named CH2, CH3 and CHC were clustered in the genus Halorubrum and that CHA1 and CH7 in the genus Haloarcula, CH8K and CH8B in the genus Halococcus and CH11 in the genus Halobacterium.

  5. Dicty_cDB: Contig-U16604-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available (EC 2.4.... 152 3e-35 Y18523_23( Y18523 |pid:none) Actinoplanes sp. SE50/110 comp...Y18523 |pid:none) Actinoplanes sp. SE50/110 complete ac... 87 2e-15 BA000045_1595( BA000045 |pid:none) Gloeo...1( AJ890146 |pid:none) Haloarcula hispanica amyH gene for... 87 2e-15 Y18523_22(

  6. HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae

    Directory of Open Access Journals (Sweden)

    Tatiana A. Demina

    2017-02-01

    Full Text Available Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha- and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus. Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera. Conserved virion architectural principles observed in sphaerolipoviruses suggest that these viruses belong to the PRD1-adenovirus structural lineage. Here we focus on archaeal alphasphaerolipoviruses and their related putative proviruses. The highest sequence similarities among alphasphaerolipoviruses are observed in the core structural elements of their virions: the two major capsid proteins, the major membrane protein, and a putative packaging ATPase. A recently described tailless icosahedral haloarchaeal virus, Haloarcula californiae icosahedral virus 1 (HCIV-1, has a double-stranded DNA genome and an internal membrane lining the capsid. HCIV-1 shares significant similarities with the other tailless icosahedral internal membrane-containing haloarchaeal viruses of the family Sphaerolipoviridae. The proposal to include a new virus species, Haloarcula virus HCIV1, into the genus Alphasphaerolipovirus was submitted to the International Committee on Taxonomy of Viruses (ICTV in 2016.

  7. Taxonomic analysis of extremely halophilic archaea isolated from 56-years-old dead sea brine samples.

    Science.gov (United States)

    Arahal, D R; Gutiérrez, M C; Volcani, B E; Ventosa, A

    2000-10-01

    A taxonomic study comprising both phenotypic and genotypic characterization, has been carried out on a total of 158 extremely halophilic aerobic archaeal strains. These strains were isolated from enrichments prepared from Dead Sea water samples dating from 1936 that were collected by B. E. Volcani for the demonstration of microbial life in the Dead Sea. The isolates were examined for 126 morphological, physiological, biochemical and nutritional tests. Numerical analysis of the data, by using the S(J) coefficient and UPGMA clustering method, showed that the isolates clustered into six phenons. Twenty-two out of the 158 strains used in this study were characterized previously (ARAHAL et al., 1996) and were placed into five phenotypic groups. The genotypic study included both the determination of the guanineplus-cytosine content of the DNA and DNA-DNA hybridization studies. For this purpose, representative strains from the six phenons were chosen. These groups were found to represent some members of three different genera - Haloarcula (phenons A, B, and C), Haloferax (phenons D and E) and Halobacterium (phenon F) - of the family Halobacteriaceae, some of them never reported to occur in the Dead Sea, such as Haloarcula hispanica, while Haloferax volcanii (phenons D and E) was described in the Dead Sea by studies carried out several decades later than Volcani's work.

  8. Anaerobic hydrocarbon and fatty acid metabolism by syntrophic bacteria and their impact on carbon steel corrosion

    Directory of Open Access Journals (Sweden)

    Christopher Neil Lyles

    2014-04-01

    Full Text Available The microbial metabolism of hydrocarbons is increasingly associated with the corrosion of carbon steel in sulfate-rich marine waters. However, how such transformations influence metal biocorrosion in the absence of an electron acceptor is not fully recognized. We grew a marine alkane-utilizing, sulfate-reducing bacterium, Desulfoglaeba alkanexedens, with either sulfate or Methanospirillum hungatei as electron acceptors, and tested the ability of the cultures to catalyze metal corrosion. Axenically, D. alkanexedens had a higher instantaneous corrosion rate and produced more pits in carbon steel coupons than when the same organism was grown in syntrophic co-culture with the methanogen. Since anaerobic hydrocarbon biodegradation pathways converge on fatty acid intermediates, the corrosive ability of a known fatty acid-oxidizing syntrophic bacterium, Syntrophus aciditrophicus was compared when grown in pure culture or in co-culture with a H2-utilizing sulfate-reducing bacterium (Desulfovibrio sp., strain G11 or a methanogen (M. hungatei. The instantaneous corrosion rates in the cultures were not substantially different, but the syntrophic, sulfate-reducing co-culture produced more pits in coupons than other combinations of microorganisms. Lactate-grown cultures of strain G11 had higher instantaneous corrosion rates and coupon pitting compared to the same organism cultured with hydrogen as an electron donor. Thus, if sulfate is available as an electron acceptor, the same microbial assemblages produce sulfide and low molecular weight organic acids that exacerbated biocorrosion. Despite these trends, a surprisingly high degree of variation was encountered with the corrosion assessments. Differences in biomass, initial substrate concentration, rates of microbial activity or the degree of end product formation did not account for the variations. We are forced to ascribe such differences to the metallurgical properties of the coupons.

  9. Anaerobic hydrocarbon and fatty acid metabolism by syntrophic bacteria and their impact on carbon steel corrosion.

    Science.gov (United States)

    Lyles, Christopher N; Le, Huynh M; Beasley, William Howard; McInerney, Michael J; Suflita, Joseph M

    2014-01-01

    The microbial metabolism of hydrocarbons is increasingly associated with the corrosion of carbon steel in sulfate-rich marine waters. However, how such transformations influence metal biocorrosion in the absence of an electron acceptor is not fully recognized. We grew a marine alkane-utilizing, sulfate-reducing bacterium, Desulfoglaeba alkanexedens, with either sulfate or Methanospirillum hungatei as electron acceptors, and tested the ability of the cultures to catalyze metal corrosion. Axenically, D. alkanexedens had a higher instantaneous corrosion rate and produced more pits in carbon steel coupons than when the same organism was grown in syntrophic co-culture with the methanogen. Since anaerobic hydrocarbon biodegradation pathways converge on fatty acid intermediates, the corrosive ability of a known fatty acid-oxidizing syntrophic bacterium, Syntrophus aciditrophicus was compared when grown in pure culture or in co-culture with a H2-utilizing sulfate-reducing bacterium (Desulfovibrio sp., strain G11) or a methanogen (M. hungatei). The instantaneous corrosion rates in the cultures were not substantially different, but the syntrophic, sulfate-reducing co-culture produced more pits in coupons than other combinations of microorganisms. Lactate-grown cultures of strain G11 had higher instantaneous corrosion rates and coupon pitting compared to the same organism cultured with hydrogen as an electron donor. Thus, if sulfate is available as an electron acceptor, the same microbial assemblages produce sulfide and low molecular weight organic acids that exacerbated biocorrosion. Despite these trends, a surprisingly high degree of variation was encountered with the corrosion assessments. Differences in biomass, initial substrate concentration, rates of microbial activity or the degree of end product formation did not account for the variations. We are forced to ascribe such differences to the metallurgical properties of the coupons.

  10. Membrane complexes of Syntrophomonas wolfei involved in syntrophic butyrate degradation and hydrogen formation

    Directory of Open Access Journals (Sweden)

    Bryan Regis Crable

    2016-11-01

    Full Text Available Syntrophic butyrate metabolism involves the thermodynamically unfavorable production of hydrogen and/or formate from the high potential electron donor, butyryl-CoA. Such redox reactions can occur only with energy input by a process called reverse electron transfer. Previous studies have demonstrated that hydrogen production from butyrate requires the presence of a proton gradient, but the biochemical machinery involved has not been clearly elucidated. In this study, the gene and enzyme systems involved in reverse electron transfer by Syntrophomonas wolfei were investigated using proteomic and gene expression approaches. S. wolfei was grown in coculture with Methanospirillum hungatei or Dehalococcoides mccartyi under conditions requiring reverse electron transfer and compared to both axenic S. wolfei cultures and cocultures grown in conditions that do not require reverse electron transfer. Blue native gel analysis of membranes solubilized from syntrophically grown cells revealed the presence of a membrane-bound hydrogenase, Hyd2, which exhibited hydrogenase activity during in gel assays. Bands containing a putative iron-sulfur (FeS oxidoreductase were detected in membranes of crotonate-grown and butyrate grown S. wolfei cells. The genes for the corresponding hydrogenase subunits, hyd2ABC, were differentially expressed at higher levels during syntrophic butyrate growth when compared to growth on crotonate. The expression of the FeS oxidoreductase gene increased when S. wolfei was grown with M. hungatei. Additional membrane-associated proteins detected included FoF1 ATP synthase subunits and several membrane transporters that may aid syntrophic growth. Furthermore, syntrophic butyrate metabolism can proceed exclusively by interspecies hydrogen transfer, as demonstrated by growth with D. mccartyi, which is unable to use formate. These results argue for the importance of Hyd2 and FeS oxidoreductase in reverse electron transfer during syntrophic

  11. [Diversity and enzyme-producing activity of culturable halophilic bacteria in Daishan Saltern of East China].

