Publications

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
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
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
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
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
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
identification of variant molecules of bacillus thermoproteolyticus ferredoxin: crystal structure reveals bound coenzyme a and an unexpected [3fe-4s] cluster associated with a canonical [4fe-4s] ligand motif.	during the purification of recombinant bacillus thermoproteolyticus ferredoxin (btfd) from escherichia coli, we have noted that some fe-s proteins were produced in relatively small amounts compared to the originally identified btfd carrying a [4fe-4s] cluster. these variants could be purified into three fe-s protein components (designated as v-i, v-ii, and v-iii) by standard chromatography procedures. uv-vis and epr spectroscopic analyses indicated that each of these variants accommodates a [3fe ...	2005	16156653
caseinoglycomacropeptide inhibits adhesion of pathogenic escherichia coli strains to human cells in culture.	caseinoglycomacropeptide (cgmp) derived from kappa-casein was investigated for its ability to inhibit the adhesion of 3 strains of verotoxigenic escherichia coli (vtec) and 3 strains of enteropathogenic escherichia coli (epec) to human ht29 tissue cell cultures. effects on adhesion of desulfovibrio desulfuricans, lactobacillus pentosus, lactobacillus casei, lactobacillus acidophilus, and lactobacillus gasseri were also investigated. generally, cgmp exerted effective anti-adhesive properties at a ...	2005	16162518
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
triple-resonance methods for complete resonance assignment of aromatic protons and directly bound heteronuclei in histidine and tryptophan residues.	a set of three experiments is described which correlate aromatic resonances of histidine and tryptophan residues with amide resonances in 13c/15n-labelled proteins. provided that backbone 1h and 15n positions of the sequentially following residues are known, this results in sequence-specific assignment of histidine 1h(delta2)/13c(delta2) and 1h(epsilon1)/13c(epsilon1) as well as tryptophan 1h(delta1)/13c(delta1), 1h(zeta2)/13c(zeta2), 1h(eta2)/13c(eta2), 1h(epsilon3)/13c(epsilon3), 1h(zeta3)/13c ...	2005	16211484
[determination of minimal concentrations of biocorrosion inhibitors by a bioluminescence method in relation to bacteria, participating in biocorrosion].	by using a bioluminescence atp assay, we have determined the minimal concentrations of some biocorrosion inhibitors (katon, khazar, vfiks-82, nitro-1, kaspii-2, and kaspii-4) suppressing most common microbial corrosion agents: desulfovibrio desulfuricans, desulfovibrio vulgaris, pseudomonas putida, pseudomonas fluorescens, and acidithiobacillus ferrooxidans. the cell titers determined by the bioluminescence method, including not only dividing cells but also their dormant living counterparts, are ...	2005	16212040
[microbial community structure analyzed by single-strand conformation polymorphism technique in sulfate-reducing reactor].	analyses of microbial community structure and the relationships between sulfate-reducing bacteria (srbs) and acidogenic bacteria (abs) in a completely stirred sulfate-reducing reactor were carried out by modified polymerase chain reaction-single-stranded conformation polymorphism (pcr-sscp) targeted eubacterial 16s ribosomal rna gene. a total of 13 bands were obtained and 6 of them (a1, a3, a4, a5, a9, a10) were sequenced. the sequences are similar to leuconostoc mesenteroides (genbank access no ...	2005	16212191
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
structure-function relationships in mitochondrial complex i of the strictly aerobic yeast yarrowia lipolytica.	the obligate aerobic yeast yarrowia lipolytica has been established as a powerful model system for the analysis of mitochondrial complex i. using a combination of genomic and proteomic approaches, a total of 37 subunits was identified. several of the accessory subunits are predicted to be stmd (single transmembrane domain) proteins. site-directed mutagenesis of y. lipolytica complex i has provided strong evidence that a significant part of the ubiquinone reducing catalytic core resides in the 49 ...	2005	16042611
biochemical differentiation and comparison of desulfovibrio species and other phenotypically similar genera.	seventeen human clinical isolates representing four species of desulfovibrio were characterized using 16s rrna gene sequences and tests for catalase, indole, nitrate, bile, urease, formate-fumarate stimulation, desulfoviridin, motility, and hydrogen sulfide production, plus susceptibility to antimicrobial agents. eighty additional strains representing 10 phenotypically similar genera (bilophila, selenomonas, capnocytophaga, campylobacter, bacteroides, sutterella, anaerobiospirillum, dialister, v ...	2005	16081948
structural determinants of protein stabilization by solutes. the important of the hairpin loop in rubredoxins.	despite their high sequence homology, rubredoxins from desulfovibrio gigas and d. desulfuricans are stabilized to very different extents by compatible solutes such as diglycerol phosphate, the major osmolyte in the hyperthermophilic archaeon archaeoglobus fulgidus[lamosa p, burke a, peist r, huber r, liu m y, silva g, rodrigues-pousada c, legall j, maycock c and santos h (2000) appl environ microbiol66, 1974-1979]. the principal structural difference between these two proteins is the absence of ...	2005	15691333
theoretical calculations on hydrogenase kinetics: explanation of the lag phase and the enzyme concentration dependence of the activity of hydrogenase uptake.	two models of the hydrogenase reaction cycle were investigated by means of theoretical calculations and model simulations. the first model is the widely accepted triangular hydrogenase reaction cycle with minor modifications; the second is a modified triangular model, where we have introduced an autocatalytic step into the reaction cycle. both models include a one-step activation reaction. the theoretical calculations and model simulations corroborate the assumed autocatalytic reaction step conc ...	2005	15951384
