Characterization of recombinant glyoxylate reductase from thermophile Thermus thermophilus HB27.

Science.gov (United States)

Ogino, Hiroyasu; Nakayama, Hitoshi; China, Hideyasu; Kawata, Takuya; Doukyu, Noriyuki; Yasuda, Masahiro

2008-01-01

A glyoxylate reductase gene from the thermophilic bacterium Thermus thermophilus HB27 (TthGR) was cloned and expressed in Escherichia coli cells. The recombinant enzyme was highly purified to homogeneity and characterized. The purified TthGR showed thermostability up to 70 degrees C. In contrast, the maximum reaction condition was relatively mild (45 degrees C and pH 6.7). Although the kcat values against co-enzyme NADH and NADPH were similar, the Km value against co-enzyme NADH was approximately 18 times higher than that against NADPH. TthGR prefers NADPH rather than NADH as an electron donor. These results indicate that a phosphate group of a co-enzyme affects the binding affinity rather than the reaction efficiency, and TthGR demands appropriate amount of phosphate for a high activity. Furthermore, it was found that the half-lives of TthGR in the presence of 25% dimethyl sulfoxide and diethylene glycol were significantly longer than that in the absence of an organic solvent.

Inhibitors of the glyoxylate cycle enzyme ICL1 in Candida albicans for potential use as antifungal agents.

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Hong-Leong Cheah

Full Text Available Candida albicans is an opportunistic pathogen that causes candidiasis in humans. In recent years, metabolic pathways in C. albicans have been explored as potential antifungal targets to treat candidiasis. The glyoxylate cycle, which enables C. albicans to survive in nutrient-limited host niches and its. Key enzymes (e.g., isocitrate lyase (ICL1, are particularly attractive antifungal targets for C. albicans. In this study, we used a new screening approach that better reflects the physiological environment that C. albicans cells experience during infection to identify potential inhibitors of ICL. Three compounds (caffeic acid (CAFF, rosmarinic acid (ROS, and apigenin (API were found to have antifungal activity against C. albicans when tested under glucose-depleted conditions. We further confirmed the inhibitory potential of these compounds against ICL using the ICL enzyme assay. Lastly, we assessed the bioavailability and toxicity of these compounds using Lipinski's rule-of-five and ADMET analysis.

Increasing L-threonine production in Escherichia coli by engineering the glyoxylate shunt and the L-threonine biosynthesis pathway.

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Zhao, Hui; Fang, Yu; Wang, Xiaoyuan; Zhao, Lei; Wang, Jianli; Li, Ye

2018-04-30

L-threonine is an important amino acid that can be added in food, medicine, or feed. Here, the influence of glyoxylate shunt on an L-threonine producing strain Escherichia coli TWF001 has been studied. The gene iclR was deleted, and the native promoter of the aceBA operon was replaced by the trc promoter in the chromosome of TWF001, the resulting strainTWF004 could produce 0.39 g L-threonine from1 g glucose after 36-h flask cultivation. Further replacing the native promoter of aspC by the trc promoter in the chromosome of TWF004 resulted in the strain TWF006. TWF006 could produce 0.42 g L-threonine from 1 g glucose after 36-h flask cultivation. Three key genes in the biosynthetic pathway of L-threonine, thrA * (a mutated thrA), thrB, and thrC were overexpressed in TWF006, resulting the strain TWF006/pFW01-thrA * BC. TWF006/pFW01-thrA * BC could produce 0.49 g L-threonine from 1 g glucose after 36-h flask cultivation. Next, the genes asd, rhtA, rhtC, or thrE were inserted into the plasmid TWF006/pFW01-thrA * BC, and TWF006 was transformed with these plasmids, resulting the strains TWF006/pFW01-thrA * BC-asd, TWF006/pFW01-thrA * BC-rhtA, TWF006/pFW01-thrA * BC-rhtC, and TWF006/pFW01-thrA * BC-thrE, respectively. These four strains could produce more L-threonine than the control strain, and the highest yield was produced by TWF006/pFW01-thrA * BC-asd; after 36-h flask cultivation, TWF006/pFW01-thrA * BC-asd could produce 15.85 g/l L-threonine, i.e., 0.53 g L-threonine per 1 g glucose, which is a 70% increase relative to the control strain TWF001. The results suggested that the combined engineering of glyoxylate shunt and L-threonine biosynthesis pathway could significantly increase the L-threonine production in E. coli.

Poly(ethyl glyoxylate)-Poly(ethylene oxide) Nanoparticles: Stimuli-Responsive Drug Release via End-to-End Polyglyoxylate Depolymerization.

Science.gov (United States)

Fan, Bo; Gillies, Elizabeth R

2017-08-07

The ability to disrupt polymer assemblies in response to specific stimuli provides the potential to release drugs selectively at certain sites or conditions in vivo. However, most stimuli-responsive delivery systems require many stimuli-initiated events to release drugs. "Self-immolative polymers" offer the potential to provide amplified responses to stimuli as they undergo complete end-to-end depolymerization following the cleavage of a single end-cap. Herein, linker end-caps were developed to conjugate self-immolative poly(ethyl glyoxylate) (PEtG) with poly(ethylene oxide) (PEO) to form amphiphilic block copolymers. These copolymers were self-assembled to form nanoparticles in aqueous solution. Cleavage of the linker end-caps were triggered by a thiol reducing agent, UV light, H 2 O 2 , and combinations of these stimuli, resulting in nanoparticle disintegration. Low stimuli concentrations were effective in rapidly disrupting the nanoparticles. Nile red, doxorubin, and curcumin were encapsulated into the nanoparticles and were selectively released upon application of the appropriate stimulus. The ability to tune the stimuli-responsiveness simply by changing the linker end-cap makes this new platform highly attractive for applications in drug delivery.

Phenylpropanoid 2,3-dioxygenase involved in the cleavage of the ferulic acid side chain to form vanillin and glyoxylic acid in Vanilla planifolia.

Science.gov (United States)

Negishi, Osamu; Negishi, Yukiko

2017-09-01

Enzyme catalyzing the cleavage of the phenylpropanoid side chain was partially purified by ion exchange and gel filtration column chromatography after (NH 4 ) 2 SO 4 precipitation. Enzyme activities were dependent on the concentration of dithiothreitol (DTT) or glutathione (GSH) and activated by addition of 0.5 mM Fe 2+ . Enzyme activity for ferulic acid was as high as for 4-coumaric acid in the presence of GSH, suggesting that GSH acts as an endogenous reductant in vanillin biosynthesis. Analyses of the enzymatic reaction products with quantitative NMR (qNMR) indicated that an amount of glyoxylic acid (GA) proportional to vanillin was released from ferulic acid by the enzymatic reaction. These results suggest that phenylpropanoid 2,3-dioxygenase is involved in the cleavage of the ferulic acid side chain to form vanillin and GA in Vanilla planifolia.

Metabolic regulation at the tricarboxylic acid and glyoxylate cycles of the lignin-degrading basidiomycete Phanerochaete chrysosporium against exogenous addition of vanillin.

Science.gov (United States)

Shimizu, Motoyuki; Yuda, Naoki; Nakamura, Tomofumi; Tanaka, Hiroo; Wariishi, Hiroyuki

2005-10-01

A proteomic differential display technique was utilized to study cellular responses of Phanerochaete chrysosporium exposed to vanillin, one of the key intermediates found during lignin biodegradation. Intracellular proteins were resolved by 2-DE and target protein spots were identified using MALDI-MS after in-gel tryptic digestions. Upon addition of vanillin to P. chrysosporium, up-regulation of homogentisate 1,2-dioxygenase, 1,4-benzoquinone reductases, aldehyde dehydrogenase, and aryl-alcohol dehydrogenase, which seem to play roles in vanillin metabolism, was observed. Furthermore, enzymes involved in glycolysis, the tricarboxylic acid cycle, the pentose-phosphate cycle, and heme biosynthesis were also activated. Up-regulation of extracellular peroxidase was also observed. One of the most unique phenomena against exogenous vanillin was a switch from the glyoxylate cycle to the tricarboxylic acid cycle, where a drastic increase in isocitrate dehydrogenase activity was observed. The exogenous addition of other aromatic compounds also caused an increase in its activity, which in turn triggered NAD(P)H production via the action of dehydrogenases in the tricarboxylic acid cycle, heme biosynthesis via the action of aminolevulinic acid synthase on succinyl-CoA, and energy production via activation of the mitochondrial electron transfer system. These metabolic shifts seem to be required for activating a metabolic system for aromatic compounds.

BisGMA/TEGDMA dental nanocomposites containing glyoxylic acid-modified high-aspect ratio hydroxyapatite nanofibers with enhanced dispersion

International Nuclear Information System (INIS)

Chen Liang; Yu Qingsong; Li Hao; Xu Changqi; Wang Yong; Shi Jian

2012-01-01

The purpose of this research was to investigate the influence of the glyoxylic acid (GA) modification of hydroxyapatite (HAP) nanofibers on their dispersion in bisphenol A glycidyl methacrylate (BisGMA)/triethylene glycol dimethacrylate (TEGDMA) dental composites and also to investigate the mechanical properties, water absorption and water solubility of the resulting dental resins and composites. Scanning/transmission electron microscopy images showed that microsized HAP nanofiber bundles could be effectively broken down into individual HAP nanofibers with an average length of ∼15 µm after the surface modification process. Fourier transform infrared spectroscopy, x-ray photoelectron spectroscopy and thermal gravimetric analysis characterization confirmed that GA was chemically grafted on the HAP nanofiber surface, hypothetically by reacting with the amine group on the HAP nanofiber surface. The enhanced dispersion of HAP nanofibers in the dental matrix led to increased biaxial flexural strength (BFS) compared with the corresponding dental resins and composites filled with untreated HAP nanofibers. In addition, impregnation of small mass fractions of the GA-modified HAP nanofibers into the BisGMA/TEGDMA dental resins (5 wt%, 10 wt%) or composites (2 wt%, 3 wt%) could also substantially improve the BFS in comparison with the controls (pure resins or dental composites filled with silica particles alone). Larger mass fractions could not increase the mechanical property further or even degraded the BFS values. Water behavior testing results indicated that the addition of the GA-modified HAP nanofibers resulted in higher water absorption and water solubility values, which are not preferred for clinical application. In summary, well-dispersed HAP nanofibers and their dental composites with enhanced mechanical properties have been successfully fabricated, but the water absorption and water solubility of such dental composites need to be further improved. (paper)

Genome-Wide Survey of Pseudomonas aeruginosa PA14 Reveals a Role for the Glyoxylate Pathway and Extracellular Proteases in the Utilization of Mucin

Science.gov (United States)

Flynn, Jeffrey M.; Phan, Chi

2017-01-01

ABSTRACT Chronic airway infections by the opportunistic pathogen Pseudomonas aeruginosa are a major cause of mortality in cystic fibrosis (CF) patients. Although this bacterium has been extensively studied for its virulence determinants, biofilm growth, and immune evasion mechanisms, comparatively little is known about the nutrient sources that sustain its growth in vivo. Respiratory mucins represent a potentially abundant bioavailable nutrient source, although we have recently shown that canonical pathogens inefficiently use these host glycoproteins as a growth substrate. However, given that P. aeruginosa, particularly in its biofilm mode of growth, is thought to grow slowly in vivo, the inefficient use of mucin glycoproteins may be relevant to its persistence within the CF airways. To this end, we used whole-genome fitness analysis, combining transposon mutagenesis with high-throughput sequencing, to identify genetic determinants required for P. aeruginosa growth using intact purified mucins as a sole carbon source. Our analysis reveals a biphasic growth phenotype, during which the glyoxylate pathway and amino acid biosynthetic machinery are required for mucin utilization. Secondary analyses confirmed the simultaneous liberation and consumption of acetate during mucin degradation and revealed a central role for the extracellular proteases LasB and AprA. Together, these studies describe a molecular basis for mucin-based nutrient acquisition by P. aeruginosa and reveal a host-pathogen dynamic that may contribute to its persistence within the CF airways. PMID:28507068

Contribution of the tricarboxylic acid (TCA) cycle and the glyoxylate shunt in Saccharomyces cerevisiae to succinic acid production during dough fermentation.

Science.gov (United States)

Rezaei, Mohammad N; Aslankoohi, Elham; Verstrepen, Kevin J; Courtin, Christophe M

2015-07-02

Succinic acid produced by yeast during bread dough fermentation can significantly affect the rheological properties of the dough. By introducing mutations in the model S288C yeast strain, we show that the oxidative pathway of the TCA cycle and the glyoxylate shunt contribute significantly to succinic acid production during dough fermentation. More specifically, deletion of ACO1 and double deletion of ACO1 and ICL1 resulted in a 36 and 77% decrease in succinic acid levels in fermented dough, respectively. Similarly, double deletion of IDH1 and IDP1 decreased succinic acid production by 85%, while also affecting the fermentation rate. By contrast, double deletion of SDH1 and SDH2 resulted in a two-fold higher succinic acid accumulation compared to the wild-type. Deletion of fumarate reductase activity (FRD1 and OSM1) in the reductive pathway of the TCA cycle did not affect the fermentation rate and succinic acid production. The changes in the levels of succinic acid produced by mutants Δidh1Δidp1 (low level) and Δsdh1Δsdh2 (high level) in fermented dough only resulted in small pH differences, reflecting the buffering capacity of dough at a pH of around 5.1. Moreover, Rheofermentometer analysis using these mutants revealed no difference in maximum dough height and gas retention capacity with the dough prepared with S288C. The impact of the changed succinic acid profile on the organoleptic or antimicrobial properties of bread remains to be demonstrated. Copyright © 2015 Elsevier B.V. All rights reserved.

Improving the Thermostability and Optimal Temperature of a Lipase from the Hyperthermophilic Archaeon Pyrococcus furiosus by Covalent Immobilization

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Roberta V. Branco

2015-01-01

Full Text Available A recombinant thermostable lipase (Pf2001Δ60 from the hyperthermophilic Archaeon Pyrococcus furiosus (PFUL was immobilized by hydrophobic interaction on octyl-agarose (octyl PFUL and by covalent bond on aldehyde activated-agarose in the presence of DTT at pH = 7.0 (one-point covalent attachment (glyoxyl-DTT PFUL and on glyoxyl-agarose at pH 10.2 (multipoint covalent attachment (glyoxyl PFUL. The enzyme’s properties, such as optimal temperature and pH, thermostability, and selectivity, were improved by covalent immobilization. The highest enzyme stability at 70°C for 48 h incubation was achieved for glyoxyl PFUL (around 82% of residual activity, whereas glyoxyl-DTT PFUL maintained around 69% activity, followed by octyl PFUL (27% remaining activity. Immobilization on glyoxyl-agarose improved the optimal temperature to 90°C, while the optimal temperature of octyl PFUL was 70°C. Also, very significant changes in activity with different substrates were found. In general, the covalent bond derivatives were more active than octyl PFUL. The E value also depended substantially on the derivative and the conditions used. It was observed that the reaction of glyoxyl-DTT PFUL using methyl mandelate as a substrate at pH 7 presented the best results for enantioselectivity E=22 and enantiomeric excess (ee (% = 91.

Alanine-glyoxylate aminotransferase 2 (AGXT2 polymorphisms have considerable impact on methylarginine and β-aminoisobutyrate metabolism in healthy volunteers.

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Anja Kittel

Full Text Available Elevated plasma concentrations of asymmetric (ADMA and symmetric (SDMA dimethylarginine have repeatedly been linked to adverse clinical outcomes. Both methylarginines are substrates of alanine-glyoxylate aminotransferase 2 (AGXT2. It was the aim of the present study to simultaneously investigate the functional relevance and relative contributions of common AGXT2 single nucleotide polymorphisms (SNPs to plasma and urinary concentrations of methylarginines as well as β-aminoisobutyrate (BAIB, a prototypic substrate of AGXT2. In a cohort of 400 healthy volunteers ADMA, SDMA and BAIB concentrations were determined in plasma and urine using HPLC-MS/MS and were related to the coding AGXT2 SNPs rs37369 (p.Val140Ile and rs16899974 (p.Val498Leu. Volunteers heterozygous or homozygous for the AGXT2 SNP rs37369 had higher SDMA plasma concentrations by 5% and 20% (p = 0.002 as well as higher BAIB concentrations by 54% and 146%, respectively, in plasma and 237% and 1661%, respectively, in urine (both p<0.001. ADMA concentrations were not affected by both SNPs. A haplotype analysis revealed that the second investigated AGXT2 SNP rs16899974, which was not significantly linked to the other AGXT2 SNP, further aggravates the effect of rs37369 with respect to BAIB concentrations in plasma and urine. To investigate the impact of the amino acid exchange p.Val140Ile, we established human embryonic kidney cell lines stably overexpressing wild-type or mutant (p.Val140Ile AGXT2 protein and assessed enzyme activity using BAIB and stable-isotope labeled [²H₆]-SDMA as substrate. In vitro, the amino acid exchange of the mutant protein resulted in a significantly lower enzyme activity compared to wild-type AGXT2 (p<0.05. In silico modeling of the SNPs indicated reduced enzyme stability and substrate binding. In conclusion, SNPs of AGXT2 affect plasma as well as urinary BAIB and SDMA concentrations linking methylarginine metabolism to the common genetic trait of hyper

Solvent Isotope-induced Equilibrium Perturbation for Isocitrate Lyase

Science.gov (United States)

Quartararo, Christine E.; Hadi, Timin; Cahill, Sean M.; Blanchard, John S.

2014-01-01

Isocitrate lyase (ICL) catalyzes the reversible retro-aldol cleavage of isocitrate to generate glyoxylate and succinate. ICL is the first enzyme of the glyoxylate shunt, which allows for the anaplerosis of citric acid cycle intermediates under nutrient limiting conditions. In Mycobacterium tuberculosis, the source of ICL for these studies, ICL is vital for the persistence phase of the bacteria’s life cycle. Solvent kinetic isotope effects (KIEs) in the direction of isocitrate cleavage of D2OV = 2.0 ± 0.1 and D2O[V/Kisocitrate] = 2.2 ± 0.3 arise from the initial deprotonation of the C2 hydroxyl group of isocitrate or the protonation of the aci-acid of succinate product of the isocitrate aldol cleavage by a solvent-derived proton. This KIE suggested that an equilibrium mixture of all protiated isocitrate, glyoxylate and succinate prepared in D2O, would undergo transient changes in equilibrium concentrations as a result of the solvent KIE and solvent-derived deuterium incorporation into both succinate and isocitrate. No change in the isotopic composition of glyoxylate was expected or observed. We have directly monitored the changing concentrations of all isotopic species of all reactants and products using a combination of NMR spectroscopy and mass spectrometry. Continuous monitoring of glyoxylate by 1H NMR spectroscopy shows a clear equilibrium perturbation in D2O. The final equilibrium isotopic composition of reactants in D2O revealed di-deuterated succinate, protiated glyoxylate, and mono-deuterated isocitrate, with the transient appearance and disappearance of mono-deuterated succinate. A model for the equilibrium perturbation of substrate species, and their time-dependent isotopic composition is presented. PMID:24261638

Stable carbon isotopic compositions of low-molecular-weight dicarboxylic acids, glyoxylic acid and glyoxal in tropical aerosols: implications for photochemical processes of organic aerosols

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Stelyus L. Mkoma

2014-10-01

Full Text Available Tropical aerosols of PM2.5 and PM10 were collected at a rural site in Morogoro, Tanzania (East Africa, and analysed for stable carbon isotopic composition (δ13C of dicarboxylic acids (C2–C9, glyoxylic acid (ωC2 and glyoxal (Gly using gas chromatography/isotope ratio mass spectrometer. PM2.5 samples showed that δ13C of oxalic (C2 acid are largest (mean, −18.3±1.7‰ followed by malonic (C3, −19.6±1.0‰ and succinic (C4, −21.8±2.2‰ acids, whereas those in PM10 are a little smaller: −19.9±3.1‰ (C2, −20.2±2.7‰ (C3 and −23.3±3.2‰ (C4. The δ13C of C2–C4 diacids showed a decreasing trend with an increase in carbon numbers. The higher δ13C values of oxalic acid can be explained by isotopic enrichment of 13C in the remaining C2 due to the atmospheric decomposition of oxalic acid or its precursors. δ13C of ωC2 and Gly that are precursors of oxalic acid also showed larger values (mean, −22.5‰ and −20.2‰, respectively in PM2.5 than those (−26.7‰ and −23.7‰ in PM10. The δ13C values of ωC2 and Gly are smaller than those of C2 in both PM2.5 and PM10. On the other hand, azelaic acid (C9; mean, −28.5‰ is more depleted in 13C, which is consistent with the previous knowledge; that is, C9 is produced by the oxidation of unsaturated fatty acids emitted from terrestrial higher plants. A significant enrichment of 13C in oxalic acid together with its negative correlations with relative abundance of C2 in total diacids and ratios of water-soluble organic carbon and organic carbon further support that a photochemical degradation of oxalic acid occurs during long-range transport from source regions.

The Krebs Uric Acid Cycle: A Forgotten Krebs Cycle.

Science.gov (United States)

Salway, Jack G

2018-05-25

Hans Kornberg wrote a paper entitled 'Krebs and his trinity of cycles' commenting that every school biology student knows of the Krebs cycle, but few know that Krebs discovered two other cycles. These are (i) the ornithine cycle (urea cycle), (ii) the citric acid cycle (tricarboxylic acid or TCA cycle), and (iii) the glyoxylate cycle that was described by Krebs and Kornberg. Ironically, Kornberg, codiscoverer of the 'glyoxylate cycle', overlooked a fourth Krebs cycle - (iv) the uric acid cycle. Copyright © 2018 Elsevier Ltd. All rights reserved.

Solvent Effects in Asymmetric Hetero Diels-Alder and Ene Reactions

DEFF Research Database (Denmark)

Johannsen, Mogens; Jørgensen, Karl Anker

1996-01-01

The use of polar solvents such as nitromethane or 2-nitropropane leads to a significant improvement of the catalytic properties of a cationic copper-Lewis acid in the hetero Diels-Alder reaction of alkyl glyoxylates with dienes; The scope of a newly developed copper(II)-bisoxazoline catalyst...... for the hetero Diels-Alder reaction is demonstrated by the reaction of different dienes with alkyl glyoxylates in nitroalkane solvents with the formation of the hetero Diels-Alder adduct in high enantiomeric excess as the major product. The synthetic application of the reaction is exemplified by an improved...

A free cyanohydrin as arms and armour of Marasmius oreades.

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Caspar, Jan; Spiteller, Peter

2015-03-02

Cyanogenic plants and fungi are widespread in nature. Although the origin of hydrocyanic acid in plants has been studied in detail, little is known about its origin in fungi. Here, we report the identification of the cyanohydrin of glyoxylic acid as the precursor of hydrocyanic acid in the fungus Marasmius oreades and several other cyanogenic fungi. Moreover, a feeding experiment revealed glycine as biosynthetic precursor of the cyanohydrin of glyoxylic acid. Thus, the cyanogenesis of M. oreades and other fungi is fundamentally different from cyanogenesis in plants. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Clustering mechanism of oxocarboxylic acids involving hydration reaction: Implications for the atmospheric models

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Liu, Ling; Kupiainen-Määttä, Oona; Zhang, Haijie; Li, Hao; Zhong, Jie; Kurtén, Theo; Vehkamäki, Hanna; Zhang, Shaowen; Zhang, Yunhong; Ge, Maofa; Zhang, Xiuhui; Li, Zesheng

2018-06-01

The formation of atmospheric aerosol particles from condensable gases is a dominant source of particulate matter in the boundary layer, but the mechanism is still ambiguous. During the clustering process, precursors with different reactivities can induce various chemical reactions in addition to the formation of hydrogen bonds. However, the clustering mechanism involving chemical reactions is rarely considered in most of the nucleation process models. Oxocarboxylic acids are common compositions of secondary organic aerosol, but the role of oxocarboxylic acids in secondary organic aerosol formation is still not fully understood. In this paper, glyoxylic acid, the simplest and the most abundant atmospheric oxocarboxylic acid, has been selected as a representative example of oxocarboxylic acids in order to study the clustering mechanism involving hydration reactions using density functional theory combined with the Atmospheric Clusters Dynamic Code. The hydration reaction of glyoxylic acid can occur either in the gas phase or during the clustering process. Under atmospheric conditions, the total conversion ratio of glyoxylic acid to its hydration reaction product (2,2-dihydroxyacetic acid) in both gas phase and clusters can be up to 85%, and the product can further participate in the clustering process. The differences in cluster structures and properties induced by the hydration reaction lead to significant differences in cluster formation rates and pathways at relatively low temperatures.

Hanford waste vitrification plant hydrogen generation study: Preliminary evaluation of alternatives to formic acid

International Nuclear Information System (INIS)

King, R.B.; Bhattacharyya, N.K.; Kumar, V.

1996-02-01

Oxalic, glyoxylic, glycolic, malonic, pyruvic, lactic, levulinic, and citric acids as well as glycine have been evaluated as possible substitutes for formic acid in the preparation of feed for the Hanford waste vitrification plant using a non-radioactive feed stimulant UGA-12M1 containing substantial amounts of aluminum and iron oxides as well as nitrate and nitrite at 90C in the presence of hydrated rhodium trichloride. Unlike formic acid none of these carboxylic acids liberate hydrogen under these conditions and only malonic and citric acids form ammonia. Glyoxylic, glycolic, malonic, pyruvic, lactic, levulinic, and citric acids all appear to have significant reducing properties under the reaction conditions of interest as indicated by the observation of appreciable amounts of N 2 O as a reduction product of,nitrite or, less likely, nitrate at 90C. Glyoxylic, pyruvic, and malonic acids all appear to be unstable towards decarboxylation at 90C in the presence of Al(OH) 3 . Among the carboxylic acids investigated in this study the α-hydroxycarboxylic acids glycolic and lactic acids appear to be the most interesting potential substitutes for formic acid in the feed preparation for the vitrification plant because of their failure to produce hydrogen or ammonia or to undergo decarboxylation under the reaction conditions although they exhibit some reducing properties in feed stimulant experiments

A weak link in metabolism: the metabolic capacity for glycine ...

Indian Academy of Sciences (India)

Prakash

2009-12-03

Dec 3, 2009 ... glyoxylate, threonine and trimethyllysine (carnitine synthesis), most of them ...... Participation of glycine in porphyrin biosynthesis. Eight glycine ...... normal and streptozotocin-induced diabetic rats; J. Dent. Res. 63 23–27.

Topological analysis of carbon flux during multi-stress adaptation in Halomonas sp. AAD12

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Hilal Mangaoglu Yoruk

2015-11-01

Conclusions: The operation of the glyoxylate shunt as the major anaplerotic pathway and the degradation of 6-phosphogluconate through the Entner–Doudoroff Pathway were the major factors in causing a distinction between the observed phenotypes.

Synthetic Progress toward Azadirachtins. 2. Enantio- and Diastereoselective Synthesis of the Right-Wing Fragment of 11-epi-Azadirachtin I.

Science.gov (United States)

Tan, Ceheng; Chen, Wei; Mu, Xinpeng; Chen, Qi; Gong, Jianxian; Luo, Tuoping; Yang, Zhen

2015-05-15

A stereoselective three-component coupling reaction of allylzinc bromide, silyl glyoxylate, and a β-lactone has been developed. This has been successfully applied to the enantio- and diastereoselective synthesis of the fully functionalized furopyran moiety of azadirachtins.

Oxidation of aqueous EDTA and associated organics and coprecipitation of inorganics by ambient iron-mediated aeration.

Science.gov (United States)

Englehardt, James D; Meeroff, Daniel E; Echegoyen, Luis; Deng, Yang; Raymo, Françisco M; Shibata, Tomoyuki

2007-01-01

Cationic metal and radionuclide contaminants can be extracted from soils to groundwater with sequestering agents such as EDTA. However, EDTA must then be removed fromthe groundwater, by advanced oxidation or specialized biological treatment. In this work, aqueous individual metal-EDTA solutions were aerated with steel wool for 25 h, at ambient pH, temperature, and pressure. Removal of approximately 99% of EDTA (0.09-1.78 mM); glyoxylic acid (0.153 mM); chelated Cd2+ (0.94 and 0.0952 mM), Pb2+ (0.0502 mM), and Hg2+ (0.0419 mM); and free chromate and vanadate was shown. EDTA was oxidized to glyoxylic acid and formaldehyde, and metals/metalloids were coprecipitated together with iron oxyhydroxide floc. Free arsenite and arsenate were each removed at 99.97%. Free Sr2+, and chelated Ni2+ were removed at 92% and 63%, respectively. Similar removals were obtained from mixtures, including 99.996+/-0.004% removal of total arsenic (95% confidence). Traces of iminodiacetic acid, nitrilotriacetic acid, and ethylenediaminetriacetic acid were detected after 25 h. Results are consistent with first-order, solution-phase oxidation of EDTA and glyoxylic acid by ferryl ion and H202, respectively, with inhibition due to sludge accumulation, and equilibrium metal coprecipitation. This ambient process, to our knowledge previously unknown, agrees with recently reported findings and shows promise for remediation of metals, metalloids, and radionuclides in wastewater, soil, and sediment.

In silico Support for Eschenmoser’s Glyoxylate Scenario

DEFF Research Database (Denmark)

Andersen, Jakob Lykke; Flamm, Christoph; Merkle, Daniel

2015-01-01

A core topic of research in prebiotic chemistry is the search for plausible synthetic routes that connect the building blocks of modern life, such as sugars, nucleotides, amino acids, and lipids to “molecular food sources” that were likely to have been abundant on early Earth. In a recent contrib...

Ach1 is involved in shuttling mitochondrial acetyl units for cytosolic C2 provision in Saccharomyces cerevisiae lacking pyruvate decarboxylase

DEFF Research Database (Denmark)

Chen, Yun; Zhang, Yiming; Siewers, Verena

2015-01-01

Saccharomyces cerevisiae, acetyl-CoA is compartmentalized in the cytosol, mitochondrion, peroxisome and nucleus, and cannot be directly transported between these compartments. With the acetyl-carnitine or glyoxylate shuttle, acetyl-CoA produced in peroxisomes or the cytoplasm can be transported...

Physiological role of vitamin B12 in a methanol-utilizing bacterium, Protaminobacter ruber

International Nuclear Information System (INIS)

Shimizu, S.; Ueda, S.; Sato, K.

1984-01-01

The methanol-utilizing bacterium Protaminobacter ruber is able to produce a relatively large amount of vitamin B 12 . The present study aims at the physiological role of vitamin B 12 in P. ruber. P. ruber was found to contain the two sequential reactions of glutamate mutase with β-methylaspartase and propionyl-CoA carboxylase with methylmalonyl-CoA mutase. Considering the presence of these enzyme systems and the reaction from mesaconyl-CoA to glyoxylate and propionyl-CoA, it could be considered that the formation of glutamate from α-ketoglutarate, the conversion of glutamate to mesaconate via β-methylaspartate, the activation of mesaconate with CoA to form mesaconyl-CoA, the cleavage of mesaconyl-CoA to glyoxylate and propionyl-CoA, the carboxylation of propionyl-CoA to methylmalonyl-CoA, and the isomerization of methylmalonyl-CoA to succinyl-CoA require cobalamine as a cofactor. 29 refs., 2 figs., 2 tabs

Differential content of glyphosate and its metabolites in Digitaria insularis biotypes

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Leonardo Bianco de Carvalho

2013-07-01

Full Text Available Experiments were carried out in controlled conditions to analyze the role of metabolism of glyphosate in Digitaria insularis (sourgrass biotypes with differential response to the herbicide. Contents of glyphosate, aminomethylphosphonic acid (AMPA, glyoxylate, and sarcosine was detected in leaf tissues by using reversed-polarity capillarity electrophoresis. Glyphosate content in the A biotype increased from 19.7 up to 65.5 µg g fresh weight-1, whereas decreasing from 19.9 down to 5.0 µg g fresh weight-1 in the B biotype, from 48 up to 168 hours after treatment. At 168 hours after treatment, percentage of the sum of AMPA, glyoxylate, and sarcosine was > 56% in the B biotype, whereas a small percentage of metabolites (< 10% was found in the A biotype. Thus, the faster herbicide degradation in the B biotype is evidence that a differential metabolism of glyphosate can be conferring its lesser susceptibility to the herbicide.

ald of Mycobacterium tuberculosis Encodes both the Alanine Dehydrogenase and the Putative Glycine Dehydrogenase

Science.gov (United States)

Giffin, Michelle M.; Modesti, Lucia; Raab, Ronald W.; Wayne, Lawrence G.

2012-01-01

The putative glycine dehydrogenase of Mycobacterium tuberculosis catalyzes the reductive amination of glyoxylate to glycine but not the reverse reaction. The enzyme was purified and identified as the previously characterized alanine dehydrogenase. The Ald enzyme was expressed in Escherichia coli and had both pyruvate and glyoxylate aminating activities. The gene, ald, was inactivated in M. tuberculosis, which resulted in the loss of all activities. Both enzyme activities were found associated with the cell and were not detected in the extracellular filtrate. By using an anti-Ald antibody, the protein was localized to the cell membrane, with a smaller fraction in the cytosol. None was detected in the extracellular medium. The ald knockout strain grew without alanine or glycine and was able to utilize glycine but not alanine as a nitrogen source. Transcription of ald was induced when alanine was the sole nitrogen source, and higher levels of Ald enzyme were measured. Ald is proposed to have several functions, including ammonium incorporation and alanine breakdown. PMID:22210765

Integrated Analysis of the Effects of Cold and Dehydration on Rice Metabolites, Phytohormones, and Gene Transcripts1[W][OPEN

Science.gov (United States)

Maruyama, Kyonoshin; Urano, Kaoru; Yoshiwara, Kyouko; Morishita, Yoshihiko; Sakurai, Nozomu; Suzuki, Hideyuki; Kojima, Mikiko; Sakakibara, Hitoshi; Shibata, Daisuke; Saito, Kazuki; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko

2014-01-01

Correlations between gene expression and metabolite/phytohormone levels under abiotic stress conditions have been reported for Arabidopsis (Arabidopsis thaliana). However, little is known about these correlations in rice (Oryza sativa ‘Nipponbare’), despite its importance as a model monocot. We performed an integrated analysis to clarify the relationships among cold- and dehydration-responsive metabolites, phytohormones, and gene transcription in rice. An integrated analysis of metabolites and gene expression indicated that several genes encoding enzymes involved in starch degradation, sucrose metabolism, and the glyoxylate cycle are up-regulated in rice plants exposed to cold or dehydration and that these changes are correlated with the accumulation of glucose (Glc), fructose, and sucrose. In particular, high expression levels of genes encoding isocitrate lyase and malate synthase in the glyoxylate cycle correlate with increased Glc levels in rice, but not in Arabidopsis, under dehydration conditions, indicating that the regulation of the glyoxylate cycle may be involved in Glc accumulation under dehydration conditions in rice but not Arabidopsis. An integrated analysis of phytohormones and gene transcripts revealed an inverse relationship between abscisic acid (ABA) signaling and cytokinin (CK) signaling under cold and dehydration stresses; these stresses increase ABA signaling and decrease CK signaling. High levels of Oryza sativa 9-cis-epoxycarotenoid dioxygenase transcripts correlate with ABA accumulation, and low levels of Cytochrome P450 (CYP) 735A transcripts correlate with decreased levels of a CK precursor in rice. This reduced expression of CYP735As occurs in rice but not Arabidopsis. Therefore, transcriptional regulation of CYP735As might be involved in regulating CK levels under cold and dehydration conditions in rice but not Arabidopsis. PMID:24515831

Malate and fumarate extend lifespan in Caenorhabditis elegans.

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Clare B Edwards

Full Text Available Malate, the tricarboxylic acid (TCA cycle metabolite, increased lifespan and thermotolerance in the nematode C. elegans. Malate can be synthesized from fumarate by the enzyme fumarase and further oxidized to oxaloacetate by malate dehydrogenase with the accompanying reduction of NAD. Addition of fumarate also extended lifespan, but succinate addition did not, although all three intermediates activated nuclear translocation of the cytoprotective DAF-16/FOXO transcription factor and protected from paraquat-induced oxidative stress. The glyoxylate shunt, an anabolic pathway linked to lifespan extension in C. elegans, reversibly converts isocitrate and acetyl-CoA to succinate, malate, and CoA. The increased longevity provided by malate addition did not occur in fumarase (fum-1, glyoxylate shunt (gei-7, succinate dehydrogenase flavoprotein (sdha-2, or soluble fumarate reductase F48E8.3 RNAi knockdown worms. Therefore, to increase lifespan, malate must be first converted to fumarate, then fumarate must be reduced to succinate by soluble fumarate reductase and the mitochondrial electron transport chain complex II. Reduction of fumarate to succinate is coupled with the oxidation of FADH2 to FAD. Lifespan extension induced by malate depended upon the longevity regulators DAF-16 and SIR-2.1. Malate supplementation did not extend the lifespan of long-lived eat-2 mutant worms, a model of dietary restriction. Malate and fumarate addition increased oxygen consumption, but decreased ATP levels and mitochondrial membrane potential suggesting a mild uncoupling of oxidative phosphorylation. Malate also increased NADPH, NAD, and the NAD/NADH ratio. Fumarate reduction, glyoxylate shunt activity, and mild mitochondrial uncoupling likely contribute to the lifespan extension induced by malate and fumarate by increasing the amount of oxidized NAD and FAD cofactors.

Multicomponent Synthesis of a N-Protected Alpha-Amino Ester: Ethyl 2-((4-Methoxyphenyl)Amino)-3-Phenylpropanoate

Science.gov (United States)

Le Gall, Erwan; Pignon, Antoine

2012-01-01

This laboratory experiment describes the preparation of a N-protected phenylalanine ethyl ester by a zinc-mediated Mannich-like multicomponent reaction between benzyl bromide, "p"-anisidine, and ethyl glyoxylate. The one-step reaction involves the in situ metallation of benzyl bromide into a benzylzinc reagent and its addition onto imine (Barbier…

Arabidopsis thaliana ggt1 photorespiratory mutants maintain leaf carbon/nitrogen balance by reducing RuBisCO content and plant growth.

Science.gov (United States)

Dellero, Younès; Lamothe-Sibold, Marlène; Jossier, Mathieu; Hodges, Michael

2015-09-01

Metabolic and physiological analyses of glutamate:glyoxylate aminotransferase 1 (GGT1) mutants were performed at the global leaf scale to elucidate the mechanisms involved in their photorespiratory growth phenotype. Air-grown ggt1 mutants showed retarded growth and development, that was not observed at high CO2 (3000 μL L(-1) ). When compared to wild-type (WT) plants, air-grown ggt1 plants exhibited glyoxylate accumulation, global changes in amino acid amounts including a decrease in serine content, lower organic acid levels, and modified ATP/ADP and NADP(+) /NADPH ratios. When compared to WT plants, their net CO2 assimilation rates (An ) were 50% lower and this mirrored decreases in ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) contents. High CO2 -grown ggt1 plants transferred to air revealed a rapid decrease of An and photosynthetic electron transfer rate while maintaining a high energetic state. Short-term (a night period and 4 h of light) transferred ggt1 leaves accumulated glyoxylate and exhibited low serine contents, while other amino acid levels were not modified. RuBisCO content, activity and activation state were not altered after a short-term transfer while the ATP/ADP ratio was lowered in ggt1 rosettes. However, plant growth and RuBisCO levels were both reduced in ggt1 leaves after a long-term (12 days) acclimation to air from high CO2 when compared to WT plants. The data are discussed with respect to a reduced photorespiratory carbon recycling in the mutants. It is proposed that the low An limits nitrogen-assimilation, this decreases leaf RuBisCO content until plants attain a new homeostatic state that maintains a constant C/N balance and leads to smaller, slower growing plants. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Transcriptional profiling of extracellular amino acid sensing in Saccharomyces cerevisiae and the role of Stp1p and Stp2p

DEFF Research Database (Denmark)

Eckert-Boulet, Nadine; Nielsen, P.S.; Friis, Carsten

2004-01-01

Tdh1p and glucokinase (Glk1p), shows increased transcription levels in either or both of the mutants. Also, most of the structural genes involved in trehalose and glycogen synthesis and a few genes in the glyoxylate cycle and the pentose phosphate pathway are derepressed in the ssy1 and stp1 stp2...

Kaleidoscopic Views in the Bone Marrow: Oxalate Crystals in a Patient Presenting with Bicytopenia

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Yelda Dere

2016-03-01

Full Text Available Pancytopenia associated with BM infiltration of different deposits is a rare condition mostly associated with amyloidosis or the accumulation of iron. One of the rarest deposits in the BM is oxalate crystals due to hyperoxaluria [1,2,3]. Primary hyperoxaluria, a genetic disorder due to mutation in the alanine glyoxylate aminotransferase gene, located on chromosome 2q37.3 and resulting in the conversion of glyoxylate to oxalate, is characterized by increased production of oxalic acid because of the specific liver enzyme deficiency and generally presents with renal stones, renal or liver failure, and oxalosis [4]. Calcium oxalate may even be deposited into various tissues such as those of the retina, peripheral nerves, arterial media, and heart [4,5]. The medical history of nephrolithiasis at early ages, characteristic appearance of birefringent crystals forming rosettes in the BM, and the envelope-like forms in the BM aspirates seen in our case supported the diagnosis of primary hyperoxaluria, which is best confirmed by genetic studies and treated with liver transplantation because of the location of the abnormal enzymes in the hepatocytes.

Cloning and expression of isocitrate lyase from human round worm Strongyloides stercoralis

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Siddiqui A.A.

2000-09-01

Full Text Available A full length cDNA (1463 bp encoding isocitrate lyase (EC 4.1.3.1 of Strongyloides stercoralis is described. The nucleotide sequence of this insert identified a cDNA coding for the isocitrate lyase. The conceptually translated amino acid sequence of the open reading frame for S. stercoralis isocitrate lyase encodes a 450 amino acid residue protein with an apparent molecular weight of 50 kDa and a predicted pl of 6.39. The sequence is 69 % A/T, reflecting a characteristic A/T codon bias of S. stercoralis. The amino acid sequence of S. stercoralis isocitrate lyase is compared with bifunctional glyoxylate cycle protein of Caenorhabditis elegans and isocitrate lyases from Chlamydomonas reinhardtii and Myxococcus xanthus. The full length cDNA of S. stercoralis was expressed in pRSET vector and bacteriophage T7 promoter based expression system. S. stercoralis lyase recombinant protein, purified via immobilized metal affinity chromatography, showed a molecular mass of 50 kDa on polyacrylamide gels. The role of isocitrate lyase in the glyoxylate cycle and energy metabolism of S. stercoralis is also discussed.

Improving Properties of a Novel β-Galactosidase from Lactobacillus plantarum by Covalent Immobilization

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Rocio Benavente

2015-04-01

Full Text Available A novel β-galactosidase from Lactobacillus plantarum (LPG was over-expressed in E. coli and purified via a single chromatographic step by using lowly activated IMAC (immobilized metal for affinity chromatography supports. The pure enzyme exhibited a high hydrolytic activity of 491 IU/mL towards o-nitrophenyl β-d-galactopyranoside. This value was conserved in the presence of different divalent cations and was quite resistant to the inhibition effects of different carbohydrates. The pure multimeric enzyme was stabilized by multipoint and multisubunit covalent attachment on glyoxyl-agarose. The glyoxyl-LPG immobilized preparation was over 20-fold more stable than the soluble enzyme or the one-point CNBr-LPG immobilized preparation at 50 °C. This β-galactosidase was successfully used in the hydrolysis of lactose and lactulose and formation of different oligosaccharides was detected. High production of galacto-oligosaccharides (35% and oligosaccharides derived from lactulose (30% was found and, for the first time, a new oligosaccharide derived from lactulose, tentatively identified as 3'-galactosyl lactulose, has been described.

Potential Inhibitors for Isocitrate Lyase of Mycobacterium tuberculosis and Non-M. tuberculosis: A Summary

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Yie-Vern Lee

2015-01-01

Full Text Available Isocitrate lyase (ICL is the first enzyme involved in glyoxylate cycle. Many plants and microorganisms are relying on glyoxylate cycle enzymes to survive upon downregulation of tricarboxylic acid cycle (TCA cycle, especially Mycobacterium tuberculosis (MTB. In fact, ICL is a potential drug target for MTB in dormancy. With the urge for new antitubercular drug to overcome tuberculosis treat such as multidrug resistant strain and HIV-coinfection, the pace of drug discovery has to be increased. There are many approaches to discovering potential inhibitor for MTB ICL and we hereby review the updated list of them. The potential inhibitors can be either a natural compound or synthetic compound. Moreover, these compounds are not necessary to be discovered only from MTB ICL, as it can also be discovered by a non-MTB ICL. Our review is categorized into four sections, namely, (a MTB ICL with natural compounds; (b MTB ICL with synthetic compounds; (c non-MTB ICL with natural compounds; and (d non-MTB ICL with synthetic compounds. Each of the approaches is capable of overcoming different challenges of inhibitor discovery. We hope that this paper will benefit the discovery of better inhibitor for ICL.

Enhancing succinic acid biosynthesis in Escherichia coli by engineering its global transcription factor, catabolite repressor/activator (Cra).

Science.gov (United States)

Zhu, Li-Wen; Xia, Shi-Tao; Wei, Li-Na; Li, Hong-Mei; Yuan, Zhan-Peng; Tang, Ya-Jie

2016-11-04

This study was initiated to improve E. coli succinate production by engineering the E. coli global transcription factor, Cra (catabolite repressor/activator). Random mutagenesis libraries were generated through error-prone PCR of cra. After re-screening and mutation site integration, the best mutant strain was Tang1541, which provided a final succinate concentration of 79.8 ± 3.1 g/L: i.e., 22.8% greater than that obtained using an empty vector control. The genes and enzymes involved in phosphoenolpyruvate (PEP) carboxylation and the glyoxylate pathway were activated, either directly or indirectly, through the mutation of Cra. The parameters for interaction of Cra and DNA indicated that the Cra mutant was bound to aceBAK, thereby activating the genes involved in glyoxylate pathway and further improving succinate production even in the presence of its effector fructose-1,6-bisphosphate (FBP). It suggested that some of the negative effect of FBP on Cra might have been counteracted through the enhanced binding affinity of the Cra mutant for FBP or the change of Cra structure. This work provides useful information about understanding the transcriptional regulation of succinate biosynthesis.

Biosynthetic mechanism of glycolate in Chromatium, 4

International Nuclear Information System (INIS)

Asami, Sumio; Takabe, Tetsuo; Akazawa, Takashi

1977-01-01

The metabolic transformation of glycolate to glycine occurring in photosynthesizing cells of Chromatium was investigated by the radioisotopic technique and by amino acid analysis. By analyzing the distribution of radiocarbon upon feeding (1- 14 C) glycolate, (2- 14 C) glyoxylate and (1- 14 C) glycine to bacterial cells, it was demonstrated that glycolate is converted to glycine via glyoxylate, and both glycolate and glycine are excreted extracellularly. Although the formation of serine was barely detected by the above two techniques in both N 2 and O 2 atmospheres, it was found that 14 CO 2 is evolved quite markedly from both (1- 14 C) glycolate and (1- 14 C) glycine fed to the Chromatium cells. Analytical results of transient changes in amino acid compositions under atmospheric changes of N 2 →O 2 and by the addition of exogenous glycolate in N 2 confirm the notion that glycolate is converted to glycine. Acidic amino acids (glutamic acid and aspartic acid) appear to take part in glycine formation as amino donors. The formation of glycine from glycolate in a N 2 atmosphere suggests that an unknown glycolate dehydrogenation reaction may operate in the overall process. (auth.)

Immobilized Lipases on Functionalized Silica Particles as Potential Biocatalysts for the Synthesis of  Fructose Oleate in an Organic Solvent/Water System

OpenAIRE

Vinicius Vescovi; Raquel L. C. Giordano; Adriano A. Mendes; Paulo W. Tardioli

2017-01-01

Lipases from Thermomyces lanuginosus (TLL) and Pseudomonas fluorescens (PFL) wereimmobilized on functionalized silica particles aiming their use in the synthesis of fructose oleate in a tert‐butyl alcohol/water system. Silica particles were chemically modified with octyl (OS), octyl plus glutaraldehyde (OSGlu), octyl plus glyoxyl(OSGlx), and octyl plus epoxy groups(OSEpx). PFL was hyperactivated on all functionalized supports (more than 100% recovered activity) using low protein loading (1 mg...

Glyoxylate as a reducing agent for manganese(III) in salen scaffold ...

Indian Academy of Sciences (India)

being the monohydrate gem-diol forms) followed by the slow electron transfer ... stress and implicated as possible therapeutic agents .... excess HGl at different pHs (1.8–2.5) were set aside ...... sion (UGC), New Delhi in terms of a Teacher Fel-.

Facultative methanotrophy: false leads, true results, and suggestions for future research.

Science.gov (United States)

Semrau, Jeremy D; DiSpirito, Alan A; Vuilleumier, Stéphane

2011-10-01

Methanotrophs are a group of phylogenetically diverse microorganisms characterized by their ability to utilize methane as their sole source of carbon and energy. Early studies suggested that growth on methane could be stimulated with the addition of some small organic acids, but initial efforts to find facultative methanotrophs, i.e., methanotrophs able to utilize compounds with carbon-carbon bonds as sole growth substrates were inconclusive. Recently, however, facultative methanotrophs in the genera Methylocella, Methylocapsa, and Methylocystis have been reported that can grow on acetate, as well as on larger organic acids or ethanol for some species. All identified facultative methanotrophs group within the Alphaproteobacteria and utilize the serine cycle for carbon assimilation from formaldehyde. It is possible that facultative methanotrophs are able to convert acetate into intermediates of the serine cycle (e.g. malate and glyoxylate), because a variety of acetate assimilation pathways convert acetate into these compounds (e.g. the glyoxylate shunt of the tricarboxylic acid cycle, the ethylmalonyl-CoA pathway, the citramalate cycle, and the methylaspartate cycle). In this review, we summarize the history of facultative methanotrophy, describe scenarios for the basis of facultative methanotrophy, and pose several topics for future research in this area. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Metabolism of allantoin in soybeans

International Nuclear Information System (INIS)

Winkler, R.G.; Polacco, J.C.; Blevins, D.G.; Randall, D.D.

1986-01-01

The metabolism of [2-7 14 C] and [4-5 14 C] allantoin has been studied in intact leaf tissue to elucidate the pathway of allantoin catabolism and its regulation. 1.3 mM [2-7 14 C] and 1.3 mM [4-5 14 C] DL allantoin release 14 CO 2 from intact leaf discs at 0.9 and 0.08 μmoles.hr -1 .g fresh wt -1 respectively. The most potent urease inhibitor known, phenyl phosphordiamidate (PPD), inhibited urease in intact tissue at concentrations from 0.1 mM to 10 mM. In contrast 14 CO 2 release from [2-7 14 C] and [4-5 14 C] allantoin was not inhibited by 1 mM PPD in 0.5 h and 1 h assays. These data are consistent with allantoate amido-hydrolase action. Intact tissue discs were incubated with [4-5 14 C] allantoin and analyzed for catabolites by ion exclusion HPLC. Allantoate, ureidoglycolate, and glyoxylate were identified by their retention time. Two 14 C labelled peaks did not migrate with known standards. They are being characterized to identify their structure. These data are consistent with a pathway of catabolism including allantoate, ureidoglycolate and glyoxylate, NH 3 and CO 2

A metabolomics-based method for studying the effect of yfcC gene in Escherichia coli on metabolism.

