Reduction of the amount of periplasmic hydrogenase in Desulfovibrio vulgaris (Hildenborough) with antisense RNA: direct evidence for an important role of this hydrogenase in lactate metabolism

Molybdate inhibits mercury methylation capacity of Pseudodesulfovibrio hydrargyri BerOc1 regardless of the growth metabolism

Molybdate inhibits sulfate respiration in sulfate-reducing bacteria (SRB). It is used as an inhibitor to indirectly evaluate the role of SRB in mercury methylation in the environment. Here, the SRB Pseudodesulfovibrio hydrargyri BerOc1 was used to assess the effect of molybdate on cell growth and mercury methylation under various metabolic conditions. Geobacter sulfurreducens PCA was used as the non-SRB counterpart strain with the ability to methylate mercury. While PCA growth and methylation are not affected by molybdate, 1 mM of molybdate inhibits BerOc1 growth under sulfate respiration (50% inhibition) but also under fumarate respiration (complete inhibition). Even more surprising, mercury methylation of BerOc1 is totally inhibited at 0.1 mM of molybdate when grown under sulfate or fumarate respiration with pyruvate as the electron donor. As molybdate is expected to reduce cellular ATP level, the lower Hg methylation observed with pyruvate could be the consequence of lower energy production. Although molybdate alters the expression of hgcA (mercury methylation marker) and sat (involved in sulfate reduction and molybdate sensitivity) in a metabolism-dependent manner, no relationship with mercury methylation rates could be found. Our results show, for the first time, a specific mercury methylation inhibition by molybdate in SRB.

Hydrogenases and H2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus

Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H₂ metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H₂ metabolism.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.

Hydrogenase activity of mineral-associated and suspended populations of Desulfovibrio desulfuricans Essex 6

The interactions between sulfate-reducing microorganisms and iron oxides influence a number of important redox-sensitive biogeochemical processes including the formation of iron sulfides. Enzymes, such as hydrogenase which catalyze the reversible oxidation of molecular hydrogen, are known to mediate electron transfer to metals and may contribute to the formation and speciation of ferrous sulfides formed at the cell-mineral interface. In the present study, we compared the whole cell hydrogenase activity of Desulfovibrio desulfuricans strain Essex 6 growing as biofilms on hematite (hematite-associated) or as suspended populations using different metabolic pathways. Hematite-associated cells exhibited significantly greater hydrogenase activity than suspended populations during sulfate respiration but not during pyruvate fermentation. The enhanced activity of the hematite-associated, sulfate-grown cells appears to be dependent on iron availability rather than a general response to surface attachment since the activity of glass-associated cells did not differ from that of suspended populations. Hydrogenase activity of pyruvate-fermenting cells was stimulated by addition of iron as soluble Fe(II)Cl2 and, in the absence of added iron, both sulfate-reducing and pyruvate-fermenting cells displayed similar rates of hydrogenase activity. These data suggest that iron exerts a stronger influence on whole cell hydrogenase activity than either metabolic pathway or mode of growth. The location of hydrogenase to the cell envelope and the enhanced activity at the hematite surface in sulfate-reducing cells may influence the redox conditions that control the species of iron sulfides on the mineral surface.

Hydrogen is a preferred intermediate in the energy-conserving electron transport chain of Methanosarcina barkeri

Methanogens use an unusual energy-conserving electron transport chain that involves reduction of a limited number of electron acceptors to methane gas. Previous biochemical studies suggested that the proton-pumping F(420)H(2) dehydrogenase (Fpo) plays a crucial role in this process during growth on methanol. However, Methanosarcina barkeri Delta fpo mutants constructed in this study display no measurable phenotype on this substrate, indicating that Fpo plays a minor role, if any. In contrast, Delta frh mutants lacking the cytoplasmic F(420)-reducing hydrogenase (Frh) are severely affected in their ability to grow and make methane from methanol, and double Delta fpo/Delta frh mutants are completely unable to use this substrate. These data suggest that the preferred electron transport chain involves production of hydrogen gas in the cytoplasm, which then diffuses out of the cell, where it is reoxidized with transfer of electrons into the energy-conserving electron transport chain. This hydrogen-cycling metabolism leads directly to production of a proton motive force that can be used by the cell for ATP synthesis. Nevertheless, M. barkeri does have the flexibility to use the Fpo-dependent electron transport chain when needed, as shown by the poor growth of the Delta frh mutant. Our data suggest that the rapid enzymatic turnover of hydrogenases may allow a competitive advantage via faster growth rates in this freshwater organism. The mutant analysis also confirms the proposed role of Frh in growth on hydrogen/carbon dioxide and suggests that either Frh or Fpo is needed for aceticlastic growth of M. barkeri.