    Science.gov (United States)

    Yang, Dan-Dan; Li, Qian; Huang, Jing-Jing; Chen, Min

    2012-11-01

    Soil and saline water samples were collected from the Daishan Saltern of East China, and the halophilic bacteria were isolated and cultured by using selective media, aimed to investigate the diversity and enzyme-producing activity of culturable halophilic bacteria in saltern environment. A total of 181 strains were isolated by culture-dependent method. Specific primers were used to amplify the 16S rRNA gene of bacteria and archaea. The operation taxonomy units (OTUs) were determined by ARDRA method, and the representative strain of each OTU was sequenced. The phylogenetic position of all the isolated strains was determined by 16S rRNA sequencing. The results showed that the isolated 181 strains displayed 21 operational taxonomic units (OTUs), of which, 12 OTUs belonged to halophilic bacteria, and the others belonged to halophilic archaea. Phylogenetic analysis indicated that there were 7 genera presented among the halophilic bacteria group, and 4 genera presented among the halophilic archaea group. The dominant halophilic strains were of Halomonas and Haloarcula, with 46.8% in halophilic bacteria and 49.1% in halophilic archaea group, respectively. Enzyme-producing analysis indicated that most strains displayed enzyme-producing activity, including the activities of producing amylase, proteinase and lipase, and the dominant strains capable of enzyme-producing were of Haloarcula. Our results showed that in the environment of Daishan Saltern, there existed a higher diversity of halophilic bacteria, being a source sink for screening enzyme-producing bacterial strains.

  12. Resistance of extremely halophilic archaea to zinc and zinc oxide nanoparticles

    Science.gov (United States)

    Salgaonkar, Bhakti B.; Das, Deepthi; Bragança, Judith Maria

    2016-02-01

    Industrialization as well as other anthropogenic activities have resulted in addition of high loads of metal and/or metal nanoparticles to the environment. In this study, the effect of one of the widely used heavy metal, zinc (Zn) and zinc oxide nanoparticles (ZnO NPs) on extremely halophilic archaea was evaluated. One representative member from four genera namely Halococcus, Haloferax, Halorubrum and Haloarcula of the family Halobacteriaceae was taken as the model organism. All the haloarchaeal genera investigated were resistant to both ZnCl2 and ZnO NPs at varying concentrations. Halococcus strain BK6 and Haloferax strain BBK2 showed the highest resistance in complex/minimal medium of up to 2.0/1.0 mM ZnCl2 and 2.0/1.0-0.5 mM ZnO NP. Accumulation of ZnCl2/ZnO NPs was seen as Haloferax strain BBK2 (287.2/549.6 mg g-1) > Halococcus strain BK6 (165.9/388.5 mg g-1) > Haloarcula strain BS2 (93.2/28.5 mg g-1) > Halorubrum strain BS17 (29.9/16.2 mg g-1). Scanning electron microscopy and energy dispersive X-ray spectroscopy (SEM-EDX) analysis revealed that bulk ZnCl2 was sorbed at a higher concentration (21.77 %) on the cell surface of Haloferax strain BBK2 as compared to the ZnO NPs (14.89 %).

  13. Butyrivibrio hungatei sp. nov. and pseudobutyrivibrio xylanivorans sp. nov., butyrate-producing bacteria from the rumen

    Czech Academy of Sciences Publication Activity Database

    Kopečný, Jan; Zorec, M.; Mrázek, Jakub; Kobayashi, Y.; Marinšek Logar, R.

    2003-01-01

    Roč. 53, č. 1 (2003), s. 201-209 ISSN 1466-5026 R&D Projects: GA ČR GA524/99/0602 Institutional research plan: CEZ:AV0Z5045916 Keywords : bacteria Subject RIV: ED - Physiology Impact factor: 3.187, year: 2003

  14. Curiously modern DNA for a "250 million-year-old" bacterium.

    Science.gov (United States)

    Nickle, David C; Learn, Gerald H; Rain, Matthew W; Mullins, James I; Mittler, John E

    2002-01-01

    Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the approximately 59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies.

  15. Population dynamics of biofilm development during start-up of a butyrate-degrading fluidized-bed reactor

    Energy Technology Data Exchange (ETDEWEB)

    Zellner, G.; Geveke, M.; Diekmann, H. (Hannover Univ. (Germany). Inst. fuer Mikrobiologie); Conway de Macario, E. (New York State Dept. of Health, Albany, NY (United States). Wadsworth Center for Laboratories and Research)

    1991-12-01

    Population dynamics during start-up of a fluidized-bed reactor with butyrate or butyrate plus acetate as sole substrates as well as biofilm development on the sand substratum were studied microbiologically, immunologically and by scanning electron microscopy. An adapted syntrophic consortium consisting of Syntrophospora sp., Methanothrix soehngenii, Methanosarcina mazei and Methanobrevibacter arboriphilus or Methanogenium sp. achieved high-rate butyrate degradation to methane and carbon dioxide. Desulfovibrio sp., Methanocorpusculum sp., and Methanobacterium sp. were also present in lower numbers. Immunological analysis demonstrated methanogens antigenically related to Methanobrevibacter ruminantium M1, Methanosarcina mazei S6, M. thermophila TM1, Methanobrevibacter arboriphilus AZ and Methanothrix soehngenii Opfikon in the biofilm. Immunological analysis also showed that the organisms isolated from the butyrate-degrading culture used as a source of inoculum were related to M. soehngenii Opfikon, Methanobacterium formicium MF and Methanospirillum hungatei JF1. (orig.).

  16. Three-dimensional crystals of ribosomes and their subunits from eu- and archaebacteria.

    Science.gov (United States)

    Glotz, C; Müssig, J; Gewitz, H S; Makowski, I; Arad, T; Yonath, A; Wittmann, H G

    1987-11-01

    Ordered three-dimensional crystals of 70S ribosomes as well as of 30S and 50S ribosomal subunits from various bacteria (E. coli, Bacillus stearothermophilus, Thermus thermophilus and Halobacterium marismortui) have been grown by vapour diffusion in hanging drops using mono- and polyalcohols. A new compact crystal form of 50S subunits has been obtained, and it is suitable for crystallographic studies at medium resolution. In addition, from one crystal form large crystals could be grown in X-ray capillaries. In all cases the crystals were obtained from functionally active ribosomal particles, and the particles from dissolved crystals retained their integrity and biological activity.

  17. Using Thermal Inactivation Kinetics to Calculate the Probability of Extreme Spore Longevity: Implications for Paleomicrobiology and Lithopanspermia

    Science.gov (United States)

    Nicholson, Wayne L.

    2003-12-01

    Thermal inactivation kinetics with extrapolation were used to model the survival probabilities of spores of various Bacillus species over time periods of millions of years at the historical ambient temperatures (25-40 °) encountered within the 250 million-year-old Salado formation, from which the putative ancient spore-forming bacterium Salibacillus marismortui strain 2-9-3 was recovered. The model indicated extremely low-to-moderate survival probabilities for spores of mesophiles, but surprisingly high survival probabilities for thermophilic spores. The significance of the results are discussed in terms of the survival probabilities of (i) terrestrial spores in ancient geologic samples and (ii) spores transported between planets within impact ejecta.

  18. Antimicrobial Activity and Mechanism of inhibition of Silver Nanoparticles against Extreme Halophilic Archaea

    Directory of Open Access Journals (Sweden)

    Rebecca Thombre

    2016-09-01

    Full Text Available Haloarchaea are salt-loving halophilic microorganism’s that inhabit marine environments, sea water, salterns, and lakes. The resistance of haloarchaea to physical extremities that challenge organismic survival is ubiquitous. Metal and antibiotic resistance of haloarchaea has been on an upsurge due to the exposure of these organisms to metal sinks and drug resistance genes augmented in their natural habitats due to anthropogenic activities and environmental pollution. The efficacy of silver nanoparticles (SNPs as a potent and broad spectrum inhibitory agent is known however, there are no reports on the inhibitory activity of SNPs against haloarchaea. In the present study, we have investigated the antimicrobial potentials of SNPs synthesized using aqueous leaf extract of Cinnamomum tamala against antibiotic resistant haloarchaeal isolates Haloferax prahovense RR8, Haloferax lucentense RR15, Haloarcula argentinensis RR10 and Haloarcula tradensis RR13. The synthesized SNPs were characterized by UV-Vis spectroscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy, dynamic light scattering, X-ray diffraction and Fourier transform infrared spectroscopy. The SNPs demonstrated potent antimicrobial activity against the haloarchaea with a minimum inhibitory concentration of 300- 400µg/ml. Growth kinetics of haloarchaea in the presence of SNPs was studied by employing the Baranyi mathematical model for microbial growth using the DMFit curve fitting programme. The C. tamala SNPs also demonstrated cytotoxic activity against human lung adenocarcinoma epithelial cell line (A540 and human breast adenocarcinoma cell line (MCF-7. The mechanism of inhibition of haloarchaea by the SNPs was investigated. The plausible mechanism proposed is the alterations and disruption of haloarchaeal membrane permeability by turbulence, inhibition of respiratory dehydrogenases and lipid peroxidation causing cellular and DNA damage resulting in cell death.

