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Desulfovibrio vulgaris

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https://www.readbyqxmd.com/read/29753939/reactivation-of-standard-nife-hydrogenase-and-bioelectrochemical-catalysis-of-proton-reduction-and-hydrogen-oxidation-in-a-mediated-electron-transfer-system
#1
Saeko Shiraiwa, Keisei So, Yu Sugimoto, Yuki Kitazumi, Osamu Shirai, Koji Nishikawa, Yoshiki Higuchi, Kenji Kano
Standard [NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F (DvMF-H2 ase) catalyzes the uptake and production of hydrogen (H2 ) and is a promising biocatalyst for future energy devices. However, DvMF-H2 ase experiences oxidative inactivation under oxidative stress to generate Ni-A and Ni-B states. It takes a long time to reactivate the Ni-A state by chemical reduction, whereas the Ni-B state is quickly reactivated under reducing conditions. Oxidative inhibition limits the application of DvMF-H2 ase in practical devices...
May 5, 2018: Bioelectrochemistry
https://www.readbyqxmd.com/read/29721040/methane-yielding-microbial-communities-processing-lactate-rich-substrates-a-piece-of-the-anaerobic-digestion-puzzle
#2
Anna Detman, Damian Mielecki, Łukasz Pleśniak, Michał Bucha, Marek Janiga, Irena Matyasik, Aleksandra Chojnacka, Mariusz-Orion Jędrysek, Mieczysław K Błaszczyk, Anna Sikora
Background: Anaerobic digestion, whose final products are methane and carbon dioxide, ensures energy flow and circulation of matter in ecosystems. This naturally occurring process is used for the production of renewable energy from biomass. Lactate, a common product of acidic fermentation, is a key intermediate in anaerobic digestion of biomass in the environment and biogas plants. Effective utilization of lactate has been observed in many experimental approaches used to study anaerobic digestion...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29700624/insight-into-the-molecular-mechanism-of-the-sulfur-oxidation-process-by-reverse-sulfite-reductase-rsir-from-sulfur-oxidizer-allochromatium-vinosum
#3
Semanti Ghosh, Angshuman Bagchi
Sulfur metabolism is one of the oldest known biochemical processes. Chemotrophic or phototrophic proteobacteria, through the dissimilatory pathway, use sulfate, sulfide, sulfite, thiosulfate or elementary sulfur by either reductive or oxidative mechanisms. During anoxygenic photosynthesis, anaerobic sulfur oxidizer Allochromatium vinosum forms sulfur globules that are further oxidized by dsr operon. One of the key redox enzymes in reductive or oxidative sulfur metabolic pathways is the DsrAB protein complex...
April 26, 2018: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29505248/sulfur-isotope-fractionation-by-sulfate-reducing-microbes-can-reflect-past-physiology
#4
André Pellerin, Christine B Wenk, Itay Halevy, Boswell A Wing
Sulfur (S) isotope fractionation by sulfate-reducing microorganisms is a direct manifestation of their respiratory metabolism. This fractionation is apparent in the substrate (sulfate) and waste (sulfide) produced. The sulfate-reducing metabolism responds to variability in the local environment, with the response determined by the underlying genotype, resulting in the expression of an "isotope phenotype". Sulfur isotope phenotypes have been used as a diagnostic tool for the metabolic activity of sulfate-reducing microorganisms in the environment...
April 3, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29476629/ph-dependent-speciation-and-hydrogen-h-2-control-u-vi-respiration-by-desulfovibrio-vulgaris
#5
Shilpi Kushwaha, Andrew K Marcus, Bruce E Rittmann
In situ bioreduction of soluble hexavalent uranium U(VI) to insoluble U(IV) (as UO2 ) has been proposed as a means of preventing U migration in the groundwater. This work focuses on the bioreduction of U(VI) and precipitation of U(IV). It uses anaerobic batch reactors with Desulfovibrio vulgaris, a well-known sulfate, iron, and U(VI) reducer, growing on lactate as the electron donor, in the absence of sulfate, and with a 30-mM bicarbonate buffering. In the absence of sulfate, D. vulgaris reduced  >90% of the total soluble U(VI) (1 mM) to form U(IV) solids that were characterized by X-ray diffraction and confirmed to be nano-crystalline uraninite with crystallite size 2...
