Publications

zinc-substituted desulfovibrio gigas desulforedoxins: resolving subunit degeneracy with nonsymmetric pseudocontact shifts.	desulfovibrio gigas desulforedoxin (dx) consists of two identical peptides, each containing one [fe-4s] center per monomer. variants with different iron and zinc metal compositions arise when desulforedoxin is produced recombinantly from escherichia coli. the three forms of the protein, the two homodimers [fe(iii)/fe(iii)]dx and [zn(ii)/zn(ii)]dx, and the heterodimer [fe(iii)/zn(ii)]dx, can be separated by ion exchange chromatography on the basis of their charge differences. once separated, the ...	2002	12237467
structural studies of the carbon monoxide complex of [nife]hydrogenase from desulfovibrio vulgaris miyazaki f: suggestion for the initial activation site for dihydrogen.	the carbon monoxide complex of [nife]hydrogenase from desulfovibrio vulgaris miyazaki f has been characterized by x-ray crystallography and absorption and resonance raman spectroscopy. nine crystal structures of the [nife]hydrogenase in the co-bound and co-liberated forms were determined at 1.2-1.4 a resolution. the exogenously added co was assigned to be bound to the ni atom at the ni-fe active site. the co was not replaced with h(2) in the dark at 100 k, but was liberated by illumination with ...	2002	12296727
ammonia production by ruminal microorganisms and enumeration, isolation, and characterization of bacteria capable of growth on peptides and amino acids from the sheep rumen.	excessive nh(3) production in the rumen is a major nutritional inefficiency in ruminant animals. experiments were undertaken to compare the rates of nh(3) production from different substrates in ruminal fluid in vitro and to assess the role of asaccharolytic bacteria in nh(3) production. ruminal fluid was taken from four rumen-fistulated sheep receiving a mixed hay-concentrate diet. the calculated rate of nh(3) production from trypticase varied from 1.8 to 19.7 nmol mg of protein(-1) min(-1) dep ...	2002	12324340
bioreduction and biocrystallization of palladium by desulfovibrio desulfuricans ncimb 8307.	the reduction of pd(ii) to pd(0) was accelerated by using the sulfate-reducing bacterium desulfovibrio desulfuricans ncimb 8307 at the expense of formate or h(2) as electron donors at ph 2-7. with formate no reduction occurred at ph 2, but with h(2) 50% of the activity was retained at ph 2, with the maximum rate (1.3-1.4 micromol min(-1) mg dry cells(-1)) seen at ph 3-7, which was similar to the rate with formate at neutral ph. excess nitrate was inhibitory to pd(ii) reduction using formate, but ...	2002	12325145
comparison of the refined crystal structures of wild-type (1.34 a) flavodoxin from desulfovibrio vulgaris and the s35c mutant (1.44 a) at 100 k.	engineered flavodoxins in which a surface residue has been replaced by an exposed cysteine are useful modules to link multi-domain redox proteins obtained by gene fusion to electrode surfaces. in the present work, the crystal structure of the s35c mutant of desulfovibrio vulgaris flavodoxin in the oxidized state has been determined and compared with a refined structure of the wild type (wt). the structure of wt flavodoxin (space group p4(3)2(1)2, unit-cell parameters a = 50.52, b = 50.52, c = 13 ...	2002	12351822
isolation of the provisionally named desulfovibrio fairfieldensis from human periodontal pockets.	sulfate-reducing bacteria have recently been associated with periodontitis and proposed to play a role in the pathogenesis of this chronic inflammatory process. eight isolates of sulfate-reducing bacteria belonging to the genus desulfovibrio were obtained from the periodontal pockets of five out of seven patients presenting with active periodontitis. a multiplex pcr was devised for their identification at the species level. all isolates were identified as desulfovibrio fairfieldensis, a recently ...	2002	12354215
sulfate respiration in desulfovibrio vulgaris hildenborough. structure of the 16-heme cytochrome c hmca at 2.5-a resolution and a view of its role in transmembrane electron transfer.	the crystal structure of the high molecular mass cytochrome c hmca from desulfovibrio vulgaris hildenborough is described. hmca contains the unprecedented number of sixteen hemes c attached to a single polypeptide chain, is associated with a membrane-bound redox complex, and is involved in electron transfer from the periplasmic oxidation of hydrogen to the cytoplasmic reduction of sulfate. the structure of hmca is organized into four tetraheme cytochrome c(3)-like domains, of which the first is ...	2002	12356749
converting the nifes carbon monoxide dehydrogenase to a hydrogenase and a hydroxylamine reductase.	substitution of one amino acid for another at the active site of an enzyme usually diminishes or eliminates the activity of the enzyme. in some cases, however, the specificity of the enzyme is changed. in this study, we report that the changing of a metal ligand at the active site of the nifes-containing carbon monoxide dehydrogenase (codh) converts the enzyme to a hydrogenase or a hydroxylamine reductase. codh with alanine substituted for cys(531) exhibits substantial uptake hydrogenase activit ...	2002	12374822
hydroxylamine reductase activity of the hybrid cluster protein from escherichia coli.	the hybrid cluster protein (hcp; formerly termed the prismane protein) has been extensively studied due to its unique spectroscopic properties. although the structural and spectroscopic characteristics are well defined, its enzymatic function, up to this point, has remained unidentified. while it was proposed that hcp acts in some step of nitrogen metabolism, a specific role for this enzyme remained unknown. recent studies of hcp purified from escherichia coli have identified a novel hydroxylami ...	2002	12374823
carbon monoxide cycling by desulfovibrio vulgaris hildenborough.	sulfate-reducing bacteria, like desulfovibrio vulgaris hildenborough, use the reduction of sulfate as a sink for electrons liberated in oxidation reactions of organic substrates. the rate of the latter exceeds that of sulfate reduction at the onset of growth, causing a temporary accumulation of hydrogen and other fermentation products (the hydrogen or fermentation burst). in addition to hydrogen, d. vulgaris was found to produce significant amounts of carbon monoxide during the fermentation burs ...	2002	12374824
pulsed electron-electron double resonance on multinuclear metal clusters: assignment of spin projection factors based on the dipolar interaction.	the interaction between two paramagnetic metal centers, a [3fe-4s](+) cluster and a [nife] center, is investigated in the hydrogenase from desulfovibrio vulgaris miyazaki f by pulsed eldor (electron-electron double resonance). the distance between the metal centers is known from x-ray crystallography. the experimental dipolar spin-spin interaction deviates from the value expected for two point-dipoles located at the centers of the metal clusters. an extended spin-coupling model accounting for th ...	2002	12381206
mercury methylation by desulfovibrio desulfuricans nd132 in the presence of polysulfides.	the extracellular speciation of mercury may control bacterial uptake and methylation. mercury-polysulfide complexes have recently been shown to be prevalent in sulfidic waters containing zero-valent sulfur. despite substantial increases in total dissolved mercury concentration, methylation rates in cultures of desulfovibrio desulfuricans nd132 equilibrated with cinnabar did not increase in the presence of polysulfides, as expected due to the large size and charged nature of most of the complexes ...	2002	12406773