development of methods for the detection and quantification of 7alpha-dehydroxylating clostridia, desulfovibrio vulgaris, methanobrevibacter smithii, and lactobacillus plantarum in human feces.	mounting evidence suggests a relationship between bacterial metabolism of certain dietary and endogenous factors and the development of colorectal cancer. deoxycholic acid (dca) is a well studied co-carcinogen and bio-transformation product of 7alpha-dehydroxylating clostridia. h2s is a cytotoxic metabolite produced primarily by sulfate-reducing bacteria (srb). the production of methane indicates low levels of active srb. lactic acid bacteria (lab) have received attention recently due to their p ...	2005	15963794
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
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
synthesis, characterization, biocide and toxicological activities of di-n-butyl- and diphenyl-tin(iv)-salicyliden-beta-amino alcohol derivatives.	the one pot reaction of salicylaldehyde 1, beta-amino alcohols 2a-2c, and di-n-butyltin(iv) oxide 3a or diphenyltin(iv) oxide 3b produced five diorganotin(iv) compounds, 4a-4c, 5a, and 5c, in good yields. all compounds were characterized by ir, (1)h, (13)c, and (119)sn nmr spectroscopy, and elemental analysis; furthermore, compounds 4b, 4c, 5a, and 5c were characterized by x-ray diffraction analysis. after the structural characterization, all of the compounds were tested in vitro against bacillu ...	2005	16022535
interaction and electron transfer between the high molecular weight cytochrome and cytochrome c3 from desulfovibrio vulgaris hildenborough: kinetic, microcalorimetric, epr and electrochemical studies.	the complex formation between the tetraheme cytochrome c3 and hexadecaheme high molecular weight cytochrome c (hmc), the structure of which has recently been resolved, has been characterized by cross-linking experiments, epr, electrochemistry and kinetic analysis, and some key parameters of the interaction were determined. the analysis of electron transfer between [fe] hydrogenase, cytochrome c3 and hmc demonstrates a redox-shuttling role of cytochrome c3 in the pathway from hydrogenase to hmc, ...	2005	15780995
structural differences between the ready and unready oxidized states of [nife] hydrogenases.	[nife] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. so far, the structural basis for this difference has not been understood because of lack of relevant crystallographic data. here, we present the crystal structure of the ready ni-b state of desulfovibrio fructosovorans [nife] hydrogenase and show it to have a putative mu-hydroxo ...	2005	15803334
structure of s35c flavodoxin mutant from desulfovibrio vulgaris in the semiquinone state.	the crystallographic structure of an engineered flavodoxin mutant from desulfovibrio vulgaris has been analysed. site-directed mutagenesis was used to substitute serine 35 with a cysteine to provide a possible covalent linkage. the crystal structure of the semiquinone form of this mutant is similar to the corresponding oxidation state of the wild-type flavodoxin. analysis of the structural changes reveals the interaction between n(5)h of the flavin and the carbonyl o atom of gly61 to be critical ...	2005	15805604
bioinformatics, genomics and evolution of non-flagellar type-iii secretion systems: a darwinian perspective.	we review the biology of non-flagellar type-iii secretion systems from a darwinian perspective, highlighting the themes of evolution, conservation, variation and decay. the presence of these systems in environmental organisms such as myxococcus, desulfovibrio and verrucomicrobium hints at roles beyond virulence. we review newly discovered sequence homologies (e.g., yopn/tyea and sepl). we discuss synapomorphies that might be useful in formulating a taxonomy of type-iii secretion. the problem of ...	2005	15808742
the hydrogenases of geobacter sulfurreducens: a comparative genomic perspective.	the hydrogenase content of the genome of geobacter sulfurreducens, a member of the family geobacteraceae within the delta-subdivision of the proteobacteria, was examined and found to be distinct from that of desulfovibrio species, another family of delta-proteobacteria on which extensive research concerning hydrogen metabolism has been conducted. four [nife]-hydrogenases are encoded in the g. sulfurreducens genome: two periplasmically oriented, membrane-bound hydrogenases, hya and hyb, and two c ...	2005	15817791
analysis of bacterial diversity in acidic pond water and compost after treatment of artificial acid mine drainage for metal removal.	the microbial population of a sludge amended leaf compost material utilized for treatment of artificial acid mine drainage was studied by culture-independent molecular methods. iron-rich and sulfurous wastewater (artificial acid mine drainage) was circulated through a column bioreactor for 16 months. after 12 months the column was inoculated with a mixed culture from an acidic pond receiving acid mine drainage from a tailings impoundment at a decommissioned site in kristineberg, north sweden. hy ...	2005	15818559
reduction of cr(vi) by immobilized cells of desulfovibrio vulgaris ncimb 8303 and microbacterium sp. ncimb 13776.	hexavalent chromium, a carcinogen and mutagen, can be reduced to cr(iii) by desulfovibrio vulgaris ncimb 8303 and microbacterium sp. ncimb 13776. this study examined cr(vi) reduction by immobilized cells of the two strains in a common solution matrix using various entrapment matrices. chitosan and pva-borate beads did not retain integrity and supported low or no reduction of cr(vi) by the cells. a commercial preparation (lentikats) was stable but also did not support cr(vi) reduction. k-carragee ...	2005	15818565
oxygen tolerance of the h2-sensing [nife] hydrogenase from ralstonia eutropha h16 is based on limited access of oxygen to the active site.	hydrogenases, abundant proteins in the microbial world, catalyze cleavage of h2 into protons and electrons or the evolution of h2 by proton reduction. hydrogen metabolism predominantly occurs in anoxic environments mediated by hydrogenases, which are sensitive to inhibition by oxygen. those microorganisms, which thrive in oxic habitats, contain hydrogenases that operate in the presence of oxygen. we have selected the h2-sensing regulatory [nife] hydrogenase of ralstonia eutropha h16 to investiga ...	2005	15849358
x-ray crystal structures of moorella thermoacetica fpra. novel diiron site structure and mechanistic insights into a scavenging nitric oxide reductase.	several members of a widespread class of bacterial and archaeal metalloflavoproteins, called fpra, likely function as scavenging nitric oxide reductases (s-nors). however, the only published x-ray crystal structure of an fpra is for a protein characterized as a rubredoxin:dioxygen oxidoreductase (roo) from desulfovibrio gigas. therefore, the crystal structure of moorella thermoacetica fpra, which has been established to function as an s-nor, was solved in three different states: as isolated, red ...	2005	15850383
