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microbial community succession during lactate amendment and electron-acceptor limitation reveals a predominance of metal-reducing pelosinus spp.determining the success of in-situ bioremediation strategies is complex. by using controlled laboratory conditions, the influence of individual variables such as u(vi), cr(vi) and electron donor and acceptors on community structure, dynamics, and the metal-reducing potential can be studied. triplicate anaerobic, continuous-flow reactors were inoculated with cr(vi) contaminated groundwater from the hanford, washington 100-h area, amended with lactate and incubated for 95 days to obtain stable, en ...201222267668
using gas chromatography/isotope ratio mass spectrometry to determine the fractionation factor for h(2) production by hydrogenases.hydrogenases catalyze the reversible formation of h(2), and they are key enzymes in the biological cycling of h(2). h isotopes have the potential to be a very useful tool in quantifying hydrogen ion trafficking in biological h(2) production processes, but there are several obstacles that have thus far limited the application of this tool. here, we describe a new method that overcomes some of these barriers and is specifically designed to measure isotopic fractionation during enzyme-catalyzed h(2 ...201222215579
Lactobacillus salivarius REN counteracted unfavorable 4-nitroquinoline-1-oxide-induced changes in colonic microflora of rats.Probiotics and carcinogens both have a significant effect on the microfloral composition of the human intestine. The objective of this study was to investigate the impact of an important carcinogen, 4-Nitroquinoline-1-Oxide on colonic microflora and the efficacy of the probiotic Lactobacillus salivarius REN as an agent of counteracting these effects. Using denaturing gradient gel electrophoresis (DGGE) combined with redundancy analysis, we demonstrated that both 4-Nitroquinoline-1-Oxide and L. s ...201122203549
Microbiology of regressive autism.This manuscript summarizes some of our earlier work on the microbiology of autism subjects' stool specimens, as compared with stools from control subjects. Our most recent data indicating that Desulfovibrio may play an important role in regressive autism is also presented. In addition, we present information on antimicrobial susceptibility patterns of Desulfovibrio using the CLSI agar dilution susceptibility technique. In addition, we summarize data from our earlier studies showing the impact of ...201122202440
identifying fermenting bacteria in anoxic tidal-flat sediments by a combination of microcalorimetry and ribosome-based stable-isotope probing.a novel approach was developed to follow the successive utilization of organic carbon under anoxic conditions by microcalorimetry, chemical analyses of fermentation products and stable-isotope probing (sip). the fermentation of (13) c-labeled glucose was monitored over 4 weeks by microcalorimetry in a stimulation experiment with tidal-flat sediments. based on characteristic heat production phases, time points were selected for quantifying fermentation products and identifying substrate-assimilat ...201122188432
comparative 16s rrna gene surveys of granular sludge from three upflow anaerobic bioreactors treating purified terephthalic acid (pta) wastewater.the microbial communities from three upflow anaerobic bioreactors treating purified terephthalic acid (pta) wastewater were characterized with 16s ribosomal rna gene sequencing surveys. universal bacterial and archaeal primers were used to compare the bioreactor communities to each other. a total of 1,733 bacterial sequences and 383 archaeal sequences were characterized. the high number of syntrophus spp. and pelotomaculum spp. found within these reactors indicates efficient removal of benzoate ...201122179636
functional characterization of crp/fnr-type global transcriptional regulators in desulfovibrio vulgaris hildenborough.crp/fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. however, little is known about the function of four annotated crp/fnr homologs (dvu0379, dvu2097, dvu2547 and dvu3111) in desulfovibrio vulgaris hildenborough. a systematic study using bioinformatic, transcriptomic, genetic and physiological approaches was conducted to characterize their roles in stress responses. similar growth phenotypes we ...201122156435
comparative electrochemical study of superoxide reductases.superoxide reductases are involved in relevant biological electron transfer reactions related to protection against oxidative stress caused by reactive oxygen species. the electrochemical features of metalloproteins belonging to the three different classes of enzymes were studied by potentio-dynamic techniques (cyclic and square wave voltammetry): desulfoferrodoxin from desulfovibrio vulgaris hildenborough, class i superoxide reductases and neelaredoxin from desulfovibrio gigas and treponema pal ...201122143105
Efficacy of natural biocide on control of microbial induced corrosion in oil pipelines mediated by Desulfovibrio vulgaris and Desulfovibrio gigas.We compared the efficacy of a natural biocide with four chemical tetrakishydroxymethyl phosphonium sulfonate, benzyl trimethyl ammonium chloride, and formaldehyde, glutaraldehyde, to control microbial induced corrosion in oil pipelines. The efficacy of biocides were monitored against Desulfovibrio vulgaris and Desulfovibrio gigas in experimental pipes by measuring cell counts, H2S production, Fe(II) production, production of extracellular polymeric substances and structure of biofilm. The treatm ...201122128548
structural and mechanistic insights into an unusual thiol disulfide oxidoreductase.cytoplasmic desulfothioredoxin (dtrx) from the anaerobe desulfovibrio vulgaris hildenborough has been identified as a new member of the thiol disulfide oxidoreductase family. the active site of dtrx contains a particular consensus sequence, cphc, never seen in the cytoplasmic thioredoxins and generally found in periplasmic oxidases. unlike canonical thioredoxins (trx), dtrx does not present any disulfide reductase activity but it presents instead an unusual disulfide isomerase activity. we have ...201122128175
Characterization of the bacterial community composition in a hypoxic zone induced by Microcystis blooms in Lake Taihu, China.Cyanobacterial blooms have become more frequent as a result of eutrophication in lakes. The accumulation and breakdown of huge cyanobacterial biomasses often cause hypoxia in lakes. However, little is known about microbial diversity in these areas. In this study, we characterized the bacterial community composition of a Microcystis-bloom-induced hypoxic area in Lake Taihu, which is a large, shallow lake, by analysing terminal restriction fragment length polymorphisms of 16S ribosomal RNA genes a ...201122126440
Abundance, Diversity and Activity of Sulfate-Reducing Prokaryotes in Heavy Metal-Contaminated Sediment from a Salt Marsh in the Medway Estuary (UK).We investigated the diversity and activity of sulfate-reducing prokaryotes (SRP) in a 3.5-m sediment core taken from a heavy metal-contaminated site in the Medway Estuary, UK. The abundance of SRPs was quantified by qPCR of the dissimilatory sulfite reductase gene ß-subunit (dsrB) and taking into account DNA extraction efficiency. This showed that SRPs were abundant throughout the core with maximum values in the top 50 cm of the sediment core making up 22.4% of the total bacterial community and ...201122124626
