Publications

characterisation of the 11 kb dna region adjacent to the gene encoding desulfovibrio gigas flavoredoxin.	flavoredoxin is an fmn binding protein that functions as an electron carrier in the sulphate metabolism of desulfovibrio gigas. the neighbouring dna regions of the gene encoding flavoredoxin were sequenced and characterised. transcript analysis of the flavoredoxin gene resulted in a positive band corresponding to the size of the coding region, suggesting that flavoredoxin is encoded by a monocystronic unit, as previously suggested by sequence analysis. analysis of the adjacent dna regions reveal ...	2005	16147877
hydrogenases in desulfovibrio vulgaris hildenborough: structural and physiologic characterisation of the membrane-bound [nifese] hydrogenase.	the genome of desulfovibrio vulgaris hildenborough (dvh) encodes for six hydrogenases (hases), making it an interesting organism to study the role of these proteins in sulphate respiration. in this work we address the role of the [nifese] hase, found to be the major hase associated with the cytoplasmic membrane. the purified enzyme displays interesting catalytic properties, such as a very high h(2) production activity, which is dependent on the presence of phospholipids or detergent, and resista ...	2005	16187073
study of the spin-spin interactions between the metal centers of desulfovibrio gigas aldehyde oxidoreductase: identification of the reducible sites of the [2fe-2s]1+,2+ clusters.	the aldehyde oxidoreductase from desulfovibrio gigas belongs to the family of molybdenum hydroxylases. besides a molybdenum cofactor which constitutes their active site, these enzymes contain two [2fe-2s](2+,1+) clusters which are believed to transfer the electrons provided by the substrate to an acceptor which is either a fad group or an electron-transferring protein. when the three metal centers of d. gigas aor are simultaneously paramagnetic, splittings due to intercenter spin-spin interactio ...	2005	16114900
gene expression analysis of the mechanism of inhibition of desulfovibrio vulgaris hildenborough by nitrate-reducing, sulfide-oxidizing bacteria.	sulfate-reducing bacteria (srb) are inhibited by nitrate-reducing, sulfide-oxidizing bacteria (nr-sob) in the presence of nitrate. this inhibition has been attributed either to an increase in redox potential or to production of nitrite by the nr-sob. nitrite specifically inhibits the final step in the sulfate reduction pathway. when the nr-sob thiomicrospira sp. strain cvo was added to mid-log phase cultures of the srb desulfovibrio vulgaris hildenborough in the presence of nitrate, sulfate redu ...	2005	16104868
deletion of flavoredoxin gene in desulfovibrio gigas reveals its participation in thiosulfate reduction.	the gene encoding desulfovibrio gigas flavoredoxin was deleted to elucidate its physiological role in the sulfate metabolism. disruption of flr gene strongly inhibited the reduction of thiosulfate and exhibited a reduced growth in the presence of sulfite with lactate as electron donor. the growth with sulfate was not however affected by the lack of this protein. additionally, flr mutant cells revealed a decrease of about 50% in the h2 consumption rate using thiosulfate as electron acceptor. alto ...	2005	16099456
cadmium accumulation and dna homology with metal resistance genes in sulfate-reducing bacteria.	cadmium resistance (0.1 to 1.0 mm) was studied in four pure and one mixed culture of sulfate-reducing bacteria (srb). the growth of the bacteria was monitored with respect to carbon source (lactate) oxidation and sulfate reduction in the presence of various concentrations of cadmium chloride. two strains desulfovibrio desulfuricans dsm 1926 and desulfococcus multivorans dsm 2059 showed the highest resistance to cadmium (0.5 mm). transmission electron microscopy of the two strains showed intracel ...	2005	16085855
structure and topology of microbial communities in the major gut compartments of melolontha melolontha larvae (coleoptera: scarabaeidae).	physicochemical gut conditions and the composition and topology of the intestinal microbiota in the major gut compartments of the root-feeding larva of the european cockchafer (melolontha melolontha) were studied. axial and radial profiles of ph, o2, h2, and redox potential were measured with microsensors. terminal restriction fragment length polymorphism (t-rflp) analysis of bacterial 16s rrna genes in midgut samples of individual larvae revealed a simple but variable and probably nonspecific c ...	2005	16085849
horizontal transfer of two operons coding for hydrogenases between bacteria and archaea.	using a phylogenetic approach, we discovered three putative horizontal transfers between bacterial and archaeal species involving large clusters of genes. one transfer involves an operon of 13 genes, called mbx, which probably was transferred into the genome of thermotoga maritima from a species belonging or close to the pyrococcus genus. the two others implied an operon of six genes, called ech, transferred independently to the genomes of thermoanaerobacter tengcongensis and desulfovibrio gigas ...	2005	15983865
effects of oxygen exposure on respiratory activities of desulfovibrio desulfuricans strain dvo1 isolated from activated sludge.	the present study addresses the effects of oxygen exposure on the aerobic and anaerobic respiratory activity of desulfovibrio desulfuricans strain dvo1. this strain was isolated from the highest sulfate-reduction positive most-probable-number dilution (10(6)) of an activated sludge sample, which had been subjected to 120 h of continuous aeration. washed cell suspensions of strain dvo1 were aerated at 50% atmospheric oxygen saturation in sulfide-free media for a period of 33 h in the presence or ...	2005	16329947
characterisation of intestinal bacteria in infant stools using real-time pcr and northern hybridisation analyses.	real-time pcr and northern hybridisations were used to quantify bacterial populations in the large gut of infants. pcr primers for rapid, sensitive, high throughput detection of bifidobacteria, bacteroides, sulphate-reducing bacteria and enterococcus faecalis, based on analysis of 16s rrna genes were used. bacterial populations were analysed in faeces from 40 infants aged 0-6, 7-12 and 13-24 months. the effects of breast versus bottle feeding was also investigated. real-time pcr indicated that b ...	2005	16329974
aerobic organic carbon mineralization by sulfate-reducing bacteria in the oxygen-saturated photic zone of a hypersaline microbial mat.	the sulfate-reducing bacterium strain srb d2 isolated from the photic zone of a hypersaline microbial mat, from lake chiprana, ne spain, respired pyruvate, alanine, and alpha-ketoglutarate but not formate, lactate, malate, succinate, and serine at significant rates under fully oxic conditions. dehydrogenase enzymes of only the former substrates are likely oxygen-tolerant as all substrates supported anaerobic sulfate reduction. no indications were found, however, that aerobic respiration supporte ...	2005	15965719
nitrate reduction by desulfovibrio desulfuricans: a periplasmic nitrate reductase system that lacks napb, but includes a unique tetraheme c-type cytochrome, napm.	many sulphate reducing bacteria can also reduce nitrite, but relatively few isolates are known to reduce nitrate. although nitrate reductase genes are absent from desulfovibrio vulgaris strain hildenborough, for which the complete genome sequence has been reported, a single subunit periplasmic nitrate reductase, napa, was purified from desulfovibrio desulfuricans strain 27774, and the structural gene was cloned and sequenced. chromosome walking methods have now been used to determine the complet ...	2005	15972253