stoichiometric redox titrations of complex metalloenzymes.		2002	12418235
thermodynamic and kinetic characterization of trihaem cytochrome c3 from desulfuromonas acetoxidans.	trihaem cytochrome c3 (also known as cytochrome c551.5 and cytochrome c7) is isolated from the periplasmic space of desulfuromonas acetoxidans, a sulfur-reducing bacterium. thermodynamic and kinetic data for the trihaem cytochrome c3 are presented and discussed in the context of the possible physiological implications of its functional properties with respect to the natural habitat of d. acetoxidans, namely as a symbiont with green sulfur bacteria working as a mini-sulfuretum. the thermodynamic ...	2002	12423372
bioremediation of chromate: thermodynamic analysis of the effects of cr(vi) on sulfate-reducing bacteria.	developing new bioremediation processes for soils and effluents polluted by cr(vi) requires the selection of the most efficient and the most heavy-metal-resistant bacteria. the effects of cr(vi) on bioenergetic metabolism in two sulfate-reducing bacteria (srb), desulfovibrio vulgaris hildenborough and desulfomicrobium norvegicum, were monitored using isothermal microcalorimetry. the complete reduction of cr(vi) to cr(iii) was studied by spectrophotometry and by speciation using a combination of ...	2002	12436319
flavin thermodynamics explain the oxygen insensitivity of enteric nitroreductases.	bacterial nitroreductases are nad(p)h-dependent flavoenzymes which catalyze the oxygen-insensitive reduction of nitroaromatics, quinones, and riboflavin derivatives. despite their broad substrate specificity, their reactivity is very specific for two-electron, not one-electron, chemistry. we now describe the thermodynamic properties of the flavin mononucleotide cofactor of enterobacter cloacae nitroreductase (nr), determined under a variety of solution conditions. the two-electron redox midpoint ...	2002	12450383
growth and chemosensory behavior of sulfate-reducing bacteria in oxygen-sulfide gradients.	growth and chemotactic behavior in oxic-anoxic gradients were studied with two freshwater and four marine strains of sulfate-reducing bacteria related to the genera desulfovibrio, desulfomicrobium or desulfobulbus. cells were grown in oxygen-sulfide counter-gradients within tubes filled with agar-solidified medium. the immobilized cells grew mainly in the anoxic zone, revealing a peak below the oxic-anoxic interface. all tested strains survived exposure to air for 8 h and all were capable of oxy ...	2002	19709210
sulfate-reducing bacteria in human feces and their association with inflammatory bowel diseases.	we have searched for sulfate-reducing bacteria in the feces of 41 healthy individuals and 110 patients from a hepato-gastro-enterology unit using a specific liquid medium (test-kit labège, compagnie française de géothermie, orléans, france). the 110 patients were separated in 22 patients presenting with inflammatory bowel diseases and 88 patients hospitalized for other lower (n=30) or upper (n=58) digestive tract diseases. sulfate-reducing bacteria were isolated from 10 healthy individuals (24%) ...	2002	19709217
sulfate-reducing bacterial community response to carbon source amendments in contaminated aquifer microcosms.	abstract microbial sulfate reduction is an important metabolic activity in many reduced habitats. however, little is known about the sulfate-reducing communities inhabiting petroleum hydrocarbon (phc)-contaminated freshwater aquifer sediments. the purpose of this study was to identify the groups of sulfate-reducing bacteria (srb) selectively stimulated when sediment from a phc-contaminated freshwater aquifer was incubated in sulfate-reducing aquifer microcosms that were amended with specific car ...	2002	19709270
susceptibility to antibiotics and biochemical properties of desulfovibrio desulfuricans strains.	susceptibility to several antibiotics and biochemical properties of intestinal and soil strains of desulfovibrio desulfuricans bacteria were investigated using the tests: atb ana, sceptor anaerobic mic/id and api zym. it was demonstrated that the d. desulfuricans strains were resistant to penicillin, cefoxitin, clindamycin, metronidazole, erythromycin, rifampicin and teicoplanin. the strains initially susceptible to imipenem became resistant to this drug following 72 h incubation with it. of 25 ...	2001	12197616
a 6940 bp dna fragment from desulfovibrio gigas contains genes coding for lipoproteins, universal stress response and transcriptional regulator protein homologues.	the nucleotide sequence of a 6940 bp dna fragment from desulfovibrio gigas, containing seven orfs was determined. orf-1 encodes a probable lipoprotein having high similarities with lytic transglycosylases. orf-2 encodes a polypeptide that does not show homologies with proteins deposited in the database, but it contains the consensus pattern of class ii aminoacyl-trna synthetases. the putative protein encoded by orf-3 possesses high similarities with universal stress response proteins from the us ...	2001	11916257
comparative analysis of polychlorinated biphenyl-dechlorinating communities in enrichment cultures using three different molecular screening techniques.	the catalysts for many microbially mediated environmental processes such as the dechlorination of polychlorinated biphenyls (pcbs) have been difficult to identify by traditional isolation techniques. numerous, as yet unsuccessful, attempts have been made to isolate and culture the dechlorinating species. to overcome this limitation, amplified rdna restriction analysis (ardra) of a clone library, denaturing gradient gel electrophoresis (dgge) and terminal restriction fragment length polymorphism ...	2001	11846761
crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase.	in anaerobic organisms, the decarboxylation of pyruvate, a crucial component of intermediary metabolism, is catalyzed by the metalloenzyme pyruvate: ferredoxin oxidoreductase (pfor) resulting in the generation of low potential electrons and the subsequent acetylation of coenzyme a (coa). pfor is the only enzyme for which a stable acetyl thiamine diphosphate (thdp)-based free radical reaction intermediate has been identified. the 1.87 a-resolution structure of the radical form of pfor from desulf ...	2001	11752578
physical, chemical, and microbiological characteristics of microbial mats (kopara) in the south pacific atolls of french polynesia.	microbial mats that develop in shallow brackish and hyposaline ponds in the rims of two french polynesian atolls (rangiroa and tetiaroa) were intensively investigated during the past three years. comparative assessment of these mats (called kopara in polynesian language) showed remarkable similarities in their composition and structure. due to the lack of iron, the color of the cyanobacterial pigments produced remained visible through the entire depth of the mats (20-40 cm depth), with alternate ...	2001	11766060
[nife] hydrogenase from desulfovibrio desulfuricans atcc 27774: gene sequencing, three-dimensional structure determination and refinement at 1.8 a and modelling studies of its interaction with the tetrahaem cytochrome c3.	the primary and three-dimensional structures of a [nife] hydrogenase isolated from d. desulfitricans atcc 27774 were determined, by nucleotide analysis and single-crystal x-ray crystallography. the three-dimensional structural model was refined to r=0.167 and rfree=0.223 using data to 1.8 a resolution. two unique structural features are observed: the [4fe-4s] cluster nearest the [nife] centre has been modified [4fe-3s-3o] by loss of one sulfur atom and inclusion of three oxygen atoms; a three-fo ...	2001	11191224
