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Desulfovibrio vulgaris

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https://www.readbyqxmd.com/read/28320772/mechanism-for-microbial-population-collapse-in-a-fluctuating-resource-environment
#1
Serdar Turkarslan, Arjun V Raman, Anne W Thompson, Christina E Arens, Mark A Gillespie, Frederick von Netzer, Kristina L Hillesland, Sergey Stolyar, Adrian López García de Lomana, David J Reiss, Drew Gorman-Lewis, Grant M Zane, Jeffrey A Ranish, Judy D Wall, David A Stahl, Nitin S Baliga
Managing trade-offs through gene regulation is believed to confer resilience to a microbial community in a fluctuating resource environment. To investigate this hypothesis, we imposed a fluctuating environment that required the sulfate-reducer Desulfovibrio vulgaris to undergo repeated ecologically relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen-consuming Methanococcus maripaludis Strikingly, the microbial community became progressively less proficient at restoring the environmentally relevant physiological state after each perturbation and most cultures collapsed within 3-7 shifts...
March 20, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28319099/the-direct-role-of-selenocysteine-in-nifese-hydrogenase-maturation-and-catalysis
#2
Marta C Marques, Cristina Tapia, Oscar Gutiérrez-Sanz, Ana Raquel Ramos, Kimberly L Keller, Judy D Wall, Antonio L De Lacey, Pedro M Matias, Inês A C Pereira
Hydrogenases are highly active enzymes for hydrogen production and oxidation. [NiFeSe] hydrogenases, in which selenocysteine is a ligand to the active site Ni, have high catalytic activity and a bias for H2 production. In contrast to [NiFe] hydrogenases, they display reduced H2 inhibition and are rapidly reactivated after contact with oxygen. Here we report an expression system for production of recombinant [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough and study of a selenocysteine-to-cysteine variant (Sec489Cys) in which, for the first time, a [NiFeSe] hydrogenase was converted to a [NiFe] type...
March 20, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28192203/electrostatic-roles-in-electron-transfer-from-nife-hydrogenase-to-cytochrome-c3-from-desulfovibrio-vulgaris-miyazaki-f
#3
Yu Sugimoto, Yuki Kitazumi, Osamu Shirai, Koji Nishikawa, Yoshiki Higuchi, Masahiro Yamamoto, Kenji Kano
Electrostatic interactions between proteins are key factors that govern the association and reaction rate. We spectroscopically determine the second-order reaction rate constant (k) of electron transfer from [NiFe] hydrogenase (H2ase) to cytochrome (cyt) c3 at various ionic strengths (I). The k value decreases with I. To analyze the results, we develop a semi-analytical formula for I dependence of k based on the assumptions that molecules are spherical and the reaction proceeds via a transition state. Fitting of the formula to the experimental data reveals that the interaction occurs in limited regions with opposite charges and with radii much smaller than those estimated from crystal structures...
February 9, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28159790/the-effects-of-sulfate-reduction-on-tce-dechlorination-by-dehalococcoides-containing-microbial-communities
#4
Xinwei Mao, Alexandra Polasko, Lisa Alvarez-Cohen
In order to elucidate interactions between sulfate reduction and dechlorination, we systematically evaluated the effects of different concentrations of sulfate and sulfide on reductive dechlorination by isolates, constructed consortia and enrichments containing Dehalococcoides sp. Sulfate (up to 5 mM) did not inhibit growth or metabolism of pure cultures of dechlorinator Dehalococcoides mccartyi 195, sulfate reducer Desulfovibrio vulgaris Hildenborough (DvH) or syntroph Syntrophomonas wolfei (S. wolfei). In contrast, sulfide (5mM) exhibited inhibitory effects on growth of the sulfate reducer and the syntroph, as well as on both dechlorination and growth rates of D...
February 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27873195/community-structure-of-a-sulfate-reducing-consortium-in-lead-contaminated-wastewater-treatment-process
#5
Yen T Nguyen, Hoa T Q Kieu, Stephanie West, Yen T Dang, Harald Horn
This study evaluated the capacity to remove lead by an indigenous consortium of five sulfate-reducing bacteria (SRB): Desulfobacterium autotrophicum, Desulfomicrobium salsugmis, Desulfomicrobium escambiense, Desulfovibrio vulgaris, and Desulfovibrio carbinolicus, using continuous moving bed biofilm reactor systems. Four continuous moving bed biofilm reactors (referred as R1-R4) were run in parallel for 40 days at lead loading rates of 0, 20, 30 and 40 mg l(-1) day(-1), respectively. The impact of lead on community structure of the SRB consortium was investigated by dsrB gene-based denaturing gradient gel electrophoresis (dsrB-based DGGE), fluorescence in situ hybridization (FISH) and chemical analysis...