Science.gov (United States)

Wang, Xiyue; Xie, Yuping; Gao, Peng; Zhang, Sufang; Tan, Haidong; Yang, Fengxu; Lian, Rongwei; Tian, Jing; Xu, Guowang

2014-04-15

Metabolomics is a potent tool to assist in identifying the function of unknown genes through analysis of metabolite changes in the context of varied genetic backgrounds. However, the availability of a universal unbiased profiling analysis is still a big challenge. In this study, we report an optimized metabolic profiling method based on gas chromatography-mass spectrometry for Escherichia coli. It was found that physiological saline at -80°C could ensure satisfied metabolic quenching with less metabolite leakage. A solution of methanol/water (21:79, v/v) was proved to be efficient for intracellular metabolite extraction. This method was applied to investigate the metabolome difference among wild-type E. coli, its yfcC deletion, and overexpression mutants. Statistical and bioinformatic analysis of the metabolic profiling data indicated that the expression of yfcC potentially affected the metabolism of glyoxylate shunt. This finding was further validated by real-time quantitative polymerase chain reactions showing that expression of aceA and aceB, the key genes in glyoxylate shunt, was upregulated by yfcC. This study exemplifies the robustness of the proposed metabolic profiling analysis strategy and its potential roles in investigating unknown gene functions in view of metabolome difference. Copyright © 2014 Elsevier Inc. All rights reserved.

Time course metabolome of Roux-en-Y gastric bypass confirms correlation between leptin, body weight and the microbiome.

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Loqmane Seridi

Full Text Available Roux-en-Y gastric bypass (RYGB is an effective way to lose weight and reverse type 2 diabetes. We profiled the metabolome of 18 obese patients (nine euglycemic and nine diabetics that underwent RYGB surgery and seven lean subjects. Plasma samples from the obese patients were collected before the surgery and one week and three months after the surgery. We analyzed the metabolome in association to five hormones (Adiponectin, Insulin, Ghrelin, Leptin, and Resistin, four peptide hormones (GIP, Glucagon, GLP1, and PYY, and two cytokines (IL-6 and TNF. PCA showed samples cluster by surgery time and many microbially driven metabolites (indoles in particular correlated with the three months after the surgery. Network analysis of metabolites revealed a connection between carbohydrate (mannosamine and glucosamine and glyoxylate and confirms glyoxylate association to diabetes. Only leptin and IL-6 had a significant association with the measured metabolites. Leptin decreased immediately after RYGB (before significant weight loss, whereas IL-6 showed no consistent response to RYGB. Moreover, leptin associated with tryptophan in support of the possible role of leptin in the regulation of serotonin synthesis pathways in the gut. These results suggest a potential link between gastric leptin and microbial-derived metabolites in the context of obesity and diabetes.

Ethanol and Acetate Acting as Carbon/Energy Sources Negatively Affect Yeast Chronological Aging

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Ivan Orlandi

2013-01-01

Full Text Available In Saccharomyces cerevisiae, the chronological lifespan (CLS is defined as the length of time that a population of nondividing cells can survive in stationary phase. In this phase, cells remain metabolically active, albeit at reduced levels, and responsive to environmental signals, thus simulating the postmitotic quiescent state of mammalian cells. Many studies on the main nutrient signaling pathways have uncovered the strong influence of growth conditions, including the composition of culture media, on CLS. In this context, two byproducts of yeast glucose fermentation, ethanol and acetic acid, have been proposed as extrinsic proaging factors. Here, we report that ethanol and acetic acid, at physiological levels released in the exhausted medium, both contribute to chronological aging. Moreover, this combined proaging effect is not due to a toxic environment created by their presence but is mainly mediated by the metabolic pathways required for their utilization as carbon/energy sources. In addition, measurements of key enzymatic activities of the glyoxylate cycle and gluconeogenesis, together with respiration assays performed in extreme calorie restriction, point to a long-term quiescent program favoured by glyoxylate/gluconeogenesis flux contrary to a proaging one based on the oxidative metabolism of ethanol/acetate via TCA and mitochondrial respiration.

Metabolism of chlorofluorocarbons and polybrominated compounds by Pseudomonas putida G786(pHG-2) via an engineered metabolic pathway.

OpenAIRE

Hur, H G; Sadowsky, M J; Wackett, L P

1994-01-01

The recombinant bacterium Pseudomonas putida G786(pHG-2) metabolizes pentachloroethane to glyoxylate and carbon dioxide, using cytochrome P-450CAM and toluene dioxygenase to catalyze consecutive reductive and oxidative dehalogenation reactions (L.P. Wackett, M.J. Sadowsky, L.N. Newman, H.-G. Hur, and S. Li, Nature [London] 368:627-629, 1994). The present study investigated metabolism of brominated and chlorofluorocarbon compounds by the recombinant strain. Under anaerobic conditions, P. putid...

Characterization and Neutralization of Arsenical-Based WWII Era Chemical Munition Fills

Science.gov (United States)

2006-08-01

of 4. Oxalic glycolic, and glyoxylic acids were the major products formed at pH values of 6 and 8. The final step is the oxidation of organic acids ...54 22. Summary of Analytical Results for the Nitric Acid Reagent ............................ 55 23. Summary of Properties of 20 wt... acid (DPAOA). Other arsenic-containing degradation products analyzed for by CE include the inorganic components, arsenate (AsO4) and m-arsenite (AsO2

Porphyromonas uenonis sp. nov., a Pathogen for Humans Distinct from P. asaccharolytica and P. endodontalis

OpenAIRE

Finegold, Sydney M.; Vaisanen, Marja-Liisa; Rautio, Merja; Eerola, Erkki; Summanen, Paula; Molitoris, Denise; Song, Yuli; Liu, Chengxu; Jousimies-Somer, Hannele

2004-01-01

Three Porphyromonas species (Porphyromonas asaccharolytica, P. endodontalis, and the novel species that is the subject of the present report, P. uenonis) are very much alike in terms of biochemical characteristics, such as enzyme profiles and cellular fatty acid contents. P. asaccharolytica is distinguished from the other two species by virtue of production of α-fucosidase and glyoxylic acid positivity. The novel species is difficult to differentiate from P. endodontalis phenotypically and wa...

The Aspergillus nidulans acuL gene encodes a mitochondrial carrier required for the utilization of carbon sources that are metabolized via the TCA cycle.

Science.gov (United States)

Flipphi, Michel; Oestreicher, Nathalie; Nicolas, Valérie; Guitton, Audrey; Vélot, Christian

2014-07-01

In Aspergillus nidulans, the utilization of acetate as sole carbon source requires several genes (acu). Most of them are also required for the utilization of fatty acids. This is the case for acuD and acuE, which encode the two glyoxylate cycle-specific enzymes, isocitrate lyase and malate synthase, respectively, but also for acuL that we have identified as AN7287, and characterized in this study. Deletion of acuL resulted in the same phenotype as the original acuL217 mutant. acuL encodes a 322-amino acid protein which displays all the structural features of a mitochondrial membrane carrier, and shares 60% identity with the Saccharomyces cerevisiae succinate/fumarate mitochondrial antiporter Sfc1p (also named Acr1p). Consistently, the AcuL protein was shown to localize in mitochondria, and partial cross-complementation was observed between the S. cerevisiae and A. nidulans homologues. Extensive phenotypic characterization suggested that the acuL gene is involved in the utilization of carbon sources that are catabolized via the TCA cycle, and therefore require gluconeogenesis. In addition, acuL proves to be co-regulated with acuD and acuE. Overall, our data suggest that AcuL could link the glyoxylate cycle to gluconeogenesis by exchanging cytoplasmic succinate for mitochondrial fumarate. Copyright © 2014 Elsevier Inc. All rights reserved.

Gene Expression Response of Trichophyton rubrum during Coculture on Keratinocytes Exposed to Antifungal Agents

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Tatiana Takahasi Komoto

2015-01-01

Full Text Available Trichophyton rubrum is the most common causative agent of dermatomycoses worldwide, causing infection in the stratum corneum, nails, and hair. Despite the high prevalence of these infections, little is known about the molecular mechanisms involved in the fungal-host interaction, particularly during antifungal treatment. The aim of this work was to evaluate the gene expression of T. rubrum cocultured with keratinocytes and treated with the flavonoid trans-chalcone and the glycoalkaloid α-solanine. Both substances showed a marked antifungal activity against T. rubrum strain CBS (MIC = 1.15 and 17.8 µg/mL, resp.. Cytotoxicity assay against HaCaT cells produced IC50 values of 44.18 to trans-chalcone and 61.60 µM to α-solanine. The interaction of keratinocytes with T. rubrum conidia upregulated the expression of genes involved in the glyoxylate cycle, ergosterol synthesis, and genes encoding proteases but downregulated the ABC transporter TruMDR2 gene. However, both antifungals downregulated the ERG1 and ERG11, metalloprotease 4, serine proteinase, and TruMDR2 genes. Furthermore, the trans-chalcone downregulated the genes involved in the glyoxylate pathway, isocitrate lyase, and citrate synthase. Considering the urgent need for more efficient and safer antifungals, these results contribute to a better understanding of fungal-host interactions and to the discovery of new antifungal targets.

Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli.

Science.gov (United States)

Sarkar, Dayanidhi; Siddiquee, Khandaker Al Zaid; Araúzo-Bravo, Marcos J; Oba, Takahiro; Shimizu, Kazuyuki

2008-11-01

To elucidate the physiological adaptation of Escherichia coli due to cra gene knockout, a total of 3,911 gene expressions were investigated by DNA microarray for continuous culture. About 50 genes were differentially regulated for the cra mutant. TCA cycle and glyoxylate shunt were down-regulated, while pentose phosphate (PP) pathway and Entner Doudoroff (ED) pathway were up-regulated in the cra mutant. The glucose uptake rate and the acetate production rate were increased with less acetate consumption for the cra mutant. To identify the genes controlled by Cra protein, the Cra recognition weight matrix from foot-printing data was developed and used to scan the whole genome. Several new Cra-binding sites were found, and some of the result was consistent with the DNA microarray data. The ED pathway was active in the cra mutant; we constructed cra.edd double genes knockout mutant to block this pathway, where the acetate overflowed due to the down-regulation of aceA,B and icd gene expressions. Then we further constructed cra.edd.iclR triple genes knockout mutant to direct the carbon flow through the glyoxylate pathway. The cra.edd.iclR mutant showed the least acetate production, resulting in the highest cell yield together with the activation of the glycolysis pathway, but the glucose consumption rate could not be improved.

Co-ordinate regulation of genes involved in storage lipid mobilization in Arabidopsis thaliana.

Science.gov (United States)

Rylott, E L; Hooks, M A; Graham, I A

2001-05-01

Molecular genetic approaches in the model plant Arabidopsis thaliana (Col0) are shedding new light on the role and control of the pathways associated with the mobilization of lipid reserves during oilseed germination and post-germinative growth. Numerous independent studies have reported on the expression of individual genes encoding enzymes from the three major pathways: beta-oxidation, the glyoxylate cycle and gluconeogenesis. However, a single comprehensive study of representative genes and enzymes from the different pathways in a single plant species has not been done. Here we present results from Arabidopsis that demonstrate the co-ordinate regulation of gene expression and enzyme activities for the acyl-CoA oxidase- and 3-ketoacyl-CoA thiolase-mediated steps of beta-oxidation, the isocitrate lyase and malate synthase steps of the glyoxylate cycle and the phosphoenolpyruvate carboxykinase step of gluconeogenesis. The mRNA abundance and enzyme activities increase to a peak at stage 2, 48 h after the onset of seed germination, and decline thereafter either to undetectable levels (for malate synthase and isocitrate lyase) or low basal levels (for the genes of beta-oxidation and gluconeogenesis). The co-ordinate induction of all these genes at the onset of germination raises the possibility that a global regulatory mechanism operates to induce the expression of genes associated with the mobilization of storage reserves during the heterotrophic growth period.

Overexpression of isocitrate lyase-glyoxylate bypass influence on metabolism in Aspergillus niger

DEFF Research Database (Denmark)

Meijer, Susan Lisette; Otero, José Manuel; Olivares Hernandez, Roberto

2009-01-01

of the cells was investigated. Inhibition of SDH was expected to lead to succinate production, but this was not observed. There was an increase in citrate and oxalate production in the wild-type strain. Furthermore, in the strain with over-expression of icl the organic acid production shifted from fumarate...... towards malate production when malonate was added to the cultivation medium. Overall, the icl over-expression and malonate addition had a significant impact on metabolism and on organic acid production profiles. Although the expected succinate and malate formation was not observed, a distinct...

The plant homolog to the human sodium/dicarboxylic cotransporter is the vacuolar malate carrier

OpenAIRE

Emmerlich, Vera; Linka, Nicole; Reinhold, Thomas; Hurth, Marco A.; Traub, Michaela; Martinoia, Enrico; Neuhaus, H. Ekkehard

2003-01-01

Malate plays a central role in plant metabolism. It is an intermediate in the Krebs and glyoxylate cycles, it is the store for CO2 in C4 and crassulacean acid metabolism plants, it protects plants from aluminum toxicity, it is essential for maintaining the osmotic pressure and charge balance, and it is therefore involved in regulation of stomatal aperture. To fulfil many of these roles, malate has to be accumulated within the large central vacuole. Many unsuccessful efforts have been made in ...

Asparagine and glycine metabolism in rat liver mitochondria and in mouse L5178Y lymphoma cells resistant or sensitive to the anticancer drug L-asparaginase

Energy Technology Data Exchange (ETDEWEB)

Keefer, J.F. Jr.

1986-01-01

Rat liver mitochondrial asparagine was found to be degraded via an aminotransferase and omega-amidase. Evidence includes oxaloacetate production from asparagine only when glyoxylate was added and production of radiolabeled ..cap alpha..-ketosuccinamate via metabolism of (U-/sup 14/C)asparagine. In the cytosol, asparagine is degraded primarily via asparaginase and subsequent transamination. A new HPLC technique for separation of citric acid cycle intermediates was developed using: ion pairing with 20 mM each to tetrabutylammonium hydroxide and Na/sub 2/SO/sub 4/; pH 7.0; isocratic elution; and detection at 210 nm. Amino acid content of mouse lymphoma cells either sensitive (L5178Y) or resistant (L5178Y/L-ASE) to the anticancer drug L-asparaginase was studied. The concentration of asparagine was 1.5 times higher and the concentrations of the essential amino acids histidine, methionine, valine and phenylalanine were two times higher in asparaginase-resistant than sensitive cells. In vivo but not in vitro studies indicated that glucine decreases in sensitive but not resistant cells upon asparaginase treatment. Asparagine and glycine metabolism was further studied using /sup 14/C radiolabel conversion of asparagine, glyoxylate, glycine and serine. Glycine metabolism is especially important in lymphomas and leukemias because these cells contain higher concentrations of glycine that other cancer and normal cells. Therefore, glycine levels were studied and were found to decrease in sensitive but not resistant cells upon asparaginase administration.

Metabolomics analysis of TiO2 nanoparticles induced toxicological effects on rice (Oryza sativa L.).

Science.gov (United States)

Wu, Biying; Zhu, Lizhong; Le, X Chris

2017-11-01

The wide occurrence and high environmental concentration of titanium dioxide nanoparticles (nano-TiO 2 ) have raised concerns about their potential toxic effects on crops. In this study, we employed a GC-MS-based metabolomic approach to investigate the potential toxicity of nano-TiO 2 on hydroponically-cultured rice (Oryza sativa L.) after exposed to 0, 100, 250 or 500 mg/L of nano-TiO 2 for fourteen days. Results showed that the biomass of rice was significantly decreased and the antioxidant defense system was significantly disturbed after exposure to nano-TiO 2 . One hundred and five identified metabolites showed significant difference compared to the control, among which the concentrations of glucose-6-phosphate, glucose-1-phosphate, succinic and isocitric acid were increased most, while the concentrations of sucrose, isomaltulose, and glyoxylic acid were decreased most. Basic energy-generating ways including tricarboxylic acid cycle and the pentose phosphate pathway, were elevated significantly while the carbohydrate synthesis metabolism including starch and sucrose metabolism, and glyoxylate and dicarboxylate metabolism were inhibited. However, the biosynthetic formation of most of the identified fatty acids, amino acids and secondary metabolites which correlated to crop quality, were increased. The results suggest that the metabolism of rice plants is distinctly disturbed after exposure to nano-TiO 2 , and nano-TiO 2 would have a mixed effect on the yield and quality of rice. Copyright © 2017 Elsevier Ltd. All rights reserved.

Regulation of flux through metabolic cycles

International Nuclear Information System (INIS)

Walsh, K.

1984-01-01

The branchpoint of the tricarboxylic acid and glyoxylate shunt was characterized in the intact organism by a multidimensional approach. Theory and methodology were developed to determine velocities for the net flow of carbon through the major steps of acetate metabolism in E. coli. Rates were assigned based on the 13 C-NMR spectrum of intracellular glutamate, measured rates of substrate incorporation into end products, the constituent composition of E. coli and a series of conservation equations which described the system at steady state. The in vivo fluxes through the branchpoint of the tricarboxylic acid and glyoxylate cycles were compared to rates calculated from the kinetic constants of the branchpoint enzymes and the intracellular concentrations of their substrates. These studies elucidated the role of isocitrate dehydrogenase phosphorylation in the Krebs cycle and led to the development of a generalized mathematical description of the sensitivity of branchpoints to regulatory control. This theoretical analysis was termed the branchpoint effect and it describes conditions which result in large changes in the flux through an enzyme even though that enzyme is not subject to direct regulatory control. The theoretical and experimental characterization of this system provided a framework to study the effects of enzyme overproduction and underproduction on metabolic processes in the cell. An in vivo method was developed to determine the extent to which an enzyme catalyzes a rate-controlling reaction. The enzyme chosen for this study was citrate synthase

Ambient iron-mediated aeration (IMA) for water reuse.

Science.gov (United States)

Deng, Yang; Englehardt, James D; Abdul-Aziz, Samer; Bataille, Tristan; Cueto, Josenrique; De Leon, Omar; Wright, Mary E; Gardinali, Piero; Narayanan, Aarthi; Polar, Jose; Tomoyuki, Shibata

2013-02-01

Global water shortages caused by rapidly expanding population, escalating water consumption, and dwindling water reserves have rendered water reuse a strategically significant approach to meet current and future water demand. This study is the first to our knowledge to evaluate the technical feasibility of iron-mediated aeration (IMA), an innovative, potentially economical, holistic, oxidizing co-precipitation process operating at room temperature, atmospheric pressure, and neutral pH, for water reuse. In the IMA process, dissolved oxygen (O₂) was continuously activated by zero-valent iron (Fe⁰) to produce reactive oxygen species (ROS) at ambient pH, temperature, and pressure. Concurrently, iron sludge was generated as a result of iron corrosion. Bench-scale tests were conducted to study the performance of IMA for treatment of secondary effluent, natural surface water, and simulated contaminated water. The following removal efficiencies were achieved: 82.2% glyoxylic acid, ~100% formaldehyde as an oxidation product of glyoxylic acid, 94% of Ca²⁺ and associated alkalinity, 44% of chemical oxygen demand (COD), 26% of electrical conductivity (EC), 98% of di-n-butyl phthalate (DBP), 80% of 17β-estradiol (E2), 45% of total nitrogen (TN), 96% of total phosphorus (TP), 99.8% of total Cr, >90% of total Ni, 99% of color, 3.2 log removal of total coliform, and 2.4 log removal of E. Coli. Removal was attributed principally to chemical oxidation, precipitation, co-precipitation, coagulation, adsorption, and air stripping concurrently occurring during the IMA treatment. Results suggest that IMA is a promising treatment technology for water reuse. Copyright © 2012 Elsevier Ltd. All rights reserved.

Directing vanillin production from ferulic acid by increased acetyl-CoA consumption in recombinant Escherichia coli.

Science.gov (United States)

Lee, Eun-Gyeong; Yoon, Sang-Hwal; Das, Amitabha; Lee, Sook-Hee; Li, Cui; Kim, Jae-Yean; Choi, Myung-Suk; Oh, Deok-Kun; Kim, Seon-Won

2009-01-01

The amplification of gltA gene encoding citrate synthase of TCA cycle was required for the efficient conversion of acetyl-CoA, generated during vanillin production from ferulic acid, to CoA, which is essential for vanillin production. Vanillin of 1.98 g/L was produced from the E. coli DH5alpha (pTAHEF-gltA) with gltA amplification in 48 h of culture at 3.0 g/L of ferulic acid, which was about twofold higher than the vanillin production of 0.91 g/L obtained by the E. coli DH5alpha (pTAHEF) without gltA amplification. The icdA gene encoding isocitrate dehydrogenase of TCA cycle was deleted to make the vanillin producing E. coli utilize glyoxylate bypass which enables more efficient conversion of acetyl-CoA to CoA in comparison with TCA cycle. The production of vanillin by the icdA null mutant of E. coli BW25113 harboring pTAHEF was enhanced by 2.6 times. The gltA amplification of the glyoxylate bypass in the icdA null mutant remarkably increased the production rate of vanillin with a little increase in the amount of vanillin production. The real synergistic effect of gltA amplification and icdA deletion was observed with use of XAD-2 resin reducing the toxicity of vanillin produced during culture. Vanillin of 5.14 g/L was produced in 24 h of the culture with molar conversion yield of 86.6%, which is the highest so far in vanillin production from ferulic acid using recombinant E. coli.

Thermal stability of products from self-irradiated Ca sup 14 CO sub 3

Energy Technology Data Exchange (ETDEWEB)

Albarran, G. (Universidad Nacional Autonoma de Mexico, Mexico City (Mexico). Inst. de Ciencias Nucleares); Collins, K.E.; Collins, C.H. (Universidade Estadual de Campinas, SP (Brazil). Inst. de Quimica)

1991-01-01

Five {sup 14}-labelled organic acids are obtained from the self-radiolysis of high specific activity Ca{sup 14}CO{sub 3}. The yields of all products decrease upon isothermal annealing at 548 K. Upon isochronal annealing (1 h), no significant changes occur up to 423 K. In the temperature interval between 476 and 673 K, the yields of formic, oxalic and glyoxylic acids decrease similarly, suggesting that they have the same precursor: the CO{sub 2}{sup -} radical. The isochronal annealing behaviours of the precursors of glycolic and acetic acids are more complex and involve other solid state species. (author).

On the distribution of catecholamines in Promesostoma balticum (Turbellaria, Neorhabdocoela, Promesostomatidae).

Science.gov (United States)

Joffe, B I

1994-01-01

The distribution of putative catecholamines has been previously studied in the nervous system of three Promesostoma species using the glyoxylic-acid-induced fluorescence (GAIF) method. In this communication, the results are reported of a similar study of Promesostoma balticum, which is classified to another group of species in the genus. Promesostoma species from two different species groups differed in the position of neurons associated with the ventral and lateral cords. All the studied species of Promesostoma demonstrated doubled dorsal neurons in so called anterior complex (AnDo), a character which differentiates this genus from the other studied Typhloplanoida.

Herring and chicken/pork meals lead to differences in plasma levels of TCA intermediates and arginine metabolites in overweight and obese men and women

DEFF Research Database (Denmark)

Vincent, Andrew; Savolainen, Otto I; Sen, Partho

2017-01-01

citrate, fumarate, isocitrate, glycolate, oxalate, agmatine and methyhistidine and increased asparagine, ornithine, glutamine and the hexosamine glucosamine. Modelling found that the tricarboxylic acid cycle, glyoxylate, and argininemetabolism were affected by the intervention. The effect on arginine...... metabolism was supported by an increase in blood nitric oxide in males on the herring diet. Conclusion: The results suggest that eating herring instead of chicken and lean pork leads to important metabolic effects, particularly on energy and amino acid metabolism. Our findings support the hypothesis...... that there are metabolic effects of herring intake unrelated to the long chain n-3 polyunsaturated fatty acid content....

Relative expression of the products of glyoxylate bypass operon: contributions of transcription and translation.

OpenAIRE

Chung, T; Resnik, E; Stueland, C; LaPorte, D C

1993-01-01

Although the genes of the aceBAK operon are expressed from the same promoter, the relative cellular levels of their products are approximately 0.3:1:0.003. Gene and operon fusions with lacZ were constructed to characterize this differential expression. The upshift in expression between aceB and aceA resulted from differences in translational efficiency. In contrast, inefficient translation and premature transcriptional termination contributed to the downshift in expression between aceA and ac...

Organic Acids: The Pools of Fixed Carbon Involved in Redox Regulation and Energy Balance in Higher Plants

Directory of Open Access Journals (Sweden)

Abir U Igamberdiev

2016-07-01

Full Text Available Organic acids are synthesized in plants as a result of the incomplete oxidation of photosynthetic products and represent the stored pools of fixed carbon accumulated due to different transient times of conversion of carbon compounds in metabolic pathways. When redox level in the cell increases, e.g., in conditions of active photosynthesis, the tricarboxylic acid (TCA cycle in mitochondria is transformed to a partial cycle supplying citrate for the synthesis of 2-oxoglutarate and glutamate (citrate valve, while malate is accumulated and participates in the redox balance in different cell compartments (via malate valve. This results in malate and citrate frequently being the most accumulated acids in plants. However, the intensity of reactions linked to the conversion of these compounds can cause preferential accumulation of other organic acids, e.g., fumarate or isocitrate, in higher concentrations than malate and citrate. The secondary reactions, associated with the central metabolic pathways, in particularly with the TCA cycle, result in accumulation of other organic acids that are derived from the intermediates of the cycle. They form the additional pools of fixed carbon and stabilize the TCA cycle. Trans-aconitate is formed from citrate or cis-aconitate, accumulation of hydroxycitrate can be linked to metabolism of 2-oxoglutarate, while 4-hydroxy-2-oxoglutarate can be formed from pyruvate and glyoxylate. Glyoxylate, a product of either glycolate oxidase or isocitrate lyase, can be converted to oxalate. Malonate is accumulated at high concentrations in legume plants. Organic acids play a role in plants in providing redox equilibrium, supporting ionic gradients on membranes, and acidification of the extracellular medium.

Transformation efficiency and formation of transformation products during photochemical degradation of TCE and PCE at micromolar concentrations.

Science.gov (United States)

Dobaradaran, Sina; Lutze, Holger; Mahvi, Amir Hossein; Schmidt, Torsten C

2014-01-08

Trichloroethene and tetrachloroethene are the most common pollutants in groundwater and two of the priority pollutants listed by the U.S. Environmental Protection Agency. In previous studies on TCE and PCE photolysis and photochemical degradation, concentration ranges exceeding environmental levels by far with millimolar concentrations of TCE and PCE have been used, and it is not clear if the obtained results can be used to explain the degradation of these contaminants at more realistic environmental concentration levels. Experiments with micromolar concentrations of TCE and PCE in aqueous solution using direct photolysis and UV/H2O2 have been conducted and product formation as well as transformation efficiency have been investigated. SPME/GC/MS, HPLC/UV and ion chromatography with conductivity detection have been used to determine intermediates of degradation. The results showed that chloride was a major end product in both TCE and PCE photodegradation. Several intermediates such as formic acid, dichloroacetic acid, dichloroacetaldehyede, chloroform, formaldehyde and glyoxylic acid were formed during both, UV and UV/H2O2 treatment of TCE. However chloroacetaldehyde and chloroacetic acid were only detected during direct UV photolysis of TCE and oxalic acid was only formed during the UV/H2O2 process. For PCE photodegradation, formic acid, di- and trichloroacetic acids were detected in both UV and UV/H2O2 systems, but formaldehyde and glyoxylic acid were only detected during direct UV photolysis. For water treatment UV/H2O2 seems to be favorable over direct UV photolysis because of its higher degradation efficiency and lower risk for the formation of harmful intermediates.

Metabolite profiling uncovers plasmid-induced cobalt limitation under methylotrophic growth conditions.

Directory of Open Access Journals (Sweden)

Patrick Kiefer

2009-11-01

Full Text Available The introduction and maintenance of plasmids in cells is often associated with a reduction of growth rate. The reason for this growth reduction is unclear in many cases.We observed a surprisingly large reduction in growth rate of about 50% of Methylobacterium extorquens AM1 during methylotrophic growth in the presence of a plasmid, pCM80 expressing the tetA gene, relative to the wild-type. A less pronounced growth delay during growth under non-methylotrophic growth conditions was observed; this suggested an inhibition of one-carbon metabolism rather than a general growth inhibition or metabolic burden. Metabolome analyses revealed an increase in pool sizes of ethylmalonyl-CoA and methylmalonyl-CoA of more than 6- and 35-fold, respectively, relative to wild type, suggesting a strongly reduced conversion of these central intermediates, which are essential for glyoxylate regeneration in this model methylotroph. Similar results were found for M. extorquens AM1 pCM160 which confers kanamycin resistance. These intermediates of the ethylmalonyl-CoA pathway have in common their conversion by coenzyme B(12-dependent mutases, which have cobalt as a central ligand. The one-carbon metabolism-related growth delay was restored by providing higher cobalt concentrations, by heterologous expression of isocitrate lyase as an alternative path for glyoxylate regeneration, or by identification and overproduction of proteins involved in cobalt import.This study demonstrates that the introduction of the plasmids leads to an apparent inhibition of the cobalt-dependent enzymes of the ethylmalonyl-CoA pathway. Possible explanations are presented and point to a limited cobalt concentration in the cell as a consequence of the antibiotic stress.

Global Transcriptional and Physiological Responses of Saccharomyces cerevisiae to Ammonium, L-Alanine, or L-Glutamine Limitation

DEFF Research Database (Denmark)

Usaite, Renata; Patil, Kiran Raosaheb; Grotkjær, Thomas

2006-01-01

-ammonium in limitation and by growing cells in an excess of ammonium. Cells grown in L-alanine-limited cultures had higher biomass yield per nitrogen mole (19%) than those from ammonium-limited cultures. Whole-genome transcript profiles were analyzed with a genome-scalle metabolic model that suggested increased anabolic...... activity in L-alanine-limited cells. The changes in these cells were found to be focused around pyruvate, acetyl coenzyme A, glyoxylate, and alpha-ketoglutarate via increased levels of ALT1, DAL7, PYC1, GDH2, and ADH5 and decreased levels of GDH3, CIT2, and ACS1 transcripts. The transcript profiles were...

SYNTHESIS OF NOVEL INDOLO[3,2-c]QUINOLINES; ETHYL 3-CHLORO-9,11-DIMETHOXY INDOLO[3,2-c]QUINOLINE-6-CARBOXYLATE

Directory of Open Access Journals (Sweden)

Tutik Dwi Wahyuningsih

2010-06-01

Full Text Available -Carboline and its derivatives are significant due to their pharmacological importance. The synthesis of indolo[3,2-c]quinolines as a benzo analog of -carboline has been carried out via an oxime ether intermediate. Reaction of 2'-glyoxylic ester with hydroxylamine hydrochloride in the presence of sodium acetate afforded the oxime acetate in 82%. It was then treated with natrium and fluoro-2,4-dinitrobenzene in ethanol to give an orange solid of oxime ether acetate which is in subsequent treatment with a base yielded a pale yellow solid of indolo[3,2-c]carboline in 43%. Keywords: -carboline, oxime, indolo[3,2-c]quinoline.

GABA transaminases from Saccharomyces cerevisiae and Arabidopsis thaliana complement function in cytosol and mitochondria.

Science.gov (United States)

Cao, Juxiang; Barbosa, Jose M; Singh, Narendra; Locy, Robert D

2013-07-01

GABA transaminase (GABA-T) catalyses the conversion of GABA to succinate semialdehyde (SSA) in the GABA shunt pathway. The GABA-T from Saccharomyces cerevisiae (ScGABA-TKG) is an α-ketoglutarate-dependent enzyme encoded by the UGA1 gene, while higher plant GABA-T is a pyruvate/glyoxylate-dependent enzyme encoded by POP2 in Arabidopsis thaliana (AtGABA-T). The GABA-T from A. thaliana is localized in mitochondria and mediated by an 18-amino acid N-terminal mitochondrial targeting peptide predicated by both web-based utilities TargetP 1.1 and PSORT. Yeast UGA1 appears to lack a mitochondrial targeting peptide and is localized in the cytosol. To verify this bioinformatic analysis and examine the significance of ScGABA-TKG and AtGABA-T compartmentation and substrate specificity on physiological function, expression vectors were constructed to modify both ScGABA-TKG and AtGABA-T, so that they express in yeast mitochondria and cytosol. Physiological function was evaluated by complementing yeast ScGABA-TKG deletion mutant Δuga1 with AtGABA-T or ScGABA-TKG targeted to the cytosol or mitochondria for the phenotypes of GABA growth defect, thermosensitivity and heat-induced production of reactive oxygen species (ROS). This study demonstrates that AtGABA-T is functionally interchangeable with ScGABA-TKG for GABA growth, thermotolerance and limiting production of ROS, regardless of location in mitochondria or cytosol of yeast cells, but AtGABA-T is about half as efficient in doing so as ScGABA-TKG. These results are consistent with the hypothesis that pyruvate/glyoxylate-limited production of NADPH mediates the effect of the GABA shunt in moderating heat stress in Saccharomyces. Copyright © 2013 John Wiley & Sons, Ltd.

The Role of Isocitrate Lyase (ICL1) in the Metabolic Adaptation of Candida albicans Biofilms

Science.gov (United States)

Ishola, Oluwaseun Ayodeji; Ting, Seng Yeat; Tabana, Yasser M; Ahmed, Mowaffaq Adam; Yunus, Muhammad Amir; Mohamed, Rafeezul; Lung Than, Leslie Thian; Sandai, Doblin

2016-01-01

Background A major characteristic of Candida biofilm cells that differentiates them from free-floating cells is their high tolerance to antifungal drugs. This high resistance is attributed to particular biofilm properties, including the accumulation of extrapolymeric substances, morphogenetic switching, and metabolic flexibility. Objectives This study evaluated the roles of metabolic processes (in particular the glyoxylate cycle) on biofilm formation, antifungal drug resistance, morphology, and cell wall components. Methods Growth, adhesion, biofilm formation, and cell wall carbohydrate composition were quantified for isogenic Candida albicans ICL1/ICL1, ICL1/icl1, and icl1/icl1 strains. The morphology and topography of these strains were compared by light microscopy and scanning electron microscopy. FKS1 (glucan synthase), ERG11 (14-α-demethylase), and CDR2 (efflux pump) mRNA levels were quantified using qRT-PCR. Results The ICL1/icl1 and icl1/icl1 strains formed similar biofilms and exhibited analogous drug-tolerance levels to the control ICL1/ICL1 strains. Furthermore, the drug sequestration ability of β-1, 3-glucan, a major carbohydrate component of the extracellular matrix, was not impaired. However, the inactivation of ICL1 did impair morphogenesis. ICL1 deletion also had a considerable effect on the expression of the FKS1, ERG11, and CDR2 genes. FKS1 and ERG11 were upregulated in ICL1/icl1 and icl1/icl1 cells throughout the biofilm developmental stages, and CDR2 was upregulated at the early phase. However, their expression was downregulated compared to the control ICL1/ICL1 strain. Conclusions We conclude that the glyoxylate cycle is not a specific determinant of biofilm drug resistance. PMID:27800147

Global changes in the proteome of Cupriavidus necator H16 during poly-(3-hydroxybutyrate) synthesis from various biodiesel by-product substrates.

Science.gov (United States)

Sharma, Parveen K; Fu, Jilagamazhi; Spicer, Victor; Krokhin, Oleg V; Cicek, Nazim; Sparling, Richard; Levin, David B

2016-12-01

Synthesis of poly-[3-hydroxybutyrate] (PHB) by Cupriavidus necator H16 in batch cultures was evaluated using three biodiesel-derived by-products as the sole carbon sources: waste glycerol (REG-80, refined to 80 % purity with negligible free fatty acids); glycerol bottom (REG-GB, with up to 65 % glycerol and 35 % free fatty acids), and free fatty acids (REG-FFA, with up to 75 % FFA and no glycerol). All the three substrates supported growth and PHB production by C. necator, with polymer accumulation ranging from 9 to 84 % cell dry weight (cdw), depending on the carbon source. To help understand these differences, proteomic analysis indicated that although C. necator H16 was able to accumulate PHB during growth on all three biodiesel by-products, no changes in the levels of PHB synthesis enzymes were observed. However, significant changes in the levels of expression were observed for two Phasin proteins involved with PHB accumulation, and for a number of gene products in the fatty acid β-oxidation pathway, the Glyoxylate Shunt, and the hydrogen (H2) synthesis pathways in C. necator cells cultured with different substrates. The glycerol transport protein (GlpF) was induced in REG-GB and REG-80 glycerol cultures only. Cupriavidus necator cells cultured with REG-GB and REG-FFA showed up-regulation of β-oxidation and Glyoxylate Shunt pathways proteins at 24 h pi, but H2 synthesis pathways enzymes were significantly down-regulated, compared with cells cultured with waste glycerol. Our data confirmed earlier observations of constitutive expression of PHB synthesis proteins, but further suggested that C. necator H16 cells growing on biodiesel-derived glycerol were under oxidative stress.

Radiolysis of Ca14CO3

International Nuclear Information System (INIS)

Sanchez, M.G.A.

1986-01-01

The partition-ion exclusion chromatography is evaluated to analyse non-ionic organic compounds obtained from radiolysis of high specific activity Ca 14 CO 3 . The Ca 14 CO 3 was irradiated by β - decay of carbon-14 or by γ rays from a cobalt-60 source. The crystals were dissolved for qualitative and quantitative analysis of the radiolytic products. Formic and oxalic acids were produced in high yields. Glyoxylic, acetic and glycolic acids, formaldehyde and methanol were produced in low yields. Quantitative determination was carried out by liquid scintillation spectroscopy and the chemical yields (G-values) were calculated for the products. Mechanisms of product formation are proposed based on thermal annealing experiments. (Author) [pt

Nitrogen fixation in peanut nodules during dark periods and detopped conditions with special reference to lipid bodies

International Nuclear Information System (INIS)

Siddique, A.M.; Bal, A.K.

1991-01-01

The peanut plant (Arachis hypogaea L.), unlike other known legumes, can sustain nitrogen fixation when prolonged periods of darkness or detopping curtail the supply of photosynthate to the nodule. This ability to withstand photosynthate stress is attributed to the presence of lipid bodies in infected nodule cells. In both dark-treated and detopped plants, the lipid bodies show a gradual decrease in numbers, suggesting their utilization as a source of energy and carbon for nitrogen fixation. Lipolytic activity can be localized in the lipid bodies, and the existence of β-oxidation pathway and glyoxylate cycle is shown by the release of 14 CO 2 from 14 C lineoleoyl coenzyme A by the nodule homogenate

Primary hyperoxaluria: spectrum of clinical and imaging findings

Energy Technology Data Exchange (ETDEWEB)

Strauss, Sara B.; Levin, Terry L. [Children' s Hospital of Montefiore Medical Center, Division of Pediatric Radiology, Department of Radiology, Bronx, NY (United States); Waltuch, Temima; Kaskel, Frederick [Children' s Hospital at Montefiore Medical Center, Division of Pediatric Nephrology, Bronx, NY (United States); Bivin, William [Allegheny General Hospital, Department of Pathology, Pittsburgh, PA (United States)

2017-01-15

Primary hyperoxaluria is a rare autosomal recessive inborn error of metabolism with three known subtypes. In primary hyperoxaluria type 1, the most common of the subtypes, a deficiency in the hepatic enzymes responsible for the metabolism of glycoxylate to glycine, leads to excessive levels of glyoxylate, which is converted to oxalate. The resultant elevation in serum and urinary oxalate that characterizes primary hyperoxaluria leads to calcium oxalate crystal deposition in multiple organ systems (oxalosis). We review the genetics, pathogenesis, variable clinical presentation and course of this disease as well as its treatment. Emphasis is placed on the characteristic imaging findings before and after definitive treatment with combined liver and renal transplantation. (orig.)

Metabolic Engineering of TCA Cycle for Production of Chemicals.

Science.gov (United States)

Vuoristo, Kiira S; Mars, Astrid E; Sanders, Johan P M; Eggink, Gerrit; Weusthuis, Ruud A

2016-03-01

The tricarboxylic acid (TCA) cycle has been used for decades in the microbial production of chemicals such as citrate, L-glutamate, and succinate. Maximizing yield is key for cost-competitive production. However, for most TCA cycle products, the maximum pathway yield is lower than the theoretical maximum yield (Y(E)). For succinate, this was solved by creating two pathways to the product, using both branches of the TCA cycle, connected by the glyoxylate shunt (GS). A similar solution cannot be applied directly for production of compounds from the oxidative branch of the TCA cycle because irreversible reactions are involved. Here, we describe how this can be overcome and what the impact is on the yield. Copyright © 2015 Elsevier Ltd. All rights reserved.

Acute oxalate nephropathy caused by ethylene glycol poisoning

Directory of Open Access Journals (Sweden)

Jung Woong Seo

2012-12-01

Full Text Available Ethylene glycol (EG is a sweet-tasting, odorless organic solvent found in many agents, such as anti-freeze. EG is composed of four organic acids: glycoaldehyde, glycolic acid, glyoxylic acid and oxalic acid in vivo. These metabolites are cellular toxins that can cause cardio-pulmonary failure, life-threatening metabolic acidosis, central nervous system depression, and kidney injury. Oxalic acid is the end product of EG, which can precipitate to crystals of calcium oxalate monohydrate in the tubular lumen and has been linked to acute kidney injury. We report a case of EG-induced oxalate nephropathy, with the diagnosis confirmed by kidney biopsy, which showed acute tubular injury of the kidneys with extensive intracellular and intraluminal calcium oxalate monohydrate crystal depositions.

Differential Metabolism of a Two-Carbon Substrate by Members of the Paracoccidioides Genus

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Lilian C. Baeza

2017-11-01

Full Text Available The genus Paracoccidioides comprises known fungal pathogens of humans and can be isolated from different infection sites. Metabolic peculiarities in different members of the Paracoccidioides led us to perform proteomic studies in the presence of the two-carbon molecule acetate, which predominates in the nutrient-poor environment of the phagosome. To investigate the expression rates of proteins of different members of Paracoccidioides, including one isolate of P. lutzii (Pb01 and three isolates of P. brasiliensis (Pb03, Pb339, and PbEPM83, using sodium acetate as a carbon source, proteins were quantified using label-free and data-independent liquid chromatography-mass spectrometry. Protein profiles of the isolates were statistically analyzed, revealing proteins that were differentially expressed when the fungus was cultivated in a non-preferential carbon source rather than glucose. A total of 1,160, 1,211, 1,280, and 1,462 proteins were reproducibly identified and relatively quantified in P. lutzii and the P. brasiliensis isolates Pb03, Pb339, and PbEPM83, respectively. Notably, 526, 435, 744, and 747 proteins were differentially expressed among P. lutzii and the P. brasiliensis isolates Pb03, Pb339, and PbEPM83, respectively, with a fold-change equal to or higher than 1.5. This analysis revealed that reorganization of metabolism occurred through the induction of proteins related to gluconeogenesis, glyoxylic/glyoxylate cycle, response to stress, and degradation of amino acids in the four isolates. The following differences were observed among the isolates: higher increases in the expression levels of proteins belonging to the TCA and respiratory chain in PbEPM83 and Pb01; increase in ethanol production in Pb01; utilization of cell wall components for gluconeogenesis in Pb03 and PbEPM83; and increased β-oxidation and methylcitrate cycle proteins in Pb01and PbEPM83. Proteomic profiles indicated that the four isolates reorganized their metabolism

Noradrenergic and cholinergic innervation of the bone marrow.

Science.gov (United States)

Artico, Marco; Bosco, Sandro; Cavallotti, Carlo; Agostinelli, Enzo; Giuliani-Piccari, Gabriella; Sciorio, Salvatore; Cocco, Lucio; Vitale, Marco

2002-07-01

Bone marrow is supplied by sensory and autonomic innervation. Although it is well established that hematopoiesis is regulated by cytokines and cell-to-cell contacts, the role played by neuromediators on the proliferation, differentiation and release of hematopoietic cells is still controversial. We studied the innervation of rat femur bone marrow by means of fluorescence histochemistry and immunohistochemistry. Glyoxylic acid-induced fluorescence was used to demonstrate catecholaminergic nerve fibers. The immunoperoxidase method with nickel amplification was applied to detect the distribution of nerve fibers using antibodies against the general neuronal marker PGP 9.5 (neuron-specific cytoplasmic protein), while the cholinacetyltransferase immunoreactivity was studied by immunohistochemistry. Our results show the presence of an extensive network of innervation in the rat bone marrow, providing a morphological basis for the neural modulation of hemopoiesis.

The role of peroxisomes in the integration of metabolism and evolutionary diversity of photosynthetic organisms

DEFF Research Database (Denmark)

Igamberdiev, A.U.; Lea, P.J.

2002-01-01

reactions to flavin-dependent oxidation, coupled to the decomposition of hydrogen peroxide by catalase. Hydrogen peroxide and superoxide originating in peroxisomes are important mediators in signal transduction pathways, particularly those involving salicylic acid. By contributing to the synthesis...... of oxalate, formate and other organic acids, peroxisomes regulate major fluxes of primary and secondary metabolism. The evolutionary diversity of algae has led to the presence of a wide range of enzymes in the peroxisomes that acre only similar to higher plants in their direct predecessors, the Charophyceae....... The appearance of seed plants was connected to the acquirement by storage tissues, of a peroxisomal fatty acid oxidation function linked to the glyoxylate cycle, which is induced during seed germination and maturation. Rearrangement of the peroxisomal photorespiratory function between different tissues of higher...

Primary hyperoxaluria type 1: clinical manifestations in infancy and prenatal diagnosis

DEFF Research Database (Denmark)

Illum, N; Lavard, L; Danpure, C J

1992-01-01

biopsy demonstrated complete absence of alanine: glyoxylate aminotransferase catalytic activity and immunoreactive protein compatible with a diagnosis of primary hyperoxaluria type 1. He died at the age of 11 months, just before liver transplantation was made possible. Fetal liver biopsy in the mother......A 9-month-old Pakistani boy of consanguineous parents presented with uraemia preceded by pyuria from 5 weeks of age. He had no history of renal calculi or macroscopic haematuria. Renal biopsy revealed severe calcium oxalate deposition in the tubuli and fibrosis of the interstitial tissue. Liver......'s subsequent pregnancy showed normal enzymatic activity. Early detection and early replacement of the missing enzyme by liver transplantation are considered to be crucial for the survival of severely affected infants with the acute neonatal form of primary hyperoxaluria type 1. Persistent pyuria could...

CO2 Capture by Absorption with Potassium Carbonate

Energy Technology Data Exchange (ETDEWEB)

Gary T. Rochelle; Eric Chen; Babatunde Oyenekan; Andrew Sexton; Jason Davis; Marcus Hilliard; Amorvadee Veawab

2006-07-28

The objective of this work is to improve the process for CO{sub 2} capture by alkanolamine absorption/stripping by developing an alternative solvent, aqueous K{sub 2}CO{sub 3} promoted by piperazine. The pilot plant data have been reconciled using 17% inlet CO{sub 2}. A rate-based model demonstrates that the stripper is primarily controlled by liquid film mast transfer resistance, with kinetics at vacuum and diffusion of reactants and products at normal pressure. An additional major unknown ion, probably glyoxylate, has been observed in MEA degradation. Precipitation of gypsum may be a feasible approach to removing sulphate from amine solutions and providing for simultaneous removal of CO{sub 2} and SO{sub 2}. Corrosion of carbon steel in uninhibited MEA solution is increased by increased amine concentration, by addition of piperazine, and by greater CO{sub 2} loading.

Prediction of bacterial growth on xenobiotics

DEFF Research Database (Denmark)

Brock, Andreas Libonati; Kästner, Matthias; Trapp, Stefan

2016-01-01

to attain predictions closer to the experimentally observed yields [3]. However, this knowledge is seldom known for xenobiotics in the environment but is needed to assess the turnover leading to biomass production, i.e. for sludge production or biogenic residues. The objectives of the present study were...... method, we evaluated it with both simple substrates (e.g. acetate, methanol, and glyoxylate) and xenobiotics (e.g 2,4-D, linuron, carbofuran, carbon tetrachloride, and toluene). Experimental data for the simple substrates were taken from [4], for xenobiotics from [6] and own experimental data. For simple...... substrates, our approach predicts yields close to experimental values and also for xenobiotics the yield predictions for most of the compounds are close to the experimentally obtained values.Overall, with our method we were able to obtain yield predictions close to experimental values with a minimum of input...

Characterization and immobilization of engineered sialidases from Trypanosoma rangeli for transsialylation

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Birgitte Zeuner

2017-04-01

Full Text Available A sialidase (EC 3.2.1.18; GH 33 from non-pathogenic Trypanosoma rangeli has been engineered with the aim of improving its transsialylation activity. Recently, two engineered variants containing 15 and 16 amino acid substitutions, respectively, were found to exhibit significantly improved transsialylation activity: both had a 14 times higher ratio between transsialylation and hydrolysis products compared to the first reported mutant TrSA5mut. In the current work, these two variants, Tr15 and Tr16, were characterized in terms of pH optimum, thermal stability, effect of acceptor-to-donor ratio, and acceptor specificity for transsialylation using casein glycomacropeptide (CGMP as sialyl donor and lactose or other human milk oligosaccharide core structures as acceptors. Both sialidase variants exhibited pH optima around pH 4.8. Thermal stability of each enzyme was comparable to that of previously developed T. rangeli sialidase variants and higher than that of the native transsialidase from T. cruzi (TcTS. As for other engineered T. rangeli sialidase variants and TcTS, the acceptor specificity was broad: lactose, galactooligosaccharides (GOS, xylooligosaccharides (XOS, and human milk oligosaccharide structures lacto-N-tetraose (LNT, lacto-N-fucopentaose (LNFP V, and lacto-N-neofucopentaose V (LNnFP V were all sialylated by Tr15 and Tr16. An increase in acceptor-to-donor ratio from 2 to 10 had a positive effect on transsialylation. Both enzymes showed high preference for formation α(2,3-linkages at the non-reducing end of lactose in the transsialylation. Tr15 was the most efficient enzyme in terms of transsialylation reaction rates and yield of 3’-sialyllactose. Finally, Tr15 was immobilized covalently on glyoxyl-functionalized silica, leading to a 1.5-fold increase in biocatalytic productivity (mg 3’-sialyllactose per mg enzyme compared to free enzyme after 6 cycles of reuse. The use of glyoxyl-functionalized silica proved to be markedly better

Rhizosphere dynamics of two riparian plant species from the water fluctuation zone of Three Gorges Reservoir, P.R. China - pH, oxygen and LMWOA monitoring during short flooding events

Science.gov (United States)

Schreiber, Christina M.; Schurr, Ulrich; Zeng, Bo; Höltkemeier, Agnes; Kuhn, Arnd J.