multi-heme cytochromes--new structures, new chemistry.	heme is one of the most pervasive cofactors in nature and the c-type cytochromes represent one of the largest families of heme-containing proteins. recent progress in bacterial genomic analysis has revealed a vast range of genes encoding novel c-type cytochromes that contain multiple numbers of heme cofactors. the genome sequence of geobacter sulfurreducens, for example, includes some one hundred genes encoding c-type cytochromes, with around seventy of these containing two, or more, heme groups ...	2005	16234915
the type i/type ii cytochrome c3 complex: an electron transfer link in the hydrogen-sulfate reduction pathway.	in desulfovibrio metabolism, periplasmic hydrogen oxidation is coupled to cytoplasmic sulfate reduction via transmembrane electron transfer complexes. type ii tetraheme cytochrome c3 (tpii-c3), nine-heme cytochrome c (9hca) and 16-heme cytochrome c (hmca) are periplasmic proteins associated to these membrane-bound redox complexes and exhibit analogous physiological function. type i tetraheme cytochrome c3 (tpi-c3) is thought to act as a mediator for electron transfer from hydrogenase to these mu ...	2005	16226767
[sulfate-reducing bacteria in gypsum karst lakes of northern lithuania].	microbiological studies were performed in three small gypsum karst lakes in northern lithuania, most typical of the region. samples were taken in different seasons of 2001. the conditions for microbial growth in the lakes are determined by elevated content of salts (from 0.5 to 2.0 g/l), dominated by so(2-)4 and ca2+ ions (up to 1.4 and 0.6 g/l, respectively). the elevated sulfate concentration is favorable for sulfate-reducing bacteria (srbs). summer and winter stratification gives rise to anae ...	2005	16400994
a method adapting microarray technology for signature-tagged mutagenesis of desulfovibrio desulfuricans g20 and shewanella oneidensis mr-1 in anaerobic sediment survival experiments.	signature-tagged mutagenesis (stm) is a powerful technique that can be used to identify genes expressed by bacteria during exposure to conditions in their natural environments. to date, there have been no reports of studies in which this approach was used to study organisms of environmental, rather than pathogenic, significance. we used a mini-tn10 transposon-bearing plasmid, pbsl180, that efficiently and randomly mutagenized desulfovibrio desulfuricans g20 in addition to shewanella oneidensis m ...	2005	16269742
electrochemical definitions of o2 sensitivity and oxidative inactivation in hydrogenases.	a new strategy is described for comparing, quantitatively, the ability of hydrogenases to tolerate exposure to o2 and anoxic oxidizing conditions. using protein film voltammetry, the inherent sensitivities to these challenges (thermodynamic potentials and rates of reactions) have been measured for enzymes from a range of mesophilic microorganisms. in the absence of o2, all the hydrogenases undergo reversible inactivation at various potentials above that of the h+/h2 redox couple, and h2 oxidatio ...	2005	16366571
desulfovibrio aerotolerans sp. nov., an oxygen tolerant sulphate-reducing bacterium isolated from activated sludge.	a new mesophilic sulphate-reducing bacterium, designated strain dvo5(t) (t=type strain), was isolated from the outermost sulphate reduction-positive most-probable-number tube (10(-6) dilution) of an activated sludge sample, which had been oxygenated at 100% air saturation for 120 h. the motile, gram-negative, curved 1 by 2-5 microm and non-spore-forming cells of strain dvo5(t) existed singly or in chains. strain dvo5(t) grew optimally at 29 degrees c, ph 6.9 and 0.05% (w/v) nacl in a medium cont ...	2005	16701597
ftir-spectroscopic studies of the fine structure of nitrocellulose treated by desulfovibrio desulfuricans.	most studies have concluded that nitrocellulose (nc) with high degree of nitrogen content is resistant to biodegradation. our results demonstrated that nc (>11%n) does undergo biotransformation in the presence of sulfate-reducing bacteria desulfovibrio desulfuricans 1388. ftir analyses indicated that the substitution of nitro groups for oh(-) groups took place. the spectrum of precipitate obtained after acetone extraction of nc resembled mainly the spectrum of native cellulose. thus the syntheti ...	2005	16701591
carbon monoxide inhibits superoxide dismutase and stimulates reactive oxygen species production by desulfovibrio desulfuricans 1388.	the hypothesis that oxidative stress characterized by enhanced superoxide generation underlies the toxicity of some factors to living organisms has been investigated. it is shown that co (5-6% in gas phase) changed some growth parameters (mu, t(d)) of the sulfate-reducing bacterium desulfovibrio desulfuricans 1388. enhanced o(2)(-) generation registered by epr spectroscopy and adrenochrome method was observed when cells were incubated under co. the sod activity in cells from the exponential grow ...	2005	16701596
activation process of [nife] hydrogenase elucidated by high-resolution x-ray analyses: conversion of the ready to the unready state.	hydrogenases catalyze oxidoreduction of molecular hydrogen and have potential applications for utilizing dihydrogen as an energy source. [nife] hydrogenase has two different oxidized states, ni-a (unready, exhibits a lag phase in reductive activation) and ni-b (ready). we have succeeded in converting ni-b to ni-a with the use of na2s and o2 and determining the high-resolution crystal structures of both states. ni-b possesses a monatomic nonprotein bridging ligand at the ni-fe active site, wherea ...	2005	16271886
role of the tetrahemic subunit in desulfovibrio vulgaris hildenborough formate dehydrogenase.	in the anaerobic sulfate-reducing bacterium desulfovibrio vulgaris hildenborough (dvh), the genome sequencing revealed the presence of three operons encoding formate dehydrogenases. fdh1 encodes an alphabetagamma trimeric enzyme containing 11 heme binding sites; fdh2 corresponds to an alphabetagamma trimeric enzyme with a tetrahemic subunit; fdh3 encodes an alphabeta dimeric enzyme. in the present work, spectroscopic measurements demonstrated that the reduction of cytochrome c(553) was obtained ...	2005	16274230
the influence of nickel on the adhesion ability of desulfovibrio desulfuricans.	the build-up of biofilms on metals surfaces may lead to severe corrosion, especially in the presence of sulphate-reducing bacteria (srb). to prevent the deterioration of material caused by biofilms it is necessary to understand the processes governing biofilm development including mechanisms of cell adhesion. additionally, corrosion of metallic surfaces due to bacteria may lead to the dissolution of metallic elements that may further affect adhesion and biofilm development. a study was carried o ...	2005	16290113
chemical activity of iron in [2fe-2s]-protein centers and fes2(100) surfaces.	iron atoms bonded to sulfur play an important role in proteins, heterogeneous catalysts, and gas sensors. first-principles density functional calculations were used to investigate the structure and chemical activity of a unique [2fe-2s] center in the split-soret cytochrome c (ssc) from desulfovibrio desulfuricans. in agreement with a previously proposed structural model [abreu et al., j. biol. inorg. chem. 2003, 8, 360], it is found that the [2fe-2s] cluster is located in a surface pocket of the ...	2005	16851284