The importance of the protein framework for the catalytic activity of [FeFe]-hydrogenases.The active center (H-cluster) of [FeFe]-hydrogenases is embedded into a hydrophobic pocket within the protein. We have analyzed several amino acids, located in the vicinity of this niche, by site-directed mutagenesis of the [FeFe]-hydrogenases from Clostridium pasteurianum (CpI) and Chlamydomonas reinhardtii (CrHydA1). These amino acids are highly conserved and predicted to be involved in H-cluster coordination. Characterization of two hydrogenase variants confirmed this hypo-thesis. The exchang ...201122110126
Desulfovibrio desulfuricans Bacteremia in an Immunocompromised Host with a Liver Graft and Ulcerative Colitis.Desulfovibrio spp. are anaerobic, sulfate-reducing, nonfermenting, Gram-negative bacteria found in the digestive tract of humans. Identification of these species with conventional methods is difficult. The reported case of a Desulfovibrio desulfuricans bacteremia occurring in an immunocompromised host with ulcerative colitis confirms that this organism may be a possible opportunistic human pathogen.201222075582
microbial reduction of structural iron in interstratified illite-smectite minerals by a sulfate-reducing bacterium.clay minerals are ubiquitous in soils, sediments, and sedimentary rocks and could coexist with sulfate-reducing bacteria (srb) in anoxic environments, however, the interactions of clay minerals and srb are not well understood. the objective of this study was to understand the reduction rate and capacity of structural fe(iii) in dioctahedral clay minerals by a mesophilic srb, desulfovibrio vulgaris and the potential role in catalyzing smectite illitization. bioreduction experiments were performed ...201122074236
Genome sequence of Desulfovibrio sp. A2, a highly copper resistant, sulfate-reducing bacterium isolated from effluents of a zinc smelter at the Urals.Desulfovibrio sp. A2 is an anaerobic gram-negative sulfate-reducing bacterium with remarkable tolerance to copper. It was isolated from wastewater effluents of a zinc smelter at the Urals. Here, we report the 4.2-Mb draft genome sequence of Desulfovibrio sp. A2 and identify potential copper resistance mechanisms.201122072648
Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase.Membrane-bound respiratory [NiFe]-hydrogenase (MBH), a H(2)-uptake enzyme found in the periplasmic space of bacteria, catalyses the oxidation of dihydrogen: H(2)???2H(+)?+?2e(-) (ref. 1). In contrast to the well-studied O(2)-sensitive [NiFe]-hydrogenases (referred to as the standard enzymes), MBH has an O(2)-tolerant H(2) oxidation activity; however, the mechanism of O(2) tolerance is unclear. Here we report the crystal structures of Hydrogenovibrio marinus MBH in three different redox condition ...201122002607
systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium.abstract: background: two component regulatory systems are the primary form of signal transduction in bacteria. although genomic binding sites have been determined for several eukaryotic and bacterial transcription factors, comprehensive identification of gene targets of two component response regulators remains challenging due to the lack of knowledge of the signals required for their activation. we focused our study on desulfovibrio vulgaris hildenborough, a sulfate reducing bacterium that en ...201121992415
analysis of the microbial community of the biocathode of a hydrogen-producing microbial electrolysis cell.the microbial electrolysis cell (mec) is a promising system for hydrogen production. still, expensive catalysts such as platinum are needed for efficient hydrogen evolution at the cathode. recently, the possibility to use a biocathode as an alternative for platinum was shown. the microorganisms involved in hydrogen evolution in such systems are not yet identified. we analyzed the microbial community of a mixed culture biocathode that was enriched in an mec bioanode. this biocathode produced 1.1 ...201121983651
gd(iii) chelates as nmr probes of protein-protein interactions. case study: rubredoxin and cytochrome c3.two cyclen-derived gd probes, [gd-dotam](3+) and [gd-dotp](5-) (dotam = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetamide; dotp = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis(methylenephosphonate)), were assessed as paramagnetic relaxation enhancement (pre)-inducing probes for characterization of protein-protein interactions. two proteins, desulfovibrio gigas rubredoxin and desulfovibrio gigas cytochrome c(3), were used as model partners. in a (1)h nmr titration it was shown that [gd-do ...201121957905
mechanistic and physiological implications of the interplay among iron-sulfur clusters in [fefe]-hydrogenases. a qm/mm perspective.key stereoelectronic properties of desulfovibrio desulfuricans [fefe]-hydrogenase (ddh) were investigated by quantum mechanical description of its complete inorganic core, which includes a fe(6)s(6) active site (the h-cluster), as well as two ancillary fe(4)s(4) assemblies (the f and f' clusters). the partially oxidized, active-ready form of ddh is able to efficiently bind dihydrogen, thus starting h(2) oxidation catalysis. the calculations allow us to unambiguously assign a mixed fe(ii)fe(i) st ...201121942468
characterization of microbial communities during anode biofilm reformation in a two-chambered microbial electrolysis cell (mec).geochip (ii) and single strand conformation polymorphism (sscp) were used to characterize anode microbial communities of a microbial electrolysis cell (mec). biofilm communities, enriched in a two-chamber mec (r1, 0.6v applied) having a coulombic efficiency (ce) of 35±4% and a hydrogen yield [formula: see text] of 31±3%, were used as the inoculum for a new reactor (r2). after three months r2 achieved stable performance with ce=38±4% and [formula: see text] few changes in the predominant populati ...201121939699
on the relationship between sialomucin and sulfomucin expression and hydrogenotrophic microbes in the human colonic mucosa.the colonic mucus layer is comprised primarily of acidomucins, which provide viscous properties and can be broadly classified into sialomucins or sulfomucins based on the presence of terminating sialic acid or sulfate groups. differences in acidomucin chemotypes have been observed in diseases such as colorectal cancer and inflammatory bowel disease, and variation in sialo- and sulfomucin content may influence microbial colonization. for example, sulfate derived from sulfomucin degradation may pr ...201121931721
Degradation of cyanobacterial biomass in anoxic tidal-flat sediments: a microcosm study of metabolic processes and community changes.To follow the anaerobic degradation of organic matter in tidal-flat sediments, a stimulation experiment with (13)C-labeled Spirulina biomass (130?mg per 21?g sediment slurry) was conducted over a period of 24 days. A combination of microcalorimetry to record process kinetics, chemical analyses of fermentation products and RNA-based stable-isotope probing (SIP) to follow community changes was applied. Different degradation phases could be identified by microcalorimetry: Within 2 days, heat output ...201121918576
Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome.The ability to conduct advanced functional genomic studies of the thousands of sequenced bacteria has been hampered by the lack of available tools for making high-throughput chromosomal manipulations in a systematic manner that can be applied across diverse species. In this work, we highlight the use of synthetic biological tools to assemble custom suicide vectors with reusable and interchangeable DNA "parts" to facilitate chromosomal modification at designated loci. These constructs enable an a ...201121908633
