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The ISME Journal Sep 2013Desulfovibrio vulgaris Hildenborough strains with significantly increased tolerance to NaCl were obtained via experimental evolution. A NaCl-evolved strain, ES9-11,...
Desulfovibrio vulgaris Hildenborough strains with significantly increased tolerance to NaCl were obtained via experimental evolution. A NaCl-evolved strain, ES9-11, isolated from a population cultured for 1200 generations in medium amended with 100 mM NaCl, showed better tolerance to NaCl than a control strain, EC3-10, cultured for 1200 generations in parallel but without NaCl amendment in medium. To understand the NaCl adaptation mechanism in ES9-11, we analyzed the transcriptional, metabolite and phospholipid fatty acid (PLFA) profiles of strain ES9-11 with 0, 100- or 250 mM-added NaCl in medium compared with the ancestral strain and EC3-10 as controls. In all the culture conditions, increased expressions of genes involved in amino-acid synthesis and transport, energy production, cation efflux and decreased expression of flagellar assembly genes were detected in ES9-11. Consistently, increased abundances of organic solutes and decreased cell motility were observed in ES9-11. Glutamate appears to be the most important osmoprotectant in D. vulgaris under NaCl stress, whereas, other organic solutes such as glutamine, glycine and glycine betaine might contribute to NaCl tolerance under low NaCl concentration only. Unsaturation indices of PLFA significantly increased in ES9-11. Branched unsaturated PLFAs i17:1 ω9c, a17:1 ω9c and branched saturated i15:0 might have important roles in maintaining proper membrane fluidity under NaCl stress. Taken together, these data suggest that the accumulation of osmolytes, increased membrane fluidity, decreased cell motility and possibly an increased exclusion of Na(+) contribute to increased NaCl tolerance in NaCl-evolved D. vulgaris.
Topics: Adaptation, Physiological; Biological Evolution; Desulfovibrio vulgaris; Energy Metabolism; Fatty Acids; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Membrane Fluidity; Sodium Chloride
PubMed: 23575373
DOI: 10.1038/ismej.2013.60 -
The ISME Journal Sep 2020Several Trichonympha protist species in the termite gut have independently acquired Desulfovibrio ectosymbionts in apparently different stages of symbiosis. Here, we...
Several Trichonympha protist species in the termite gut have independently acquired Desulfovibrio ectosymbionts in apparently different stages of symbiosis. Here, we obtained the near-complete genome sequence of Desulfovibrio phylotype ZnDsv-02, which attaches to the surface of Trichonympha collaris cells, and compared it with a previously obtained genome sequence of 'Candidatus Desulfovibrio trichonymphae' phylotype Rs-N31, which is almost completely embedded in the cytoplasm of Trichonympha agilis. Single-nucleotide polymorphism analysis indicated that although Rs-N31 is almost clonal, the ZnDsv-02 population on a single host cell is heterogeneous. Despite these differences, the genome of ZnDsv-02 has been reduced to 1.6 Mb, which is comparable to that of Rs-N31 (1.4 Mb), but unlike other known ectosymbionts of protists with a genome similar in size to their free-living relatives. Except for the presence of a lactate utilization pathway, cell-adhesion components and anti-phage defense systems in ZnDsv-02, the overall gene-loss pattern between the two genomes is very similar, including the loss of genes responsive to environmental changes. Our study suggests that genome reduction can occur in ectosymbionts, even when they can be transmitted horizontally and obtain genes via lateral transfer, and that the symbiont genome size depends heavily on their role in the symbiotic system.
Topics: Animals; Desulfovibrio; Evolution, Molecular; Gastrointestinal Microbiome; Hypermastigia; Isoptera; Phylogeny; Symbiosis
PubMed: 32483307
DOI: 10.1038/s41396-020-0688-1 -
Journal of Bacteriology Dec 1989Phylogenetic relationships among 20 nonsporeforming and two endospore-forming species of sulfate-reducing eubacteria were inferred from comparative 16S rRNA sequencing.... (Comparative Study)
Comparative Study
Phylogenetic relationships among 20 nonsporeforming and two endospore-forming species of sulfate-reducing eubacteria were inferred from comparative 16S rRNA sequencing. All genera of mesophilic sulfate-reducing eubacteria except the new genus Desulfomicrobium and the gliding Desulfonema species were included. The sporeforming species Desulfotomaculum ruminis and Desulfotomaculum orientis were found to be gram-positive organisms sharing 83% 16S rRNA sequence similarity, indicating that this genus is diverse. The gram-negative nonsporeforming species could be divided into seven natural groups: group 1, Desulfovibrio desulfuricans and other species of this genus that do not degrade fatty acids (this group also included "Desulfomonas" pigra); group 2, the fatty acid-degrading "Desulfovibrio" sapovorans; group 3, Desulfobulbus species; group 4, Desulfobacter species; group 5, Desulfobacterium species and "Desulfococcus" niacini; group 6, Desulfococcus multivorans and Desulfosarcina variabilis; and group 7, the fatty acid-oxidizing "Desulfovibrio" baarsii. (The quotation marks are used to indicate the need for taxonomic revision.) Groups 1 to 3 are incomplete oxidizers that form acetate as an end product; groups 4 to 7 are complete oxidizers. The data were consistent with and refined relationships previously inferred by oligonucleotide catalogs of 16S rRNA. Although the determined relationships are generally consistent with the existing classification based on physiology and other characteristics, the need for some taxonomic revision is indicated.