[detection of srps in injection water of shenli oil field by fish].	fluorescence in situ hybridization (fish) with 16s rrna-targeted oligonucleotide probes was applied for analyzing the structure of sulfate reducing prokaryotes (srps) community in injection water of shengli oil field. eight probes and their various combinations were used to detect srps in the water. results showed srps detected in the water were diverse, which followed in 4 bacterial phyla and 1 archaeal phylum. total amount of srps was 2.86 x 10(4) cells/ml, accounting for 20% of total cells of ...	2006	16850843
succinate dehydrogenase functioning by a reverse redox loop mechanism and fumarate reductase in sulphate-reducing bacteria.	sulphate- or sulphur-reducing bacteria with known or draft genome sequences (desulfovibrio vulgaris, desulfovibrio desulfuricans g20, desulfobacterium autotrophicum [draft], desulfotalea psychrophila and geobacter sulfurreducens) all contain sdhcab or frdcab gene clusters encoding succinate : quinone oxidoreductases. frdd or sdhd genes are missing. the presence and function of succinate dehydrogenase versus fumarate reductase was studied. desulfovibrio desulfuricans (strain essex 6) grew by fuma ...	2006	16849807
the adaptive genome of desulfovibrio vulgaris hildenborough.	peculiar attributes revealed by sequencing the genome of desulfovibrio vulgaris hildenborough are analyzed, particularly in relation to the presence of a phosphotransferase system (pts). the pts is a typical bacterial carbohydrate transport system functioning via group translocation. novel avenues for investigations are proposed emphasizing the metabolic diversity of d. vulgaris hildenborough, especially the likely utilization of mannose-type sugars. comparative analysis with pts from other gram ...	2006	16842335
photoinduced hydrogen production by direct electron transfer from photosystem i cross-linked with cytochrome c3 to [nife]-hydrogenase.	the photosynthetic reaction center is an efficient molecular device for the conversion of light energy to chemical energy. in a previous study, we synthesized the hydrogenase/photosystem i (psi) complex, in which ralstonia hydrogenase was linked to the cytoplasmic side of synechocystis psi, to modify psi so that it photoproduced molecular hydrogen (h2). in that study, hydrogenase was fused with a psi subunit, psae, and the resulting hydrogenase-psae fusion protein was self-assembled with psae-fr ...	2006	16836469
correlation between mrna and protein abundance in desulfovibrio vulgaris: a multiple regression to identify sources of variations.	parallel profiling of mrna and protein on a global scale and integrative analysis of these two data types could provide additional insights into the metabolic mechanisms underlying complex biological systems. however, because mrna and protein abundance are affected by many cellular and physical processes, there have been conflicting results on their correlation. using whole-genome microarray and lc-ms/ms proteomic data collected from desulfovibrio vulgaris grown under three different conditions, ...	2006	16310166
the active site of the [fefe]-hydrogenase from desulfovibrio desulfuricans. ii. redox properties, light sensitivity and co-ligand exchange as observed by infrared spectroscopy.	in [fefe]-hydrogenases, the h cluster (hydrogen-activating cluster) contains a di-iron centre ([2fe]h subcluster, a (l)(co)(cn)fe(mu-rs2)(mu-co)fe(cyss)(co)(cn) group) covalently attached to a cubane iron-sulphur cluster ([4fe-4s]h subcluster). the cys-thiol functions as the link between one iron (called fe1) of the [2fe]h subcluster and one iron of the cubane subcluster. the other iron in the [2fe]h subcluster is called fe2. the light sensitivity of the desulfovibrio desulfuricans enzyme in a v ...	2006	16323019
direct force measurement of bacteria adhesion on metal in aqueous media.	the adhesion of bacteria on metal surfaces in aqueous media and the development of biofilm and resultant biofouling are important phenomena in both the natural environment and engineering systems. this work reports on the use of a force microscopy technique to measure bacterial metal adhesion by two anaerobic sulphate-reducing bacteria (desulfovibrio desulfuricans and a local marine isolate) and an aerobe (pseudomonas sp.). using a modified bacteria tip, the atomic force microscope was able to q ...	2006	17163038
[microbial community structure in different wastewater treatment processes characterized by single-strand-conformation polymorphism (sscp) technique].	in order to investigate microbial community structures in different wastewater treatment processes and understand the relationship between the structures and the status of processes, the microbial community diversity, variety and distribution in five wastewater treatment processes were studied by a culture-independent genetic fingerprinting technique single-strand-conformation polymorphism (sscp). the five processes included a denitrification and phosphorus removal bioreactor (n), chinese tradit ...	2006	16881324
superoxide reduction mechanism of archaeoglobus fulgidus one-iron superoxide reductase.	superoxide reductases (sors), iron-centered enzymes responsible for reducing superoxide (o2(-)) to hydrogen peroxide, are found in many anaerobic and microaerophilic prokaryotes. the rapid reaction with an exogenous electron donor renders the reductase activity catalytic. here, we demonstrate using pulse radiolysis that the initial reaction between o2(-) and archaeoglobus fulgidus neelaredoxin, a one-iron sor, leads to a short-lived transient that immediately disappears to yield a solvent-bound ...	2006	16866373
isolation of sulfate-reducing bacteria from tunisian marine sediments and description of desulfovibrio bizertensis sp. nov.	several strains of sulfate-reducing bacteria were isolated from marine sediments recovered near tunis, korbous and bizerte, tunisia. they all showed characteristics consistent with members of the genus desulfovibrio. one of these strains, designated mb3(t), was characterized further. cells of strain mb3(t) were slender, curved, vibrio-shaped, motile, gram-negative, non-spore-forming rods. they were positive for desulfoviridin as bisulfite reductase. strain mb3(t) grew at temperatures of 15-45 de ...	2006	17158997
reclassification of the sulfate- and nitrate-reducing bacterium desulfovibrio vulgaris subsp. oxamicus as desulfovibrio oxamicus sp. nov., comb. nov.	desulfovibrio vulgaris subsp. oxamicus (type strain, dsm 1925(t)) was found to use nitrate as a terminal electron acceptor, the latter being reduced to ammonium. phylogenetic studies indicated that strain dsm 1925(t) was distantly related to the type strain of desulfovibrio vulgaris (95.4 % similarity of the small-subunit rrna gene) and had as its closest phylogenetic relatives two other nitrate- and sulfate-reducing bacteria, namely desulfovibrio termitidis (99.4 % similarity) and desulfovibrio ...	2006	16825618
a proteomic view of desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry.	direct lc-ms/ms was used to examine the proteins extracted from exponential or stationary phase desulfovibrio vulgaris cells that had been grown on a minimal medium containing either lactate or formate as the primary carbon source. across all four growth conditions, 976 gene products were identified with high confidence, which is equal to approximately 28% of all predicted proteins in the d. vulgaris genome. bioinformatic analysis showed that the proteins identified were distributed among almost ...	2006	16819729