oxygen exposure increases resistance of desulfovibrio vulgaris hildenborough to killing by hydrogen peroxide.inactivation of perr by oxidative stress and a corresponding increase in expression of the perr regulon genes is part of the oxidative stress defense in a variety of anaerobic bacteria. diluted anaerobic, nearly sulfide-free cultures of mutant and wild-type desulfovibrio vulgaris (10(5)-10(6) colony-forming units/ml) were treated with 0 to 2,500 μm h(2)o(2) for only 5 min to prevent readjustment of gene expression. survivors were then scored by plating. the wild type and perr mutant had 50% surv ...201121894573
Structural reorganization renders enhanced metalloprotein stability.The enhanced stability of a mesophilic metalloprotein was assessed using biophysical spectroscopies. Significant local structural interconversions during thermal insult account for a reorganization of the protein scaffold, without disturbing the active metal site. This cushioning mechanism is proposed to be a generic property of metalloproteins contributing to enhanced stability.201121894348
sustainable syntrophic growth of dehalococcoides ethenogenes strain 195 with desulfovibrio vulgaris hildenborough and methanobacterium congolense: global transcriptomic and proteomic analyses.dehalococcoides ethenogenes strain 195 (de195) was grown in a sustainable syntrophic association with desulfovibrio vulgaris hildenborough (dvh) as a co-culture, as well as with dvh and the hydrogenotrophic methanogen methanobacterium congolense (mc) as a tri-culture using lactate as the sole energy and carbon source. in the co- and tri-cultures, maximum dechlorination rates of de195 were enhanced by approximately three times (11.0±0.01 μmol per day for the co-culture and 10.1±0.3 μmol per day f ...201121881617
biogeochemical characteristics of kuan-tzu-ling, chung-lun and bao-lai hot springs in southern taiwan.hot springs are the important natural sources of geothermally heated groundwater from the earth's crust. kuan-tzu-ling (ktl), chung-lun (cl) and bao-lai (bl) are well-known hot springs in southern taiwan. fluid and mud (sediments) samples were collected from the eruption points of three hot springs for detailed biogeochemical characterization. the fluid sample displays relatively high concentrations of na(+) and cl(-) compared with k(+), mg(2+), ca(2+), no(2) (-), and so(4) (2-), suggesting a po ...201121879853
Desulfobaculum xiamenensis gen. nov., sp. nov., a member of the family Desulfovibrionaceae isolated from marine mangrove sediment.A taxonomic study was carried out on strain P1(T), which was isolated from mangrove sediment samples collected from Qinglan Port (Hainan, China). Cells were curved rods, motile with a single polar flagellum. The strain was non-spore-forming with cell size of 0.6 &times 1.5-2.2 µm. Catalase and oxidase activities were not detected. Growth was observed in the temperature range 22-44 °C (optimum 35-40 °C) and pH range 5.5-8.5 (optimum 7.0). NaCl was required for growth, and tolerated up to 3.5% (op ...201121873514
molecular analysis of the biomass of a fluidized bed reactor treating synthetic vinasse at anaerobic and micro-aerobic conditions.the microbial communities (bacteria and archaea) established in an anaerobic fluidized bed reactor used to treat synthetic vinasse (betaine, glucose, acetate, propionate, and butyrate) were characterized by denaturing gradient gel electrophoresis (dgge) and phylogenetic analysis. this study was focused on the competitive and syntrophic interactions between the different microbial groups at varying influent substrate to sulfate ratios of 8, 4, and 2 and anaerobic or micro-aerobic conditions. acet ...201121861082
complete debromination of tetra- and penta-brominated diphenyl ethers by a coculture consisting of dehalococcoides and desulfovibrio species.polybrominated diphenyl ethers (pbdes) are widespread global contaminants due to their extensive usage as flame retardants. among the 209 pbde congeners, tetra-brominated diphenyl ether (tetra-bde) (congener 47) and penta-bdes (congeners 99 and 100) are the most abundant, toxic, and bioaccumulative congeners in the environment. however, little is known about microorganisms that carry out debromination of these congeners under anaerobic conditions. in this study, we describe a coculture gy2 consi ...201121859110
evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough.we used high-resolution tiling microarrays and 5' rna sequencing to identify transcripts in desulfovibrio vulgaris hildenborough, a model sulfate-reducing bacterium. we identified the first nucleotide position for 1,124 transcripts, including 54 proteins with leaderless transcripts and another 72 genes for which a major transcript initiates within the upstream protein-coding gene, which confounds measurements of the upstream gene's expression. sequence analysis of these promoters showed that d. ...201121840973
structural insights into dissimilatory sulfite reductases: structure of desulforubidin from desulfomicrobium norvegicum.dissimilatory sulfite reductases (dsirs) are crucial enzymes in bacterial sulfur-based energy metabolism, which are likely to have been present in some of the earliest life forms on earth. several classes of dsirs have been proposed on the basis of different biochemical and spectroscopic properties, but it is not clear whether this corresponds to actual physiological or structural differences. here, we describe the first structure of a dsir from the desulforubidin class isolated from desulfomicr ...201121833321
development of a small-scale bioreactor method to monitor the molecular diversity and environmental impacts of bacterial biofilm communities from an acid mine drainage impacted creek.shamokin creek is a tributary of the susquehanna river in central pennsylvania that is heavily impacted by the acid mine drainage (amd) caused by the oxidation of pyrite from the region's extensive anthracite coal mining industry. recent studies have begun to characterize the microbial communities present in this and other amd-impacted waters, but varying environmental conditions have complicated attempts to determine the ecological impacts of individual bacterial species within these communitie ...201121821067
metabolism of h2 by desulfovibrio desulfuricans g20 during syntrophic growth on lactate.syntrophic growth involves the oxidation of organic compounds and subsequent transfer of electrons to a h2- or formate-consuming microorganism. in order to identify genes specifically involved in syntrophic growth, a mutant library of desulfovibrio desulfuricans g20 was screened for loss of the ability to grow syntrophically with methanospirillum hungatei. a collection of twenty mutants with an impaired ability to grow syntrophically was obtained. all twenty mutants grew in pure culture on lacta ...201121798981
diversity and composition of sulfate- and sulfite-reducing prokaryotes as affected by marine-freshwater gradient and sulfate availability.sulfate- and sulfite-reducing prokaryotes (ssrp) communities play a key role in both sulfur and carbon cycles. in estuarine ecosystems, sulfate concentrations change with tides and could be limited in tidal freshwater reach or deep sediments. in a subtropical estuary of northern taiwan in december 2007, we examined the compositional changes of ssrp communities. we examined three sites: from the lower estuarine brackish-water reach (site gr and mangrove vegetation site, gm) to the upper estuarine ...201121785985