June 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29429007/cr-vi-reduction-and-physiological-toxicity-are-impacted-by-resource-ratio-in-desulfovibrio-vulgaris
#6
Lauren C Franco, Sadie Steinbeisser, Grant M Zane, Judy D Wall, Matthew W Fields
Desulfovibrio spp. are capable of heavy metal reduction and are well-studied systems for understanding metal fate and transport in anaerobic environments. Desulfovibrio vulgaris Hildenborough was grown under environmentally relevant conditions (i.e., temperature, nutrient limitation) to elucidate the impacts on Cr(VI) reduction on cellular physiology. Growth at 20 °C was slower than 30 °C and the presence of 50 μM Cr(VI) caused extended lag times for all conditions, but once growth resumed the growth rate was similar to that without Cr(VI)...
March 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29411481/glycoside-hydrolase-dish-from-desulfovibrio-vulgaris-degrades-the-n-acetylgalactosamine-component-of-diverse-biofilms
#7
Lei Zhu, Venkata G Poosarla, Sooyeon Song, Thammajun L Wood, Daniel S Miller, Bei Yin, Thomas K Wood
Biofilms of sulfate-reducing bacteria (SRB) produce H2 S, which contributes to corrosion. Although bacterial cells in biofilms are cemented together, they often dissolve their own biofilm to allow the cells to disperse. Using Desulfovibrio vulgaris as a model SRB, we sought polysaccharide-degrading enzymes that disperse its biofilm. Using a whole-genome approach, we identified eight enzymes as putative extracellular glycoside hydrolases including DisH (DVU2239, dispersal hexosaminidase), an enzyme that we demonstrated here, by utilizing various p-nitrooligosaccharide substrates, to be an N-acetyl-β-D-hexosaminidase...
February 6, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29377633/constraint-based-modelling-captures-the-metabolic-versatility-of-desulfovibrio-vulgaris
#8
Jason J Flowers, Matthew A Richards, Nitin Baliga, Birte Meyer, David A Stahl
A refined Desulfovibrio vulgaris Hildenborough flux balance analysis (FBA) model (iJF744) was developed, incorporating 1016 reactions that include 744 genes and 951 metabolites. A draft model was first developed through automatic model reconstruction using the ModelSeed Server and then curated based on existing literature. The curated model was further refined by incorporating three recently proposed redox reactions involving the Hdr-Flx and Qmo complexes and a lactate dehydrogenase (LdhAB, DVU 3027-3028) indicated by mutation and transcript analyses to serve electron transfer reactions central to syntrophic and respiratory growth...
April 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29324779/filling-gaps-in-bacterial-amino-acid-biosynthesis-pathways-with-high-throughput-genetics
#9
Morgan N Price, Grant M Zane, Jennifer V Kuehl, Ryan A Melnyk, Judy D Wall, Adam M Deutschbauer, Adam P Arkin
For many bacteria with sequenced genomes, we do not understand how they synthesize some amino acids. This makes it challenging to reconstruct their metabolism, and has led to speculation that bacteria might be cross-feeding amino acids. We studied heterotrophic bacteria from 10 different genera that grow without added amino acids even though an automated tool predicts that the bacteria have gaps in their amino acid synthesis pathways. Across these bacteria, there were 11 gaps in their amino acid biosynthesis pathways that we could not fill using current knowledge...
January 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29245150/mobilization-of-arsenic-on-nano-tio-2-in-soil-columns-with-sulfate-reducing-bacteria
#10
Ting Luo, Li Ye, Tingshan Chan, Chuanyong Jing
Arsenic (As) remediation in contaminated water using nanoparticles is promising. However, the fate and transport of As associated with nano-adsorbents in natural environment is poorly understood. To investigate the fate of adsorbed As on nano-TiO2 in changed redox condition from oxic to anoxic, we added the As(V)-TiO2 suspension in groundwater to an autoclaved soil column which inoculated a sulfate-reducing bacterium, Desulfovibrio vulgaris DP4. The dissolved As(V) in effluent increased to 798 μg/L for the biotic column and to 1510 μg/L for the abiotic control, and dissolved As(III) was observed only in biotic column...