biosynthesis of hopanoids by sulfate-reducing bacteria (genus desulfovibrio).	sulfate reduction accounts for about a half of the remineralization of organic carbon in anoxic marine shelf regions. moreover, it was already a major microbial process in the very early ocean at least 2.4 billion years before the present. here we demonstrate for the first time the capability of sulfate-reducing bacteria (srb) to biosynthesize hopanoids, compounds that are quantitatively important and widely distributed biomarkers in recent and fossil sediments dating back to the late archean. w ...	2006	16817930
a humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism.	our colons harbor trillions of microbes including a prominent archaeon, methanobrevibacter smithii. to examine the contributions of archaea to digestive health, we colonized germ-free mice with bacteroides thetaiotaomicron, an adaptive bacterial forager of the polysaccharides that we consume, with or without m. smithii or the sulfate-reducing bacterium desulfovibrio piger. whole-genome transcriptional profiling of b. thetaiotaomicron, combined with mass spectrometry, revealed that, unlike d. pig ...	2006	16782812
study of nitrate stress in desulfovibrio vulgaris hildenborough using itraq proteomics.	the response of desulfovibrio vulgaris hildenborough (dvh), a sulphate-reducing bacterium, to nitrate stress was examined using quantitative proteomic analysis. dvh was stressed with 105 mm sodium nitrate (nano(3)), a level that caused a 50% inhibition in growth. the protein profile of stressed cells was compared with that of cells grown in the absence of nitrate using the itraq peptide labelling strategy and tandem liquid chromatography separation coupled with mass spectrometry (quadrupole time ...	2006	16772278
epr and redox properties of periplasmic nitrate reductase from desulfovibrio desulfuricans atcc 27774.	nitrate reductases are enzymes that catalyze the conversion of nitrate to nitrite. we report here electron paramagnetic resonance (epr) studies in the periplasmic nitrate reductase isolated from the sulfate-reducing bacteria desulfovibrio desulfuricans atcc 27774. this protein, belonging to the dimethyl sulfoxide reductase family of mononuclear mo-containing enzymes, comprises a single 80-kda subunit and contains a mo bis(molybdopterin guanosine dinucleotide) cofactor and a [4fe-4s] cluster. epr ...	2006	16791644
characterization of bacterial community associated to biofilms of corroded oil pipelines from the southeast of mexico.	microbial communities associated to biofilms promote corrosion of oil pipelines. the community structure of bacteria in the biofilm formed in oil pipelines is the basic knowledge to understand the complexity and mechanisms of metal corrosion. to assess bacterial diversity, biofilm samples were obtained from x52 steel coupons corroded after 40 days of exposure to normal operation and flow conditions. the biofilm samples were directly used to extract metagenomic dna, which was used as template to ...	2006	16765858
rapid and reversible reactions of [nife]-hydrogenases with sulfide.	rapid and reversible binding of sulfide to [nife]-hydrogenases (particularly the enzyme from desulfovibrio vulgaris) under weakly acidic conditions (ph 6) has been studied by protein film voltammetry, which tracks the formation of different species as a function of potential. sulfide (most likely entering as h2s) rapidly attacks the active site during h2 oxidation. the inactive adduct is formed (and is stable) only at potentials substantially more positive than the comparable species formed with ...	2006	16756292
[sulfate-reducing bacteria in reservoirs of the yavoriv sulfur field].	fifteen cultures of bacteria which perform dissimilation sulfate reduction have been isolated from the reservoirs of the yavoriv sulfur deposit. electron-microscopic investigations have shown that the cells of all cultures are of vibroid, spiral and bacillary form. they form no spores. they grow in the medium with sulfates and lactates and do not use propionate and acetate. in the medium with lactate all the cultures accumulated acetate in the medium. cells of all the studied bacteria contain de ...	2006	17388124
redox chemistry of low-ph forms of tetrahemic cytochrome c3.	desulfovibrio vulgaris hildenborough cytochrome c(3) contains four hemes in a low-spin state with bis-histidinyl coordination. high-spin forms of cytochrome c(3) can be generated by protonation of the axial ligands in order to probe spin equilibrium (low-spin/high-spin). the spin alterations occurring at acid ph, the associated changes in redox potentials, as well as the reactivity towards external ligands were followed by the conjunction of square wave voltammetry and uv-visible, cd, nmr and ep ...	2006	17084898
sequential and structural analysis of [nife]-hydrogenase-maturation proteins from desulfovibrio vulgaris miyazaki f.	the complete primary structure of the hyn-region in the genome of desulfovibrio vulgaris miyazaki f (dvmf), encoding the [nife]-hydrogenase and two maturation proteins has been identified. besides the formerly reported genes for the large and small subunits, this region comprises genes encoding an endopeptidase (hync) and a putative chaperone (hynd). the complete genomic region covers 4086 nucleotides including the previously published upstream located promoter region and the sequences of the st ...	2006	16902753
a variant system i for cytochrome c biogenesis in archaea and some bacteria has a novel ccme and no ccmh.	c-type cytochromes are characterized by post-translational covalent attachment of heme to thiols that occur in a cys-xxx-xxx-cys-his motif. three distinct biogenesis systems are known for this heme attachment. archaea are now shown to contain a significantly modified form of cytochrome c maturation system i (the ccm system). the most notable adaptation relative to the well-studied apparatus from proteobacteria and plants is a novel form of the heme chaperone ccme, lacking the highly conserved hi ...	2006	16920107
the tmc complex from desulfovibrio vulgaris hildenborough is involved in transmembrane electron transfer from periplasmic hydrogen oxidation.	three membrane-bound redox complexes have been reported in desulfovibrio spp., whose genes are not found in the genomes of other sulfate reducers such as desulfotalea psycrophila and archaeoglobus fulgidus. these complexes contain a periplasmic cytochrome c subunit of the cytochrome c(3) family, and their presence in these organisms probably correlates with the presence of a pool of periplasmic cytochromes c(3), also absent in the two other sulfate reducers. in this work we report the isolation ...	2006	16922512
the role of the hybrid cluster protein in oxidative stress defense.	hybrid cluster proteins (hcp) contain two types of fe/s clusters, namely a [4fe-4s](2+/1+) or [2fe-2s](2+/1+) cluster and a novel type of hybrid cluster, [4fe-2s-2o], in the as-isolated state. although first isolated from anaerobic sulfate-reducing bacteria, the analysis of the genomic sequences reveals that genes encoding putative hybrid cluster proteins are present in a wide range of organisms, aerobic, anaerobic, or facultative, from the bacteria, archaea, and eukarya domains. despite a detai ...	2006	16928682
human inflammatory bowel disease does not associate with lawsonia intracellularis infection.	there is increasing evidence that bacterial infection of the intestinal mucosa may contribute to the pathogenesis of inflammatory bowel diseases (ibd). in pigs, an obligate intracellular bacterium, lawsonia intracellularis (li), was shown to cause proliferative enteropathy (pe) of which some forms display histological and clinical similarities to human ibd. since li-similar desulfovibrio spp. may infect human cells, we hypothesized that li might be associated with the development of human ibd.	2006	16984651