marine microbial community response to inorganic and organic sediment amendments in laboratory mesocosms.sediment amendments provide promising strategies of enhancing sequestration of heavy metals and degradation of organic contaminants. the impacts of sediment amendments for metal and organic remediation including apatite, organoclay (and apatite and organoclay in geotextile mats), acetate, and chitin on environmental microbial communities in overlying water and sediment profiles are reported here. these experiments were performed concurrent with an ecotoxicity evaluation (data submitted in compan ...201121784523
[in process citation]. 201121774184
the mechanism of formate oxidation by metal-dependent formate dehydrogenases.metal-dependent formate dehydrogenases (fdh) from prokaryotic organisms are members of the dimethyl sulfoxide reductase family of mononuclear molybdenum-containing and tungsten-containing enzymes. fdhs catalyze the oxidation of the formate anion to carbon dioxide in a redox reaction that involves the transfer of two electrons from the substrate to the active site. the active site in the oxidized state comprises a hexacoordinated molybdenum or tungsten ion in a distorted trigonal prismatic geomet ...201121773834
bacterial growth phase influences methylmercury production by the sulfate-reducing bacterium desulfovibrio desulfuricans nd132.the effect of bacterial growth phase is an aspect of mercury (hg) methylation that previous studies have not investigated in detail. here we consider the effect of growth phase (mid-log, late-log and late stationary phase) on hg methylation by the known methylator desulfovibrio desulfuricans nd132. we tested the addition of hg alone (chloride-complex), hg with suwannee river natural organic matter (srnom) (unequilibrated), and hg equilibrated with srnom on monomethylmercury (mmhg) production by ...201121762955
x-ray crystal structure of arsenite-inhibited xanthine oxidase: µ-sulfido,µ-oxo double bridge between molybdenum and arsenic in the active site.xanthine oxidoreductase is a molybdenum-containing enzyme that catalyzes the hydroxylation reaction of sp(2)-hybridized carbon centers of a variety of substrates, including purines, aldehydes, and other heterocyclic compounds. the complex of arsenite-inhibited xanthine oxidase has been characterized previously by uv-vis, electron paramagnetic resonance, and x-ray absorption spectroscopy (xas), and the catalytically essential sulfido ligand of the square-pyrimidal molybdenum center has been sugge ...201121761899
microfluidic fluorescence in situ hybridization and flow cytometry (µflowfish).we describe an integrated microfluidic device (µflowfish) capable of performing 16s rrna fluorescence in situ hybridization (fish) followed by flow cytometric detection for identifying bacteria in natural microbial communities. the device was used for detection of species involved in bioremediation of cr(vi) and other metals in groundwater samples from a highly-contaminated environmental site (hanford, wa, usa). the µflowfish seamlessly integrates two components: a hybridization chamber formed b ...201121755095
abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon.hydrogenotrophic microbiota have a significant impact on colonic health; however, little is known about their diversity and ecology in situ. here, molecular-based methods and multivariate analyses were used to examine the abundance and diversity of mucosa-associated hydrogenotrophic microbes in 90 biopsies collected from right colon, left colon and rectum of 25 healthy subjects. functional genes of all three hydrogenotrophic groups were detected in at least one colonic region of all subjects. me ...201121753800
genetics and molecular biology of the electron flow for sulfate respiration in desulfovibrio.progress in the genetic manipulation of the desulfovibrio strains has provided an opportunity to explore electron flow pathways during sulfate respiration. most bacteria in this genus couple the oxidation of organic acids or ethanol with the reduction of sulfate, sulfite, or thiosulfate. both fermentation of pyruvate in the absence of an alternative terminal electron acceptor, disproportionation of fumarate and growth on h(2) with co(2) during sulfate reduction are exhibited by some strains. the ...201121747813
towards a rigorous network of protein-protein interactions of the model sulfate reducer desulfovibrio vulgaris hildenborough.protein-protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. the aforementioned tools have been extensively applied to study escherichia coli and other aerobes and more recently to study the stress response behavior of desulfovibrio vulgaris hildenborough, a model obligate anaerobe and sulfate reducer and the subject of this study. here we carried out affinity purification follow ...201121738675
oxygen reduction in the strict anaerobe desulfovibrio vulgaris hildenborough: characterization of two membrane-bound oxygen reductases.although desulfovibrio vulgaris hildenborough (dvh) is a strictly anaerobic bacterium, it is able to consume oxygen in different cellular compartments, including extensive periplasmic o(2) reduction with hydrogen as electron donor. the genome of dvh revealed the presence of cydab and cox genes, encoding a quinol oxidase bd and a cytochrome c oxidase, respectively. in the membranes of dvh, we detected both quinol oxygen reductase [inhibited by heptyl-hydroxyquinoline-n-oxide (hqno)] and cytochrom ...201121737501
combating bacterial colonization on metals via polymer coatings: relevance to marine and medical applications.metals are widely used in engineering as well as medical applications. however, their surfaces are easily colonized by bacteria that form biofilms. among the numerous concerns with biofilm formation, biocorrosion is of particular importance in industry, because structural integrity may be compromised, leading to technical failures. in the food industry and medical field, biofilms also pose health risks. to inhibit bacterial colonization, the surfaces of metals can be coated with a polymeric laye ...201121732600
large sulfur isotope fractionation does not require disproportionation.the composition of sulfur isotopes in sedimentary sulfides and sulfates traces the sulfur cycle throughout earth's history. in particular, depletions of sulfur-34 ((34)s) in sulfide relative to sulfate exceeding 47 per mil (ôç¦) often serve as a proxy for the disproportionation of intermediate sulfur species in addition to sulfate reduction. here, we demonstrate that a pure, actively growing culture of a marine sulfate-reducing bacterium can deplete (34)s by up to 66ôç¦ during sulfate reduction ...201121719675
[a case of desulfovibrio desulfuricans cultured from blood in japan].we report a case of desulfovibrio desulfuricans bacteremia in a 60-year-old-man. in our case, anaerobic blood culture bottle turned out positive after five days' incubation. gram stain showed the presence of slightly-curved gram negative rod. suspecting campylobacter and helicobacter, we added microaerobic culture while tentatively reporting campylobacter to the physician. we then added anaerobic culturing with brucella hk (rs) agar because microaerobic culture proved the absence of microaerophi ...201121706860