2010-05-01

Since the construction of the Three Gorges Dam at the Yangtze River in China, the reservoir management created a new 30m water fluctuation zone 45-75m above the original water level. Only species well adapted to long-time flooding (up to several months) will be able to vegetate the river banks and replace the original vegetation. To investigate how common species of the riverbanks cope with submergence, Alternanthera philoxeroides Mart. and Arundinella anomala Steud., two flooding resistant riparian species, have been examined in a rhizotron environment. Short-time (2 days waterlogging, 2 days flooding, 2 days recovery) flooding cycles in the original substrate and long time (14 days waterlogging, flooding, recovery) flooding cycles, in original substrate and sterile glass bead substrate, have been simulated in floodable two-way access rhizotrons. Oxygen- and pH-sensitive foils (planar optodes, PreSens) automatically monitored root reaction in a confined space (2cm2 each) on the backside of the rhizotron, while soil solution samples were taken 2 times a day from the other side of the rhizotron at the corresponding area through filter and steel capillaries. The samples were analyzed by capillary electrophoresis for low molecular weight organic acids (LMWOA, i.e. oxalic, formic, succinic, malic, acetic, glyoxylic, lactic and citric acid). Results show diurnal rhythms of rhizospheric acidification for both species in high resolution, combined with oxygen entry into the root surrounding during waterlogged state. Flooding caused stronger acidification in the rhizosphere, that were however not accompanied by increased occurrence of LMWOA except for acetic and glyoxylic acid. First results from longer flooding periods show stable diurnal rhythms during waterlogging, but no strongly increased activity during the flooding event. Performance of the two species is not hampered by being waterlogged, and they follow a silencing strategy during a longer phase of anoxia without

Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G

Science.gov (United States)

2011-01-01

Background Malate synthase, one of the two enzymes unique to the glyoxylate cycle, is found in all three domains of life, and is crucial to the utilization of two-carbon compounds for net biosynthetic pathways such as gluconeogenesis. In addition to the main isoforms A and G, so named because of their differential expression in E. coli grown on either acetate or glycolate respectively, a third distinct isoform has been identified. These three isoforms differ considerably in size and sequence conservation. The A isoform (MSA) comprises ~530 residues, the G isoform (MSG) is ~730 residues, and this third isoform (MSH-halophilic) is ~430 residues in length. Both isoforms A and G have been structurally characterized in detail, but no structures have been reported for the H isoform which has been found thus far only in members of the halophilic Archaea. Results We have solved the structure of a malate synthase H (MSH) isoform member from Haloferax volcanii in complex with glyoxylate at 2.51 Å resolution, and also as a ternary complex with acetyl-coenzyme A and pyruvate at 1.95 Å. Like the A and G isoforms, MSH is based on a β8/α8 (TIM) barrel. Unlike previously solved malate synthase structures which are all monomeric, this enzyme is found in the native state as a trimer/hexamer equilibrium. Compared to isoforms A and G, MSH displays deletion of an N-terminal domain and a smaller deletion at the C-terminus. The MSH active site is closely superimposable with those of MSA and MSG, with the ternary complex indicating a nucleophilic attack on pyruvate by the enolate intermediate of acetyl-coenzyme A. Conclusions The reported structures of MSH from Haloferax volcanii allow a detailed analysis and comparison with previously solved structures of isoforms A and G. These structural comparisons provide insight into evolutionary relationships among these isoforms, and also indicate that despite the size and sequence variation, and the truncated C-terminal domain of the H

Purification, crystallization and preliminary X-ray analysis of isocitrate dehydrogenase kinase/phosphatase from Escherichia coli

International Nuclear Information System (INIS)

Zheng, Jimin; Lee, Daniel C.; Jia, Zongchao

2009-01-01

Isocitrate dehydrogenase kinase/phosphatase has been crystallized in three different crystal forms. Data were collected from each crystal form for structure determination. The Escherichia coli aceK gene encodes isocitrate dehydrogenase kinase/phosphatase (EC 2.7.11.5), a bifunctional protein that phosphorylates and dephosphorylates isocitrate dehydrogenase (IDH), resulting in its inactivation and activation, respectively. This reversible (de)phosphorylation directs isocitrate, an intermediate of the citric acid cycle, to either go through the full cycle or to enter the glyoxylate bypass. In the present study, the AceK protein from E. coli has been purified and crystallized. Three crystal forms were obtained from very similar crystallization conditions. The crystals belong to space groups P4 1 2 1 2, P3 2 21 and P2 1 2 1 2 1 and diffracted X-rays to resolutions of 2.9, 3.0 and 2.7 Å, respectively

An investigation of an autonomic innervation of the vertebral artery using monoamine histofluorescence

Directory of Open Access Journals (Sweden)

JA Mitchell

2009-06-01

Full Text Available Blood flow to the hindbrain, via the paired vertebral arteries, must be uncompromised for adequate neurological functioning of its vital centres. Therefore, it would seem unlikely that the intracranial vertebral artery would need to vasoconstrict, thus reducing its blood flow. In order to investigate the existence and location of a noradrenaline-mediated constrictor mechanism in the wall of the intracranial vertebral artery, transverse sections of ten baboon and ten monkey vessels were stained with sucrose-potassium phosphate-glyoxylic acid (counterstained with malachite-green. This method allows the visualisation of catecholaminergic nerves when the sections are exposed to ultraviolet light. In this study of primate vascular tissue, however, none of the monkey or baboon vertebral artery sections showed the presence of noradrenergic nerves in the tunica media – tunica adventitia junction or penetrating the tunica media of the arteries. These findings indicate that the intracranial vertebral artery does not have a neurogenic vasomotor function in primates.

Transcriptome analysis of acyl-homoserine lactone-based quorum sensing regulation in Yersinia pestis [corrected].

Directory of Open Access Journals (Sweden)

Christopher N LaRock

Full Text Available The etiologic agent of bubonic plague, Yersinia pestis, senses self-produced, secreted chemical signals in a process named quorum sensing. Though the closely related enteric pathogen Y. pseudotuberculosis uses quorum sensing system to regulate motility, the role of quorum sensing in Y. pestis has been unclear. In this study we performed transcriptional profiling experiments to identify Y. pestis quorum sensing regulated functions. Our analysis revealed that acyl-homoserine lactone-based quorum sensing controls the expression of several metabolic functions. Maltose fermentation and the glyoxylate bypass are induced by acyl-homoserine lactone signaling. This effect was observed at 30°C, indicating a potential role for quorum sensing regulation of metabolism at temperatures below the normal mammalian temperature. It is proposed that utilization of alternative carbon sources may enhance growth and/or survival during prolonged periods in natural habitats with limited nutrient sources, contributing to maintenance of plague in nature.

Co-immobilization of cyclohexanone monooxygenase and glucose-6-phosphate dehydrogenase onto polyethylenimine-porous agarose polymeric composite using γ irradiation to use in biotechnological processes

International Nuclear Information System (INIS)

Atia, K.S.

2005-01-01

The co-immobilization of cyclohexanone monooxygenase (CHMO) and glucose-6-phosphate dehydrogenase (G6PDH) was optimized by completely coating, via covalent immobilization, the surface aldehyde groups of porous agarose (glyoxyl-agarose) with amine groups of polyethylenimine (PEI). The highest immobilization efficiency (∼87%) (activity of enzyme per amount of immobilized enzyme) was obtained with a CHMO/G6PDH ratio 2:1. The effects of different ratios of the support to the amount of enzymes (CHMO:G6PDH=2:1), the optimum incubation pH and the incubation time on the enzymatic activity of the enzymes were determined and found to be 5:1, 8.5 and 30 min, respectively. Subjecting the co-immobilized enzymes to doses of γ-radiation (5-100 kGy) resulted in complete loss in the activity of the free enzymes at a dose of 40 kGy, while the co-immobilized ones showed relatively high resistance to γ-radiation up to a dose of 50 kGy

Carbon and hydrogen metabolism of green algae in light and dark

Energy Technology Data Exchange (ETDEWEB)

1990-01-01

After adaptation to a hydrogen metabolism, Chlamydomonas reinhardtii can photoanaerobically metabolize acetate with the evolution of H{sub 2} and CO{sub 2}. An enzyme profile of the chloroplastic, cytoplasmic, and mitochondrial fractions were obtained with a cellular fractionation procedure that incorporated cell wall removal by autolysine, digestion of the plasmalemma with digitonin and fractionation by differential centrifugation on a Percoll step gradient. The sequence of events leading to the photo-evolution of H{sub 2} from acetate includes the conversion of acetate into succinate via the extraplastidic glyoxylate cycle, the oxidation of succinate to fumarate by chloroplastic succinic dehydrogenase and the oxidation of malate to oxaloacetate in the chloroplast by NAD dependent malate dehydrogenase. The level of potential activity of the enzymes was sufficient to accommodate the observed rate of gas evolution. The isolated darkened chloroplast evolves aerobically CO{sub 2} from glucose indicating a chloroplastic respiratory pathway. Evolution of CO{sub 2} is blocked by mitochondrial inhibitors.

Metabolic peculiarities of the citric acid overproduction from glucose in yeasts Yarrowia lipolytica.

Science.gov (United States)

Kamzolova, Svetlana V; Morgunov, Igor G

2017-11-01

Comparative study of 43 natural yeast strains belonging to 20 species for their capability for overproduction of citric acid (CA) from glucose under nitrogen limitation of cell growth was carried out. As a result, natural strain Yarrowia lipolytica VKM Y-2373 was selected. The effect of growth limitation by biogenic macroelements (nitrogen, phosphorus, or sulfur) on the CA production by the selected strain was studied. It was shown that yeasts Y. lipolytica grown under deficiency of nitrogen, phosphorus, or sulfur were able to excrete CA in industrially sufficient amounts (80-85g/L with the product yield (Y CA ) of 0.70-0.75g/g and the process selectivity of 92.5-95.3%). Based on the obtained data on activities of enzymes involved in the initial stages of glucose oxidation, the cycle of tricarboxylic acids, and the glyoxylate cycle, the conception of the mechanism responsible for the CA overproduction from glucose in Y. lipolytica was formulated. Copyright © 2017 Elsevier Ltd. All rights reserved.

Organic products from Ca14Co3 autoradiolysis: effects of thermal annealing

International Nuclear Information System (INIS)

Albarran S, M.G.; Collins, K.E.; Collins, C.H.

1986-01-01

Autoradiolysis of Ca 14 Co 3 produces several different low molecular mass organic compounds which can be conveniently observed after ion exclusion-partition chromatographic separation of the dissolved sample, provided that the solid was prepared with high specific activity carbon-14 and has been stored for a sufficiently long period. Subsequent thermal annealing changes the distribution of these observed compounds, demonstrating that chemical reactions of the precursor species take place in the solid Ca 14 Co 3 matrix. Specifically, the following products were observed after an autoradiolytic dose of 5 MGy: methanol, formaldehyde, formic acid, oxalic acid, glyoxylic acid, glycolic acid and acetic acid, with-G-values ranging from 5x10 -6 to 2x10 -3 . Isochronal annealing to 500 0 C markedly changes the yields of carbon-14 labelled formic and acetic acids but has lesser effects on the other acidic products. This indicates that several different precursor species are present in the autoradiolyzed solid. (Author) [pt

Fiat lux! Phylogeny and bioinformatics shed light on GABA functions in plants.

Science.gov (United States)

Renault, Hugues

2013-06-01

The non-protein amino acid γ-aminobutyric acid (GABA) accumulates in plants in response to a wide variety of environmental cues. Recent data point toward an involvement of GABA in tricarboxylic acid (TCA) cycle activity and respiration, especially in stressed roots. To gain further insights into potential GABA functions in plants, phylogenetic and bioinformatic approaches were undertaken. Phylogenetic reconstruction of the GABA transaminase (GABA-T) protein family revealed the monophyletic nature of plant GABA-Ts. However, this analysis also pointed to the common origin of several plant aminotransferases families, which were found more similar to plant GABA-Ts than yeast and human GABA-Ts. A computational analysis of AtGABA-T co-expressed genes was performed in roots and in stress conditions. This second approach uncovered a strong connection between GABA metabolism and glyoxylate cycle during stress. Both in silico analyses open new perspectives and hypotheses for GABA metabolic functions in plants.

Fiat lux!

Science.gov (United States)

Renault, Hugues

2013-01-01

The non-protein amino acid γ-aminobutyric acid (GABA) accumulates in plants in response to a wide variety of environmental cues. Recent data point toward an involvement of GABA in tricarboxylic acid (TCA) cycle activity and respiration, especially in stressed roots. To gain further insights into potential GABA functions in plants, phylogenetic and bioinformatic approaches were undertaken. Phylogenetic reconstruction of the GABA transaminase (GABA-T) protein family revealed the monophyletic nature of plant GABA-Ts. However, this analysis also pointed to the common origin of several plant aminotransferases families, which were found more similar to plant GABA-Ts than yeast and human GABA-Ts. A computational analysis of AtGABA-T co-expressed genes was performed in roots and in stress conditions. This second approach uncovered a strong connection between GABA metabolism and glyoxylate cycle during stress. Both in silico analyses open new perspectives and hypotheses for GABA metabolic functions in plants. PMID:23518583

(13)C-metabolic flux analysis of lipid accumulation in the oleaginous fungus Mucor circinelloides.

Science.gov (United States)

Zhao, Lina; Zhang, Huaiyuan; Wang, Liping; Chen, Haiqin; Chen, Yong Q; Chen, Wei; Song, Yuanda

2015-12-01

The oleaginous fungus Mucor circinelloides is of industrial interest because it can produce high levels of polyunsaturated fatty acid γ-linolenic acid. M. circinelloides CBS 277.49 is able to accumulate less than 15% of cell dry weight as lipids, while M. circinelloides WJ11 can accumulate lipid up to 36%. In order to better understand the mechanisms behind the differential lipid accumulation in these two strains, tracer experiments with (13)C-glucose were performed with the growth of M. circinelloides and subsequent gas chromatography-mass spectrometric detection of (13)C-patterns in proteinogenic amino acids was carried out to identify the metabolic network topology and estimate intracellular fluxes. Our results showed that the high oleaginous strain WJ11 had higher flux of pentose phosphate pathway and malic enzyme, lower flux in tricarboxylic acid cycle, higher flux in glyoxylate cycle and ATP: citrate lyase, together, it might provide more NADPH and substrate acetyl-CoA for fatty acid synthesis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Enhanced saccharification of sugarcane bagasse using soluble cellulase supplemented with immobilized β-glucosidase.

Science.gov (United States)

Borges, Diogo Gontijo; Baraldo, Anderson; Farinas, Cristiane Sanchez; Giordano, Raquel de Lima Camargo; Tardioli, Paulo Waldir

2014-09-01

The β-glucosidase (BG) enzyme plays a vital role in the hydrolysis of lignocellulosic biomass. Supplementation of the hydrolysis reaction medium with BG can reduce inhibitory effects, leading to greater conversion. In addition, the inclusion of immobilized BG can be a useful way of increasing enzyme stability and recyclability. BG was adsorbed on polyacrylic resin activated by carboxyl groups (BG-PC) and covalently attached to glyoxyl-agarose (BG-GA). BG-PC exhibited similar behavior to soluble BG in the hydrolysis of cellobiose, while BG-GA hydrolyzed the same substrate at a lower rate. However, the thermal stability of BG-GA was higher than that of free BG. Hydrolysis of pretreated sugarcane bagasse catalyzed by soluble cellulase supplemented with immobilized BG improved the conversion by up to 40% after 96 h of reaction. Both derivatives remained stable up to the third cycle and losses of activity were less than 50% after five cycles. Copyright © 2014 Elsevier Ltd. All rights reserved.

Proteomic and metabolomic profiles of marine Vibrio sp. 010 in response to an antifoulant challenge

KAUST Repository

Chandramouli, Kondethimmanahalli; Dash, Swagatika; Zhang, Yu; Ravasi, Timothy; Qian, Peiyuan

2013-01-01

Vibrio spp. have the ability to form biofilms, which may contribute to the subsequent successful colonization by microfouling and macrofouling organisms. The effects of an antifouling compound, poly-ether B, on Vibrio sp. 010 were investigated using flow cytometry, proteomics, and metabolomics. A 2-D gel-based proteomic analysis was used to identify proteins responsive to poly-ether B treatment. The profiles of biofilm metabolites were analyzed by ultra-performance liquid chromatography-mass spectrometry. Poly-ether B caused a significant reduction in viability. The proteins affected by the treatment were related to nucleotide metabolism, the glyoxylate cycle, and stress responses. Metabolites such as tripeptides, fatty acids, and quorum-sensing molecules were regulated differentially. Down-regulation of proteins and metabolites potentially led to a loss in colonisation ability, thereby affecting the structure of the biofilm. These results suggest that the proteins and metabolites identified may serve as target molecules for potent antifouling compounds. © 2013 Copyright Taylor and Francis Group, LLC.

Bilateral native nephrectomy to reduce oxalate stores in children at the time of combined liver-kidney transplantation for primary hyperoxaluria type 1.

Science.gov (United States)

Lee, Eliza; Ramos-Gonzalez, Gabriel; Rodig, Nancy; Elisofon, Scott; Vakili, Khashayar; Kim, Heung Bae

2018-05-01

Primary hyperoxaluria type-1 (PH-1) is a rare genetic disorder in which normal hepatic metabolism of glyoxylate is disrupted resulting in diffuse oxalate deposition and end-stage renal disease (ESRD). While most centers agree that combined liver-kidney transplant (CLKT) is the appropriate treatment for PH-1, perioperative strategies for minimizing recurrent oxalate-related injury to the transplanted kidney remain unclear. We present our management of children with PH-1 and ESRD on hemodialysis (HD) who underwent CLKT at our institution from 2005 to 2015. On chart review, three patients (2 girls, 1 boy) met study criteria. Two patients received deceased-donor split-liver grafts, while one patient received a whole liver graft. All patients underwent bilateral native nephrectomy at transplant to minimize the total body oxalate load. Median preoperative serum oxalate was 72 μmol/L (range 17.8-100). All patients received HD postoperatively until predialysis serum oxalate levels fell stores and may mitigate damage to the renal allograft.

daf-16/FoxO promotes gluconeogenesis and trehalose synthesis during starvation to support survival.

Science.gov (United States)

Hibshman, Jonathan D; Doan, Alexander E; Moore, Brad T; Kaplan, Rebecca Ew; Hung, Anthony; Webster, Amy K; Bhatt, Dhaval P; Chitrakar, Rojin; Hirschey, Matthew D; Baugh, L Ryan

2017-10-24

daf-16 /FoxO is required to survive starvation in Caenorhabditis elegans , but how daf-16I FoxO promotes starvation resistance is unclear. We show that daf-16 /FoxO restructures carbohydrate metabolism by driving carbon flux through the glyoxylate shunt and gluconeogenesis and into synthesis of trehalose, a disaccharide of glucose. Trehalose is a well-known stress protectant, capable of preserving membrane organization and protein structure during abiotic stress. Metabolomic, genetic, and pharmacological analyses confirm increased trehalose synthesis and further show that trehalose not only supports survival as a stress protectant but also serves as a glycolytic input. Furthermore, we provide evidence that metabolic cycling between trehalose and glucose is necessary for this dual function of trehalose. This work demonstrates that daf-16 /FoxO promotes starvation resistance by shifting carbon metabolism to drive trehalose synthesis, which in turn supports survival by providing an energy source and acting as a stress protectant.

Limited uptake, translocation and enhanced metabolic degradation contribute to glyphosate tolerance in Mucuna pruriens var. utilis plants.

Science.gov (United States)

Rojano-Delgado, Antonia María; Cruz-Hipolito, Hugo; De Prado, Rafael; Luque de Castro, María Dolores; Franco, Antonio Rodríguez

2012-01-01

Velvet bean (Mucuna pruriens, Fabaceae) plants exhibits an innate, very high resistance (i.e., tolerance) to glyphosate similar to that of plants which have acquired resistance to this herbicide as a trait. We analyzed the uptake of [(14)C]-glyphosate by leaves and its translocation to meristematic tissues, and used scanning electron micrographs to further analyze the cuticle and 3D capillary electrophoresis to investigate a putative metabolism capable of degrading the herbicide. Velvet bean exhibited limited uptake of glyphosate and impaired translocation of the compound to meristematic tissues. Also, for the first time in a higher plant, two concurrent pathways capable of degrading glyphosate to AMPA, Pi, glyoxylate, sarcosine and formaldehyde as end products were identified. Based on the results, the innate tolerance of velvet bean to glyphosate is possibly a result of the combined action of the previous three traits, namely: limited uptake, impaired translocation and enhanced degradation. Copyright © 2011 Elsevier Ltd. All rights reserved.

A General Tool for Engineering the NAD/NADP Cofactor Preference of Oxidoreductases.

Science.gov (United States)

Cahn, Jackson K B; Werlang, Caroline A; Baumschlager, Armin; Brinkmann-Chen, Sabine; Mayo, Stephen L; Arnold, Frances H

2017-02-17

The ability to control enzymatic nicotinamide cofactor utilization is critical for engineering efficient metabolic pathways. However, the complex interactions that determine cofactor-binding preference render this engineering particularly challenging. Physics-based models have been insufficiently accurate and blind directed evolution methods too inefficient to be widely adopted. Building on a comprehensive survey of previous studies and our own prior engineering successes, we present a structure-guided, semirational strategy for reversing enzymatic nicotinamide cofactor specificity. This heuristic-based approach leverages the diversity and sensitivity of catalytically productive cofactor binding geometries to limit the problem to an experimentally tractable scale. We demonstrate the efficacy of this strategy by inverting the cofactor specificity of four structurally diverse NADP-dependent enzymes: glyoxylate reductase, cinnamyl alcohol dehydrogenase, xylose reductase, and iron-containing alcohol dehydrogenase. The analytical components of this approach have been fully automated and are available in the form of an easy-to-use web tool: Cofactor Specificity Reversal-Structural Analysis and Library Design (CSR-SALAD).

Regulation of metabolic products and gene expression in Fusarium asiaticum by agmatine addition.

Science.gov (United States)

Suzuki, Tadahiro; Kim, Young-Kyung; Yoshioka, Hifumi; Iwahashi, Yumiko

2013-05-01

The metabolic products resulting from the cultivation of F. asiaticum in agmatine were identified using capillary electrophoresis-time of flight mass spectrometry. Glyoxylic acid was detected from fungal cultures grown in agmatine, while it was absent in control cells. The abundance of other metabolic products of the glycolytic pathway also increased because of agmatine; however, there was no increase in the amounts of pyruvic acid or metabolites from the tricarboxylic acid cycle. Moreover, gene expression levels within Fusarium asiaticum exposed to agmatine were analyzed by DNA microarray. Changes in gene expression levels directed the changes in metabolic products. Our results suggest that acetyl coenzyme A, which is a starting substrate for the biosynthesis of deoxynivalenol (DON), was simultaneously produced by activated β-oxidation. Furthermore, the content of 4-aminobutyrate (GABA) was increased in the agmatine addition culture medium. GABA can be synthesized from agmatine through putrescine and might influence the regulation of DON-related genes.

Proteomic and metabolomic profiles of marine Vibrio sp. 010 in response to an antifoulant challenge

KAUST Repository

Chandramouli, Kondethimmanahalli

2013-08-01

Vibrio spp. have the ability to form biofilms, which may contribute to the subsequent successful colonization by microfouling and macrofouling organisms. The effects of an antifouling compound, poly-ether B, on Vibrio sp. 010 were investigated using flow cytometry, proteomics, and metabolomics. A 2-D gel-based proteomic analysis was used to identify proteins responsive to poly-ether B treatment. The profiles of biofilm metabolites were analyzed by ultra-performance liquid chromatography-mass spectrometry. Poly-ether B caused a significant reduction in viability. The proteins affected by the treatment were related to nucleotide metabolism, the glyoxylate cycle, and stress responses. Metabolites such as tripeptides, fatty acids, and quorum-sensing molecules were regulated differentially. Down-regulation of proteins and metabolites potentially led to a loss in colonisation ability, thereby affecting the structure of the biofilm. These results suggest that the proteins and metabolites identified may serve as target molecules for potent antifouling compounds. © 2013 Copyright Taylor and Francis Group, LLC.

Proteins involved in flor yeast carbon metabolism under biofilm formation conditions.

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Moreno-García, Jaime; García-Martínez, Teresa; Moreno, Juan; Mauricio, Juan Carlos

2015-04-01

A lack of sugars during the production of biologically aged wines after fermentation of grape must causes flor yeasts to metabolize other carbon molecules formed during fermentation (ethanol and glycerol, mainly). In this work, a proteome analysis involving OFFGEL fractionation prior to LC/MS detection was used to elucidate the carbon metabolism of a flor yeast strain under biofilm formation conditions (BFC). The results were compared with those obtained under non-biofilm formation conditions (NBFC). Proteins associated to processes such as non-fermentable carbon uptake, the glyoxylate and TCA cycles, cellular respiration and inositol metabolism were detected at higher concentrations under BFC than under the reference conditions (NBFC). This study constitutes the first attempt at identifying the flor yeast proteins responsible for the peculiar sensory profile of biologically aged wines. A better metabolic knowledge of flor yeasts might facilitate the development of effective strategies for improved production of these special wines. Copyright © 2014 Elsevier Ltd. All rights reserved.

Phosphorylation of glyoxysomal malate synthase from castor oil seed endosperm and cucumber cotyledon

International Nuclear Information System (INIS)

Yang, Y.P; Randall, D.D.

1989-01-01

Glyoxysomal malate synthase (MS) was purified to apparent homogeneity from 3-d germinating castor oil seed endosperm by a relatively simple procedure including two sucrose density gradient centrifugations. Antibodies raised to the caster oil seed MS crossreacted with MS from cucumber cotyledon. MS was phosphorylated in both tissues in an MgATP dependent reaction. The phosphorylation pattern was similar for both enzymes and both enzymes were inhibited by NaF, NaMo, (NH 4 )SO 4 , glyoxylate and high concentration of MgCl 2 (60 mM), but was not inhibited by NaCl and malate. Further characterization of the phosphorylation of MS from castor oil seed endosperms showed that the 5S form of MS is the form which is labelled by 32 P. The addition of exogenous alkaline phosphatase to MS not only decreased enzyme activity, but could also dephosphorylate phospho-MS. The relationship between dephosphorylation of MS and the decrease of MS activity is currently under investigation

Interactions of Neuropathogenic Escherichia coli K1 (RS218) and Its Derivatives Lacking Genomic Islands with Phagocytic Acanthamoeba castellanii and Nonphagocytic Brain Endothelial Cells

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Yousuf, Farzana Abubakar; Yousuf, Zuhair; Iqbal, Junaid; Siddiqui, Ruqaiyyah; Khan, Hafsa; Khan, Naveed Ahmed

2014-01-01

Here we determined the role of various genomic islands in E. coli K1 interactions with phagocytic A. castellanii and nonphagocytic brain microvascular endothelial cells. The findings revealed that the genomic islands deletion mutants of RS218 related to toxins (peptide toxin, α-hemolysin), adhesins (P fimbriae, F17-like fimbriae, nonfimbrial adhesins, Hek, and hemagglutinin), protein secretion system (T1SS for hemolysin), invasins (IbeA, CNF1), metabolism (D-serine catabolism, dihydroxyacetone, glycerol, and glyoxylate metabolism) showed reduced interactions with both A. castellanii and brain microvascular endothelial cells. Interestingly, the deletion of RS218-derived genomic island 21 containing adhesins (P fimbriae, F17-like fimbriae, nonfimbrial adhesins, Hek, and hemagglutinin), protein secretion system (T1SS for hemolysin), invasins (CNF1), metabolism (D-serine catabolism) abolished E. coli K1-mediated HBMEC cytotoxicity in a CNF1-independent manner. Therefore, the characterization of these genomic islands should reveal mechanisms of evolutionary gain for E. coli K1 pathogenicity. PMID:24818136

Interactions of Neuropathogenic Escherichia coli K1 (RS218 and Its Derivatives Lacking Genomic Islands with Phagocytic Acanthamoeba castellanii and Nonphagocytic Brain Endothelial Cells

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Farzana Abubakar Yousuf

2014-01-01

Full Text Available Here we determined the role of various genomic islands in E. coli K1 interactions with phagocytic A. castellanii and nonphagocytic brain microvascular endothelial cells. The findings revealed that the genomic islands deletion mutants of RS218 related to toxins (peptide toxin, α-hemolysin, adhesins (P fimbriae, F17-like fimbriae, nonfimbrial adhesins, Hek, and hemagglutinin, protein secretion system (T1SS for hemolysin, invasins (IbeA, CNF1, metabolism (D-serine catabolism, dihydroxyacetone, glycerol, and glyoxylate metabolism showed reduced interactions with both A. castellanii and brain microvascular endothelial cells. Interestingly, the deletion of RS218-derived genomic island 21 containing adhesins (P fimbriae, F17-like fimbriae, nonfimbrial adhesins, Hek, and hemagglutinin, protein secretion system (T1SS for hemolysin, invasins (CNF1, metabolism (D-serine catabolism abolished E. coli K1-mediated HBMEC cytotoxicity in a CNF1-independent manner. Therefore, the characterization of these genomic islands should reveal mechanisms of evolutionary gain for E. coli K1 pathogenicity.

daf-16/FoxO promotes gluconeogenesis and trehalose synthesis during starvation to support survival

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Hibshman, Jonathan D; Doan, Alexander E; Moore, Brad T; Kaplan, Rebecca EW; Hung, Anthony; Webster, Amy K; Bhatt, Dhaval P; Chitrakar, Rojin; Hirschey, Matthew D

2017-01-01

daf-16/FoxO is required to survive starvation in Caenorhabditis elegans, but how daf-16IFoxO promotes starvation resistance is unclear. We show that daf-16/FoxO restructures carbohydrate metabolism by driving carbon flux through the glyoxylate shunt and gluconeogenesis and into synthesis of trehalose, a disaccharide of glucose. Trehalose is a well-known stress protectant, capable of preserving membrane organization and protein structure during abiotic stress. Metabolomic, genetic, and pharmacological analyses confirm increased trehalose synthesis and further show that trehalose not only supports survival as a stress protectant but also serves as a glycolytic input. Furthermore, we provide evidence that metabolic cycling between trehalose and glucose is necessary for this dual function of trehalose. This work demonstrates that daf-16/FoxO promotes starvation resistance by shifting carbon metabolism to drive trehalose synthesis, which in turn supports survival by providing an energy source and acting as a stress protectant. PMID:29063832

Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction. Reprinted from Biotechnology and Bioengineering, Vol. 41, Pp 633-646 (1993).

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Vallino, J J; Stephanopoulos, G

2000-03-20

The two main contributions of this article are the solidification of Corynebacterium glutamicum biochemistry guided by bioreaction network analysis, and the determination of basal metabolic flux distributions during growth and lysine synthesis. Employed methodology makes use of stoichiometrically based mass balances to determine flux distributions in the C. glutamicum metabolic network. Presented are a brief description of the methodology, a thorough literature review of glutamic acid bacteria biochemistry, and specific results obtained through a combination of fermentation studies and analysis-directed intracellular assays. The latter include the findings of the lack of activity of glyoxylate shunt, and that phosphoenolpyruvate carboxylase (PPC) is the only anaplerotic reaction expressed in C. glutamicum cultivated on glucose minimal media. Network simplifications afforded by the above findings facilitated the determination of metabolic flux distributions under a variety of culture conditions and led to the following conclusions. Both the pentose phosphate pathway and PPC support significant fluxes during growth and lysine overproduction, and that flux partitioning at the glucosa-6-phosphate branch point does not appear to limit lysine synthesis. Copyright 1993 John Wiley & Sons, Inc.

The Glycerate and Phosphorylated Pathways of Serine Synthesis in Plants: The Branches of Plant Glycolysis Linking Carbon and Nitrogen Metabolism.

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Igamberdiev, Abir U; Kleczkowski, Leszek A

2018-01-01

Serine metabolism in plants has been studied mostly in relation to photorespiration where serine is formed from two molecules of glycine. However, two other pathways of serine formation operate in plants and represent the branches of glycolysis diverging at the level of 3-phosphoglyceric acid. One branch (the glycerate - serine pathway) is initiated in the cytosol and involves glycerate formation from 3-phosphoglycerate, while the other (the phosphorylated serine pathway) operates in plastids and forms phosphohydroxypyruvate as an intermediate. Serine formed in these pathways becomes a precursor of glycine, formate and glycolate accumulating in stress conditions. The pathways can be linked to GABA shunt via transamination reactions and via participation of the same reductase for both glyoxylate and succinic semialdehyde. In this review paper we present a hypothesis of the regulation of redox balance in stressed plant cells via participation of the reactions associated with glycerate and phosphorylated serine pathways. We consider these pathways as important processes linking carbon and nitrogen metabolism and maintaining cellular redox and energy levels in stress conditions.

Curcumin improves alcoholic fatty liver by inhibiting fatty acid biosynthesis.

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Guo, Chang; Ma, Jingfan; Zhong, Qionghong; Zhao, Mengyuan; Hu, Tianxing; Chen, Tong; Qiu, Longxin; Wen, Longping

2017-08-01

Alcoholic fatty liver is a threat to human health. It has been long known that abstinence from alcohol is the most effective therapy, other effective therapies are not available for the treatment in humans. Curcumin has a great potential for anti-oxidation and anti-inflammation, but the effect on metabolic reconstruction remains little known. Here we performed metabolomic analysis by gas chromatography/mass spectrometry and explored ethanol pathogenic insight as well as curcumin action pattern. We identified seventy-one metabolites in mouse liver. Carbohydrates and lipids were characteristic categories. Pathway analysis results revealed that ethanol-induced pathways including biosynthesis of unsaturated fatty acids, fatty acid biosynthesis and pentose and glucuronate interconversions were suppressed by curcumin. Additionally, ethanol enhanced galactose metabolism and pentose phosphate pathway. Glyoxylate and dicarboxylate metabolism and pyruvate metabolism were inhibited in mice fed ethanol diet plus curcumin. Stearic acid, oleic acid and linoleic acid were disease biomarkers and therapical biomarkers. These results reflect the landscape of hepatic metabolism regulation. Our findings illustrate ethanol pathological pathway and metabolic mechanism of curcumin therapy. Copyright © 2017. Published by Elsevier Inc.

Conformational Stability, Structural Parameters And Vibrational Assignments of Allantoin

International Nuclear Information System (INIS)

Haman, S.

2008-01-01

Allantoin 2,5-Dioxo-4-imidazolinyl) urea , the diureide of glyoxylic acid, is a crystallisable oxidation product of uric acid found in allantoic and amniotic fluids, in fetal urine and in many plants. It is a healing, moisturizing, soothing and anti-irritating, keratolytic and non-toxic agent useful in dermatological, cosmetic and veterinary preparation. The optimized geometries and energies of the low-energy conformers of allantoin have been calculated using density functional theory (Daft) method. The calculations were performed with Beck's nonlocal three-parameter hybrid functional in combination with the Lee, Yang, and Parr correlation functional (By-play) using the 6-311++G(d,p) basis set. We calculated the infrared frequencies and intensities of the most stable conformers in order to assist in the assignment of the vibrational bands in the experimental spectrum. The B3LYP/6-311+G(d,p) harmonic force constants were scaled by applying the scaled quantum mechanical force field (SQM) technique. The calculated vibrational spectra were interpreted and band assignments were reported

Systematic engineering of TCA cycle for optimal production of a four-carbon platform chemical 4-hydroxybutyric acid in Escherichia coli.

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Choi, Sol; Kim, Hyun Uk; Kim, Tae Yong; Lee, Sang Yup

2016-11-01

To address climate change and environmental problems, it is becoming increasingly important to establish biorefineries for the production of chemicals from renewable non-food biomass. Here we report the development of Escherichia coli strains capable of overproducing a four-carbon platform chemical 4-hybroxybutyric acid (4-HB). Because 4-HB production is significantly affected by aeration level, genome-scale metabolic model-based engineering strategies were designed under aerobic and microaerobic conditions with emphasis on oxidative/reductive TCA branches and glyoxylate shunt. Several different metabolic engineering strategies were employed to develop strains suitable for fermentation both under aerobic and microaerobic conditions. It was found that microaerobic condition was more efficient than aerobic condition in achieving higher titer and productivity of 4-HB. The final engineered strain produced 103.4g/L of 4-HB by microaerobic fed-batch fermentation using glycerol. The aeration-dependent optimization strategy of TCA cycle will be useful for developing microbial strains producing other reduced derivative chemicals of TCA cycle intermediates. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Proteome and membrane fatty acid analyses on Oligotropha carboxidovorans OM5 grown under chemolithoautotrophic and heterotrophic conditions.

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Debarati Paul

Full Text Available Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405 is a chemolithoautotrophic bacterium able to utilize CO and H(2 to derive energy for fixation of CO(2. Thus, it is capable of growth using syngas, which is a mixture of varying amounts of CO and H(2 generated by organic waste gasification. O. carboxidovorans is capable also of heterotrophic growth in standard bacteriologic media. Here we characterize how the O. carboxidovorans proteome adapts to different lifestyles of chemolithoautotrophy and heterotrophy. Fatty acid methyl ester (FAME analysis of O. carboxidovorans grown with acetate or with syngas showed that the bacterium changes membrane fatty acid composition. Quantitative shotgun proteomic analysis of O. carboxidovorans grown in the presence of acetate and syngas showed production of proteins encoded on the megaplasmid for assimilating CO and H(2 as well as proteins encoded on the chromosome that might have contributed to fatty acid and acetate metabolism. We found that adaptation to chemolithoautotrophic growth involved adaptations in cell envelope, oxidative homeostasis, and metabolic pathways such as glyoxylate shunt and amino acid/cofactor biosynthetic enzymes.

Pool of resistance mechanisms to glyphosate in Digitaria insularis.

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de Carvalho, Leonardo Bianco; Alves, Pedro Luis da Costa Aguiar; González-Torralva, Fidel; Cruz-Hipolito, Hugo Enrique; Rojano-Delgado, Antonia María; De Prado, Rafael; Gil-Humanes, Javier; Barro, Francisco; de Castro, María Dolores Luque

2012-01-18

Digitaria insularis biotypes resistant to glyphosate have been detected in Brazil. Studies were carried out in controlled conditions to determine the role of absorption, translocation, metabolism, and gene mutation as mechanisms of glyphosate resistance in D. insularis. The susceptible biotype absorbed at least 12% more (14)C-glyphosate up to 48 h after treatment (HAT) than resistant biotypes. High differential (14)C-glyphosate translocation was observed at 12 HAT, so that >70% of the absorbed herbicide remained in the treated leaf in resistant biotypes, whereas 42% remained in the susceptible biotype at 96 HAT. Glyphosate was degraded to aminomethylphosphonic acid (AMPA), glyoxylate, and sarcosine by >90% in resistant biotypes, whereas a small amount of herbicide (up to 11%) was degraded by the susceptible biotype up to 168 HAT. Two amino acid changes were found at positions 182 and 310 in EPSPS, consisting of a proline to threonine and a tyrosine to cysteine substitution, respectively, in resistant biotypes. Therefore, absorption, translocation, metabolism, and gene mutation play an important role in the D. insularis glyphosate resistance.

Fermentation characteristics in conversion of organic acids obtained by oxidation of low-rank coals to poly({beta}-hydroxybutyrate) using A. eutrophus cells with some analysis on metabolic flux distribution; Kattan no ekisosanka de erareru yukisan wo suiso saikin wo riyoshite pori {beta}-hidorokishi rakusan (PHB) ni henkansaseru tameno baiyo kogakuteki kento to taisha ryusoku bunpu shisutemu kaiseki

Energy Technology Data Exchange (ETDEWEB)

Tsujimoto, Shoko.; Shin, Huidong.; Shimizu, Kazuyuki. [Kyushu Institute of Technology, Fukuoka (Japan). Department of Biochemical engineering and science; Mae, Kazuhiro.; Miura, Koichi. [Kyoto University, Kyoto (Japan). Department of Chemical Engineering

1999-03-10

Fermentation characteristics are investigated for the conversion of glycolate, acetate, formate, and malonate obtained by the oxidation of low-rank coals to poly ({beta}-hydrox butyrate) (PHB) using A. eutrophus cells. Based on the cultivation experiments using one of the organic acids as a sole carbon source, it is found that acetate is the most effectively converted to PHB. When mixed organic acids are used, formate is preferentially consumed, followed by acetate, and finally glycolate. Although malate can not be utilized, it is implied that it might change the pathway flux distributions based on the metabolic flux analysis. Namely, it shows competitive inhibition to succinate dehydrogenase so that its addition during fermentation results in flux reduction from succinate to maleic acid as well as glyoxylate flux and gluconeogenesis flux. It is also found that NADPH generated from isocitrate is preferentially utilized for the reaction from {alpha}-ketoglutarate to glutamate when NH{sub 3} concentration is high, while it is eventually used for the PHB production from acetoacetyl CoA as NH{sub 3} concentration decreases. (author)

Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP.

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Kim, Donghyuk; Seo, Sang Woo; Gao, Ye; Nam, Hojung; Guzman, Gabriela I; Cho, Byung-Kwan; Palsson, Bernhard O

2018-04-06

Two major transcriptional regulators of carbon metabolism in bacteria are Cra and CRP. CRP is considered to be the main mediator of catabolite repression. Unlike for CRP, in vivo DNA binding information of Cra is scarce. Here we generate and integrate ChIP-exo and RNA-seq data to identify 39 binding sites for Cra and 97 regulon genes that are regulated by Cra in Escherichia coli. An integrated metabolic-regulatory network was formed by including experimentally-derived regulatory information and a genome-scale metabolic network reconstruction. Applying analysis methods of systems biology to this integrated network showed that Cra enables optimal bacterial growth on poor carbon sources by redirecting and repressing glycolysis flux, by activating the glyoxylate shunt pathway, and by activating the respiratory pathway. In these regulatory mechanisms, the overriding regulatory activity of Cra over CRP is fundamental. Thus, elucidation of interacting transcriptional regulation of core carbon metabolism in bacteria by two key transcription factors was possible by combining genome-wide experimental measurement and simulation with a genome-scale metabolic model.

Redistribution of metabolic fluxes in Chlorella protothecoides by variation of media nitrogen concentration

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Saratram Gopalakrishnan

2015-12-01

Full Text Available In this study, the Elementary Metabolite Unit (EMU algorithm was employed to calculate intracellular fluxes for Chlorella protothecoides using previously generated growth and mass spec data. While the flux through glycolysis remained relatively constant, the pentose phosphate pathway (PPP flux increased from 3% to 20% of the glucose uptake during nitrogen-limited growth. The TCA cycle flux decreased from 94% to 38% during nitrogen-limited growth while the flux of acetyl-CoA into lipids increased from 58% to 109% of the glucose uptake, increasing total lipid accumulation. Phosphoenolpyruvate carboxylase (PEPCase activity was higher during nitrogen-sufficient growth. The glyoxylate shunt was found to be partially active in both cases, indicating the nutrient nature has an impact on flux distribution. It was found that the total NADPH supply within the cell remained almost constant under both conditions. In summary, algal cells substantially reorganize their metabolism during the switch from carbon-limited (nitrogen-sufficient to nitrogen-limited (carbon-sufficient growth. Keywords: Microalgae, Biofuels, Chlorella, MFA, EMU algorithm

Proteomic profile response of Paracoccidioides lutzii to the antifungal argentilactone

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Renata Silva Do Prado

2015-06-01

Full Text Available The dimorphic fungi Paracoccidioides spp. are the etiological agents of paracoccidioidomycosis (PCM, a mycosis of high incidence in Brazil. The toxicity of drug treatment and the emergence of resistant organisms have led to research for new candidates for drugs. In this study, we demonstrate that the natural product argentilactone was not cytotoxic or genotoxic to MRC5 cells at the IC50 concentration to the fungus. We also verified the proteomic profile of Paracoccidioides lutzii after incubation with argentilactone using a label free quantitative proteome nanoUPLC-MSE. The results of this study indicated that the fungus has a global metabolic adaptation in the presence of argentilactone. Enzymes of important pathways, such as glycolysis, the Krebs cycle and the glyoxylate cycle, were repressed, which drove the metabolism to the methylcytrate cycle and beta-oxidation. Proteins involved in cell rescue, defense and stress response were induced. In this study, alternative metabolic pathways adopted by the fungi were elucidated, helping to elucidate the course of action of the compound studied.

Effects of nitrogen infiltration into plant tissue on the metabolism of carbon, with special reference to Themeda triandra Forssk

Energy Technology Data Exchange (ETDEWEB)

Amory, A M

1983-01-01

The infiltration of nitrate and ammonia into Themeda triandra and Zea mays leaf tissue influenced the carbon dioxide gas exchange characteristics: 1) the carbon dioxide compensation point increased, 2) the net photosynthetic rate was increased by the nitrate ion and decreased by the ammonium ion, and 3) dark respiration was unaffected. /sup 14/CO/sub 2/ assimilation and the partitioning of /sup 14/C by Themeda triandra leaves were influenced by the infiltration of both forms of nitrogen; the amino acid fraction changed in both composition and concentration. Nitrogen infiltration increased the activities of the following enzymes: aspartate amino-transferase, PEP carboxylase and RuBP carboxylase. Methionine sulphoximine (inhibitor of glutamate synthetase) increased the carbon dioxide compensation point and formate pool size. Infiltration of nitrate and ammonia enhanced the /sup 14/C uptake from labelled glycolate, glyoxylate and formate into the water soluble fraction of Themeda triandra leaves. The activities of RuBP carboxylase and RuBP oxygenase (to a greater extent) were increased by the addition of nitrate and ammonia in vitro.

The radiolytic and radiolytically induced gas generation in Hanford waste tanks

International Nuclear Information System (INIS)

Jonah, C.D.; Meisel, D.; Sauer, M.C. Jr.

1994-01-01

A task force operating in ANL/CHM has been developing a mechanistic understanding of the radiolytic processes that lead to the generation and retention of gases within tanks of radioactive waste at the Hanford site. This chemistry is one of the important factors that must be considered in devising remediation procedures to eliminate the great potential hazard of these tanks. A quantitative description of much of the chemistry involved in the production of H 2 and, to a lesser extent, in the production of N 2 O has been achieved. Direct radiolytic generation was experimentally quantified and this new information was utilized in computer modeling to provide predictive capabilities so that changes of chemical composition of various waste tanks under different remediation procedures could be assessed. Oxygen in the waste solutions is effectively consumed upon irradiation and thus is of no concern. The mechanism of the radiolytic degradation of the chelators was established. The end products are simple organic molecules, in particularly, formaldehyde and glyoxylate, that are very efficient in the thermal generation of H 2

Urinary Metabolomic Study of Chlorogenic Acid in a Rat Model of Chronic Sleep Deprivation Using Gas Chromatography-Mass Spectrometry

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Wei-ni Ma

2018-01-01

Full Text Available The urinary metabolomic study based on gas chromatography-mass spectrometry (GC-MS had been developed to investigate the possible antidepressant mechanism of chlorogenic acid (CGA in a rat model of sleep deprivation (SD. According to pattern recognition analysis, there was a clear separation among big platform group (BP, sleep deprivation group (SD, and the CGA (model + CGA, and CGA group was much closer to the BP group by showing a tendency of recovering towards BP group. Thirty-six significantly changed metabolites related to antidepressant by CGA were identified and used to explore the potential mechanism. Combined with the result of the classic behavioral tests and biochemical indices, CGA has significant antidepressant effects in a rat model of SD, suggesting that the mechanism of action of CGA might be involved in regulating the abnormal pathway of nicotinate and nicotinamide metabolism; glyoxylate and dicarboxylate metabolism; glycine, serine, and threonine metabolism; and arginine and proline metabolism. Our results also show that metabolomics analysis based on GC-MS is a useful tool for exploring biomarkers involved in depression and elucidating the potential therapeutic mechanisms of Chinese medicine.

Physiologically based pharmacokinetic modeling of dibromoacetic acid in F344 rats

International Nuclear Information System (INIS)

Matthews, Jessica L.; Schultz, Irvin R.; Easterling, Michael R.; Melnick, Ronald L.

2010-01-01

A novel physiologically based pharmacokinetic (PBPK) model structure, which includes submodels for the common metabolites (glyoxylate (GXA) and oxalate (OXA)) that may be involved in the toxicity or carcinogenicity of dibromoacetic acid (DBA), has been developed. Particular attention is paid to the representation of hepatic metabolism, which is the primary elimination mechanism. DBA-induced suicide inhibition is modeled by irreversible covalent binding of the intermediate metabolite α-halocarboxymethylglutathione (αH1) to the glutathione-S-transferase zeta (GSTzeta) enzyme. We also present data illustrating the presence of a secondary non-GSTzeta metabolic pathway for DBA, but not dichloroacetic acid (DCA), that produces GXA. The model is calibrated with plasma and urine concentration data from DBA exposures in female F344 rats through intravenous (IV), oral gavage, and drinking water routes. Sensitivity analysis is performed to confirm identifiability of estimated parameters. Finally, model validation is performed with data sets not used during calibration. Given the structural similarity of dihaloacetates (DHAs), we hypothesize that the PBPK model presented here has the capacity to describe the kinetics of any member or mixture of members of this class in any species with the alteration of chemical-and species-specific parameters.

Production of itaconic acid from acetate by engineering acid-tolerant Escherichia coli W.

Science.gov (United States)

Noh, Myung Hyun; Lim, Hyun Gyu; Woo, Sung Hwa; Song, Jinyi; Jung, Gyoo Yeol

2018-03-01

Utilization of abundant and cheap carbon sources can effectively reduce the production cost and enhance the economic feasibility. Acetate is a promising carbon source to achieve cost-effective microbial processes. In this study, we engineered an Escherichia coli strain to produce itaconic acid from acetate. As acetate is known to inhibit cell growth, we initially screened for a strain with a high tolerance to 10 g/L of acetate in the medium, and the W strain was selected as the host. Subsequently, the WC strain was obtained by overexpression of cad (encoding cis-aconitate decarboxylase) using a synthetic promoter and 5' UTR. However, the WC strain produced only 0.13 g/L itaconic acid because of low acetate uptake. To improve the production, the acetate assimilating pathway and glyoxylate shunt pathway were amplified by overexpression of pathway genes as well as its deregulation. The resulting strain, WCIAG4 produced 3.57 g/L itaconic acid (16.1% of theoretical maximum yield) after 88 hr of fermentation with rapid acetate assimilation. These efforts support that acetate can be a potential feedstock for biochemical production with engineered E. coli. © 2017 Wiley Periodicals, Inc.