binding of ligands originates small perturbations on the microscopic thermodynamic properties of a multicentre redox protein.	nmr and visible spectroscopy coupled to redox measurements were used to determine the equilibrium thermodynamic properties of the four haems in cytochrome c3 under conditions in which the protein was bound to ligands, the small anion phosphate and the protein rubredoxin with the iron in the active site replaced by zinc. comparison of these results with data for the isolated cytochrome shows that binding of ligands causes only small changes in the reduction potentials of the haems and their pairw ...	2005	15853810
desulfovibrio brasiliensis sp. nov., a moderate halophilic sulfate-reducing bacterium from lagoa vermelha (brazil) mediating dolomite formation.	a novel halotolerant sulfate-reducing bacterium, desulfovibrio brasiliensis strain lvform1, was isolated from sediments of a dolomite-forming hypersaline coastal lagoon, lagoa vermelha, in the state of rio de janeiro, brazil. the cells are vibrio-shaped and 0.30 to 0.45 microm by 1.0 to 3.5 microm in size. these bacteria mediate the precipitation of dolomite [camg(co3)2] in culture experiments. the strain was identified as a member of the genus desulfovibrio in the delta-subclass of the proteoba ...	2005	15856133
nested pcr-denaturing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities.	here, we describe a three-step nested-pcr-denaturing gradient gel electrophoresis (dgge) strategy to detect sulfate-reducing bacteria (srb) in complex microbial communities from industrial bioreactors. in the first step, the nearly complete 16s rrna gene was amplified using bacterial primers. subsequently, this product was used as a template in a second pcr with group-specific srb primers. a third round of amplification was conducted to obtain fragments suitable for dgge. the largest number of b ...	2005	15870318
reoxidation of reduced uranium with iron(iii) (hydr)oxides under sulfate-reducing conditions.	in cultures of desulfovibrio desulfuricans 620 the effects of iron(iii) (hydr)oxides (hematite, goethite, and ferrihydrite) on microbial reduction and reoxidation of uranium (u) were evaluated under lactate-limited sulfate-reducing conditions. with lactate present, g20 reduced u(vi) in both 1,4-piperazinediethanesulfonate (pipes) and bicarbonate buffer. once lactate was depleted, however, microbially reduced u served as an electron donor to reduce fe(iii) present in iron(iii) (hydr)oxides. with ...	2005	15871237
effect of inorganic phosphate on fmn binding and loop flexibility in desulfovibrio desulfuricans apo-flavodoxin.	the complex between flavin mononucleotide (fmn) and apo-flavodoxin is dominated by isoalloxazine-stacking interactions and 5'-phosphate hydrogen bonds. we show here that fmn binding to desulfovibrio desulfuricans apo-flavodoxin is faster and the affinity is higher in the presence of inorganic phosphate as compared to in its absence (i=110 mm, ph 7, 20 degrees c). the transition-state of complex formation was investigated by phi-value analysis using trp60ala and tyr98ala apo-flavodoxin variants. ...	2005	15876370
reductive dechlorination of tetrachloroethene to trans-dichloroethene and cis-dichloroethene by pcb-dechlorinating bacterium df-1.	polychlorinated biphenyls (pcbs) and chlorinated ethenes (ces) are known to pollute sediment, soil, and groundwater. the anaerobic dechlorination of these compounds is an integral part of their biodegradation in polluted environments. we report for the first time the dechlorination of tetrachloroethene (pce) and trichloroethene (tce) by bacterium df-1. this pcb and chlorobenzene dechlorinating bacterium dechlorinated pce to tce, which was then converted into trans-1,2-dichloroethene (trans-dce) ...	2005	15884359
high-resolution crystal structures of desulfovibrio vulgaris (hildenborough) nigerythrin: facile, redox-dependent iron movement, domain interface variability, and peroxidase activity in the rubrerythrins.	high-resolution crystal structures of desulfovibrio vulgaris nigerythrin (dvngr), a member of the rubrerythrin (rbr) family, demonstrate an approximately 2-a movement of one iron (fe1) of the diiron site from a carboxylate to a histidine ligand upon conversion of the mixed-valent ([fe2(ii),fe1(iii)]) to diferrous states, even at cryogenic temperatures. this glu<-->his ligand "toggling" of one iron, which also occurs in dvrbr, thus, appears to be a characteristic feature of rbr-type diiron sites. ...	2005	15895271
biodegradation of cyclic nitramines by tropical marine sediment bacteria.	undersea deposition of unexploded ordnance (uxo) constitutes a potential source of contamination of marine environments by hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (hmx). the goal of the present study was to determine microbial degradation of rdx and hmx in a tropical marine sediment sampled from a coastal uxo field in the region of oahu island in hawaii. sediment mixed cultures growing in marine broth 2216 (21 degrees c) anaerobically mi ...	2005	15915354
anaerobic purification and crystallization to improve the crystal quality: ferredoxin ii from desulfovibrio gigas.	sulfate-reducing bacteria (srb), which are strict anaerobes, contain an electron-transfer chain from pyridine nucleotides to molecular oxygen. this unique enzymatic equipment allows the bacterium to produce atp when exposed to air from the degradation of internal reserves of polyglucose. ferredoxin ii (fd ii) is a small electron-transfer protein isolated from the strict anaerobic sulfate-reducing bacterium desulfovibrio gigas. the protein contains 58 amino acids and an iron-sulfur cluster. the c ...	2005	15930639
characterization of sulfate reducing bacteria isolated from cooling towers.	in this study, the occurrence and metabolic capacities of sulfate reducing bacteria (srb) were studied in 36 water samples taken from cooling towers of 30 different buildings, such as hotels and business centres in istanbul. srb were present in 14 cooling towers out of 30 (46.6%) buildings and while the lowest concentration of srb was 10 cells/ml, the highest concentration was determined as 10(4) cells/ml. after the distribution of srb within cooling towers was determined, several strains of srb ...	2005	15931988