Third generation biofuels via direct cellulose fermentation

Consolidated bioprocessing (CBP) is a system in which cellulase production, substrate hydrolysis, and fermentation are accomplished in a single process step by cellulolytic microorganisms. CBP offers the potential for lower biofuel production costs due to simpler feedstock processing, lower energy inputs, and higher conversion efficiencies than separate hydrolysis and fermentation processes, and is an economically attractive near-term goal for "third generation" biofuel production. In this review article, production of third generation biofuels from cellulosic feedstocks will be addressed in respect to the metabolism of cellulolytic bacteria and the development of strategies to increase biofuel yields through metabolic engineering.

Identification of genes that confer sediment fitness to Desulfovibrio desulfuricans G20

Signature-tagged mutants of Desulfovibrio desulfuricans G20 were screened, and 97 genes crucial for sediment fitness were identified. These genes belong to functional categories including signal transduction, binding and transport, insertion elements, and others. Mutants with mutations in genes encoding proteins involved in amino acid biosynthesis, hydrogenase activity, and DNA repair were further characterized.

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.

Construction and physiological studies of hydrogenase depleted mutants of Desulfovibrio fructosovorans

Desulfovibrio fructosovorans possesses two periplasmic hydrogenases (a nickel-iron and an iron hydrogenase) and a cytoplasmic NADP-dependent hydrogenase. The hydAB genes encoding the periplasmic iron hydrogenase were replaced, in the wild-type strain as well as in single mutants depleted of one of the other two hydrogenases, by the acc1 gene encoding resistance to gentamycin. Molecular characterization and remaining activity measurements of the resulting single and double mutants were performed. All mutated strains exhibited similar growth when H(2) was the electron donor but they grew differently on fructose, lactate or pyruvate as electron donors. Our results indicate that the loss of one enzyme might be compensated by another even though hydrogenases have different localization in the cells.

Effects of deletion of genes encoding Fe-only hydrogenase of Desulfovibrio vulgaris Hildenborough on hydrogen and lactate metabolism

The physiological properties of a hyd mutant of Desulfovibrio vulgaris Hildenborough, lacking periplasmic Fe-only hydrogenase, have been compared with those of the wild-type strain. Fe-only hydrogenase is the main hydrogenase of D. vulgaris Hildenborough, which also has periplasmic NiFe- and NiFeSe-hydrogenases. The hyd mutant grew less well than the wild-type strain in media with sulfate as the electron acceptor and H(2) as the sole electron donor, especially at a high sulfate concentration. Although the hyd mutation had little effect on growth with lactate as the electron donor for sulfate reduction when H(2) was also present, growth in lactate- and sulfate-containing media lacking H(2) was less efficient. The hyd mutant produced, transiently, significant amounts of H(2) under these conditions, which were eventually all used for sulfate reduction. The results do not confirm the essential role proposed elsewhere for Fe-only hydrogenase as a hydrogen-producing enzyme in lactate metabolism (W. A. M. van den Berg, W. M. A. M. van Dongen, and C. Veeger, J. Bacteriol. 173:3688-3694, 1991). This role is more likely played by a membrane-bound, cytoplasmic Ech-hydrogenase homolog, which is indicated by the D. vulgaris genome sequence. The physiological role of periplasmic Fe-only hydrogenase is hydrogen uptake, both when hydrogen is and when lactate is the electron donor for sulfate reduction.