Carnosine and anserine homeostasis in skeletal muscle and heart is controlled by β‐alanine transamination

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Blancquaert, Laura; Baba, Shahid P.; Kwiatkowski, Sebastian; Stautemas, Jan; Stegen, Sanne; Barbaresi, Silvia; Chung, Weiliang; Boakye, Adjoa A.; Hoetker, J. David; Bhatnagar, Aruni; Delanghe, Joris; Vanheel, Bert; Veiga‐da‐Cunha, Maria; Derave, Wim

2016-01-01

Key points Using recombinant DNA technology, the present study provides the first strong and direct evidence indicating that β‐alanine is an efficient substrate for the mammalian transaminating enzymes 4‐aminobutyrate‐2‐oxoglutarate transaminase and alanine‐glyoxylate transaminase.The concentration of carnosine and anserine in murine skeletal and heart muscle depends on circulating availability of β‐alanine, which is in turn controlled by degradation of β‐alanine in liver and kidney.Chronic oral β‐alanine supplementation is a popular ergogenic strategy in sports because it can increase the intracellular carnosine concentration and subsequently improve the performance of high‐intensity exercises. The present study can partly explain why the β‐alanine supplementation protocol is so inefficient, by demonstrating that exogenous β‐alanine can be effectively routed toward oxidation. Abstract The metabolic fate of orally ingested β‐alanine is largely unknown. Chronic β‐alanine supplementation is becoming increasingly popular for improving high‐intensity exercise performance because it is the rate‐limiting precursor of the dipeptide carnosine (β‐alanyl‐l‐histidine) in muscle. However, only a small fraction (3–6%) of the ingested β‐alanine is used for carnosine synthesis. Thus, the present study aimed to investigate the putative contribution of two β‐alanine transamination enzymes, namely 4‐aminobutyrate‐2‐oxoglutarate transaminase (GABA‐T) and alanine‐glyoxylate transaminase (AGXT2), to the homeostasis of carnosine and its methylated analogue anserine. We found that, when transfected into HEK293T cells, recombinant mouse and human GABA‐T and AGXT2 are able to transaminate β‐alanine efficiently. The reaction catalysed by GABA‐T is inhibited by vigabatrin, whereas both GABA‐T and AGXT2 activity is inhibited by aminooxyacetic acid (AOA). Both GABA‐T and AGXT2 are highly expressed in the mouse liver and

Synthesis and chemical characterization of the novel agronomically relevant pentadentate chelate 2-(2-((2-hydroxybenzyl)amino)ethylamino)-2-(2-hydroxyphenyl)acetic acid (DCHA).

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López-Rayo, Sandra; Hernández, Diana; Lucena, Juan J; Escudero, Rosa; Gómez-Gallego, Mar; Sierra, Miguel A

2010-07-14

Iron chelates analogous to o,o-EDDHA/Fe(3+) are the fertilizers chosen to treat iron chlorosis in plants growing on calcareous soil. The isomer o,p-EDDHA/Fe(3+) presents less stability but faster assimilation by the plant than o,o-EDDHA/Fe(3+), because only five coordinating groups are able to complex Fe(3+). The new chelating agent 2-(2-((2-hydroxybenzyl)amino)ethylamino)-2-(2-hydroxyphenyl)acetic acid (DCHA) has been synthesized to obtain an iron fertilizer with intermediate stability between o,o-EDDHA/Fe(3+) and o,p-EDDHA/Fe(3+) and with fast assimilation. Its synthesis has been done starting from phenol, N-acetylethylendiamine, glyoxylic acid, and NaOH in a three-step sequence. The purity of the DCHA chelating agent, its protonation, and Ca(2+), Mg(2+), Fe(3+), and Cu(2+) stability constants, together with its ability to maintain iron in solution in different agronomic conditions, have been determined. The results indicate that the chelate DCHA/Fe(3+) has intermediate stability between those of o,o-EDDHA/Fe(3+) and o,p-EDDHA/Fe(3+) complexes and that it is capable of maintaining the Fe(3+) in agronomic conditions. This new chelating agent may be effective in correcting iron chlorosis in plants.

Use of an adipocyte model to study the transcriptional adaptation of Mycobacterium tuberculosis to store and degrade host fat

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Shivangi Rastogi

2016-01-01

Full Text Available During its persistence in the infected host, Mycobacterium tuberculosis (Mtb accumulates host-derived fatty acids in intracytoplasmic lipid inclusions as triacylglycerols which serve primarily as carbon and energy reserves. The Mtb genome codes for more than 15 triacylglycerol synthases, 24 lipase/esterases, and seven cutinase-like proteins. Hence, we looked at the expression of the corresponding genes in intracellular bacilli persisting amidst the host triacylglycerols. We used the Mtb infected murine adipocyte model to ensure persistence and transcripts were quantified using real-time reverse transcriptase polymerase chain reaction. Dormancy and glyoxylate metabolism was confirmed by the upregulated expression of dosR and icl, respectively, by intra-adipocyte bacilli compared with in vitro growing bacilli. The study revealed that tgs1, tgs2, Rv3371, and mycolyltransferase Ag85A are the predominant triacylglycerol synthases, while lipF, lipH, lipJ, lipK, lipN, lipV, lipX, lipY, culp5, culp7, and culp6 are the predominant lipases/esterases used by Mtb for the storage and degradation of host-derived fat. Moreover, it was observed that many of these enzymes are used by Mtb during active replication rather than during nonreplicating persistence, indicating their probable function in cell wall synthesis.

Changes in δ(13)C of dark respired CO2 and organic matter of different organs during early ontogeny in peanut plants.

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Ghashghaie, Jaleh; Badeck, Franz W; Girardin, Cyril; Sketriené, Diana; Lamothe-Sibold, Marlène; Werner, Roland A

2015-01-01

Carbon isotope composition in respired CO2 and organic matter of individual organs were measured on peanut seedlings during early ontogeny in order to compare fractionation during heterotrophic growth and transition to autotrophy in a species with lipid seed reserves with earlier results obtained on beans. Despite a high lipid content in peanut seeds (48%) compared with bean seeds (1.5%), the isotope composition of leaf- and root-respired CO2 as well as its changes during ontogeny were similar to already published data on bean seedlings: leaf-respired CO2 became (13)C-enriched reaching -21.5‰, while root-respired CO2 became (13)C-depleted reaching around -31‰ at the four-leaf stage. The opposite respiratory fractionation in leaves vs. roots already reported for C3 herbs was thus confirmed for peanuts. However, contrarily to beans, the peanut cotyledon-respired CO2 was markedly (13)C-enriched, and its (13)C-depletion was noted from the two-leaf stage onwards only. Carbohydrate amounts being very low in peanut seeds, this cannot be attributed solely to their use as respiratory substrate. The potential role of isotope fractionation during glyoxylate cycle and/or gluconeogenesis on the (13)C-enriched cotyledon-respired CO2 is discussed.

Studies on the nature of intermediates in enzyme mechanisms

International Nuclear Information System (INIS)

Clark, J.D.

1988-01-01

The reaction pathway followed by malate synthase has been studied by the double isotope fractionation method to determine whether the reaction is stepwise or concerted. A primary deuterium kinetic isotope effect ( D V/K) of 1.3 ± 0.1 has been found using [ 2 H 3 ]acetyl-CoA as substrate. The 13 C isotope effect at the aldehydic carbon of glyoxylate has also been measured. For this determination, the malate product was quantitatively transformed into a new sample of malate having the carbon of interest at C-4. This material was decarboxylated to produce the appropriate CO 2 for isotope ratio mass spectrometric analysis. If the essential Zn(II) ion of yeast aldolase interacts with the carbonyl groups of bound substrates, we can expect that these will be more reactive toward reduction by borohydrides than those free in solution. Tritiated sodium borohydride was therefore used to reduce the substrates of yeast aldolase in the presence and absence of enzyme, and the enantiomeric and diastereomeric ratios of the products were analyzed. Experiments were conducted in an effort to distinguish between endocyclic and exocyclic cleavage in the hydrolysis catalyzed by lysozyme. Tritiated sodium borohydride was used in an attempt to trap the putative oxocarbonium intermediate

Mannich reactions of alkynes: the role of sub-stoichiometric amounts of stable polymeric alkynylcopper (I) compounds in the catalytic cycle (abstract)

International Nuclear Information System (INIS)

Khan, A.N.; Buckley, B.R.; Heaney, H.

2011-01-01

The rapid development of the use of organocopper reagents and catalysts in organic synthesis since the middle of the last century has been comprehensively documented. The advantages of using heterogeneous catalysts include ease of work-up and purification, reduction in waste disposal, and the ability to recycle catalysts. Reactions of terminal alkynes that involve copper(I) catalysts have been widely studied, in particular as a result of the search for atom efficiency. Ligand associated alkynylcopper(I) derivatives have been reported many times, for example in copper(I) catalysed alkyne-azide cycloaddition (CuAAC) reactions. Our interest in Mannich reactions, and also in alkynylcopper(I) pre-catalysts, prompted this study of reactions of alkynes with secondary amines with aldehydes. Early studies of Mannich reactions involving alkynes almost always involved formaldehyde, exceptions included imines and derivatives of glyoxylic esters. An efficient one-pot three-component coupling of an aldehyde, alkyne, and amine to generate propargyl amines has been effected by microwave heating in water using a polymeric alkynylcopper(I) complex as catalyst (Scheme 1). This reaction utilizes water as a solvent which provides a green-approach for such reactions. This method has proved to be applicable to a wide range of substrates. (author)

Investigation on the Metabolic Regulation of pgi gene knockout Escherichia coli by Enzyme Activities and Intracellular Metabolite Concentrations

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Nor ‘Aini, A. R.

2006-01-01

Full Text Available An integrated analysis of the cell growth characteristics, enzyme activities, intracellular metabolite concentrations was made to investigate the metabolic regulation of pgi gene knockout Escherichia coli based on batch culture and continuous culture which was performed at the dilution rate of 0.2h-1. The enzymatic study identified that pathways of pentose phosphate, ED pathway and glyoxylate shunt were all active in pgi mutant. The glycolysis enzymes i.e glyceraldehyde-3-phosphate dehydrogenase, fructose diphosphatase, pyruvate kinase, triose phosphate isomerase were down regulated implying that the inactivation of pgi gene reduced the carbon flux through glycolytic pathway. Meanwhile, the pentose phosphate pathway was active as a major route for intermediary carbohydrate metabolism instead of glycolysis. The pentose phosphate pathway generates most of the major reducing co-factor NADPH as shown by the increased of NADPH/NADP+ ratio in the mutant when compared with the parent strain. The fermentative enzymes such as acetate kinase and lactate dehydrogenase were down regulated in the mutant. Knockout of pgi gene results in the significant increase in the intracellular concentration of glucose-6-phosphate and decrease in the concentration of oxaloacetate. The slow growth rate of the mutant was assumed to be affected by the accumulation of glucose-6-phosphate and imbalance of NADPH reoxidation.

The Deletion of the Succinate Dehydrogenase Gene KlSDH1 in Kluyveromyces lactis Does Not Lead to Respiratory Deficiency

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Saliola, Michele; Bartoccioni, Paola Chiara; De Maria, Ilaria; Lodi, Tiziana; Falcone, Claudio

2004-01-01

We have isolated a Kluyveromyces lactis mutant unable to grow on all respiratory carbon sources with the exception of lactate. Functional complementation of this mutant led to the isolation of KlSDH1, the gene encoding the flavoprotein subunit of the succinate dehydrogenase (SDH) complex, which is essential for the aerobic utilization of carbon sources. Despite the high sequence conservation of the SDH genes in Saccharomyces cerevisiae and K. lactis, they do not have the same relevance in the metabolism of the two yeasts. In fact, unlike SDH1, KlSDH1 was highly expressed under both fermentative and nonfermentative conditions. In addition to this, but in contrast with S. cerevisiae, K. lactis strains lacking KlSDH1 were still able to grow in the presence of lactate. In these mutants, oxygen consumption was one-eighth that of the wild type in the presence of lactate and was normal with glucose and ethanol, indicating that the respiratory chain was fully functional. Northern analysis suggested that alternative pathway(s), which involves pyruvate decarboxylase and the glyoxylate cycle, could overcome the absence of SDH and allow (i) lactate utilization and (ii) the accumulation of succinate instead of ethanol during growth on glucose. PMID:15189981

Increased riboflavin production from activated bleaching earth by a mutant strain of Ashbya gossypii.

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Tajima, Satoshi; Itoh, Yoko; Sugimoto, Takashi; Kato, Tatsuya; Park, Enoch Y

2009-10-01

The production of riboflavin from vegetable oil was increased using a mutant strain of Ashbya gossypii. This mutant was generated by treating the wild-type strain with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Riboflavin production was 10-fold higher in the mutant compared to the wild-type strain. The specific intracellular catalase activity after 3 d of culture was 6-fold higher in the mutant than in the wild-type strain. For the mutant, riboflavin production in the presence of 40 mM hydrogen peroxide was 16% less than that in the absence of hydrogen peroxide, whereas it was 56% less for the wild-type strain. The isocitrate lyase (ICL) activity of the mutant was 0.26 mU/mg of protein during the active riboflavin production phase, which was 2.6-fold higher than the wild-type strain. These data indicate that the mutant utilizes the carbon flux from the TCA cycle to the glyoxylate cycle more efficiently than the wild-type strain, resulting in enhanced riboflavin production. This novel mutant has the potential to be of use for industrial-scale riboflavin production from waste-activated bleaching earth (ABE), thereby transforming a useless material into a valuable bioproduct.

Hormonal regulation of gluconeogenesis in cereal aleurone is strongly cultivar-dependent and gibberellin action involves SLENDER1 but not GAMYB.

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Eastmond, Peter J; Jones, Russell L

2005-11-01

Storage oil is a major constituent in the cereal aleurone layer. The aim of this study was to investigate how gibberellin (GA) and abscisic acid (ABA) regulate conversion of oil to sugar in barley aleurone. The activity of the glyoxylate cycle enzyme isocitrate lyase (ICL) was surveyed in eight barley cultivars. Surprisingly, some cultivars do not require GA for the induction of ICL (e.g. Himalaya), whereas some do (e.g. Golden Promise). Furthermore, in Golden Promise, GA also stimulates triacylglycerol breakdown and enhances the net flux of carbon from acetate to sugar. In contrast, ABA strongly represses ICL activity and the flux of carbon from oil to sugar in both Golden Promise and Himalaya. Biolistics using a promoter reporter showed that GA and ABA regulate ICL at the level of transcription. Studies using barley and rice mutants and pharmacological agents show that GA-dependent induction of ICL activity is mediated by SLENDER1 and requires cGMP, but does not involve the transcription factor GAMYB. Gibberellin and ABA therefore act antagonistically to regulate gluconeogenesis in the aleurone layer as well as controlling the production and secretion of hydrolases into the starchy endosperm. We suggest that the variation between different barley cultivars might be a result of selective breeding to alter seed dormancy.

The malate synthase of Paracoccidioides brasiliensis is a linked surface protein that behaves as an anchorless adhesin

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Pereira Maristela

2009-12-01

Full Text Available Abstract Background The pathogenic fungus Paracoccidioides brasiliensis is the agent of paracoccidioidomycosis (PCM. This is a pulmonary mycosis acquired by inhalation of fungal airborne propagules that can disseminate to several organs and tissues leading to a severe form of the disease. Adhesion and invasion to host cells are essential steps involved in the internalization and dissemination of pathogens. Inside the host, P. brasiliensis may use the glyoxylate cycle for intracellular survival. Results Here, we provide evidence that the malate synthase of P. brasiliensis (PbMLS is located on the fungal cell surface, and is secreted. PbMLS was overexpressed in Escherichia coli, and polyclonal antibody was obtained against this protein. By using Confocal Laser Scanning Microscopy, PbMLS was detected in the cytoplasm and in the cell wall of the mother, but mainly of budding cells of the P. brasiliensis yeast phase. PbMLSr and its respective polyclonal antibody produced against this protein inhibited the interaction of P. brasiliensis with in vitro cultured epithelial cells A549. Conclusion These observations indicated that cell wall-associated PbMLS could be mediating the binding of fungal cells to the host, thus contributing to the adhesion of fungus to host tissues and to the dissemination of infection, behaving as an anchorless adhesin.

Multifaceted roles of metabolic enzymes of the Paracoccidioides species complex

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Caroline Maria Marcos

2014-12-01

Full Text Available Paracoccidioides species are dimorphic fungi, and are the etiologic agents of paracoccidioidomycosis (PCM, a serious disease of multiple organs. The large number of tissues colonized by this fungus suggests the presence of a variety of surface molecules involved in adhesion. A surprising finding is that the majority of enzymes in the glycolytic pathway, tricarboxylic acid (TCA cycle and glyoxylate cycle in Paracoccidioides spp. has adhesive properties that aid in the interaction with the host extracellular matrix, and so act as ‘moonlighting’ proteins. Moonlighting proteins have multiple functions and add another dimension to cellular complexity, while benefiting cells in several ways. This phenomenon occurs in both eukaryotes and prokaryotes. For example, moonlighting proteins from the glycolytic pathway or TCA cycle can play roles in bacterial pathogens, either by acting as proteins secreted in a conventional pathway or not and/or as cell surface component that facilitate adhesion or adherence . This review outlines the multifuncionality exposed by a variety of Paracoccidioides spp. enzymes including aconitase, aldolase, glyceraldehyde-3-phosphate dehydrogenase, isocitrate lyase, malate synthase, triose phosphate isomerase, fumarase and enolase. The roles that moonlighting activities play in the virulence characteristics of this fungus and several other human pathogens during their interactions with the host are discussed.

Comparative proteomics analysis of engineered Saccharomyces cerevisiae with enhanced biofuel precursor production.

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Xiaoling Tang

Full Text Available The yeast Saccharomyces cerevisiae was metabolically modified for enhanced biofuel precursor production by knocking out genes encoding mitochondrial isocitrate dehydrogenase and over-expression of a heterologous ATP-citrate lyase. A comparative iTRAQ-coupled 2D LC-MS/MS analysis was performed to obtain a global overview of ubiquitous protein expression changes in S. cerevisiae engineered strains. More than 300 proteins were identified. Among these proteins, 37 were found differentially expressed in engineered strains and they were classified into specific categories based on their enzyme functions. Most of the proteins involved in glycolytic and pyruvate branch-point pathways were found to be up-regulated and the proteins involved in respiration and glyoxylate pathway were however found to be down-regulated in engineered strains. Moreover, the metabolic modification of S. cerevisiae cells resulted in a number of up-regulated proteins involved in stress response and differentially expressed proteins involved in amino acid metabolism and protein biosynthesis pathways. These LC-MS/MS based proteomics analysis results not only offered extensive information in identifying potential protein-protein interactions, signal pathways and ubiquitous cellular changes elicited by the engineered pathways, but also provided a meaningful biological information platform serving further modification of yeast cells for enhanced biofuel production.

Distribution and Evolution of Peroxisomes in Alveolates (Apicomplexa, Dinoflagellates, Ciliates)

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Ludewig-Klingner, Ann-Kathrin; Michael, Victoria; Jarek, Michael; Brinkmann, Henner

2018-01-01

Abstract The peroxisome was the last organelle to be discovered and five decades later it is still the Cinderella of eukaryotic compartments. Peroxisomes have a crucial role in the detoxification of reactive oxygen species, the beta-oxidation of fatty acids, and the biosynthesis of etherphospholipids, and they are assumed to be present in virtually all aerobic eukaryotes. Apicomplexan parasites including the malaria and toxoplasmosis agents were described as the first group of mitochondriate protists devoid of peroxisomes. This study was initiated to reassess the distribution and evolution of peroxisomes in the superensemble Alveolata (apicomplexans, dinoflagellates, ciliates). We established transcriptome data from two chromerid algae (Chromera velia, Vitrella brassicaformis), and two dinoflagellates (Prorocentrum minimum, Perkinsus olseni) and identified the complete set of essential peroxins in all four reference species. Our comparative genome analysis provides unequivocal evidence for the presence of peroxisomes in Toxoplasma gondii and related genera. Our working hypothesis of a common peroxisomal origin of all alveolates is supported by phylogenetic analyses of essential markers such as the import receptor Pex5. Vitrella harbors the most comprehensive set of peroxisomal proteins including the catalase and the glyoxylate cycle and it is thus a promising model organism to investigate the functional role of this organelle in Apicomplexa. PMID:29202176

Pathway confirmation and flux analysis of central metabolicpathways in Desulfovibrio vulgaris Hildenborough using gaschromatography-mass spectrometry and fourier transform-ion cyclotronresonance mass spectrometry

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Tang, Yinjie; Pingitore, Francesco; Mukhopadhyay, Aindrila; Phan,Richard; Hazen, Terry C.; Keasling, Jay D.

2006-07-11

It has been proposed that during growth under anaerobic oroxygen-limited conditions Shewanella oneidensis MR-1 uses theserine-isocitrate lyase pathway common to many methylotrophic anaerobes,in which formaldehyde produced from pyruvate is condensed with glycine toform serine. The serine is then transformed through hydroxypyruvate andglycerate to enter central metabolism at phosphoglycerate. To examine itsuse of the serine-isocitrate lyase pathway under anaerobic conditions, wegrew S. oneidensis MR-1 on [1-13C]lactate as the sole carbon source witheither trimethylamine N-oxide (TMAO) or fumarate as an electron acceptor.Analysis of cellular metabolites indicates that a large percentage(>75 percent) of lactate was partially oxidized to either acetate orpyruvate. The 13C isotope distributions in amino acids and other keymetabolites indicate that, under anaerobic conditions, a complete serinepathway is not present, and lactate is oxidized via a highly reversibleserine degradation pathway. The labeling data also suggest significantactivity in the anaplerotic (malic enzyme and phosphoenolpyruvatecarboxylase) and glyoxylate shunt (isocitrate lyase and malate synthase)reactions. Although the tricarboxylic acid (TCA) cycle is often observedto be incomplete in many other anaerobes (absence of 2-oxoglutaratedehydrogenase activity), isotopic labeling supports the existence of acomplete TCA cycle in S. oneidensis MR-1 under TMAO reductioncondition.

Differential metabolism of Mycoplasma species as revealed by their genomes

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Fabricio B.M. Arraes

2007-01-01

Full Text Available The annotation and comparative analyses of the genomes of Mycoplasma synoviae and Mycoplasma hyopneumonie, as well as of other Mollicutes (a group of bacteria devoid of a rigid cell wall, has set the grounds for a global understanding of their metabolism and infection mechanisms. According to the annotation data, M. synoviae and M. hyopneumoniae are able to perform glycolytic metabolism, but do not possess the enzymatic machinery for citrate and glyoxylate cycles, gluconeogenesis and the pentose phosphate pathway. Both can synthesize ATP by lactic fermentation, but only M. synoviae can convert acetaldehyde to acetate. Also, our genome analysis revealed that M. synoviae and M. hyopneumoniae are not expected to synthesize polysaccharides, but they can take up a variety of carbohydrates via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS. Our data showed that these two organisms are unable to synthesize purine and pyrimidine de novo, since they only possess the sequences which encode salvage pathway enzymes. Comparative analyses of M. synoviae and M. hyopneumoniae with other Mollicutes have revealed differential genes in the former two genomes coding for enzymes that participate in carbohydrate, amino acid and nucleotide metabolism and host-pathogen interaction. The identification of these metabolic pathways will provide a better understanding of the biology and pathogenicity of these organisms.

The plant homolog to the human sodium/dicarboxylic cotransporter is the vacuolar malate carrier.

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Emmerlich, Vera; Linka, Nicole; Reinhold, Thomas; Hurth, Marco A; Traub, Michaela; Martinoia, Enrico; Neuhaus, H Ekkehard

2003-09-16

Malate plays a central role in plant metabolism. It is an intermediate in the Krebs and glyoxylate cycles, it is the store for CO2 in C4 and crassulacean acid metabolism plants, it protects plants from aluminum toxicity, it is essential for maintaining the osmotic pressure and charge balance, and it is therefore involved in regulation of stomatal aperture. To fulfil many of these roles, malate has to be accumulated within the large central vacuole. Many unsuccessful efforts have been made in the past to identify the vacuolar malate transporter; here, we describe the identification of the vacuolar malate transporter [A. thaliana tonoplast dicarboxylate transporter (AttDT)]. This transporter exhibits highest sequence similarity to the human sodium/dicarboxylate cotransporter. Independent T-DNA [portion of the Ti (tumor-inducing) plasmid that is transferred to plant cells] Arabidopsis mutants exhibit substantially reduced levels of leaf malate, but respire exogenously applied [14C]malate faster than the WT. An AttDT-GFP fusion protein was localized to vacuole. Vacuoles isolated from Arabidopsis WT leaves exhibited carbonylcyanide m-chlorophenylhydrazone and citrate inhibitable malate transport, which was not stimulated by sodium. Vacuoles isolated from mutant plants import [14C]-malate at strongly reduced rates, confirming that this protein is the vacuolar malate transporter.

Impact of Trichloroethylene Exposure on the Microbial Diversity and Protein Expression in Anaerobic Granular Biomass at 37°C and 15°C

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Alma Siggins

2012-01-01

Full Text Available Granular biomass from a laboratory-scale anaerobic bioreactor trial was analysed to identify changes in microbial community structure and function in response to temperature and trichloroethylene (TCE. Two bioreactors were operated at 37°C, while two were operated at 15°C. At the time of sampling, one of each temperature pair of bioreactors was exposed to process failure-inducing concentrations of TCE (60 mg L−1 while the other served as a TCE-free control. Bacterial community structure was investigated using denaturing gradient gel electrophoresis (DGGE and 16S rRNA gene clone library analysis. Temperature was identified as an important factor for bacterial community composition, while minor differences were associated with trichloroethylene supplementation. Proteobacteria was the dominant phylum in all bioreactors, while clone library analysis revealed a higher proportion of Bacteroidetes-, Chloroflexi-, and Firmicutes-like clones at 15°C than at 37°C. Comparative metaproteomics in the presence and absence of TCE was carried out by two-dimensional gel electrophoresis (2-DGE, and 28 protein spots were identified, with putative functions related to cellular processes, including methanogenesis, glycolysis, the glyoxylate cycle, and the methyl malonyl pathway. A good agreement between metaproteomic species assignment and phylogenetic information was observed, with 10 of the identified proteins associated with members of the phylum Proteobacteria.

Functional Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System.

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Hideto Takami

Full Text Available In this study, the metabolic and physiological potential evaluator system based on Kyoto Encyclopedia of Genes and Genomes (KEGG functional modules was employed to establish a functional classification of archaeal species and to determine the comprehensive functions (functionome of the previously uncultivated thermophile "Candidatus Caldiarchaeum subterraneum" (Ca. C. subterraneum. A phylogenetic analysis based on the concatenated sequences of proteins common among 142 archaea and 2 bacteria, and among 137 archaea and 13 unicellular eukaryotes suggested that Ca. C. subterraneum is closely related to thaumarchaeotic species. Consistent with the results of the phylogenetic analysis, clustering and principal component analyses based on the completion ratio patterns for all KEGG modules in 79 archaeal species suggested that the overall metabolic and physiological potential of Ca. C. subterraneum is similar to that of thaumarchaeotic species. However, Ca. C. subterraneum possessed almost no genes in the modules required for nitrification and the hydroxypropionate-hydroxybutyrate cycle for carbon fixation, unlike thaumarchaeotic species. However, it possessed all genes in the modules required for central carbohydrate metabolism, such as glycolysis, pyruvate oxidation, the tricarboxylic acid (TCA cycle, and the glyoxylate cycle, as well as multiple sets of sugar and branched chain amino acid ABC transporters. These metabolic and physiological features appear to support the predominantly aerobic character of Ca. C. subterraneum, which lives in a subsurface thermophilic microbial mat community with a heterotrophic lifestyle.

The investigation of anti-inflammatory activity of Yi Guanjian decoction by serum metabonomics approach.

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Shui, Sufang; Cai, Xiaorong; Huang, Rongqing; Xiao, Bingkun; Yang, Jianyun

2017-01-30

Yi Guanjian (YGJ), one of the Chinese herbal medicines most commonly used in western countries, reported to possess significant anti-inflammatary effects that inhibit the process of inflammation. However, the mechanisms underlying its anti-inflammation effects remain largely unresolved. This study was aimed to investigate the anti-inflammatory activity of YGJ and to explore its potential anti-inflammatory mechanisms by serum metabonomics approach. An xylene-induced mouse right-ear-edema model was used as an inflammatory response in vivo model. Ear edema, prostaglandin E2 (PGE 2 ) and Tumor-Necrosis-Factor-alpha (TNF-α) were detected. Then, serum metabolic profiling was analyzed and pathway analysis performed on the biomarkers reversed after YGJ administration and further integration of metabolic networks. The results showed that YGJ alleviated ear edema and decreased serum PGE 2 and TNF-α levels. Fourteen biomarkers were screened, and the levels were all reversed to different degrees after YGJ administration. These biomarkers were mainly related to linoleic acid metabolism, taurine and hypotaurine metabolism, glyoxylate and dicarboxylate metabolism, glycine, serine and threonine metabolism and citrate cycle (TCA cycle). In metabolic networks, glycine and pyruvate were node molecules. This indicated that YGJ could significantly inhibit inflammatory response triggered by acute local stimulation and exerted anti-inflammatory activity mainly by regulating node molecules. Copyright © 2016 Elsevier B.V. All rights reserved.

First confirmation and characterization of target and non-target site resistance to glyphosate in Palmer amaranth (Amaranthus palmeri) from Mexico.

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Dominguez-Valenzuela, Jose Alfredo; Gherekhloo, Javid; Fernández-Moreno, Pablo Tomás; Cruz-Hipolito, Hugo Enrique; Alcántara-de la Cruz, Ricardo; Sánchez-González, Eduardo; De Prado, Rafael

2017-06-01

Following the introduction of glyphosate-resistant (GR)-cotton crops in Mexico, farmers have relied upon glyphosate as being the only herbicide for in-season weed control. Continuous use of glyphosate within the same year and over multiple successive years has resulted in the selection of glyphosate resistance in Palmer amaranth (Amarantus palmeri). Dose-response assays confirmed resistance in seven different accessions. The resistance ratio based on GR 50 values (50% growth reduction) varied between 12 and 83. At 1000 μM glyphosate, shikimic acid accumulation in the S-accession was 30- to 2-fold higher at compared to R-accessions. At 96 h after treatment, 35-44% and 61% of applied 14 C-glyphosate was taken up by leaves of plants from R- and S-accessions, respectively. At this time, a significantly higher proportion of the glyphosate absorbed remained in the treated leaf of R-plants (55-69%) compared to S-plants (36%). Glyphosate metabolism was low and did not differ between resistant and susceptible plants. Glyphosate was differentially metabolized to AMPA and glyoxylate in plants of R- and S-accessions, although it was low in both accessions (glyphosate collected from GR-cotton crops from Mexico. This is the first study demonstrating glyphosate-resistance in Palmer amaranth from Mexico. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Gluconeogenesis from Storage Wax in the Cotyledons of Jojoba Seedlings 1

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Moreau, Robert A.; Huang, Anthony H. C.

1977-01-01

The cotyledons of jojoba (Simmondsia chinensis) seeds contained 50 to 60% of their weight as intracellular wax esters. During germination there was a gradual decrease in the wax content with a concomitant rise in soluble carbohydrates, suggesting that the wax played the role of a food reserve. Thin layer chromatography revealed that both the fatty alcohol and fatty acid were metabolized. The disappearance of wax was matched with an increase of catalase, a marker enzyme of the gluconeogenic process in other fatty seedlings. Subcellular organelles were isolated by sucrose gradient centrifugation from the cotyledons at the peak stage of germination. The enzymes of the β oxidation of fatty acid and of the glyoxylate cycle were localized in the glyoxysomes but not in the mitochondria. The glyoxysomes had specific activities of individual enzymes similar to those of the castor bean glyoxysomes. An active alkaline lipase was detected in the wax bodies at the peak stage of germination but not in the ungerminated seeds. No lipase was detected in glyoxysomes or mitochondria. After the wax in the wax bodies had been extracted with diethyl ether, the organelle membrane was isolated and it still retained the alkaline lipase. The gluconeogenesis from wax in the jojoba seedling appears to be similar, but with modification, to that from triglyceride in other fatty seedlings. Images PMID:16660087

Gluconeogenesis from storage wax in the cotyledons of jojoba seedlings.

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Moreau, R A; Huang, A H

1977-08-01

The cotyledons of jojoba (Simmondsia chinensis) seeds contained 50 to 60% of their weight as intracellular wax esters. During germination there was a gradual decrease in the wax content with a concomitant rise in soluble carbohydrates, suggesting that the wax played the role of a food reserve. Thin layer chromatography revealed that both the fatty alcohol and fatty acid were metabolized. The disappearance of wax was matched with an increase of catalase, a marker enzyme of the gluconeogenic process in other fatty seedlings. Subcellular organelles were isolated by sucrose gradient centrifugation from the cotyledons at the peak stage of germination. The enzymes of the beta oxidation of fatty acid and of the glyoxylate cycle were localized in the glyoxysomes but not in the mitochondria. The glyoxysomes had specific activities of individual enzymes similar to those of the castor bean glyoxysomes. An active alkaline lipase was detected in the wax bodies at the peak stage of germination but not in the ungerminated seeds. No lipase was detected in glyoxysomes or mitochondria. After the wax in the wax bodies had been extracted with diethyl ether, the organelle membrane was isolated and it still retained the alkaline lipase. The gluconeogenesis from wax in the jojoba seedling appears to be similar, but with modification, to that from triglyceride in other fatty seedlings.

Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways.

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Lee, Yun; Lafontaine Rivera, Jimmy G; Liao, James C

2014-09-01

Metabolic pathways in cells must be sufficiently robust to tolerate fluctuations in expression levels and changes in environmental conditions. Perturbations in expression levels may lead to system failure due to the disappearance of a stable steady state. Increasing evidence has suggested that biological networks have evolved such that they are intrinsically robust in their network structure. In this article, we presented Ensemble Modeling for Robustness Analysis (EMRA), which combines a continuation method with the Ensemble Modeling approach, for investigating the robustness issue of non-native pathways. EMRA investigates a large ensemble of reference models with different parameters, and determines the effects of parameter drifting until a bifurcation point, beyond which a stable steady state disappears and system failure occurs. A pathway is considered to have high bifurcational robustness if the probability of system failure is low in the ensemble. To demonstrate the utility of EMRA, we investigate the bifurcational robustness of two synthetic central metabolic pathways that achieve carbon conservation: non-oxidative glycolysis and reverse glyoxylate cycle. With EMRA, we determined the probability of system failure of each design and demonstrated that alternative designs of these pathways indeed display varying degrees of bifurcational robustness. Furthermore, we demonstrated that target selection for flux improvement should consider the trade-offs between robustness and performance. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Variation in the transcriptional response of threatened coral larvae to elevated temperatures.

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Polato, Nicholas R; Altman, Naomi S; Baums, Iliana B

2013-03-01

Coral populations have declined worldwide largely due to increased sea surface temperatures. Recovery of coral populations depends in part upon larval recruitment. Many corals reproduce during the warmest time of year when further increases in temperature can lead to low fertilization rates of eggs and high larval mortality. Microarray experiments were designed to capture and assess variability in the thermal stress responses of Acropora palmata larvae from Puerto Rico. Transcription profiles showed a striking acceleration of normal developmental gene expression patterns with increased temperature. The transcriptional response to heat suggested rapid depletion of larval energy stores via peroxisomal lipid oxidation and included key enzymes that indicated the activation of the glyoxylate cycle. High temperature also resulted in expression differences in key developmental signalling genes including the conserved WNT pathway that is critical for pattern formation and tissue differentiation in developing embryos. Expression of these and other important developmental and thermal stress genes such as ferritin, heat shock proteins, cytoskeletal components, cell adhesion and autophagy proteins also varied among larvae derived from different parent colonies. Disruption of normal developmental and metabolic processes will have negative impacts on larval survival and dispersal as temperatures rise. However, it appears that variation in larval response to high temperature remains despite the dramatic population declines. Further research is needed to determine whether this variation is heritable or attributable to maternal effects. © 2013 Blackwell Publishing Ltd.

Impact of environmental volatile organic compounds on otitis media in children: Correlation between exposure and urinary metabolites.

Science.gov (United States)

Kim, So Young; Son, Bu-Soon; Park, Hee-Jin; Oh, Seung Ha; Lee, Jun Ho; Suh, Myung-Hwan; Park, Moo Kyun

2017-02-01

Volatile organic compounds (VOCs) induce inflammatory responses. Tobacco smoke contains numerous VOCs and is a risk factor for otitis media effusion (OME); however, no previous studies have investigated the association between VOCs and OME. We used urinary metabolites and exposure to environmental risk factors to investigate the association between VOC and polycyclic aromatic hydrocarbon exposure and recurrent OME in children. Children with recurrent OME who visited the Otorhinolaryngology Department of Seoul National University Hospital between November 2014 and June 2015 were prospectively enrolled in the study. Recurrent OME was defined as more than two OME episodes over a 6-month period lasting longer than 2 months. The control group consisted of children without OME in the last year. Demographic information, including age, sex, and previous medical history was obtained, and endoscopic examinations of the tympanic membrane were performed. Urinary concentrations of 1-hydroxypyrene, 2-naphthol, hippuric acid, trans, trans-muconic acid (t,t-MA), mandelic acid, phenyl glyoxylic acid, and methyl hippuric acid were analyzed using high-performance liquid chromatography/tandem mass spectroscopy. Environmental factors assessed included house type, age, renovations, the presence of furniture children with OME and 39 controls. Age and sex did not differ between groups. Exposure to passive smoking was significantly more common in the OME group than in the controls (P children. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

An impaired metabolic response to hydrostatic pressure explains Alcanivorax borkumensis recorded distribution in the deep marine water column

KAUST Repository

Scoma, Alberto

2016-08-12

Alcanivorax borkumensis is an ubiquitous model organism for hydrocarbonoclastic bacteria, which dominates polluted surface waters. Its negligible presence in oil-contaminated deep waters (as observed during the Deepwater Horizon accident) raises the hypothesis that it may lack adaptive mechanisms to hydrostatic pressure (HP). The type strain SK2 was tested under 0.1, 5 and 10 MPa (corresponding to surface water, 500 and 1000 m depth, respectively). While 5 MPa essentially inactivated SK2, further increase to 10 MPa triggered some resistance mechanism, as indicated by higher total and intact cell numbers. Under 10 MPa, SK2 upregulated the synthetic pathway of the osmolyte ectoine, whose concentration increased from 0.45 to 4.71 fmoles cell-1. Central biosynthetic pathways such as cell replication, glyoxylate and Krebs cycles, amino acids metabolism and fatty acids biosynthesis, but not β-oxidation, were upregulated or unaffected at 10 MPa, although total cell number was remarkably lower with respect to 0.1 MPa. Concomitantly, expression of more than 50% of SK2 genes was downregulated, including genes related to ATP generation, respiration and protein translation. Thus, A. borkumensis lacks proper adaptation to HP but activates resistance mechanisms. These consist in poorly efficient biosynthetic rather than energy-yielding degradation-related pathways, and suggest that HP does represent a major driver for its distribution at deep-sea.

Molecular Recognition of PTS-1 Cargo Proteins by Pex5p: Implications for Protein Mistargeting in Primary Hyperoxaluria

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Noel Mesa-Torres

2015-02-01

Full Text Available Peroxisomal biogenesis and function critically depends on the import of cytosolic proteins carrying a PTS1 sequence into this organelle upon interaction with the peroxin Pex5p. Recent structural studies have provided important insights into the molecular recognition of cargo proteins by Pex5p. Peroxisomal import is a key feature in the pathogenesis of primary hyperoxaluria type 1 (PH1, where alanine:glyoxylate aminotransferase (AGT undergoes mitochondrial mistargeting in about a third of patients. Here, we study the molecular recognition of PTS1 cargo proteins by Pex5p using oligopeptides and AGT variants bearing different natural PTS1 sequences, and employing an array of biophysical, computational and cell biology techniques. Changes in affinity for Pex5p (spanning over 3–4 orders of magnitude reflect different thermodynamic signatures, but overall bury similar amounts of molecular surface. Structure/energetic analyses provide information on the contribution of ancillary regions and the conformational changes induced in Pex5p and the PTS1 cargo upon complex formation. Pex5p stability in vitro is enhanced upon cargo binding according to their binding affinities. Moreover, we provide evidence that the rational modulation of the AGT: Pex5p binding affinity might be useful tools to investigate mistargeting and misfolding in PH1 by pulling the folding equilibria towards the native and peroxisomal import competent state.

LC–MS Proteomics Analysis of the Insulin/IGF-1-Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism

Energy Technology Data Exchange (ETDEWEB)

Depuydt, Geert; Xie, Fang; Petyuk, Vladislav A.; Smolders, Arne; Brewer, Heather M.; Camp, David G.; Smith, Richard D.; Braeckman, Bart P.

2014-04-04

The insulin/IGF-1 receptor is a major known determinant of dauer formation, stress resistance, longevity, and metabolism in Caenorhabditis elegans. In the past, whole-genome transcript profiling was used extensively to study differential gene expression in response to reduced insulin/IGF-1 signaling, including the expression levels of metabolism-associated genes. Taking advantage of the recent developments in quantitative liquid chromatography mass spectrometry (LC–MS)-based proteomics, we profiled the proteomic changes that occur in response to activation of the DAF-16 transcription factor in the germline-less glp-4(bn2);daf-2(e1370) receptor mutant. Strikingly, the daf-2 profile suggests extensive reorganization of intermediary metabolism, characterized by the upregulation of many core intermediary metabolic pathways. These include glycolysis/gluconeogenesis, glycogenesis, pentose phosphate cycle, citric acid cycle, glyoxylate shunt, fatty acid β-oxidation, one-carbon metabolism, propionate and tyrosine catabolism, and complexes I, II, III, and V of the electron transport chain. Interestingly, we found simultaneous activation of reciprocally regulated metabolic pathways, which is indicative of spatiotemporal coordination of energy metabolism and/or extensive post-translational regulation of these enzymes. Finally, this restructuring of daf-2 metabolism is reminiscent to that of hypometabolic dauers, allowing the efficient and economical utilization of internal nutrient reserves and possibly also shunting metabolites through alternative energy-generating pathways to sustain longevity.

LC-MS Proteomics Analysis of the Insulin/IGF-1 Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism

Energy Technology Data Exchange (ETDEWEB)

Depuydt, Geert G.; Xie, Fang; Petyuk, Vladislav A.; Smolders, Arne; Brewer, Heather M.; Camp, David G.; Smith, Richard D.; Braeckman, Bart P.

2014-02-20

The insulin/IGF-1 receptor is a major known determinant of dauer formation, stress resistance, longevity and metabolism in C. elegans. In the past, whole-genome transcript profiling was used extensively to study differential gene expression in response to reduced insulin/IGF-1 signaling, including expression levels of metabolism-associated genes. Taking advantage of the recent developments in quantitative liquid chromatography mass-spectrometry (LC-MS) based proteomics, we profiled the proteomic changes that occur in response to activation of the DAF-16 transcription factor in the germline-less glp-4(bn2); daf-2(e1370) receptor mutant. Strikingly, the daf-2 profile suggests extensive reorganization of intermediary metabolism, characterized by the up-regulation of many core intermediary metabolic pathways. These include, glycolysis/gluconeogenesis, glycogenesis, pentose phosphate cycle, citric acid cycle, glyoxylate shunt, fatty acid β-oxidation, one-carbon metabolism, propionate and tyrosine catabolism, and complex I, II, III and V of the electron transport chain. Interestingly, we found simultaneous activation of reciprocally regulated metabolic pathways, which is indicative for spatio-temporal coordination of energy metabolism and/or extensive post-translational regulation of these enzymes. This restructuring of daf-2 metabolism is reminiscent to that of hypometabolic dauers, allowing the efficient and economical utilization of internal nutrient reserves, possibly also shunting metabolites through alternative energy-generating pathways, in order to sustain longevity.

Analysis of the enzymatic properties of a broad family of alanine aminotransferases.

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Chandra H McAllister

Full Text Available Alanine aminotransferase (AlaAT has been studied in a variety of organisms due to the involvement of this enzyme in mammalian processes such as non-alcoholic hepatocellular damage, and in plant processes such as C4 photosynthesis, post-hypoxic stress response and nitrogen use efficiency. To date, very few studies have made direct comparisons of AlaAT enzymes and fewer still have made direct comparisons of this enzyme across a broad spectrum of organisms. In this study we present a direct kinetic comparison of glutamate:pyruvate aminotransferase (GPAT activity for seven AlaATs and two glutamate:glyoxylate aminotransferases (GGAT, measuring the K(M values for the enzymes analyzed. We also demonstrate that recombinant expression of AlaAT enzymes in Eschericia coli results in differences in bacterial growth inhibition, supporting previous reports of AlaAT possessing bactericidal properties, attributed to lipopolysaccharide endotoxin recognition and binding. A probable lipopolysaccharide binding region within the AlaAT enzymes, homologous to a region of a lipopolysaccharide binding protein (LBP in humans, was also identified in this study. The AlaAT enzyme differences identified here indicate that AlaAT homologues have differentiated significantly and the roles these homologues play in vivo may also have diverged significantly. Specifically, the differing kinetics of AlaAT enzymes and how this may alter the nitrogen use efficiency in plants is discussed.

The Shewanella oneidensis MR-1 Fluxome under Various OxygenConditions

Energy Technology Data Exchange (ETDEWEB)

Tang, Yinjie J.; Hwang, Judy S.; Wemmer, David E.; Keasling, Jay D.

2006-03-17

The central metabolic fluxes of Shewanella oneidensis MR-1were examined under carbon-limited (aerobic) and oxygen-limited(micro-aerobic) chemostat conditions using 13C labeled lactate as thesole carbon source. The carbon labeling patterns of key amino acids inbiomass were probed using both GC-MS and 13C-NMR. Based on the genomeannotation, a metabolic pathway model was constructed to quantify thecentral metabolic flux distributions. The model showed that thetricarboxylic acid (TCA) cycle is the major carbon metabolism route underboth conditions. The Entner-Doudoroff and pentose phosphate pathways weremainly utilized for biomass synthesis (flux below 5 percent of thelactate uptake rate). The anapleurotic reactions (pyruvate to malate andoxaloacetate to phosphoenolpyruvate) and the glyoxylate shunt wereactive. Under carbon-limited conditions, a substantial amount of carbonwas oxidized via the highly reversible serine metabolic pathway. Fluxesthrough the TCA cycle were less whereas acetate production was more underoxygen limitation than under carbon limitation. Although fluxdistributions under aerobic, micro-aerobic, and shake-flask cultureconditions were dramatically different, the relative flux ratios of thecentral metabolic reactions did not vary significantly. Hence, S.oneidensis metabolism appears to be quite robust to environmentalchanges. Our study also demonstrates the merit of coupling GC-MS with 13CNMR for metabolic flux analysis to reduce the use of 13C labeledsubstrates and to obtain more accurate flux values.

Rewiring yeast acetate metabolism through MPC1 loss of function leads to mitochondrial damage and decreases chronological lifespan

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Ivan Orlandi

2014-11-01

Full Text Available During growth on fermentable substrates, such as glucose, pyruvate, which is the end-product of glycolysis, can be used to generate acetyl-CoA in the cytosol via acetaldehyde and acetate, or in mitochondria by direct oxidative decarboxylation. In the latter case, the mitochondrial pyruvate carrier (MPC is responsible for pyruvate transport into mitochondrial matrix space. During chronological aging, yeast cells which lack the major structural subunit Mpc1 display a reduced lifespan accompanied by an age-dependent loss of autophagy. Here, we show that the impairment of pyruvate import into mitochondria linked to Mpc1 loss is compensated by a flux redirection of TCA cycle intermediates through the malic enzyme-dependent alternative route. In such a way, the TCA cycle operates in a “branched” fashion to generate pyruvate and is depleted of intermediates. Mutant cells cope with this depletion by increasing the activity of glyoxylate cycle and of the pathway which provides the nucleocytosolic acetyl-CoA. Moreover, cellular respiration decreases and ROS accumulate in the mitochondria which, in turn, undergo severe damage. These acquired traits in concert with the reduced autophagy restrict cell survival of the mpc1∆ mutant during chronological aging. Conversely, the activation of the carnitine shuttle by supplying acetyl-CoA to the mitochondria is sufficient to abrogate the short-lived phenotype of the mutant.

LC–MS Proteomics Analysis of the Insulin/IGF-1-Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism

Science.gov (United States)

2015-01-01

The insulin/IGF-1 receptor is a major known determinant of dauer formation, stress resistance, longevity, and metabolism in Caenorhabditis elegans. In the past, whole-genome transcript profiling was used extensively to study differential gene expression in response to reduced insulin/IGF-1 signaling, including the expression levels of metabolism-associated genes. Taking advantage of the recent developments in quantitative liquid chromatography mass spectrometry (LC–MS)-based proteomics, we profiled the proteomic changes that occur in response to activation of the DAF-16 transcription factor in the germline-less glp-4(bn2);daf-2(e1370) receptor mutant. Strikingly, the daf-2 profile suggests extensive reorganization of intermediary metabolism, characterized by the upregulation of many core intermediary metabolic pathways. These include glycolysis/gluconeogenesis, glycogenesis, pentose phosphate cycle, citric acid cycle, glyoxylate shunt, fatty acid β-oxidation, one-carbon metabolism, propionate and tyrosine catabolism, and complexes I, II, III, and V of the electron transport chain. Interestingly, we found simultaneous activation of reciprocally regulated metabolic pathways, which is indicative of spatiotemporal coordination of energy metabolism and/or extensive post-translational regulation of these enzymes. This restructuring of daf-2 metabolism is reminiscent to that of hypometabolic dauers, allowing the efficient and economical utilization of internal nutrient reserves and possibly also shunting metabolites through alternative energy-generating pathways to sustain longevity. PMID:24555535

Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using gas chromatography-mass spectrometry and fourier transform-ion cyclotron resonance mass spectrometry

International Nuclear Information System (INIS)

Tang, Yinjie; Pingitore, Francesco; Mukhopadhyay, Aindrila; Phan, Richard; Hazen, Terry C.; Keasling, Jay D.