in vitro and in vivo sulfate reduction in the gut contents of the termite mastotermes darwiniensis and the rose-chafer pachnoda marginata.	sulfate-reducing bacteria (srb) from termites have been assigned to the genus desulfovibrio. desulfovibrio intestinalis lives in the gut of the australian termite mastotermes darwiniensis. for the first time we were able to enrich and identify a sulfate-reducing bacterium from the gut of the rose-chafer pachnoda marginata, which showed the highest 16s rdna sequence identity (93%) to desulfovibrio intestinalis and desulfovibrio strain stl1. compared to mastotermes darwiniensis (1x10(7) cells of s ...	2005	15942866
desulfovibrio putealis sp. nov., a novel sulfate-reducing bacterium isolated from a deep subsurface aquifer.	a novel sulfate-reducing bacterium was isolated from a well that collected water from a deep aquifer at a depth of 430 m in the paris basin, france. the strain, designated b7-43t, was made up of vibrioid cells that were motile by means of a single polar flagellum. cells contained desulfoviridin. in the presence of sulfate, the following substrates were used as energy and carbon sources: lactate, pyruvate, malate, fumarate, ethanol, butanol, acetate/h2 and glycine. sulfite and thiosulfate were al ...	2005	15653861
epr experiments to elucidate the structure of the ready and unready states of the [nife] hydrogenase of desulfovibrio vulgaris miyazaki f.	isolation and purification of the [nife] hydrogenase of desulfovibrio vulgaris miyazaki f under aerobic conditions leads to a mixture of two states, ni-a (unready) and ni-b (ready). the two states are distinguished by different activation times and different epr spectra. hyscore and endor data and dft calculations show that both states have an exchangeable proton, albeit with a different (1)h hyperfine coupling. this proton is assigned to the bridging ligand between ni and fe. for ni-b, a hydrox ...	2005	15667250
on the relationship between affinity for molecular hydrogen and the physiological directionality of hydrogenases.	the physiological significance of the generic reaction h(2)<-->2[h] is not always clear because hydrogenases may function in the breakdown of molecular hydrogen or in its synthesis or in both directions. fe-hydrogenases have nevertheless been most often associated with proton reduction and nife-hydrogenases with hydrogen oxidation. a re-determination of the k(m) of h(2) oxidation by pyrococcus furiosus nife-hydrogenase-i and by desulfovibrio vulgaris fe-hydrogenase suggests that affinity for hyd ...	2005	15667251
construction of a [nife]-hydrogenase deletion mutant of desulfovibrio vulgaris hildenborough.	a mutant of desulfovibrio vulgaris hildenborough lacking a gene for [nife] hydrogenase was generated. growth studies, performed for the mutant in comparison with the wild-type, showed no strong differences during the exponential growth phase. however, the mutant cells died more rapidly in the stationary growth phase.	2005	15667264
applications of bacterial hydrogenases in waste decontamination, manufacture of novel bionanocatalysts and in sustainable energy.	bacterial hydrogenases have been harnessed to the removal of heavy metals from solution by reduction to less soluble metal species. for pd(ii), its bioreduction results in the deposition of cell-bound pd(0)-nanoparticles that are ferromagnetic and have a high catalytic activity. hydrogenases can also be used synthetically in the production of hydrogen from sugary wastes through breakdown of formate produced by fermentation. the bio-h(2) produced can be used to power an electrical device using a ...	2005	15667270
transcriptional regulation of a hybrid cluster (prismane) protein.	hcp (hybrid-cluster protein) contains two fe/s clusters, one of which is a hybrid [4fe-2s-2o] cluster. despite intensive study, its physiological function has not been reported. the escherichia coli hcp gene is located in a two-gene operon with hcr, which encodes an nadh-dependent hcp reductase. e. coli hcp is detected after anaerobic growth with nitrate or nitrite: possible roles for it in hydroxylamine or nitric oxide reduction have been proposed. to study the regulation and role of hcp, an hc ...	2005	15667305
synthesis of the h-cluster framework of iron-only hydrogenase.	the metal-sulphur active sites of hydrogenases catalyse hydrogen evolution or uptake at rapid rates. understanding the structure and function of these active sites--through mechanistic studies of hydrogenases, synthetic assemblies and in silico models--will help guide the design of new materials for hydrogen production or uptake. here we report the assembly of the iron-sulphur framework of the active site of iron-only hydrogenase (the h-cluster), and show that it functions as an electrocatalyst ...	2005	15703741
production of antimicrobial substances by bacillus subtilis lfe-1, b. firmus ho-1 and b. licheniformis t6-5 isolated from an oil reservoir in brazil.	forty bacillus strains isolated from a brazilian oil reservoir were tested against each other to select strains producing antimicrobial substances (ams). three strains, bacillus subtilis (lfe-1), bacillus firmus (h2o-1) and bacillus licheniformis (t6-5), were selected due to their ability to inhibit more than 65% of the bacillus strains tested. these three strains were also investigated for their capability to inhibit sulphate-reducing bacteria (srb). furthermore, physiological and biochemical c ...	2005	15715870
a flavo-diiron protein from desulfovibrio vulgaris with oxidase and nitric oxide reductase activities. evidence for an in vivo nitric oxide scavenging function.	a few members of a widespread class of bacterial and archaeal flavo-diiron proteins, dubbed fpras, have been shown to function as either oxidases (dioxygen reductases) or scavenging nitric oxide reductases, but the questions of which of these functions dominates in vivo for a given fpra and whether all fpras function as oxidases or nitric oxide reductases remain to be clarified. to address these questions, an fpra has been characterized from the anaerobic sulfate-reducing bacterium desulfovibrio ...	2005	15736966
combined spectroscopic/computational study of binuclear fe(i)-fe(i) complexes: implications for the fully-reduced active-site cluster of fe-only hydrogenases.	the fe(i)-fe(i) dimer complex [fe2(pdt)(co)4(cn)2][et4n]2 (2), where pdt = 1,3-propane dithiolate, serves as a model of the fully reduced [2fe]h component of the h cluster, which is the active site for catalysis in fe-only hydrogenases (fehases). electronic absorption, magnetic circular dichroism (mcd), and resonance raman (rr) spectroscopies have been employed to characterize both the ground and excited states of 2 as well as those of the related complex fe2(pdt)(co)6 (1). these results have be ...	2005	15762706