Antisense RNA strategies for metabolic engineering of Clostridium acetobutylicum

We examined the effectiveness of antisense RNA (as RNA) strategies for metabolic engineering of Clostridium acetobutylicum. Strain ATCC 824(pRD4) was developed to produce a 102-nucleotide asRNA with 87% complementarity to the butyrate kinase (BK) gene. Strain ATCC 824(pRD4) exhibited 85 to 90% lower BK and acetate kinase specific activities than the control strain. Strain ATCC 824(pRD4) also exhibited 45 to 50% lower phosphotransbutyrylase (PTB) and phosphotransacetylase specific activities than the control strain. This strain exhibited earlier induction of solventogenesis, which resulted in 50 and 35% higher final concentrations of acetone and butanol, respectively, than the concentrations in the control. Strain ATCC 824(pRD1) was developed to putatively produce a 698-nucleotide asRNA with 96% complementarity to the PTB gene. Strain ATCC 824(pRD1) exhibited 70 and 80% lower PTB and BK activities, respectively, than the control exhibited. It also exhibited 300% higher levels of a lactate dehydrogenase activity than the control exhibited. The growth yields of ATCC 824(pRD1) were 28% less than the growth yields of the control. While the levels of acids were not affected in ATCC 824(pRD1) fermentations, the acetone and butanol concentrations were 96 and 75% lower, respectively, than the concentrations in the control fermentations. The lower level of solvent production by ATCC 824(pRD1) was compensated for by approximately 100-fold higher levels of lactate production. The lack of any significant impact on butyrate formation fluxes by the lower PTB and BK levels suggests that butyrate formation fluxes are not controlled by the levels of the butyrate formation enzymes.

A unified model describing the role of hydrogen in the growth of desulfovibrio vulgaris under different environmental conditions

A unified model for the growth of Desulfovibrio vulgaris under different environmental conditions is presented. The model assumes the existence of two electron transport mechanisms functioning simultaneously. One mechanism results in the evolution and consumption of hydrogen, as in the hydrogen-cycling model. The second mechanism assumes a direct transport of electrons from the donor to the acceptor, without the participation of H2. A combination of kinetic and thermodynamic conditions control the flow of electrons through each pathway. The model was calibrated using batch experiments with D. vulgaris grown on lactate, in the presence and absence of sulfate, and was verified using additional batch experiments under different conditions. The model captured the general trends of consumption of substrates and accumulation of products, including the transient accumulation and consumption of H2. Furthermore, the model estimated that 48% of the electrons transported from lactate to sulfate involved H2 production, indicating that hydrogen cycling is a fundamental process in D. vulgaris. The presence of simultaneous electron transport mechanisms might provide D. vulgaris with important ecological advantages, because it facilitates a rapid response to changes in environmental conditions. This model increases our ability to study the microbial ecology of anaerobic environments and the role of Desulfovibrio species in a variety of environments. Copyright 1998 John Wiley & Sons, Inc.

Characterization of the [NiFe] hydrogenase from the sulfate reducer Desulfovibrio vulgaris Hildenborough

The [NiFe] hydrogenase from Desulfovibrio vulgaris Hildenborough was isolated from the cytoplasmic membranes and characterized by EPR spectroscopy. It has a total molecular mass of 98.7 kDa (subunits of 66.4 and 32.3 kDa), and contains 1 nickel and 12 Fe atoms per heterodimer. The catalytic activities for hydrogen consumption and production were determined to be 174 and 89 mumol H2.min-1.mg-1, respectively. As isolated, under aerobic conditions, this hydrogenase exhibits EPR signals characteristic of the nickel centers in [NiFe] hydrogenases (Ni-A signal at gx,y,z = 2.32, 2.23 and approximately 2.0 and Ni-B signal at gx,y,z = 2.33, 2.16 and approximately 2.0) as well as an intense quasi-isotropic signal centered at g = 2.02 due to the oxidized [3Fe-4S] center. The redox profile under hydrogen atmosphere is remarkably similar to that of other [NiFe] hydrogenases. The signals observed for the oxidized state disappear, first being substituted by the Ni-C type signal (gx,y,z = 2.19, 2.14, approximately 2.01), which upon long incubation under hydrogen yields the split Ni-C signal due to interaction with the reduced [4Fe-4S] centers.