January 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27817891/biogenic-platinum-and-palladium-nanoparticles-as-new-catalysts-for-the-removal-of-pharmaceutical-compounds
#6
Mónica Martins, Cláudia Mourato, Sandra Sanches, João Paulo Noronha, M T Barreto Crespo, Inês A C Pereira
Pharmaceutical products (PhP) are one of the most alarming emergent pollutants in the environment. Therefore, it is of extreme importance to investigate efficient PhP removal processes. Biologic synthesis of platinum nanoparticles (Bio-Pt) has been reported, but their catalytic activity was never investigated. In this work, we explored the potential of cell-supported platinum (Bio-Pt) and palladium (Bio-Pd) nanoparticles synthesized with Desulfovibrio vulgaris as biocatalysts for removal of four PhP: ciprofloxacin, sulfamethoxazole, ibuprofen and 17β-estradiol...
January 1, 2017: Water Research
https://www.readbyqxmd.com/read/27702753/fractionation-of-sulfur-and-hydrogen-isotopes-in-desulfovibrio-vulgaris-with-perturbed-dsrc-expression
#7
William D Leavitt, Sofia S Venceslau, Inês A C Pereira, David T Johnston, Alexander S Bradley
Dissimilatory sulfate reduction is the central microbial metabolism in global sulfur cycling. Understanding the importance of sulfate reduction to Earth's biogeochemical S cycle requires aggregating single-cell processes with geochemical signals. For sulfate reduction, these signals include the ratio of stable sulfur isotopes preserved in minerals, as well as the hydrogen isotope ratios and structures of microbial membrane lipids preserved in organic matter. In this study we cultivated the model sulfate reducer, Desulfovibrio vulgaris DSM 644(T), to investigate how these parameters were perturbed by changes in expression of the protein DsrC...
October 3, 2016: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/27686721/fermentative-hydrogen-production-in-an-up-flow-anaerobic-biofilm-reactor-inoculated-with-a-co-culture-of-clostridium-acetobutylicum-and-desulfovibrio-vulgaris
#8
Cristian Barca, David Ranava, Marielle Bauzan, Jean-Henry Ferrasse, Marie-Thérèse Giudici-Orticoni, Audrey Soric
Dark fermentation systems often show low H2 yields and unstable H2 production, as the result of the variability of microbial dynamics and metabolic pathways. Recent batch investigations have demonstrated that an artificial consortium of two anaerobic bacteria, Clostridium acetobutylicum and Desulfovibrio vulgaris Hildenborough, may redirect metabolic fluxes and improve H2 yields. This study aimed at evaluating the scale-up from batch to continuous H2 production in an up-flow anaerobic packed-bed reactor (APBR) continuously fed with a glucose-medium...
December 2016: Bioresource Technology
https://www.readbyqxmd.com/read/27671526/regulation-sensory-domains-and-roles-of-two-desulfovibrio-desulfuricans-atcc27774-crp-family-transcription-factors-hcpr1-and-hcpr2-in-response-to-nitrosative-stress
#9
Ian T Cadby, Susan A Ibrahim, Matthew Faulkner, David J Lee, Douglas Browning, Stephen J Busby, Andrew L Lovering, Melanie R Stapleton, Jeffrey Green, Jeffrey A Cole
In silico analyses identified a Crp/Fnr family transcription factor (HcpR) in sulfate-reducing bacteria that controls expression of the hcp gene, which encodes the hybrid cluster protein and contributes to nitrosative stress responses. There is only one hcpR gene in the model sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, but two copies in Desulfovibrio desulfuricans 27774, which can use nitrate as an alternative electron acceptor to sulfate. Structures of the D. desulfuricans hcpR1, hcpR2 and hcp operons are reported...