electric-field-induced redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: surface-enhanced resonance raman spectroscopy and simulation studies.	the tetraheme protein cytochrome c(3) (cyt-c(3)) from desulfovibrio gigas, immobilized on a self-assembled monolayer (sam) of 11-mercaptoundecanoic acid, is studied by theoretical and spectroscopic methods. molecular dynamics simulations indicate that the protein docks to the negatively charged sam via its lysine-rich domain around the exposed heme iv. complex formation is associated with only little protein structural perturbations. this finding is in line with the resonance raman and surface-e ...	2005	15764652
rubredoxin acts as an electron donor for neelaredoxin in archaeoglobus fulgidus.	archaeoglobus fulgidus neelaredoxin (nlr) is an electron donor:superoxide oxidoreductase. the reaction of superoxide with reduced nlr is almost diffusion-limited, but the overall efficiency for detoxifying superoxide in vivo depends on the rate of reduction of nlr by electron donors. here, we report the purification and characterization of the two type i rubredoxins from a. fulgidus (af0880 and af1349) and show that they act as efficient electron donors for neelaredoxin, in vitro, with a second- ...	2005	15766568
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
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
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
[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
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
buildup of polyelectrolyte-protein multilayer assemblies on gold electrodes. role of the hydrophobic effect.	the buildup of layer-by-layer assemblies onto gold surfaces from water-soluble charged polyelectrolytes and proteins is examined using quartz crystal microgravimetry (qcm) and electrochemical techniques. polyelectrolytes such as poly(styrenesulfonate) and poly(ester sulfonic acid) (eastman aq-29d polymer) adsorb spontaneously onto gold, contrary to poly(ethyleneimine). from the modification of the gold surface with a thiol and specific adsorption of polymers under polarization conditions, it is ...	2004	15773101
[choice of isolation procedure for endotoxins from the outer membrane of the bacteria desulfovibrio desulfuricans].	the chemical structure determining properties and biological functions of endotoxins derived from desulfovibrio desulfuricans species has not been recognized, which considerably hinders the choice of an effective extraction procedure of these lipopolysaccharides (lps) from the bacterial outer cell membrane. we aimed at selecting the most effective method of lps isolation from d. desulfuricans in terms of the most efficient extraction solution, the appropriate conditions of isolation and adequate ...	2004	15773506
dehalogenation of chlorinated aromatic compounds using a hybrid bioinorganic catalyst on cells of desulfovibrio desulfuricans.	a novel bioinorganic catalyst was obtained via reduction of pd(ii) to pd0 on to the surface of cells of desulfovibrio desulfuricans at the expense of h2. palladised biomass, supplied with formate or h2 as an electron donor, catalysed the dehalogenation of 2-chlorophenol and polychlorinated biphenyls. in the example of 2,3,4,5-tetrachlorobiphenyl, the bioinorganic catalyst promoted a rate of chloride release of 9.33 +/- 0.17 nmol min(-1) mg (-1) and only approximately 5% of this value was obtaine ...	2004	15672233
the genome of desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold arctic sediments.	desulfotalea psychrophila is a marine sulfate-reducing delta-proteobacterium that is able to grow at in situ temperatures below 0 degrees c. as abundant members of the microbial community in permanently cold marine sediments, d. psychrophila-like bacteria contribute to the global cycles of carbon and sulfur. here, we describe the genome sequence of d. psychrophila strain lsv54, which consists of a 3 523 383 bp circular chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14 66 ...	2004	15305914
changes in the nitrocellulose molecule induced by sulfate-reducing bacteria desulfovibrio desulfuricans 1,388. the enzymes participating in this process.	the appearance of unsubstituted glucopyranose residues in nitrocellulose (nc) induced by desulfovibrio desulfuricans was established by (13)c-nmr spectroscopy. after contact with bacterial cells, the degree of substitution by nitro groups in nc decreased from 2.59 to 2.40. the bacteria possess intra- and extracellular nitroesterase activities, which are responsible for denitration of the polymer. the presence of nc in the growth medium influences the extracellular nitroesterase activity. it is s ...	2004	15310283
roles of noncoordinated aromatic residues in redox regulation of cytochrome c3 from desulfovibrio vulgaris miyazaki f.	the roles of aromatic residues in redox regulation of cytochrome c(3) were investigated by site-directed mutagenesis at every aromatic residue except for axial ligands (phe20, tyr43, tyr65, tyr66, his67, and phe76). the mutations at phe20 induced large chemical shift changes in the nmr signals for hemes 1 and 3, and large changes in the microscopic redox potentials of hemes 1 and 3. the nmr signals of the axial ligands of hemes 1 and 3 were also affected. analysis of the nature of the mutations ...	2004	15323546
overexpression and purification of treponema pallidum rubredoxin; kinetic evidence for a superoxide-mediated electron transfer with the superoxide reductase neelaredoxin.	superoxide reductases are a class of non-haem iron enzymes which catalyse the monovalent reduction of the superoxide anion o2- into hydrogen peroxide and water. treponema pallidum (tp), the syphilis spirochete, expresses the gene for a superoxide reductase called neelaredoxin, having the iron protein rubredoxin as the putative electron donor necessary to complete the catalytic cycle. in this work, we present the first cloning, overexpression in escherichia coli and purification of the tp rubredo ...	2004	15328557
structure of superoxide reductase bound to ferrocyanide and active site expansion upon x-ray-induced photo-reduction.	some sulfate-reducing and microaerophilic bacteria rely on the enzyme superoxide reductase (sor) to eliminate the toxic superoxide anion radical (o2-). sor catalyses the one-electron reduction of o2- to hydrogen peroxide at a nonheme ferrous iron center. the structures of desulfoarculus baarsii sor (mutant e47a) alone and in complex with ferrocyanide were solved to 1.15 and 1.7 a resolution, respectively. the latter structure, the first ever reported of a complex between ferrocyanide and a pro ...	2004	15341736