prediction and characterization of missing proteomic data in desulfovibrio vulgaris.proteomic datasets are often incomplete due to identification range and sensitivity issues. it becomes important to develop methodologies to estimate missing proteomic data, allowing better interpretation of proteomic datasets and metabolic mechanisms underlying complex biological systems. in this study, we applied an artificial neural network to approximate the relationships between cognate transcriptomic and proteomic datasets of desulfovibrio vulgaris, and to predict protein abundance for the ...201121687592
complete genome sequence and updated annotation of desulfovibrio alaskensis g20.desulfovibrio alaskensis g20 (formerly desulfovibrio desulfuricans g20) is a gram-negative mesophilic sulfate-reducing bacterium (srb), known to corrode ferrous metals and to reduce toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms. we present the 3.7-mb genome sequence to provide insights into its physiology.201121685289
new spectroscopic and electrochemical insights on a class i superoxide reductase: evidence for an intramolecular electron-transfer pathway.sors (superoxide reductases) are enzymes involved in bacterial resistance to reactive oxygen species, catalysing the reduction of superoxide anions to hydrogen peroxide. so far three structural classes have been identified. class i enzymes have two iron-centre-containing domains. most studies have focused on the catalytic iron site (centre ii), yet the role of centre i is poorly understood. the possible roles of this iron site were approached by an integrated study using both classical and fast ...201121682694
epr characterization of the new qrc complex from sulfate reducing bacteria and its ability to form a supercomplex with hydrogenase and tpic3.the quinone-reductase complex (qrc) is a respiratory complex with type i cytochrome c(3):menaquinone reductase activity, recently described in sulfate-reducing bacteria. qrc is related to the complex iron-sulfur molybdoenzyme family and to the alternative complex iii. in this work we report a detailed characterization of the redox properties of the metal cofactors of qrc using epr spectroscopy, which allowed the determination of the reduction potentials of five out of six hemes c, one [3fe-4s](1 ...201121651911
genome sequence of mercury-methylating and pleomorphic desulfovibrio africanus strain walvis bay.desulfovibrio africanus strain walvis bay is an anaerobic sulfate-reducing bacterium (srb) capable of producing methylmercury (mehg), a potent human neurotoxin. the mechanism of methylation by this and other organisms is unknown. we present the 4.2 mb genome sequence to provide further insight into microbial mercury methylation and sulfate-reducing bacteria.201121642452
[nife]- and [fes]-cofactors in the membrane-bound hydrogenase of ralstonia eutropha investigated by x-ray absorption spectroscopy: insights into o2-tolerant h2-cleavage.molecular features that enable certain [nife] hydrogenases to catalyze hydrogen (h2) conversion in the presence of dioxygen (o2) were investigated in the present study. by means of x-ray absorption spectroscopy (xas) we compared the [nife] active site and fes clusters in the o2-tolerant membrane-bound hydrogenase (mbh) of ralstonia eutropha and the o2-sensitive periplasmic hydrogenase (ph) of desulfovibrio gigas. fe-xas indicated an unusual complement of iron-sulfur centers in the mbh, likely ba ...201121618994
dynamic microbial response of sulfidogenic wastewater biofilm to nitrate.nitrate is one of the chemicals often added to wastewater to control hydrogen sulfide production by sulfate-reducing bacteria (srb). while the effect of nitrate in various srb pure cultures is well documented, the effect observed in mixed microbial communities is not consistent. this study investigates the response of mixed srb communities to nitrate, by examining the changes in activity and community composition of sulfidogenic wastewater biofilm over a 10-day period with 10 mmol l(-1) nitrate ...201121611797
use of immunomagnetic separation for the detection of desulfovibrio vulgaris from environmental samples.immunomagnetic separation (ims) has proved highly efficient for recovering microorganisms from heterogeneous samples. current investigation targeted the separation of viable cells of the sulfate-reducing bacterium, desulfovibrio vulgaris. streptavidin-coupled paramagnetic beads and biotin labeled antibodies raised against surface antigens of this microorganism were used to capture d. vulgaris cells in both bioreactor grown laboratory samples and from extremely low-biomass environmental soil and ...201121605602
methods for engineering sulfate reducing bacteria of the genus desulfovibrio.sulfate reducing bacteria (srb) are physiologically important given their nearly ubiquitous presence and have important applications in the areas of bioremediation and bioenergy. this chapter provides details on the steps used for homologous-recombination mediated chromosomal manipulation of desulfovibrio vulgaris hildenborough, a well-studied sulfate reducer. more specifically, we focus on the implementation of a "parts" based approach for suicide vector assembly, important aspects of anaerobic ...201121601101
structural redox control in a 7fe ferredoxin isolated from desulfovibrio alaskensis.the redox behaviour of a ferredoxin (fd) from desulfovibrio alaskensis was characterized by electrochemistry. the protein was isolated and purified, and showed to be a tetramer containing one [3fe-4s] and one [4fe-4s] centre. this ferredoxin has high homology with fdi from desulfovibrio vulgaris miyazaki and hildenborough and fdiii from desulfovibrio africanus. from differential pulse voltammetry the following signals were identified: [3fe-4s](+1/0) (e(0')=-158±5mv); [4fe-4s](+2/+1) (e(0')=-474± ...201121600857
[regulation of sulfates, hydrogen sulfide and heavy metals level in technogenic reservoirs by sulfate-reducing bacteria].sulfate-reducing bacteria desulfovibrio desulfuricans ya-11 in the presence of sulfates and organic compounds in the medium reduce sulfates to hydrogen sulfide (dissimilatory sulfate reduction). heavy metals in concentration over 2 mm inhibit this process. pb2+, zn2+, ni2+, co2+, fe2+ and cd2+ ions in concentration 1-1.5 mm display insignificant inhibiting effect on sulfate reduction process, and metals precipitate in the form of sulfides. at concentrations of heavy metals 2-3 mm one can observe ...201121598657
predicting a human gut microbiota's response to diet in gnotobiotic mice.the interrelationships between our diets and the structure and operations of our gut microbial communities are poorly understood. a model community of ten sequenced human gut bacteria was introduced into gnotobiotic mice, and changes in species abundance and microbial gene expression were measured in response to randomized perturbations of four defined ingredients in the host diet. from the responses, we developed a statistical model that predicted over 60% of the variation in species abundance ...201121596954
desulfovibrio species are potentially important in regressive autism.autism is a complex disorder with no specific diagnostic test so the disease is defined by its characteristics including cognitive defects, social, communication and behavioral problems, repetitive behaviors, unusual sensitivity to stimuli such as noise, restricted interests, and self stimulation. the incidence of this disease has increased remarkably in recent years and was 110/10,000 children (∼1%) in multiple areas of the us in 2007. the financial burden on families and communities is enormou ...201121592674