March 2018: Environmental Pollution
https://www.readbyqxmd.com/read/29149671/silver-nanoparticles-stimulate-the-proliferation-of-sulfate-reducing-bacterium-desulfovibrio-vulgaris
#11
Zhaoyu Chen, Ji Lu, Shu-Hong Gao, Min Jin, Philip L Bond, Ping Yang, Zhiguo Yuan, Jianhua Guo
The intensive use of silver nanoparticles (AgNPs) in cosmetics and textiles causes their release into sewer networks of urban water systems. Although a few studies have investigated antimicrobial activities of nanoparticles against environmental bacteria, little is known about potential impacts of the released AgNPs on sulfate reducing bacteria in sewers. Here, we investigated the effect of AgNPs on Desulfovibrio vulgaris Hidenborough (D. vulgaris), a typical sulfate-reducing bacterium (SRB) in sewer systems...
February 1, 2018: Water Research
https://www.readbyqxmd.com/read/29138306/key-metabolites-and-mechanistic-changes-for-salt-tolerance-in-an-experimentally-evolved-sulfate-reducing-bacterium-desulfovibrio-vulgaris
#12
Aifen Zhou, Rebecca Lau, Richard Baran, Jincai Ma, Frederick von Netzer, Weiling Shi, Drew Gorman-Lewis, Megan L Kempher, Zhili He, Yujia Qin, Zhou Shi, Grant M Zane, Liyou Wu, Benjamin P Bowen, Trent R Northen, Kristina L Hillesland, David A Stahl, Judy D Wall, Adam P Arkin, Jizhong Zhou
Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29042504/unintended-laboratory-driven-evolution-reveals-genetic-requirements-for-biofilm-formation-by-desulfovibrio-vulgaris-hildenborough
#13
Kara B De León, Grant M Zane, Valentine V Trotter, Gregory P Krantz, Adam P Arkin, Gareth P Butland, Peter J Walian, Matthew W Fields, Judy D Wall
Biofilms of sulfate-reducing bacteria (SRB) are of particular interest as members of this group are culprits in corrosion of industrial metal and concrete pipelines as well as being key players in subsurface metal cycling. Yet the mechanism of biofilm formation by these bacteria has not been determined. Here we show that two supposedly identical wild-type cultures of the SRB Desulfovibrio vulgaris Hildenborough maintained in different laboratories have diverged in biofilm formation. From genome resequencing and subsequent mutant analyses, we discovered that a single nucleotide change within DVU1017, the ABC transporter of a type I secretion system (T1SS), was sufficient to eliminate biofilm formation in D...
October 17, 2017: MBio
https://www.readbyqxmd.com/read/29033913/biochemical-function-molecular-structure-and-evolution-of-an-atypical-thioredoxin-reductase-from-desulfovibrio-vulgaris
#14
Odile Valette, Tam T T Tran, Christine Cavazza, Elodie Caudeville, Gaël Brasseur, Alain Dolla, Emmanuel Talla, Laetitia Pieulle
Thioredoxin reductase (TR) regulates the intracellular redox environment by reducing thioredoxin (Trx). In anaerobes, recent findings indicate that the Trx redox network is implicated in the global redox regulation of metabolism but also actively participates in protecting cells against O2 . In the anaerobe Desulfovibrio vulgaris Hildenborough ( Dv H), there is an intriguing redundancy of the Trx system which includes a classical system using NADPH as electron source, a non-canonical system using NADH and an isolated TR (DvTRi)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28925553/dispersal-and-inhibitory-roles-of-mannose-2-deoxy-d-glucose-and-n-acetylgalactosaminidase-on-the-biofilm-of-desulfovibrio-vulgaris
#15
Venkata G Poosarla, Thammajun L Wood, Lei Zhu, Daniel S Miller, Bei Yin, Thomas K Wood
Biofilms of sulfate-reducing bacteria (SRB) are often the major cause of microbiologically influenced corrosion. The representative SRB Desulfovibrio vulgaris has previously been shown to have a biofilm that consists primarily of protein. In this study, by utilizing lectin staining, we identified that the biofilm of D. vulgaris also consists of the matrix components mannose, fucose and N-acetylgalactosamine (GalNAc), with mannose predominating. Based on these results, we found that the addition of mannose and the nonmetabolizable mannose analog 2-deoxy-d-glucose inhibits the biofilm formation of D...