  19. Noninvasive optical inhibition with a red-shifted microbial rhodopsin

    DEFF Research Database (Denmark)

    Chuong, Amy S; Miri, Mitra L; Busskamp, Volker

    2014-01-01

    Optogenetic inhibition of the electrical activity of neurons enables the causal assessment of their contributions to brain functions. Red light penetrates deeper into tissue than other visible wavelengths. We present a red-shifted cruxhalorhodopsin, Jaws, derived from Haloarcula (Halobacterium......) salinarum (strain Shark) and engineered to result in red light-induced photocurrents three times those of earlier silencers. Jaws exhibits robust inhibition of sensory-evoked neural activity in the cortex and results in strong light responses when used in retinas of retinitis pigmentosa model mice. We also...... demonstrate that Jaws can noninvasively mediate transcranial optical inhibition of neurons deep in the brains of awake mice. The noninvasive optogenetic inhibition opened up by Jaws enables a variety of important neuroscience experiments and offers a powerful general-use chloride pump for basic and applied...

  20. Bacterioruberin and salinixanthin carotenoids of extremely halophilic Archaea and Bacteria: A Raman spectroscopic study

    Science.gov (United States)

    Jehlička, J.; Edwards, H. G. M.; Oren, A.

    2013-04-01

    Laboratory cultures of a number of red extremely halophilic Archaea (Halobacterium salinarum strains NRC-1 and R1, Halorubrum sodomense, Haloarcula valismortis) and of Salinibacter ruber, a red extremely halophilic member of the Bacteria, have been investigated by Raman spectroscopy using 514.5 nm excitation to characterize their carotenoids. The 50-carbon carotenoid α-bacterioruberin was detected as the major carotenoid in all archaeal strains. Raman spectroscopy also detected bacterioruberin as the main pigment in a red pellet of cells collected from a saltern crystallizer pond. Salinibacter contains the C40-carotenoid acyl glycoside salinixanthin (all-E, 2'S)-2'-hydroxy-1'-[6-O-(methyltetradecanoyl)-β-D-glycopyranosyloxy]-3',4'-didehydro-1',2'-dihydro-β,ψ-carotene-4-one), for which the Raman bands assignments of are given here for the first time.

  1. Expression of gentisate 1,2-dioxygenase (gdoA) genes involved in aromatic degradation in two haloarchaeal genera.

    Science.gov (United States)

    Fairley, D J; Wang, G; Rensing, C; Pepper, I L; Larkin, M J

    2006-12-01

    Gentisate-1,2-dioxygenase genes (gdoA), with homology to a number of bacterial dioxygenases, and genes encoding a putative coenzyme A (CoA)-synthetase subunit (acdB) and a CoA-thioesterase (tieA) were identified in two haloarchaeal isolates. In Haloarcula sp. D1, gdoA was expressed during growth on 4-hydroxybenzoate but not benzoate, and acdB and tieA were not expressed during growth on any of the aromatic substrates tested. In contrast, gdoA was expressed in Haloferax sp. D1227 during growth on benzoate, 3-hydroxybenzoate, cinnamate and phenylpropionate, and both acdB and tieA were expressed during growth on benzoate, cinnamate and phenylpropionate, but not on 3-hydroxybenzoate. This pattern of induction is consistent with these genes encoding steps in a CoA-mediated benzoate pathway in this strain.

  2. Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry

    DEFF Research Database (Denmark)

    Kirpekar, F; Douthwaite, S; Roepstorff, P

    2000-01-01

    RNases in parallel combined with further fragmentation by Post Source Decay (PSD). This approach allows fast and sensitive screening of a purified RNA for posttranscriptional modification, and has been applied on 5S rRNA from two thermophilic microorganisms, the bacterium Bacillus stearothermophilus...... that is clearly conserved with respect to both sequence and position in B. stearothermophilus and H. halobium and to some degree also in H. marismortui. However, no analogous modification was identified in the latter three organisms. We further find that the 5' end of H. halobium 5S rRNA is dephosphorylated......, in contrast to the other 5S rRNA species investigated. The method additionally gives an immediate indication of whether the expected RNA sequence is in agreement with the observed fragment masses. Discrepancies with two of the published 5S rRNA sequences were identified and are reported here....

  3. Diversity of halophilic archaea from six hypersaline environments in Turkey.

    Science.gov (United States)

    Ozcan, Birgul; Ozcengiz, Gulay; Coleri, Arzu; Cokmus, Cumhur

    2007-06-01

    The diversity of archaeal strains from six hypersaline environments in Turkey was analyzed by comparing their phenotypic characteristics and 16S rDNA sequences. Thirty-three isolates were characterized in terms of their phenotypic properties including morphological and biochemical characteristics, susceptibility to different antibiotics, and total lipid and plasmid contents, and finally compared by 16S rDNA gene sequences. The results showed that all isolates belong to the family Halobacteriaceae. Phylogenetic analyses using approximately 1,388 bp comparisions of 16S rDNA sequences demonstrated that all isolates clustered closely to species belonging to 9 genera, namely Halorubrum (8 isolates), Natrinema (5 isolates), Haloarcula (4 isolates), Natronococcus (4 isolates), Natrialba (4 isolates), Haloferax (3 isolates), Haloterrigena (3 isolates), Halalkalicoccus (1 isolate), and Halomicrobium (1 isolate). The results revealed a high diversity among the isolated halophilic strains and indicated that some of these strains constitute new taxa of extremely halophilic archaea.

  4. Structure of halophilic malate dehydrogenase in multimolar KCl solutions from neutron scattering and ultracentrifugation

    International Nuclear Information System (INIS)

    Calmettes, P.

    1987-01-01

    The structure and solvent interactions of malate dehydrogenase from Halobacterium marismortui in multimolar KCl solvents are found to be similar to those in multimolar NaCl solvents reported previously (G. Zaccai, E. Wachtel and H. Eisenberg, J. Mol. Biol. 190 (1986) 97). KCl rather than NaCl is predominant in physiological medium. At salt concentrations up to about 3.0 M, the protein (a dimer of M 87000 g/mol) can be considered to occupy an invariant volume in which it is associated with about 4100 molecules of water and about 520 molecules of salt. At very low resolution, the enzyme particle appears to have a compact protein core and protruding protein parts in interaction with the water and salt components, structural features that are not observed in non-halophilic mitochondrial malate dehydrogenase. The above conclusions were drawn from the analysis of neutron scattering and ultracentrifugation data, and the complementarity of these approaches is discussed extensively. 24 refs.; 7 figs.; 4 tabs

  5. The interaction of Plutonium with Bacteria in the Repository Environment

    International Nuclear Information System (INIS)

    Gillow, J. B.; Francis, A. J.; Lucero, D. A.; Papenguth, H. W.

    2000-01-01

    Microorganisms in the nuclear waste repository environment may interact with plutonium through (1) sorption, (2) intracellular accumulation, and (3) transformation speciation. These interactions may retard or enhance the mobility of Pu by precipitation reactions, biocolloid formation, or production of more soluble species. Current and planned radioactive waste repository environments, such as deep subsurface halite and granite formations, are considered extreme relative to life processes in the near-surface terrestrial environment. There is a paucity of information on the biotransformation of radionuclides by microorganisms present in such extreme environments. In order to gain a better understanding of the interaction of plutonium with microorganisms present in the waste repository sites we investigated a pure culture (Halomonas sp.) and a mixed culture of bacteria (Haloarcula sinaiiensis, Marinobacter hydrocarbonoclasticus, Altermonas sp., and a γ-proteobacterium) isolated from the Waste Isolation Pilot Plant (WIPP) site and an Acetobacterium sp. from alkaline groundwater at the Grimsel Test Site in Switzerland

  6. PA-1, a Versatile Anaerobe Obtained in Pure Culture, Catabolizes Benzenoids and Other Compounds in Syntrophy with Hydrogenotrophs, and P-2 plus Wolinella sp. Degrades Benzenoids

    Science.gov (United States)

    Barik, Sudhakar; Brulla, W. J.; Bryant, M. P.