modeling the active sites of metalloenzymes. 4. predictions of the unready states of [nife] desulfovibrio gigas hydrogenase from density functional theory.	density functional theory has been used to predict the structures of a variety of active site models for the unready states, ni-a and ni-su, of the [nife] hydrogenase from desulfovibrio gigas. by comparing available experimental results on ni-a, ni-su, and ni-si with the computational results on these model complexes, we have been able to identify the most likely formulas and structures for the active sites of ni-a and ni-su. ni-a is predicted to be a ni(iii)-fe(ii) species with the bridging hyd ...	2001	11195380
cooperativity between electrons and protons in a monomeric cytochrome c(3): the importance of mechano-chemical coupling for energy transduction.	to fully understand the structural bases for the mechanisms of biological energy transduction, it is essential to determine the microscopic thermodynamic parameters which describe the properties of each centre involved in the reactions, as well as its interactions with the others. these interactions between centres can then be interpreted in the light of structural features of the proteins. redox titrations of cytochrome c(3) from desulfovibrio desulfuricans atcc 27774 followed by nmr and visibl ...	2001	11948869
a membrane-bound cytochrome c3: a type ii cytochrome c3 from desulfovibrio vulgaris hildenborough.	a new tetraheme cytochrome c3 was isolated from the membranes of desulfovibrio vulgaris hildenborough (dvh). this cytochrome has a molecular mass of 13.4 kda and a pi of 5.5 and contains four heme c groups with apparent reduction potentials of -170 mv, -235 mv, -260 mv and -325 mv at ph 7.6. the complete sequence of the new cytochrome, retrieved from the preliminary data of the dvh genome, shows that this cytochrome is homologous to the "acidic" cytochrome c3 from desulfovibrio africanus (da). a ...	2001	11948878
degradation of dibenzothiophene by sulfate-reducing bacteria cultured in the presence of only nitrogen gas.	to remove sulfur compounds in petroleum, we isolated sulfate-reducing bacteria that could degrade dibenzothiophene in the presence of only nitrogen gas. among the 19 strains isolated, some could grow in the presence of 10% (v/v) kerosene and of which two strains were identified as desulfomicrobium escambium and desulfovibrio longreachii. gas chromatography of the ethyl-acetate extract of bacterial cultures, in which 10% or more of the dibenzothiophene initially present was degraded, gave five un ...	2001	16232954
microbial communities and exopolysaccharides from polynesian mats.	microbial mats present in two shallow atolls of french polynesia were characterized by high amounts of exopolysaccharides associated with cyanobacteria as the predominating species. cyanobacteria were found in the first centimeters of the gelatinous mats, whereas deeper layers showing the occurrence of the sulfate reducers desulfovibrio and desulfobacter species as determined by the presence of specific biomarkers. exopolysaccharides were extracted from these mats and partially characterized. al ...	2001	14961381
rubrerythrin and rubredoxin oxidoreductase in desulfovibrio vulgaris: a novel oxidative stress protection system.	evidence is presented for an alternative to the superoxide dismutase (sod)-catalase oxidative stress defense system in desulfovibrio vulgaris (strain hildenborough). this alternative system consists of the nonheme iron proteins, rubrerythrin (rbr) and rubredoxin oxidoreductase (rbo), the product of the rbo gene (also called desulfoferrodoxin). a deltarbo strain of d. vulgaris was found to be more sensitive to internal superoxide exposure than was the wild type. unlike rbo, expression of plasmid- ...	2001	11114906
equilibrium unfolding of dimeric desulfoferrodoxin involves a monomeric intermediate: iron cofactors dissociate after polypeptide unfolding.	here we report the conformational stability of homodimeric desulfoferrodoxin (dfx) from desulfovibrio desulfuricans (atcc 27774). the dimer is formed by two dfx monomers linked through beta-strand interactions in two domains; in addition, each monomer contains two different iron centers: one fe-(s-cys)(4) center and one fe-[s-cys+(n-his)(4)] center. the dissociation constant for dfx was determined to be 1 microm (deltag = 34 kj/mol of dimer) from the concentration dependence of aromatic residue ...	2001	11305909
superoxide reductase from desulfoarculus baarsii: reaction mechanism and role of glutamate 47 and lysine 48 in catalysis.	superoxide reductase (sor) is a small metalloenzyme that catalyzes reduction of o(2)()(-) to h(2)o(2) and thus provides an antioxidant mechanism against superoxide radicals. its active site contains an unusual mononuclear ferrous center, which is very efficient during electron transfer to o(2)()(-) [lombard, m., fontecave, m., touati, d., and nivière, v. (2000) j. biol. chem. 275, 115-121]. the reaction of the enzyme from desulfoarculus baarsii with superoxide was studied by pulse radiolysis m ...	2001	11305919
coexistence of a sulphate-reducing desulfovibrio species and the dehalorespiring desulfitobacterium frappieri tce1 in defined chemostat cultures grown with various combinations of sulfate and tetrachloroethene.	a two-member co-culture consisting of the dehalorespiring desulfitobacterium frappieri tce1 and the sulphate-reducing desulfovibrio sp. strain sulf1 was obtained via anaerobic enrichment from soil contaminated with tetrachloroethene (pce). in this co-culture, pce dechlorination to cis-dichloroethene was due to the activity of the dehalorespiring bacterium only. chemostat experiments with lactate as the primary electron donor for both strains along with varying sulphate and pce concentrations sho ...	2001	11321548
coiiiedta- reduction by desulfovibrio vulgaris and propagation of reactions involving dissolved sulfide and polysulfides.	the migration of 60co, dominantly via transport of co-edta complexes, into surface water and groundwater is a recognized concern at many nuclear production and storage sites. reduction of coiiiedta- to coiiedta2- should decrease the mobility of 60co in natural environments by stimulating ligand displacement with fe(iii) or al(iii) or by precipitation of cosx in sulfidic environments. in this study, we examine direct (enzymatic) and indirect (metabolite) reduction processes of coiiiedta- by the s ...	2001	11329708
the 'strict' anaerobe desulfovibrio gigas contains a membrane-bound oxygen-reducing respiratory chain.	sulfate-reducing bacteria are considered as strict anaerobic microorganisms, in spite of the fact that some strains have been shown to tolerate the transient presence of dioxygen. this report shows that membranes from desulfovibrio gigas grown in fumarate/sulfate contain a respiratory chain fully competent to reduce dioxygen to water. in particular, a membrane-bound terminal oxygen reductase, of the cytochrome bd family, was isolated, characterized, and shown to completely reduce oxygen to water ...	2001	11343703
two crystal structures of the cytoplasmic molybdate-binding protein modg suggest a novel cooperative binding mechanism and provide insights into ligand-binding specificity.	the x-ray structures of the cytoplasmic molybdate-binding protein modg from azotobacter vinelandii in two different crystal forms have been determined. for such a small protein it is remarkably complex. each 14.3 kda subunit contains two small beta-barrel domains, which display an ob-fold motif, also seen in the related structure of mode, a molybdenum-dependent transcriptional regulator, and very recently in the mop protein that, like modg, has been implicated in molybdenum homeostasis within th ...	2001	11352591