Genetic diversity and expression of the [NiFe] hydrogenase large-subunit gene of Desulfovibrio spp. in environmental samples

The genetic diversity and expression of the [NiFe] hydrogenase large-subunit gene of Desulfovibrio spp. in environmental samples were determined in order to show in parallel the existing and active members of Desulfovibrio populations. DNA and total RNA were extracted from different anaerobic bioreactor samples; RNA was transcribed into cDNA. Subsequently, PCR was performed to amplify a ca.-440-bp fragment of the [NiFe] hydrogenase large-subunit gene and its mRNA. Denaturing gradient gel electrophoresis analysis was used to separate the PCR products according to their sequence and thereby to visualize the individual community members. Desulfovibrio strains corresponding to amplified [NiFe] hydrogenase transcripts were regarded as metabolically active, because in pure cultures transcripts were detectable in exponentially growing cells but not in cultures in the stationary phase. DNA sequencing and comparative sequence analysis were used to identify the detected organisms on the basis of their [NiFe] hydrogenase sequences. The genes of characterized Desulfovibrio spp. showed a considerable extent of divergence (ca. 30%), whereas sequences obtained from bacterial populations of the bioreactors showed a low level of variation and indicated the coexistence of closely related strains probably belonging to the species Desulfovibrio sulfodismutans. Under methanogenic conditions, all detected populations were active; under denitrifying conditions, no [NiFe] hydrogenase mRNA was visible. Changes in activity and composition of Desulfovibrio populations caused by changes in the environmental conditions could be monitored by using the approach described in this study.

Dissimilatory sulfite reductase revisited. The desulfoviridin molecule does contain 20 iron ions, extensively demetallated sirohaem, and an S = 9/2 iron-sulfur cluster

Assimilatory sulfite reductase contains a sirohaem that is very weakly coupled to a [4Fe-4S] cubane, i.e. five iron atoms in total. Dissimilatory sulfite reductase is a complex system with 20 Fe atoms/alpha 2 beta 2 gamma 2 hexamer. A recent revision of the purification procedure for the Desulfovibrio vulgaris dissimilatory enzyme has afforded a preparation of only 10 Fe atoms hexamer, this has led to the convulsion that the topology of prosthetic groups parallels that of the assimilatory system [Wolfe, B. M., Lui, S. M. & Cowan, J. A. (1994) Eur. J. Biochem. 223, 79-89]. The new purification procedure has been reproduced but the claimed molecular properties are not reproducible. The highly purified, active desulfoviridin contains 20, not 10, Fe atoms/molecule: the sirohaem is extensively dematallated, not metallated; and the S = 9/2 iron-sulfur cluster is present, not absent.

Characterization of the prismane protein from Desulfovibrio vulgaris (Hildenborough) by low-temperature magnetic circular dichroic spectroscopy

The prismane protein of Desulfovibrio vulgaris (Hildenborough) contains a putative [6Fe-6S] cluster. This novel iron-sulfur cluster has been characterized here by magnetic circular dichroism (MCD) spectroscopy. Three paramagnetic redox states of the cluster, [6Fe-6S]5+, [6Fe-6S]4+ and [6Fe-6S]3+, each show a distinctive low-temperature MCD spectrum which is unlike that observed for any other iron-sulfur clusters. Magnetization data for the prismane protein in these three redox states indicate ground state spins that are in accordance with previous EPR assignments. For the protein as isolated, with the [6Fe-6S]5+ form of the cluster, magnetizations show an exceptionally steep initial slope that can be fit to a ground state of spin S = 9/2. For the semi-reduced protein, the cluster in the [6Fe-6S]4+ form, magnetizations show an initial slope characteristic for a ground state of spin S = 4. For the dithionite-reduced protein, with the [6Fe-6S]3+ form of the cluster, magnetizations are typical for a ground state of spin S = 1/2.

Characterization of a ferredoxin from Desulfovibrio vulgaris (Hildenborough) that interacts with RNA

The purification and characterization of a ferredoxin from Desulfovibrio vulgaris (Hildenborough) is described. The protein can be isolated in two forms; the major form is strongly complexed to RNA, while a minor form is free from nucleic acid. Bound RNA cannot be removed by digestion with nucleases, or by heating to 70 degrees C, and it can only be partially removed by rechromatography. The ultraviolet/visible spectrum shows typical absorption maxima at 280 nm and 400 nm for the RNA-free ferredoxin. The RNA-bound protein exhibits an additional strong peak at 260 nm. The RNA can be extracted from the protein with phenol. The ferredoxin is a dimer of subunits, each of 7.5 kDa; its pI is 3.9. The protein contains a [4Fe-4S](2+;1+) cluster with an EPR spectrum (g = 1.90, 1.93 and 2.05) in the reduced state. A reduction potential of -360 mV was determined for the RNA-free ferredoxin with reversible voltammetry at glassy carbon. From the temperature dependence of the reduction potential, the unusually high standard reaction entropy was calculated as delta S degree = -230 J.K-1.mol-1. No electrochemical response was obtained with the RNA-bound ferredoxin. Binding of RNA appears to require the presence of an intact cluster, since the absence of absorption at 400 nm runs in parallel with the absence of absorption at 260 nm. The possibility is discussed that the binding to the RNA has a regulatory function and is controlled by the state of the cluster.