the effect of decreasing alkalinity on microbial community dynamics in a sulfate-reducing bioreactor as analyzed by pcr-sscp.	pcr-single-strand conformation polymorphism (sscp) and southern blotting techniques were adopted to investigate microbial community dynamics in a sulfate-reducing bioreactor caused by decreasing influent alkalinity. experimental results indicated that the sulfate-removal rate approached 87% in 25 d under the conditions of influent alkalinity of 4000 mg/l (as caco3) and sulfate-loading rate of 4.8 g/(l*d), which indicated that the bioreactor started up successfully. the analysis of microbial comm ...	2006	16989283
synergistic inhibition of microbial sulfide production by combinations of the metabolic inhibitor nitrite and biocides.	mics of six broad-spectrum biocides and two specific metabolic inhibitors and fractional inhibitory concentration indexes (ficis) for controlling a sulfide-producing consortium were determined. nitrite was synergistic (fici<1) with all but one biocide due to its specific inhibition of dissimilatory sulfite reductase. hence, combining nitrite with biocides allows more efficient and cost-effective control of sulfate-reducing bacteria.	2006	16997976
recovery of temperate desulfovibrio vulgaris bacteriophage using a novel host strain.	a novel sulfate-reducing bacterium (strain depue) closely related to desulfovibrio vulgaris ssp. vulgaris strain hildenborough was isolated from the sediment of a heavy-metal impacted lake using established techniques. although few physiological differences between strains depue and hildenborough were observed, pulse-field gel electrophoresis (pfge) revealed a significant genome reduction in strain depue. comparative whole-genome microarray and polymerase chain reaction analyses demonstrated tha ...	2006	17014494
heme biosynthesis in methanosarcina barkeri via a pathway involving two methylation reactions.	the methanogenic archaeon methanosarcina barkeri synthesizes protoheme via precorrin-2, which is formed from uroporphyrinogen iii in two consecutive methylation reactions utilizing s-adenosyl-l-methionine. the existence of this pathway, previously exclusively found in the sulfate-reducing delta-proteobacterium desulfovibrio vulgaris, was demonstrated for m. barkeri via the incorporation of two methyl groups from methionine into protoheme.	2006	17028275
correlation of mrna expression and protein abundance affected by multiple sequence features related to translational efficiency in desulfovibrio vulgaris: a quantitative analysis.	the modest correlation between mrna expression and protein abundance in large-scale data sets is explained in part by experimental challenges, such as technological limitations, and in part by fundamental biological factors in the transcription and translation processes. among various factors affecting the mrna-protein correlation, the roles of biological factors related to translation are poorly understood. in this study, using experimental mrna expression and protein abundance data collected f ...	2006	17028312
lc-ms/ms based proteomic analysis and functional inference of hypothetical proteins in desulfovibrio vulgaris.	high efficiency capillary liquid chromatography-tandem mass spectrometry (lc-ms/ms) was used to examine the proteins extracted from desulfovibrio vulgaris cells across six treatment conditions. while our previous study provided a proteomic overview of the cellular metabolism based on proteins with known functions [w. zhang, m.a. gritsenko, r.j. moore, d.e. culley, l. nie, k. petritis, e.f. strittmatter, d.g. camp ii, r.d. smith, f.j. brockman, a proteomic view of the metabolism in desulfovibrio ...	2006	16982031
interaction of desulfovibrio desulfuricans biofilms with stainless steel surface and its impact on bacterial metabolism.	to study the influence of some metallic elements of stainless steel 304 (ss 304) on the development and activity of a sulfate-reducing bacterial biofilm, using as comparison a reference nonmetallic material polymethylmethacrylate (pmma).	2006	17040232
a 1,1,1-trichloroethane-degrading anaerobic mixed microbial culture enhances biotransformation of mixtures of chlorinated ethenes and ethanes.	1,1,1-trichloroethane (1,1,1-tca) is a common groundwater pollutant as a result of improper disposal and accidental spills. it is often found as a cocontaminant with trichloroethene (tce) and inhibits some tce-degrading microorganisms. 1,1,1-tca removal is therefore required for effective bioremediation of sites contaminated with mixed chlorinated organics. this study characterized ms, a 1,1,1-tca-degrading, anaerobic, mixed microbial culture derived from a 1,1,1-tca-contaminated site in the nor ...	2006	17056695
crystal structure of rubredoxin from desulfovibrio gigas to ultra-high 0.68 a resolution.	rubredoxin (d.g. rd) is a small non-heme iron-sulfur protein shown to function as a redox coupling protein from the sulfate reducing bacteria desulfovibrio gigas. the protein is generally purified from anaerobic bacteria in which it is thought to be involved in electron transfer or exchange processes. rd transfers an electron to oxygen to form water as part of a unique electron transfer chain, composed by nadh:rubredoxin oxidoreductase (nro), rubredoxin and rubredoxin:oxygen oxidoreductase (roo) ...	2006	16930541
rubredoxin:oxygen oxidoreductase enhances survival of desulfovibrio vulgaris hildenborough under microaerophilic conditions.	genes for superoxide reductase (sor), rubredoxin (rub), and rubredoxin:oxygen oxidoreductase (roo) are located in close proximity in the chromosome of desulfovibrio vulgaris hildenborough. protein blots confirmed the absence of roo from roo mutant and sor-rub-roo (srr) mutant cells and its presence in sor mutant and wild-type cells grown under anaerobic conditions. oxygen reduction rates of the roo and srr mutants were 20 to 40% lower than those of the wild type and the sor mutant, indicating th ...	2006	16923892
palladium and gold removal and recovery from precious metal solutions and electronic scrap leachates by desulfovibrio desulfuricans.	biomass of desulfovibrio desulfuricans was used to recover au(iii) as au(0) from test solutions and from waste electronic scrap leachate. au(0) was precipitated extracellularly by a different mechanism from the biodeposition of pd(0). the presence of cu(2+) ( approximately 2000 mg/l) in the leachate inhibited the hydrogenase-mediated removal of pd(ii) but pre-palladisation of the cells in the absence of added cu(2+) facilitated removal of pd(ii) from the leachate and more than 95% of the pd(ii) ...	2006	16909331
cr(vi) detoxification by desulfovibrio vulgaris strain hildenborough: microbe-metal interactions studies.	toxic heavy metals constitute a worldwide environmental pollution problem. bioremediation technologies represent efficient alternatives to the classic cleaning-up of contaminated soil and ground water. most toxic heavy metals such as chromium are less soluble and toxic when reduced than when oxidized. sulfate-reducing bacteria (srb) are able to reduce heavy metals by a chemical reduction via the production of h2s and by a direct enzymatic process involving hydrogenases and c3 cytochromes. we hav ...	2006	16896506
spectroelectrochemical characterization of the [nife] hydrogenase of desulfovibrio vulgaris miyazaki f.	the active site in the [nife] hydrogenase of desulfovibrio vulgaris miyazaki f has been investigated by fourier transform infrared (ftir) spectroscopy. analysis of the spectra allowed the three diatomic inorganic ligands to fe in this enzyme to be identified as one co molecule and two cn(-) molecules. furthermore, ph-dependent redox titrations were performed to determine the midpoint potentials as well as the pk value of the respective reactions and revealed that each single-electron redox trans ...	2006	16893172