spectroscopic investigation and determination of reactivity and structure of the tetraheme cytochrome c3 from desulfovibrio desulfuricans essex 6.	cytochrome c3, a small (14-kda) soluble tetraheme protein was isolated from the periplasmic fraction of desulfovibrio desulfuricans strain essex 6. its major physiological function appears to be that of an electron carrier for the periplasmic hydrogenase. it has been also shown to interact with the high-molecular-mass cytochrome complex in the cytoplasmic membrane, which eventually feeds electrons into the membraneous quinone pool, as well as with the membrane-associated dissimilatory sulfite re ...	2001	11358521
the rate of formation of cytochrome c553 is not dependent on the nature of the unfolded state.		2001	11370667
tungsten-containing formate dehydrogenase from desulfovibrio gigas: metal identification and preliminary structural data by multi-wavelength crystallography.	the tungsten-containing formate dehydrogenase (w-fdh) isolated from desulfovibrio gigas has been crystallized in space group p2(1), with cell parameters a = 73.8 a, b = 111.3 a, c = 156.6 a and beta = 93.7 degrees. these crystals diffract to beyond 2.0 a on a synchrotron radiation source. w-fdh is a heterodimer (92 kda and 29 kda subunits) and two w-fdh molecules are present in the asymmetric unit. although a molecular replacement solution was found using the periplasmic nitrate reductase as a s ...	2001	11372198
recent theoretical predictions of the active site for the observed forms in the catalytic cycle of ni-fe hydrogenase.	various states or forms of the active site in ni-fe hydrogenase, both catalytically active and inactive forms, have been identified and investigated experimentally. until recently, the geometric structure of each form remained an open question. several recent theoretical studies with density functional theory have attempted to redress this deficiency. in this commentary, the similarities and differences among the structures proposed by these studies will be addressed.	2001	11372206
the influence of fluid shear and aici3 on the material properties of pseudomonas aeruginosa pao1 and desulfovibrio sp. ex265 biofilms.	an understanding of the material properties of biofilms is important when describing how biofilms physically interact with their environment. in this study, aerobic biofilms of pseudomonas aeruginosa pao1 and anaerobic sulfate-reducing bacteria (srb) biofilms of desulfovibrio sp. ex265 were grown under different fluid shear stresses (tau g) in a chemostat recycle loop. individual biofilm microcolonies were deformed by varying the fluid wall shear stress (tau w). the deformation was quantified in ...	2001	11381956
the effect of culture media on antigenic expression in sulfate-reducing bacteria.	the importance of sulfate-reducing bacteria (srb) in nature has been widely recognized for many years. however, little is known about the ecology of srb. the problem has been detecting, classifying, and quantifying these organisms. there are many shortcomings in the use of culture media for this purpose. as an alternative, fluorescent antibody (fa) techniques were considered as a method for the detection and identification of srb. antisera were prepared against whole cells of different species o ...	2001	11400049
identifying regulators of transcription in an obligate intracellular pathogen: a metal-dependent repressor in chlamydia trachomatis.	a prominent feature exhibited by chlamydia trachomatis growing in an iron-limiting environment is a differential pattern of protein expression. in many bacteria, iron-responsive proteins are regulated at the level of transcription by a family of repressors resembling the escherichia coli ferric uptake regulator (fur) protein. although the chlamydial genome sequencing project did not unveil an obvious fur homologue, a detailed examination indicated five unassigned open reading frames (orfs) that ...	2001	11401709
relativistic dft calculations of the paramagnetic intermediates of [nife] hydrogenase. implications for the enzymatic mechanism.		2001	11403633
isolation of desulfomicrobium orale sp. nov. and desulfovibrio strain ny682, oral sulfate-reducing bacteria involved in human periodontal disease.	the species of sulfate-reducing bacteria that prevail in sites affected by periodontal disease may be different from those commonly occurring in the digestive tracts of healthy individuals. ten strains of mesophilic sulfate-reducing bacteria (srb) were isolated from subgingival plaque in periodontal lesions of ten patients with periodontitis. characterization on the basis of morphological, physiological and phylogenetic properties demonstrated two distinct types of oral srb. one strain was a cur ...	2001	11411671
identification of a small tetraheme cytochrome c and a flavocytochrome c as two of the principal soluble cytochromes c in shewanella oneidensis strain mr1.	two abundant, low-redox-potential cytochromes c were purified from the facultative anaerobe shewanella oneidensis strain mr1 grown anaerobically with fumarate. the small cytochrome was completely sequenced, and the genes coding for both proteins were cloned and sequenced. the small cytochrome c contains 91 residues and four heme binding sites. it is most similar to the cytochromes c from shewanella frigidimarina (formerly shewanella putrefaciens) ncimb400 and the unclassified bacterial strain h1 ...	2001	11425747
mechanistic study of microbial control of hydrogen sulfide production in oil reservoirs.	microbial control of biogenic production of hydrogen sulfide in oil fields was studied in a model system consisting of pure cultures of the nitrate-reducing, sulfide-oxidizing bacterium (nr-sob) thiomicrospira sp. strain cvo and the sulfate-reducing bacterium (srb) desulfovibrio sp. strain lac6, as well as in microbial cultures enriched from produced water of a canadian oil reservoir. the presence of nitrate at concentrations up to 20 mm had little effect on the rate of sulfate reduction by a pu ...	2001	11427944
molecular characterization of desulfovibrio gigas neelaredoxin, a protein involved in oxygen detoxification in anaerobes.	desulfovibrio gigas neelaredoxin is an iron-containing protein of 15 kda, having a single iron site with a his(4)cys coordination. neelaredoxins and homologous proteins are widespread in anaerobic prokaryotes and have superoxide-scavenging activity. to further understand its role in anaerobes, its genomic organization and expression in d. gigas were studied and its ability to complement escherichia coli superoxide dismutase deletion mutant was assessed. in d. gigas, neelaredoxin is transcribed a ...	2001	11443075
identification of the gene encoding nadh-rubredoxin oxidoreductase in clostridium acetobutylicum.	nadh-rubredoxin oxidoreductase (nror), a flavoprotein from the obligately anaerobe clostridium acetobutylicum is encoded by an orf (nror) of 1140 nucleotides. whereas primary structure analysis reveals that nror has amino acid sequence patterns homologous with those involved in fad and nad-binding, the enzyme is distantly related to other flavoproteins in the databank. nror is highly active for reducing clostridial rubredoxin (rd) especially against c. acetobutylicum rd with an efficiency (k(cat ...	2001	11444870