December 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27486032/desulfovibrio-vulgaris-cbik-p-cobaltochelatase-evolution-of-a-haem-binding-protein-orchestrated-by-the-incorporation-of-two-histidine-residues
#10
Susana A L Lobo, Marco A M Videira, Isabel Pacheco, Mark N Wass, Martin J Warren, Miguel Teixeira, Pedro M Matias, Célia V Romão, Lígia M Saraiva
The sulfate-reducing bacteria of the Desulfovibrio genus make three distinct modified tetrapyrroles, haem, sirohaem and adenosylcobamide, where sirohydrochlorin acts as the last common biosynthetic intermediate along the branched tetrapyrrole pathway. Intriguingly, D. vulgaris encodes two sirohydrochlorin chelatases, CbiK(P) and CbiK(C) , that insert cobalt/iron into the tetrapyrrole macrocycle but are thought to be distinctly located in the periplasm and cytoplasm respectively. Fusing GFP onto the C-terminus of CbiK(P) confirmed that the protein is transported to the periplasm...
August 3, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27477318/sulfate-reducing-bacteria-slow-intestinal-transit-in-a-bismuth-reversible-fashion-in-mice
#11
N L Ritz, D M Lin, M R Wilson, L L Barton, H C Lin
BACKGROUND: Hydrogen sulfide (H2 S) serves as a mammalian cell-derived gaseous neurotransmitter. The intestines are exposed to a second source of this gas by sulfate-reducing bacteria (SRB). Bismuth subsalicylate binds H2 S rendering it insoluble. The aim of this study was to test the hypothesis that SRB may slow intestinal transit in a bismuth-reversible fashion. METHODS: Eighty mice were randomized to five groups consisting of Live SRB, Killed SRB, SRB+Bismuth, Bismuth, and Saline...
January 2017: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/27456760/photoactivation-of-the-ni-sir-state-to-the-ni-sia-state-in-nife-hydrogenase-ft-ir-study-on-the-light-reactivity-of-the-ready-ni-sir-state-and-as-isolated-enzyme-revisited
#12
Hulin Tai, Liyang Xu, Seiya Inoue, Koji Nishikawa, Yoshiki Higuchi, Shun Hirota
The Ni-SIr state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F was photoactivated to its Ni-SIa state by Ar(+) laser irradiation at 514.5 nm, whereas the Ni-SL state was light induced from a newly identified state, which was less active than any other identified state and existed in the "as-isolated" enzyme.
August 10, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27379039/enhanced-biocide-mitigation-of-field-biofilm-consortia-by-a-mixture-of-d-amino-acids
#13
Yingchao Li, Ru Jia, Hussain H Al-Mahamedh, Dake Xu, Tingyue Gu
Microbiologically influenced corrosion (MIC) is a major problem in the oil and gas industry as well as in many other industries. Current treatment methods rely mostly on pigging and biocide dosing. Biocide resistance is a growing concern. Thus, it is desirable to use biocide enhancers to improve the efficacy of existing biocides. D-Amino acids are naturally occurring. Our previous work demonstrated that some D-amino acids are biocide enhancers. Under a biocide stress of 50 ppm (w/w) hydroxymethyl phosphonium sulfate (THPS) biocide, 1 ppm D-tyrosine and 100 ppm D-methionine used separately successfully mitigated the Desulfovibrio vulgaris biofilm on carbon steel coupons...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27371588/antimicrobial-effects-of-free-nitrous-acid-on-desulfovibrio-vulgaris-implications-for-sulfide-induced-corrosion-of-concrete
#14
Shu-Hong Gao, Jun Yuan Ho, Lu Fan, David J Richardson, Zhiguo Yuan, Philip L Bond
Hydrogen sulfide produced by sulfate-reducing bacteria (SRB) in sewers causes odor problems and asset deterioration due to the sulfide-induced concrete corrosion. Free nitrous acid (FNA) was recently demonstrated as a promising antimicrobial agent to alleviate hydrogen sulfide production in sewers. However, details of the antimicrobial mechanisms of FNA are largely unknown. Here, we report the multiple-targeted antimicrobial effects of FNA on the SRB Desulfovibrio vulgaris Hildenborough by determining the growth, physiological, and gene expression responses to FNA exposure...