    1985-01-01

    Methanogenic enrichments catabolizing 13 mM phenylacetate or 4 mM phenol were established at 37°C, using a 10% inoculum from a municipal anaerobic digester. By using agar roll tubes of the basal medium plus 0.1% yeast extract-25 mM fumarate, a hydrogenotrophic lawn of Wolinella succinogenes and phenol or phenylacetate, strains P-2 and PA-1, respectively, were isolated in coculture with W. succinogenes. With the lawn deleted, PA-1 was isolated in pure culture. Strain P-2 is apparently a new species of anaerobic, motile, gram-negative, spindle-shaped, small rod that as yet has been grown only in coculture with W. succinogenes. It used phenol, hydrocinnamate, benzoate, and phenylacetate as energy sources. Product recovery by the coculture, per mole of phenol and 4.4 mol of fumarate used, included 2.03, 0.12, 0.08, and 3.23 mol, respectively, of acetate, propionate, butyrate, and succinate. Carbon recovery was 75% and H recovery was 80%, although CO2 and a few other possible products were not determined. That P-2 is an obligate proton-reducing acetogen and possible pathways for its degradation of phenol are discussed. Strain PA-1 is apparently a new species of anaerobic, motile, relatively small, gram-negative rod. It utilized compounds such as phenylacetate, hydrocinnamate, benzoate, phenol, resorcinol, gallate, 4-aminophenol, 2-aminobenzoate, pyruvate, Casamino Acids, and aspartate as energy sources in coculture with W. succinogenes. Per mole of phenylacetate and 1.44 mol of fumarate used, 1.04, 0.53, and 0.78 mol of acetate, propionate, and succinate, respectively, were recovered from the coculture. Only about 50% of the carbon and H were recovered. In coculture with Methanospirillum hungatei, 0.96 mol of acetate and 0.25 mol of methane were recovered per mol of pyruvate used; 0.90 mol of acetate and 0.33 mol of methane, per mol of fumarate used; 0.93 mol of acetate and 0.54 mol of methane, per mol of aspartate used; and 1.71 mol of acetate and 0.57 mol of methane

  7. Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal

    Science.gov (United States)

    Vreeland, Russell H.; Rosenzweig, William D.; Powers, Dennis W.

    2000-10-01

    Bacteria have been found associated with a variety of ancient samples, however few studies are generally accepted due to questions about sample quality and contamination. When Cano and Borucki isolated a strain of Bacillus sphaericus from an extinct bee trapped in 25-30 million-year-old amber, careful sample selection and stringent sterilization techniques were the keys to acceptance. Here we report the isolation and growth of a previously unrecognized spore-forming bacterium (Bacillus species, designated 2-9-3) from a brine inclusion within a 250million-year-old salt crystal from the Permian Salado Formation. Complete gene sequences of the 16S ribosomal DNA show that the organism is part of the lineage of Bacillus marismortui and Virgibacillus pantothenticus. Delicate crystal structures and sedimentary features indicate the salt has not recrystallized since formation. Samples were rejected if brine inclusions showed physical signs of possible contamination. Surfaces of salt crystal samples were sterilized with strong alkali and acid before extracting brines from inclusions. Sterilization procedures reduce the probability of contamination to less than 1 in 10 9.

  8. Catalytic properties of thermophilic lactate dehydrogenase and halophilic malate dehydrogenase at high temperature and low water activity.

    Science.gov (United States)

    Hecht, K; Wrba, A; Jaenicke, R

    1989-07-15

    Thermophilic lactate dehydrogenases from Thermotoga maritima and Bacillus stearothermophilus are stable up to temperature limits close to the optimum growth temperature of their parent organisms. Their catalytic properties are anomalous in that Km shows a drastic increase with increasing temperature. At low temperatures, the effect levels off. Extreme halophilic malate dehydrogenase from Halobacterium marismortui exhibits a similar anomaly. Increasing salt concentration (NaCl) leads to an optimum curve for Km, oxaloacctate while Km, NADH remains constant. Previous claims that the activity of halophilic malate dehydrogenase shows a maximum at 1.25 M NaCl are caused by limiting substrate concentration; at substrate saturation, specific activity of halophilic malate dehydrogenase reaches a constant value at ionic strengths I greater than or equal to 1 M. Non-halophilic (mitochondrial) malate dehydrogenase shows Km characteristics similar to those observed for the halophilic enzyme. The drastic decrease in specific activity of the mitochondrial enzyme at elevated salt concentrations is caused by the salt-induced increase in rigidity of the enzyme, rather than gross structural changes.

  9. Polysaccharides from Extremophilic Microorganisms

    Science.gov (United States)

    Nicolaus, B.; Moriello, V. Schiano; Lama, L.; Poli, A.; Gambacorta, A.

    2004-02-01

    Several marine thermophilic strains were analyzed for exopolysaccharide production. The screening process revealed that a significant number of thermophilic microorganisms were able to produce biopolymers, and some of them also revealed interesting chemical compositions. We have identified four new polysaccharides from thermophilic marine bacteria, with complex primary structures and with different repetitive units: a galacto-mannane type from strain number 4004 and mannane type for the other strains. The thermophilic Bacillus thermantarcticus produces two exocellular polysaccharides (EPS 1, EPS 2) that give the colonies a typical mucous character. The exopolysaccharide fraction was produced with all substrates assayed, although a higher yield 400 mg liter-1 was obtained with mannose as carbon and energy source. NMR spectra confirmed that EPS 1 was a heteropolysaccharide of which the repeating unit was constituted by four different α-D-mannoses and three different β-D-glucoses. It seems to be close to some xantan polymers. EPS 2 was a mannan. Four different α-D-mannoses were found as the repeating unit. Production and chemical studies of biopolymers produced by halophilic archaea, Haloarcula species were also reported.

  10. Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels.

    Directory of Open Access Journals (Sweden)

    Naseer Sangwan

    Full Text Available This paper presents the characterization of the microbial community responsible for the in-situ bioremediation of hexachlorocyclohexane (HCH. Microbial community structure and function was analyzed using 16S rRNA amplicon and shotgun metagenomic sequencing methods for three sets of soil samples. The three samples were collected from a HCH-dumpsite (450 mg HCH/g soil and comprised of a HCH/soil ratio of 0.45, 0.0007, and 0.00003, respectively. Certain bacterial; (Chromohalobacter, Marinimicrobium, Idiomarina, Salinosphaera, Halomonas, Sphingopyxis, Novosphingobium, Sphingomonas and Pseudomonas, archaeal; (Halobacterium, Haloarcula and Halorhabdus and fungal (Fusarium genera were found to be more abundant in the soil sample from the HCH-dumpsite. Consistent with the phylogenetic shift, the dumpsite also exhibited a relatively higher abundance of genes coding for chemotaxis/motility, chloroaromatic and HCH degradation (lin genes. Reassembly of a draft pangenome of Chromohalobacter salaxigenes sp. (∼8X coverage and 3 plasmids (pISP3, pISP4 and pLB1; 13X coverage containing lin genes/clusters also provides an evidence for the horizontal transfer of HCH catabolism genes.

  11. Assessing the Effect of Pretreatments on the Structure and Functionality of Microbial Communities for the Bioconversion of Microalgae to Biogas

    Directory of Open Access Journals (Sweden)

    Olivia Córdova

    2018-06-01

    Full Text Available Microalgae biomethanization is driven by anaerobic sludge associated microorganisms and is generally limited by the incomplete hydrolysis of the microalgae cell wall, which results in a low availability of microalgal biomass for the methanogenic community. The application of enzymatic pretreatments, e.g., with hydrolytic enzymes, is among the strategies used to work around the incomplete hydrolysis of the microalgae cell wall. Despite the proven efficacy of these pretreatments in increasing biomethanization, the changes that a given pretreatment may cause to the anaerobic sludge associated microorganisms during biomethanization are still unknown. This study evaluated the changes in the expression of the metatranscriptome of anaerobic sludge associated microorganisms during Chlorella sorokiniana biomethanization without pretreatment (WP (control and pretreated with commercial cellulase in order to increase the solubilization of the microalgal organic matter. Pretreated microalgal biomass experienced significant increases in biogas the production. The metatranscriptomic analysis of control samples showed functionally active microalgae cells, a bacterial community dominated by γ- and δ-proteobacteria, and a methanogenic community dominated by Methanospirillum hungatei. In contrast, pretreated samples were characterized by the absence of active microalgae cells and a bacteria population dominated by species of the Clostridia class. These differences are also related to the differential activation of metabolic pathways e.g., those associated with the degradation of organic matter during its biomethanization.

  12. Isolation and characterization from solar salterns of North Algeria of a haloarchaeon producing a new halocin.

    Science.gov (United States)

    Mazguene, Souhila; Rossi, Mosè; Gogliettino, Marta; Palmieri, Gianna; Cocca, Ennio; Mirino, Sara; Imadalou-Idres, Nacera; Benallaoua, Said

    2018-03-01

    Halophilic archaea, thriving in hypersaline environments, synthesize antimicrobial substances with an unknown role, called halocins. It has been suggested that halocin production gives transient competitive advantages to the producer strains and represents one of the environmental factors influencing the microbial community composition. Herein, we report on the antibacterial activity of a new haloarchaeon selected from solar salterns of the northern coast of Algeria. A total of 81 halophilic strains, isolated from the microbial consortia, were screened for the production of antimicrobial compounds by interspecies competition test and against a collection of commercial haloarchaea. On the basis of the partial 16S rRNA sequencing, the most efficient halocin producer was recognized as belonging to Haloferax (Hfx) sp., while the best indicator microorganism, showing high sensitivity toward halocin, was related to Haloarcula genus. The main morphological, physiological and biochemical properties of Hfx were investigated and a partial purification of the produced halocin was allowed to identify it as a surface membrane protein with a molecular mass between 30 and 40 kDa. Therefore, in this study, we isolated a new strain belonging to Haloferax genus and producing a promising antimicrobial compound useful for applications in health and food industries.