2006-01-01

It has been proposed that during growth under anaerobic or oxygen-limited conditions Shewanella oneidensis MR-1 uses the serine-isocitrate lyase pathway common to many methylotrophic anaerobes, in which formaldehyde produced from pyruvate is condensed with glycine to form serine. The serine is then transformed through hydroxypyruvate and glycerate to enter central metabolism at phosphoglycerate. To examine its use of the serine-isocitrate lyase pathway under anaerobic conditions, we grew S. oneidensis MR-1 on [1-13C] lactate as the sole carbon source with either trimethylamine N-oxide (TMAO) or fumarate as an electron acceptor. Analysis of cellular metabolites indicates that a large percentage (>75 percent) of lactate was partially oxidized to either acetate or pyruvate. The 13C isotope distributions in amino acids and other key metabolites indicate that, under anaerobic conditions, a complete serine pathway is not present, and lactate is oxidized via a highly reversible serine degradation pathway. The labeling data also suggest significant activity in the anaplerotic (malic enzyme and phosphoenolpyruvatecarboxylase) and glyoxylate shunt (isocitrate lyase and malate synthase) reactions. Although the tricarboxylic acid (TCA) cycle is often observed to be incomplete in many other anaerobes (absence of 2-oxoglutaratede hydrogenase activity), isotopic labeling supports the existence of a complete TCA cycle in S. oneidensis MR-1 under TMAO reduction condition

Ethylene- and diethylene glycol metabolism, toxicity and treatment

International Nuclear Information System (INIS)

Wiener, H.L.

1986-01-01

Each year numerous men and domestic animals suffer from ethylene glycol (EG) poisoning. The present approach to treating EG poisoning by administering ethanol is aimed at preventing the oxidation of EG to glycolate, the toxic mediator. When treatment is delayed or the amount of EG consumed is large, successful treatment is rarely obtained, since the concentration of glycolate becomes excessive. In an effort to develop a better approach to treating EG poisoning, studies were conducted to determine the feasibility of using pig liver glycolic acid oxidase (GAO) as a means of enzyme therapy in male rats receiving EG. Pig liver GAO was active in vitro in rat blood, oxidizing glycolate to glyoxylate. When injected intravenously into male rats, GAO had an approximate half-life of twenty five minutes and its elimination followed first order kinetics. Despite activity in vitro, native pig liver GAO did not display detectable activity in vivo. Diethylene glycol (DEG) when ingested also results in toxicity. The metabolism and toxicity of DEG was investigated in male Wistar rats using [ 14 C]-DEG synthesized from [U- 14 C]-EG and ethylene oxide and purified by high performance liquid chromatography. (2-Hydroxyethoxy)acetic acid (HEAA) was identified as the major product of DEG oxidation. These results suggest that the treatment of DEG poisoning should follow the same regimen as treatment for EG poisoning

Impact of Xanthylium Derivatives on the Color of White Wine.

Science.gov (United States)

Bührle, Franziska; Gohl, Anita; Weber, Fabian

2017-08-19

Xanthylium derivatives are yellow to orange pigments with a glyoxylic acid bridge formed by dimerization of flavanols, which are built by oxidative cleavage of tartaric acid. Although their structure and formation under wine-like conditions are well established, knowledge about their color properties and their occurrence and importance in wine is deficient. Xanthylium cations and their corresponding esters were synthesized in a model wine solution and isolated via high-performance countercurrent chromatography (HPCCC) and solid phase extraction (SPE). A Three-Alternative-Forced-Choice (3-AFC) test was applied to reveal the color perception threshold of the isolated compounds in white wine. Their presence and color impact was assessed in 70 different wines (58 white and 12 rosé wines) by UHPLC-DAD-ESI-MS n and the storage stability in wine was determined. The thresholds in young Riesling wine were 0.57 mg/L (cations), 1.04 mg/L (esters) and 0.67 mg/L (1:1 ( w / w ) mixture), respectively. The low thresholds suggest a possible impact on white wine color, but concentrations in wines were below the threshold. The stability study showed the degradation of the compounds during storage under several conditions. Despite the low perception threshold, xanthylium derivatives might have no direct impact on white wine color, but might play a role in color formation as intermediate products in polymerization and browning.

Reconstitution of TCA cycle with DAOCS to engineer Escherichia coli into an efficient whole cell catalyst of penicillin G.

Science.gov (United States)

Lin, Baixue; Fan, Keqiang; Zhao, Jian; Ji, Junjie; Wu, Linjun; Yang, Keqian; Tao, Yong

2015-08-11

Many medically useful semisynthetic cephalosporins are derived from 7-aminodeacetoxycephalosporanic acid (7-ADCA), which has been traditionally made by the polluting chemical method. Here, a whole-cell biocatalytic process based on an engineered Escherichia coli strain expressing 2-oxoglutarate-dependent deacetoxycephalosporin C synthase (DAOCS) for converting penicillin G to G-7-ADCA is developed. The major engineering strategy is to reconstitute the tricarboxylic acid (TCA) cycle of E. coli to force the metabolic flux to go through DAOCS catalyzed reaction for 2-oxoglutarate to succinate conversion. Then the glyoxylate bypass was disrupted to eliminate metabolic flux that may circumvent the reconstituted TCA cycle. Additional engineering steps were taken to reduce the degradation of penicillin G and G-7-ADCA in the bioconversion process. These steps include engineering strategies to reduce acetate accumulation in the biocatalytic process and to knock out a host β-lactamase involved in the degradation of penicillin G and G-7-ADCA. By combining these manipulations in an engineered strain, the yield of G-7-ADCA was increased from 2.50 ± 0.79 mM (0.89 ± 0.28 g/L, 0.07 ± 0.02 g/gDCW) to 29.01 ± 1.27 mM (10.31 ± 0.46 g/L, 0.77 ± 0.03 g/gDCW) with a conversion rate of 29.01 mol%, representing an 11-fold increase compared with the starting strain (2.50 mol%).

Effects of light on respiration and development of photosynthetic cells. Renewal application and progress report, March 1-November 1, 1980

Energy Technology Data Exchange (ETDEWEB)

Gibbs, M.

1980-11-20

The oxyhydrogen reaction in the presence and absence of CO/sub 2/ was studied in H/sub 2/- adapted Scenedesmus obliquus by monitoring the initial rates of H/sub 2/, O/sub 2/, and /sup 14/CO/sub 2/ uptake and the effect of inhibitors on these rates. Glucose and acetate respiration was competitive with H/sub 2/ uptake. KCN inhibited equally respiration and the oxyhydrogen reaction in the presence and absence of CO/sub 2/. It was concluded that the oxyhydrogen reaction both in the absence and presence of CO/sub 2/ has properties in common with components of respiration and photosynthesis. Participation of these two processes in the oxyhydrogen reaction would require a closely linked shuttle between mitochondrion and chloroplast. Protoplasts and chloroplasts will be isolated from a H/sub 2/-adapted alga in order to elucidate the cooperation between the two organelles. Acetate was shown to stimulate H/sub 2/ photoproduction in H/sub 2/-adapted algae even more so than an uncoupler of electron transport. The role of these compounds will be evaluated either in terms of the glyoxylate cycle or electron acceptors resulting in formation of alcohols. The term chloroplast respiration was proposed to account for the breakdown of polyglucan within the chloroplast. A means of reoxidizing reduced pyridine nucleotide was required to complete the cycle. A new enzyme ascorbic acid reduced pyridine nucleotide peroxidase was isolated from the chloroplast. The characterization of this enzyme will continue.

Metabolism of chlorofluorocarbons and polybrominated compounds by Pseudomonas putida G786(pHG-2) via an engineered metabolic pathway.

Science.gov (United States)

Hur, H G; Sadowsky, M J; Wackett, L P

1994-11-01

The recombinant bacterium Pseudomonas putida G786(pHG-2) metabolizes pentachloroethane to glyoxylate and carbon dioxide, using cytochrome P-450CAM and toluene dioxygenase to catalyze consecutive reductive and oxidative dehalogenation reactions (L.P. Wackett, M.J. Sadowsky, L.N. Newman, H.-G. Hur, and S. Li, Nature [London] 368:627-629, 1994). The present study investigated metabolism of brominated and chlorofluorocarbon compounds by the recombinant strain. Under anaerobic conditions, P. putida G786(pHG-2) reduced 1,1,2,2-tetrabromoethane, 1,2-dibromo-1,2-dichloroethane, and 1,1,1,2-tetrachloro-2,2-difluoroethane to products bearing fewer halogen substituents. Under aerobic conditions, P. putida G786(pHG-2) oxidized cis- and trans-1,2-dibromoethenes, 1,1-dichloro-2,2-difluoroethene, and 1,2-dichloro-1-fluoroethene. Several compounds were metabolized by sequential reductive and oxidative reactions via the constructed metabolic pathway. For example, 1,1,2,2-tetrabromoethane was reduced by cytochrome P-450CAM to 1,2-dibromoethenes, which were subsequently oxidized by toluene dioxygenase. The same pathway metabolized 1,1,1,2-tetrachloro-2,2-difluoroethane to oxalic acid as one of the final products. The results obtained in this study indicate that P. putida G786(pHG-2) metabolizes polyfluorinated, chlorinated, and brominated compounds and further demonstrates the value of using a knowledge of catabolic enzymes and recombinant DNA technology to construct useful metabolic pathways.

Kinetics and oxidative mechanism for H2O2-enhanced iron-mediated aeration (IMA) treatment of recalcitrant organic compounds in mature landfill leachate

International Nuclear Information System (INIS)

Deng Yang; Englehardt, James D.

2009-01-01

A hydrogen peroxide (H 2 O 2 )-enhanced iron (Fe 0 )-mediated aeration (IMA) process has been recently demonstrated to effectively remove organic wastes from mature landfill leachate. In this paper, the kinetics and oxidative mechanisms of the enhanced IMA treatment were studied. Bench-scale full factorial tests were conducted in an orbital shaker reactor for treatment of a mature leachate with an initial chemical oxygen demand (COD) of 900-1200 mg/L. At the maximum aeration rate (8.3 mL air/min mL sample), process variables significantly influencing the rates of H 2 O 2 decay and COD removal were pH (3.0-8.0), initial H 2 O 2 doses (0.21-0.84 M), and Fe 0 surface area concentrations (0.06-0.30 m 2 /L). Empirical kinetic models were developed and verified for the degradation of H 2 O 2 and COD. High DO maintained by a high aeration rate slowed the H 2 O 2 self-decomposition, accelerated Fe 0 consumption, and enhanced the COD removal. In hydroxyl radical (OH·) scavenging tests, the rate of removal of glyoxylic acid (target compound) was not inhibited by the addition of para-chlorobenzoic acid (OH· scavenger) at pH 7.0-7.5, ruling out hydroxyl radical as the principal oxidant in neutral-weakly basic solution. These experimental results show that this enhanced IMA technology is a potential alternative for the treatment of high strength recalcitrant organic wastewaters.

Kinetics and oxidative mechanism for H2O2-enhanced iron-mediated aeration (IMA) treatment of recalcitrant organic compounds in mature landfill leachate.

Science.gov (United States)

Deng, Yang; Englehardt, James D

2009-09-30

A hydrogen peroxide (H(2)O(2))-enhanced iron (Fe(0))-mediated aeration (IMA) process has been recently demonstrated to effectively remove organic wastes from mature landfill leachate. In this paper, the kinetics and oxidative mechanisms of the enhanced IMA treatment were studied. Bench-scale full factorial tests were conducted in an orbital shaker reactor for treatment of a mature leachate with an initial chemical oxygen demand (COD) of 900-1200 mg/L. At the maximum aeration rate (8.3 mL air/min mL sample), process variables significantly influencing the rates of H(2)O(2) decay and COD removal were pH (3.0-8.0), initial H(2)O(2) doses (0.21-0.84 M), and Fe(0) surface area concentrations (0.06-0.30 m(2)/L). Empirical kinetic models were developed and verified for the degradation of H(2)O(2) and COD. High DO maintained by a high aeration rate slowed the H(2)O(2) self-decomposition, accelerated Fe(0) consumption, and enhanced the COD removal. In hydroxyl radical (OH*) scavenging tests, the rate of removal of glyoxylic acid (target compound) was not inhibited by the addition of para-chlorobenzoic acid (OH* scavenger) at pH 7.0-7.5, ruling out hydroxyl radical as the principal oxidant in neutral-weakly basic solution. These experimental results show that this enhanced IMA technology is a potential alternative for the treatment of high strength recalcitrant organic wastewaters.

Tailorable thiolated trimethyl chitosans for covalently stabilized nanoparticles.

Science.gov (United States)

Verheul, Rolf J; van der Wal, Steffen; Hennink, Wim E

2010-08-09

A novel four-step method is presented to synthesize partially thiolated trimethylated chitosan (TMC) with a tailorable degree of quaternization and thiolation. First, chitosan was partially N-carboxylated with glyoxylic acid and sodium borohydride. Next, the remaining amines were quantitatively dimethylated with formaldehyde and sodium borohydride and then quaternized with iodomethane in NMP. Subsequently, these partially carboxylated TMCs dissolved in water were reacted with cystamine at pH 5.5 using EDC as coupling agent. After addition of DTT and dialysis, thiolated TMCs were obtained, varying in degree of quaternization (25-54%) and degree of thiolation (5-7%), as determined with (1)H NMR and Ellman's assay. Gel permeation chromatography with light scattering detection indicated limited intermolecular cross-linking. All thiolated TMCs showed rapid oxidation to yield disulfide cross-linked TMC at pH 7.4, while the thiolated polymers were rather stable at pH 4.0. When Calu-3 cells were used, XTT and LDH cell viability tests showed a slight reduction in cytotoxicity for thiolated TMCs as compared to the nonthiolated polymers with similar DQs. Positively charged nanoparticles loaded with fluorescently labeled ovalbumin were made from thiolated TMCs and thiolated hyaluronic acid. The stability of these particles was confirmed in 0.8 M NaCl, in contrast to particles made from nonthiolated polymers that dissociated under these conditions, demonstrating that the particles were held together by intermolecular disulfide bonds.

A metabolic signature of long life in Caenorhabditis elegans

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Viney Jonathan M

2010-02-01

Full Text Available Abstract Background Many Caenorhabditis elegans mutations increase longevity and much evidence suggests that they do so at least partly via changes in metabolism. However, up until now there has been no systematic investigation of how the metabolic networks of long-lived mutants differ from those of normal worms. Metabolomic technologies, that permit the analysis of many untargeted metabolites in parallel, now make this possible. Here we use one of these, 1H nuclear magnetic resonance spectroscopy, to investigate what makes long-lived worms metabolically distinctive. Results We examined three classes of long-lived worms: dauer larvae, adult Insulin/IGF-1 signalling (IIS-defective mutants, and a translation-defective mutant. Surprisingly, these ostensibly different long-lived worms share a common metabolic signature, dominated by shifts in carbohydrate and amino acid metabolism. In addition the dauer larvae, uniquely, had elevated levels of modified amino acids (hydroxyproline and phosphoserine. We interrogated existing gene expression data in order to integrate functional (metabolite-level changes with transcriptional changes at a pathway level. Conclusions The observed metabolic responses could be explained to a large degree by upregulation of gluconeogenesis and the glyoxylate shunt as well as changes in amino acid catabolism. These responses point to new possible mechanisms of longevity assurance in worms. The metabolic changes observed in dauer larvae can be explained by the existence of high levels of autophagy leading to recycling of cellular components. See associated minireview: http://jbiol.com/content/9/1/7

Effect of conservative treatment on the renal outcome of children with primary hyperoxaluria type 1.

Science.gov (United States)

Fargue, Sonia; Harambat, Jérôme; Gagnadoux, Marie-France; Tsimaratos, Michel; Janssen, Françoise; Llanas, Brigitte; Berthélémé, Jean-Pierre; Boudailliez, Bernard; Champion, Gérard; Guyot, Claude; Macher, Marie-Alice; Nivet, Hubert; Ranchin, Bruno; Salomon, Rémi; Taque, Sophie; Rolland, Marie-Odile; Cochat, Pierre

2009-10-01

Primary hyperoxaluria type 1 results from alanine:glyoxylate aminotransferase deficiency. Due to genotype/phenotype heterogeneity in this autosomal recessive disorder, the renal outcome is difficult to predict in these patients and the long-term impact of conservative management in children is unknown. We report here a multicenter retrospective study on the renal outcome in 27 affected children whose biological diagnosis was based on either decreased enzyme activity or identification of mutations in the patient or his siblings. The median age at first symptoms was 2.4 years while that at initiation of conservative treatment was 4.1 years; 6 children were diagnosed upon family screening. The median follow-up was 8.7 years. At diagnosis, 15 patients had an estimated glomerular filtration rate (eGFR) below 90, and 7 children already had stage 2-3 chronic kidney disease. The median baseline eGFR was 74, which rose to 114 with management in the 22 patients who did not require renal replacement therapy. Overall, 20 patients had a stable eGFR, however, 7 exhibited a decline in eGFR of over 20 during the study period. In a Cox regression model, the only variable significantly associated with deterioration of renal function was therapeutic delay with a relative risk of 1.7 per year. Our study strongly suggests that early and aggressive conservative management may preserve renal function of compliant children with this disorder, thereby avoiding dialysis and postponing transplantation.

Reconstruction of a metabolic regulatory network in Escherichia coli for purposeful switching from cell growth mode to production mode in direct GABA fermentation from glucose.

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Soma, Yuki; Fujiwara, Yuri; Nakagawa, Takuya; Tsuruno, Keigo; Hanai, Taizo

2017-09-01

γ-aminobutyric acid (GABA) is a drug and functional food additive and is used as a monomer for producing the biodegradable plastic, polyamide 4. Recently, direct GABA fermentation from glucose has been developed as an alternative to glutamate-based whole cell bioconversion. Although total productivity in fermentation is determined by the specific productivity and cell amount responsible for GABA production, the optimal metabolic state for GABA production conflicts with that for bacterial cell growth. Herein, we demonstrated metabolic state switching from the cell growth mode based on the metabolic pathways of the wild type strain to a GABA production mode based on a synthetic metabolic pathway in Escherichia coli through rewriting of the metabolic regulatory network and pathway engineering. The GABA production mode was achieved by multiple strategies such as conditional interruption of the TCA and glyoxylate cycles, engineering of GABA production pathway including a bypass for precursor metabolite supply, and upregulation of GABA transporter. As a result, we achieved 3-fold improvement in total GABA production titer and yield (4.8g/L, 49.2% (mol/mol glucose)) in batch fermentation compared to the case without metabolic state switching (1.6g/L, 16.4% (mol/mol glucose)). This study reports the highest GABA production performance among previous reports on GABA fermentation from glucose using engineered E. coli. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Differential representation of liver proteins in obese human subjects suggests novel biomarkers and promising targets for drug development in obesity.

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Caira, Simonetta; Iannelli, Antonio; Sciarrillo, Rosaria; Picariello, Gianluca; Renzone, Giovanni; Scaloni, Andrea; Addeo, Pietro

2017-12-01

The proteome of liver biopsies from human obese (O) subjects has been compared to those of nonobese (NO) subjects using two-dimensional gel electrophoresis (2-DE). Differentially represented proteins were identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS)-based peptide mass fingerprinting (PMF) and nanoflow-liquid chromatography coupled to electrospray-tandem mass spectrometry (nLC-ESI-MS/MS). Overall, 61 gene products common to all of the liver biopsies were identified within 65 spots, among which 25 ones were differently represented between O and NO subjects. In particular, over-representation of short-chain acyl-CoA dehydrogenase, Δ(3,5)-Δ(2,4)dienoyl-CoA isomerase, acetyl-CoA acetyltransferase, glyoxylate reductase/hydroxypyruvate reductase, fructose-biphosphate aldolase B, peroxiredoxin I, protein DJ-1, catalase, α- and β-hemoglobin subunits, 3-mercaptopyruvate S-transferase, calreticulin, aminoacylase 1, phenazine biosynthesis-like domain-containing protein and a form of fatty acid-binding protein, together with downrepresentation of glutamate dehydrogenase, glutathione S-transferase A1, S-adenosylmethionine synthase 1A and a form of apolipoprotein A-I, was associated with the obesity condition. Some of these metabolic enzymes and antioxidant proteins have already been identified as putative diagnostic markers of liver dysfunction in animal models of steatosis or obesity, suggesting additional investigations on their role in these syndromes. Their differential representation in human liver was suggestive of their consideration as obesity human biomarkers and for the development of novel antiobesity drugs.

Detection and quantification of α-keto-δ-(N(G),N(G)-dimethylguanidino)valeric acid: a metabolite of asymmetric dimethylarginine.

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Martens-Lobenhoffer, Jens; Rodionov, Roman N; Drust, Andreas; Bode-Böger, Stefanie M

2011-12-15

Nitric oxide is an ubiquitary cell signaling substance. Its enzymatic production rate by nitric oxide synthase is regulated by the concentrations of the substrate L-arginine and the competitive inhibitor asymmetric dimethylarginine (ADMA). A newly recognized elimination pathway for ADMA is the transamination to α-keto-δ-(N(G),N(G)-dimethylguanidino)valeric acid (DMGV) by the enzyme alanine-glyoxylate aminotransferase 2 (AGXT2). This pathway has been proven to be relevant for nitric oxide regulation, but up to now no method exists for the determination of DMGV in biological fluids. We have developed a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the quantification of DMGV. D(6)-DMGV was used as internal standard. Samples were purified online by column switching, and separation was achieved on a porous graphitic carbon column. The calibration was linear over ranges of 10 to 200 nmol/L for plasma and 0.1 to 20 μmol/L for urine. The intra- and interday accuracies and precisions in plasma and urine were better than 10%. In plasma samples, DMGV was present in concentrations between 19.1 and 77.5 nmol/L. In urine samples, concentrations between 0.0114 and 1.03 μmol/mmol creatinine were found. This method can be used as a tool for the scientific investigation of the ADMA conversion to DMGV via the enzyme AGXT2. Copyright © 2011 Elsevier Inc. All rights reserved.

Mechanisms leading to oligomers and SOA through aqueous photooxidation: insights from OH radical oxidation of acetic acid and methylglyoxal

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Y. Tan

2012-01-01

Full Text Available Previous experiments have demonstrated that the aqueous OH radical oxidation of methylglyoxal produces low volatility products including pyruvate, oxalate and oligomers. These products are found predominantly in the particle phase in the atmosphere, suggesting that methylglyoxal is a precursor of secondary organic aerosol (SOA. Acetic acid plays a central role in the aqueous oxidation of methylglyoxal and it is a ubiquitous product of gas phase photochemistry, making it a potential "aqueous" SOA precursor in its own right. However, the fate of acetic acid upon aqueous-phase oxidation is not well understood. In this research, acetic acid (20 μM–10 mM was oxidized by OH radicals, and pyruvic acid and methylglyoxal experimental samples were analyzed using new analytical methods, in order to better understand the formation of SOA from acetic acid and methylglyoxal. Glyoxylic, glycolic, and oxalic acids formed from acetic acid and OH radicals. In contrast to the aqueous OH radical oxidation of methylglyoxal, the aqueous OH radical oxidation of acetic acid did not produce succinic acid and oligomers. This suggests that the methylgloxal-derived oligomers do not form through the acid catalyzed esterification pathway proposed previously. Using results from these experiments, radical mechanisms responsible for oligomer formation from methylglyoxal oxidation in clouds and wet aerosols are proposed. The importance of acetic acid/acetate as an SOA precursor is also discussed. We hypothesize that this and similar chemistry is central to the daytime formation of oligomers in wet aerosols.

Bromopyruvate, an active site-directed inactivator of E. coli 2-keto-4-hydroxyglutarate(KHG) aldolase, modifies glutamic acid residue-45

International Nuclear Information System (INIS)

Vlahos, C.J.; Dekker, E.E.

1987-01-01

E. coli KHG-aldolase (2-keto-4-hydroxyglutarate ↔ pyruvate + glyoxylate), a novel trimeric Class I aldolase, requires one active-site lysine residue (Lys 133)/subunit for Schiff-base formation as well as one arginine residue (Arg 49)/subunit for catalytic activity. The substrate analog, 3-bromopyruvate (BRPY), causes a time- and concentration-dependent loss of KHG-aldolase activity. This inactivation is regarded as active site-directed since: (a) BRPY modification results in complete loss of enzymatic activity; (b) saturation kinetics are exhibited, suggesting that a reversible complex is formed between the aldolase and BRPY prior to the rate-limiting inactivation step; (c) over 90% of the initial aldolase activity is protected by either substrate, pyruvate or KHG; (d) 1.1 mol of 14 C-BRPY is bound/enzyme subunit. Peptide isolation and sequencing show that the incorporated radioactivity is associated with residue Glu-45. Denaturation of the enzyme with guanidine x HCl following treatment with excess 14 C-BRPY allows for the incorporation of carbon-14 at Cys-159 and Cys-180 as well. The presence of pyruvate protects Glu-45 from being esterified but does not prevent the alkylation of the two cysteine residues. These results suggest that Glu-45 is essential for the catalytic activity of E. coli KHG-aldolase, most likely functioning as the active-site amphoteric proton donor/acceptor moiety that is involved in the overall mechanism of the reaction catalyzed by this enzyme

Proteomic analysis in nitrogen-deprived Isochrysis galbana during lipid accumulation.

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Pingping Song

Full Text Available The differentially co-expressed proteins in N-deprived and N-enriched I. galbana were comparatively analyzed by using two dimensional electrophoresis (2-DE and matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight-mass spectrometry (MALDI-TOF/TOF-MS with the aim of better understanding lipid metabolism in this oleaginous microalga. Forty-five of the 900 protein spots showed dramatic changes in N-deprived I. galbana compared with the N-enriched cells. Of these, 36 protein spots were analyzed and 27 proteins were successfully identified. The identified proteins were classified into seven groups by their molecular functions, including the proteins related to energy production and transformation, substance metabolism, signal transduction, molecular chaperone, transcription and translation, immune defense and cytoskeleton. These altered proteins slowed cell growth and photosynthesis of I. galbana directly or indirectly, but at the same time increased lipid accumulation. Eight key enzymes involved in lipid metabolism via different pathways were identified as glyceraldehyde-3-phosphate dehydrogenase (GAPDH, phosphoglycerate kinase (PGK, enolase, aspartate aminotransferase (AST, fumarate hydratase (FH, citrate synthase (CS, O-acetyl-serine lyase (OAS-L and ATP sulfurylase (ATPS. The results suggested that the glycolytic pathway and citrate transport system might be the main routes for lipid anabolism in N-deprived I. galbana, and that the tricarboxylic acid (TCA cycle, glyoxylate cycle and sulfur assimilation system might be the major pathways involved in lipid catabolism.

Characterization of phosphorylated isocitrate dehydrogenase and purification of the isocitrate dehydrogenase kinase/phosphatase of Escherichia coli

International Nuclear Information System (INIS)

Malloy, P.J.

1985-01-01

NADP + -specific isocitrate dehydrogenase (IDH; EC 1.1.1.42) was shown to be phosphorylated with ( 32 P)-orthophosphate in vivo in several strains of Escherichia coli. In strain KC 13, an adenylate cyclase deficient mutant, the specific activity of IDH decreased 70% when acetate was added to stationary phase cultures grown on glucose. The enzyme was immunoprecipitated from sonic extracts and shown to contain 32 P by sodium dodecyl sulfate polyacrylamide gel electrophoresis and autoradiography. The results demonstrate that unlike many eukaryotic protein kinases, the protein kinase involved in the phosphorylation of IDH in E. coli does not require cyclic adenosine monophosphate for catalysis. Similarly, the phosphorylation of IDH was demonstrated in E. coli mutants deficient in either isocitrate lyase or malate synthase. The incorporation of 32 P in IDH was demonstrated following SDS-PAGE and autoradiography of the immunoprecipitated enzyme. These results suggest that the conditions required for the phosphorylation of IDH do not depend on the functioning of the glyoxylate shunt. Following in vivo 32 P-labeling of E. coli strain F143/KL259 in the presence of acetate, 32 P-labeled IDH was isolated from sonicated extracts of the cells. The 32 P-enzyme was carboxylmethylated and digested with trypsin. A single 32 P-labeled peptide was isolated from the tryptic digest. Amino acid analysis of the purified 32 P-labeled peptide showed that the peptide contains seven amino acids, including a single phosphorylated serine residue

Metabolic response of Candida albicans to phenylethyl alcohol under hyphae-inducing conditions.

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Han, Ting-Li; Tumanov, Sergey; Cannon, Richard D; Villas-Boas, Silas G

2013-01-01

Phenylethyl alcohol was one of the first quorum sensing molecules (QSMs) identified in C. albicans. This extracellular signalling molecule inhibits the hyphal formation of C. albicans at high cell density. Little is known, however, about the underlying mechanisms by which this QSM regulates the morphological switches of C. albicans. Therefore, we have applied metabolomics and isotope labelling experiments to investigate the metabolic changes that occur in C. albicans in response to phenylethyl alcohol under defined hyphae-inducing conditions. Our results showed a global upregulation of central carbon metabolism when hyphal development was suppressed by phenylethyl alcohol. By comparing the metabolic changes in response to phenylethyl alcohol to our previous metabolomic studies, we were able to short-list 7 metabolic pathways from central carbon metabolism that appear to be associated with C. albicans morphogenesis. Furthermore, isotope-labelling data showed that phenylethyl alcohol is indeed taken up and catabolised by yeast cells. Isotope-labelled carbon atoms were found in the majority of amino acids as well as in lactate and glyoxylate. However, isotope-labelled carbon atoms from phenylethyl alcohol accumulated mainly in the pyridine ring of NAD(+)/NADH and NADP(-/)NADPH molecules, showing that these nucleotides were the main products of phenylethyl alcohol catabolism. Interestingly, two metabolic pathways where these nucleotides play an important role, nitrogen metabolism and nicotinate/nicotinamide metabolism, were also short-listed through our previous metabolomics works as metabolic pathways likely to be closely associated with C. albicans morphogenesis.

Production of L-carnitine by secondary metabolism of bacteria

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Iborra José L

2007-10-01

Full Text Available Abstract The increasing commercial demand for L-carnitine has led to a multiplication of efforts to improve its production with bacteria. The use of different cell environments, such as growing, resting, permeabilized, dried, osmotically stressed, freely suspended and immobilized cells, to maintain enzymes sufficiently active for L-carnitine production is discussed in the text. The different cell states of enterobacteria, such as Escherichia coli and Proteus sp., which can be used to produce L-carnitine from crotonobetaine or D-carnitine as substrate, are analyzed. Moreover, the combined application of both bioprocess and metabolic engineering has allowed a deeper understanding of the main factors controlling the production process, such as energy depletion and the alteration of the acetyl-CoA/CoA ratio which are coupled to the end of the biotransformation. Furthermore, the profiles of key central metabolic activities such as the TCA cycle, the glyoxylate shunt and the acetate metabolism are seen to be closely interrelated and affect the biotransformation efficiency. Although genetically modified strains have been obtained, new strain improvement strategies are still needed, especially in Escherichia coli as a model organism for molecular biology studies. This review aims to summarize and update the state of the art in L-carnitine production using E. coli and Proteus sp, emphasizing the importance of proper reactor design and operation strategies, together with metabolic engineering aspects and the need for feed-back between wet and in silico work to optimize this biotransformation.

Carbohydrate metabolism in ripening banana and its alteration on gamma irradiation in relation to delay in ripening

International Nuclear Information System (INIS)

Surendranathan, K.K.; Nair, P.M.

1980-01-01

Ripening, of climacteric class of fruits like banana, is accompanied with an upsurge in respiration, indicating a change in metabolism from hexose monophosphate (HMP) shunt pathway to glycolytic pathway. The key enzyme in glycolytic pathway, namely, phosphofructokinase, is activated and this activation paralleled with the increase in respiration rate. The enhancement in the activity of enzymes of glycolytic and Kreb's cycle help the fruit to assimilate energy as ATP produced from the breakdown and oxidation of storage starch. The demand for energy supply is great for the different ripening processes. Gamma irradiation of the fruit at the preclimacteric stage delayed the onset of climacteric to about 7 to 8 days, thereby extending the ripening to 15-20 days. This delay was brought about by the alterations in the metabolism of carbohydrate. There is a predominance of HMP pathway in irradiated banana. This along with the activation of phosphatases like FDPase and F-6-Pase restricted the entrance of sugar phosphate esters to Kreb's cycle for oxidation. The functioning of Kreb's cycle is also affected by the inhibition of succinic dehydrogenase. But activation of glyoxylate shunt pathway helped to maintain the levels of Kreb's cycle intermediates, like citrate and malate, although energy production is reduced. Finally the activation of gluconeogenic pathway helps in channelling the metabolites back to sugars. All these metabolic changes cause a considerable depletion in the production of ATP. (auth.)

Flux analysis of central metabolic pathways in Geobactermetallireducens during reduction of solubleFe(III)-NTA

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Tang, Yinjie J.; Chakraborty, Romy; Garcia-Martin, Hector; Chu,Jeannie; Hazen, Terry C.; Keasling, Jay D.

2007-01-01

We analyzed the carbon fluxes in the central metabolism ofGeobacter metallireducens strain GS-15 using 13C isotopomer modeling.Acetate labeled in the 1st or 2nd position was the sole carbon source,and Fe-NTA was the sole terminal electron acceptor. The measured labeledacetate uptake rate was 21 mmol/gdw/h in the exponential growth phase.The resulting isotope labeling pattern of amino acids allowed an accuratedetermination of the in vivo global metabolic reaction rates (fluxes)through the central metabolic pathways using a computational isotopomermodel. The tracer experiments showed that G. metallireducens containedcomplete biosynthesis pathways for essential metabolism, and this strainmight also have an unusual isoleucine biosynthesis route (usingacetyl-CoA and pyruvate as the precursors). The model indicated that over90 percent of the acetate was completely oxidized to CO2 via a completetricarboxylic acid (TCA) cycle while reducing iron. Pyruvate carboxylaseand phosphoenolpyruvate carboxykinase were present under theseconditions, but enzymes in the glyoxylate shunt and malic enzyme wereabsent. Gluconeogenesis and the pentose phosphate pathway were mainlyemployed for biosynthesis and accounted for less than 3 percent of totalcarbon consumption. The model also indicated surprisingly highreversibility in the reaction between oxoglutarate and succinate. Thisstep operates close to the thermodynamic equilibrium possibly becausesuccinate is synthesized via a transferase reaction, and the conversionof oxoglutarate to succinate is a rate limiting step for carbonmetabolism. These findings enable a better understanding of therelationship between genome annotation and extant metabolic pathways inG. metallireducens.

Formation of aqueous-phase α-hydroxyhydroperoxides (α-HHP: potential atmospheric impacts

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R. Zhao

2013-06-01

Full Text Available The focus of this work is on quantifying the degree of the aqueous-phase formation of α-hydroxyhydroperoxides (α-HHPs via reversible nucleophilic addition of H2O2 to aldehydes. Formation of this class of highly oxygenated organic hydroperoxides represents a poorly characterized aqueous-phase processing pathway that may lead to enhanced SOA formation and aerosol toxicity. Specifically, the equilibrium constants of α-HHP formation have been determined using proton nuclear-magnetic-resonance (1H NMR spectroscopy and proton-transfer-reaction mass spectrometry (PTR-MS. Significant α-HHP formation was observed from formaldehyde, acetaldehyde, propionaldehyde, glycolaldehyde, glyoxylic acid, and methylglyoxal, but not from methacrolein and ketones. Low temperatures enhanced the formation of α-HHPs but slowed their formation rates. High inorganic salt concentrations shifted the equilibria toward the hydrated form of the aldehydes and slightly suppressed α-HHP formation. Using the experimental equilibrium constants, we predict the equilibrium concentration of α-HHPs to be in the μM level in cloud water, but it may also be present in the mM level in aerosol liquid water (ALW, where the concentrations of H2O2 and aldehydes can be high. Formation of α-HHPs in ALW may significantly affect the effective Henry's law constants of H2O2 and aldehydes but may not affect their gas-phase levels. The photochemistry and reactivity of this class of atmospheric species have not been studied.

60 YEARS OF POMC: From POMC and α-MSH to PAM, molecular oxygen, copper, and vitamin C.

Science.gov (United States)

Kumar, Dhivya; Mains, Richard E; Eipper, Betty A

2016-05-01

A critical role for peptide C-terminal amidation was apparent when the first bioactive peptides were identified. The conversion of POMC into adrenocorticotropic hormone and then into α-melanocyte-stimulating hormone, an amidated peptide, provided a model system for identifying the amidating enzyme. Peptidylglycine α-amidating monooxygenase (PAM), the only enzyme that catalyzes this modification, is essential; mice lacking PAM survive only until mid-gestation. Purification and cloning led to the discovery that the amidation of peptidylglycine substrates proceeds in two steps: peptidylglycine α-hydroxylating monooxygenase catalyzes the copper- and ascorbate-dependent α-hydroxylation of the peptidylglycine substrate; peptidyl-α-hydroxyglycine α-amidating lyase cleaves the N-C bond, producing amidated product and glyoxylate. Both enzymes are contained in the luminal domain of PAM, a type 1 integral membrane protein. The structures of both catalytic cores have been determined, revealing how they interact with metals, molecular oxygen, and substrate to catalyze both reactions. Although not essential for activity, the intrinsically disordered cytosolic domain is essential for PAM trafficking. A phylogenetic survey led to the identification of bifunctional membrane PAM in Chlamydomonas, a unicellular eukaryote. Accumulating evidence points to a role for PAM in copper homeostasis and in retrograde signaling from the lumen of the secretory pathway to the nucleus. The discovery of PAM in cilia, cellular antennae that sense and respond to environmental stimuli, suggests that much remains to be learned about this ancient protein. © 2016 Society for Endocrinology.

Succinate overproduction: A case study of computational strain design using a comprehensive Escherichia coli kinetic model

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Ali eKhodayari

2015-01-01

Full Text Available Computational strain design prediction accuracy has been the focus for many recent efforts through the selective integration of kinetic information into metabolic models. In general, kinetic model prediction quality is determined by the range and scope of genetic and/or environmental perturbations used during parameterization. In this effort, we apply the k-OptForce procedure on a kinetic model of E. coli core metabolism constructed using the Ensemble Modeling (EM method and parameterized using multiple mutant strains data under aerobic respiration with glucose as the carbon source. Minimal interventions are identified that improve succinate yield under both aerobic and anaerobic conditions to test the fidelity of model predictions under both genetic and environmental perturbations. Under aerobic condition, k-OptForce identifies interventions that match existing experimental strategies pointing at a number of unexplored flux redirections such as routing glyoxylate flux through the glycerate metabolism to improve succinate yield. Many of the identified interventions rely on the kinetic descriptions and would not be discoverable by a purely stoichiometric description. In contrast, under fermentative (anaerobic conditions, k-OptForce fails to identify key interventions including up-regulation of anaplerotic reactions and elimination of competitive fermentative products. This is due to the fact that the pathways activated under anaerobic conditions were not properly parameterized as only aerobic flux data were used in the model construction. This study shed light on the importance of condition-specific model parameterization and provides insight onto how to augment kinetic models so as to correctly respond to multiple environmental perturbations.

Gaseous environment of plants and activity of enzymes of carbohydrate catabolism

International Nuclear Information System (INIS)

Ivanov, B.F.; Zemlyanukhin, A.A.; Igamberdiev, A.U.; Salam, A.M.M.

1989-01-01

The authors investigated the action of hypoxia and high CO 2 concentration in the atmosphere on activity of phosphofructokinase, aldolase, glucose phosphate isomerase, glucose-6-phosphate dehydrogenase, lactate dehydrogenase, alcohol dehydrogenase, and isocitrate lyase in pea seedlings (Pisum sativum L.), corn scutella (Zea mays L.), and hemp cotyledons (Cannabis sativa L.). The first 4-12h of hypoxia witnessed suppression of enzymes of the initial stages of glycolysis (glucose-6-phosphate isomerase, phosphofructokinase)and activation of enzymes of its final stages (alcohol dehydrogenase and lactate dehydrogenase) and enzymes linking glycolysis and the pentose phosphate pathway (aldolase and glucose-6-phosphate dehydrogenase). An excess of CO 2 in the environment accelerated and amplified this effect. At the end of a 24-h period of anaerobic incubation, deviations of enzyme activity from the control were leveled in both gaseous environments. An exception was observed in the case of phosphofructokinase, whose activity increased markedly at this time in plants exposed to CO 2 . Changes in activity of the enzymes were coupled with changes in their kinetic parameters (apparent K m and V max values). The activity of isocitrate lyase was suppressed in both variants of hypoxic gaseous environments, a finding that does not agree with the hypothesis as to participation of the glyoxylate cycle in the metabolic response of plants to oxygen stress. Thus, temporary inhibition of the system of glycolysis and activation of the pentose phosphate pathway constituted the initial response of the plants to O 2 stress, and CO 2 intensified this metabolic response

Kinetics and oxidative mechanism for H{sub 2}O{sub 2}-enhanced iron-mediated aeration (IMA) treatment of recalcitrant organic compounds in mature landfill leachate

Energy Technology Data Exchange (ETDEWEB)

Deng Yang, E-mail: yang.deng@upr.edu [Department of Civil Engineering and Surveying, University of Puerto Rico, PO BOX 9041, Mayaguez, PR 00681 (Puerto Rico); Englehardt, James D. [Department of Civil, Architectural and Environmental Engineering, University of Miami, PO BOX 248294, Coral Gables, FL 33124-0630 (United States)

2009-09-30

A hydrogen peroxide (H{sub 2}O{sub 2})-enhanced iron (Fe{sup 0})-mediated aeration (IMA) process has been recently demonstrated to effectively remove organic wastes from mature landfill leachate. In this paper, the kinetics and oxidative mechanisms of the enhanced IMA treatment were studied. Bench-scale full factorial tests were conducted in an orbital shaker reactor for treatment of a mature leachate with an initial chemical oxygen demand (COD) of 900-1200 mg/L. At the maximum aeration rate (8.3 mL air/min mL sample), process variables significantly influencing the rates of H{sub 2}O{sub 2} decay and COD removal were pH (3.0-8.0), initial H{sub 2}O{sub 2} doses (0.21-0.84 M), and Fe{sup 0} surface area concentrations (0.06-0.30 m{sup 2}/L). Empirical kinetic models were developed and verified for the degradation of H{sub 2}O{sub 2} and COD. High DO maintained by a high aeration rate slowed the H{sub 2}O{sub 2} self-decomposition, accelerated Fe{sup 0} consumption, and enhanced the COD removal. In hydroxyl radical (OH{center_dot}) scavenging tests, the rate of removal of glyoxylic acid (target compound) was not inhibited by the addition of para-chlorobenzoic acid (OH{center_dot} scavenger) at pH 7.0-7.5, ruling out hydroxyl radical as the principal oxidant in neutral-weakly basic solution. These experimental results show that this enhanced IMA technology is a potential alternative for the treatment of high strength recalcitrant organic wastewaters.

Engineering of red cells of Arabidopsis thaliana and comparative genome-wide gene expression analysis of red cells versus wild-type cells.

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Shi, Ming-Zhu; Xie, De-Yu

2011-04-01

We report metabolic engineering of Arabidopsis red cells and genome-wide gene expression analysis associated with anthocyanin biosynthesis and other metabolic pathways between red cells and wild-type (WT) cells. Red cells of A. thaliana were engineered for the first time from the leaves of production of anthocyanin pigment 1-Dominant (pap1-D). These red cells produced seven anthocyanin molecules including a new one that was characterized by LC-MS analysis. Wild-type cells established as a control did not produce anthocyanins. A genome-wide microarray analysis revealed that nearly 66 and 65% of genes in the genome were expressed in the red cells and wild-type cells, respectively. In comparison with the WT cells, 3.2% of expressed genes in the red cells were differentially expressed. The expression levels of 14 genes involved in the biosynthetic pathway of anthocyanin were significantly higher in the red cells than in the WT cells. Microarray and RT-PCR analyses demonstrated that the TTG1-GL3/TT8-PAP1 complex regulated the biosynthesis of anthocyanins. Furthermore, most of the genes with significant differential expression levels in the red cells versus the WT cells were characterized with diverse biochemical functions, many of which were mapped to different metabolic pathways (e.g., ribosomal protein biosynthesis, photosynthesis, glycolysis, glyoxylate metabolism, and plant secondary metabolisms) or organelles (e.g., chloroplast). We suggest that the difference in gene expression profiles between the two cell lines likely results from cell types, the overexpression of PAP1, and the high metabolic flux toward anthocyanins.

Regulation of Lactobacillus plantarum contamination on the carbohydrate and energy related metabolisms of Saccharomyces cerevisiae during bioethanol fermentation.

Science.gov (United States)

Dong, Shi-Jun; Lin, Xiang-Hua; Li, Hao

2015-11-01

During the industrial bioethanol fermentation, Saccharomyces cerevisiae cells are often stressed by bacterial contaminants, especially lactic acid bacteria. Generally, lactic acid bacteria contamination can inhibit S. cerevisiae cell growth through secreting lactic acid and competing with yeast cells for micronutrients and living space. However, whether are there still any other influences of lactic acid bacteria on yeast or not? In this study, Lactobacillus plantarum ATCC 8014 was co-cultivated with S. cerevisiae S288c to mimic the L. plantarum contamination in industrial bioethanol fermentation. The contaminative L. plantarum-associated expression changes of genes involved in carbohydrate and energy related metabolisms in S. cerevisiae cells were determined by quantitative real-time polymerase chain reaction to evaluate the influence of L. plantarum on carbon source utilization and energy related metabolism in yeast cells during bioethanol fermentation. Contaminative L. plantarum influenced the expression of most of genes which are responsible for encoding key enzymes involved in glucose related metabolisms in S. cerevisiae. Specific for, contaminated L. plantarum inhibited EMP pathway but promoted TCA cycle, glyoxylate cycle, HMP, glycerol synthesis pathway, and redox pathway in S. cerevisiae cells. In the presence of L. plantarum, the carbon flux in S. cerevisiae cells was redistributed from fermentation to respiratory and more reducing power was produced to deal with the excess NADH. Moreover, L. plantarum contamination might confer higher ethanol tolerance to yeast cells through promoting accumulation of glycerol. These results also highlighted our knowledge about relationship between contaminative lactic acid bacteria and S. cerevisiae during bioethanol fermentation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Further studies on O2-resistant photosynthesis and photorespiration in a tobacco mutant with enhanced catalase activity

International Nuclear Information System (INIS)

Zelitch, I.

1990-01-01

The increase in net photosynthesis in M 4 progeny of an O 2 -resistant tobacco (Nicotiana tabacum) mutant relative to wild-type plants at 21 and 42% O 2 has been confirmed and further investigated. Self-pollination of an M 3 mutant produced M 4 progeny segregating high catalase phenotypes (average 40% greater than wild type) at a frequency of about 60%. The high catalase phenotype cosegregated precisely with O 2 -resistant photosynthesis. About 25% of the F 1 progeny of reciprocal crosses between the same M 3 mutant and wild type had high catalase activity, whether the mutant was used as the maternal or paternal parent, indicating nuclear inheritance. In high-catalase mutants the activity of NADH-hydroxypyruvate reductase, another peroxisomal enzyme, was the same as wild type. The mutants released 15% less photorespiratory CO 2 as a percent of net photosynthesis in CO 2 -free 21% O 2 and 36% less in CO 2 -free 42% O 2 compared with wild type. The mutant leaf tissue also released less 14 CO 2 per [1- 14 C]glycolate metabolized than wild type in normal air, consistent with less photorespiration in the mutant. The O 2 -resistant photosynthesis appears to be caused by a decrease in photorespiration especially under conditions of high O 2 where the stoichiometry of CO 2 release per glycolate metabolized is expected to be enhanced. The higher catalase activity in the mutant may decrease the nonenzymatic peroxidation of keto-acids such as hydroxypyruvate and glyoxylate by photorespiratory H 2 O 2

The novel zinc cluster regulator Tog1 plays important roles in oleate utilization and oxidative stress response in Saccharomyces cerevisiae

Energy Technology Data Exchange (ETDEWEB)

Thepnok, Piyasuda; Ratanakhanokchai, Khanok; Soontorngun, Nitnipa, E-mail: nitnipa.soo@kmutt.ac.th

2014-08-08

Highlights: • TOG1 deletion results in defective growth on non-fermentable carbon sources. • Removal of TOG1 sensitizes cells to oxidative stress. • Tog1 directly binds and activates expression of oleate utilizing genes. • The Δtog1 cells display reduced peroxisomal content in oleate culture. • S. cerevisiae zinc cluster Tog1 is a novel activator of oleate utilization. - Abstract: Many zinc cluster proteins have been shown to play a role in the transcriptional regulation of glucose-repressible genes during glucose exhaustion and diauxic shift. Here, we studied an additional member of this family called Yer184c (herein called Tog1) for transcriptional regulator of oleate. Our results showed that a Δtog1 strain displays impaired growth with several non-fermentable carbons. Tog1 is also implicated in oxidative stress tolerance. Importantly, during the glucose–oleate shift, combined results from quantitative real time-PCR and chromatin immunoprecipitation (ChIP) experiments showed that Tog1 acts as a direct activator of oleate utilizing genes, encoded key enzymes in β-Oxidation and NADPH regeneration (POX1, FOX2, POT1 and IDP2), the glyoxylate shunt (MLS1 and ICL1), and gluconeogenesis (PCK1 and FBP1). A transmission electron microscopy (TEM) analysis of the Δtog1 strain assayed with oleate also revealed a substantial decrease in peroxisome abundance that is vital for fatty acid oxidation. Overall, our results clearly demonstrated that Tog1 is a newly characterized zinc cluster regulator that functions in the complex network of non-fermentable carbon metabolism in Saccharomycescerevisiae.

General metabolism of Laribacter hongkongensis: a genome-wide analysis

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Curreem Shirly O

2011-04-01

Full Text Available Abstract Background Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea. In this study, we performed an in-depth annotation of the genes and pathways of the general metabolism of L. hongkongensis and correlated them with its phenotypic characteristics. Results The L. hongkongensis genome possesses the pentose phosphate and gluconeogenesis pathways and tricarboxylic acid and glyoxylate cycles, but incomplete Embden-Meyerhof-Parnas and Entner-Doudoroff pathways, in agreement with its asaccharolytic phenotype. It contains enzymes for biosynthesis and β-oxidation of saturated fatty acids, biosynthesis of all 20 universal amino acids and selenocysteine, the latter not observed in Neisseria gonorrhoeae, Neisseria meningitidis and Chromobacterium violaceum. The genome contains a variety of dehydrogenases, enabling it to utilize different substrates as electron donors. It encodes three terminal cytochrome oxidases for respiration using oxygen as the electron acceptor under aerobic and microaerophilic conditions and four reductases for respiration with alternative electron acceptors under anaerobic conditions. The presence of complete tetrathionate reductase operon may confer survival advantage in mammalian host in association with diarrhea. The genome contains CDSs for incorporating sulfur and nitrogen by sulfate assimilation, ammonia assimilation and nitrate reduction. The existence of both glutamate dehydrogenase and glutamine synthetase/glutamate synthase pathways suggests an importance of ammonia metabolism in the living environments that it may encounter. Conclusions The L. hongkongensis genome possesses a variety of genes and pathways for carbohydrate, amino acid and lipid metabolism, respiratory chain and sulfur and nitrogen metabolism. These allow the bacterium to utilize various substrates for energy production and survive in different environmental niches.