a theoretical study of spin states in ni-s4 complexes and models of the [nife] hydrogenase active site.	we have applied density functional theory, using both pure (bp86) and hybrid (b3lyp and b3lyp*) functionals, to investigate structural parameters and reaction energies for nickel(ii)-sulfur coordination compounds, as well as for small cluster models of the ni-si and ni-r redox state of [nife] hydrogenases. results obtained investigating experimentally well-characterized complexes show that bp86 is well suited to describe the structural features of this class of compounds. however, the singlet-tr ...	2004	15365900
roll with the flow: microbial masters of redox chemistry.		2004	15381191
inhibition and aerobic inactivation kinetics of desulfovibrio fructosovorans nife hydrogenase studied by protein film voltammetry.	we have used protein film voltammetry to study the nife hydrogenase from desulfovibrio fructosovorans. we show how measurements of transient activity following the addition in the electrochemical cell of h(2), co, or o(2) allow simple and virtually instantaneous determinations of the michaelis constant, inhibition constant, or rate of inactivation, respectively, thus opening new opportunities to study the active site of nife hydrogenases. the binding and release of co occur within a fraction of ...	2004	15382953
epr spectroscopy of protein microcrystals oriented in a liquid crystalline polymer medium.	correlation of the g-tensor of a paramagnetic active center of a protein with its structure provides a unique experimental information on the electronic structure of the metal site. to address this problem, we made solid films containing metalloprotein (desulfovibrio gigas cytochrome c(3)) microcrystals. the microcrystals in a liquid crystalline polymer medium (water/hydroxypropylcellulose) were partially aligned by a shear flow. a strong orientation effect of the metalloprotein was observed by ...	2004	15388083
desulfovibrio bastinii sp. nov. and desulfovibrio gracilis sp. nov., moderately halophilic, sulfate-reducing bacteria isolated from deep subsurface oilfield water.	two moderately halophilic, mesophilic, sulfate-reducing bacteria were isolated from production-water samples from emeraude oilfield, congo. motile, vibrioid cells of srl4225t grew optimally at a concentration of 4 % nacl, at ph 5.8-6.2, with a minimal ph for growth of 5.2, showing that it is a moderately acidophilic bacterium. cells of srl6146t were motile, curved or vibrioid, long and thin rods. optimal growth was obtained at a concentration of 5-6 % nacl, at ph 6.8-7.2. the nutritional require ...	2004	15388730
desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir.	a novel sulphate-reducing bacterium (al1t) was recovered from a soured oil well in purdu bay, alaska. light and atomic force microscopy observations revealed that cells were gram-negative, vibrio-shaped and motile by means of a single polar flagellum. the carbon and energy sources used by the isolate and the salinity, temperature and ph ranges facilitating its growth proved to be typical of a partial lactate-oxidizing, moderately halophilic, mesophilic, sulphate-reducing bacterium. analysis of t ...	2004	15388739
[stages of biofilm formation by sulfate-reducing bacteria].	taxis to fe3+ ions and adhesion to steel-3 of sulphate-reducing bacteria different by corrosion activity have been investigated. it has been shown that taxis activity of cells from the postgate medium "b" was higher than from the buffer. aggressive strains desulfovibrio indonensis, desulfovibrio sp. possessed higher activity taxis with respect to fe3+ ions. it has been noted that aggressive strains of sulphate-reducing bacteria adhered more actively to the steel surface and formed more powerful ...	2004	15456221
thermal unfolding of apo and holo desulfovibrio desulfuricans flavodoxin: cofactor stabilizes folded and intermediate states.	we here compare thermal unfolding of the apo and holo forms of desulfovibrio desulfuricans flavodoxin, which noncovalently binds a flavin mononucleotide (fmn) cofactor. in the case of the apo form, fluorescence and far-uv circular dichroism (cd) detected transitions are reversible but do not overlap (t(m) of 50 and 60 degrees c, respectively, ph 7). the thermal transitions for the holo form follow the same pattern but occur at higher temperatures (t(m) of 60 and 67 degrees c for fluorescence and ...	2004	15461458
bacterial community associated with black band disease in corals.	black band disease (bbd) is a virulent polymicrobial disease primarily affecting massive-framework-building species of scleractinian corals. while it has been well established that the bbd bacterial mat is dominated by a cyanobacterium, the quantitative composition of the bbd bacterial mat community has not described previously. terminal-restriction fragment length polymorphism (t-rflp) analysis was used to characterize the infectious bacterial community of the bacterial mat causing bbd. these a ...	2004	15466538
isolation of sulfate-reducing bacteria from the terrestrial deep subsurface and description of desulfovibrio cavernae sp. nov.	deep subsurface sandstones in the area of berlin (germany) located 600 to 1060 m below the surface were examined for the presence of viable microorganisms. the in situ temperatures at the sampling sites ranged from 37 to 45 degrees c. investigations focussed on sulfate-reducing bacteria able to grow on methanol and triethylene glycol, which are added as chemicals to facilitate the long-term underground storage of natural gas. seven strains were isolated from porewater brines in the porous sandst ...	2004	15490555
cofactor-apoprotein hydrogen bonding in oxidized and fully reduced flavodoxin monitored by trans-hydrogen-bond scalar couplings.	hydrogen bonding plays a key role in the tight binding of the fmn cofactor and the regulation of its redox properties in flavodoxins. hydrogen bonding interactions can be directly observed in solution by multidimensional heteronuclear nmr spectroscopy through the scalar couplings between donor and acceptor nuclei. here we report on the detection of intermolecular trans-hydrogen-bond couplings ((h)j) between the flavin ring system and the backbone of desulfovibrio vulgaris flavodoxin in the oxidi ...	2004	15515086