Involvement of a single periplasmic hydrogenase for both hydrogen uptake and production in some Desulfovibrio species

Various sulphate-reducing bacteria differing in the number of genes encoding hydrogenase were shown to ferment lactate in coculture with Methanospirillum hungatei, in the absence of sulphate. The efficiency of interspecies H2 transfer carried out by these species of sulphate-reducing bacteria does not appear to correlate with the distribution of genes coding for hydrogenase. Desulfovibrio vulgaris Groningen, which possesses only the gene for [NiFe] hydrogenase, oxidizes hydrogen in the presence of sulphate and produces some hydrogen during fermentation of pyruvate without electron acceptor. The hydrogenase of D. vulgaris was purified and characterized. It exhibits a molecular mass of 87 kDa and is composed of two different subunits (60 and 28 kDa). D. vulgaris hydrogenase contains 10.6 iron atoms, 0.9 nickel atom and 12 acid-labile sulphur atoms/molecule, and the absorption spectrum of the enzyme is characteristic of an iron-sulphur protein. Maximal H2 uptake and H2 evolution activities were 332 and 230 units/mg protein, respectively. D. vulgaris cells contain exclusively the [NiFe] hydrogenase, whatever the growth conditions, as shown by biochemical and immunological studies. Immunocytolocalization in ultrathin frozen sections of cells grown on lactate and sulphate, on H2 and sulphate and on pyruvate showed that the [NiFe] hydrogenase was located in the periplasmic space. Labelling was enhanced in cells grown on H2 and sulphate and on pyruvate. The results enable us to conclude that D. vulgaris Groningen contains a single hydrogenase of the [NiFe] type, located in the periplasmic space like that described for D. gigas. This enzyme appears to be involved in both H2 uptake and H2 production, depending on the growth conditions.

Overproduction of the prismane protein from Desulfovibrio desulfuricans ATCC 27774 in Desulfovibrio vulgaris (Hildenborough) and EPR spectroscopy of the [6Fe-6S] cluster in different redox states

The Desulfovibrio desulfuricans ATCC 27774 prismane protein was isolated from a Desulfovibrio vulgaris (Hildenborough) strain that contained the gene for this protein in expression vector pSUP104. A redox titration demonstrated that the [Fe-S] cluster in this protein may attain four different redox states, indicated as +3, +4, +5 and +6, with midpoint potentials for the transitions of approx. -220, +50/-25 and +370 mV, respectively. EPR spectra of the protein in the various redox states are reminiscent of those of the D. vulgaris prismane protein (Pierik et al. (1992) Eur. J. Biochem. 206, 705-719), but differ in details. In the +5-state, virtually all the iron is in a S = 9/2 spin state, indicative for a cluster that is more complex than common [4Fe-4S] or [2Fe-2S] clusters. Similarity of the EPR spectrum of the protein in the +3-state with those of inorganic [6Fe-6S] model compounds suggests that the cluster in the protein is also [6Fe-6S]. In the +4-state of the protein a broad signal due to an integer-spin system can be detected with normal-mode EPR. A dramatic sharpening-up and increase of intensity of this band (g = 14.7) is observed with parallel-mode EPR. In accordance with the chemically determined iron content of the protein (6.0 +/- 0.45 moles of iron/mole of protein), the spectroscopic data indicate one [6Fe-6S] cluster in this protein. We did not find evidence for a previous claim (Moura et al. (1992) J. Biol. Chem. 267, 4489-4496) that the D. desulfuricans protein contains two [6Fe-6S] clusters.