use of 16s rrna-targeted oligonucleotide probes to investigate the distribution of sulphate-reducing bacteria in estuarine sediments.	the distribution of sulphate-reducing bacteria (srbs) in three anaerobic sediments, one predominantly freshwater and low sulphate and two predominantly marine and high sulphate, on the river tama, tokyo, japan, was investigated using 16s rrna-targeted oligonucleotide probes. hybridisation results and sulphate reduction measurements indicated that srbs are a minor part of the bacterial population in the freshwater sediments. only desulfobulbus and desulfobacterium were detected, representing 1.6% ...	2001	11451520
the genetic organization of desulfovibrio desulphuricans atcc 27774 bacterioferritin and rubredoxin-2 genes: involvement of rubredoxin in iron metabolism.	the anaerobic bacterium desulfovibrio desulphuricans atcc 27774 contains a unique bacterioferritin, isolated with a stable di-iron centre and having iron-coproporphyrin iii as its haem cofactor, as well as a type 2 rubredoxin with an unusual spacing of four amino acid residues between the first two binding cysteines. the genes encoding for these two proteins were cloned and sequenced. the deduced amino acid sequence of the bacterioferritin shows that it is among the most divergent members of thi ...	2001	11454214
crystallographic and ftir spectroscopic evidence of changes in fe coordination upon reduction of the active site of the fe-only hydrogenase from desulfovibrio desulfuricans.	fe-only hydrogenases, as well as their nife counterparts, display unusual intrinsic high-frequency ir bands that have been assigned to co and cn(-) ligation to iron in their active sites. ftir experiments performed on the fe-only hydrogenase from desulfovibrio desulfuricans indicate that upon reduction of the active oxidized form, there is a major shift of one of these bands that is provoked, most likely, by the change of a co ligand from a bridging position to a terminal one. indeed, the crysta ...	2001	11456758
mössbauer characterization of the iron-sulfur clusters in desulfovibrio vulgaris hydrogenase.	the periplasmic hydrogenase of desulfovibrio vulgaris (hildenbourough) is an all fe-containing hydrogenase. it contains two ferredoxin type [4fe-4s] clusters, termed the f clusters, and a catalytic h cluster. recent x-ray crystallographic studies on two fe hydrogenases revealed that the h cluster is composed of two sub-clusters, a [4fe-4s] cluster ([4fe-4s](h)) and a binuclear fe cluster ([2fe](h)), bridged by a cysteine sulfur. the aerobically purified d. vulgaris hydrogenase is stable in air. ...	2001	11456963
modeling the active sites in metalloenzymes. 3. density functional calculations on models for [fe]-hydrogenase: structures and vibrational frequencies of the observed redox forms and the reaction mechanism at the diiron active center.	optimized structures for the redox species of the diiron active site in [fe]-hydrogenase as observed by ftir and for species in the catalytic cycle for the reversible h(2) oxidation have been determined by density-functional calculations on the active site model, [(l)(co)(cn)fe(mu-pdt)(mu-co)fe(co)(cn)(l')](q)(l = h(2)o, co, h(2), h(-); pdt = sch(2)ch(2)ch(2)s, l' = ch(3)s(-), ch(3)sh; q = 0, 1-, 2-, 3-). analytical dft frequencies on model complexes (mu-pdt)fe(2)(co)(6) and [(mu-pdt)fe(2)(co)(4 ...	2001	11457105
a capable bridging ligand for fe-only hydrogenase: density functional calculations of a low-energy route for heterolytic cleavage and formation of dihydrogen.		2001	11457119
self-consistent karplus parametrization of 3j couplings depending on the polypeptide side-chain torsion chi1.	recently proposed self-consistent 3j coupling analysis (schmidt, j. m.; blümel, m.; löhr, f.; rüterjans, h. j. biomol. nmr 1999, 14, 1-12) has been carried out to calibrate karplus parameters constituting the empirical dependence of 3j coupling constants on the chi1 dihedral angle in amino acid side chains. the procedure involves simultaneous least-squares optimization of six sets of three karplus coefficients related to all six 3j coupling types accessible in 15n,13c-labeled proteins. a simple ...	2001	11459487
in the facultative sulphate/nitrate reducer desulfovibrio desulfuricans atcc 27774, the nine-haem cytochrome c is part of a membrane-bound redox complex mainly expressed in sulphate-grown cells.	the bacterium desulfovibrio desulfuricans atcc 27774 belongs to the group of sulphate reducers also capable of utilising nitrate as its terminal electron acceptor for anaerobic growth. one of the complex multihaem proteins found in nitrate- or sulphate-grown cells of desulfovibrio desulfuricans atcc 27774 is the nine-haem cytochrome c. the present work shows that the gene encoding for desulfovibrio desulfuricans atcc 27774 nine-haem cytochrome c is part of an operon formed by the gene cluster 9h ...	2001	11470160
the mechanism of superoxide scavenging by archaeoglobus fulgidus neelaredoxin.	neelaredoxin is a mononuclear iron protein widespread among prokaryotic anaerobes and facultative aerobes, including human pathogens. it has superoxide scavenging activity, but the exact mechanism by which this process occurs has been controversial. in this report, we present the study of the reaction of superoxide with the reduced form of neelaredoxin from the hyperthermophilic archaeon archaeoglobus fulgidus by pulse radiolysis. this protein reduces superoxide very efficiently (k = 1.5 x 10(9) ...	2001	11489883
crystal structures of a novel ferric reductase from the hyperthermophilic archaeon archaeoglobus fulgidus and its complex with nadp+.	studies performed within the last decade have indicated that microbial reduction of fe(iii) to fe(ii) is a biologically significant process. the ferric reductase (fer) from archaeoglobus fulgidus is the first reported archaeal ferric reductase and it catalyzes the flavin-mediated reduction of ferric iron complexes using nad(p)h as the electron donor. based on its catalytic activity, the a. fulgidus fer resembles the bacterial and eukaryotic assimilatory type of ferric reductases. however, the hi ...	2001	11525168
biological degradation of 2,4,6-trinitrotoluene.	nitroaromatic compounds are xenobiotics that have found multiple applications in the synthesis of foams, pharmaceuticals, pesticides, and explosives. these compounds are toxic and recalcitrant and are degraded relatively slowly in the environment by microorganisms. 2,4,6-trinitrotoluene (tnt) is the most widely used nitroaromatic compound. certain strains of pseudomonas and fungi can use tnt as a nitrogen source through the removal of nitrogen as nitrite from tnt under aerobic conditions and the ...	2001	11527999
a member of the delta subgroup of proteobacteria from a pyogenic liver abscess is a typical sulfate reducer of the genus desulfovibrio.	strain fh26001/95 (atcc 700045) was previously isolated from a pyogenic liver abscess from a human. comparative 16s rrna gene sequence analysis showed that this strain is related to members of the delta subgroup of the proteobacteria, within a cluster of sulfate-reducing bacteria (desulfovibrio spp.) and non-sulfate-reducing bacteria (bilophila wadsworthia and lawsonia spp.). the phenotype of strain fh26001/95 was found to be typical of members of the genus desulfovibrio. growth and substrate tr ...	2001	11158153
five-gene cluster in clostridium thermoaceticum consisting of two divergent operons encoding rubredoxin oxidoreductase- rubredoxin and rubrerythrin-type a flavoprotein- high-molecular-weight rubredoxin.	a five-gene cluster encoding four nonheme iron proteins and a flavoprotein from the thermophilic anaerobic bacterium clostridium thermoaceticum (moorella thermoacetica) was cloned and sequenced. based on analysis of deduced amino acid sequences, the genes were identified as rub (rubredoxin), rbo (rubredoxin oxidoreductase), rbr (rubrerythrin), fpra (type a flavoprotein), and a gene referred to as hrb (high-molecular-weight rubredoxin). northern blot analysis demonstrated that the five-gene clust ...	2001	11160086