how sulphate-reducing microorganisms cope with stress: lessons from systems biology.sulphate-reducing microorganisms (srms) are a phylogenetically diverse group of anaerobes encompassing distinct physiologies with a broad ecological distribution. as srms have important roles in the biogeochemical cycling of carbon, nitrogen, sulphur and various metals, an understanding of how these organisms respond to environmental stresses is of fundamental and practical importance. in this review, we highlight recent applications of systems biology tools in studying the stress responses of s ...201121572460
active transport, substrate specificity, and methylation of hg(ii) in anaerobic bacteria.the formation of methylmercury (mehg), which is biomagnified in aquatic food chains and poses a risk to human health, is effected by some iron- and sulfate-reducing bacteria (ferb and srb) in anaerobic environments. however, very little is known regarding the mechanism of uptake of inorganic hg by these organisms, in part because of the inherent difficulty in measuring the intracellular hg concentration. by using the ferb geobacter sulfurreducens and the srb desulfovibrio desulfuricans nd132 as ...201121555571
correlations of fecal bacterial communities with age and living region for the elderly living in bama, guangxi, china.bama county (guangxi, china) is famous for its longevous population. in this study, intestinal microflora of 17 healthy elderly subjects of different ages and from different regions (rural and urban) in bama, were analyzed by denaturing gradient gel electrophoresis (dgge). significant effects of age and living region on the whole intestinal bacterial communities were observed by redundancy analysis (rda). a total of 11 bacterial strains that were correlated with age and living region were identi ...201121538237
the anaerobe-specific orp complex of desulfovibrio vulgaris hildenborough is encoded by two divergent operons co-regulated by {sigma}54 and a cognate transcriptional regulator.analysis of sequenced bacterial genomes revealed that genomes encode more than 30 % of hypothetical and conserved hypothetical proteins of unknown function. among proteins of unknown function that are conserved in anaerobes, some might be determinant in the anaerobic way of life. this study focuses on two divergent clusters specifically found in anaerobic microorganisms and mainly composed of genes encoding conserved hypothetical proteins. we show that the two gene clusters dvu2103-dvu2104-dvu21 ...201121531797
crystal structure and spectroscopic studies of a stable mixed-valent state of the hemerythrin-like domain of a bacterial chemotaxis protein.the bacterial chemotaxis protein of desulfovibrio vulgaris dcrh (dcrh-hr) functions as an o(2)-sensing protein. this protein has a hemerythrin-like domain that includes a nonheme diiron center analogous to the diiron center of the hemerythrin (hr) family. interestingly, the o(2) affinity of dcrh-hr is 3.3 × 10(6) m(-1), a value 25-fold higher than that of the pectinaria gouldii hr. this high affinity arises from the fast association of the o(2) ligand with dcrh-hr (k(on) = 5.3 × 10(8) m(-1) s(-1 ...201121528842
state of the art; microbiology in health and disease. intestinal bacterial flora in autism.autism of the regressive variety is selected as an example of the importance of intestinal bacterial microflora in disease other than classical infection. our studies have indicated that intestinal bacteria play a role in this disease since it responds to oral vancomycin, a drug that is not absorbed from the gi tract. pyrosequencing studies document an abnormal gut microflora in regressive autism subjects as compared to controls. finally, we present preliminary evidence suggesting that desulfovi ...201121524713
the sulfate-reducing bacterium desulfovibrio desulfuricans nd132 as a model for understanding bacterial mercury methylation.we propose the use of desulfovibrio desulfuricans nd132 as a model species for understanding the mechanism of microbial hg methylation. strain nd132 is an anaerobic dissimilatory sulfate-reducing bacterium (dsrb), isolated from estuarine mid-chesapeake bay sediments. it was chosen for study because of its exceptionally high rates of hg methylation in culture and its metabolic similarity to the lost strain d. desulfuricans ls, the only organism for which methylation pathways have been partially d ...201121515733
tungsten and molybdenum regulation of formate dehydrogenase expression in desulfovibrio vulgaris hildenborough.formate is an important energy substrate for sulfate-reducing bacteria in natural environments, and both molybdenum- and tungsten-containing formate dehydrogenases have been reported in these organisms. in this work, we studied the effect of both metals on the levels of the three formate dehydrogenases encoded in the genome of desulfovibrio vulgaris hildenborough, with lactate, formate, or hydrogen as electron donors. using western blot analysis, quantitative real-time pcr, activity-stained gels ...201121498650
oriented immobilization of a membrane-bound hydrogenase onto an electrode for direct electron transfer.the interaction of redox enzymes with electrodes is of great interest for studying the catalytic mechanisms of redox enzymes and for bioelectronic applications. efficient electron transport between the biocatalysts and the electrodes has achieved more success with soluble enzymes than with membrane enzymes because of the higher structural complexity and instability of the latter proteins. in this work, we report a strategy for immobilizing a membrane-bound enzyme onto gold electrodes with a cont ...201121491850
culturable diversity of lithotrophic haloalkaliphilic sulfate-reducing bacteria in soda lakes and the description of desulfonatronum thioautotrophicum sp. nov., desulfonatronum thiosulfatophilum sp. nov., desulfonatronovibrio thiodismutans sp. nov., and desulfonatronovibrio magnus sp. nov.soda lake sediments usually contain high concentrations of sulfide indicating active sulfate reduction. monitoring of sulfate-reducing bacteria (srb) in soda lakes demonstrated a dominance of two groups of culturable srb belonging to the order desulfovibrionales specialized in utilization of inorganic electron donors, such as formate, h(2) and thiosulfate. the most interesting physiological trait of the novel haloalkaliphilic srb isolates was their ability to grow lithotrophically by dismutation ...201121479878
effects of molybdate and tungstate on expression levels and biochemical characteristics of formate dehydrogenases produced by desulfovibrio alaskensis ncimb 13491.formate dehydrogenases (fdhs) are enzymes that catalyze the formate oxidation to carbon dioxide and that contain either mo or w in a mononuclear form in the active site. in the present work, the influence of mo and w salts on the production of fdh by desulfovibrio alaskensis ncimb 13491 was studied. two different fdhs, one containing w (w-fdh) and a second incorporating either mo or w (mo/w-fdh), were purified. both enzymes were isolated from cells grown in a medium supplemented with 1 μm molybd ...201121478344
overestimation of the abundance of sulfate-reducing bacteria in human feces by quantitative pcr targeting the desulfovibrio 16s rrna gene.the dominant genus of sulfate-reducing bacteria (srb) in humans is desulfovibrio, and quantitative pcr (qpcr) targeting the 16s rrna gene is often used in assays. we show that the 16s rrna gene assay overestimated srb abundance in feces from 24 adults compared to qpcr assays using primers targeting two genes involved in srb energy metabolism.201121460115