December 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28884159/a-reexamination-of-thioredoxin-reductase-from-thermoplasma-acidophilum-a-thermoacidophilic-euryarchaeon-identifies-it-as-an-nadh-dependent-enzyme
#16
Dwi Susanti, Usha Loganathan, Austin Compton, Biswarup Mukhopadhyay
Flavin-containing Trx reductase (TrxR) of Thermoplasma acidophilum (Ta), a thermoacidophilic facultative anaerobic archaeon, lacks the structural features for the binding of 2'-phosphate of nicotinamide adenine dinucleotide phosphate (NADPH), and this feature has justified the observed lack of activity with NADPH; NADH has also been reported to be ineffective. Our recent phylogenetic analysis identified Ta-TrxR as closely related to the NADH-dependent enzymes of Thermotoga maritima and Desulfovibrio vulgaris, both being anaerobic bacteria...
August 31, 2017: ACS Omega
https://www.readbyqxmd.com/read/28874410/identification-and-characterization-of-the-major-porin-of-desulfovibrio-vulgaris-hildenborough
#17
Lucy Zeng, Etsuko Wooton, David A Stahl, Peter J Walian
Due in large part to their ability to facilitate the diffusion of a diverse range of solutes across the outer membrane (OM) of Gram-negative bacteria, the porins represent one of the most prominent and important bacterial membrane protein superfamilies. Notably, for the Gram-negative bacterium Desulfovibrio vulgaris Hildenborough, a model organism for studies of sulfate-reducing bacteria, no genes for porins have been identified or proposed in its annotated genome. Results from initial biochemical studies suggested that the product of the DVU0799 gene, which is one of the most abundant proteins of the D...
December 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28770667/autophagy-counters-lps-mediated-suppression-of-lysozyme
#18
Sudha B Singh, Henry C Lin
Impaired Paneth cell expression of antimicrobial protein (AMP) lysozyme is found in patients with Crohn's disease with the autophagy gene ATG16L1 risk allele, in mice with mutations in autophagy genes Atg16L1, Atg5 and Atg7, and in Irgm1 knockout mice. Defective autophagy is also associated with expansion of resident Gram-negative bacteria in the intestinal lumen. These findings suggest that autophagy may control extracellular resident microbes by governing expression of lysozyme. To test the hypothesis that autophagy may have a defensive role in host response to resident extracellular microbes, we investigated the relationship between gut microbes, autophagy, and lysozyme...
August 2017: Innate Immunity
https://www.readbyqxmd.com/read/28550300/experimental-quantum-chemical-and-molecular-dynamic-simulations-studies-on-the-corrosion-inhibition-of-mild-steel-by-some-carbazole-derivatives
#19
Henry U Nwankwo, Lukman O Olasunkanmi, Eno E Ebenso
Five selected carbazole derivatives, namely carbazole, 3,6-dibromocarbazole, 2-hydroxycarbazole, 1,2,3,4-tetrahydrocarbazole and 9-(2-ethylhexyl)carbazole-3,6-dicarboxaldehyde were investigated for their inhibitive effects on Desulfovibrio vulgaris (D. vulgaris) induced corrosion of mild steel and in 1 M HCl medium using weight loss, potentiodynamic polarization and electrochemical impedance spectroscopy (EIS) techniques. The carbazole derivatives were found to be mixed type inhibitors with predominantly cathodic inhibitive effects for mild steel in 1 M HCl...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28506671/modeling-of-flux-binding-and-substitution-of-urea-molecules-in-the-urea-transporter-dvut
#20
Hai-Tian Zhang, Zhe Wang, Tao Yu, Jian-Ping Sang, Xian-Wu Zou, Xiaoqin Zou
Urea transporters (UTs) are transmembrane proteins that transport urea molecules across cell membranes and play a crucial role in urea excretion and water balance. Modeling the functional characteristics of UTs helps us understand how their structures accomplish the functions at the atomic level, and facilitates future therapeutic design targeting the UTs. This study was based on the crystal structure of Desulfovibrio vulgaris urea transporter (dvUT). To model the binding behavior of urea molecules in dvUT, we constructed a cooperative binding model...
September 2017: Journal of Molecular Graphics & Modelling
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