dissimilatory sulfite reductase (desulfoviridin) of the taurine-degrading, non-sulfate-reducing bacterium bilophila wadsworthia rzatau contains a fused dsrb-dsrd subunit.	a dissimilatory sulfite reductase (dsr) was purified from the anaerobic, taurine-degrading bacterium bilophila wadsworthia rzatau to apparent homogeneity. the enzyme is involved in energy conservation by reducing sulfite, which is formed during the degradation of taurine as an electron acceptor, to sulfide. according to its uv-visible absorption spectrum with maxima at 392, 410, 583, and 630 nm, the enzyme belongs to the desulfoviridin type of dsrs. the sulfite reductase was isolated as an alpha ...	2001	11160104
analysis of the desulfovibrio gigas transcriptional unit containing rubredoxin (rd) and rubredoxin-oxygen oxidoreductase (roo) genes and upstream orfs.	rubredoxin-oxygen oxidoreductase, an 86-kda homodimeric flavoprotein, is the final component of a soluble electron transfer chain that couples nadh oxidation with oxygen reduction to water from the sulfate-reducing bacterium desulfovibrio gigas. a 4.2-kb fragment of d. gigas chromosomal dna containing the roo gene and the rubredoxin gene was sequenced. additional open reading frames designated as orf-1, orf-2, and orf-3 were also identified in this dna fragment. orf-1 encodes a protein exhibitin ...	2001	11162545
three-dimensional structure of the nonaheme cytochrome c from desulfovibrio desulfuricans essex in the fe(iii) state at 1.89 a resolution.	a nine heme group containing cytochrome c isolated from the soluble and membrane fractions of desulfovibrio desulfuricans essex, termed nonaheme cytochrome c, was crystallized, and the structure was solved using the multiple wavelength anomalous dispersion (mad) phasing method. refinement was carried out to a resolution of 1.89 a, and anisotropic temperature factors were addressed to the iron and sulfur atoms in the model. the structure revealed two cytochrome c(3) like domains with the typical ...	2001	11170457
nonaheme cytochrome c, a new physiological electron acceptor for [ni,fe] hydrogenase in the sulfate-reducing bacterium desulfovibrio desulfuricans essex: primary sequence, molecular parameters, and redox properties.	a nonaheme cytochrome c was purified to homogeneity from the soluble and the membrane fractions of the sulfate-reducing bacterium desulfovibrio desulfuricans essex. the gene encoding for the protein was cloned and sequenced. the primary structure of the multiheme protein was highly homologous to that of the nonaheme cytochrome c from d. desulfuricans atcc 27774 and to that of the 16-heme hmca protein from desulfovibrio vulgaris hildenborough. the analysis of the sequence downstream of the gene e ...	2001	11170458
two-iron rubredoxin of pseudomonas oleovorans: production, stability and characterization of the individual iron-binding domains by optical, cd and nmr spectroscopies.	a minigene encoding the c-terminal domain of the 2fe rubredoxin of pseudomonas oleovorans was created from the parental alk g gene contained in the expression plasmid pkk223-3. the vector directed the high-level production of the c-terminal domain of this rubredoxin; a simple procedure was used to purify the recombinant domain in the 1fe form. the 1fe form of the c-terminal domain was readily converted into the apoprotein and cadmium forms after precipitation with trichloroacetic acid and resolu ...	2001	11171083
structure determination of bacterioferritin from desulfovibrio desulfuricans by the mad method at the fe k-edge.	bacterioferritins constitute a subfamily of heme ferritins, proteins involved in iron storage and homeostasis. the protein isolated from desulfovibrio desulfuricans atcc 27774 is a homodimer of mass 52 kda. the monomers are linked by an iron-coproporphyrin group and each monomer contains a diferric center. the 24-monomer clusters found in the crystal are probably the functional particles. mad data from cubic bacterioferritin crystals were collected at the k-shell iron edge. preliminary phasing w ...	2001	11173495
cloning and expression of the catalase gene from the anaerobic bacterium desulfovibrio vulgaris (miyazaki f).	we identified a gene encoding a catalase from the anaerobic bacteria desulfovibrio vulgaris (miyazaki f), and the expression of its gene in escherichia coli. the 3.3-kbp dna fragment isolated from d. vulgaris (miyazaki f) by double digestion with ecori and sali was found to produce a protein that binds protoheme ix as a prosthetic group in e. coli. this dna fragment contained a putative open reading frame (kat) and one part of another open reading frame (orf-1). the amino acid sequence of the am ...	2001	11226874
purification and characterization of homo- and hetero-dimeric acetate kinases from the sulfate-reducing bacterium desulfovibrio vulgaris.	two distinct forms of acetate kinase were purified to homogeneity from a sulfate-reducing bacterium desulfovibrio vulgaris miyazaki f. the enzymes were separated from the soluble fraction of the cells on anion exchange columns. one acetate kinase (ak-i) was a homodimer (alpha(s)(2)) and the other (ak-ii) was a heterodimer (alpha(s)alpha(l)). on sds-page, alpha(l) and alpha(s) subunits migrated as bands of 49.3 and 47.8 kda, respectively, but they had an identical n-terminal amino acid sequence. ...	2001	11226881
enzymatic reduction of chromate: comparative studies using sulfate-reducing bacteria. key role of polyheme cytochromes c and hydrogenases.	various sulfate-reducing bacteria of the genera desulfovibrio and desulfomicrobium were tested and compared for enzymatic reduction of chromate. our study demonstrated that the ability to reduce chromate is widespread among sulfate-reducing bacteria. among them, desulfomicrobium norvegicum reduced cr(vi) with the highest reaction rate. this strain grew in the presence of up to 500 microm chromate, but cr(vi) reduction in the absence of sulfate was not associated with growth. the presence of chro ...	2001	11234966
evaluation of the hydrogen bonding interactions and their effects on the oxidation-reduction potentials for the riboflavin complex of the desulfovibrio vulgaris flavodoxin.	the oxidation-reduction potentials for the riboflavin complex of the desulfovibrio vulgaris flavodoxin are substantially different from those of the flavin mononucleotide (fmn) containing native protein, with the midpoint potential for the semiquinone-hydroquinone couple for the riboflavin complex being 180 mv less negative. this increase has been attributed to the absence in the riboflavin complex of unfavorable electrostatic effects of the dianionic 5'-phosphate of the fmn on the stability of ...	2001	11245795
crystal structure of the 100 kda arsenite oxidase from alcaligenes faecalis in two crystal forms at 1.64 a and 2.03 a.	arsenite oxidase from alcaligenes faecalis ncib 8687 is a molybdenum/iron protein involved in the detoxification of arsenic. it is induced by the presence of aso(2-) (arsenite) and functions to oxidize as(iii)o(2-), which binds to essential sulfhydryl groups of proteins and dithiols, to the relatively less toxic as(v)o(4)(3-) (arsenate) prior to methylation.	2001	11250197