targeting intermediates of [fefe]-hydrogenase by co and cn vibrational signatures.in this work, we employ density functional theory to assign vibrational signatures of [fefe]-hydrogenase intermediates to molecular structures. for this purpose, we perform an exhaustive analysis of structures and harmonic vibrations of a series of cn and co containing model clusters of the [fefe]-hydrogenase enzyme active site considering also different charges, counterions, and solvents. the pure density functional bp86 in combination with a triple-? polarized basis set produce reliable molecu ...201121443182
[role of exopolymeric substances of corrosion-aggressive bacteria in the biofilm formation on the steel surface].it had been done the comparative study of the exopolymeric substances (eps) synthesized by the sulfidogenic microbial community and monocultures of desulfovibrio sp. 10, bacillus subtilis 36 and pseudomonas aeruginosa 27 under various growth models as biofilm and plankton was performed. it was established that biofilm-produced exopolymers contained increased amount of glucose and fucose, while planktonic ones had more amount of mannose and rhamnose. the amount of rhamnose was 24% of the total am ...201121442946
the crystal structure of cupriavidus necator nitrate reductase in oxidized and partially reduced states.the periplasmic nitrate reductase (napab) from cupriavidus necator is a heterodimeric protein that belongs to the dimethyl sulfoxide reductase family of mononuclear mo-containing enzymes and catalyzes the reduction of nitrate to nitrite. the protein comprises a large catalytic subunit (napa, 91 kda) containing the molybdenum active site plus one [4fe-4s] cluster, as well as a small subunit (napb, 17 kda), which is a diheme c-type cytochrome involved in electron transfer. crystals of the oxidized ...201121419779
a microscopic model for gas diffusion dynamics in a [nife]-hydrogenase.we describe and apply a microscopic model for the calculation of gas diffusion rates in a [nife]-hydrogenase. this enzyme has attracted much interest for use as a h(2) oxidising catalyst in biofuel cells, but a major problem is their inhibition by co and o(2). in our model, the diffusive hopping of gas molecules in the protein interior is coarse grained using a master equation approach with transition rates estimated from equilibrium and non-equilibrium pulling simulations. propagating the rate ...201121409188
oxygen uptake rates in the hyperthermophilic anaerobe thermotoga maritima grown in a bioreactor under controlled oxygen exposure: clues to its defence strategy against oxidative stress.a 2.3-l bioreactor was specially adapted to grow hyperthermophilic microorganisms under controlled conditions of temperature, ph, redox potential and dissolved o(2). using this bioreactor regulated at 80-¦c and ph 7.0, we demonstrated that thermotoga maritima recovered its growth despite being exposed to oxygen for a short time (30-ámin with a maximum concentration of 23-á++m of dissolved oxygen). under these conditions, we demonstrated that o(2) uptake rate, estimated at 73.6-á++moles o(2)-ámin ...201121400100
strategy for microbiome analysis using 16s rrna gene sequence analysis on the illumina sequencing platform.understanding the identity and changes of organisms in the urogenital and other microbiomes of the human body may be key to discovering causes and new treatments of many ailments, such as vaginosis. high-throughput sequencing technologies have recently enabled discovery of the great diversity of the human microbiome. the cost per base of many of these sequencing platforms remains high (thousands of dollars per sample); however, the illumina genome analyzer (iga) is estimated to have a cost per b ...201121361774
genome sequence of the mercury-methylating strain desulfovibrio desulfuricans nd132.desulfovibrio desulfuricans strain nd132 is an anaerobic sulfate-reducing bacterium (srb) capable of producing methylmercury (mehg), a potent human neurotoxin. the mechanism of methylation by this and other organisms is unknown. we present the 3.8-mb genome sequence to provide further insight into microbial mercury methylation.201121357488
enzyme-based amperometric platform to determine the polymorphic response in drug metabolism by cytochromes p450."personalized medicine" is a new concept in health care, one aspect of which defines the specificity and dosage of drugs according to effectiveness and safety for each patient. dosage strongly depends from the rate of metabolism which is primarily regulated by the activity of cytochrome p450. in addition to the need for a genetic characterization of the patients, there is also the necessity to determine the drug-clearance properties of the polymorphic p450 enzyme. to address this issue, human p4 ...201121348440
simultaneous analyses of photoinduced electron transfer in the wild type and four single substitution isomers of the fmn binding protein from desulfovibrio vulgaris, miyazaki f.the mechanism of photoinduced electron transfer (pet) from the aromatic amino acids (trp32, tyr35 and trp106) to the excited flavin mononucleotide (fmn) in the wild type (wt) and four single amino acid substitution isomers (e13t, e13q, w32a and w32y) of fmn binding protein (fbp) from the desulfovibrio vulgaris (miyazaki f) were simultaneously analyzed (method a) with the marcus-hush (mh) theory and kakitani-mataga (km) theory using ultrafast fluorescence dynamics of these proteins. in addition, ...201121347481
local magnetism in palladium bionanomaterials probed by muon spectroscopy.palladium bionanomaterial was manufactured using the sulfate-reducing bacterium, desulfovibrio desulfuricansm, to reduce soluble pd(ii) ions to cell-bound pd(0) in the presence of hydrogen. the biomaterial was examined using a superconducting quantum interference device (squid) to measure bulk magnetisation and by muon spin rotation spectroscopy (µsr) which is uniquely able to probe the local magnetic environment inside the sample. results showed behaviour attributable to interaction of muons bo ...201121331587
communication: accurate determination of side-chain torsion angle ?1 in proteins: phenylalanine residues.quantitative side-chain torsion angle ?(1) determinations of phenylalanine residues in desulfovibrio vulgaris flavodoxin are carried out using exclusively the correlation between the experimental vicinal coupling constants and theoretically determined karplus equations. karplus coefficients for nine vicinal coupling related with the torsion angle ?(1) were calculated using the b3lyp functional and basis sets of different size. optimized ?(1) angles are in outstanding agreement with those previou ...201121322654
desulfovibrio arcticus sp. nov., a psychrotolerant sulfate-reducing bacterium from a cryopeg of the varandey peninsula.a psychrotolerant mesophilic sulfate-reducing bacterium, strain b15(t), was isolated from the supercooled water brine in the permafrost on the varandey peninsula (the coast of barents sea). the cells of strain b15(t) were gram-negative motile vibrions (3-4 × 0.4-0.5 µm) with a single polar flagellum. they were positive for desulfoviridin as a bisulfite reductase. strain b15(t) grew at temperatures of -2-28°c (optimum 24°c) and at salinity of 0-2.0% (optimum 0.2%). the strain was able to use hydr ...201121317277