plasticity of the domain structure in flgj, a bacterial protein involved in flagellar rod formation.	bacterial flagellar rod structure is built across the peptidoglycan (pg) layer. a salmonella enterica flagellar protein flgj is believed to consist of two functional domains, the n-terminal half acting as a scaffold or cap essential for rod assembly and the c-terminal half acting as a pg hydrolase (pgase) that makes a hole in the pg layer to facilitate rod penetration. in this study, molecular data analyses were conducted on flgj data sets sampled from a variety of bacterial species, and three t ...	2006	17283383
structural basis for o2 sensing by the hemerythrin-like domain of a bacterial chemotaxis protein: substrate tunnel and fluxional n terminus.	the methyl-accepting chemotaxis protein, dcrh, from the anaerobic sulfate-reducing bacterium, desulfovibrio vulgaris (hildenborough), has a hemerythrin-like domain, dcrh-hr, at its c terminus. dcrh-hr was previously shown to contain a diiron site that binds o2, suggesting an o2-sensing function. x-ray crystal structures of diferric (met-), azido-diferric (azidomet-), and diferrous (deoxy-) dcrh-hr reveal a "substrate tunnel" distinct from that in invertebrate hemerythrins. this tunnel is propose ...	2006	16866347
[application of "microring an" to "level 1": presumptive identification of anaerobic gram-negative bacilli].	commonly isolated anaerobic gram-negative rods (4 genus 64 strains), some other important gram-negative anaerobic species (9 genus 45 strains), and cigar-shaped clostridia (11 strains) were studied on their susceptibility patterns to 6 agents on "microring an". some modifications were made in the methods and interpretation of results. susceptibility patterns to erythromycin, rifampicin, colistin, benzylpenicillin, kanamycin, and vancomycin were following (sensitive [s], intermediate [i], resista ...	2006	17822332
spectroelectrochemistry of type ii cytochrome c3 on a glycosylated self-assembled monolayer.	a modified silver electrode was prepared by the self-assembly of a thiol-derivatized neoglycoconjugate, forming a 2d surface with maltose functionality. this self-assembled-monolayer-modified electrode was utilized for adsorption and spectroelectrochemical studies of tetraheme-containing type ii cytochrome c3. the glycosylated surface allowed for the determination of the hemes' redox potentials and demonstrated enhanced spectroelectrochemical performance, in comparison to the widely used self-as ...	2006	17106964
x-ray structure of the membrane-bound cytochrome c quinol dehydrogenase nrfh reveals novel haem coordination.	oxidation of membrane-bound quinol molecules is a central step in the respiratory electron transport chains used by biological cells to generate atp by oxidative phosphorylation. a novel family of cytochrome c quinol dehydrogenases that play an important role in bacterial respiratory chains was recognised in recent years. here, we describe the first structure of a cytochrome from this family, nrfh from desulfovibrio vulgaris, which forms a stable complex with its electron partner, the cytochrome ...	2006	17139260
electrochemical investigations of the interconversions between catalytic and inhibited states of the [fefe]-hydrogenase from desulfovibrio desulfuricans.	studies of the catalytic properties of the [fefe]-hydrogenase from desulfovibrio desulfuricans by protein film voltammetry, under a h2 atmosphere, reveal and establish a variety of interesting properties not observed or measured quantitatively with other techniques. the catalytic bias (inherent ability to oxidize hydrogen vs reduce protons) is quantified over a wide ph range: the enzyme is proficient at both h2 oxidation (from ph > 6) and h2 production (ph < 6). hydrogen production is inhibited ...	2006	17177431
environment. spain's prestige oil spill resurfaces.		2006	17185574
biochemical and spectroscopic characterization of an aldehyde oxidoreductase isolated from desulfovibrio aminophilus.	aldehyde oxidoreductase (aor) activity has been found in a number of sulfate-reducing bacteria. the enzyme that is responsible for the conversion of aldehydes to carboxylic acids is a mononuclear molybdenum enzyme belonging to the xanthine oxidase family. we report here the purification and characterization of aor isolated from the sulfate-reducing bacterium desulfovibrio (d.) aminophilus dsm 12254, an aminolytic strain performing thiosulfate dismutation. the enzyme is a homodimer (ca. 200 kda), ...	2006	16290059
improved methodology for bioremoval of black crusts on historical stone artworks by use of sulfate-reducing bacteria.	an improved methodology to remove black crusts from stone by using desulfovibrio vulgaris subsp. vulgaris atcc 29579, a sulfate-reducing bacterium, is presented. the strain removed 98% of the sulfates of the crust in a 45-h treatment. precipitation of black iron sulfide was avoided using filtration of a medium devoid of iron. among three cell carriers, carbogel proved to be superior to both sepiolite and hydrobiogel-97, as it allowed an easy application of the bacteria, kept the system in a stat ...	2006	16672524
integrated analysis of transcriptomic and proteomic data of desulfovibrio vulgaris: zero-inflated poisson regression models to predict abundance of undetected proteins.	motivation: integrated analysis of global scale transcriptomic and proteomic data can provide important insights into the metabolic mechanisms underlying complex biological systems. however, because the relationship between protein abundance and mrna expression level is complicated by many cellular and physical processes, sophisticated statistical models need to be developed to capture their relationship. results: in this study, we describe a novel data-driven statistical model to integrate whol ...	2006	16675466
changes in organic matter biodegradability influencing sulfate reduction in an aquifer contaminated by landfill leachate.	in situ experiments were conducted to measure sulfate reduction rates and identify rate-limiting factors in a shallow, alluvial aquifer contaminated with municipal landfill leachate. single-well, push-pull tests conducted in a well adjacent to the landfill with > 8 mm dissolved organic carbon (doc) exhibited a sulfate reduction rate of 3.2 mumol so4(-2) (l sediment)(-1) day(-1), a value in close agreement with laboratory-derived estimates. identical tests conducted in wells located 90 m downgrad ...	2006	16680512
oxidative stress and heat-shock responses in desulfovibrio vulgaris by genome-wide transcriptomic analysis.	sulfate-reducing bacteria such as desulfovibrio vulgaris have developed a set of responses that allow them to survive in hostile environments. to obtain further knowledge of the protective mechanisms employed by d. vulgaris in response to oxidative stress and heat shock, we performed a genome-wide transcriptomic analysis to determine the cellular responses to both stimuli. the results showed that 130 genes were responsive to oxidative stress, while 427 genes were responsive to heat-shock. functi ...	2006	16680520
[adhesion of sulphate-reducing bacteria to steel under cathode polarization].	adhesion of different (as to their corrosion aggression) strains of sulphate-reducing bacteria to steel has been studied under cathode polarization at various potentials: -800, -900, -1000, -1200 mv. it has been established that cathode polarization differently affects the adhesion of strain of sulphate-reducing bacteria with various aggression to steel. correlation between the bacterial strains aggression and the number of cells adhered to metal have been noted. the cells of aggressive strains ...	2006	16686219