Topics: Base Sequence; Desulfovibrio; Gram-Negative Anaerobic Bacteria; Molecular Sequence Data; Oligonucleotide Probes; Oxidation-Reduction; Phylogeny; RNA, Ribosomal; RNA, Ribosomal, 16S; RNA-Directed DNA Polymerase; Spores, Bacterial; Sulfates
PubMed: 2480344
DOI: 10.1128/jb.171.12.6689-6695.1989 -
Gut Apr 2004Desulfovibrios produce sulphide, which is toxic to colonic epithelial cells. These bacteria have previously been linked to ulcerative colitis. Traditional methods of...
BACKGROUND
Desulfovibrios produce sulphide, which is toxic to colonic epithelial cells. These bacteria have previously been linked to ulcerative colitis. Traditional methods of culturing these organisms are slow, and often unreliable, while molecular approaches are either non-quantitative or lack sensitivity.
AIMS
To develop a sensitive method for quantitating desulfovibrios in stools and biopsy tissue, and to investigate the effects of age and disease on these bacteria.
METHODS
Rectal biopsies were taken from 10 colitis patients and 10 healthy controls. Stool samples were obtained from 10 healthy infants (mean age 1.01 (0.18) years), 10 healthy young adults (26.7 (1.2) years), and 10 healthy elderly people (71.7 (1.2) years). Primers were designed and developed for analysing Desulfovibrio populations in the bowel using real time polymerase chain reaction (PCR).
RESULTS
The PCR primers were highly specific for desulfovibrios. Large numbers (approximately 10(6)-10(7)/g) occurred in biopsies in colitis patients and healthy subjects, and no disease related differences were observed. Measurements of mucosal desulfovibrios over 12 months showed marked changes in some patients. Infants (10(6)-10(7)/g) and elderly people (10(7)-10(8)/g) had significantly higher numbers of desulfovibrios in stools compared with young adults (10(5)/g).
CONCLUSIONS
Real time PCR analysis of desulfovibrios was an efficient and accurate method for studying these potentially harmful microorganisms. Desulfovibrios were ubiquitous in the bowel, irrespective of age. As rectal mucosae were heavily colonised in health and disease, if these bacteria play a role in colitis, some host defect, possibly in sulphide detoxication pathways or in bacterial antigen handling, is required for manifestations of pathogenicity.
Topics: Adult; Age Factors; Aged; Bacteriological Techniques; Base Sequence; Biopsy; Colitis, Ulcerative; DNA, Bacterial; Desulfovibrio; Feces; Female; Humans; Intestinal Mucosa; Male; Middle Aged; Molecular Sequence Data; Polymerase Chain Reaction; RNA, Bacterial; RNA, Ribosomal, 16S; Rectum; Sequence Alignment
PubMed: 15016746
DOI: 10.1136/gut.2003.031245 -
Scientific Reports Nov 2017The sulfate reducing bacterium Desulfovibrio desulfuricans inhabits both the human gut and external environments. It can reduce nitrate and nitrite as alternative...
The sulfate reducing bacterium Desulfovibrio desulfuricans inhabits both the human gut and external environments. It can reduce nitrate and nitrite as alternative electron acceptors to sulfate to support growth. Like other sulphate reducing bacteria, it can also protect itself against nitrosative stress caused by NO generated when nitrite accumulates. By combining in vitro experiments with bioinformatic and RNA-seq data, metabolic responses to nitrate or NO and how nitrate and nitrite reduction are coordinated with the response to nitrosative stress were revealed. Although nitrate and nitrite reduction are tightly regulated in response to substrate availability, the global responses to nitrate or NO were largely regulated independently. Multiple NADH dehydrogenases, transcription factors of unknown function and genes for iron uptake were differentially expressed in response to electron acceptor availability or nitrosative stress. Amongst many fascinating problems for future research, the data revealed a YtfE orthologue, Ddes_1165, that is implicated in the repair of nitrosative damage. The combined data suggest that three transcription factors coordinate this regulation in which NrfS-NrfR coordinates nitrate and nitrite reduction to minimize toxicity due to nitrite accumulation, HcpR1 serves a global role in regulating the response to nitrate, and HcpR2 regulates the response to nitrosative stress.
