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Desulfovibrio vulgaris

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https://www.readbyqxmd.com/read/29324779/filling-gaps-in-bacterial-amino-acid-biosynthesis-pathways-with-high-throughput-genetics
#1
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-tio2-in-soil-columns-with-sulfate-reducing-bacteria
#2
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...
December 12, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/29149671/silver-nanoparticles-stimulate-the-proliferation-of-sulfate-reducing-bacterium-desulfovibrio-vulgaris
#3
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...
November 8, 2017: 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
#4
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
#5
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
#6
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 (DvH), 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
#7
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 non-metabolizable mannose analog 2-deoxy-D-glucose inhibits the biofilm formation of D...
September 19, 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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28458201/reduction-of-adsorbed-as-v-on-nano-tio2-by-sulfate-reducing-bacteria
#13
Ting Luo, Li Ye, Cheng Ding, Jinlong Yan, Chuanyong Jing
Reduction of surface-bound arsenate [As(V)] and subsequent release into the aqueous phase contribute to elevated As in groundwater. However, this natural process is not fully understood, especially in the presence of sulfate-reducing bacteria (SRB). Gaining mechanistic insights into solid-As(V)-SRB interactions motivated our molecular level study on the fate of nano-TiO2 bound As(V) in the presence of Desulfovibrio vulgaris DP4, a strain of SRB, using incubation and in situ ATR-FTIR experiments. The incubation results clearly revealed the reduction of As(V), either adsorbed on nano-TiO2 or dissolved, in the presence of SRB...
November 15, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28436827/reductive-precipitation-of-sulfate-and-soluble-fe-iii-by-desulfovibrio-vulgaris-electron-donor-regulates-intracellular-electron-flow-and-nano-fes-crystallization
#14
Chen Zhou, Yun Zhou, Bruce E Rittmann
Fully understanding the metabolism of SRB provides fundamental guidelines for allowing the microorganisms to provide more beneficial services in water treatment and resource recovery. The electron-transfer pathway of sulfate respiration by Desulfovibrio vulgaris is well studied, but still partly unresolved. Here we provide deeper insight by comprehensively monitoring metabolite changes during D. vulgaris metabolism with two electron donors, lactate and pyruvate, in presence or absence of citrate-chelated soluble Fe(III) as an additional competing electron acceptor...
August 1, 2017: Water Research
https://www.readbyqxmd.com/read/28419704/robustness-of-a-model-microbial-community-emerges-from-population-structure-among-single-cells-of-a-clonal-population
#15
Anne W Thompson, Serdar Turkarslan, Christina E Arens, Adrián López García de Lomana, Arjun V Raman, David A Stahl, Nitin S Baliga
Microbial populations can withstand, overcome and persist in the face of environmental fluctuation. Previously, we demonstrated how conditional gene regulation in a fluctuating environment drives dilution of condition-specific transcripts, causing a population of Desulfovibrio vulgaris Hildenborough (DvH) to collapse after repeatedly transitioning from sulfate respiration to syntrophic conditions with the methanogen Methanococcus maripaludis. Failure of the DvH to successfully transition contributed to the collapse of this model community...
August 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28365342/a-continuous-system-for-biocatalytic-hydrogenation-of-co2-to-formate
#16
Cláudia Mourato, Mónica Martins, Sofia M da Silva, Inês A C Pereira
In this work a novel bioprocess for hydrogenation of CO2 to formate was developed, using whole cell catalysis by a sulfate-reducing bacterium. Three Desulfovibrio species were tested (D. vulgaris Hildenborough, D. alaskensis G20, and D. desulfuricans ATCC 27774), of which D. desulfuricans showed the highest activity, producing 12mM of formate in batch, with a production rate of 0.09mMh(-1). Gene expression analysis indicated that among the three formate dehydrogenases and five hydrogenases, the cytoplasmic FdhAB and the periplasmic [FeFe] HydAB are the main enzymes expressed in D...
July 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28320772/mechanism-for-microbial-population-collapse-in-a-fluctuating-resource-environment
#17
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
#18
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...
May 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
#19
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...
May 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28159790/effects-of-sulfate-reduction-on-trichloroethene-dechlorination-by-dehalococcoides-containing-microbial-communities
#20
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 the growth or metabolism of pure cultures of the dechlorinator Dehalococcoides mccartyi 195, the sulfate reducer Desulfovibrio vulgaris Hildenborough, or the syntroph Syntrophomonas wolfei In contrast, sulfide at 5 mM exhibited inhibitory effects on growth of the sulfate reducer and the syntroph, as well as on both dechlorination and growth rates of D...
April 15, 2017: Applied and Environmental Microbiology
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