Cytochrome c553 from Desulfovibrio vulgaris (Hildenborough). Electrochemical properties and electron transfer with hydrogenase

An electrochemical study of the periplasmic cytochrome c553 of Desulfovibrio vulgaris (Hildenborough) is presented. The dependence of the midpoint potential on temperature and pH was studied with cyclic voltammetry. The voltammograms obtained were reversible and revealed that this cytochrome showed fast electron transfer on a bare glassy carbon electrode. The midpoint potential at pH 7.0 and 25 degrees C was found to be 62 mV versus the normal hydrogen electrode. It was observed that the temperature dependence was discontinuous with a transition temperature at 32 degrees C. The standard reaction entropy at the growth temperature of the organism (37 degrees C) was calculated to be delta S degree ' = -234 J mol-1 K-1. The pH dependence of the midpoint potential could be described with one pK of the oxidized form with a value of 10.6. The second-order rate constant for electron transfer between cytochrome c553 and the Fe-hydrogenase from D. vulgaris (H) was also determined with cyclic voltammetry. The equivalent rate constant for cytochrome c3 and hydrogenase was measured for comparison. The second-order rate constants are 2 x 10(7) M-1 s-1 for cytochrome c553 and 2 x 10(8) M-1 s-1 for cytochrome c3. The kinetic parameters of the hydrogenase for both cytochromes were determined using the spectrophotometric hydrogen consumption assay. With cytochrome c553 this resulted in a Km of 46 microM and a maximum turnover number of 7.1 x 10(2) s-1 in the H2 consumption assay. The values with cytochrome c3 were 17 microM and 6.4 x 10(2) s-1, respectively. The importance of the different kinetic parameters for contrasting models proposed to describe the function of the Fe-hydrogenase are discussed.

Metabolism of sulfate-reducing prokaryotes

Dissimilatory sulfate reduction is carried out by a heterogeneous group of bacteria and archaea that occur in environments with temperatures up to 105 degrees C. As a group together they have the capacity to metabolize a wide variety of compounds ranging from hydrogen via typical organic fermentation products to hexadecane, toluene, and several types of substituted aromatics. Without exception all sulfate reducers activate sulfate to APS; the natural electron donor(s) for the ensuing APS reductase reaction is not known. The same is true for the reduction of the product bisulfite; in addition there is still some uncertainty as to whether the pathway to sulfide is a direct six-electron reduction of bisulfite or whether it involves trithionate and thiosulfate as intermediates. The study of the degradation pathways of organic substrates by sulfate-reducing prokaryotes has led to the discovery of novel non-cyclic pathways for the oxidation of the acetyl moiety of acetyl-CoA to CO2. The most detailed knowledge is available on the metabolism of Desulfovibrio strains, both on the pathways and enzymes involved in substrate degradation and on electron transfer components and terminal reductases. Problems encountered in elucidating the flow of reducing equivalents and energy transduction are the cytoplasmic localization of the terminal reductases and uncertainties about the electron donors for the reactions catalyzed by these enzymes. New developments in the study of the metabolism of sulfate-reducing bacteria and archaea are reviewed.

DcrA, a c-type heme-containing methyl-accepting protein from Desulfovibrio vulgaris Hildenborough, senses the oxygen concentration or redox potential of the environment

The amino acid sequence of DcrA from Desulfovibrio vulgaris Hildenborough, a strictly anaerobic, sulfate-reducing bacterium, indicated homology with the methyl-accepting chemotaxis proteins from enteric bacteria (A. Dolla, R. Fu, M. J. Brumlik, and G. Voordouw, J. Bacteriol. 174:1726-1733, 1992). The homology is restricted to the cytoplasmic C-terminal signaling domain. The periplasmic N-terminal sensor domain was found to contain a unique sequence, CHHCH, corresponding to a consensus c-type heme binding site. A pretreated, DcrA-specific polyclonal antiserum, generated against DcrA protein overproduced in Escherichia coli, was used for immunoprecipitation of 35S-labeled DcrA from D. vulgaris and Desulfovibrio desulfuricans G200(pJRFR2), a transconjugant that overexpresses functional DcrA. Labeling of the latter with the heme precursor 5-amino-[4-14C]levulinic acid, followed by immunoprecipitation, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and fluorography, confirmed the presence of c-type heme, while labeling with L-[methyl-3H]methionine in the absence of protein synthesis confirmed that DcrA is a methyl-accepting protein. The base liability of the incorporated radioactivity indicated methyl ester formation like that occurring in the methyl-accepting chemotaxis proteins of enteric bacteria. L-[methyl-3H]methionine labeling of D. desulfuricans G200(pJRFR2) under different conditions indicated that methyl labeling of DcrA decreased upon addition of oxygen and increased upon subsequent addition of the reducing agent dithionite. These results indicate that DcrA may serve as a sensor of oxygen concentration and/or redox potential.