Topics: Desulfovibrio desulfuricans; Gene Expression Regulation, Bacterial; Nitrates; Nitric Oxide; Nitrites; Nitrosative Stress; Transcriptome
PubMed: 29176637
DOI: 10.1038/s41598-017-16403-4 -
Journal of the American Chemical Society May 2012When enzymes are optimized for biotechnological purposes, the goal often is to increase stability or catalytic efficiency. However, many enzymes reversibly convert their...
When enzymes are optimized for biotechnological purposes, the goal often is to increase stability or catalytic efficiency. However, many enzymes reversibly convert their substrate and product, and if one is interested in catalysis in only one direction, it may be necessary to prevent the reverse reaction. In other cases, reversibility may be advantageous because only an enzyme that can operate in both directions can turnover at a high rate even under conditions of low thermodynamic driving force. Therefore, understanding the basic mechanisms of reversibility in complex enzymes should help the rational engineering of these proteins. Here, we focus on NiFe hydrogenase, an enzyme that catalyzes H(2) oxidation and production, and we elucidate the mechanism that governs the catalytic bias (the ratio of maximal rates in the two directions). Unexpectedly, we found that this bias is not mainly determined by redox properties of the active site, but rather by steps which occur on sites of the proteins that are remote from the active site. We evidence a novel strategy for tuning the catalytic bias of an oxidoreductase, which consists in modulating the rate of a step that is limiting only in one direction of the reaction, without modifying the properties of the active site.
Topics: Catalytic Domain; Desulfovibrio; Hydrogenase; Models, Molecular; Mutation; Oxidation-Reduction; Thermodynamics
PubMed: 22540997
DOI: 10.1021/ja301802r -
Acta Crystallographica. Section F,... May 2024Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO to formate, with biotechnological...
Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO to formate, with biotechnological applications envisaged in climate-change mitigation. The role of Met405 in the active site of Desulfovibrio vulgaris formate dehydrogenase AB (DvFdhAB) has remained elusive. However, its proximity to the metal site and the conformational change that it undergoes between the resting and active forms suggests a functional role. In this work, the M405S variant was engineered, which allowed the active-site geometry in the absence of methionine S interactions with the metal site to be revealed and the role of Met405 in catalysis to be probed. This variant displayed reduced activity in both formate oxidation and CO reduction, together with an increased sensitivity to oxygen inactivation.
Topics: Desulfovibrio vulgaris; Formate Dehydrogenases; Catalytic Domain; Crystallography, X-Ray; Oxidation-Reduction; Models, Molecular; Formates; Carbon Dioxide; Bacterial Proteins
PubMed: 38699971
DOI: 10.1107/S2053230X24003911 -
Journal of Bacteriology Dec 1961Peck, H. D., Jr. (Oak Ridge National Laboratory, Oak Ridge, Tenn.). Enzymatic basis for assimilatory and dissimilatory sulfate reduction. J. Bacteriol. 82: 933-939....
Peck, H. D., Jr. (Oak Ridge National Laboratory, Oak Ridge, Tenn.). Enzymatic basis for assimilatory and dissimilatory sulfate reduction. J. Bacteriol. 82: 933-939. 1961.-Two pathways for the reduction of sulfate to sulfite in bacteria have been previously described. The substrate for sulfate reduction by extracts of yeast is 3'-phosphoadenosine-5'-phosphosulfate (PAPS) and, in contrast, the substrate for sulfate reduction in extracts of Desulfovibrio desulfuricans is adenosine-5'-phosphosulfate (APS). The enzymes catalyzing these reductions have been termed PAPS-reductase and APS-reductase, respectively. Since yeasts are "assimilatory sulfate reducers", i.e., reduce only enough sulfate to satisfy nutritional requirements for sulfur, and D. desulfuricans is a "dissimilatory sulfate reducer", i.e., utilizes sulfate as its terminal electron acceptor in anaerobic respiration, the pathway of sulfate reduction was determined in 25 microorganisms to ascertain whether there is a correlation between the pathway of sulfate reduction and the physiological role of sulfate in the metabolism of bacteria. Assimilatory sulfate reducers reduced sulfate in the form of PAPS, and, with one exception, APS-reductase was found only in dissimilatory sulfate reducers. APS-reductase was also found in the Thiobacilli in high specific activity and is involved in the oxidation of reduced sulfur compounds to sulfate.