a tale of two ferredoxins: sequence similarity and structural differences.	sequence similarity between proteins is usually considered a reliable indicator of homology. pyruvate-ferredoxin oxidoreductase and quinol-fumarate reductase contain ferredoxin domains that bind [fe-s] clusters and are involved in electron transport. profile-based methods for sequence comparison, such as psi-blast and hmmer, suggest statistically significant similarity between these domains.	2006	16603087
relation between mrna expression and sequence information in desulfovibrio vulgaris: combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mrna abundance.	the context-dependent expression of genes is the core for biological activities, and significant attention has been given to identification of various factors contributing to gene expression at genomic scale. however, so far this type of analysis has been focused either on relation between mrna expression and non-coding sequence features such as upstream regulatory motifs or on correlation between mrna abundance and non-random features in coding sequences (e.g., codon usage and amino acid usage) ...	2006	16603130
changing the ligation of the distal [4fe4s] cluster in nife hydrogenase impairs inter- and intramolecular electron transfers.	in nife hydrogenases, electrons are transferred from the active site to the redox partner via a chain of three iron-sulfur clusters, and the surface-exposed [4fe4s] cluster has an unusual his(cys)3 ligation. when this histidine (h184 in desulfovibrio fructosovorans) is changed into a cysteine or a glycine, a distal cubane is still assembled but the oxidative activity of the mutants is only 1.5 and 3% of that of the wt, respectively. we compared the activities of the wt and engineered enzymes for ...	2006	16608357
hydrogen bonding affects the [nife] active site of desulfovibrio vulgaris miyazaki f hydrogenase: a hyperfine sublevel correlation spectroscopy and density functional theory study.	pulse electron paramagnetic resonance and hyperfine sublevel correlation spectroscopy have been used to investigate nitrogen coordination of the active site of [nife] hydrogenase of desulfovibrio vulgaris miyazaki f in its oxidized "ready" state. the obtained (14)n hyperfine (a = [+1.32, +1.32, +2.07] mhz) and nuclear quadrupole (e(2)qq/h = -1.9 mhz, eta = 0.37) coupling constants were assigned to the n(epsilon) of a highly conserved histidine (his88) by studying a hydrogenase preparation in whi ...	2006	16610917
the repetitive dna elements called crisprs and their associated genes: evidence of horizontal transfer among prokaryotes.	we have found direct dna repeats 21-47 bp in length interspersed with nonrepetitive sequences of similar length, or clustered regularly interspaced short palindromic repeats (crisprs) in a wide range of diverse prokaryotes, including many archaeal and eubacterial species. a number of cas, crispr-associated genes have also been characterized in many of the same organisms. phylogenetic analysis of these cas genes suggests that the crispr loci have been propagated via hgt, horizontal gene transfer. ...	2006	16612537
selenium is involved in regulation of periplasmic hydrogenase gene expression in desulfovibrio vulgaris hildenborough.	desulfovibrio vulgaris hildenborough is a good model organism to study hydrogen metabolism in sulfate-reducing bacteria. hydrogen is a key compound for these organisms, since it is one of their major energy sources in natural habitats and also an intermediate in the energy metabolism. the d. vulgaris hildenborough genome codes for six different hydrogenases, but only three of them, the periplasmic-facing [fefe], [feni]1, and [fenise] hydrogenases, are usually detected. in this work, we studied t ...	2006	16621815
desulfovibrio alkalitolerans sp. nov., a novel alkalitolerant, sulphate-reducing bacterium isolated from district heating water.	a novel alkalitolerant, sulphate-reducing bacterium (strain rt2t) was isolated from alkaline district heating water. strain rt2t was a motile vibrio (0.5-0.8 microm wide and 1.4-1.9 microm long) and grew at ph 6.9-9.9 (optimum at ph 9.0-9.4) and at 16-47 degrees c (optimum at 43 degrees c). the genomic dna g+c content was 64.7 mol%. a limited number of compounds were used as electron donors with sulphate as electron acceptor, including lactate, pyruvate, formate and hydrogen/acetate. sulphite an ...	2006	16627648
afm study of the effect of metronidazole on surface structures of sulfate-reducing bacteria.	the effect of metronidazole (me) on sulfate-reducing bacteria (srb) was studied by atomic force microscopy (afm) in this paper. topography images of srb cell show that after exposure to me individual cell shape is sharply modified. topography and phase images of srb cell wall show that after exposure to me not only the roughness of the cell wall increases but also the physical performance of srb surface is changed to be uniform. afm frictional loops show that after exposure to me, srb surface fr ...	2006	16701623
culture and identification of desulfovibrio spp. from corals infected by black band disease on dominican and florida keys reefs.	black band disease (bbd) of corals is characterized as a pathogenic microbial consortium composed of a wide variety of microorganisms. together, many of these microorganisms contribute to an active sulfur cycle that produces anoxia and high levels of sulfide adjacent to the coral surface, conditions that are lethal to coral tissue. sulfate-reducing bacteria, as sulfide producers, are an important component of the sulfur cycle and the black band community. previous molecular survey studies have s ...	2006	16703774
toxic effects of uranium on desulfovibrio desulfuricans g20.	the toxic effects of u(vi) were studied using desulfovibrio desulfuricans g20 in a medium containing bicarbonate or 1,4-piperazinediethane sulfonic acid disodium salt monohydrate (pipes) buffer (each at 30 mm and ph 7). uranium(vi) toxicity was dependent on the medium buffer and was observed in terms of longer lag times and, in some cases, no measurable growth. the minimum inhibiting concentration was 140 microm u(vi) in pipes-buffered medium. this is 36-fold lower than that reported previously ...	2006	16704053
uranium reduction.	the dramatic decrease in solubility accompanying the reduction of u(vi) to u(iv), producing the insoluble mineral uraninite, has been viewed as a potential mechanism for sequestration of environmental uranium contamination. in the past 15 years, it has been firmly established that a variety of bacteria exhibit this reductive capacity. to obtain an understanding of the microbial metal metabolism, to develop a practical approach for the acceleration of in situ bioreduction, and to predict the long ...	2006	16704344
salt stress in desulfovibrio vulgaris hildenborough: an integrated genomics approach.	the ability of desulfovibrio vulgaris hildenborough to reduce, and therefore contain, toxic and radioactive metal waste has made all factors that affect the physiology of this organism of great interest. increased salinity is an important and frequent fluctuation faced by d. vulgaris in its natural habitat. in liquid culture, exposure to excess salt resulted in striking elongation of d. vulgaris cells. using data from transcriptomics, proteomics, metabolite assays, phospholipid fatty acid profil ...	2006	16707698