  13. Characterization and antimicrobial potential of extremely halophilic archaea isolated from hypersaline environments of the Algerian Sahara.

    Science.gov (United States)

    Quadri, Inès; Hassani, Imene Ikrame; l'Haridon, Stéphane; Chalopin, Morgane; Hacène, Hocine; Jebbar, Mohamed

    2016-01-01

    Halophilic archaea were isolated from different chotts and sebkha, dry salt lakes and salt flat respectively, of the Algerian Sahara and characterized using phenotypic and phylogenetic approaches. From 102 extremely halophilic strains isolated, forty three were selected and studied. These strains were also screened for their antagonistic potential and the production of hydrolytic enzymes. Sequencing of the 16S rRNA genes and phylogenetic analysis allowed the identification of 10 archaeal genera within the class Halobacteria: Natrinema (13 strains), Natrialba (12 strains), Haloarcula (4 strains), Halopiger (4 strains), Haloterrigena (3 strains), Halorubrum (2 strains), Halostagnicola (2 strains), Natronococcus, Halogeometricum and Haloferax (1 strain each). The most common producers of antimicrobial compounds belong to the genus Natrinema while the most hydrolytic isolates, with combined production of several enzymes, belong to the genus Natrialba. The strain affiliated to Halopiger djelfamassilliensis was found to produce some substances of interest (halocins, anti-Candida, enzymes). After partial purification and characterization of one of the strains Natrinema gari QI1, we found similarities between the antimicrobial compound and the halocin C8. Therefore, the gene encoding halocin C8 was amplified and sequenced. Copyright © 2016 Elsevier GmbH. All rights reserved.

  14. Effect of phosphorus addition on the reductive transformation of pentachlorophenol (PCP) and iron reduction with microorganism involvement.

    Science.gov (United States)

    Wang, Yongkui; Liu, Xianli; Huang, Jiexun; Xiao, Wensheng; Zhang, Jiaquan; Yin, Chunqin

    2017-10-01

    The transformation of phosphorus added to the soil environment has been proven to be influenced by the Fe biochemical process, which thereby may affect the transformation of organic chlorinated contaminants. However, the amount of related literatures regarding this topic is limited. This study aimed to determine the effects of phosphorus addition on pentachlorophenol (PCP) anaerobic transformation, iron reduction, and paddy soil microbial community structure. Results showed that the transformation of phosphorus, iron, and PCP were closely related to the microorganisms. Moreover, phosphorus addition significantly influenced PCP transformation and iron reduction, which promoted and inhibited these processes at low and high concentrations, respectively. Both the maximum reaction rate of PCP transformation and the maximum Fe(II) amount produced were obtained at 1 mmol/L phosphorus concentration. Among the various phosphorus species, dissolved P and NaOH-P considerably changed, whereas only slight changes were observed for the remaining phosphorus species. Microbial community structure analysis demonstrated that adding low concentration of phosphorus promoted the growth of Clostridium bowmanii, Clostridium hungatei, and Clostridium intestinale and Pseudomonas veronii. By contrast, high-concentration phosphorus inhibited growth of these microorganisms, similar to the curves of PCP transformation and iron reduction. These observations indicated that Clostridium and P. veronii, especially Clostridium, played a vital role in the transformation of related substances in the system. All these findings may serve as a reference for the complicated reactions among the multiple components of soils.

  15. Fermentative degradation of polyethylene glycol by a strictly anaerobic, gram-negative, nonsporeforming bacterium, Pelobacter venetianus sp. nov.

    Science.gov (United States)

    Schink, B; Stieb, M

    1983-06-01

    The synthetic polyether polyethylene glycol (PEG) with a molecular weight of 20,000 was anaerobically degraded in enrichment cultures inoculated with mud of limnic and marine origins. Three strains (Gra PEG 1, Gra PEG 2, and Ko PEG 2) of rod-shaped, gram-negative, nonsporeforming, strictly anaerobic bacteria were isolated in mineral medium with PEG as the sole source of carbon and energy. All strains degraded dimers, oligomers, and polymers of PEG up to a molecular weight of 20,000 completely by fermentation to nearly equal amounts of acetate and ethanol. The monomer ethylene glycol was not degraded. An ethylene glycol-fermenting anaerobe (strain Gra EG 12) isolated from the same enrichments was identified as Acetobacterium woodii. The PEG-fermenting strains did not excrete extracellular depolymerizing enzymes and were inhibited by ethylene glycol, probably owing to a blocking of the cellular uptake system. PEG, some PEG-containing nonionic detergents, 1,2-propanediol, 1,2-butanediol, glycerol, and acetoin were the only growth substrates utilized of a broad variety of sugars, organic acids, and alcohols. The isolates did not reduce sulfate, sulfur, thiosulfate, or nitrate and were independent of growth factors. In coculture with A. woodii or Methanospirillum hungatei, PEGs and ethanol were completely fermented to acetate (and methane). A marine isolate is described as the type strain of a new species, Pelobacter venetianus sp. nov. Its physiology and ecological significance, as well as the importance and possible mechanism of anaerobic polyether degradation, are discussed.

  16. Utilization of waste as biogas substrateby dominan microbes identified

    Science.gov (United States)

    Nurlina, E.; Sambasri, S.; Hartati, E.; Safitri, R.; Hodijat, A.

    2018-05-01

    Indonesia as the tropics have a source of biomass feedstock which is very large, so the waste biomass can be used optimally as an energy source in the form of biogas. This study was conducted to obtain alternative energy from domestic waste materials, given the limited availability of petroleum and natural gas sourced from fossil fuels. This methodology is an experimental method, the process conditions at room temperature 25-27 °C, pH adjusted to the growth of microbes to produce biogas, retention time 20-60 days, the bioreactor is operated with a batch system, the volume of waste in the bioreactor is made permanent, so that the production of biogas in large scale will increase the pressure inside the bioreactor. Biogas is formed accommodated then distributed to the stove. Factors that determine the formation of biogas is a microbial species capable methanogens convert acetate into biogas. From the results of microbial identification of the isolates in the bioreactor, has identified three types of bacteria methanogens namely Methanospirillum hungatei, Methanobacterium polustre and Methanolacinapoynteri. The results of this study, domestic waste can be utilized as a substrate in biogas production, with the highest methane composition reaches 50.79%. This result is expected to increase public knowledge to utilize the waste into biogas as a renewable energy to sufficient the energy needs of household, so it does not depend on the energy derived from fossil fuels.

  17. Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.

    Science.gov (United States)

    Yoon, Jung-Hoon; Oh, Tae-Kwang; Park, Yong-Ha

    2004-11-01

    A Gram-variable, endospore-forming moderately halophilic rod, strain SF-121, was isolated from a marine solar saltern of the Yellow Sea in Korea. The result of 16S rRNA gene sequence analysis showed that strain SF-121 has highest sequence similarity (99.7 %) with the type strain of Bacillus halodenitrificans. Phylogenetic analyses based on 16S rRNA gene sequences revealed that B. halodenitrificans DSM 10037(T) and strain SF-121 are more closely related to the genus Virgibacillus than to the genus Bacillus. Strain SF-121 and B. halodenitrificans DSM 10037(T) exhibited 16S rRNA gene similarity levels of 95.3-97.5 % with the type strains of Virgibacillus species and 94.0 % with the type strain of Bacillus subtilis. DNA-DNA relatedness and phenotypic data indicated that B. halodenitrificans DSM 10037(T) and strain SF-121 are members of the same species. B. halodenitrificans DSM 10037(T) and strain SF-121 exhibited DNA-DNA relatedness values of 9-11 % with the type strains of Virgibacillus carmonensis and Virgibacillus marismortui. On the basis of the phenotypic, chemotaxonomic, phylogenetic and genetic data, B. halodenitrificans should be reclassified in the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.

  18. Link Between Capacity for Current Production and Syntrophic Growth in Geobacter species

    Directory of Open Access Journals (Sweden)

    Amelia-Elena eRotaru

    2015-07-01

    Full Text Available Electrodes are unnatural electron acceptors, and it is yet unknown how some Geobacter species evolved to use electrodes as terminal electron acceptors. Analysis of different Geobacter species revealed that they varied in their capacity for current production. G. metallireducens and G. hydrogenophilus generated high current densities (ca. 0.05 mA/cm2, comparable to G. sulfurreducens. G. bremensis, G. chapellei, G. humireducens, and G. uranireducens, produced much lower currents (ca. 0.05 mA/cm2 and G. bemidjiensis was previously found to not produce current. There was no correspondence between the effectiveness of current generation and Fe(III oxide reduction rates. Some high-current-density strains (G. metallireducens and G. hydrogenophilus reduced Fe(III-oxides as fast as some low-current-density strains (G. bremensis, G. humireducens, and G. uranireducens whereas other low-current-density strains (G. bemidjiensis and G. chapellei reduced Fe(III oxide as slowly as G. sulfurreducens, a high-current-density strain. However, there was a correspondence between the ability to produce higher currents and the ability to grow syntrophically. G. hydrogenophilius was found to grow in co-culture with Methanosarcina barkeri, which is capable of direct interspecies electron transfer (DIET, but not with Methanospirillium hungatei capable only of H2 or formate transfer. Conductive granular activated carbon (GAC stimulated metabolism of the G. hydrogenophilus - M. barkeri co-culture, consistent with electron exchange via DIET. These findings, coupled with the previous finding that G. metallireducens and G. sulfurreducens are also capable of DIET, suggest that evolution to optimize DIET has fortuitiously conferred the capability for high-density current production to some Geobacter species.