Comparative Genomics of Regulation of Fatty Acid and Branched-chain Amino Acid Utilization in Proteobacteria

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Kazakov, Alexey E.; Rodionov, Dmitry A.; Arkin, Adam Paul; Dubchak, Inna; Gelfand, Mikhail S.; Alm, Eric

2008-10-31

Bacteria can use branched-chain amino acids (ILV, i.e. isoleucine, leucine, valine) and fatty acids (FA) as sole carbon and energy sources convering ILV into acetyl-CoA, propanoyl-CoA and propionyl-CoA, respectively. In this work, we used the comparative genomic approach to identify candidate transcriptional factors and DNA motifs that control ILV and FA utilization pathways in proteobacteria. The metabolic regulons were characterized based on the identification and comparison of candidate transcription factor binding sites in groups of phylogenetically related genomes. The reconstructed ILV/FA regulatory network demonstrates considerable variability and involves six transcriptional factors from the MerR, TetR and GntR families binding to eleven distinct DNA motifs. The ILV degradation genes in gamma- and beta-proteobacteria are mainly regulated by anovel regulator from the MerR family (e.g., LiuR in Pseudomonas aeruginosa) (40 species), in addition, the TetR-type regulator LiuQ was identified in some beta-proteobacteria (8 species). Besides the core set of ILV utilization genes, the LiuR regulon in some lineages is expanded to include genes from other metabolic pathways, such as the glyoxylate shunt and glutamate synthase in the Shewanella species. The FA degradation genes are controlled by four regulators including FadR in gamma-proteobacteria (34 species), PsrA in gamma- and beta-proteobacteria (45 species), FadP in beta-proteobacteria (14 species), and LiuR orthologs in alpha-proteobacteria (22 species). The remarkable variability of the regulatory systems associated with the FA degradation pathway is discussed from the functional and evolutionary points of view.

Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics

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Carlo Berg

2018-02-01

Full Text Available Marine and brackish surface waters are highly dynamic habitats that undergo repeated seasonal variations in microbial community composition and function throughout time. While succession of the various microbial groups has been well investigated, little is known about the underlying gene-expression of the microbial community. We investigated microbial interactions via metatranscriptomics over a spring to fall seasonal cycle in the brackish Baltic Sea surface waters, a temperate brackish water ecosystem periodically promoting massive cyanobacterial blooms, which have implications for primary production, nutrient cycling, and expansion of hypoxic zones. Network analysis of the gene expression of all microbes from 0.22 to 200 μm in size and of the major taxonomic groups dissected the seasonal cycle into four components that comprised genes peaking during different periods of the bloom. Photoautotrophic nitrogen-fixing Cyanobacteria displayed the highest connectivity among the microbes, in contrast to chemoautotrophic ammonia-oxidizing Thaumarchaeota, while heterotrophs dominated connectivity among pre- and post-bloom peaking genes. The network was also composed of distinct functional connectivities, with an early season balance between carbon metabolism and ATP synthesis shifting to a dominance of ATP synthesis during the bloom, while carbon degradation, specifically through the glyoxylate shunt, characterized the post-bloom period, driven by Alphaproteobacteria as well as by Gammaproteobacteria of the SAR86 and SAR92 clusters. Our study stresses the exceptionally strong biotic driving force executed by cyanobacterial blooms on associated microbial communities in the Baltic Sea and highlights the impact cyanobacterial blooms have on functional microbial community composition.

Porphyromonas uenonis sp. nov., a pathogen for humans distinct from P. asaccharolytica and P. endodontalis.

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Finegold, Sydney M; Vaisanen, Marja-Liisa; Rautio, Merja; Eerola, Erkki; Summanen, Paula; Molitoris, Denise; Song, Yuli; Liu, Chengxu; Jousimies-Somer, Hannele

2004-11-01

Three Porphyromonas species (Porphyromonas asaccharolytica, P. endodontalis, and the novel species that is the subject of the present report, P. uenonis) are very much alike in terms of biochemical characteristics, such as enzyme profiles and cellular fatty acid contents. P. asaccharolytica is distinguished from the other two species by virtue of production of alpha-fucosidase and glyoxylic acid positivity. The novel species is difficult to differentiate from P. endodontalis phenotypically and was designated a P. endodontalis-like organism for some time. However, P. endodontalis is recovered almost exclusively from oral sources and also grows poorly on Biolog Universal Agar, both characteristics that are in contrast to those of the other two organisms. Furthermore, P. uenonis is glycerol positive in the Biolog AN Microplate system. Both P. asaccharolytica and P. uenonis are positive by 13 other tests in the Biolog system, whereas P. endodontalis is negative by all of these tests. P. asaccharolytica grew well in both solid and liquid media without supplementation with 5% horse serum, whereas the other two species grew poorly without supplementation. Sequencing of 16S rRNA revealed about 10% divergence between the novel species and P. endodontalis but less than 2% sequence difference between the novel species and P. asaccharolytica. Subsequent DNA-DNA hybridization studies documented that the novel organism was indeed distinct from P. asaccharolytica. We propose the name Porphyromonas uenonis for the novel species. We have recovered P. uenonis from four clinical infections in adults, all likely of intestinal origin, and from the feces of six children.

Porphyromonas uenonis sp. nov., a Pathogen for Humans Distinct from P. asaccharolytica and P. endodontalis

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Finegold, Sydney M.; Vaisanen, Marja-Liisa; Rautio, Merja; Eerola, Erkki; Summanen, Paula; Molitoris, Denise; Song, Yuli; Liu, Chengxu; Jousimies-Somer, Hannele

2004-01-01

Three Porphyromonas species (Porphyromonas asaccharolytica, P. endodontalis, and the novel species that is the subject of the present report, P. uenonis) are very much alike in terms of biochemical characteristics, such as enzyme profiles and cellular fatty acid contents. P. asaccharolytica is distinguished from the other two species by virtue of production of α-fucosidase and glyoxylic acid positivity. The novel species is difficult to differentiate from P. endodontalis phenotypically and was designated a P. endodontalis-like organism for some time. However, P. endodontalis is recovered almost exclusively from oral sources and also grows poorly on Biolog Universal Agar, both characteristics that are in contrast to those of the other two organisms. Furthermore, P. uenonis is glycerol positive in the Biolog AN Microplate system. Both P. asaccharolytica and P. uenonis are positive by 13 other tests in the Biolog system, whereas P. endodontalis is negative by all of these tests. P. asaccharolytica grew well in both solid and liquid media without supplementation with 5% horse serum, whereas the other two species grew poorly without supplementation. Sequencing of 16S rRNA revealed about 10% divergence between the novel species and P. endodontalis but less than 2% sequence difference between the novel species and P. asaccharolytica. Subsequent DNA-DNA hybridization studies documented that the novel organism was indeed distinct from P. asaccharolytica. We propose the name Porphyromonas uenonis for the novel species. We have recovered P. uenonis from four clinical infections in adults, all likely of intestinal origin, and from the feces of six children. PMID:15528728

Diagnosis of rare inherited glyoxalate metabolic disorders through in-situ analysis of renal stones

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Jacob, D. E.; Grohe, B.; Hoppe, B.; Beck, B. B.; Tessadri, R.

2012-04-01

The primary hyperoxalurias type I - III constitute rare autosomal-recessive inherited disorders of the human glyoxylate metabolism. By mechanisms that are ill understood progressive nephrocalcinosis and recurrent urolithiasis (kidney stone formation) often starting in early childhood, along with their secondary complications results in loss of nephron mass which progresses to end-stage renal failure over time. In the most frequent form, end-stage renal failure (ESRF) is the rule and combined liver/kidney transplantation respectively pre-emptive liver transplantation are the only causative treatment today. Hence, this contributes significantly to healthcare costs and early diagnosis is extremely important for a positive outcome for the patient. We are developing a stone-based diagnostic method by in-detail multi-methods investigation of the crystalline moiety in concert with urine and stone proteomics. Stone analysis will allow faster analysis at low-impact for the patients in the early stages of the disease. First results from combined spectroscopic (Raman, FTIR)and geochemical micro-analyses (Electron Microprobe and Laser Ablation ICP-MS) are presented here that show significant differences between stones from hyperoxaluria patients and those formed by patients without this disorder (idiopathic stones). Major differences exist in chemistry as well as in morphology and phase composition of the stones. Ca/P ratios and Mg contents differentiate between oxalate-stones from hyperoxaluria patients and idiopathic stones. Results show that also within the different subtypes of primary hyperoxaluria significant differences can be found in stone composition. These imply differences in stone formation which could be exploited for new therapeutic pathways. Furthermore, the results provide important feedback for suspected but yet unconfirmed cases of primary hyperoxaluria when used in concert with the genetic methods routinely applied.

Proteomic analysis reveals that iron availability alters the metabolic status of the pathogenic fungus Paracoccidioides brasiliensis.

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Ana F A Parente

Full Text Available Paracoccidioides brasiliensis is a thermodimorphic fungus and the causative agent of paracoccidioidomycosis (PCM. The ability of P. brasiliensis to uptake nutrients is fundamental for growth, but a reduction in the availability of iron and other nutrients is a host defense mechanism many pathogenic fungi must overcome. Thus, fungal mechanisms that scavenge iron from host may contribute to P. brasiliensis virulence. In order to better understand how P. brasiliensis adapts to iron starvation in the host we compared the two-dimensional (2D gel protein profile of yeast cells during iron starvation to that of iron rich condition. Protein spots were selected for comparative analysis based on the protein staining intensity as determined by image analysis. A total of 1752 protein spots were selected for comparison, and a total of 274 out of the 1752 protein spots were determined to have changed significantly in abundance due to iron depletion. Ninety six of the 274 proteins were grouped into the following functional categories; energy, metabolism, cell rescue, virulence, cell cycle, protein synthesis, protein fate, transcription, cellular communication, and cell fate. A correlation between protein and transcript levels was also discovered using quantitative RT-PCR analysis from RNA obtained from P. brasiliensis under iron restricting conditions and from yeast cells isolated from infected mouse spleens. In addition, western blot analysis and enzyme activity assays validated the differential regulation of proteins identified by 2-D gel analysis. We observed an increase in glycolytic pathway protein regulation while tricarboxylic acid cycle, glyoxylate and methylcitrate cycles, and electron transport chain proteins decreased in abundance under iron limiting conditions. These data suggest a remodeling of P. brasiliensis metabolism by prioritizing iron independent pathways.

Composition and Predicted Metabolic Capacity of Upper and Lower Airway Microbiota of Healthy Dogs in Relation to the Fecal Microbiota.

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Ericsson, Aaron C; Personett, Alexa R; Grobman, Megan E; Rindt, Hansjorg; Reinero, Carol R

2016-01-01

The upper and lower airways of healthy humans are reported to harbor stable and consistent bacterial populations, and the composition of these communities is altered in individuals affected with several respiratory diseases. Data regarding the presence of airway microbiota in other animals are scant and a better understanding of the composition and metabolic function of such bacterial populations is essential for the development of novel therapeutic and diagnostic modalities for use in both veterinary and human medicine. Based on targeted next-generation sequencing of feces and samples collected at multiple levels of the airways from 16 healthy female dogs, we demonstrate that canine airways harbor a topographically continuous microbiota with increasing relative abundance of proteobacterial species from the upper to lower airways. The lung-associated microbiota, as assessed via bronchoalveolar lavage fluid (BALF), was the most consistent between dogs and was dominated by three distinct taxa, two of which were resolved to the species level and one to the level of family. The gene content of the nasal, oropharyngeal, and lung-associated microbiota, predicted using the Phylogenetic Investigations into Communities by Reconstruction of Unobserved States (PICRUSt) software, provided information regarding the glyoxylate and citrate cycle metabolic pathways utilized by these bacterial populations to colonize such nutrient-poor, low-throughput environments. These data generated in healthy subjects provide context for future analysis of diseased canine airways. Moreover, as dogs have similar respiratory anatomy, physiology, and immune systems as humans, are exposed to many of the same environmental stimuli, and spontaneously develop similar respiratory diseases, these data support the use of dogs as a model species for prospective studies of the airway microbiota, with findings translatable to the human condition.

Deep-Sea Trench Microbiology Down to 10.9 Kilometers Below the Surface

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Bartlett, D. H.

2012-12-01

Deep-sea trenches, extending to more than 10.9 km below the sea surface, are among the most remote and infrequently sampled habitats. As a result a global perspective of microbial diversity and adaptation is lacking in these extreme settings. I will present the results of studies of deep-sea trench microbes collected in the Puerto Rico Trench (PRT), Tonga Trench, New Britain Trench and Mariana Trench. The samples collected include sediment, seawater and animals in baited traps. The analyses to be described include microbial community activity and viability measurements as a function of hydrostatic pressure, microbial culturing at high pressure under various physiological conditions, phylogenetics and metagenome and single-cell genome characterizations. Most of the results to date stem from samples recovered from the PRT. The deep-sea PRT Trench microbes have more in common at the species level with other deep-sea microbial communities previously characterized in the Pacific Ocean and the Mediterranean Sea than with the microbial populations above them in shallow waters. They also harbor larger genomes with more genes assigned to signal transduction, transcription, replication, recombination and repair and inorganic ion transport. The overrepresented transporters in the PRT metagenome include di- and tri-carboxylate transporters that correspond to the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. But, perhaps the most dramatic adaptational feature of the PRT microbes is heavy metal resistance, as reflected in the high numbers of metal efflux systems present. Single-cell genomics approaches have proven particularly useful for placing PRT metagenomic data into context.

Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain

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Tang, Yinjie J.; Sapra, Rajat; Joyner, Dominique; Hazen, Terry C.; Myers, Samuel; Reichmuth, David; Blanch, Harvey; Keasling, Jay D.

2009-01-20

A recently discovered thermophilic bacterium, Geobacillus thermoglucosidasius M10EXG, ferments a range of C5 (e.g., xylose) and C6 sugars (e.g., glucose) and istolerant to high ethanol concentrations (10percent, v/v). We have investigated the central metabolism of this bacterium using both in vitro enzyme assays and 13C-based flux analysis to provide insights into the physiological properties of this extremophile and explore its metabolism for bio-ethanol or other bioprocess applications. Our findings show that glucose metabolism in G. thermoglucosidasius M10EXG proceeds via glycolysis, the pentose phosphate pathway, and the TCA cycle; the Entner?Doudoroff pathway and transhydrogenase activity were not detected. Anaplerotic reactions (including the glyoxylate shunt, pyruvate carboxylase, and phosphoenolpyruvate carboxykinase) were active, but fluxes through those pathways could not be accuratelydetermined using amino acid labeling. When growth conditions were switched from aerobic to micro-aerobic conditions, fluxes (based on a normalized glucose uptake rate of 100 units (g DCW)-1 h-1) through the TCA cycle and oxidative pentose phosphate pathway were reduced from 64+-3 to 25+-2 and from 30+-2 to 19+-2, respectively. The carbon flux under micro-aerobic growth was directed formate. Under fully anerobic conditions, G. thermoglucosidasius M10EXG used a mixed acid fermentation process and exhibited a maximum ethanol yield of 0.38+-0.07 mol mol-1 glucose. In silico flux balance modeling demonstrates that lactate and acetate production from G. thermoglucosidasius M10EXG reduces the maximum ethanol yieldby approximately threefold, thus indicating that both pathways should be modified to maximize ethanol production.

Metabolic evolution and a comparative omics analysis of Corynebacterium glutamicum for putrescine production.

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Li, Zhen; Shen, Yu-Ping; Jiang, Xuan-Long; Feng, Li-Shen; Liu, Jian-Zhong

2018-02-01

Putrescine is widely used in the industrial production of bioplastics, pharmaceuticals, agrochemicals, and surfactants. Because the highest titer of putrescine is much lower than that of its precursor L-ornithine reported in microorganisms to date, further work is needed to increase putrescine production in Corynebacterium glutamicum. We first compared 7 ornithine decarboxylase genes and found that the Enterobacter cloacae ornithine decarboxylase gene speC1 was most suitable for putrescine production in C. glutamicum. Increasing NADPH availability and blocking putrescine oxidation and acetylation were chosen as targets for metabolic engineering. The putrescine producer C. glutamicum PUT4 was first constructed by deleting puo, butA and snaA genes, and replacing the fabG gene with E. cloacae speC1. After adaptive evolution with C. glutamicum PUT4, the evolved strain C. glutamicum PUT-ALE, which produced an 96% higher amount of putrescine compared to the parent strain, was obtained. The whole genome resequencing indicates that the SNPs located in the odhA coding region may be associated with putrescine production. The comparative proteomic analysis reveals that the pentose phosphate and anaplerotic pathway, the glyoxylate cycle, and the ornithine biosynthetic pathway were upregulated in the evolved strain C. glutamicum PUT-ALE. The aspartate family, aromatic, and branched chain amino acid and fatty acid biosynthetic pathways were also observed to be downregulated in C. glutamicum PUT-ALE. Reducing OdhA activity by replacing the odhA native start codon GTG with TTG and overexpression of cgmA or pyc458 further improved putrescine production. Repressing the carB, ilvH, ilvB and aroE expression via CRISPRi also increased putrescine production by 5, 9, 16 and 19%, respectively.

The switch from fermentation to respiration in Saccharomyces cerevisiae is regulated by the Ert1 transcriptional activator/repressor.

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Gasmi, Najla; Jacques, Pierre-Etienne; Klimova, Natalia; Guo, Xiao; Ricciardi, Alessandra; Robert, François; Turcotte, Bernard

2014-10-01

In the yeast Saccharomyces cerevisiae, fermentation is the major pathway for energy production, even under aerobic conditions. However, when glucose becomes scarce, ethanol produced during fermentation is used as a carbon source, requiring a shift to respiration. This adaptation results in massive reprogramming of gene expression. Increased expression of genes for gluconeogenesis and the glyoxylate cycle is observed upon a shift to ethanol and, conversely, expression of some fermentation genes is reduced. The zinc cluster proteins Cat8, Sip4, and Rds2, as well as Adr1, have been shown to mediate this reprogramming of gene expression. In this study, we have characterized the gene YBR239C encoding a putative zinc cluster protein and it was named ERT1 (ethanol regulated transcription factor 1). ChIP-chip analysis showed that Ert1 binds to a limited number of targets in the presence of glucose. The strongest enrichment was observed at the promoter of PCK1 encoding an important gluconeogenic enzyme. With ethanol as the carbon source, enrichment was observed with many additional genes involved in gluconeogenesis and mitochondrial function. Use of lacZ reporters and quantitative RT-PCR analyses demonstrated that Ert1 regulates expression of its target genes in a manner that is highly redundant with other regulators of gluconeogenesis. Interestingly, in the presence of ethanol, Ert1 is a repressor of PDC1 encoding an important enzyme for fermentation. We also show that Ert1 binds directly to the PCK1 and PDC1 promoters. In summary, Ert1 is a novel factor involved in the regulation of gluconeogenesis as well as a key fermentation gene. Copyright © 2014 by the Genetics Society of America.

Regulatory and Metabolic Networks for the Adaptation of Pseudomonas aeruginosa Biofilms to Urinary Tract-Like Conditions

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Dohnt, Katrin; Haddad, Isam; Jänsch, Lothar; Klein, Johannes; Narten, Maike; Pommerenke, Claudia; Scheer, Maurice; Schobert, Max; Schomburg, Dietmar; Thielen, Bernhard; Jahn, Dieter

2013-01-01

Biofilms of the Gram-negative bacterium Pseudomonas aeruginosa are one of the major causes of complicated urinary tract infections with detrimental outcome. To develop novel therapeutic strategies the molecular adaption strategies of P. aeruginosa biofilms to the conditions of the urinary tract were investigated thoroughly at the systems level using transcriptome, proteome, metabolome and enzyme activity analyses. For this purpose biofilms were grown anaerobically in artificial urine medium (AUM). Obtained data were integrated bioinformatically into gene regulatory and metabolic networks. The dominating response at the transcriptome and proteome level was the adaptation to iron limitation via the broad Fur regulon including 19 sigma factors and up to 80 regulated target genes or operons. In agreement, reduction of the iron cofactor-dependent nitrate respiratory metabolism was detected. An adaptation of the central metabolism to lactate, citrate and amino acid as carbon sources with the induction of the glyoxylate bypass was observed, while other components of AUM like urea and creatinine were not used. Amino acid utilization pathways were found induced, while fatty acid biosynthesis was reduced. The high amounts of phosphate found in AUM explain the reduction of phosphate assimilation systems. Increased quorum sensing activity with the parallel reduction of chemotaxis and flagellum assembly underscored the importance of the biofilm life style. However, reduced formation of the extracellular polysaccharide alginate, typical for P. aeruginosa biofilms in lungs, indicated a different biofilm type for urinary tract infections. Furthermore, the obtained quorum sensing response results in an increased production of virulence factors like the extracellular lipase LipA and protease LasB and AprA explaining the harmful cause of these infections. PMID:23967252

Regulatory and metabolic networks for the adaptation of Pseudomonas aeruginosa biofilms to urinary tract-like conditions.

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Petra Tielen

Full Text Available Biofilms of the Gram-negative bacterium Pseudomonas aeruginosa are one of the major causes of complicated urinary tract infections with detrimental outcome. To develop novel therapeutic strategies the molecular adaption strategies of P. aeruginosa biofilms to the conditions of the urinary tract were investigated thoroughly at the systems level using transcriptome, proteome, metabolome and enzyme activity analyses. For this purpose biofilms were grown anaerobically in artificial urine medium (AUM. Obtained data were integrated bioinformatically into gene regulatory and metabolic networks. The dominating response at the transcriptome and proteome level was the adaptation to iron limitation via the broad Fur regulon including 19 sigma factors and up to 80 regulated target genes or operons. In agreement, reduction of the iron cofactor-dependent nitrate respiratory metabolism was detected. An adaptation of the central metabolism to lactate, citrate and amino acid as carbon sources with the induction of the glyoxylate bypass was observed, while other components of AUM like urea and creatinine were not used. Amino acid utilization pathways were found induced, while fatty acid biosynthesis was reduced. The high amounts of phosphate found in AUM explain the reduction of phosphate assimilation systems. Increased quorum sensing activity with the parallel reduction of chemotaxis and flagellum assembly underscored the importance of the biofilm life style. However, reduced formation of the extracellular polysaccharide alginate, typical for P. aeruginosa biofilms in lungs, indicated a different biofilm type for urinary tract infections. Furthermore, the obtained quorum sensing response results in an increased production of virulence factors like the extracellular lipase LipA and protease LasB and AprA explaining the harmful cause of these infections.

Anti-bacterial activity of Achatina CRP and its mechanism of action.

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Mukherjee, Sandip; Barman, Soma; Mandal, Narayan Chandra; Bhattacharya, Shelley

2014-07-01

The physiological role of C-reactive protein (CRP), the classical acute-phase protein, is not well documented, despite many reports on biological effects of CRP in vitro and in model systems in vivo. It has been suggested that CRP protects mice against lethal toxicity of bacterial infections by implementing immunological responses. In Achatina fulica CRP is a constitutive multifunctional protein in haemolymph and considered responsible for their survival in the environment for millions of years. The efficacy of Achatina CRP (ACRP) was tested against both Salmonella typhimurium and Bacillus subtilis infections in mice where endogenous CRP level is negligible even after inflammatory stimulus. Further, growth curves of the bacteria revealed that ACRP (50 microg/mL) is bacteriostatic against gram negative salmonellae and bactericidal against gram positive bacilli. ACRP induced energy crises in bacterial cells, inhibited key carbohydrate metabolic enzymes such as phosphofructokinase in glycolysis, isocitrate dehydrogenase in TCA cycle, isocitrate lyase in glyoxylate cycle and fructose-1,6-bisphosphatase in gluconeogenesis. ACRP disturbed the homeostasis of cellular redox potential as well as reduced glutathione status, which is accompanied by an enhanced rate of lipid peroxidation. Annexin V-Cy3/CFDA dual staining clearly showed ACRP induced apoptosis-like death in bacterial cell population. Moreover, immunoblot analyses also indicated apoptosis-like death in ACRP treated bacterial cells, where activation of poly (ADP-ribose) polymerase-1 (PARP) and caspase-3 was noteworthy. It is concluded that metabolic impairment by ACRP in bacterial cells is primarily due to generation of reactive oxygen species and ACRP induced anti-bacterial effect is mediated by metabolic impairment leading to apoptosis-like death in bacterial cells.

Extreme intrafamilial variability of Saudi brothers with primary hyperoxaluria type 1

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Alfadhel M

2012-08-01

Full Text Available Majid Alfadhel,1 Khalid A Alhasan,2 Mohammed Alotaibi,3 Khalid Al Fakeeh41Division of Genetics, Department of Pediatrics, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia; 2Division of Nephrology Department of Pediatrics, King Saud University King Khalid University Hospital, Riyadh, Saudi Arabia; 3Department of Radiology, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia; 4Division of Nephrology, Department of Pediatrics, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi ArabiaBackground: Primary hyperoxaluria type 1 (PH1 is characterized by progressive renal insufficiency culminating in end-stage renal disease, and a wide range of clinical features related to systemic oxalosis in different organs. It is caused by autosomal recessive deficiency of alanine:glyoxylate aminotransferase due to a defect in AGXT gene.Case report: Two brothers (one 6 months old; the other 2 years old presented with acute renal failure and urinary tract infection respectively. PH1 was confirmed by high urinary oxalate level, demonstration of oxalate crystals in bone biopsy, and pathogenic homozygous known AGXT gene mutation. Despite the same genetic background, same sex, and shared environment, the outcome of the two siblings differs widely. While one of them died earlier with end-stage renal disease and multiorgan failure caused by systemic oxalosis, the older brother is pyridoxine responsive with normal development and renal function.Conclusion: Clinicians should be aware of extreme intrafamilial variability of PH1 and international registries are needed to characterize the genotype-phenotype correlation in such disorder.Keywords: primary hyperoxaluria, oxalosis, PH1, intrafamilial variability

Regulatory and metabolic networks for the adaptation of Pseudomonas aeruginosa biofilms to urinary tract-like conditions.

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Tielen, Petra; Rosin, Nathalie; Meyer, Ann-Kathrin; Dohnt, Katrin; Haddad, Isam; Jänsch, Lothar; Klein, Johannes; Narten, Maike; Pommerenke, Claudia; Scheer, Maurice; Schobert, Max; Schomburg, Dietmar; Thielen, Bernhard; Jahn, Dieter

2013-01-01

Biofilms of the Gram-negative bacterium Pseudomonas aeruginosa are one of the major causes of complicated urinary tract infections with detrimental outcome. To develop novel therapeutic strategies the molecular adaption strategies of P. aeruginosa biofilms to the conditions of the urinary tract were investigated thoroughly at the systems level using transcriptome, proteome, metabolome and enzyme activity analyses. For this purpose biofilms were grown anaerobically in artificial urine medium (AUM). Obtained data were integrated bioinformatically into gene regulatory and metabolic networks. The dominating response at the transcriptome and proteome level was the adaptation to iron limitation via the broad Fur regulon including 19 sigma factors and up to 80 regulated target genes or operons. In agreement, reduction of the iron cofactor-dependent nitrate respiratory metabolism was detected. An adaptation of the central metabolism to lactate, citrate and amino acid as carbon sources with the induction of the glyoxylate bypass was observed, while other components of AUM like urea and creatinine were not used. Amino acid utilization pathways were found induced, while fatty acid biosynthesis was reduced. The high amounts of phosphate found in AUM explain the reduction of phosphate assimilation systems. Increased quorum sensing activity with the parallel reduction of chemotaxis and flagellum assembly underscored the importance of the biofilm life style. However, reduced formation of the extracellular polysaccharide alginate, typical for P. aeruginosa biofilms in lungs, indicated a different biofilm type for urinary tract infections. Furthermore, the obtained quorum sensing response results in an increased production of virulence factors like the extracellular lipase LipA and protease LasB and AprA explaining the harmful cause of these infections.

Differential filamentation of Candida albicans and Candida dubliniensis Is governed by nutrient regulation of UME6 expression.

LENUS (Irish Health Repository)

O'Connor, Leanne

2010-09-01

Candida dubliniensis is closely related to Candida albicans; however, it is responsible for fewer infections in humans and is less virulent in animal models of infection. C. dubliniensis forms fewer hyphae in vivo, and this may contribute to its reduced virulence. In this study we show that, unlike C. albicans, C. dubliniensis fails to form hyphae in yeast extract-peptone-dextrose (YPD) medium supplemented with 10% (vol\\/vol) fetal calf serum (YPDS medium). However, C. dubliniensis filaments in water plus 10% (vol\\/vol) fetal calf serum (WS), and this filamentation is inhibited by the addition of peptone and glucose. Repression of filamentation in YPDS medium could be partly overcome by preculture in synthetic Lee\\'s medium. Unlike C. albicans, inoculation of C. dubliniensis in YPDS medium did not result in increased UME6 transcription. However, >100-fold induction of UME6 was observed when C. dubliniensis was inoculated in nutrient-poor WS medium. The addition of increasing concentrations of peptone to WS medium had a dose-dependent effect on reducing UME6 expression. Transcript profiling of C. dubliniensis hyphae in WS medium identified a starvation response involving expression of genes in the glyoxylate cycle and fatty acid oxidation. In addition, a core, shared transcriptional response with C. albicans could be identified, including expression of virulence-associated genes including SAP456, SAP7, HWP1, and SOD5. Preculture in nutrient-limiting medium enhanced adherence of C. dubliniensis, epithelial invasion, and survival following coculture with murine macrophages. In conclusion, C. albicans, unlike C. dubliniensis, appears to form hyphae in liquid medium regardless of nutrient availability, which may account for its increased capacity to cause disease in humans.

Catabolism of biomass-derived sugars in fungi and metabolic engineering as a tool for organic acid production

Energy Technology Data Exchange (ETDEWEB)

Koivistoinen, O.

2013-11-01

gene ladB was identified and the deletion of the gene resulted in growth arrest on galactitol indicating that the enzyme is an essential part of the oxido-reductive galactose pathway in fungi. The last step of this pathway converts D-sorbitol to D-fructose by sorbitol dehydrogenase encoded by sdhA gene. Sorbitol dehydrogenase was found to be a medium chain dehydrogenase and transcription analysis suggested that the enzyme is involved in D-galactose and D-sorbitol catabolism. The thesis also demonstrates how the understanding of cell metabolism can be used to engineer yeast to produce glycolic acid. Glycolic acid is a chemical, which can be used for example in the cosmetic industry and as a precursor for biopolymers. Currently, glycolic acid is produced by chemical synthesis in a process requiring toxic formaldehyde and fossil fuels. Thus, a biochemical production route would be preferable from a sustainability point of view. Yeasts do not produce glycolic acid under normal conditions but it is a desired production host for acid production because of its natural tolerance to low pH conditions. As a proof of concept, pure model substrates, e.g. D-xylose and ethanol, were used as starting materials for glycolic acid production but the knowledge can be further applied to an expanded substrate range such as biomass derived sugars. Already the introduction of a heterologous glyoxylate reductase gene resulted in glycolic acid production in the yeasts S. cerevisiae and Kluyveromyces lactis. Further modifications of the glyoxylate cycle increased the production of glycolic acid and it was successfully produced in bioreactor cultivation. The challenge of biotechnology is to produce high value products from cheap raw materials in an economically feasible way. This thesis gives more basic understanding to the topic in the form of new information regarding L-rhamnose and D-galactose metabolism in eukaryotic microbes as well as provides an example on how cell metabolism can be

Extending the spectrum of α-dicarbonyl compounds in vivo.

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Henning, Christian; Liehr, Kristin; Girndt, Matthias; Ulrich, Christof; Glomb, Marcus A

2014-10-10

Maillard α-dicarbonyl compounds are known as central intermediates in advanced glycation end product (AGE) formation. Glucose is the primary source of energy for the human body, whereas l-threo-ascorbic acid (vitamin C) is an essential nutrient, involved in a variety of enzymatic reactions. Thus, the Maillard degradation of glucose and ascorbic acid is of major importance in vivo. To understand the complex mechanistic pathways of AGE formation, it is crucial to extend the knowledge on plasma concentrations of reactive key α-dicarbonyl compounds (e.g. 1-deoxyglucosone). With the present work, we introduce a highly sensitive LC-MS/MS multimethod for human blood plasma based on derivatization with o-phenylenediamine under acidic conditions. The impact of workup and reaction conditions, particularly of pH, was thoroughly evaluated. A comprehensive validation provided the limit of detection, limit of quantitation, coefficients of variation, and recovery rates. The method includes the α-dicarbonyls 1-deoxyglucosone, 3-deoxyglucosone, glucosone, Lederer's glucosone, dehydroascorbic acid, 2,3-diketogulonic acid, 1-deoxypentosone, 3-deoxypentosone, 3,4-dideoxypentosone, pentosone, 1-deoxythreosone, 3-deoxythreosone, threosone, methylglyoxal, glyoxal; the α-keto-carboxylic acids pyruvic acid and glyoxylic acid; and the dicarboxylic acid oxalic acid. The method was then applied to the analyses of 15 healthy subjects and 24 uremic patients undergoing hemodialysis. The comparison of the results revealed a clear shift in the product spectrum. In most cases, the plasma levels of target analytes were significantly higher. Thus, this is the first time that a complete spectrum of α-dicarbonyl compounds relevant in vivo has been established. The results provide further insights into the chemistry of AGE formation and will be helpful to find specific markers to differentiate between the various precursors of glycation. © 2014 by The American Society for Biochemistry and

An incomplete TCA cycle increases survival of Salmonella Typhimurium during infection of resting and activated murine macrophages.

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Bowden, Steven D; Ramachandran, Vinoy K; Knudsen, Gitte M; Hinton, Jay C D; Thompson, Arthur

2010-11-08

In comparison to the comprehensive analyses performed on virulence gene expression, regulation and action, the intracellular metabolism of Salmonella during infection is a relatively under-studied area. We investigated the role of the tricarboxylic acid (TCA) cycle in the intracellular replication of Salmonella Typhimurium in resting and activated macrophages, epithelial cells, and during infection of mice. We constructed deletion mutations of 5 TCA cycle genes in S. Typhimurium including gltA, mdh, sdhCDAB, sucAB, and sucCD. We found that the mutants exhibited increased net intracellular replication in resting and activated murine macrophages compared to the wild-type. In contrast, an epithelial cell infection model showed that the S. Typhimurium ΔsucCD and ΔgltA strains had reduced net intracellular replication compared to the wild-type. The glyoxylate shunt was not responsible for the net increased replication of the TCA cycle mutants within resting macrophages. We also confirmed that, in a murine infection model, the S. Typhimurium ΔsucAB and ΔsucCD strains are attenuated for virulence. Our results suggest that disruption of the TCA cycle increases the ability of S. Typhimurium to survive within resting and activated murine macrophages. In contrast, epithelial cells are non-phagocytic cells and unlike macrophages cannot mount an oxidative and nitrosative defence response against pathogens; our results show that in HeLa cells the S. Typhimurium TCA cycle mutant strains show reduced or no change in intracellular levels compared to the wild-type. The attenuation of the S. Typhimurium ΔsucAB and ΔsucCD mutants in mice, compared to their increased net intracellular replication in resting and activated macrophages suggest that Salmonella may encounter environments within the host where a complete TCA cycle is advantageous.

Transcriptome and Multivariable Data Analysis of Corynebacterium glutamicum under Different Dissolved Oxygen Conditions in Bioreactors

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Sun, Yang; Guo, Wenwen; Wang, Fen; Peng, Feng; Yang, Yankun; Dai, Xiaofeng; Liu, Xiuxia; Bai, Zhonghu

2016-01-01

Dissolved oxygen (DO) is an important factor in the fermentation process of Corynebacterium glutamicum, which is a widely used aerobic microbe in bio-industry. Herein, we described RNA-seq for C. glutamicum under different DO levels (50%, 30% and 0%) in 5 L bioreactors. Multivariate data analysis (MVDA) models were used to analyze the RNA-seq and metabolism data to investigate the global effect of DO on the transcriptional distinction of the substance and energy metabolism of C. glutamicum. The results showed that there were 39 and 236 differentially expressed genes (DEGs) under the 50% and 0% DO conditions, respectively, compared to the 30% DO condition. Key genes and pathways affected by DO were analyzed, and the result of the MVDA and RNA-seq revealed that different DO levels in the fermenter had large effects on the substance and energy metabolism and cellular redox balance of C. glutamicum. At low DO, the glycolysis pathway was up-regulated, and TCA was shunted by the up-regulation of the glyoxylate pathway and over-production of amino acids, including valine, cysteine and arginine. Due to the lack of electron-acceptor oxygen, 7 genes related to the electron transfer chain were changed, causing changes in the intracellular ATP content at 0% and 30% DO. The metabolic flux was changed to rebalance the cellular redox. This study applied deep sequencing to identify a wealth of genes and pathways that changed under different DO conditions and provided an overall comprehensive view of the metabolism of C. glutamicum. The results provide potential ways to improve the oxygen tolerance of C. glutamicum and to modify the metabolic flux for amino acid production and heterologous protein expression. PMID:27907077

Different Covalent Immobilizations Modulate Lipase Activities of Hypocrea pseudokoningii

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Marita G. Pereira

2017-09-01

Full Text Available Enzyme immobilization can promote several advantages for their industrial application. In this work, a lipase from Hypocrea pseudokoningii was efficiently linked to four chemical supports: agarose activated with cyanogen bromide (CNBr, glyoxyl-agarose (GX, MANAE-agarose activated with glutaraldehyde (GA and GA-crosslinked with glutaraldehyde. Results showed a more stable lipase with both the GA-crosslinked and GA derivatives, compared to the control (CNBr, at 50 °C, 60 °C and 70 °C. Moreover, all derivatives were stabilized when incubated with organic solvents at 50%, such as ethanol, methanol, n-propanol and cyclohexane. Furthermore, lipase was highly activated (4-fold in the presence of cyclohexane. GA-crosslinked and GA derivatives were more stable than the CNBr one in the presence of organic solvents. All derivatives were able to hydrolyze sardine, açaí (Euterpe oleracea, cotton seed and grape seed oils. However, during the hydrolysis of sardine oil, GX derivative showed to be 2.3-fold more selectivity (eicosapentaenoic acid (EPA/docosahexaenoic acid (DHA ratio than the control. Additionally, the types of immobilization interfered with the lipase enantiomeric preference. Unlike the control, the other three derivatives preferably hydrolyzed the R-isomer of 2-hydroxy-4-phenylbutanoic acid ethyl ester and the S-isomer of 1-phenylethanol acetate racemic mixtures. On the other hand, GX and CNBr derivatives preferably hydrolyzed the S-isomer of butyryl-2-phenylacetic acid racemic mixture while the GA and GA-crosslink derivatives preferably hydrolyzed the R-isomer. However, all derivatives, including the control, preferably hydrolyzed the methyl mandelate S-isomer. Moreover, the derivatives could be used for eight consecutive cycles retaining more than 50% of their residual activity. This work shows the importance of immobilization as a tool to increase the lipase stability to temperature and organic solvents, thus enabling the possibility of

Molecular time-course and the metabolic basis of entry into dauer in Caenorhabditis elegans.

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Pan-Young Jeong

Full Text Available When Caenorhabditis elegans senses dauer pheromone (daumone, signaling inadequate growth conditions, it enters the dauer state, which is capable of long-term survival. However, the molecular pathway of dauer entry in C. elegans has remained elusive. To systematically monitor changes in gene expression in dauer paths, we used a DNA microarray containing 22,625 gene probes corresponding to 22,150 unique genes from C. elegans. We employed two different paths: direct exposure to daumone (Path 1 and normal growth media plus liquid culture (Path 2. Our data reveal that entry into dauer is accomplished through the multi-step process, which appears to be compartmentalized in time and according to metabolic flux. That is, a time-course of dauer entry in Path 1 shows that dauer larvae formation begins at post-embryonic stage S4 (48 h and is complete at S6 (72 h. Our results also suggest the presence of a unique adaptive metabolic control mechanism that requires both stage-specific expression of specific genes and tight regulation of different modes of fuel metabolite utilization to sustain the energy balance in the context of prolonged survival under adverse growth conditions. It is apparent that worms entering dauer stage may rely heavily on carbohydrate-based energy reserves, whereas dauer larvae utilize fat or glyoxylate cycle-based energy sources. We created a comprehensive web-based dauer metabolic database for C. elegans (www.DauerDB.org that makes it possible to search any gene and compare its relative expression at a specific stage, or evaluate overall patterns of gene expression in both paths. This database can be accessed by the research community and could be widely applicable to other related nematodes as a molecular atlas.

Extracellular ammonia at sites of pulmonary infection with Coccidioides posadasii contributes to severity of the respiratory disease.

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Wise, Hua Zhang; Hung, Chiung-Yu; Whiston, Emily; Taylor, John W; Cole, Garry T

2013-01-01

Coccidioides is the causative agent of a potentially life-threatening respiratory disease of humans. A feature of this mycosis is that pH measurements of the microenvironment of pulmonary abscesses are consistently alkaline due to ammonia production during the parasitic cycle. We previously showed that enzymatically active urease is partly responsible for elevated concentrations of extracellular ammonia at sites of lung infection and contributes to both localized host tissue damage and exacerbation of the respiratory disease in BALB/c mice. Disruption of the urease gene (URE) of Coccidioides posadasii only partially reduced the amount of ammonia detected during in vitro growth of the parasitic phase, suggesting that other ammonia-producing pathways exist that may also contribute to the virulence of this pathogen. Ureidoglycolate hydrolase (Ugh) expressed by bacteria, fungi and higher plants catalyzes the hydrolysis of ureidoglycolate to yield glyoxylate and the release CO2 and ammonia. This enzymatic pathway is absent in mice and humans. Ureidoglycolate hydrolase gene deletions were conducted in a wild type (WT) isolate of C. posadasii as well as the previously generated Δure knock-out strain. Restorations of UGH in the mutant stains were performed to generate and evaluate the respective revertants. The double mutant revealed a marked decrease in the amount of extracellular ammonia without loss of reproductive competence in vitro compared to both the WT and Δure parental strains. BALB/c mice challenged intranasally with the Δugh/Δure mutant showed 90% survival after 30 days, decreased fungal burden, and well-organized pulmonary granulomas. We conclude that loss of both Ugh and Ure activity significantly reduced the virulence of this fungal pathogen. Copyright © 2013 Elsevier Ltd. All rights reserved.

Composition and Predicted Metabolic Capacity of Upper and Lower Airway Microbiota of Healthy Dogs in Relation to the Fecal Microbiota.

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Aaron C Ericsson

Full Text Available The upper and lower airways of healthy humans are reported to harbor stable and consistent bacterial populations, and the composition of these communities is altered in individuals affected with several respiratory diseases. Data regarding the presence of airway microbiota in other animals are scant and a better understanding of the composition and metabolic function of such bacterial populations is essential for the development of novel therapeutic and diagnostic modalities for use in both veterinary and human medicine. Based on targeted next-generation sequencing of feces and samples collected at multiple levels of the airways from 16 healthy female dogs, we demonstrate that canine airways harbor a topographically continuous microbiota with increasing relative abundance of proteobacterial species from the upper to lower airways. The lung-associated microbiota, as assessed via bronchoalveolar lavage fluid (BALF, was the most consistent between dogs and was dominated by three distinct taxa, two of which were resolved to the species level and one to the level of family. The gene content of the nasal, oropharyngeal, and lung-associated microbiota, predicted using the Phylogenetic Investigations into Communities by Reconstruction of Unobserved States (PICRUSt software, provided information regarding the glyoxylate and citrate cycle metabolic pathways utilized by these bacterial populations to colonize such nutrient-poor, low-throughput environments. These data generated in healthy subjects provide context for future analysis of diseased canine airways. Moreover, as dogs have similar respiratory anatomy, physiology, and immune systems as humans, are exposed to many of the same environmental stimuli, and spontaneously develop similar respiratory diseases, these data support the use of dogs as a model species for prospective studies of the airway microbiota, with findings translatable to the human condition.

Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication*

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Kito, Keiji; Ito, Haruka; Nohara, Takehiro; Ohnishi, Mihoko; Ishibashi, Yuko; Takeda, Daisuke

2016-01-01

Omics analysis is a versatile approach for understanding the conservation and diversity of molecular systems across multiple taxa. In this study, we compared the proteome expression profiles of four yeast species (Saccharomyces cerevisiae, Saccharomyces mikatae, Kluyveromyces waltii, and Kluyveromyces lactis) grown on glucose- or glycerol-containing media. Conserved expression changes across all species were observed only for a small proportion of all proteins differentially expressed between the two growth conditions. Two Kluyveromyces species, both of which exhibited a high growth rate on glycerol, a nonfermentative carbon source, showed distinct species-specific expression profiles. In K. waltii grown on glycerol, proteins involved in the glyoxylate cycle and gluconeogenesis were expressed in high abundance. In K. lactis grown on glycerol, the expression of glycolytic and ethanol metabolic enzymes was unexpectedly low, whereas proteins involved in cytoplasmic translation, including ribosomal proteins and elongation factors, were highly expressed. These marked differences in the types of predominantly expressed proteins suggest that K. lactis optimizes the balance of proteome resource allocation between metabolism and protein synthesis giving priority to cellular growth. In S. cerevisiae, about 450 duplicate gene pairs were retained after whole-genome duplication. Intriguingly, we found that in the case of duplicates with conserved sequences, the total abundance of proteins encoded by a duplicate pair in S. cerevisiae was similar to that of protein encoded by nonduplicated ortholog in Kluyveromyces yeast. Given the frequency of haploinsufficiency, this observation suggests that conserved duplicate genes, even though minor cases of retained duplicates, do not exhibit a dosage effect in yeast, except for ribosomal proteins. Thus, comparative proteomic analyses across multiple species may reveal not only species-specific characteristics of metabolic processes under

Integrated operation of the photorespiratory cycle and cytosolic metabolism in the modulation of primary nitrogen assimilation and export of organic N-transport compounds from leaves: a hypothesis.

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Misra, Jitendra B

2014-02-15

Photorespiration is generally considered to be an essentially dissipative process, although it performs some protective and essential functions. A theoretical appraisal indicates that the loss of freshly assimilated CO2 due to photorespiration in well-watered plants may not be as high as generally believed. Even under moderately adverse conditions, these losses may not exceed 10%. The photorespiratory metabolism of the source leaves of well-watered and well-nourished crop plants ought to be different from that of other leaves because the fluxes of the export of both carbohydrates and organic N-transport compounds in source leaves is quite high. With a heuristic approach that involved the dovetailing of certain metabolic steps with the photorespiratory cycle (PR-cycle), a novel network is proposed to operate in the source-leaves of well-watered and well-nourished plants. This network allows for the diversion of metabolites from their cyclic-routes in sizeable quantities. With the removal of considerable quantities of glycine and serine from the cyclic route, the number of RuBP oxygenation events would be several times those of the formation of hydroxypyruvate. Thus, to an extreme extent, photorespiratory metabolism would become open-ended and involve much less futile recycling of glycine and serine. Conversion of glyoxylate to glycine has been proposed to be a crucial step in the determination of the relative rates of the futile (cyclic) and anabolic (open-ended) routes. Thus, in the source leaves of well-watered and well-nourished plants, the importance of the cyclic route is limited to the salvaging of photorespiratory intermediates for the regeneration of RuBP. The proposed network is resilient enough to coordinate the rates of the assimilation of carbon and nitrogen in accordance with the moisture and N-fertility statuses of the soil. Copyright © 2013 Elsevier GmbH. All rights reserved.

Fatty acid synthesis by spinach chloroplasts, 2

International Nuclear Information System (INIS)

Yamada, Mitsuhiro; Nakamura, Yasunori

1975-01-01

By incorporation of 3 H 2 O into the fatty acid chain in the presence of unlabelled precursor, we showed that fatty acids are synthesized from PGA, PEP and pyruvate by intact spinach chloroplasts in the light. 13 C-tracer experiments confirmed that 1-C of pyruvate is decarboxylated and 2-C is incorporated into fatty acids by the chloroplasts. The patterns of fatty acids synthesized from PGA and pyruvate were the same as that from acetate. The highest rate of fatty acid synthesis was reached at the physiological concentration of PGA (3 mM) and pyruvate (1 mM). These results indicate the operation of the following path in the chloroplasts in light: PGA→PEP→pyruvate→acetylCoA→fatty acids. Since citrate and OAA were much less active and malate and glyoxylate were inert as precursors for fatty acid synthesis, PEP or pyruvate carboxylation, citrate lyase reaction and malate synthetase reaction are not involved in the formation of acetylCoA and fatty acids. Since pyruvate was much more effective as a substrate for fatty acid synthesis than lactate, acetaldehyde or acetate, direct decarboxylation path is considered to be the primary path from pyruvate to acetylCoA. The insignificant effect of chloroplast-washing on fatty acid synthesis from PGA and pyruvate indicates that the glycolytic path from PGA to pyruvate is associated with the chloroplasts. Since pyruvate was more effectively incorporated into fatty acids than acetylCoA, it is unlikely that pyruvate decarboxylation to acetylCoA is due to mitochondria contaminating the chloroplast preparation. On the basis of measurements of 3 H 2 O incorporation in the light and dark, the activity of fatty acid synthesis in spincah leaves appears to be shared by the activities in chloroplasts (87%) and other organelles (13%). (author)

Spatio-temporal distributions of dicarboxylic acids, ω-oxocarboxylic acids, pyruvic acid, α-dicarbonyls and fatty acids in the marine aerosols from the North and South Pacific

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Hoque, Mir Md. Mozammal; Kawamura, Kimitaka; Uematsu, Mitsuo

2017-03-01

Aerosol samples (TSP) were collected during a cruise in the North (3°05‧N-34°02‧N) and South (6°59‧S-25°46‧S) Pacific to investigate the spatio-temporal distributions of water-soluble dicarboxylic acids and related compounds. The molecular distributions of diacids were characterized by the predominance of oxalic (C2) acid followed by malonic (C3) and then succinic (C4) acid. However, we found a predominance of C4 over C3 in the aerosol sample that was collected in the western North Pacific Rim with a heavy influence from continental air masses. Atmospheric abundances of short chain diacids (C2-C4) are 2-3 times higher in the North Pacific than in the South Pacific. During the cruise, abundances of C2 in the western North Pacific are 5 times higher than those in the rest of the samples collected. Moreover, the aerosol samples collected in the western North Pacific demonstrated that glyoxylic (ωC2) acid and methylglyoxal (MeGly) were dominant together with C2. We found a strong correlation between C2 and ωC2 (r = 0.87) and C2 and MeGly (r = 0.97) in the western North Pacific aerosols but the correlations are significantly weak in the samples from the central North Pacific and Southern Ocean. Diacids were found to account for 1.6 to 14% of organic carbon with higher values in the western North Pacific. These results, together with 7-day backward air mass trajectories, indicate that ωC2 and MeGly are both originated from the photochemical oxidation of continent-derived organic precursors including isoprene, which can serve as precursors for the production of C2 during long-range atmospheric transport.