[effect of corrosion inhibitor on adhesion of sulfate-reducing bacteria to steel and their production of exopolymer complex].	it was shown in the laboratory investigations that the cells of sulphate-reducing bacteria of both aggressive desulfovibrio sp. strain kiev-10 and nonaggressive desulfovibrio desulfuricans strain kiev-45 strains can produce exopolysaccharides (eps). plankton (freely floating) cells of sulphate-reducing bacteria produce greater quantity of eps than the cells of the biofilm formed on steel. the inducing effect of metal on eps synthesis by sulphate-reducing bacteria has been established. the conten ...	2004	15515905
direct monitoring of the electron pool effect of cytochrome c3 by highly sensitive eqcm measurements.	cytochrome c(3) from desulfovibrio vulgaris has four hemes per molecule, and a redox change at the hemes alters the conformation of the protein, leading to a redox-dependent change in the interaction of cytochrome c(3) with redox partners (an electron acceptor or an electron donor). the redox-dependent change in this interaction was directly monitored by the high-performance electrochemical quartz crystal microbalance (eqcm) technique that has been improved to give high sensitivity in solution. ...	2004	15517437
reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria.	relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. the recent availability of complete finished or draft-quality genome sequences for seven representatives allowed us to investigate the genetic and regulatory factors in a number of key pathways involved in the biosynthesis of building blocks and cofactors, metal-ion homeostasis, stress response, and energy metabolism using a combination of regulatory ...	2004	15535866
physiological and gene expression analysis of inhibition of desulfovibrio vulgaris hildenborough by nitrite.	a desulfovibrio vulgaris hildenborough mutant lacking the nrfa gene for the catalytic subunit of periplasmic cytochrome c nitrite reductase (nrfha) was constructed. in mid-log phase, growth of the wild type in medium containing lactate and sulfate was inhibited by 10 mm nitrite, whereas 0.6 mm nitrite inhibited the nrfa mutant. lower concentrations (0.04 mm) inhibited the growth of both mutant and wild-type cells on plates. macroarray hybridization indicated that nitrite upregulates the nrfha ge ...	2004	15547266
sulfate-reducing bacteria in tubes constructed by the marine infaunal polychaete diopatra cuprea.	marine infaunal burrows and tubes greatly enhance solute transport between sediments and the overlying water column and are sites of elevated microbial activity. biotic and abiotic controls of the compositions and activities of burrow and tube microbial communities are poorly understood. the microbial communities in tubes of the marine infaunal polychaete diopatria cuprea collected from two different sediment habitats were examined. the bacterial communities in the tubes from a sandy sediment di ...	2004	15574900
multiple orientations in a physiological complex: the pyruvate-ferredoxin oxidoreductase-ferredoxin system.	ferredoxin i from desulfovibrio africanus (da fdi) is a small acidic [4fe-4s] cluster protein that exchanges electrons with pyruvate-ferredoxin oxidoreductase (pfor), a key enzyme in the energy metabolism of anaerobes. the thermodynamic properties and the electron transfer between pfor and either native or mutated fdi have been investigated by microcalorimetry and steady-state kinetics, respectively. the association constant of the pfor-fdi complex is 3.85 x 10(5) m(-1), and the binding affinity ...	2004	15581360
continuous removal of cr(vi) from aqueous solution catalysed by palladised biomass of desulfovibrio vulgaris.	growth-decoupled cells of desulfovibrio vulgaris ncimb 8303 can be used to reduce pd(ii) to cell-bound pd(0) (bio-pd(0)), a bioinorganic catalyst capable of reducing hexavalent chromium to less toxic cr(iii), using formate as the electron donor. magnetic resonance imaging showed that bio-pd(0), immobilized in chitosan and agar beads, is distinguishable from the surrounding gel and is evenly dispersed within the immobilization matrix. agar-immobilized bio-pd(0) and 'chemical pd(0)' were packed in ...	2004	15604792
an orientation-selected endor and hyscore study of the ni-c active state of desulfovibrio vulgaris miyazaki f hydrogenase.	electron nuclear double resonance (endor) and hyperfine sublevel correlation spectroscopy (hyscore) are applied to study the active site of catalytic [nife]-hydrogenase from desulfovibrio vulgaris miyazaki f in the reduced ni-c state. these techniques offer a powerful tool for detecting nearby magnetic nuclei, including a metal-bound substrate hydrogen, and for mapping the spin density distribution of the unpaired electron at the active site. the observed hyperfine couplings are assigned via com ...	2004	15611882
sulphate respiration from hydrogen in desulfovibrio bacteria: a structural biology overview.	sulphate-reducing organisms are widespread in anaerobic enviroments, including the gastrointestinal tract of man and other animals. the study of these bacteria has attracted much attention over the years, due also to the fact that they can have important implications in industry (in biocorrosion and souring of oil and gas deposits), health (in inflamatory bowel diseases) and the environment (bioremediation). the characterization of the various components of the electron transport chain associate ...	2004	15950057
fmn binding and unfolding of desulfovibrio desulfuricans flavodoxin: "hidden" intermediates at low denaturant concentrations.	the flavin mononucleotide (fmn) cofactor in desulfovibrio desulfuricans flavodoxin stays associated with the polypeptide upon guanidine hydrochloride (guhcl) induced unfolding. using isothermal titration calorimetry (itc), we determined the affinity of fmn for the flavodoxin polypeptide as a function of both urea and guhcl concentrations (ph 7, 25 degrees c). the fmn affinity for folded and guhcl-unfolded flavodoxin differs 10-fold, which is in agreement with the difference in thermodynamic stab ...	2004	15698959
inhibiting mild steel corrosion from sulfate-reducing bacteria using antimicrobial-producing biofilms in three-mile-island process water.	biofilms were used to produce gramicidin s (a cyclic decapeptide) to inhibit corrosion-causing, sulfate-reducing bacteria (srb). in laboratory studies these biofilms protected mild steel 1010 continuously from corrosion in the aggressive, cooling service water of the amergen three-mile-island (tmi) nuclear plant, which was augmented with reference srb. the growth of both reference srb (gram-positive desulfosporosinus orientis and gram-negative desulfovibrio vulgaris) was shown to be inhibited by ...	2004	12898064