  19. Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes.

    Science.gov (United States)

    Meyer, Birte; Kuehl, Jennifer V; Deutschbauer, Adam M; Arkin, Adam P; Stahl, David A

    2013-11-01

    The mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers obligately linked by interspecies metabolite exchange in syntrophic consortia that may include sulfate reducing species such as Desulfovibrio. To evaluate the metabolic flexibility of syntrophic Desulfovibrio to adapt to naturally fluctuating methanogenic environments, we studied Desulfovibrio alaskensis strain G20 grown in chemostats under respiratory and syntrophic conditions with alternative methanogenic partners, Methanococcus maripaludis and Methanospirillum hungatei, at different growth rates. Comparative whole-genome transcriptional analyses, complemented by G20 mutant strain growth experiments and physiological data, revealed a significant influence of both energy source availability (as controlled by dilution rate) and methanogen on the electron transfer systems, ratios of interspecies electron carriers, energy generating systems, and interspecies physical associations. A total of 68 genes were commonly differentially expressed under syntrophic versus respiratory lifestyle. Under low-energy (low-growth-rate) conditions, strain G20 further had the capacity to adapt to the metabolism of its methanogenic partners, as shown by its differing gene expression of enzymes involved in the direct metabolic interactions (e.g., periplasmic hydrogenases) and the ratio shift in electron carriers used for interspecies metabolite exchange (hydrogen/formate). A putative monomeric [Fe-Fe] hydrogenase and Hmc (high-molecular-weight-cytochrome c3) complex-linked reverse menaquinone (MQ) redox loop become increasingly important for the reoxidation of the lactate-/pyruvate oxidation-derived redox pair, DsrC(red) and Fd(red), relative to the Qmo-MQ-Qrc (quinone-interacting membrane-bound oxidoreductase; quinone-reducing complex) loop. Together, these data underscore the high enzymatic and metabolic adaptive flexibility that likely sustains

  20. First characterization of extremely halophilic 2-deoxy-D-ribose-5-phosphate aldolase.

    Science.gov (United States)

    Ohshida, Tatsuya; Hayashi, Junji; Satomura, Takenori; Kawakami, Ryushi; Ohshima, Toshihisa; Sakuraba, Haruhiko

    2016-10-01

    2-Deoxy-d-ribose-5-phosphate aldolase (DERA) catalyzes the aldol reaction between two aldehydes and is thought to be a potential biocatalyst for the production of a variety of stereo-specific materials. A gene encoding DERA from the extreme halophilic archaeon, Haloarcula japonica, was overexpressed in Escherichia coli. The gene product was successfully purified, using procedures based on the protein's halophilicity, and characterized. The expressed enzyme was stable in a buffer containing 2 M NaCl and exhibited high thermostability, retaining more than 90% of its activity after heating at 70 °C for 10 min. The enzyme was also tolerant to high concentrations of organic solvents, such as acetonitrile and dimethylsulfoxide. Moreover, H. japonica DERA was highly resistant to a high concentration of acetaldehyde and retained about 35% of its initial activity after 5-h' exposure to 300 mM acetaldehyde at 25 °C, the conditions under which E. coli DERA is completely inactivated. The enzyme exhibited much higher activity at 25 °C than the previously characterized hyperthermophilic DERAs (Sakuraba et al., 2007). Our results suggest that the extremely halophilic DERA has high potential to serve as a biocatalyst in organic syntheses. This is the first description of the biochemical characterization of a halophilic DERA. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Identification of moderately halophilic bacteria from Thai fermented fish ( pla-ra ) and proposal of Virgibacillus siamensis sp. nov.

    Science.gov (United States)

    Tanasupawat, Somboon; Chamroensaksri, Nitcha; Kudo, Takuji; Itoh, Takashi

    2010-10-01

    Forty-one isolates of moderately halophilic bacteria were isolated from fermented fish (pla-ra) in Thailand. On the basis of their phenotypic and chemotaxonomic characteristics, DNA-DNA relatedness and 16S rRNA gene sequences analyses, they were divided into six groups. The isolates in Group I to V were Gram-positive rod-shaped bacteria. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan and menaquinone with seven isoprene units (MK-7). An isolate in Group VI was a Gram-negative rod-shaped bacterium. The DNA G+C contents of tested strains ranged from 36.5-63 mol%. Ten strains (Group I) were identified as Virgibacillus dokdonensis, 13 isolates (Group II) as V. halodenitrificans, 14 isolates (Group III) as V. marismortui, 1 isolate (Group IV) as Virgibacillus sp., 2 isolates (Group V) as Bacillus vietnamnensis, and 1 isolate (Group VI) as Chromohalobacter salexigens. Isolate MS3-4 in Group IV was closely related to V. carmonensis KCTC 3819(T) (95.9%). This strain contained anteiso-C(15:0) (55.8%) and anteiso-C(17:0) (17.7%) as major cellular fatty acids and had phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid as polar lipids. The DNA G+C content of MS3-4 was 38.0 mol%. The strain from Group IV is proposed as Virgibacillus siamensis sp. nov. and MS3-4(T) is the type strain (JCM 15395(T) =PCU 312(T) =TISTR 1957(T)).

  2. Isolation and identification of culturable extremely halophilic archaea of Inche-Boroun wetland

    Directory of Open Access Journals (Sweden)

    Mehrnoosh Rasooli

    2013-11-01

    Full Text Available Haloarchaeal diversity of Inche-Boroun wetland in north of Iran in Golestan province was investigated by using culture-dependent methods. Sampling was carried out in May and September 2010. In each sampling, 4 distinct region of wetland were analyzed by using complex media like MGM, JCM168, MH1 and an alkaliphilic medium containing 23% salts. After incubation at 40ºC, a total of 406 isolates were prepared and 2.1×106 CFU/ml were obtained in culture media. Among all isolates, 361 isolates were obtained from MGM and 39 isolates from JCM 168, 3 isolates from MH1 and 3 isolate from alkaliphilic media. Initial morphological, biochemical and physiological tests were performed. According to the results, 45 isolates were selected and phylogenetic analysis of 16S rRNA was performed for them. Among selected strains, 40 isolates belonged to Halobacteriacaea and were related to Haloarcula, Halorubrum, Haloferax, Halobellus, Halogeometricum, Halobacterium, Halolamina, Halorhabdus and Halostagnicola (respectively 30, 27.5, 17.5, 10, 5.2, 2.6, 2.6, 2.6 and 2.6 percent of Haloarchaeal strains. A total of 5 strains belonged to the kingdom of Bacteria and were related to Rhodovibrio, Pseudomonas and Salicola (respectively 40, 40 and 20 percent of bacterial strains. According to our results and the limited numbers of haloarchaeal genera that having been discovered until now, it seemed that the culturable prokaryotic populations in this hypersaline environment was diverse.

  3. A proteomic view at the biochemistry of syntrophic butyrate oxidation in Syntrophomonas wolfei.

    Directory of Open Access Journals (Sweden)

    Alexander Schmidt

    Full Text Available In syntrophic conversion of butyrate to methane and CO2, butyrate is oxidized to acetate by secondary fermenting bacteria such as Syntrophomonas wolfei in close cooperation with methanogenic partner organisms, e.g., Methanospirillum hungatei. This process involves an energetically unfavourable shift of electrons from the level of butyryl-CoA oxidation to the substantially lower redox potential of proton and/or CO2 reduction, in order to transfer these electrons to the methanogenic partner via hydrogen and/or formate. In the present study, all prominent membrane-bound and soluble proteins expressed in S. wolfei specifically during syntrophic growth with butyrate, in comparison to pure-culture growth with crotonate, were examined by one- and two-dimensional gel electrophoresis, and identified by peptide fingerprinting-mass spectrometry. A membrane-bound, externally oriented, quinone-linked formate dehydrogenase complex was expressed at high level specifically during syntrophic butyrate oxidation, comprising a selenocystein-linked catalytic subunit with a membrane-translocation pathway signal (TAT, a membrane-bound iron-sulfur subunit, and a membrane-bound cytochrome. Soluble hydrogenases were expressed at high levels specifically during growth with crotonate. The results were confirmed by native protein gel electrophoresis, by formate dehydrogenase and hydrogenase-activity staining, and by analysis of formate dehydrogenase and hydrogenase activities in intact cells and cell extracts. Furthermore, constitutive expression of a membrane-bound, internally oriented iron-sulfur oxidoreductase (DUF224 was confirmed, together with expression of soluble electron-transfer flavoproteins (EtfAB and two previously identified butyryl-CoA dehydrogenases. Our findings allow to depict an electron flow scheme for syntrophic butyrate oxidation in S. wolfei. Electrons derived from butyryl-CoA are transferred through a membrane-bound EtfAB:quinone oxidoreductase (DUF

  4. Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae.