structures and comparison of the y98h (2.0 a) and y98w (1.5 a) mutants of flavodoxin (desulfovibrio vulgaris).	the structures for two mutants at the tyr98 site of desulfovibrio vulgaris flavodoxin have been determined. the first, a tyrosine-to-histidine (y98h) variant, was determined at the moderately high resolution of 2.0 a, while the tyrosine-to-tryptophan variant (y98w) yielded very high resolution data (beyond 1.5 a) allowing a detailed look at the water structure, alternate side-chain conformations and the planarity of the fmn. both structures were solved by molecular replacement beginning with the ...	2001	11264581
a simple, rapid, and highly efficient gene expression system for multiheme cytochromes c.	the genes of tetraheme cytochrome c3 and hexadecaheme high-molecular-weight cytochrome c from desulfovibrio vulgaris could be overexpressed as holoproteins in shewanella oneidensis tsp-c using puc-type vectors of e. coli. surprisingly, s. oneidensis was transformed directly by puc-type vectors through electroporation. the yields of the recombinant proteins in this expression system were much higher than the previously reported ones.	2001	11272827
metabolism of benzoate, cyclohex-1-ene carboxylate, and cyclohexane carboxylate by "syntrophus aciditrophicus" strain sb in syntrophic association with h(2)-using microorganisms.	the metabolism of benzoate, cyclohex-1-ene carboxylate, and cyclohexane carboxylate by "syntrophus aciditrophicus" in cocultures with hydrogen-using microorganisms was studied. cyclohexane carboxylate, cyclohex-1-ene carboxylate, pimelate, and glutarate (or their coenzyme a [coa] derivatives) transiently accumulated during growth with benzoate. identification was based on comparison of retention times and mass spectra of trimethylsilyl derivatives to the retention times and mass spectra of authe ...	2001	11282627
colonic infection by bilophila wadsworthia in pigs.	bilophila wadsworthia is a common inhabitant of the human colon and has been associated with appendicitis and other local sites of inflammation in humans. challenge-exposure or prevalence studies in laboratory and other animals have not been reported. b. wadsworthia is closely related phylogenetically to desulfovibrio sp. and lawsonia intracellularis, which are considered colon pathogens. we developed a pcr specific for b. wadsworthia dna. samples of bacterial dna extracted from the feces of pig ...	2001	11283090
conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytochrome.	cell metabolism relies on energy transduction usually performed by complex membrane-spanning proteins that couple different chemical processes, e.g. electron and proton transfer in proton-pumps. there is great interest in determining at the molecular level the structural details that control these energy transduction events, particularly those involving multiple electrons and protons, because tight control is required to avoid the production of dangerous reactive intermediates. tetraheme cytochr ...	2001	11551953
antimicrobial susceptibilities of clinical desulfovibrio isolates.	the antimicrobial susceptibilities of 16 clinical isolates of desulfovibrio spp. were determined. all or most isolates were susceptible to imipenem (mic(90) [mic at which 90% of the isolates tested were inhibited], 0.5 microg/ml), metronidazole (mic(90), 0.25 microg/ml), clindamycin (mic(90), 4 microg/ml), and chloramphenicol (mic(90), 16 microg/ml) but were resistant or intermediate to penicillin g (mic(90), 64 microg/ml), piperacillin (mic(90), 256 microg/ml), piperacillin-tazobactam (mic(90), ...	2001	11557495
[formation of microbial populations on the surface of protective coatings].	formation of microbial cenosis on the surface of polyethylene-, polyurethane- and oil-bitumen-based protective coatings was studied in dynamics during 1, 3, 7, 14 and 21 days. it has been shown that the biofilm was formed on the protective materials during 14 days and consisted of ammonifying, denitrifying, hydrocarbon-oxidizing and sulphate-reducing bacteria referred to pseudomonas, arthrobacter, bacillus and kesulfovibrio genera. the bacteria which form the biofilm on coatings possess high den ...	2001	11558243
a role for rubredoxin in oxidative stress protection in desulfovibrio vulgaris: catalytic electron transfer to rubrerythrin and two-iron superoxide reductase.	desulfovibrio vulgaris rubredoxin, which contains a single [fe(scys)4] site, is shown to be a catalytically competent electron donor to two enzymes from the same organism, namely, rubrerythrin and two-iron superoxide reductase (a.k.a. rubredoxin oxidoreductase or desulfoferrodoxin). these two enzymes have been implicated in catalytic reduction of hydrogen peroxide and superoxide, respectively, during periods of oxidative stress in d. vulgaris, but their proximal electron donors had not been char ...	2001	11566030
reduction of technetium(vii) by desulfovibrio fructosovorans is mediated by the nickel-iron hydrogenase.	resting cells of the sulfate-reducing bacterium desulfovibrio fructosovorans grown in the absence of sulfate had a very high tc(vii)-reducing activity, which led to the formation of an insoluble black precipitate. the involvement of a periplasmic hydrogenase in tc(vii) reduction was indicated (i) by the requirement for hydrogen as an electron donor, (ii) by the tolerance of this activity to oxygen, and (iii) by the inhibition of this activity by cu(ii). moreover, a mutant carrying a deletion in ...	2001	11571159
direct detection of 16s rrna in soil extracts by using oligonucleotide microarrays.	we report on the development and validation of a simple microarray method for the direct detection of intact 16s rrna from unpurified soil extracts. total rnas from geobacter chapellei and desulfovibrio desulfuricans were hybridized to an oligonucleotide array consisting of universal and species-specific 16s rrna probes. pcr-amplified products from geobacter and desulfovibrio were easily and specifically detected under a range of hybridization times, temperatures, and buffers. however, reproduci ...	2001	11571176
copper-induced inhibition of growth of desulfovibrio desulfuricans g20: assessment of its toxicity and correlation with those of zinc and lead.	the toxicity of copper [cu(ii)] to sulfate-reducing bacteria (srb) was studied by using desulfovibrio desulfuricans g20 in a medium (mtm) developed specifically to test metal toxicity to srb (r. k. sani, g. geesey, and b. m. peyton, adv. environ. res. 5:269-276, 2001). the effects of cu(ii) toxicity were observed in terms of inhibition in total cell protein, longer lag times, lower specific growth rates, and in some cases no measurable growth. at only 6 microm, cu(ii) reduced the maximum specifi ...	2001	11571183
control of biogenic h(2)s production with nitrite and molybdate.	the effects of the metabolic inhibitors, sodium nitrite and ammonium molybdate, on production of h(2)s by a pure culture of the sulfate-reducing bacterium (srb) desulfovibrio sp. strain lac6 and a consortium of srb, enriched from produced water of a canadian oil field, were investigated. addition of 0.1 mm nitrite or 0.024 mm molybdate at the start of growth prevented the production of h(2)s by strain lac6. with exponentially growing cultures, higher levels of inhibitors, 0.25 mm nitrite or 0.09 ...	2001	11571618
effect of hydrogen-bond networks in controlling reduction potentials in desulfovibrio vulgaris (hildenborough) cytochrome c3 probed by site-specific mutagenesis.	cytochromes c3 isolated from desulfovibrio spp. are periplasmic proteins that play a central role in energy transduction by coupling the transfer of electrons and protons from hydrogenase. comparison between the oxidized and reduced structures of cytochrome c3 isolated from desulfovibrio vulgaris (hildenborough) show that the residue threonine 24, located in the vicinity of heme iii, reorients between these two states [messias, a. c., kastrau, d. h. w., costa, h. s., legall, j., turner, d. l., s ...	2001	11583171