Topics: Bacteria; Desulfovibrio desulfuricans; Oxidation-Reduction; Oxidoreductases; Oxidoreductases Acting on Sulfur Group Donors; Sulfates; Sulfur
PubMed: 14484818
DOI: 10.1128/jb.82.6.933-939.1961 -
Applied and Environmental Microbiology Jul 2003The toxicity of Al to Desulfovibrio desulfuricans G20 was assessed over a period of 8 weeks in a modified lactate C medium buffered at four initial pHs (5.0, 6.5, 7.2,...
The toxicity of Al to Desulfovibrio desulfuricans G20 was assessed over a period of 8 weeks in a modified lactate C medium buffered at four initial pHs (5.0, 6.5, 7.2, and 8.3) and treated with five levels of added Al (0, 0.01, 0.1, 1.0, and 10 mM). At pH 5, cell population densities decreased significantly and any effect of Al was negligible compared to that of the pH. At pHs 6.5 and 7.2, the cell population densities increased by 30-fold during the first few days and then remained stable for soluble-Al concentrations of <5 x 10(-5) M. In treatments having total-Al concentrations of > or =1 mM, soluble-Al concentrations exceeded 5 x 10(-5) M and limited cell population growth substantially and proportionally. At pH 8.3, soluble-Al concentrations were below the 5 x 10(-5) M toxicity threshold and cell population density increases of 20- to 40-fold were observed. An apparent cell population response to added Al at pH 8.3 was attributed to the presence of large, spirilloidal bacteria (accounting for as much as 80% of the cells at the 10 mM added Al level). Calculations of soluble-Al speciation for the pH 6.5 and 7.2 treatments that showed Al toxicity suggested the possible presence of the Al(13)O(4)(OH)(24)(H(2)O)(12)(7+) "tridecamer" cation and an inverse correlation of the tridecamer concentration and the cell population density. Analysis by (27)Al nuclear magnetic resonance spectroscopy, however, yielded no evidence of this species in freshly prepared samples or those taken 800 days after inoculation. Exclusion of the tridecamer species from the aqueous speciation calculations at pHs 6.5 and 7.2 yielded inverse correlations of the neutral Al(OH)(3) and anionic Al(OH)(4)(-) monomeric species with cell population density, suggesting that one or both of these ions bear primary responsibility for the toxicity observed.
Topics: Aluminum; Colony Count, Microbial; Desulfovibrio; Hydrogen-Ion Concentration; Solubility; Solutions
PubMed: 12839782
DOI: 10.1128/AEM.69.7.4057-4066.2003 -
Journal of Proteome Research Dec 2012Cell membranes represent the "front line" of cellular defense and the interface between a cell and its environment. To determine the range of proteins and protein...
Cell membranes represent the "front line" of cellular defense and the interface between a cell and its environment. To determine the range of proteins and protein complexes that are present in the cell membranes of a target organism, we have utilized a "tagless" process for the system-wide isolation and identification of native membrane protein complexes. As an initial subject for study, we have chosen the Gram-negative sulfate-reducing bacterium Desulfovibrio vulgaris. With this tagless methodology, we have identified about two-thirds of the outer membrane- associated proteins anticipated. Approximately three-fourths of these appear to form homomeric complexes. Statistical and machine-learning methods used to analyze data compiled over multiple experiments revealed networks of additional protein-protein interactions providing insight into heteromeric contacts made between proteins across this region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be essential for the detection and characterization of environment-driven changes in the outer membrane proteome and in the modeling of stress response pathways. The workflow utilized here should be effective for the global characterization of membrane protein complexes in a wide range of organisms.
Topics: Bacterial Outer Membrane Proteins; Cell Membrane; Chromatography, Ion Exchange; Desulfovibrio vulgaris; Detergents; Electrophoresis, Polyacrylamide Gel; Escherichia coli; High-Throughput Screening Assays; Mass Spectrometry; Membrane Proteins; Molecular Weight; Multiprotein Complexes; Periplasm; Protein Interaction Mapping; Protein Interaction Maps; Proteome; Proteomics; Sequence Homology, Amino Acid; Solubility
PubMed: 23098413
DOI: 10.1021/pr300548d