    Science.gov (United States)

    Pawlowski, Alice; Rissanen, Ilona; Bamford, Jaana K H; Krupovic, Mart; Jalasvuori, Matti

    2014-06-01

    A new family of viruses named Sphaerolipoviridae has been proposed recently. It comprises icosahedral, tailless haloarchaeal viruses with an internal lipid membrane located between the protein capsid and the dsDNA genome. The proposed family Sphaerolipoviridae was divided into two genera: Alphasphaerolipovirus, including Haloarcula hispanica viruses SH1, PH1 and HHIV-2, and Betasphaerolipovirus, including Natrinema virus SNJ1. Here, we propose to expand the family Sphaerolipoviridae to include a group of bacteriophages infecting extreme thermophilic Thermus thermophilus and sharing a number of structural and genomic properties with archaeal sphaerolipoviruses. This new group comprises two members, lytic phage P23-77 and temperate phage IN93, as well as putative members P23-72 and P23-65H. In addition, several related proviruses have been discovered as integrated elements in bacterial genomes of the families Thermus and Meiothermus. Morphology of the virus particles and the overall capsid architecture of these bacteriophages resembles that of archaeal members of the Sphaerolipoviridae, including an unusual capsid arrangement in a T = 28 dextro lattice. Alpha- and betasphaerolipoviruses share with P23-77-like bacteriophages a conserved block of core genes that encode a putative genome-packaging ATPase and the two major capsid proteins (MCPs). The recently determined X-ray structure of the small and large MCPs of P23-77 revealed a single beta-barrel (jelly-roll) fold that is superimposable with the cryo-EM density maps of the SH1 capsomers. Given the common features of these viruses, we propose to include the so far unclassified P23-77-like bacteriophages into a new genus, "Gammasphaerolipovirus", within the family Sphaerolipoviridae.

  5. Isolation, characterization and exploring biotechnological potential of halophilic archaea from salterns of western India.

    Science.gov (United States)

    Singh, Aparna; Singh, Anil Kumar

    2018-01-01

    Thirteen halophilic archaea were isolated from Kandla and Bhayander salt pans. These isolates were grouped into three different genera Halobacterium, Haloferax and Haloarcula based on morphological and biochemical characterization, polar lipid analysis, Amplified 16S rDNA restriction analysis (ARDRA) and 16S rDNA sequence analysis. Biochemical characterization suggested the ability of isolates to produce protease, amylase and poly-hydroxybutyrate (PHB) indicating their biotechnological potential. The isolates were further screened for the amount of extracellular protease produced. Halobacterium sp. SP1(1) showed significant protease production compared to other isolates. Protease producing ability of the isolate was influenced by several factors such as NaCl concentration, type of protein source, metal ions and surfactants, and presence of amino acid supplements in the production medium. Soybean flour, FeCl 3 and dicotylsulfosuccinate were found to increase protease production by 2.36, 1.54 and 1.26 folds, respectively compared to production in basal medium. Effect of organic solvents used in paints (n-decane, n-undecane and n-dodecane) was also investigated on protease production by the isolate. Protease production by Halobacterium sp. SP1(1) was enhanced by 1.2 folds in presence of n-decane compared to control. Furthermore, the ability of isolate to hydrolyse fish protein was investigated using three different edible fishes (Pomfret, Flat fish and Seer fish) as sole protein source. Pomfret was found to be a good protein source for protease production by the isolate. These results revealed that Halobacterium sp. SP1(1) may have potential for paint-based antifouling coating preparations and fish sauce preparation by virtue of its extracellular protease.

  6. Transfer of Natrialba asiatica B1T to Natrialba taiwanensis sp. nov. and description of Natrialba aegyptiaca sp. nov., a novel extremely halophilic, aerobic, non-pigmented member of the Archaea from Egypt that produces extracellular poly(glutamic acid).

    Science.gov (United States)

    Hezayen, F F; Rehm, B H; Tindall, B J; Steinbüchel, A

    2001-05-01

    A novel extremely halophilic member of the Archaea, strain 40T, was isolated from Egypt (Aswan). This isolate requires at least 1.6 M sodium chloride for growth and exhibits optimal growth between 37 and 42 degrees C. Determination of the entire 16S rRNA gene sequence revealed the highest similarity to the type strain of Natrialba asiatica (> 99%). Polar lipid analysis indicated that strain 40T and Natrialba asiatica have essentially identical compositions, indicating that the former is a member of genus Natrialba. However, physiological and biochemical data provided evidence that Natrialba asiatica strains B1T and 172P1T, as well as strain 40T, are sufficiently different to be divided in three different species. The G+C content of strain 40T was 61.5+/-0.6 mol%. In addition, DNA-DNA hybridization data supported the placement of the isolate in a new species in the genus Natrialba, Natrialba aegyptiaca sp. nov., and indicated that Natrialba asiatica strain B1T should also be placed in a separate species, Natrialba taiwanensis sp. nov. Morphological studies of strain 40T indicated clearly that this isolate appears in three completely different cell shapes (cocci, rods, tetrads) under different conditions of growth, including different sodium chloride concentrations and different growth temperatures. Another interesting property of strain 40T is the ability to produce an extracellular polymer, which was found to be composed predominantly of glutamic acid (85% w/w), representing poly(glutamic acid), carbohydrates (12.5% w/w) and unidentified compounds (2.5% w/w). Among the Archaea, production of an extracellular polysaccharide has been described for some members of the genera Haloferax and Haloarcula.

  7. Prokaryotic diversity in one of the largest hypersaline coastal lagoons in the world.

    Science.gov (United States)

    Clementino, M M; Vieira, R P; Cardoso, A M; Nascimento, A P A; Silveira, C B; Riva, T C; Gonzalez, A S M; Paranhos, R; Albano, R M; Ventosa, A; Martins, O B

    2008-07-01

    Araruama Lagoon is an environment characterized by high salt concentrations. The low raining and high evaporation rates in this region favored the development of many salty ponds around the lagoon. In order to reveal the microbial composition of this system, we performed a 16S rRNA gene survey. Among archaea, most clones were related to uncultured environmental Euryarchaeota. In lagoon water, we found some clones related to Methanomicrobia and Methanothermococcus groups, while in the saline pond water members related to the genus Haloarcula were detected. Bacterial community was dominated by clones related to Gamma-proteobacteria, Actinobacteria, and Synechococcus in lagoon water, while Salinibacter ruber relatives dominated in saline pond. We also detected the presence of Alpha-proteobacteria, Pseudomonas-like bacteria and Verrucomicrobia. Only representatives of the genus Ralstonia were cosmopolitan, being observed in both systems. The detection of a substantial number of clones related to uncultured archaea and bacteria suggest that the hypersaline waters of Araruama harbor a pool of novel prokaryotic phylotypes, distinct from those observed in other similar systems. We also observed clones related to halophilic genera of cyanobacteria that are specific for each habitat studied. Additionally, two bacterioplankton molecular markers with ecological relevance were analyzed, one is linked to nitrogen fixation (nifH) and the other is linked to carbon fixation by bacterial photosynthesis, the protochlorophyllide genes, revealing a specific genetic distribution in this ecosystem. This is the first study of the biogeography and community structure of microbial assemblages in Brazilian tropical hypersaline environments. This work is directed towards a better understanding of the free-living prokaryotic diversity adapted to life in hypersaline waters.

  8. Structural and functional implications in the eubacterial ribosome as revealed by protein-rRNA and antibiotic contact sites.

    Science.gov (United States)

    Wittmann-Liebold, B; Uhlein, M; Urlaub, H; Müller, E C; Otto, A; Bischof, O

    1995-01-01

    Contact sites between protein and rRNA in 30S and 50S ribosomal subunits of Escherichia coli and Bacillus stearothermophilus were investigated at the molecular level using UV and 2-iminothiolane as cross-linkers. Thirteen ribosomal proteins (S3, S4, S7, S14, S17, L2, L4, L6, L14, L27, L28, L29, and L36) from these organisms were cross-linked in direct contact with the RNAs, and the peptide stretches as well as amino acids involved were identified. Further, the binding sites of puromycin and spiramycin were established at the peptide level in several proteins that were found to constitute the antibiotic-binding sites. Peptide stretches of puromycin binding were identified from proteins S7, S14, S18, L18, AND L29; those of spiramycin attachment were derived from proteins S12, S14, L17, L18, L27, and L35. Comparison of the RNA-peptide contact sites with the peptides identified for antibiotic binding and with those altered in antibiotic-resistant mutants clearly showed identical peptide areas to be involved and, hence, demonstrated the functional importance of these peptides. Further evidence for a functional implication of ribosomal proteins in the translational process came from complementation experiments in which protein L2 from Halobacterium marismortui was incorporated into the E. coli ribosomes that were active. The incorporated protein was present in 50S subunits and 70S particles, in disomes, and in higher polysomes. These results clearly demonstrate the functional implication of protein L2 in protein biosynthesis. Incorporation studies with a mutant of HmaL2 with a replacement of histidine-229 by glycine completely abolished the functional activity of the ribosome. Accordingly, protein L2 with histidine-229 is a crucial element of the translational machinery.