Non Target Site Tolerance Mechanisms Describe Tolerance to Glyphosate in Avena sterilis

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Pablo Tomas Fernandez-Moreno

2016-08-01

Full Text Available Sterile wild oat (Avena sterilis L. is an autogamous grass established in warm climate regions. This species has been used as a cover crop in Mediterranean perennial crops during the spring period prior to initiating competition with the main crop for water and nutrients. However, such cover crops need to be controlled (by glyphosate or tillage before the beginning of summer period (due to the possibility of intense drought stress. In 2011, the olive grove farmers of southern Spain expressed dissatisfaction because of the ineffective control with glyphosate on A. sterilis. Experiments were conducted to determine whether the continued use of glyphosate over a 5 year period had selected a new resistant or tolerant species. The GR50 values obtained for A. sterilis were 297.12 and 245.23 g ae ha-1 for exposed (E and un-exposed (UE glyphosate accessions, respectively. The spray retention and shikimic acid accumulation exhibited a non-significant difference between the two accessions. The results of 14C- glyphosate absorption was the same in the two accessions (E and UE, while the translocation from the treated leaf to the rest of the shoots and roots was similar in A. sterilis accessions. Glyphosate metabolism to aminomethylphosphonic acid (AMPA and glyoxylate was similar in both accessions, but increased after treatment with glyphosate, indicating that metabolism plays an important role in tolerance. Both A. sterilis accessions, present similarity in the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS activity enzyme with different glyphosate concentrations and without glyphosate, confirming that both accessions present the same genomic characteristics. The above-mentioned results indicate that innate tolerance to glyphosate in A. sterilis is probably and partly due to reduced herbicide absorption and translocation and metabolism compared to the susceptibility of other grasses weeds like Chloris inflata, Eleusine indica and Lolium rigidum.

Non-target Site Tolerance Mechanisms Describe Tolerance to Glyphosate in Avena sterilis.

Science.gov (United States)

Fernández-Moreno, Pablo T; Alcantara-de la Cruz, Ricardo; Cruz-Hipólito, Hugo E; Rojano-Delgado, Antonia M; Travlos, Ilias; De Prado, Rafael

2016-01-01

Sterile wild oat (Avena sterilis L.) is an autogamous grass established in warm climate regions. This species has been used as a cover crop in Mediterranean perennial crops during the spring period prior to initiating competition with the main crop for water and nutrients. However, such cover crops need to be controlled (by glyphosate or tillage) before the beginning of summer period (due to the possibility of intense drought stress). In 2011, the olive grove farmers of southern Spain expressed dissatisfaction because of the ineffective control with glyphosate on A. sterilis. Experiments were conducted to determine whether the continued use of glyphosate over a 5 year period had selected a new resistant or tolerant species. The GR50 values obtained for A. sterilis were 297.12 and 245.23 g ae ha(-1) for exposed (E) and un-exposed (UE) glyphosate accessions, respectively. The spray retention and shikimic acid accumulation exhibited a non-significant difference between the two accessions. The results of (14)C- glyphosate absorption was the same in the two accessions (E and UE), while the translocation from the treated leaf to the rest of the shoots and roots was similar in A. sterilis accessions. Glyphosate metabolism to aminomethylphosphonic acid (AMPA) and glyoxylate was similar in both accessions, but increased after treatment with glyphosate, indicating that metabolism plays an important role in tolerance. Both A. sterilis accessions, present similarity in the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) activity enzyme with different glyphosate concentrations and without glyphosate, confirming that both accessions present the same genomic characteristics. The above-mentioned results indicate that innate tolerance to glyphosate in A. sterilis is probably and partly due to reduced herbicide absorption and translocation and metabolism compared to the susceptibility of other grasses weeds like Chloris inflata, Eleusine indica, and Lolium rigidum.

Enhanced vulnerability of human proteins towards disease-associated inactivation through divergent evolution.

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Medina-Carmona, Encarnación; Fuchs, Julian E; Gavira, Jose A; Mesa-Torres, Noel; Neira, Jose L; Salido, Eduardo; Palomino-Morales, Rogelio; Burgos, Miguel; Timson, David J; Pey, Angel L

2017-09-15

Human proteins are vulnerable towards disease-associated single amino acid replacements affecting protein stability and function. Interestingly, a few studies have shown that consensus amino acids from mammals or vertebrates can enhance protein stability when incorporated into human proteins. Here, we investigate yet unexplored relationships between the high vulnerability of human proteins towards disease-associated inactivation and recent evolutionary site-specific divergence of stabilizing amino acids. Using phylogenetic, structural and experimental analyses, we show that divergence from the consensus amino acids at several sites during mammalian evolution has caused local protein destabilization in two human proteins linked to disease: cancer-associated NQO1 and alanine:glyoxylate aminotransferase, mutated in primary hyperoxaluria type I. We demonstrate that a single consensus mutation (H80R) acts as a disease suppressor on the most common cancer-associated polymorphism in NQO1 (P187S). The H80R mutation reactivates P187S by enhancing FAD binding affinity through local and dynamic stabilization of its binding site. Furthermore, we show how a second suppressor mutation (E247Q) cooperates with H80R in protecting the P187S polymorphism towards inactivation through long-range allosteric communication within the structural ensemble of the protein. Our results support that recent divergence of consensus amino acids may have occurred with neutral effects on many functional and regulatory traits of wild-type human proteins. However, divergence at certain sites may have increased the propensity of some human proteins towards inactivation due to disease-associated mutations and polymorphisms. Consensus mutations also emerge as a potential strategy to identify structural hot-spots in proteins as targets for pharmacological rescue in loss-of-function genetic diseases. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please

Crystal structure of the S187F variant of human liver alanine: Aminotransferase associated with primary hyperoxaluria type I and its functional implications

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Oppici, Elisa; Fodor, Krisztian; Paiardini, Alessandro; Williams, Chris; Voltattorni, Carla Borri; Wilmanns, Matthias; Cellini, Barbara

2013-01-01

The substitution of Ser187, a residue located far from the active site of human liver peroxisomal alanine:glyoxylate aminotransferase (AGT), by Phe gives rise to a variant associated with primary hyperoxaluria type I. Unexpectedly, previous studies revealed that the recombinant form of S187F exhibits a remarkable loss of catalytic activity, an increased pyridoxal 5′-phosphate (PLP) binding affinity and a different coenzyme binding mode compared with normal AGT. To shed light on the structural elements responsible for these defects, we solved the crystal structure of the variant to a resolution of 2.9 Å. Although the overall conformation of the variant is similar to that of normal AGT, we noticed: (i) a displacement of the PLP-binding Lys209 and Val185, located on the re and si side of PLP, respectively, and (ii) slight conformational changes of other active site residues, in particular Trp108, the base stacking residue with the pyridine cofactor moiety. This active site perturbation results in a mispositioning of the AGT-pyridoxamine 5′-phosphate (PMP) complex and of the external aldimine, as predicted by molecular modeling studies. Taken together, both predicted and observed movements caused by the S187F mutation are consistent with the following functional properties of the variant: (i) a 300- to 500-fold decrease in both the rate constant of L-alanine half-transamination and the kcat of the overall transamination, (ii) a different PMP binding mode and affinity, and (iii) a different microenvironment of the external aldimine. Proposals for the treatment of patients bearing S187F mutation are discussed on the basis of these results. Proteins 2013; 81:1457–1465. © 2013 Wiley Periodicals, Inc. PMID:23589421

Succinate production positively correlates with the affinity of the global transcription factor Cra for its effector FBP in Escherichia coli.

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Wei, Li-Na; Zhu, Li-Wen; Tang, Ya-Jie

2016-01-01

Effector binding is important for transcription factors, affecting both the pattern and function of transcriptional regulation to alter cell phenotype. Our previous work suggested that the affinity of the global transcription factor catabolite repressor/activator (Cra) for its effector fructose-1,6-bisphosphate (FBP) may contribute to succinate biosynthesis. To support this hypothesis, single-point and three-point mutations were proposed through the semi-rational design of Cra to improve its affinity for FBP. For the first time, a positive correlation between succinate production and the affinity of Cra for FBP was revealed in Escherichia coli . Using the best-fit regression function, a cubic equation was used to examine and describe the relationship between succinate production and the affinity of Cra for FBP, demonstrating a significant positive correlation between the two factors (coefficient of determination R 2  = 0.894, P  = 0.000 Cra and DNA showed that Cra bound to the promoter regions of pck and aceB to activate the corresponding genes. Normally, Cra-regulated operons under positive control are deactivated in the presence of FBP. Therefore, theoretically, the enhanced affinity of Cra for FBP will inhibit the activation of pck and aceB . However, the activation of genes involved in CO 2 fixation and the glyoxylate pathway was further improved by the Cra mutant, ultimately contributing to succinate biosynthesis. Enhanced binding of Cra to FBP or active site mutations may eliminate the repressive effect caused by FBP, thus leading to increased activation of genes associated with succinate biosynthesis in the Cra mutant. This work demonstrates an important transcriptional regulation strategy in the metabolic engineering of succinate production and provides useful information for better understanding of the regulatory mechanisms of transcription factors.

Mechanisms for formation of organic acids in gas-phase reactions of ozone and hydroxyl radical with dialkenes and unsaturated carbonyls

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Chien, Chao-Jung

2001-07-01

Carboxylic acids are ubiquitous throughout the troposphere and may contribute significant fractions of the free acidity in some remote areas. One of the important sources of these carboxylic acids is thought to be photochemical transformation of biogenic hydrocarbons such as isoprene. For the work reported here, atmospheric samples from University of North Carolina dual outdoor environmental chamber under simulated urban atmospheric conditions were analyzed for carboxylic acids. Both OH radicals and O3 initiated photooxidation reaction experiments were performed for isoprene, along with its structural analogs, 1,3-butadiene and 2,3-dimethyl-1,3-butadiene, and their primary photooxidation products, methacrolein, acrolein, and methyl vinyl ketone. Among the detected carboxylic acids were formic, acetic, and several multifunctional carboxylic acids, including methacrylic, acrylic, glyoxylic, and glycolic acids. Quantification of most carboxylic acid products was also established. Formation yields of carboxylic acids from the reactions of O3 with studied compounds were determined, and time-concentration series of the reactants and carboxylic acid products were measured to facilitate mechanism formulation. While the reaction mechanisms of Criegee biradicals arising from decomposition of primary ozonides are proposed to account for the observed carboxylic acid products in the ozonolysis of unsaturated hydrocarbons, reactions of peroxy acyl radicals with HO2 and/or other peroxy radicals are thought to be responsible for the formation of carboxylic acids during the OH-initiated reactions in the presence of NOx. In this study, smog chamber simulations have also been performed for selected compounds using Morpho, a photochemical kinetic simulation software package. Explicit photochemical mechanisms with O 3 and OH radicals that lead to formation of carboxylic acids were elaborated and implemented, and the simulation results were compared with those from other chemical

Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence.

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Atteyet F Yassin

Full Text Available The permanent draft genome sequence of Actinotignum schaalii DSM 15541T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM systems, type II toxin-antitoxin (TA, CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA and topisomerase IV (ParC enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH

Metabolic Interplay between Peroxisomes and Other Subcellular Organelles Including Mitochondria and the Endoplasmic Reticulum

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Wanders, Ronald J. A.; Waterham, Hans R.; Ferdinandusse, Sacha

2016-01-01

Peroxisomes are unique subcellular organelles which play an indispensable role in several key metabolic pathways which include: (1.) etherphospholipid biosynthesis; (2.) fatty acid beta-oxidation; (3.) bile acid synthesis; (4.) docosahexaenoic acid (DHA) synthesis; (5.) fatty acid alpha-oxidation; (6.) glyoxylate metabolism; (7.) amino acid degradation, and (8.) ROS/RNS metabolism. The importance of peroxisomes for human health and development is exemplified by the existence of a large number of inborn errors of peroxisome metabolism in which there is an impairment in one or more of the metabolic functions of peroxisomes. Although the clinical signs and symptoms of affected patients differ depending upon the enzyme which is deficient and the extent of the deficiency, the disorders involved are usually (very) severe diseases with neurological dysfunction and early death in many of them. With respect to the role of peroxisomes in metabolism it is clear that peroxisomes are dependent on the functional interplay with other subcellular organelles to sustain their role in metabolism. Indeed, whereas mitochondria can oxidize fatty acids all the way to CO2 and H2O, peroxisomes are only able to chain-shorten fatty acids and the end products of peroxisomal beta-oxidation need to be shuttled to mitochondria for full oxidation to CO2 and H2O. Furthermore, NADH is generated during beta-oxidation in peroxisomes and beta-oxidation can only continue if peroxisomes are equipped with a mechanism to reoxidize NADH back to NAD+, which is now known to be mediated by specific NAD(H)-redox shuttles. In this paper we describe the current state of knowledge about the functional interplay between peroxisomes and other subcellular compartments notably the mitochondria and endoplasmic reticulum for each of the metabolic pathways in which peroxisomes are involved. PMID:26858947

New biotechnological perspectives of a NADH oxidase variant from Thermus thermophilus HB27 as NAD+-recycling enzyme

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Rocha-Martín Javier

2011-11-01

Full Text Available Abstract Background The number of biotransformations that use nicotinamide recycling systems is exponentially growing. For this reason one of the current challenges in biocatalysis is to develop and optimize more simple and efficient cofactor recycling systems. One promising approach to regenerate NAD+ pools is the use of NADH-oxidases that reduce oxygen to hydrogen peroxide while oxidizing NADH to NAD+. This class of enzymes may be applied to asymmetric reduction of prochiral substrates in order to obtain enantiopure compounds. Results The NADH-oxidase (NOX presented here is a flavoenzyme which needs exogenous FAD or FMN to reach its maximum velocity. Interestingly, this enzyme is 6-fold hyperactivated by incubation at high temperatures (80°C under limiting concentrations of flavin cofactor, a change that remains stable even at low temperatures (37°C. The hyperactivated form presented a high specific activity (37.5 U/mg at low temperatures despite isolation from a thermophile source. Immobilization of NOX onto agarose activated with glyoxyl groups yielded the most stable enzyme preparation (6-fold more stable than the hyperactivated soluble enzyme. The immobilized derivative was able to be reactivated under physiological conditions after inactivation by high solvent concentrations. The inactivation/reactivation cycle could be repeated at least three times, recovering full NOX activity in all cases after the reactivation step. This immobilized catalyst is presented as a recycling partner for a thermophile alcohol dehydrogenase in order to perform the kinetic resolution secondary alcohols. Conclusion We have designed, developed and characterized a heterogeneous and robust biocatalyst which has been used as recycling partner in the kinetic resolution of rac-1-phenylethanol. The high stability along with its capability to be reactivated makes this biocatalyst highly re-useable for cofactor recycling in redox biotransformations.

Fatty acid synthesis by spinach chloroplasts, 2. The path from PGA to fatty acids

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Yamada, Mitsuhiro; Nakamura, Yasunori [Tokyo Univ. (Japan). Coll. of General Education

1975-02-01

By incorporation of /sup 3/H/sub 2/O into the fatty acid chain in the presence of unlabelled precursor, we showed that fatty acids are synthesized from PGA, PEP and pyruvate by intact spinach chloroplasts in the light. /sup 13/C-tracer experiments confirmed that 1-C of pyruvate is decarboxylated and 2-C is incorporated into fatty acids by the chloroplasts. The patterns of fatty acids synthesized from PGA and pyruvate were the same as that from acetate. The highest rate of fatty acid synthesis was reached at the physiological concentration of PGA (3 mM) and pyruvate (1 mM). These results indicate the operation of the following path in the chloroplasts in light: PGA..-->..PEP..-->..pyruvate..-->..acetylCoA..-->..fatty acids. Since citrate and OAA were much less active and malate and glyoxylate were inert as precursors for fatty acid synthesis, PEP or pyruvate carboxylation, citrate lyase reaction and malate synthetase reaction are not involved in the formation of acetylCoA and fatty acids. Since pyruvate was much more effective as a substrate for fatty acid synthesis than lactate, acetaldehyde or acetate, direct decarboxylation path is considered to be the primary path from pyruvate to acetylCoA. The insignificant effect of chloroplast-washing on fatty acid synthesis from PGA and pyruvate indicates that the glycolytic path from PGA to pyruvate is associated with the chloroplasts. Since pyruvate was more effectively incorporated into fatty acids than acetylCoA, it is unlikely that pyruvate decarboxylation to acetylCoA is due to mitochondria contaminating the chloroplast preparation. On the basis of measurements of /sup 3/H/sub 2/O incorporation in the light and dark, the activity of fatty acid synthesis in spincah leaves appears to be shared by the activities in chloroplasts (87%) and other organelles (13%).

The BvgAS Regulon of Bordetella pertussis

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Kyung Moon

2017-10-01

Full Text Available Nearly all virulence factors in Bordetella pertussis are activated by a master two-component system, BvgAS, composed of the sensor kinase BvgS and the response regulator BvgA. When BvgS is active, BvgA is phosphorylated (BvgA~P, and virulence-activated genes (vags are expressed [Bvg(+ mode]. When BvgS is inactive and BvgA is not phosphorylated, virulence-repressed genes (vrgs are induced [Bvg(− mode]. Here, we have used transcriptome sequencing (RNA-seq and reverse transcription-quantitative PCR (RT-qPCR to define the BvgAS-dependent regulon of B. pertussis Tohama I. Our analyses reveal more than 550 BvgA-regulated genes, of which 353 are newly identified. BvgA-activated genes include those encoding two-component systems (such as kdpED, multiple other transcriptional regulators, and the extracytoplasmic function (ECF sigma factor brpL, which is needed for type 3 secretion system (T3SS expression, further establishing the importance of BvgA~P as an apex regulator of transcriptional networks promoting virulence. Using in vitro transcription, we demonstrate that the promoter for brpL is directly activated by BvgA~P. BvgA-FeBABE cleavage reactions identify BvgA~P binding sites centered at positions −41.5 and −63.5 in bprL. Most importantly, we show for the first time that genes for multiple and varied metabolic pathways are significantly upregulated in the B. pertussis Bvg(− mode. These include genes for fatty acid and lipid metabolism, sugar and amino acid transporters, pyruvate dehydrogenase, phenylacetic acid degradation, and the glycolate/glyoxylate utilization pathway. Our results suggest that metabolic changes in the Bvg(− mode may be participating in bacterial survival, transmission, and/or persistence and identify over 200 new vrgs that can be tested for function.

C1-Pathways in Methyloversatilis universalis FAM5: Genome Wide Gene Expression and Mutagenesis Studies

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Nathan M. Good

2015-04-01

Full Text Available Methyloversatilis universalis FAM5 utilizes single carbon compounds such as methanol or methylamine as a sole source of carbon and energy. Expression profiling reveals distinct sets of genes altered during growth on methylamine vs methanol. As expected, all genes for the N-methylglutamate pathway were induced during growth on methylamine. Among other functions responding to the aminated source of C1-carbon, are a heme-containing amine dehydrogenase (Qhp, a distant homologue of formaldehyde activating enzyme (Fae3, molybdenum-containing formate dehydrogenase, ferredoxin reductase, a set of homologues to urea/ammonium transporters and amino-acid permeases. Mutants lacking one of the functional subunits of the amine dehydrogenase (ΔqhpA or Δfae3 showed no growth defect on C1-compounds. M. universalis FAM5 strains with a lesion in the H4-folate pathway were not able to use any C1-compound, methanol or methylamine. Genes essential for C1-assimilation (the serine cycle and glyoxylate shunt and H4MTP-pathway for formaldehyde oxidation showed similar levels of expression on both C1-carbon sources. M. universalis FAM5 possesses three homologs of the formaldehyde activating enzyme, a key enzyme of the H4MTP-pathway. Strains lacking the canonical Fae (fae1 lost the ability to grow on both C1-compounds. However, upon incubation on methylamine the fae1-mutant produced revertants (Δfae1R, which regained the ability to grow on methylamine. Double and triple mutants (Δfae1RΔfae3, or Δfae1RΔfae2 or Δfae1RΔfae2Δfae3 constructed in the revertant strain background showed growth similar to the Δfae1R phenotype. The metabolic pathways for utilization of methanol and methylamine in Methyloversatilis universalis FAM5 are reconstructed based on these gene expression and phenotypic data.

Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics.

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Mizuno, Carolina Megumi; Rodriguez-Valera, Francisco; Ghai, Rohit

2015-02-10

The genomes of four novel marine Actinobacteria have been assembled from large metagenomic data sets derived from the Mediterranean deep chlorophyll maximum (DCM). These are the first marine representatives belonging to the order Acidimicrobiales and only the second group of planktonic marine Actinobacteria to be described. Their streamlined genomes and photoheterotrophic lifestyle suggest that they are planktonic, free-living microbes. A novel rhodopsin clade, acidirhodopsins, related to freshwater actinorhodopsins, was found in these organisms. Their genomes suggest a capacity to assimilate C2 compounds, some using the glyoxylate bypass and others with the ethylmalonyl-coenzyme A (CoA) pathway. They are also able to derive energy from dimethylsulfopropionate (DMSP), sulfonate, and carbon monoxide oxidation, all commonly available in the marine habitat. These organisms appear to be prevalent in the deep photic zone at or around the DCM. The presence of sister clades to the marine Acidimicrobiales in freshwater aquatic habitats provides a new example of marine-freshwater transitions with potential evolutionary insights. Despite several studies showing the importance and abundance of planktonic Actinobacteria in the marine habitat, a representative genome was only recently described. In order to expand the genomic repertoire of marine Actinobacteria, we describe here the first Acidimicrobidae genomes of marine origin and provide insights about their ecology. They display metabolic versatility in the acquisition of carbon and appear capable of utilizing diverse sources of energy. One of the genomes harbors a new kind of rhodopsin related to the actinorhodopsin clade of freshwater origin that is widespread in the oceans. Our data also support their preference to inhabit the deep chlorophyll maximum and the deep photic zone. This work contributes to the perception of marine actinobacterial groups as important players in the marine environment with distinct and

Impact of Increasing Levels of Oxygen Consumption on the Evolution of Color, Phenolic, and Volatile Compounds of Nebbiolo Wines.

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Petrozziello, Maurizio; Torchio, Fabrizio; Piano, Federico; Giacosa, Simone; Ugliano, Maurizio; Bosso, Antonella; Rolle, Luca

2018-01-01

Since the end of the last century, many works have been carried out to verify the effect of controlled oxygen intake on the chemical and organoleptic characteristics of red wines. In spite of the large number of studies on this subject, oxygen remains a cutting-edge research topic in oenology. Oxygen consumption leads to complex and not univocal changes in wine composition, sometimes positive such as color stabilization, softening of mouthfeel, increase of aroma complexity. However, the variability of these effects, which depend both on the oxygenation conditions and the composition of the wine, require more efforts in this research field to effectively manage wine oxygen exposure. The present study is focused on the evolution of the chemical composition of four different Nebbiolo wines, each of them added with 4 different doses of oxygen (7, 14, 21, and 28 mg/L total intake) during the first month of storage. In this perspective, the evolution over time of wine color and polyphenols was studied. Acetaldehyde, glyceraldehyde and glyoxylic acid were quantified by HPLC. These compounds can play a role in wine aging creating condensed colored and stable products involving anthocyanins with or without tannins. Moreover, some volatile aldehydes correlated with oxidized olfactory notes, including methional and (E)-2-alkenals, have been quantified by GC-MS. Overall, during storage a decrease of color intensity, total and free anthocyanins and an increase in polymeric pigments (in particular the contribution to the red color of pigments not-bleachable by SO 2 or dTAT%) and some minor aldehydes was observed. Nevertheless, the differences in color parameters between the samples with different doses of oxygen were modest. These evidences were in contrast with an evident and detectable increase of free acetaldehyde content at increasing doses of oxygen measured after 60 days of storage. The effect of oxygen on color and production of SO 2 non-bleachable pigments during aging

Impact of Increasing Levels of Oxygen Consumption on the Evolution of Color, Phenolic, and Volatile Compounds of Nebbiolo Wines

Science.gov (United States)

Petrozziello, Maurizio; Torchio, Fabrizio; Piano, Federico; Giacosa, Simone; Ugliano, Maurizio; Bosso, Antonella; Rolle, Luca

2018-01-01

Since the end of the last century, many works have been carried out to verify the effect of controlled oxygen intake on the chemical and organoleptic characteristics of red wines. In spite of the large number of studies on this subject, oxygen remains a cutting-edge research topic in oenology. Oxygen consumption leads to complex and not univocal changes in wine composition, sometimes positive such as color stabilization, softening of mouthfeel, increase of aroma complexity. However, the variability of these effects, which depend both on the oxygenation conditions and the composition of the wine, require more efforts in this research field to effectively manage wine oxygen exposure. The present study is focused on the evolution of the chemical composition of four different Nebbiolo wines, each of them added with 4 different doses of oxygen (7, 14, 21, and 28 mg/L total intake) during the first month of storage. In this perspective, the evolution over time of wine color and polyphenols was studied. Acetaldehyde, glyceraldehyde and glyoxylic acid were quantified by HPLC. These compounds can play a role in wine aging creating condensed colored and stable products involving anthocyanins with or without tannins. Moreover, some volatile aldehydes correlated with oxidized olfactory notes, including methional and (E)-2-alkenals, have been quantified by GC-MS. Overall, during storage a decrease of color intensity, total and free anthocyanins and an increase in polymeric pigments (in particular the contribution to the red color of pigments not-bleachable by SO2 or dTAT%) and some minor aldehydes was observed. Nevertheless, the differences in color parameters between the samples with different doses of oxygen were modest. These evidences were in contrast with an evident and detectable increase of free acetaldehyde content at increasing doses of oxygen measured after 60 days of storage. The effect of oxygen on color and production of SO2 non-bleachable pigments during aging

Design of a species-specific PCR method for the detection of the heat-resistant fungi Talaromyces macrosporus and Talaromyces trachyspermus.

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Yamashita, S; Nakagawa, H; Sakaguchi, T; Arima, T-H; Kikoku, Y

2018-01-01

Heat-resistant fungi occur sporadically and are a continuing problem for the food and beverage industry. The genus Talaromyces, as a typical fungus, is capable of producing the heat-resistant ascospores responsible for the spoilage of processed food products. Isocitrate lyase, a signature enzyme of the glyoxylate cycle, is required for the metabolism of non-fermentable carbon compounds, like acetate and ethanol. Here, species-specific primer sets for detection and identification of DNA derived from Talaromyces macrosporus and Talaromyces trachyspermus were designed based on the nucleotide sequences of their isocitrate lyase genes. Polymerase chain reaction (PCR) using a species-specific primer set amplified products specific to T. macrosporus and T. trachyspermus. Other fungal species, such as Byssochlamys fulva and Hamigera striata, which cause food spoilage, were not detected using the Talaromyces-specific primer sets. The detection limit for each species-specific primer set was determined as being 50 pg of template DNA, without using a nested PCR method. The specificity of each species-specific primer set was maintained in the presence of 1,000-fold amounts of genomic DNA from other fungi. The method also detected fungal DNA extracted from blueberry inoculated with T. macrosporus. This PCR method provides a quick, simple, powerful and reliable way to detect T. macrosporus and T. trachyspermus. Polymerase chain reaction (PCR)-based detection is rapid, convenient and sensitive compared with traditional methods of detecting heat-resistant fungi. In this study, a PCR-based method was developed for the detection and identification of amplification products from Talaromyces macrosporus and Talaromyces trachyspermus using primer sets that target the isocitrate lyase gene. This method could be used for the on-site detection of T. macrosporus and T. trachyspermus in the near future, and will be helpful in the safety control of raw materials and in food and beverage

Substrates and oxygen dependent citric acid production by Yarrowia lipolytica: insights through transcriptome and fluxome analyses.

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Sabra, Wael; Bommareddy, Rajesh Reddy; Maheshwari, Garima; Papanikolaou, Seraphim; Zeng, An-Ping

2017-05-08

Unlike the well-studied backer yeast where catabolite repression represents a burden for mixed substrate fermentation, Yarrowia lipolytica, an oleaginous yeast, is recognized for its potential to produce single cell oils and citric acid from different feedstocks. These versatilities of Y. lipolytica with regards to substrate utilization make it an attractive host for biorefinery application. However, to develop a commercial process for the production of citric acid by Y. lipolytica, it is necessary to better understand the primary metabolism and its regulation, especially for growth on mixed substrate. Controlling the dissolved oxygen concentration (pO 2 ) in Y. lipolytica cultures enhanced citric acid production significantly in cultures grown on glucose in mono- or dual substrate fermentations, whereas with glycerol as mono-substrate no significant effect of pO 2 was found on citrate production. Growth on mixed substrate with glucose and glycerol revealed a relative preference of glycerol utilization by Y. lipolytica. Under optimized conditions with pO 2 control, the citric acid titer on glucose in mono- or in dual substrate cultures was 55 and 50 g/L (with productivity of 0.6 g/L*h in both cultures), respectively, compared to a maximum of 18 g/L (0.2 g/L*h) with glycerol in monosubstrate culture. Additionally, in dual substrate fermentation, glycerol limitation was found to trigger citrate consumption despite the presence of enough glucose in pO 2 -limited culture. The metabolic behavior of this yeast on different substrates was investigated at transcriptomic and 13 C-based fluxomics levels. Upregulation of most of the genes of the pentose phosphate pathway was found in cultures with highest citrate production with glucose in mono- or in dual substrate fermentation with pO 2 control. The activation of the glyoxylate cycle in the oxygen limited cultures and the imbalance caused by glycerol limitation might be the reason for the re-consumption of citrate in

Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy.

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Michael Volpers

Full Text Available The strong advances in synthetic biology enable the engineering of novel functions and complex biological features in unprecedented ways, such as implementing synthetic autotrophic metabolism into heterotrophic hosts. A key challenge for the sustainable production of fuels and chemicals entails the engineering of synthetic autotrophic organisms that can effectively and efficiently fix carbon dioxide by using sustainable energy sources. This challenge involves the integration of carbon fixation and energy uptake systems. A variety of carbon fixation pathways and several types of photosystems and other energy uptake systems can be chosen and, potentially, modularly combined to design synthetic autotrophic metabolism. Prior to implementation, these designs can be evaluated by the combination of several computational pathway analysis techniques. Here we present a systematic, integrated in silico analysis of photo-electro-autotrophic pathway designs, consisting of natural and synthetic carbon fixation pathways, a proton-pumping rhodopsin photosystem for ATP regeneration and an electron uptake pathway. We integrated Flux Balance Analysis of the heterotrophic chassis Escherichia coli with kinetic pathway analysis and thermodynamic pathway analysis (Max-min Driving Force. The photo-electro-autotrophic designs are predicted to have a limited potential for anaerobic, autotrophic growth of E. coli, given the relatively low ATP regenerating capacity of the proton pumping rhodopsin photosystems and the high ATP maintenance of E. coli. If these factors can be tackled, our analysis indicates the highest growth potential for the natural reductive tricarboxylic acid cycle and the synthetic pyruvate synthase-pyruvate carboxylate -glyoxylate bicycle. Both carbon fixation cycles are very ATP efficient, while maintaining fast kinetics, which also results in relatively low estimated protein costs for these pathways. Furthermore, the synthetic bicycles are highly

¹³C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation.

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Dany J V Beste

2011-07-01

Full Text Available Mycobacterium tuberculosis requires the enzyme isocitrate lyase (ICL for growth and virulence in vivo. The demonstration that M. tuberculosis also requires ICL for survival during nutrient starvation and has a role during steady state growth in a glycerol limited chemostat indicates a function for this enzyme which extends beyond fat metabolism. As isocitrate lyase is a potential drug target elucidating the role of this enzyme is of importance; however, the role of isocitrate lyase has never been investigated at the level of in vivo fluxes. Here we show that deletion of one of the two icl genes impairs the replication of Mycobacterium bovis BCG at slow growth rate in a carbon limited chemostat. In order to further understand the role of isocitrate lyase in the central metabolism of mycobacteria the effect of growth rate on the in vivo fluxes was studied for the first time using ¹³C-metabolic flux analysis (MFA. Tracer experiments were performed with steady state chemostat cultures of BCG or M. tuberculosis supplied with ¹³C labeled glycerol or sodium bicarbonate. Through measurements of the ¹³C isotopomer labeling patterns in protein-derived amino acids and enzymatic activity assays we have identified the activity of a novel pathway for pyruvate dissimilation. We named this the GAS pathway because it utilizes the Glyoxylate shunt and Anapleurotic reactions for oxidation of pyruvate, and Succinyl CoA synthetase for the generation of succinyl CoA combined with a very low flux through the succinate--oxaloacetate segment of the tricarboxylic acid cycle. We confirm that M. tuberculosis can fix carbon from CO₂ into biomass. As the human host is abundant in CO₂ this finding requires further investigation in vivo as CO₂ fixation may provide a point of vulnerability that could be targeted with novel drugs. This study also provides a platform for further studies into the metabolism of M. tuberculosis using ¹³C-MFA.

Molecular distributions of dicarboxylic acids, ketocarboxylic acids and α-dicarbonyls in biomass burning aerosols: implications for photochemical production and degradation in smoke layers

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A. Hoffer

2010-03-01

Full Text Available Aerosols in the size class <2.5 μm (6 daytime and 9 nighttime samples were collected at a pasture site in Rondônia, Brazil, during the intensive biomass burning period of 16–26 September 2002 as part of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia – Smoke, Aerosols, Clouds, Rainfall and Climate (LBA-SMOCC. Homologous series of dicarboxylic acids (C2–C11 and related compounds (ketocarboxylic acids and α-dicarbonyls were identified using gas chromatography (GC and GC/mass spectrometry (GC/MS. Among the species detected, oxalic acid was found to be the most abundant, followed by succinic, malonic and glyoxylic acids. Average concentrations of total dicarboxylic acids, ketocarboxylic acids and α-dicarbonyls in the aerosol samples were 2180, 167 and 56 ng m−3, respectively. These are 2–8, 3–11 and 2–16 times higher, respectively, than those reported in urban aerosols, such as in 14 Chinese megacities. Higher ratios of dicarboxylic acids and related compounds to biomass burning tracers (levoglucosan and K+ were found in the daytime than in the nighttime, suggesting the importance of photochemical production. On the other hand, higher ratios of oxalic acid to other dicarboxylic acids and related compounds normalized to biomass burning tracers (levoglucosan and K+ in the daytime provide evidence for the possible degradation of dicarboxylic acids (≥C3 in this smoke-polluted environment. Assuming that these and related compounds are photo-chemically oxidized to oxalic acid in the daytime, and given their linear relationship, they could account for, on average, 77% of the formation of oxalic acid. The remaining portion of oxalic acid may have been directly emitted from biomass burning as suggested by a good correlation with the biomass burning tracers (K+, CO and ECa and organic carbon (OC. However, photochemical production from other precursors could not be excluded.

Chemical characteristics of dicarboxylic acids and related organic compounds in PM2.5 during biomass-burning and non-biomass-burning seasons at a rural site of Northeast China.

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Cao, Fang; Zhang, Shi-Chun; Kawamura, Kimitaka; Liu, Xiaoyan; Yang, Chi; Xu, Zufei; Fan, Meiyi; Zhang, Wenqi; Bao, Mengying; Chang, Yunhua; Song, Wenhuai; Liu, Shoudong; Lee, Xuhui; Li, Jun; Zhang, Gan; Zhang, Yan-Lin

2017-12-01

Fine particulate matter (PM2.5) samples were collected using a high-volume air sampler and pre-combusted quartz filters during May 2013 to January 2014 at a background rural site (47 ∘ 35 N, 133 ∘ 31 E) in Sanjiang Plain, Northeast China. A homologous series of dicarboxylic acids (C 2 -C 11 ) and related compounds (oxoacids, α-dicarbonyls and fatty acids) were analyzed by using a gas chromatography (GC) and GC-MS method employing a dibutyl ester derivatization technique. Intensively open biomass-burning (BB) episodes during the harvest season in fall were characterized by high mass concentrations of PM2.5, dicarboxylic acids and levoglucosan. During the BB period, mass concentrations of dicarboxylic acids and related compounds were increased by up to >20 times with different factors for different organic compounds (i.e., succinic (C 4 ) acid > oxalic (C 2 ) acid > malonic (C 3 ) acid). High concentrations were also found for their possible precursors such as glyoxylic acid (ωC 2 ), 4-oxobutanoic acid, pyruvic acid, glyoxal, and methylglyoxal as well as fatty acids. Levoglucosan showed strong correlations with carbonaceous aerosols (OC, EC, WSOC) and dicarboxylic acids although such good correlations were not observed during non-biomass-burning seasons. Our results clearly demonstrate biomass burning emissions are very important contributors to dicarboxylic acids and related compounds. The selected ratios (e.g., C 3 /C 4 , maleic acid/fumaric acid, C 2 /ωC 2 , and C 2 /levoglucosan) were used as tracers for secondary formation of organic aerosols and their aging process. Our results indicate that organic aerosols from biomass burning in this study are fresh without substantial aging or secondary production. The present chemical characteristics of organic compounds in biomass-burning emissions are very important for better understanding the impacts of biomass burning on the atmosphere aerosols. Copyright © 2017 Elsevier Ltd. All rights reserved.

Simultaneous analysis of multiple Mycobacterium tuberculosis knockdown mutants in vitro and in vivo.

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Antje Blumenthal

2010-12-01

Full Text Available Mycobacterium tuberculosis (Mtb represents one of the most persistent bacterial threats to human health and new drugs are needed to limit its impact. Conditional knockdown mutants can help validate new drug targets, but the analysis of individual mutants is laborious and time consuming. Here, we describe quantitative DNA tags (qTags and their use to simultaneously analyze conditional Mtb knockdown mutants that allowed silencing the glyoxylate and methylcitrate cycles (via depletion of isocitrate lyase, ICL, the serine protease Rv3671c, and the core subunits of the mycobacterial proteasome, PrcB and PrcA. The impact of gene silencing in multi-strain cultures was determined by measuring the relative abundance of mutant-specific qTags with real-time PCR. This achieved accurate quantification over a broad range of qTag abundances and depletion of ICL, Rv3671c, or PrcBA resulted in the expected impairment of growth of Mtb with butyrate as the primary carbon source, survival during oxidative stress, acid stress and starvation. The impact of depleting ICL, Rv3671c, or PrcBA in multi-strain mouse infections was analyzed with two approaches. We first measured the relative abundance of mutant-specific qTags in total chromosomal DNA isolated from bacteria that were recovered from infected lungs on agar plates. We then developed a two-step amplification procedure, which allowed us to measure the abundances of individual mutants directly in infected lung tissue. Both strategies confirmed that inactivation of Rv3671c and PrcBA severely reduced persistence of Mtb in mice. The multi-strain infections furthermore suggested that silencing ICL not only prevented growth of Mtb during acute infections but also prevented survival of Mtb during chronic infections. Analyses of the ICL knockdown mutant in single-strain infections confirmed this and demonstrated that silencing of ICL during chronic infections impaired persistence of Mtb to the extent that the pathogen

Dicarboxylic acids, oxoacids, benzoic acid, α-dicarbonyls, WSOC, OC, and ions in spring aerosols from Okinawa Island in the western North Pacific Rim: size distributions and formation processes

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Deshmukh, Dhananjay K.; Kawamura, Kimitaka; Lazaar, Manuel; Kunwar, Bhagawati; Boreddy, Suresh K. R.

2016-04-01

Size-segregated aerosols (nine stages from 11.3 µm in diameter) were collected at Cape Hedo, Okinawa, in spring 2008 and analyzed for water-soluble diacids (C2-C12), ω-oxoacids (ωC2-ωC9), pyruvic acid, benzoic acid, and α-dicarbonyls (C2-C3) as well as water-soluble organic carbon (WSOC), organic carbon (OC), and major ions (Na+, NH4+, K+, Mg2+, Ca2+, Cl-, NO3-, SO42-, and MSA-). In all the size-segregated aerosols, oxalic acid (C2) was found to be the most abundant species, followed by malonic and succinic acids, whereas glyoxylic acid (ωC2) was the dominant oxoacid and glyoxal (Gly) was more abundant than methylglyoxal. Diacids (C2-C5), ωC2, and Gly as well as WSOC and OC peaked at fine mode (0.65-1.1 µm) whereas azelaic (C9) and 9-oxononanoic (ωC9) acids peaked at coarse mode (3.3-4.7 µm). Sulfate and ammonium were enriched in fine mode, whereas sodium and chloride were in coarse mode. Strong correlations of C2-C5 diacids, ωC2 and Gly with sulfate were observed in fine mode (r = 0.86-0.99), indicating a commonality in their secondary formation. Their significant correlations with liquid water content in fine mode (r = 0.82-0.95) further suggest an importance of the aqueous-phase production in Okinawa aerosols. They may also have been directly emitted from biomass burning in fine mode as supported by strong correlations with potassium (r = 0.85-0.96), which is a tracer of biomass burning. Bimodal size distributions of longer-chain diacid (C9) and oxoacid (ωC9) with a major peak in the coarse mode suggest that they were emitted from the sea surface microlayers and/or produced by heterogeneous oxidation of biogenic unsaturated fatty acids on sea salt particles.

Transcriptional and metabolic response of recombinant Escherichia coli to spatial dissolved oxygen tension gradients simulated in a scale-down system.

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Lara, Alvaro R; Leal, Lidia; Flores, Noemí; Gosset, Guillermo; Bolívar, Francisco; Ramírez, Octavio T

2006-02-05

Escherichia coli, expressing recombinant green fluorescent protein (GFP), was subjected to dissolved oxygen tension (DOT) oscillations in a two-compartment system for simulating gradients that can occur in large-scale bioreactors. Cells were continuously circulated between the anaerobic (0% DOT) and aerobic (10% DOT) vessels of the scale-down system to mimic an overall circulation time of 50 s, and a mean residence time in the anaerobic and aerobic compartments of 33 and 17 s, respectively. Transcription levels of mixed acid fermentation genes (ldhA, poxB, frdD, ackA, adhE, pflD, and fdhF), measured by quantitative RT-PCR, increased between 1.5- to over 6-fold under oscillatory DOT compared to aerobic cultures (constant 10% DOT). In addition, the transcription level of fumB increased whereas it decreased for sucA and sucB, suggesting that the tricarboxylic acid cycle was functioning as two open branches. Gene transcription levels revealed that cytrochrome bd, which has higher affinity to oxygen but lower energy efficiency, was preferred over cytochrome bO3 in oscillatory DOT cultures. Post-transcriptional processing limited heterologous protein production in the scale-down system, as inferred from similar gfp transcription but 19% lower GFP concentration compared to aerobic cultures. Simulated DOT gradients also affected the transcription of genes of the glyoxylate shunt (aceA), of global regulators of aerobic and anaerobic metabolism (fnr, arcA, and arcB), and other relevant genes (luxS, sodA, fumA, and sdhB). Transcriptional changes explained the observed alterations in overall stoichiometric and kinetic parameters, and production of ethanol and organic acids. Differences in transcription levels between aerobic and anaerobic compartments were also observed, indicating that E. coli can respond very fast to intermittent DOT conditions. The transcriptional responses of E. coli to DOT gradients reported here are useful for establishing rational scale-up criteria and

Size Distributions and Formation Pathways of Organic and Inorganic Constituents in Spring Aerosols from Okinawa Island in the Western North Pacific Rim: An Outflow Region of Asian Dusts

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Deshmukh, D. K.; Lazaar, M.; Kawamura, K.; Kunwar, B.; Tachibana, E.; Boreddy, S. K. R.

2015-12-01

Size-segregated aerosols (9-stages) were collected at Okinawa Island in the western North Pacific Rim in spring 2008. The samples were analyzed for diacids (C2-C12), ω-oxoacids (ωC2-ωC9), a-dicarbonyls (C2-C3), organic carbon (OC), water-soluble OC (WSOC) and major ions to understand the sources and atmospheric processes in the outflow region of Asian pollutants. The molecular distribution of diacids showed the predominance of oxalic acid (C2) followed by malonic and succinic acids in all the size-segregated aerosols. ω-Oxoacids showed the predominance of glyoxylic acid (ωC2) whereas glyoxal (Gly) was more abundant than methylglyoxal in all the sizes. The abundant presence of sulfate as well as phthalic and adipic acids in Okinawa aerosols suggested a significant contribution of anthropogenic sources in East Asia via long-range atmospheric transport. Diacids (C2-C5), ωC2 and Gly as well as WSOC and OC peaked at 0.65-1.1 µm in fine mode whereas azelaic (C9) and 9-oxononanoic (ωC9) acids peaked at 3.3-4.7 µm in coarse mode. Sulfate and ammonium are enriched in fine mode whereas sodium and chloride are in coarse mode. An important mechanism for the formation of these organic species in Okinawa aerosols is probably gas phase oxidation of VOCs and subsequent in-cloud processing during long-range transport. Their characteristics size distribution implies that fine particles enriched with these organic and inorganic species could act as CCN to develop the cloud cover over the western North Pacific. The major peak of C9 and ωC9 on coarse mode suggest that they are produced by photooxidation of unsaturated fatty acids mainly derived from phytoplankton via heterogeneous reactions on sea spray particles. This study demonstrates that anthropogenic aerosols emitted from East Asia have significant influence on the compositions of organic and inorganic aerosols in the western North Pacific Rim.

Engineering Pseudomonas putida KT2440 for efficient ethylene glycol utilization.

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Franden, Mary Ann; Jayakody, Lahiru N; Li, Wing-Jin; Wagner, Neil J; Cleveland, Nicholas S; Michener, William E; Hauer, Bernhard; Blank, Lars M; Wierckx, Nick; Klebensberger, Janosch; Beckham, Gregg T

2018-06-07

Ethylene glycol is used as a raw material in the production of polyethylene terephthalate, in antifreeze, as a gas hydrate inhibitor in pipelines, and for many other industrial applications. It is metabolized by aerobic microbial processes via the highly toxic intermediates glycolaldehyde and glycolate through C2 metabolic pathways. Pseudomonas putida KT2440, which has been engineered for environmental remediation applications given its high toxicity tolerance and broad substrate specificity, is not able to efficiently metabolize ethylene glycol, despite harboring putative genes for this purpose. To further expand the metabolic portfolio of P. putida, we elucidated the metabolic pathway to enable ethylene glycol via systematic overexpression of glyoxylate carboligase (gcl) in combination with other genes. Quantitative reverse transcription polymerase chain reaction demonstrated that all of the four genes in genomic proximity to gcl (hyi, glxR, ttuD, and pykF) are transcribed as an operon. Where the expression of only two genes (gcl and glxR) resulted in growth in ethylene glycol, improved growth and ethylene glycol utilization were observed when the entire gcl operon was expressed. Both glycolaldehyde and glyoxal inhibit growth in concentrations of ethylene glycol above 50 mM. To overcome this bottleneck, the additional overexpression of the glycolate oxidase (glcDEF) operon removes the glycolate bottleneck and minimizes the production of these toxic intermediates, permitting growth in up to 2 M (~124 g/L) and complete consumption of 0.5 M (31 g/L) ethylene glycol in shake flask experiments. In addition, the engineered strain enables conversion of ethylene glycol to medium-chain-length polyhydroxyalkanoates (mcl-PHAs). Overall, this study provides a robust P. putida KT2440 strain for ethylene glycol consumption, which will serve as a foundational strain for further biocatalyst development for applications in the remediation of waste polyester plastics and

Importance of relative humidity in the oxidative ageing of organic aerosols: case study of the ozonolysis of maleic acid aerosol

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P. J. Gallimore

2011-12-01

Full Text Available Many important atmospheric aerosol processes depend on the chemical composition of the aerosol, e.g. water uptake and particle cloud interactions. Atmospheric ageing processes, such as oxidation reactions, significantly and continuously change the chemical composition of aerosol particles throughout their lifetime. These ageing processes are often poorly understood. In this study we utilize an aerosol flow tube set up and an ultra-high resolution mass spectrometer to explore the effect of relative humidity (RH in the range of <5–90% on the ozonolysis of maleic acid aerosol which is employed as model organic aerosol system. Due to the slow reaction kinetics relatively high ozone concentrations of 160–200 ppm were used to achieve an appreciable degree of oxidation of maleic acid. The effect of oxidative ageing on the hygroscopicity of maleic acid particles is also investigated using an electrodynamic balance and thermodynamic modelling. RH has a profound effect on the oxidation of maleic acid particles. Very little oxidation is observed at RH < 50% and the only observed reaction products are glyoxylic acid and formic acid. In comparison, when RH > 50% there are about 15 oxidation products identified. This increased oxidation was observed even when the particles were exposed to high humidities long after a low RH ozonolysis reaction. This result might have negative implications for the use of water as an extraction solvent for the analysis of oxidized organic aerosols. These humidity-dependent differences in the composition of the ozonolyzed aerosol demonstrate that water is both a key reactant in the oxidation scheme and a determinant of particle phase and hence diffusivity. The measured chemical composition of the processed aerosol is used to model the hygroscopic growth, which compares favourably with water uptake results from the electrodynamic balance measurements. A reaction mechanism is presented which takes into account the RH dependent

Impact of Increasing Levels of Oxygen Consumption on the Evolution of Color, Phenolic, and Volatile Compounds of Nebbiolo Wines

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Maurizio Petrozziello

2018-04-01

Full Text Available Since the end of the last century, many works have been carried out to verify the effect of controlled oxygen intake on the chemical and organoleptic characteristics of red wines. In spite of the large number of studies on this subject, oxygen remains a cutting-edge research topic in oenology. Oxygen consumption leads to complex and not univocal changes in wine composition, sometimes positive such as color stabilization, softening of mouthfeel, increase of aroma complexity. However, the variability of these effects, which depend both on the oxygenation conditions and the composition of the wine, require more efforts in this research field to effectively manage wine oxygen exposure. The present study is focused on the evolution of the chemical composition of four different Nebbiolo wines, each of them added with 4 different doses of oxygen (7, 14, 21, and 28 mg/L total intake during the first month of storage. In this perspective, the evolution over time of wine color and polyphenols was studied. Acetaldehyde, glyceraldehyde and glyoxylic acid were quantified by HPLC. These compounds can play a role in wine aging creating condensed colored and stable products involving anthocyanins with or without tannins. Moreover, some volatile aldehydes correlated with oxidized olfactory notes, including methional and (E-2-alkenals, have been quantified by GC-MS. Overall, during storage a decrease of color intensity, total and free anthocyanins and an increase in polymeric pigments (in particular the contribution to the red color of pigments not-bleachable by SO2 or dTAT% and some minor aldehydes was observed. Nevertheless, the differences in color parameters between the samples with different doses of oxygen were modest. These evidences were in contrast with an evident and detectable increase of free acetaldehyde content at increasing doses of oxygen measured after 60 days of storage. The effect of oxygen on color and production of SO2 non-bleachable pigments

Redox proteomics changes in the fungal pathogen Trichosporon asahii on arsenic exposure: identification of protein responses to metal-induced oxidative stress in an environmentally-sampled isolate.