impact of nitrate-mediated microbial control of souring in oil reservoirs on the extent of corrosion.	the effect of microbial control of souring on the extent of corrosion was studied in a model system consisting of pure cultures of the nitrate-reducing, sulfide-oxidizing bacterium (nr-sob) thiomicrospira sp. strain cvo and the sulfate-reducing bacterium (srb) desulfovibrio sp. strain lac6, as well as in an srb consortium enriched from produced water from a canadian oil reservoir. the average corrosion rate induced by the srb consortium (1.4 g x m(-2) x day(-1)) was faster than that observed in ...	2001	11587574
[extracellular metabolites of hydrocarbon-oxidizing bacteria as a substrate for sulfate reduction].	the relationship between bacterial oxidation of hydrocarbons and sulfate reduction was studied in the experimental system with liquid paraffin was used as a source of organic compounds inoculated with silt taken from a reservoir. pseudomonads dominated in the hydrocarbon-oxidizing silt bacteriocenosis. however, rhodococcus and arthrobacteria amounted to not more than 3%. arthrobacteria dominated the microbial association formed in the paraffin film of the model system. sulfate-reducing bacteria ...	2001	11605466
modeling nickel hydrogenases: synthesis and structure of a distorted octahedral complex with an unprecedented [nis(4)h(2)] core.		2001	11681879
role of a highly conserved ypitp motif in 2-oxoacid:ferredoxin oxidoreductase: heterologous expression of the gene from sulfolobus sp.strain 7, and characterization of the recombinant and variant enzymes.	2-oxoacid:ferredoxin oxidoreductase from sulfolobus sp. strain 7, an aerobic and thermoacidophilic crenoarchaeon, catalyses the coenzyme a-dependent oxidative decarboxylation of pyruvate and 2-oxoglutarate, a cognate zn-7fe-ferredoxin serving as an electron acceptor. it comprises two subunits, a (632 amino acids) and b (305 amino acids). to further elucidate its structure and function, we constructed a gene expression system. the wild-type recombinant enzyme was indistinguishable from the natura ...	2001	11683888
periplasmic oxygen reduction by desulfovibrio species.	washed cells of desulfovibrio vulgaris strain marburg (dsm 2119) reduced oxygen to water with h(2) as electron donor at a mean rate of 253 nmol o(2) min(-1) (mg protein)(-1). after separating the periplasm from the cells, more than 60% of the cytochrome c activity and 90% of the oxygen-reducing activity were found in the periplasmic fraction. oxygen reduction and the reduction of cytochrome c with h(2) were inhibited by cucl(2). after further separation of the periplasm by ultrafiltration (exclu ...	2001	11685376
both ph and carbon flux influence the level of rubredoxin in clostridium butyricum.	the rubredoxin expression level in clostridium butyricum dsm 5431 grown in continuous culture was monitored using primer extension analyses of the rub gene and a specific enzymatic assay of the iron-sulfur protein. in this way, we showed that variations in rubredoxin content and in rub mrna level were influenced by the ph of the culture and were directly dependent on the carbon flux. the maximum rubredoxin level reached 1227.3 pmol (mg of proteins)(-1) (i.e. 0.7% of the total protein content) un ...	2001	11685512
nmr structure of desulfovibrio gigas rubredoxin: a model for studying protein stabilization by compatible solutes.	rubredoxins are small, soluble proteins that display a wide variation in thermostability, despite having a high degree of sequence similarity they also vary in the extent to which they are stabilized by solutes such as diglycerol phosphate. hence, they provide excellent models for studying the mechanisms of thermostabilization. nuclear magnetic resonance (nmr) spectroscopy can be used to investigate interactions between molecules, as well as subtle changes in conformation in solution, and also p ...	2001	11699644
improved measurement of (3)j(h(alpha)(i),n(i+1)) coupling constants in h(2)o dissolved proteins.	a modification to the recently proposed alpha/beta-hn(co)ca-j trosy pulse sequence (p. permi et al., j. magn. reson. 146, 255-259 (2000)) makes it possible to determine (3)j(h(alpha)(i), n(i+1)) coupling constants from a single e.cosy-type cross-peak pattern rather than from two (1)h(alpha) spin-state-edited subspectra. advantages are increased (15)n resolution, critical to extracting accurate (1)h(alpha)-(15)n coupling constants, and minimized differential relaxation due to nested (13)c(alpha) ...	2001	11700083
modeling the active sites in metalloenzymes 5. the heterolytic bond cleavage of h(2) in the [nife] hydrogenase of desulfovibrio gigas by a nucleophilic addition mechanism.	the h(2) activation catalyzed by an fe(ii)-ni(iii) model of the [nife] hydrogenase of desulfovibrio gigas has been investigated by density functional theory (dft/b3lyp) calculations on the neutral and anionic active site complexes, [(co)(cn)(2)fe(mu-sh)(2)ni(sh)(sh(2))](0) and [(co)(cn)(2)fe(mu-sh)(2)ni(sh)(2)](-). the results suggest that the reaction proceeds by a nucleophilic addition mechanism that cleaves the h-h bond heterolytically. the terminal cysteine residue cys530 in the [nife] hydro ...	2001	11703120
structure refinement of the aldehyde oxidoreductase from desulfovibrio gigas (mop) at 1.28 a.	the sulfate-reducing bacterium aldehyde oxidoreductase from desulfovibrio gigas (mop) is a member of the xanthine oxidase family of enzymes. it has 907 residues on a single polypeptide chain, a molybdopterin cytosine dinucleotide (mcd) cofactor and two [2fe-2s] iron-sulfur clusters. synchrotron data to almost atomic resolution were collected for improved cryo-cooled crystals of this enzyme in the oxidized form. the cell constants of a=b=141.78 a and c=160.87 a are about 2% shorter than those of ...	2001	11713686
characterization of recombinant desulfovibrio gigas ferredoxin.	dg ferredoxin gene was cloned using the polymerase chain reaction (pcr), inserted into vector pt7-7, and overexpressed in escherichia coli (e. coli) grown in aerobic media. the recombinant protein is a dimer and contains a [3fe-4s] cluster per monomer. epr and (1)h nmr data of recombinant and wild-type protein are compared.	2001	11716522
comparative biology of incq and incq-like plasmids.	plasmids belonging to escherichia coli incompatibility group q are relatively small (approximately 5 to 15 kb) and able to replicate in a remarkably broad range of bacterial hosts. these include gram-positive bacteria such as brevibacterium and mycobacterium and gram-negative bacteria such as agrobacterium, desulfovibrio, and cyanobacteria. these plasmids are mobilized by several self-transmissible plasmids into an even more diverse range of organisms including yeasts, plants, and animal cells. ...	2001	11729261
influence of electrochemical properties in determining the sensitivity of [4fe-4s] clusters in proteins to oxidative damage.	interconversion between [4fe-4s] cubane and [3fe-4s] cuboidal states represents one of the simplest structural changes an iron-sulphur cluster can undertake. this reaction is implicated in oxidative damage and in modulation of the activity and regulation of certain enzymes, and it is therefore important to understand the factors governing cluster stability and the processes that activate cluster conversion. in the present study, protein film voltammetry has been used to induce and monitor the ox ...	2001	11736664