  9. Anaerobic Co-digestion for Enhanced Renewable Energy and Green House Gas Emission Reduction

    Energy Technology Data Exchange (ETDEWEB)

    Navaratnam, Navaneethan; Zitomer, Daniel

    2012-05-01

    system. These increases were great than anticipated based on theoretical methane production from the additional chemical oxygen demand (COD) of the co-digestates. Co-digestion of the most promising wastes with primary sludge was estimated to generate enough electricity to power more than 2500 houses. Synergistic outcomes of co-digestion may be caused by chances in microbial community resulting in more rapid methane production rate and higher specific methanogenic activities of the biomass against acetate, propionate and H2 as substrates. The presence of Methanospirillum hungatei correlated to higher SMAs in the Co-Digester 1 system. In subsequent full-scale testing, acid whey in addition to primary sludge increased methane production by 16 %, biogas methane content by 5%, methane yield per VS destroyed by 9% ( from 650 to 710 L CH4 / kg VSdestroyed ) and volatile solids removal by 20%. Co-digestion is a promising technology to increase renewable energy production and convert municipal digesters into regional renewable energy facilities.

  10. Halolactibacillus halophilus gen. nov., sp. nov. and Halolactibacillus miurensis sp. nov., halophilic and alkaliphilic marine lactic acid bacteria constituting a phylogenetic lineage in Bacillus rRNA group 1.

    Science.gov (United States)

    Ishikawa, Morio; Nakajima, Kazuyuki; Itamiya, Yuko; Furukawa, Sayumi; Yamamoto, Yasushi; Yamasato, Kazuhide

    2005-11-01

    Eleven novel strains of marine-inhabiting lactic acid bacteria that were isolated from living and decaying marine organisms collected from a temperate area of Japan are described. The isolates were motile with peritrichous flagella and non-sporulating. They lacked catalase, quinones and cytochromes. Fermentation products from glucose were lactate, formate, acetate and ethanol. Lactate yield as percentage conversion from glucose was affected by the pH of the fermentation medium: approximately 55 % at the optimal growth pH of 8.0, greater than approximately 70 % at pH 7.0 and less than approximately 30 % at pH 9.0. The molar ratio of the other three products was the same at each cultivation pH, approximately 2 : 1 : 1. Carbohydrates and related compounds were aerobically metabolized to acetate and pyruvate as well as lactate. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. The optimum NaCl concentration for growth was 2.0-3.0 % (w/v), with a range of 0-25.5 %. The optimum pH for growth was 8.0-9.5, with a range of 6.0-10.0. The G+C content of the DNA was 38.5-40.7 mol%. The isolates constituted two genomic species (DNA-DNA relatedness of less than 41 %) each characterized by sugar fermentation profiles. The cell-wall peptidoglycan of both phenotypes contained meso-diaminopimelic acid. The major cellular fatty acids were C(16 : 0) and a-C(13 : 0). Comparative sequence analysis of the 16S rRNA genes revealed that these isolates represent novel species constituting a phylogenetic unit outside the radiation of typical lactic acid bacteria and an independent line of descent within the group composed of the halophilic/halotolerant/alkaliphilic and/or alkalitolerant species in Bacillus rRNA group 1, with 94.8-95.1 % similarity to the genus Paraliobacillus, 93.7-94.1 % to the genus Gracilibacillus and 93.8-94.2 % to Virgibacillus marismortui. On the basis of possession of physiological and biochemical characteristics common to typical lactic acid

  11. Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface

    Science.gov (United States)

    Sanford, Robert A.; Boyanov, Maxim I.; Kemner, Kenneth M.; O'Loughlin, Edward J.; Chang, Yun-juan; Locke, Randall A.; Weber, Joseph R.; Egan, Sheila M.; Mackie, Roderick I.; Cann, Isaac; Fouke, Bruce W.

    2016-01-01

    ABSTRACT A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H2 as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C). At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe2O3). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe3(PO4)2] and siderite (FeCO3). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well-understood iron-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov. IMPORTANCE A novel iron-reducing species, Orenia metallireducens sp. nov., strain Z6, was isolated from groundwater collected from a geological formation located 2.02 km below land surface in the Illinois Basin, USA

  12. MICROBIAL FERMENTATION OF ABUNDANT BIOPOLYMERS: CELLULOSE AND CHITIN

    Energy Technology Data Exchange (ETDEWEB)

    Leschine, Susan

    2009-10-31

    that the chitinase and cellulase systems of this bacterium are distinct in terms of the proteins involved and the regulation of their production. 4. Characterization of the chitinase system of C. uda. A 70,000-Mr endochitinase, designated ChiA, was purified from C. uda culture supernatant fluids and characterized. 5. Analysis of chiA, which codes for the major enzymatic component of the chitinase system of C. uda. The gene encoding the endochitinase ChiA in C. uda was cloned, its complete nucleotide sequence was determined and its implications were investigated. 6. Formation of biofilms by C. uda on cellulose and chitin. Microscopic observations indicated that, under conditions of nitrogen limitation, C. uda cells grew as a biofilm attached tightly to the surface of cellulose or chitin. 7. Development of tools for a genetic approach to studies of cellulose fermentation by cellulolytic clostridia. We have explored the potential of various techniques, and obtained evidence indicating that Tn916 mutagenesis may be particularly effective in this regard. As part of this research, we identified the presence of a plasmid in one strain, which was cloned, sequenced, and analyzed for its utility in the development of vectors for genetic studies. 8. Effects of humic substances on cellulose degradation by anaerobic cellulolytic microbes. We determined that humic substances play an important role in the anaerobic cellulose decomposition and in the physiology of cellulose-fermenting soil bacteria. 9. Nitrogenases of cellulolytic clostridia. We described a nitrogenase gene from a cellulolytic clostridium and presented evidence, based on sequence analyses and conserved gene order, for lateral gene transfer between this bacterium and a methanogenic archaeon. 10. Characterization of Clostridium hungatei, a new N2-fixing cellulolytic species isolated from a methanogenic consortium from soil. 11. Understanding the molecular architecture of the multicomplex cellulase-xylanase system of

  13. Microbial Oxidation of Hg(0) - Its Effect on Hg Stable Isotope Fractionation and Methylmercury Production

    Energy Technology Data Exchange (ETDEWEB)

    Yee, Nathan [Rutgers Univ., New Brunswick, NJ (United States); Barkay, Tamar [Rutgers Univ., New Brunswick, NJ (United States); Reinfelder, John [Rutgers Univ., New Brunswick, NJ (United States)

    2016-06-28

    relationship between Hg concentrations and rates of denitrification in enrichment cultures. In part III of our project, we examined in more detail the effects of microbial interactions on Hg transformations. We discovered that both sulfate reducing and iron reducing bacteria coexist in freshwater sediments and both microbial groups contribute to mercury methylation. We showed that mercury methylation by sulfate reducing and iron reducing bacteria are temporally and spatially separated processes. We also discovered that methanogens can methylate mercury. We showed that Methanospirillum hungatei JF-1 methylated Hg at comparable rates, but with higher yields, than those observed for sulfate-reducing bacteria and iron-reducing bacteria. Finally, we demonstrated that syntrophic interactions between different microbial groups increase mercury methylation rates. We showed that Hg methylation rates are stimulated via inter-species hydrogen and acetate transfer (i) from sulfate-reducing bacteria to methanogens and (ii) from fermenters to the sulfate-reducing bacteria. In part IV of the project, we studied Hg bioavailability and Hg isotope fractionation. We demonstrated that thiol-bound Hg is bioavailable to mercury resistant bacteria. We found that uptake of Hg from Hg-glutathione and Hg-cysteine complexes does not require functioning glutathione and cystine/cysteine transport systems. We demonstrated that a wide range of methylmercury complexes (e.g. MeHgOH, MeHg-cysteine, and MeHg-glutathione) are bioavailable to mercury resistant bacteria. The rate of MeHg demethylation varies more between different species of mercury resistant bacteria than among MeHg complexes. We showed that microbial demethylation of MeHg depends more on the species of microorganism than on the types and relative concentrations of thiols or other MeHg ligands present. Finally, we demonstrated that Hg methylation by Geobacter sulfurreducens PCA and Desulfovibrio desulfuricans ND132 imparts mass