a new function of the desulfovibrio vulgaris hildenborough [fe] hydrogenase in the protection against oxidative stress.	sulfate-reducing bacteria, like desulfovibrio vulgaris hildenborough, have developed a set of reactions allowing them to survive in oxic environments and even to reduce molecular oxygen to water. d. vulgaris contains a cytoplasmic superoxide reductase (sor) and a periplasmic superoxide dismutase (sod) involved in the elimination of superoxide anions. to assign the function of sod, the periplasmic [fe] hydrogenase activity was followed in both wild-type and sod deletant strains. this activity was ...	2004	14594815
incorporation of either molybdenum or tungsten into formate dehydrogenase from desulfovibrio alaskensis ncimb 13491; epr assignment of the proximal iron-sulfur cluster to the pterin cofactor in formate dehydrogenases from sulfate-reducing bacteria.	we report the characterization of the molecular properties and epr studies of a new formate dehydrogenase (fdh) from the sulfate-reducing organism desulfovibrio alaskensis ncimb 13491. fdhs are enzymes that catalyze the two-electron oxidation of formate to carbon dioxide in several aerobic and anaerobic organisms. d. alaskensis fdh is a heterodimeric protein with a molecular weight of 126+/-2 kda composed of two subunits, alpha=93+/-3 kda and beta=32+/-2 kda, which contains 6+/-1 fe/molecule, 0. ...	2004	14669076
a glutamate is the essential proton transfer gate during the catalytic cycle of the [nife] hydrogenase.	kinetic, epr, and fourier transform infrared spectroscopic analysis of desulfovibrio fructosovorans [nife] hydrogenase mutants targeted to glu-25 indicated that this amino acid participates in proton transfer between the active site and the protein surface during the catalytic cycle. replacement of that glutamic residue by a glutamine did not modify the spectroscopic properties of the enzyme but cancelled the catalytic activity except the para-h(2)/ortho-h(2) conversion. this mutation impaired t ...	2004	14688251
improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraints.	protein comparative modeling has useful applications in large-scale structural initiatives and in rational design of drug targets in medicinal chemistry. the reliability of a homology model is dependent on the sequence identity between the query and the structural homologue used as a template for modeling. here, we present a method for the utilization and conservation of important structural features of template structures by providing additional spatial restraints in comparative modeling progra ...	2004	14691673
molecular basis for redox-bohr and cooperative effects in cytochrome c3 from desulfovibrio desulfuricans atcc 27774: crystallographic and modeling studies of oxidized and reduced high-resolution structures at ph 7.6.	the tetraheme cytochrome c3 is a small metalloprotein with ca. 13,000 da found in sulfate-reducing bacteria, which is believed to act as a partner of hydrogenase. the three-dimensional structure of the oxidized and reduced forms of cytochrome c3 from desulfovibrio desulfuricans atcc 27774 at ph 7.6 were determined using high-resolution x-ray crystallography and were compared with the previously determined oxidized form at ph 4.0. theoretical calculations were performed with both structures, usin ...	2004	14705030
periplasmic cytochrome c3 of desulfovibrio vulgaris is directly involved in h2-mediated metal but not sulfate reduction.	kinetic parameters and the role of cytochrome c(3) in sulfate, fe(iii), and u(vi) reduction were investigated in desulfovibrio vulgaris hildenborough. while sulfate reduction followed michaelis-menten kinetics (k(m) = 220 micro m), loss of fe(iii) and u(vi) was first-order at all concentrations tested. initial reduction rates of all electron acceptors were similar for cells grown with h(2) and sulfate, while cultures grown using lactate and sulfate had similar rates of metal loss but lower sulfa ...	2004	14711670
superoxide reductase from desulfoarculus baarsii: identification of protonation steps in the enzymatic mechanism.	superoxide reductase (sor) is a metalloenzyme that catalyzes the reduction of o2*- to h2o2 and provides an antioxidant mechanism in some anaerobic and microaerophilic bacteria. its active site contains an unusual mononuclear ferrous center (center ii). protonation processes are essential for the reaction catalyzed by sor, since two protons are required for the formation of h2o2. we have investigated the acido-basic and ph dependence of the redox properties of the active site of sor from desulfoa ...	2004	14730986
thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the central indian ridge.	a thermophilic, marine, anaerobic, chemolithoautotrophic, sulfate-reducing bacterium, strain cir29812t, was isolated from a deep-sea hydrothermal vent site at the kairei vent field on the central indian ridge. cells were gram-negative motile rods that did not form spores. the temperature range for growth was 55-80 degrees c, with an optimum at 70 degrees c. the nacl concentration range for growth was 10-35 g l(-1), with an optimum at 25 g l(-1). the ph range for growth was 6-6.7, with an optimum ...	2004	14742485
cloning and expression of the enolase gene from desulfovibrio vulgaris (miyazaki f).	the gene encoding an enolase from desulfovibrio vulgaris (miyazaki f) was cloned and overexpressed in escherichia coli. a 2.1-kb dna fragment, isolated from d. vulgaris (miyazaki f) by double digestion with psti and bamhi, contained an enolase gene (eno) and part of the methylenetetrahydrofolate dehydrogenase gene (fold). the nucleotide sequence of eno indicates that the protein monomer is composed of 434 amino acids. an expression system for eno under control of the t7 promoter was constructed ...	2004	14746912
enzymatic mechanism of fe-only hydrogenase: density functional study on h-h making/breaking at the diiron cluster with concerted proton and electron transfers.	the mechanism of the enzymatic hydrogen bond forming/breaking (2h(+) + 2e<==>h(2)) and the plausible charge and spin states of the catalytic diiron subcluster [fefe](h) of the h cluster in fe-only hydrogenases are probed computationally by the density functional theory. it is found that the active center [fefe](h) can be rationally simulated as [[h](ch(3)s)(co)(cn(-))fe(p)(co(b))(mu-srs)fe(d)(co)(cn(-))l], where the monovalence [h] stands for the [4fe4s](h)(2+) subcluster bridged to the [fefe](h ...	2004	14753812