global transcriptomic analysis of desulfovibrio vulgaris on different electron donors.	whole-genome microarrays of desulfovibrio vulgaris were used to determine relative transcript levels in cells grown to exponential or stationary phase on a medium containing either lactate or formate as electron donor. the results showed that 158 and 477 genes were differentially expressed when comparing exponential to stationary phase in lactate- or formate-based media, respectively; and 505 and 355 genes were responsive to the electron donor used at exponential or stationary phase, respectivel ...	2006	16710634
oxygen defense in sulfate-reducing bacteria.	sulfate-reducing bacteria (srb) are strict anaerobes that are often found in biotopes where oxic conditions can temporarily exist. the bacteria have developed several defense strategies in order to survive exposure to oxygen. these strategies includes peculiar behaviors in the presence of oxygen, like aggregation or aerotaxis, and enzymatic systems dedicated to the reduction and the elimination of oxygen and its reactive species. sulfate-reducing bacteria, and specially desulfovibrio species, po ...	2006	16713001
folding of desulfovibrio desulfuricans flavodoxin is accelerated by cofactor fly-casting.	folding of cofactor-binding proteins involves ligand binding in addition to polypeptide folding. we here assess the kinetic folding/binding landscape for desulfovibrio desulfuricans flavodoxin that coordinates an fmn cofactor. the apo-form folds in a two-step process involving a burst-phase intermediate. studies on tyr98ala and trp60ala variants reveal that these aromatics-that stack with the fmn in the holo-form-are not participating in the apo-protein folding pathway. however, these residues a ...	2006	16730634
pathways of h2 toward the active site of [nife]-hydrogenase.	hydrogenases catalyze the reversible oxidation of molecular hydrogen (h(2)), but little is known about the diffusion of h(2) toward the active site. here we analyze pathways for h(2) permeation using molecular dynamics (md) simulations in explicit solvent. various md simulation replicates were done, to improve the sampling of the system states. h(2) easily permeates hydrogenase in every simulation and it moves preferentially in channels. all h(2) molecules that reach the active site made their a ...	2006	16731562
solution structure of hndac: a thioredoxin-like domain involved in the nadp-reducing hydrogenase complex.	the nadp-reducing hydrogenase complex from desulfovibrio fructosovorans is a heterotetramer encoded by the hndabcd operon. sequence analysis indicates that the hndc subunit (52 kda) corresponds to the nadp-reducing unit, and the hndd subunit (63.5 kda) is homologous to clostridium pasteurianum hydrogenase. the role of hnda and hndb subunits (18.8 kda and 13.8 kda, respectively) in the complex remains unknown. the hnda subunit belongs to the [2fe-2s] ferredoxin family typified by c. pasteurianum ...	2006	16731971
low strength wastewater treatment under low temperature conditions by a novel sulfur redox action process.	the objective of this research is to make a novel wastewater treatment process activated by a sulfur-redox cycle action of microbes in low temperature conditions. this action is carried out by sulfate-reducing bacteria (srb) and sulfur-oxidizing bacteria (sob). the process was comprised of a uasb reactor as pre-treatment and an aerobic downflow hanging sponge (dhs) reactor as post-treatment. as the results of reactor operation, the whole process achieved that over 90% of codcr removal efficiency ...	2006	16749445
energetic consequences of nitrite stress in desulfovibrio vulgaris hildenborough, inferred from global transcriptional analysis.	many of the proteins that are candidates for bioenergetic pathways involved with sulfate respiration in desulfovibrio spp. have been studied, but complete pathways and overall cell physiology remain to be resolved for many environmentally relevant conditions. in order to understand the metabolism of these microorganisms under adverse environmental conditions for improved bioremediation efforts, desulfovibrio vulgaris hildenborough was used as a model organism to study stress response to nitrite, ...	2006	16751553
a chemotaxis operon in the bacterium desulfovibrio gigas is induced under several growth conditions.	the chemosensory system of bacteria controls their motility and behaviour in different environments. in the present study, we report the identification of the first chemotaxis operon in desulfovibrio gigas. amino acid sequence analysis revealed seven coding regions for polypeptides with a high similarity to chemotaxis proteins from other organisms. d. gigas chemotaxis operon has a similar genetic organisation to chemotaxis operons found in the sequenced genomes of desulfovibrio desulfuricans and ...	2006	16753818
crystallization and preliminary structure determination of the membrane-bound complex cytochrome c nitrite reductase from desulfovibrio vulgaris hildenborough.	the cytochrome c nitrite reductase (cnir) isolated from desulfovibrio vulgaris hildenborough is a membrane-bound complex formed of nrfa and nrfh subunits. the catalytic subunit nrfa is a soluble pentahaem cytochrome c that forms a physiological dimer of about 120 kda. the electron-donor subunit nrfh is a membrane-anchored tetrahaem cytochrome c of about 18 kda molecular weight and belongs to the napc/nirt family of quinol dehydrogenases, for which no structures are known. crystals of the native ...	2006	16754983
carriage, quantification, and predominance of methanogens and sulfate-reducing bacteria in faecal samples.	to determine carriage rates and densities of methanogens and sulfate-reducing bacteria in adults and children using molecular methods, and to also determine if a reciprocal relationship exists between these organisms.	2006	16834722
temporal transcriptomic analysis as desulfovibrio vulgaris hildenborough transitions into stationary phase during electron donor depletion.	desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the stationary phase during electron donor depletion. in addition to temporal transcriptomics, total protein, carbohydrate, lactate, acetate, and sulfate levels were measured. the microarray data were examined for statistically significant expression changes, hierarchical cluster analysis, and promote ...	2006	16885312
toxic effects of dissolved heavy metals on desulfovibrio vulgaris and desulfovibrio sp. strains.	biological treatment of metal-containing wastewaters with sulphate-reducing bacteria (srb) is an attractive technique for the bioremediation of this kind of medium. in order to design a suitable engineering process to address this environmental problem, it is crucial to understand the inhibitory effect of dissolved heavy metals on these bacteria. batch studies were carried out to evaluate the toxic effects of several heavy metal ions [cr(iii), cu(ii), mn(ii), ni(ii) and zn(ii)] on two cultures o ...	2006	16386832
characterization of the desulfovibrio desulfuricans atcc 27774 dsrmkjop complex--a membrane-bound redox complex involved in the sulfate respiratory pathway.	sulfate-reducing organisms use sulfate as an electron acceptor in an anaerobic respiratory process. despite their ubiquitous occurrence, sulfate respiration is still poorly characterized. genome analysis of sulfate-reducing organisms sequenced to date permitted the identification of only two strictly conserved membrane complexes. we report here the purification and characterization of one of these complexes, dsrmkjop, from desulfovibrio desulfuricans atcc 27774. the complex has hemes of the c an ...	2006	16388601