The operon for the Fe-hydrogenase in Desulfovibrio vulgaris (Hildenborough): mapping of the transcript and regulation of expression

The genes for the subunits of the Fe-only hydrogenase from Desulfovibrio vulgaris are transcribed as a 1.9 kb mRNA; the operon contains no other genes besides those encoding the two subunits. The transcriptional start site of the operon was mapped. Determination of hydrogenase activity and hydrogenase mRNA levels indicates a growth-phase dependent regulation of hydrogenase expression at transcriptional level. However, it has not yet been possible to localize the sequences required for regulation and expression of the genes.

Overproduction of prismane protein in Desulfovibrio vulgaris (Hildenborough): evidence for a second S = 1/2-spin system in the one-electron reduced state

The gene encoding the prismane protein from Desulfovibrio vulgaris (Hildenborough) was inserted into broad-host-range vector pSUP104. The recombinant plasmid, pJSP104, was transferred to D. vulgaris by conjugal plasmid transfer. In the transconjugant D. vulgaris cells the prismane protein was 25-fold overproduced. The overproduced prismane protein was characterized by molecular mass, isoelectric point, iron content and spectroscopical properties. Both the iron content and the ultraviolet/visible spectrum are identical to the wild-type protein indicating that iron incorporation in the overproduced protein is complete. EPR spectra of the dithionite-reduced form of the overproduced protein indicated that the Fe-S cluster might occur in a similar structure as found in inorganic model compounds containing a [6Fe-6S] prismane core. The as-isolated overproduced protein showed the presence of a second S = 1/2 spin system that was also detected in the corresponding prismane protein from D. desulfuricans (ATCC 27774), but not in the protein from wild-type D. vulgaris. This additional signal was irreversibly transformed to the 'wild-type' high-spin and low-spin systems upon two reduction/re-oxidation cycles. It is shown that the EPR spectroscopy of the overproduced prismane protein is very similar to that of the D. desulfuricans enzyme and, with the exception of the second S = 1/2 spin system, to that of the prismane protein from wild-type D. vulgaris. Contrary to claims for the D. desulfuricans protein, it is shown here that all data can be fully explained assuming a single [6Fe-6S] cluster, that might be titrated into four different redox states and occurs in up to three different spin systems in the one-electron reduced state.

The primary structure of a protein containing a putative [6Fe-6S] prismane cluster from Desulfovibrio vulgaris (Hildenborough)

The gene encoding a protein containing a putative [6Fe-6S] prismane cluster has been cloned from Desulfovibrio vulgaris (Hildenborough) and sequenced. The gene encodes a polypeptide composed of 553 amino acids (60,161 Da). The DNA-derived amino acid sequence was partly confirmed by N-terminal sequencing of the purified protein and of fragments of the protein generated by CNBr cleavage. Furthermore, the C-terminal sequence was verified by digestion with carboxypeptidases A and B. The polypeptide contains nine Cys residues. Four of these residues are gathered in a Cys-Xaa2-Cys-Xaa7-Cys-Xaa5-Cys motif located towards the N-terminus of the protein. No relevant sequence similarity was found with other proteins, including those with high-spin Fe-S clusters (nitrogenase, hydrogenase), with one significant exception: the stretch containing the first four Cys residues spans two submotifs, Cys-Xaa2-Cys and Lys-Gly-Xaa-Cys-Gly, separated by 11 residues, that are also present in high-spin Fe-S cluster containing CO dehydrogenase. Western-blot analysis demonstrates cross-reactivity of antibodies raised against the purified protein both in Desulfovibrio strains and other sulfate-reducing bacteria. Hybridization of the cloned gene with genomic DNA of several other Desulfovibrio species indicates that homologous sequences are generally present in the genus Desulfovibrio.