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Sidra Ilyas

Full Text Available Trichosporon asahii is a yeast pathogen implicated in opportunistic infections. Cultures of an isolate collected from industrial wastewater were exposed for 2 days to 100 mg/L sodium arsenite (NaAsO2 and cadmium (CdCl2. Both metals reduced glutathione transferase (GST activity but had no effect on superoxide dismutase or catalase. NaAsO2 exposure increased glutathione reductase activity while CdCl2 had no effect. Protein thiols were labeled with 5-iodoacetamido fluorescein followed by one dimensional electrophoresis which revealed extensive protein thiol oxidation in response to CdCl2 treatment but thiol reduction in response to NaAsO2. Two dimensional electrophoresis analyses showed that the intensity of some protein spots was enhanced on treatment as judged by SameSpots image analysis software. In addition, some spots showed decreased IAF fluorescence suggesting thiol oxidation. Selected spots were excised and tryptic digested for identification by MALDI-TOF/TOF MS. Twenty unique T. asahii proteins were identified of which the following proteins were up-regulated in response to NaAsO2: 3-isopropylmalate dehydrogenase, phospholipase B, alanine-glyoxylate aminotransferase, ATP synthase alpha chain, 20S proteasome beta-type subunit Pre3p and the hypothetical proteins A1Q1_08001, A1Q2_03020, A1Q1_06950, A1Q1_06913. In addition, the following showed decreased thiol-associated fluorescence consistent with thiol oxidation; aconitase; aldehyde reductase I; phosphoglycerate kinase; translation elongation factor 2; heat shock protein 70 and hypothetical protein A1Q2_04745. Some proteins showed both increase in abundance coupled with decrease in IAF fluorescence; 3-hydroxyisobutyryl-CoA hydrolase; homoserine dehydrogenase Hom6 and hypothetical proteins A1Q2_03020 and A1Q1_00754. Targets implicated in redox response included 10 unique metabolic enzymes, heat shock proteins, a component of the 20S proteasome and translation elongation factor 2. These data

Fluxomics of the Eastern Oyster for Environmental Stress Studies

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Andrey P. Tikunov

2014-01-01

Full Text Available The metabolism of 2-13C/15N-glycine and U-13C-glucose was determined in four tissue blocks (adductor muscle, stomach and digestive gland, mantle, and gills of the Eastern oyster (Crassostrea virginica using proton (1H and carbon-13 (13C nuclear magnetic resonance (NMR spectroscopy. The oysters were treated in aerated seawater with three treatments (5.5 mM U-13C-glucose, 2.7 mM 2-13C/15N-glycine, and 5.5 mM U-13C-glucose plus 2.7 mM 2-13C/15N-glycine and the relative mass balance and 13C fractional enrichments were determined in the four tissue blocks. In all tissues, glycine was metabolized by the glycine cycle forming serine exclusively in the mitochondria by the glycine cleavage system forming 2,3-13C-serine. In muscle, a minor amount of serine-derived pyruvate entered the Krebs cycle as substantiated by detection of a trace of 2,3-13C-aspartate. In all tissues, U-13C-glucose formed glycogen by glycogen synthesis, alanine by glycolysis, and glutamate and aspartate through the Krebs cycle. Alanine was formed exclusively from glucose via alanine transaminase and not glycine via alanine-glyoxylate transaminase. Based on isotopomer analysis, pyruvate carboxylase and pyruvate dehydrogenase appeared to be equal points for pyruvate entry into the Krebs cycle. In the 5.5 mM U-13C-glucose plus 2.7 mM 2-13C/15N-glycine emergence treatment used to simulate 12 h of “low tide”, oysters accumulated more 13C-labeled metabolites, including both anaerobic glycolytic and aerobic Krebs cycle intermediates. The aerobic metabolites could be the biochemical result of the gaping behavior of mollusks during emergence. The change in tissue distribution and mass balance of 13C-labeled nutrients (U-13C-glucose and 2-13C/15N-glycine provides the basis for a new quantitative fluxomic method for elucidating sub-lethal environmental effects in marine organisms called whole body mass balance phenotyping (WoMBaP.

Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci

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Sehgal Deepmala

2012-01-01

Full Text Available Abstract Background Identification of genes underlying drought tolerance (DT quantitative trait loci (QTLs will facilitate understanding of molecular mechanisms of drought tolerance, and also will accelerate genetic improvement of pearl millet through marker-assisted selection. We report a map based on genes with assigned functional roles in plant adaptation to drought and other abiotic stresses and demonstrate its use in identifying candidate genes underlying a major DT-QTL. Results Seventy five single nucleotide polymorphism (SNP and conserved intron spanning primer (CISP markers were developed from available expressed sequence tags (ESTs using four genotypes, H 77/833-2, PRLT 2/89-33, ICMR 01029 and ICMR 01004, representing parents of two mapping populations. A total of 228 SNPs were obtained from 30.5 kb sequenced region resulting in a SNP frequency of 1/134 bp. The positions of major pearl millet linkage group (LG 2 DT-QTLs (reported from crosses H 77/833-2 × PRLT 2/89-33 and 841B × 863B were added to the present consensus function map which identified 18 genes, coding for PSI reaction center subunit III, PHYC, actin, alanine glyoxylate aminotransferase, uridylate kinase, acyl-CoA oxidase, dipeptidyl peptidase IV, MADS-box, serine/threonine protein kinase, ubiquitin conjugating enzyme, zinc finger C- × 8-C × 5-C × 3-H type, Hd3, acetyl CoA carboxylase, chlorophyll a/b binding protein, photolyase, protein phosphatase1 regulatory subunit SDS22 and two hypothetical proteins, co-mapping in this DT-QTL interval. Many of these candidate genes were found to have significant association with QTLs of grain yield, flowering time and leaf rolling under drought stress conditions. Conclusions We have exploited available pearl millet EST sequences to generate a mapped resource of seventy five new gene-based markers for pearl millet and demonstrated its use in identifying candidate genes underlying a major DT-QTL in this species. The reported gene

Glyphosate-Resistant Parthenium hysterophorus in the Caribbean Islands: Non Target Site Resistance and Target Site Resistance in Relation to Resistance Levels.

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Enzo Bracamonte

2016-12-01

Full Text Available Glyphosate has been the most intensely herbicide used worldwide for decades, and continues to be a single tool for controlling weeds in woody crops. However, the adoption of this herbicide in a wide range of culture systems has led to the emergence of resistant weeds. Glyphosate has been widely used primarily on citrus in the Caribbean area, but a study of resistance in the Caribbean islands of Cuba and the Dominican Republic has never been carried out. Unfortunately, Parthenium hysterophorus has developed glyphosate-resistance in both islands, independently. The resistance level and mechanisms of different P. hysterophorus accessions (three collected in Cuba (Cu-R and four collected in the Dominican Republic (Do-R have been studied under greenhouse and laboratory conditions. In in vivo assays (glyphosate dose causing 50% reduction in above-ground vegetative biomass and survival, the resistance factor levels showed susceptible accessions (Cu-S≥Do-S, low-resistance accessions (Cu-R3Do-R2>Cu-R2>Do-R3>Do-R4>Cu-R3>>Cu-S≥Do-S. Glyphosate was degraded to aminomethylphosphonic acid, glyoxylate and sarcosine by >88% in resistant accessions except in Cu-R3 and Do-R4 resistant accessions (51.12 and 44.21, respectively, whereas a little glyphosate (<9.32% was degraded in both susceptible accessions at 96 h after treatment. There were significant differences between P. hysterophorus accessions in the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS activity enzyme with and without different glyphosate rates. The R accessions showed values of between 0.026 and 0.21 µmol µg-1 TSP protein min-1 basal EPSPS activity values with respect to the S (0.024 and 0.025 accessions. The same trend was found in the EPSPS enzyme activity treated with glyphosate, where a higher enzyme activity inhibition (glyphosate µM corresponded to greater resistance levels in P. hysterophorus accessions. One amino acid substitution was found at position 106 in EPSPS, consisting

Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling.

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Renee M Petri

Full Text Available Subacute rumen acidotic (SARA conditions are a consequence of high grain feeding. Recent work has shown that the pattern of grain feeding can significantly impact the rumen epimural microbiota. In a continuation of these works, the objective of this study was to determine the role of grain feeding patterns on the colonization and associated changes in predicted functional properties of the fiber-adherent microbial community over a 48 h period. Eight rumen-cannulated Holstein cows were randomly assigned to interrupted or continuous 60%-grain challenge model (n = 4 per model to induce SARA conditions. Cows in the continuous model were challenged for 4 weeks, whereas cows of interrupted model had a 1-wk break in between challenges. To determine dynamics of rumen fiber-adherent microbial community we incubated the same hay from the diet samples for 24 and 48 h in situ during the baseline (no grain fed, week 1 and 4 of the continuous grain feeding model as well as during the week 1 following the break in the interrupted model. Microbial DNA was extracted and 16SrRNA amplicon (V3-V5 region sequencing was done with the Illumina MiSeq platform. A significant decrease (P 0.1% relative abundance in the rumen, 18 of which were significantly impacted by the feeding challenge model. Correlation analysis of the significant OTUs to rumen pH as an indicator of SARA showed genus Succiniclasticum had a positive correlation to SARA conditions regardless of treatment. Predictive analysis of functional microbial properties suggested that the glyoxylate/dicarboxylate pathway was increased in response to SARA conditions, decreased between 24h to 48h of incubation, negatively correlated with propanoate metabolism and positively correlated to members of the Veillonellaceae family including Succiniclasticum spp. This may indicate an adaptive response in bacterial metabolism under SARA conditions. This research clearly indicates that changes to the colonizing fiber

Proteomic Analysis of Copper-Binding Proteins in Excess Copper-Stressed Roots of Two Rice (Oryza sativa L. Varieties with Different Cu Tolerances.

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Chen Chen

Full Text Available To better understand the mechanisms involved in the heavy metal stress response and tolerance in plants, a proteomic approach was used to investigate the differences in Cu-binding protein expression in Cu-tolerant and Cu-sensitive rice varieties. Cu-binding proteins from Cu-treated rice roots were separated using a new IMAC method in which an IDA-sepharose column was applied prior to the Cu-IMAC column to remove metal ions from protein samples. More than 300 protein spots were reproducibly detected in the 2D gel. Thirty-five protein spots exhibited changes greater than 1.5-fold in intensity compared to the control. Twenty-four proteins contained one or more of nine putative metal-binding motifs reported by Smith et al., and 19 proteins (spots contained one to three of the top six motifs reported by Kung et al. The intensities of seven protein spots were increased in the Cu-tolerant variety B1139 compared to the Cu-sensitive variety B1195 (p<0.05 and six protein spots were markedly up-regulated in B1139, but not detectable in B1195. Four protein spots were significantly up-regulated in B1139, but unchanged in B1195 under Cu stress. In contrast, two protein spots were significantly down-regulated in B1195, but unchanged in B1139. These Cu-responsive proteins included those involved in antioxidant defense and detoxification (spots 5, 16, 21, 22, 28, 29 and 33, pathogenesis (spots 5, 16, 21, 22, 28, 29 and 33, regulation of gene transcription (spots 8 and 34, amino acid synthesis (spots 8 and 34, protein synthesis, modification, transport and degradation (spots 1, 2, 4, 10, 15, 19, 30, 31, 32 and 35, cell wall synthesis (spot 14, molecular signaling (spot 3, and salt stress (spots 7, 9 and 27; together with other proteins, such as a putative glyoxylate induced protein, proteins containing dimeric alpha-beta barrel domains, and adenosine kinase-like proteins. Our results suggest that these proteins, together with related physiological processes, play

Dicarboxylic acids, oxoacids, benzoic acid, α-dicarbonyls, WSOC, OC, and ions in spring aerosols from Okinawa Island in the western North Pacific Rim: size distributions and formation processes

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D. K. Deshmukh

2016-04-01

Full Text Available Size-segregated aerosols (nine stages from < 0.43 to > 11.3 µm in diameter were collected at Cape Hedo, Okinawa, in spring 2008 and analyzed for water-soluble diacids (C2–C12, ω-oxoacids (ωC2–ωC9, pyruvic acid, benzoic acid, and α-dicarbonyls (C2–C3 as well as water-soluble organic carbon (WSOC, organic carbon (OC, and major ions (Na+, NH4+, K+, Mg2+, Ca2+, Cl−, NO3−, SO42−, and MSA−. In all the size-segregated aerosols, oxalic acid (C2 was found to be the most abundant species, followed by malonic and succinic acids, whereas glyoxylic acid (ωC2 was the dominant oxoacid and glyoxal (Gly was more abundant than methylglyoxal. Diacids (C2–C5, ωC2, and Gly as well as WSOC and OC peaked at fine mode (0.65–1.1 µm whereas azelaic (C9 and 9-oxononanoic (ωC9 acids peaked at coarse mode (3.3–4.7 µm. Sulfate and ammonium were enriched in fine mode, whereas sodium and chloride were in coarse mode. Strong correlations of C2–C5 diacids, ωC2 and Gly with sulfate were observed in fine mode (r =  0.86–0.99, indicating a commonality in their secondary formation. Their significant correlations with liquid water content in fine mode (r =  0.82–0.95 further suggest an importance of the aqueous-phase production in Okinawa aerosols. They may also have been directly emitted from biomass burning in fine mode as supported by strong correlations with potassium (r =  0.85–0.96, which is a tracer of biomass burning. Bimodal size distributions of longer-chain diacid (C9 and oxoacid (ωC9 with a major peak in the coarse mode suggest that they were emitted from the sea surface microlayers and/or produced by heterogeneous oxidation of biogenic unsaturated fatty acids on sea salt particles.

Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets

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Ina Koch

2017-06-01

Full Text Available Motivation:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpretation of the large amount of biological data remain a big challenge, not only because data sets for metabolic paths are still incomplete. Moreover, they are often inconsistent, because they are coming from different experiments of various scales, regarding, for example, accuracy and/or significance. Here, theoretical modeling is powerful to formulate hypotheses for pathways and the dynamics of the metabolism, even if the biological data are incomplete. To develop reliable mathematical models they have to be proven for consistency. This is still a challenging task because many verification techniques fail already for middle-sized models. Consequently, new methods, like decomposition methods or reduction approaches, are developed to circumvent this problem.Methods: We present a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. We used the Petri net formalism to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency we applied concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs.Results: We formulated the core metabolism of Arabidopsis thaliana based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism. By applying network decomposition and reduction techniques at steady-state conditions, we suggest a straightforward mathematical modeling process. We demonstrate that potential steady-state pathways exist, which provide the

Suppressor screen and phenotype analyses revealed an emerging role of the Monofunctional peroxisomal enoyl-CoA hydratase 2 in compensated cell enlargement

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Mana eKatano

2016-02-01

Full Text Available Efficient use of seed nutrient reserves is crucial for germination and establishment of plant seedlings. Mobilizing seed oil reserves in Arabidopsis involves β-oxidation, the glyoxylate cycle, and gluconeogenesis, which provide essential energy and the carbon skeletons needed to sustain seedling growth until photoautotrophy is acquired. We demonstrated that H+-PPase activity is required for gluconeogenesis. Lack of H+-PPase in fugu5 mutants increases cytosolic pyrophosphate (PPi levels, which partially reduces sucrose synthesis de novo and inhibits cell division. In contrast, post-mitotic cell expansion in cotyledons was unusually enhanced, a phenotype called compensation. Therefore, it appears that PPi inhibits several cellular functions, including cell cycling, to trigger compensated cell enlargement (CCE. Here, we mutagenized fugu5-1 seeds with 12C6+ heavy-ion irradiation and screened mutations that restrain CCE to gain insight into the genetic pathway(s involved in CCE. We isolated A#3-1, in which cell size was severely reduced, but cell number remained similar to that of original fugu5-1. Moreover, cell number decreased in A#3-1 single mutant (A#3-1sm, similar to that of fugu5-1, but cell size was almost equal to that of the wild type. Surprisingly, A#3-1 mutation did not affect CCE in other compensation exhibiting mutant backgrounds, such as an3-4 and fugu2-1/fas1-6. Subsequent map-based cloning combined with genome sequencing and HRM curve analysis identified enoyl-CoA hydratase 2 (ECH2 as the causal gene of A#3-1. The above phenotypes were consistently observed in the ech2-1 allele and supplying sucrose restored the morphological and cellular phenotypes in fugu5-1, ech2-1, A#3-1sm, fugu5-1 ech2-1 and A#3-1;fugu5-1. Taken together, these results suggest that defects in either H+-PPase or ECH2 compromise cell proliferation due to defects in mobilizing stored lipids. In contrast, ECH2 alone likely promotes CCE during the post-mitotic cell

Proteomics reveal energy metabolism and mitogen-activated protein kinase signal transduction perturbation in human Borna disease virus Hu-H1-infected oligodendroglial cells.

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Liu, X; Yang, Y; Zhao, M; Bode, L; Zhang, L; Pan, J; Lv, L; Zhan, Y; Liu, S; Zhang, L; Wang, X; Huang, R; Zhou, J; Xie, P

2014-05-30

Borna disease virus (BDV) is a neurotropic, non-cytolytic RNA virus which replicates in the cell nucleus targeting mainly hippocampal neurons, but also astroglial and oligodendroglial cells in the brain. BDV is associated with a large spectrum of neuropsychiatric pathologies in animals. Its relationship to human neuropsychiatric illness still remains controversial. We could recently demonstrate that human BDV strain Hu-H1 promoted apoptosis and inhibited cell proliferation in a human oligodendroglial cell line (OL cells) whereas laboratory BDV strain V acted contrariwise. Here, differential protein expression between BDV Hu-H1-infected OL cells and non-infected OL cells was assessed through a proteomics approach, using two-dimensional electrophoresis followed by matrix-assisted laser desorption ionization-time of flight tandem mass spectrometry. A total of 63 differential host proteins were identified in BDV Hu-H1-infected OL cells compared to non-infected OL cells. We found that most changes referred to alterations related to the pentose phosphate pathway, glyoxylate and dicarboxylate metabolism, the tricarboxylic acid (TCA) cycle, and glycolysis /gluconeogenesis. By manual querying, two differential proteins were found to be associated with mitogen-activated protein kinase (MAPK) signal transduction. Five key signaling proteins of this pathway (i.e., p-Raf, p-MEK, p-ERK1/2, p-RSK, and p-MSK) were selected for Western blotting validation. p-ERK1/2 and p-RSK were found to be significantly up-regulated, and p-MSK was found to be significantly down-regulated in BDV Hu-H1-infected OL cells compared to non-infected OL cell. Although BDV Hu-H1 constitutively activated the ERK-RSK pathway, host cell proliferation and nuclear translocation of activated pERK in BDV Hu-H1-infected OL cells were impaired. These findings indicate that BDV Hu-H1 infection of human oligodendroglial cells significantly perturbs host energy metabolism, activates the downstream ERK-RSK complex of

A Proteomic Signature of Dormancy in the Actinobacterium Micrococcus luteus.

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Mali, Sujina; Mitchell, Morgan; Havis, Spencer; Bodunrin, Abiodun; Rangel, Jonathan; Olson, Gabriella; Widger, William R; Bark, Steven J

2017-07-15

Dormancy is a protective state in which diverse bacteria, including Mycobacterium tuberculosis , Staphylococcus aureus , Treponema pallidum (syphilis), and Borrelia burgdorferi (Lyme disease), curtail metabolic activity to survive external stresses, including antibiotics. Evidence suggests dormancy consists of a continuum of interrelated states, including viable but nonculturable (VBNC) and persistence states. VBNC and persistence contribute to antibiotic tolerance, reemergence from latent infections, and even quorum sensing and biofilm formation. Previous studies indicate that the protein mechanisms regulating persistence and VBNC states are not well understood. We have queried the VBNC state of Micrococcus luteus NCTC 2665 (MI-2665) by quantitative proteomics combining gel electrophoresis, high-performance liquid chromatography, and tandem mass spectrometry to elucidate some of these mechanisms. MI-2665 is a nonpathogenic actinobacterium containing a small (2.5-Mb), high-GC-content genome which exhibits a well-defined VBNC state induced by nutrient deprivation. The MI-2665 VBNC state demonstrated a loss of protein diversity accompanied by increased levels of 18 proteins that are conserved across actinobacteria, 14 of which have not been previously identified in VNBC. These proteins implicate an anaplerotic strategy in the transition to VBNC, including changes in the glyoxylate shunt, redox and amino acid metabolism, and ribosomal regulatory processes. Our data suggest that MI-2665 is a viable model for dissecting the protein mechanisms underlying the VBNC stress response and provide the first protein-level signature of this state. We expect that this protein signature will enable future studies deciphering the protein mechanisms of dormancy and identify novel therapeutic strategies effective against antibiotic-tolerant bacterial infections. IMPORTANCE Dormancy is a protective state enabling bacteria to survive antibiotics, starvation, and the immune system

Differential gene expression in tomato fruit and Colletotrichum gloeosporioides during colonization of the RNAi-SlPH tomato line with reduced fruit acidity and higher pH.

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Barad, Shiri; Sela, Noa; Dubey, Amit K; Kumar, Dilip; Luria, Neta; Ment, Dana; Cohen, Shahar; Schaffer, Arthur A; Prusky, Dov

2017-08-04

The destructive phytopathogen Colletotrichum gloeosporioides causes anthracnose disease in fruit. During host colonization, it secretes ammonia, which modulates environmental pH and regulates gene expression, contributing to pathogenicity. However, the effect of host pH environment on pathogen colonization has never been evaluated. Development of an isogenic tomato line with reduced expression of the gene for acidity, SlPH (Solyc10g074790.1.1), enabled this analysis. Total RNA from C. gloeosporioides colonizing wild-type (WT) and RNAi-SlPH tomato lines was sequenced and gene-expression patterns were compared. C. gloeosporioides inoculation of the RNAi-SlPH line with pH 5.96 compared to the WT line with pH 4.2 showed 30% higher colonization and reduced ammonia accumulation. Large-scale comparative transcriptome analysis of the colonized RNAi-SlPH and WT lines revealed their different mechanisms of colonization-pattern activation: whereas the WT tomato upregulated 13-LOX (lipoxygenase), jasmonic acid and glutamate biosynthesis pathways, it downregulated processes related to chlorogenic acid biosynthesis II, phenylpropanoid biosynthesis and hydroxycinnamic acid tyramine amide biosynthesis; the RNAi-SlPH line upregulated UDP-D-galacturonate biosynthesis I and free phenylpropanoid acid biosynthesis, but mainly downregulated pathways related to sugar metabolism, such as the glyoxylate cycle and L-arabinose degradation II. Comparison of C. gloeosporioides gene expression during colonization of the WT and RNAi-SlPH lines showed that the fungus upregulates ammonia and nitrogen transport and the gamma-aminobutyric acid metabolic process during colonization of the WT, while on the RNAi-SlPH tomato, it mainly upregulates the nitrate metabolic process. Modulation of tomato acidity and pH had significant phenotypic effects on C. gloeosporioides development. The fungus showed increased colonization on the neutral RNAi-SlPH fruit, and limited colonization on the WT acidic fruit

Inhibition of bovine kidney alpha-ketoglutarate dehydrogenase complex by reduced nicotinamide adenine dinucleotide in the presence or absence of calcium ion and effect of adenosine 5'-diphosphate on reduced nicotinamide adenine dinucleotide inhibition.

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Lawlis, V B; Roche, T E

1981-04-28

Micromolar Ca2+ markedly reduces NADH inhibition of bovine kidney alpha-ketoglutarate dehydrogenase complex [Lawlis, V. B., & Roche, T. E. (1980) Mol. Cell. Biochem. 32, 147-152]. Product inhibition patterns from initial velocity studies conducted at less than 10(-9) M or at 1.5 X 10(-5) M Ca2+ with NAD+, CoA, or alpha-ketoglutarate as the variable substrate showed that NADH was a noncompetitive inhibitor with respect to each of these substrates, except at high NAD+ concentrations, where reciprocal plots were nonlinear and the inhibition pattern for NADH vs. NAD+ changed from a noncompetitive to a competitive pattern. From slope and intercept replots, 2-fold to 12-fold higher inhibition constants were estimated for inhibition by NADH vs. the various substrates in the presence of 1.5 X 10(-5) M Ca2+ than for inhibition at less than 10(-9) M Ca2+. These inhibition patterns and the lack of an effect of Ca2+ on the inhibition of the dihydrolipoyl dehydrogenase component suggested that Ca2+-modulated NADH inhibition occurs at an allosteric site with competitive binding at the site by high levels of NAD+. Decarboxylation of alpha-keto[1-14C]glutarate by the resolved alpha-ketoglutarate dehydrogenase component was investigated in the presence of 5.0 mM glyoxylate which served as an efficient acceptor. NADH (0.2 mM) or 1.0 mM ATP inhibited the partial reaction whereas 15 muM Ca2+, 1.0 mM ADP, or 10 mM NAD+ stimulated the partial reaction and reduced NADH inhibition of this reaction. Thus these effectors alter the activity of the alpha-ketoglutarate dehydrogenase complex by binding at allosteric sites on the alpha-ketoglutarate dehydrogenase component. Inhibition by NADH over a wide range of NADH/NAD+ ratios was measured under conditions in which the level of alpha-ketoglutarate was adjusted to give matching control activities at less than 10(-9) M Ca2+ or 1.5 X 10(-5) M Ca2+ in either the presence or the absence of 1.6 mM ADP. These studies establish that both Ca2+ and ADP

Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA: identification of a putative ligand binding pocket at the dimeric interface

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Chittori Sagar

2012-10-01

Full Text Available Abstract Background Bacteria such as Escherichia coli and Salmonella typhimurium can utilize acetate as the sole source of carbon and energy. Acetate kinase (AckA and phosphotransacetylase (Pta, key enzymes of acetate utilization pathway, regulate flux of metabolites in glycolysis, gluconeogenesis, TCA cycle, glyoxylate bypass and fatty acid metabolism. Results Here we report kinetic characterization of S. typhimurium AckA (StAckA and structures of its unliganded (Form-I, 2.70 Å resolution and citrate-bound (Form-II, 1.90 Å resolution forms. The enzyme showed broad substrate specificity with kcat/Km in the order of acetate > propionate > formate. Further, the Km for acetyl-phosphate was significantly lower than for acetate and the enzyme could catalyze the reverse reaction (i.e. ATP synthesis more efficiently. ATP and Mg2+ could be substituted by other nucleoside 5′-triphosphates (GTP, UTP and CTP and divalent cations (Mn2+ and Co2+, respectively. Form-I StAckA represents the first structural report of an unliganded AckA. StAckA protomer consists of two domains with characteristic βββαβαβα topology of ASKHA superfamily of proteins. These domains adopt an intermediate conformation compared to that of open and closed forms of ligand-bound Methanosarcina thermophila AckA (MtAckA. Spectroscopic and structural analyses of StAckA further suggested occurrence of inter-domain motion upon ligand-binding. Unexpectedly, Form-II StAckA structure showed a drastic change in the conformation of residues 230–300 compared to that of Form-I. Further investigation revealed electron density corresponding to a citrate molecule in a pocket located at the dimeric interface of Form-II StAckA. Interestingly, a similar dimeric interface pocket lined with largely conserved residues could be identified in Form-I StAckA as well as in other enzymes homologous to AckA suggesting that ligand binding at this pocket may influence the function of these

The role of Cra in regulating acetate excretion and osmotic tolerance in E. coli K-12 and E. coli B at high density growth.

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Son, Young-Jin; Phue, Je-Nie; Trinh, Loc B; Lee, Sang Jun; Shiloach, Joseph

2011-06-30

E. coli B (BL21), unlike E.coli K-12 (JM109) is insensitive to glucose concentration and, therefore, grows faster and produces less acetate than E. coli K-12, especially when growing to high cell densities at high glucose concentration. By performing genomic analysis, it was demonstrated that the cause of this difference in sensitivity to the glucose concentration is the result of the differences in the central carbon metabolism activity. We hypothesized that the global transcription regulator Cra (FruR) is constitutively expressed in E. coli B and may be responsible for the different behaviour of the two strains. To investigate this possibility and better understand the function of Cra in the two strains, cra - negative E. coli B (BL21) and E. coli K-12 (JM109) were prepared and their growth behaviour and gene expression at high glucose were evaluated using microarray and real-time PCR. The deletion of the cra gene in E. coli B (BL21) minimally affected the growth and maximal acetate accumulation, while the deletion of the same gene in E.coli K-12 (JM109) caused the cells to stop growing as soon as acetate concentration reached 6.6 g/L and the media conductivity reached 21 mS/cm. ppsA (gluconeogenesis gene), aceBA (the glyoxylate shunt genes) and poxB (the acetate producing gene) were down-regulated in both strains, while acs (acetate uptake gene) was down-regulated only in E.coli B (BL21). These transcriptional differences had little effect on acetate and pyruvate production. Additionally, it was found that the lower growth of E. coli K-12 (JM109) strain was the result of transcription inhibition of the osmoprotectant producing bet operon (betABT). The transcriptional changes caused by the deletion of cra gene did not affect the activity of the central carbon metabolism, suggesting that Cra does not act alone; rather it interacts with other pleiotropic regulators to create a network of metabolic effects. An unexpected outcome of this work is the finding that cra

Divergent Evolution of the Transcriptional Network Controlled by Snf1-Interacting Protein Sip4 in Budding Yeasts.

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Constance Mehlgarten

Full Text Available Cellular responses to starvation are of ancient origin since nutrient limitation has always been a common challenge to the stability of living systems. Hence, signaling molecules involved in sensing or transducing information about limiting metabolites are highly conserved, whereas transcription factors and the genes they regulate have diverged. In eukaryotes the AMP-activated protein kinase (AMPK functions as a central regulator of cellular energy homeostasis. The yeast AMPK ortholog SNF1 controls the transcriptional network that counteracts carbon starvation conditions by regulating a set of transcription factors. Among those Cat8 and Sip4 have overlapping DNA-binding specificity for so-called carbon source responsive elements and induce target genes upon SNF1 activation. To analyze the evolution of the Cat8-Sip4 controlled transcriptional network we have compared the response to carbon limitation of Saccharomyces cerevisiae to that of Kluyveromyces lactis. In high glucose, S. cerevisiae displays tumor cell-like aerobic fermentation and repression of respiration (Crabtree-positive while K. lactis has a respiratory-fermentative life-style, respiration being regulated by oxygen availability (Crabtree-negative, which is typical for many yeasts and for differentiated higher cells. We demonstrate divergent evolution of the Cat8-Sip4 network and present evidence that a role of Sip4 in controlling anabolic metabolism has been lost in the Saccharomyces lineage. We find that in K. lactis, but not in S. cerevisiae, the Sip4 protein plays an essential role in C2 carbon assimilation including induction of the glyoxylate cycle and the carnitine shuttle genes. Induction of KlSIP4 gene expression by KlCat8 is essential under these growth conditions and a primary function of KlCat8. Both KlCat8 and KlSip4 are involved in the regulation of lactose metabolism in K. lactis. In chromatin-immunoprecipitation experiments we demonstrate binding of both, KlSip4 and

Experimental american trypanomiasis in rats: sympathetic denervation, parasitism and inflammatory process Desnervação simpática, parasitismo e processo inflamatório durante a doença de Chagas experimental, em ratos

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Conceição R. S. Machado

1989-12-01

Full Text Available Tissue parasitism, inflammatory process (histologic methods and sympathetic denervation (glyoxylic acid-induced histofluorescence for demonstration of catecholamines were studied in the heart (atrium and verntricle and the submandibular gland of rats infected with the Y strain of Trypanosoma cruzi. In the heart paralleling intense parasitism and inflammatory process, the sympathetic denervation started at day 6 of infection and at the end of the acute phase (day 20 practically no varicose nerve terminals were found in both myocardium and vessels. In the submandibular gland, in spite of the rarity of anastigote pseudocysts and the scarcity of inflammatory foci, slight to moderate (days 13-15 of infection or moderate to severe denervation (day 20 was found. At day 120 of infection both organs exhibited normal pattern of sympathetic innervation and only the heart showed some inflammatory foci and rare psudocysts (ventricle. Our data suggest the involvement of circulating factors in the sympathetic denervation phenomena but indicate that local inflammatory process is, at least, an aggravating factor.Parasitismo tecidual, processo inflamatório (métodos histológicos e desnervação simpática (histofluorescência induzida por ácido glioxílico para demosntração de catecolaminas foram estudados no coração (átrio e ventrículo e na glândula submandibular de ratos infectados com cepa Y de Trypanosoma cruzi. No coração, em paralelo com intenso parasitismo e processo inglamatório, a desnervação simpática iniciuo-se no 6º dia de infecção e ao fim da fase aguda (20º dia praticamente nenhuma terminação nervosa varicosa foi encontrada tanto no miocárdio como em vasos. Na glândula submandibular, apesar da raridade de ninhos de amastigotas e da escassez de focos inflamatórios, encontram-se discreta e moderada 13º-15º dia de infeccção ou moderada a severa (20º dia desnervação. Aos 120 dias de infecção, ambos os órgãos exibiram

Size distributions of dicarboxylic acids, ketocarboxylic acids, α-dicarbonyls and fatty acids in atmospheric aerosols from Tanzania, East Africa during wet and dry seasons

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Mkoma, S. L.; Kawamura, K.

2012-09-01

Atmospheric aerosol samples of PM2.5 and PM10 were collected during the wet and dry seasons in 2011 from a rural site in Tanzania and analysed for water-soluble dicarboxylic acids, ketocarboxylic acids, α-dicarbonyls and fatty acids using a gas chromatography (GC) and GC/mass spectrometry. Here we report the size distribution and sources of diacids and related compounds for wet and dry seasons. Oxalic acid (C2) was found as the most abundant diacid species followed by succinic and/or malonic acids whereas glyoxylic acid and glyoxal were the dominant ketoacids and α-dicarbonyls, respectively in both seasons in PM2.5 and PM10. Mean concentration of C2 in PM2.5 (121.5± 46.6 ng m-3) was lower in wet season than dry season (258.1± 69.5 ng m-3). Similarly, PM10 samples showed lower concentration of C2 (168.6 ± 42.4 ng m-3) in wet season than dry season (292.4± 164.8 ng m-3). Relative abundances of C2 in total diacids were 65.4% and 67.1% in PM2.5 and 64.6% and 63.9% in PM10 in the wet and dry seasons, respectively. Total concentrations of diacids (289-362 m-3), ketoacids (37.8-53.7ng m-3), and α-dicarbonyls (5.7-7.8 ng m-3) in Tanzania are higher to those reported at a rural background site in Nylsvley (South Africa) but comparable or lower to those reported from sites in Asia and Europe. Diacids and ketoacids were found to be present mainly in the fine fraction in both seasons (total α-dicarbonyls in the dry season), suggesting a production of organic aerosols from pyrogenic sources and photochemical oxidations. The averaged contributions of total diacid carbon to aerosol total carbon were 1.4% in PM2.5 and 2.1% in PM10 in wet season and 3.3% in PM2.5 and 3.9% in PM10 in dry season whereas those to water-soluble organic carbon were 2.2% and 4.7% inPM2.5 and 3.1% and 5.8% in PM10 during the wet and dry seasons, respectively. These ratios suggest an enhanced photochemical oxidation of organic precursors and heterogeneous reactions on aerosols under strong solar

Molecular composition of dicarboxylic acids, ketocarboxylic acids, α-dicarbonyls and fatty acids in atmospheric aerosols from Tanzania, East Africa during wet and dry seasons

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Mkoma, S. L.; Kawamura, K.

2013-02-01

Atmospheric aerosol samples of PM2.5 and PM10 were collected during the wet and dry seasons in 2011 from a rural site in Tanzania and analysed for water-soluble dicarboxylic acids, ketocarboxylic acids, α-dicarbonyls, and fatty acids using a gas chromatography/flame ionization detector (GC/FID) and GC/mass spectrometry. Here we report the molecular composition and sources of diacids and related compounds for wet and dry seasons. Oxalic acid (C2) was found as the most abundant diacid species followed by succinic and/or malonic acids whereas glyoxylic acid and glyoxal were the dominant ketoacid and α-dicarbonyl, respectively in both seasons in PM2.5 and PM10. Mean concentration of C2 in PM2.5 (121 ± 47 ng m-3) was lower in wet season than dry season (258 ± 69 ng m-3). Similarly, PM10 samples showed lower concentration of C2 (169 ± 42 ng m-3) in wet season than dry season (292 ± 165 ng m-3). Relative abundances of C2 in total diacids were 65% and 67% in PM2.5 and 65% and 64% in PM10 in the wet and dry seasons, respectively. Total concentrations of diacids (289-362 ng m-3), ketoacids (37.8-53.7 ng m-3), and α-dicarbonyls (5.7-7.8 ng m-3) in Tanzania are higher than those reported at a rural background site in Nylsvley (South Africa) but comparable or lower than those reported from sites in Asia and Europe. Diacids and ketoacids were found to be present mainly in PM2.5 in both seasons (total α-dicarbonyls in the dry season), suggesting a production of organic acids from pyrogenic sources and photochemical oxidations. Averaged contributions of total diacids to aerosol total carbon were 1.4% in PM2.5 and 2.1% in PM10 during wet season and 3.3% in PM2.5 and 3.9% in PM10 during dry season whereas those to water-soluble organic carbon were 2.2% and 4.7% in PM2.5 during wet season and 3.1% and 5.8% in PM10 during dry season. The higher ratios in dry season suggest an enhanced photochemical oxidation of organic precursors probably via heterogeneous reactions on

Metabolic transcription analysis of engineered Escherichia coli strains that overproduce L-phenylalanine

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Gosset Guillermo

2007-09-01

Full Text Available Abstract Background The rational design of L-phenylalanine (L-Phe overproducing microorganisms has been successfully achieved by combining different genetic strategies such as inactivation of the phosphoenolpyruvate: phosphotransferase transport system (PTS and overexpression of key genes (DAHP synthase, transketolase and chorismate mutase-prephenate dehydratase, reaching yields of 0.33 (g-Phe/g-Glc, which correspond to 60% of theoretical maximum. Although genetic modifications introduced into the cell for the generation of overproducing organisms are specifically targeted to a particular pathway, these can trigger unexpected transcriptional responses of several genes. In the current work, metabolic transcription analysis (MTA of both L-Phe overproducing and non-engineered strains using Real-Time PCR was performed, allowing the detection of transcriptional responses to PTS deletion and plasmid presence of genes related to central carbon metabolism. This MTA included 86 genes encoding enzymes of glycolysis, gluconeogenesis, pentoses phosphate, tricarboxylic acid cycle, fermentative and aromatic amino acid pathways. In addition, 30 genes encoding regulatory proteins and transporters for aromatic compounds and carbohydrates were also analyzed. Results MTA revealed that a set of genes encoding carbohydrate transporters (galP, mglB, gluconeogenic (ppsA, pckA and fermentative enzymes (ldhA were significantly induced, while some others were down-regulated such as ppc, pflB, pta and ackA, as a consequence of PTS inactivation. One of the most relevant findings was the coordinated up-regulation of several genes that are exclusively gluconeogenic (fbp, ppsA, pckA, maeB, sfcA, and glyoxylate shunt in the best PTS- L-Phe overproducing strain (PB12-ev2. Furthermore, it was noticeable that most of the TCA genes showed a strong up-regulation in the presence of multicopy plasmids by an unknown mechanism. A group of genes exhibited transcriptional responses to

Light absorption and the photoformation of hydroxyl radical and singlet oxygen in fog waters

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Kaur, R.; Anastasio, C.

2017-09-01

The atmospheric aqueous-phase is a rich medium for chemical transformations of organic compounds, in part via photooxidants generated within the drops. Here we measure light absorption, photoformation rates and steady-state concentrations of two photooxidants - hydroxyl radical (•OH) and singlet molecular oxygen (1O2*) - in 8 illuminated fog waters from Davis, California and Baton Rouge, Louisiana. Mass absorption coefficients for dissolved organic compounds (MACDOC) in the samples are large, with typical values of 10,000-15,000 cm2 g-C-1 at 300 nm, and absorption extends to wavelengths as long as 450-600 nm. While nitrite and nitrate together account for an average of only 1% of light absorption, they account for an average of 70% of •OH photoproduction. Mean •OH photoproduction rates in fogs at the two locations are very similar, with an overall mean of 1.2 (±0.7) μM h-1 under Davis winter sunlight. The mean (±1σ) lifetime of •OH is 1.6 (±0.6) μs, likely controlled by dissolved organic compounds. Including calculated gas-to-drop partitioning of •OH, the average aqueous concentration of •OH is approximately 2 × 10-15 M (midday during Davis winter), with aqueous reactions providing approximately one-third of the hydroxyl radical source. At this concentration, calculated lifetimes of aqueous organics are on the order of 10 h for compounds with •OH rate constants of 1 × 1010 M-1 s-1 or higher (e.g., substituted phenols such as syringol (6.4 h) and guaiacol (8.4 h)), and on the order of 100 h for compounds with rate constants near 1 × 109 M-1 s-1 (e.g., isoprene oxidation products such as glyoxal (152 h), glyoxylic acid (58 h), and pyruvic acid (239 h)). Steady-state concentrations of 1O2* are approximately 100 times higher than those of •OH, in the range of (0.1-3.0) × 10-13 M. Since 1O2* is a more selective oxidant than •OH, it will only react appreciably with electron-rich species such as dimethyl furan (lifetime of 2.0 h) and

Molecular composition of dicarboxylic acids, ketocarboxylic acids, α-dicarbonyls and fatty acids in atmospheric aerosols from Tanzania, East Africa during wet and dry seasons

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S. L. Mkoma

2013-02-01

Full Text Available Atmospheric aerosol samples of PM_2.5 and PM₁₀ were collected during the wet and dry seasons in 2011 from a rural site in Tanzania and analysed for water-soluble dicarboxylic acids, ketocarboxylic acids, α-dicarbonyls, and fatty acids using a gas chromatography/flame ionization detector (GC/FID and GC/mass spectrometry. Here we report the molecular composition and sources of diacids and related compounds for wet and dry seasons. Oxalic acid (C₂ was found as the most abundant diacid species followed by succinic and/or malonic acids whereas glyoxylic acid and glyoxal were the dominant ketoacid and α-dicarbonyl, respectively in both seasons in PM_2.5 and PM₁₀. Mean concentration of C₂ in PM_2.5 (121 ± 47 ng m⁻³ was lower in wet season than dry season (258 ± 69 ng m⁻³. Similarly, PM₁₀ samples showed lower concentration of C₂ (169 ± 42 ng m⁻³ in wet season than dry season (292 ± 165 ng m⁻³. Relative abundances of C₂ in total diacids were 65% and 67% in PM_2.5 and 65% and 64% in PM₁₀ in the wet and dry seasons, respectively. Total concentrations of diacids (289–362 ng m⁻³, ketoacids (37.8–53.7 ng m⁻³, and α-dicarbonyls (5.7–7.8 ng m⁻³ in Tanzania are higher than those reported at a rural background site in Nylsvley (South Africa but comparable or lower than those reported from sites in Asia and Europe. Diacids and ketoacids were found to be present mainly in PM_2.5 in both seasons (total α-dicarbonyls in the dry season, suggesting a production of organic acids from pyrogenic sources and photochemical oxidations. Averaged contributions of total diacids to aerosol total carbon were 1.4% in PM_2.5 and 2.1% in PM₁₀ during wet season and 3.3% in PM_2.5 and 3.9% in PM₁₀ during

Molecular distribution, seasonal variation, chemical transformation and sources of dicarboxylic acids and related compounds in atmospheric aerosols at remote marine Gosan site, Jeju Island

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Kundu, S.; Kawamura, K.; Lee, M.

2009-12-01

: A homologous series of C2-C12 α, ω-dicarboxylic acids, ω-oxocarboxylic acids (C2-C9), pyruvic acid and α-dicarbonyls (C2-C3) were detected in atmospheric aerosols collected between April 2003 and April 2004 from remote marine Gosan site (33°29‧ N, 126°16‧ E) located in Jeju Island, South Korea. They were determined using a GC-FID and GC/MS. Total diacid concentration ranged from 130 to 1911 ng m-3 (av. 642 ng m-3), whereas total oxoacid concentration ranged from 7 to 155 ng m-3 (av. 43 ng m-3), and pyruvic acid and α-dicarbonyls ranged from 0.5 to 15 ng m-3 (av. 5 ng m-3) and 2-108 ng m-3 (av. 17.3 ng m-3), respectively. Oxalic (C2) acid was the most abundant in all seasons followed by malonic (C3) or succinic (C4) acid, and phthalic (Ph) acid. The concentration of diacids decreased with an increase in carbon number except for azelaic (C9) acid, which was more abundant than suberic (C8) acid. Glyoxylic acid was predominant ω-oxoacid contributing to 92% of total ω-oxoacid. Total diacids, oxoacids and dicarbonyls showed maximum concentrations in spring and occasionally in winter, while minimum concentrations were observed in summer. Air mass trajectory analysis suggests that either spring or winter maxima can be explained by strong continental outflow associated with cold front passages, while summer minima are associated with warm southerly flows, which transport clean marine air from low latitudes to Jeju Island. The comparison between total diacid concentration level of this study and other study results of urban and remote sites of East Asia reveals that Gosan site is more heavily influenced by the continental outflow from China. The seasonal variation of malonic/succinic (C3/C4), malic/succinic (hC4/C4), fumaric/maleic (F/M), oxalic/pyruvic (C2/Py) and oxalic/Glyoxal (C2/Gly) ratios showed maxima in summer due to an enhanced photo-production and degradation of diacids and related compounds. Throughout all seasons C3/C4 ratio at Gosan site, located

Final Report for Grant No. DE-FG02-97ER62492 ''Engineering Deinococcus radiodurans for Metal Remediation in Radioactive Mixed Waste Sites''

International Nuclear Information System (INIS)

Michael J.; Daly, Ph.D.

2005-01-01

2000 closely matches the Aims proposed in our second NABIR application and is summarized as follows. We have further refined expression vectors for D. radiodurans and successfully tested engineered strains in natural DOE sediment and groundwater samples. Further, we have shown that D. geothermalis is transformable with plasmids and integration vectors designed for D. radiodurans. This was demonstrated by engineering Hg(II)-resistant D. geothermalis strains capable of reducing Hg(II) at elevated temperatures and under chronic irradiation. Additionally, we showed that D. geothermalis, like D. radiodurans, is naturally capable of reducing U(VI), Cr(VI), and Fe(III). These characteristics support the prospective development of this thermophilic radiophile for bioremediation of radioactive mixed waste environments with temperatures as high as 55 C, of which there are many examples. Our annotation of the D. radiodurans genome has been an important guide throughout this project period and continues to be a source of inspiration in the development of new genetic technologies dedicated to this bacterium. For example, our genome analyses have enabled us to achieve engineering goals that were unattainable in our first NABIR project (1997-2000), where uncertainties relating to its metabolic configuration prevented efforts to expand its metabolic capabilities. As just one example, we showed that D. radiodurans has a functioning tricarboxylic acid (TCA) cycle glyoxylate bypass which could be integrated with toluene oxidation. And, we successfully engineered D. radiodurans to derive carbon and energy from complete toluene mineralization and showed that toluene oxidation can be coupled to cellular biosynthesis, survival, as well as its native and engineered metal reducing capabilities. We have also constructed a whole genome microarray for D. radiodurans covering ∼94% of its predicted genes and have successfully used the array to examine the response of cells to radiation and other

Characterization of polar organic compounds and source analysis of fine organic aerosols in Hong Kong

Science.gov (United States)

Li, Yunchun

Organic aerosols, as an important fraction of airborne particulate mass, significantly affect the environment, climate, and human health. Compared with inorganic species, characterization of individual organic compounds is much less complete and comprehensive because they number in thousands or more and are diverse in chemical structures. The source contributions of organic aerosols are far from being well understood because they can be emitted from a variety of sources as well as formed from photochemical reactions of numerous precursors. This thesis work aims to improve the characterization of polar organic compounds and source apportionment analysis of fine organic carbon (OC) in Hong Kong, which consists of two parts: (1) An improved analytical method to determine monocarboxylic acids, dicarboxylic acids, ketocarboxylic acids, and dicarbonyls collected on filter substrates has been established. These oxygenated compounds were determined as their butyl ester or butyl acetal derivatives using gas chromatography-mass spectrometry. The new method made improvements over the original Kawamura method by eliminating the water extraction and evaporation steps. Aerosol materials were directly mixed with the BF 3/BuOH derivatization agent and the extracting solvent hexane. This modification improves recoveries for both the more volatile and the less water-soluble compounds. This improved method was applied to study the abundances and sources of these oxygenated compounds in PM2.5 aerosol samples collected in Hong Kong under different synoptic conditions during 2003-2005. These compounds account for on average 5.2% of OC (range: 1.4%-13.6%) on a carbon basis. Oxalic acid was the most abundant species. Six C2 and C3 oxygenated compounds, namely oxalic, malonic, glyoxylic, pyruvic acids, glyoxal, and methylglyoxal, dominated this suite of oxygenated compounds. More efforts are therefore suggested to focus on these small compounds in understanding the role of oxygenated

Isolation of Metals from Liquid Wastes: Reactive in Turbulent Thermal Reactors

International Nuclear Information System (INIS)

Wendt, Jost O.L.

2001-01-01

that DOE has already experienced problems with organic complexants added to precipitate radionuclides. For example, the Defense Nuclear Facilities Safety Board has expressed, in a formal Recommendation to the Secretary of Energy, its concern about the evolution of benzene vapor in concentrations greater then the lower flammability limit from tanks to which sodium tetraphenylborate has been added to precipitate 137Cs in the ''In-Tank Precipitation'' (ITP) process at the Savannah River Site. Other species added to the waste in the ITP process are sodium titanate (to adsorb 90Sr and Pu), and oxalic acid. Avoiding addition of organics to radioactive waste has the additional advantage that is likely to significantly reduce the rate of radiolytic and radiolytically-induced hydrogen generation (c.f. Meisel et al., [1993]), in which it is shown that removal of organics reduces the rate of hydrogen generation in simulated waste from Hanford tank 241-SY-101 by over 70%. Organic species already present are destroyed with very high efficiency. This attribute is especially attractive with respect to high-level tank waste at the Hanford Site, in which large amounts of citrate, glyoxylate, EDTA (ethylenediaminetetraacetic acid), and HEDTA [N-(2- hydroxyethyl)-ethylenediaminetriacetic acid] were added to precipitate radionuclides. These organic species are important in the thermal and radiolytic generation of methane, hydrogen, and nitrous oxide, flammable mixtures of which are episodically vented from 25 tanks on Hanford's Flammable Gas Watch List [Hopkins, 1994]. The same basic approach can be used to treat a broad range of liquid wastes, in each case concentrating the metals (regardless of liquid-phase oxidation state or association with chelators or absorbents) using a collectible sorbent, and destroying any organic species present. In common with the Army's approach (see section 2.2) to the thermal destruction of a 10 range of chemical warfare agents (GB, VX, and two blister