a bacterial consortium isolated from an icelandic fumarole displays exceptionally high levels of sulfate reduction and metals resistance.the soils of three fumaroles and one mining site, all with high metal content, were surveyed for the presence of metal-resistant sulfate-reducing bacteria and their potential application in the bioremediation of acid mine drainages. by means of selective soil enrichments a bacterial consortium was isolated from an icelandic fumarole that displayed very high sulfate reduction in the presence of a mixture of 0.75 g/l of fe, 0.20 g/l of zn and 0.080 g/l of cu. under these conditions the bacterial c ...201121296493
on understanding proton transfer to the biocatalytic [fe-fe](h) sub-cluster in [fe-fe]h(2)ases: qm/mm md simulations.proton transfer to the [fe-fe](h) sub-cluster in the desulfovibrio desulfuricans (ddh) and clostridium pasteurianum (cpi) [fe-fe] hydrogenases was investigated by a combination of first principles and empirical molecular dynamics simulations. pathways that can be inferred from the x-ray crystal structures of ddh and cpi, i.e., (glu159?ser198?glu156?water460?cys178?dtma([fe-fe](h)) and (glu282?ser319?glu279?water612?cys299), respectively, were considered. proton transfer from cys178 to dtma in th ...201121296047
(1)h, (13)c and (15)n chemical shift assignments of the thioredoxin from the obligate anaerobe desulfovibrio vulgaris hildenborough.thioredoxins are ubiquitous key antioxidant enzymes which play an essential role in cell defense against oxidative stress. they maintain the redox homeostasis owing to the regulation of thiol-disulfide exchange. in the present paper, we report the full resonance assignments of (1)h, (13)c and (15)n atoms for the reduced and oxidized forms of desulfovibrio vulgaris hildenborough thioredoxin 1 (trx1). 2d and 3d heteronuclear nmr experiments were performed using uniformly (15)n-, (13)c-labelled trx ...201121287302
isocyanide in biochemistry? a theoretical investigation of the electronic effects and energetics of cyanide ligand protonation in [fefe]-hydrogenases.the presence of fe-bound cyanide ligands in the active site of the proton-reducing enzymes [fefe]-hydrogenases has led to the hypothesis that such brønsted-lowry bases could be protonated during the catalytic cycle, thus implying that hydrogen isocyanide (hnc) might have a relevant role in such crucial microbial metabolic paths. we present a hybrid quantum mechanical/molecular mechanical (qm/mm) study of the energetics of cn(-) protonation in the enzyme, and of the effects that cyanide protonati ...201121274947
an hcpr homologue from desulfovibrio desulfuricans and its possible role in nitrate reduction and nitrosative stress.the escherichia coli crp (camp receptor protein), is a global regulator of transcription that modulates gene expression by activation or repression at a range of promoters in e. coli. a major function is to regulate the selection of nutrients required for growth. the anaerobic sulfate-reducing bacterium desulfovibrio desulfuricans atcc27774 is capable of utilizing sulfate, nitrite and nitrate as terminal electron acceptors. in the presence of both sulfate and nitrate, sulfate is reduced preferen ...201121265778
quantitative evaluation of transcriptional activation of nf-κb p65 and p50 subunits and iκbα encoding genes in colon cancer cells by desulfovibrio desulfuricans endotoxin.quantification of p65, p50 and iκbα mrnas was performed by real time qrt-pcr in caco-2 cells treated with 10, 50, and 100 μg/ml of desulfovibrio desulfuricans lps for 1, 6, 12, and 24 h. a strong increase in expression of p65 and iλbα genes was induced by 10 and 100 μg/ml of lps at 1 h; after 6 h higher transcript amounts of both genes were observed at 100 μg/ml lps. the p65 expression level was significantly increased by 50 and 100 μg/ml at 12 h and lowered by all lps doses at 24 h. no signific ...201021253915
[desulfovibrio fairfieldensis bacteremia associated with acute sigmoiditis]. 201121208758
formaldehyde--a rapid and reversible inhibitor of hydrogen production by [fefe]-hydrogenases.dihydrogen (h(2)) production by [fefe]-hydrogenases is strongly inhibited by formaldehyde (methanal) in a reaction that is rapid, reversible, and specific to this type of hydrogenase. this discovery, using three [fefe]-hydrogenases that are homologous about the active site but otherwise structurally distinct, was made by protein film electrochemistry, which measures the activity (as electrical current) of enzymes immobilized on an electrode; importantly, the inhibitor can be removed after additi ...201121204519
study of the thiol/disulfide redox systems of the anaerobe desulfovibrio vulgaris points out pyruvate:ferredoxin oxidoreductase as a new target for thioredoxin 1.sulfate reducers have developed a multifaceted adaptative strategy to survive against oxidative stresses. along with this oxidative stress response, we recently characterized an elegant reversible disulfide bond-dependent protective mechanism in the pyruvate:ferredoxin oxidoreductase (pfor) of various desulfovibrio species. here, we searched for thiol redox systems involved in this mechanism. using thiol fluorescent labeling, we show that glutathione is not the major thiol/disulfide balance-cont ...201121199874
original design of an oxygen-tolerant [nife] hydrogenase: major effect of a valine-to-cysteine mutation near the active site.hydrogenases are efficient biological catalysts of h(2) oxidation and production. most of them are inhibited by o(2), and a prerequisite for their use in biotechnological applications under air is to improve their oxygen tolerance. we have previously shown that exchanging the residue at position 74 in the large subunit of the oxygen-sensitive [nife] hydrogenase from desulfovibrio fructosovorans could impact the reaction of the enzyme with o(2) (dementin, s.; j. am. chem. soc. 2009, 131, 10156-10 ...201021175174
macromolecular crowding tunes folding landscape of parallel α/β protein, apoflavodoxin.proteins normally fold in crowded cellular environments. here we use a set of desulfovibrio desulfuricans apoflavodoxin variants to assess--with residue-specific resolution--how apoflavodoxin's folding landscape is tuned by macromolecular crowding. we find that, under crowded conditions, initial topological frustration is reduced, subsequent folding requires less ordering in the transition state, and β-strand 1 becomes more important in guiding the process. we propose that conditions more closel ...201021175168
evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization.the class ii chelatases associated with heme, siroheme, and cobalamin biosynthesis are structurally related enzymes that insert a specific metal ion (fe(2+) or co(2+)) into the center of a modified tetrapyrrole (protoporphyrin or sirohydrochlorin). the structures of two related class ii enzymes, cbix(s) from archaeoglobus fulgidus and cbik from salmonella enterica, that are responsible for the insertion of cobalt along the cobalamin biosynthesis pathway are presented in complex with their metall ...201021173279
nitrite reduction by xanthine oxidase family enzymes: a new class of nitrite reductases.mammalian xanthine oxidase (xo) and desulfovibrio gigas aldehyde oxidoreductase (aor) are members of the xo family of mononuclear molybdoenzymes that catalyse the oxidative hydroxylation of a wide range of aldehydes and heterocyclic compounds. much less known is the xo ability to catalyse the nitrite reduction to nitric oxide radical (no). to assess the competence of other xo family enzymes to catalyse the nitrite reduction and to shed some light onto the molecular mechanism of this reaction, we ...201021170563
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