September 15, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27327240/conformational-difference-between-two-subunits-in-flavin-mononucleotide-binding-protein-dimers-from-desulfovibrio-vulgaris-mf-molecular-dynamics-simulation
#15
Nadtanet Nunthaboot, Kiattisak Lugsanangarm, Somsak Pianwanit, Sirirat Kokpol, Fumio Tanaka, Takeshi Nakanishi, Masaya Kitamura
The structural and dynamical properties of five FMN binding protein (FBP) dimers, WT (wild type), E13K (Glu13 replaced by Lys), E13R (Glu13 replaced by Arg), E13T (Glu13 replaced by Thr) and E13Q (Glu13 replaced by Gln), were investigated using a method of molecular dynamics simulation (MDS). In crystal structures, subunit A (Sub A) and subunit B (Sub B) were almost completely equivalent in all of the five FBP dimers. However, the predicted MDS structures of the two subunits were not equivalent in solution, revealed by the distances and inter-planar angles between isoalloxazine (Iso) and aromatic amino acids (Trp32, Tyr35 and Trp106) as well as the hydrogen bonding pairs between Iso and nearby amino acids...
October 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27299565/metabolic-dynamics-of-desulfovibrio-vulgaris-biofilm-grown-on-a-steel-surface
#16
Yang Zhang, Guangsheng Pei, Lei Chen, Weiwen Zhang
In this study, a comparative metabolomics approach combining gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) was applied first between planktonic cells and biofilms and then between pure cultures and biofilms of Desulfovibrio vulgaris. The results revealed that the overall metabolic level of the biofilm cells was down-regulated, especially for metabolites related to the central carbon metabolism, compared to the planktonic cells and the pure culture of D. vulgaris...
August 2016: Biofouling
https://www.readbyqxmd.com/read/27270746/electron-transfer-pathways-of-formate-driven-h2-production-in-desulfovibrio
#17
Mónica Martins, Cláudia Mourato, Fabio O Morais-Silva, Claudina Rodrigues-Pousada, Gerrit Voordouw, Judy D Wall, Inês A C Pereira
The potential of sulfate-reducing bacteria (SRB) as biocatalysts for H2 production from formate was recently demonstrated, but the electron transfer pathways involved were not described. In the present work, we analyzed the H2 production capacity of five Desulfovibrio strains: Desulfovibrio vulgaris, Desulfovibrio desulfuricans, Desulfovibrio alaskensis, Desulfovibrio fructosivorans, and Desulfovibrio gigas. D. vulgaris showed the highest H2 productivity (865 mL Lmedium (-1)), and D. gigas the lowest one (374 mL Lmedium (-1) of H2)...
September 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27258948/a-stable-genetic-polymorphism-underpinning-microbial-syntrophy
#18
Tobias Großkopf, Simone Zenobi, Mark Alston, Leighton Folkes, David Swarbreck, Orkun S Soyer
Syntrophies are metabolic cooperations, whereby two organisms co-metabolize a substrate in an interdependent manner. Many of the observed natural syntrophic interactions are mandatory in the absence of strong electron acceptors, such that one species in the syntrophy has to assume the role of electron sink for the other. While this presents an ecological setting for syntrophy to be beneficial, the potential genetic drivers of syntrophy remain unknown to date. Here, we show that the syntrophic sulfate-reducing species Desulfovibrio vulgaris displays a stable genetic polymorphism, where only a specific genotype is able to engage in syntrophy with the hydrogenotrophic methanogen Methanococcus maripaludis...
December 2016: ISME Journal
https://www.readbyqxmd.com/read/27199927/comparison-of-transcriptional-heterogeneity-of-eight-genes-between-batch-desulfovibrio-vulgaris-biofilm-and-planktonic-culture-at-a-single-cell-level
#19
Zhenhua Qi, Lei Chen, Weiwen Zhang
Sulfate-reducing bacteria (SRB) biofilm formed on metal surfaces can change the physicochemical properties of metals and cause metal corrosion. To enhance understanding of differential gene expression in Desulfovibrio vulgaris under planktonic and biofilm growth modes, a single-cell based RT-qPCR approach was applied to determine gene expression levels of 8 selected target genes in four sets of the 31 individual cells isolated from each growth condition (i.e., biofilm formed on a mild steel (SS) and planktonic cultures, exponential and stationary phases)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27099342/quantitative-tagless-copurification-a-method-to-validate-and-identify-protein-protein-interactions
#20
Maxim Shatsky, Ming Dong, Haichuan Liu, Lee Lisheng Yang, Megan Choi, Mary E Singer, Jil T Geller, Susan J Fisher, Steven C Hall, Terry C Hazen, Steven E Brenner, Gareth Butland, Jian Jin, H Ewa Witkowska, John-Marc Chandonia, Mark D Biggin
Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification of endogenous proteins through orthogonal chromatography steps...
June 2016: Molecular & Cellular Proteomics: MCP
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