Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

ABSTRACT The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe] hydrogenase, an [NiFeSe] hydrogenase, and two [NiFe] hydrogenases encoded by the hyd, hys, hyn1, and hyn2 genes, respectively. In order to understand their cellular functions, we have compared the growth rates of existing (hyd and hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those of the wild type in defined media in which lactate or hydrogen at either 5 or 50% (vol/vol) was used as the sole electron donor for sulfate reduction. Only strains missing the [Fe] hydrogenase were significantly affected during growth with lactate or with 50% (vol/vol) hydrogen as the sole electron donor. When the cells were grown at low (5% [vol/vol]) hydrogen concentrations, those missing the [NiFeSe] hydrogenase suffered the greatest impairment. The growth rate data correlated strongly with gene expression results obtained from microarray hybridizations and real-time PCR using mRNA extracted from cells grown under the three conditions. Expression of the hys genes followed the order 5% hydrogen > 50% hydrogen > lactate, whereas expression of the hyd genes followed the reverse order. These results suggest that growth with lactate and 50% hydrogen is associated with high intracellular hydrogen concentrations, which are best captured by the higher activity, lower affinity [Fe] hydrogenase. In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase.

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Uranium Reduction by Desulfovibrio desulfuricans Strain G20 and a Cytochrome c3 Mutant

Applied and Environmental Microbiology ◽

10.1128/aem.68.6.3129-3132.2002 ◽

2002 ◽

Vol 68 (6) ◽

pp. 3129-3132 ◽

Cited By ~ 94

Author(s):

Rayford B. Payne ◽

Darren M. Gentry ◽

Barbara J. Rapp-Giles ◽

Laurence Casalot ◽

Judy D. Wall

Keyword(s):

Electron Donor ◽

Desulfovibrio Desulfuricans ◽

Desulfovibrio Vulgaris ◽

In Vitro Experiments ◽

Wild Type ◽

Cytochrome C3 ◽

Uranium Reduction

ABSTRACT Previous in vitro experiments with Desulfovibrio vulgaris strain Hildenborough demonstrated that extracts containing hydrogenase and cytochrome c 3 could reduce uranium(VI) to uranium(IV) with hydrogen as the electron donor. To test the involvement of these proteins in vivo, a cytochrome c 3 mutant of D. desulfuricans strain G20 was assayed and found to be able to reduce U(VI) with lactate or pyruvate as the electron donor at rates about one-half of those of the wild type. With electrons from hydrogen, the rate was more severely impaired. Cytochrome c 3 appears to be a part of the in vivo electron pathway to U(VI), but additional pathways from organic donors can apparently bypass this protein.

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The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

Nature Biotechnology ◽

10.1038/nbt959 ◽

2004 ◽

Vol 22 (5) ◽

pp. 554-559 ◽

Cited By ~ 388

Author(s):

John F Heidelberg ◽

Rekha Seshadri ◽

Shelley A Haveman ◽

Christopher L Hemme ◽

Ian T Paulsen ◽

...

Keyword(s):

Genome Sequence ◽

Desulfovibrio Vulgaris ◽

Sulfate Reducing ◽

Desulfovibrio Vulgaris Hildenborough

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Functional characterization of the early steps of tetrapyrrole biosynthesis and modification in Desulfovibrio vulgaris Hildenborough

Biochemical Journal ◽

10.1042/bj20090151 ◽

2009 ◽

Vol 420 (2) ◽

pp. 317-326 ◽

Cited By ~ 24

Author(s):

Susana A. L. Lobo ◽

Amanda Brindley ◽

Martin J. Warren ◽

Lígia M. Saraiva

Keyword(s):

Functional Characterization ◽

Desulfovibrio Vulgaris ◽

Decarboxylase Activity ◽

Sulfate Reducing ◽

Porphobilinogen Synthase ◽

Desulfovibrio Vulgaris Hildenborough ◽

The Individual ◽

Individual Enzyme ◽

Relevant Gene

The biosynthesis of the tetrapyrrole framework has been investigated in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough by characterization of the enzymes required for the transformation of aminolaevulinic acid into sirohydrochlorin. PBG (porphobilinogen) synthase (HemB) was found to be a zinc-dependent enzyme that exists in its native state as a homohexamer. PBG deaminase (HemC) was shown to contain the dipyrromethane cofactor. Uroporphyrinogen III synthase is found fused with a uroporphyrinogen III methyltransferase (HemD-CobA). Both activities could be demonstrated in this amalgamated protein and the individual enzyme activities were separated by dissecting the relevant gene to allow the production of two distinct proteins. A gene annotated in the genome as a bifunctional precorrin-2 dehydrogenase/sirohydrochlorin ferrochelatase was in fact shown to act only as a dehydrogenase and is simply capable of synthesizing sirohydrochlorin rather than sirohaem. Genome analysis also reveals a lack of any uroporphyrinogen III decarboxylase, an enzyme necessary for the classical route to haem synthesis. However, the genome does encode some predicted haem d1 biosynthetic enzymes even though the bacterium does not contain the cd1 nitrite reductase. We suggest that sirohydrochlorin acts as a substrate for haem synthesis using a novel pathway that involves homologues of the d1 biogenesis system. This explains why the uroporphyrinogen III synthase is found fused with the methyltransferase, bypassing the need for uroporphyrinogen III decarboxylase activity.

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Effects of Deletion of Genes Encoding Fe-Only Hydrogenase of Desulfovibrio vulgaris Hildenborough on Hydrogen and Lactate Metabolism

Journal of Bacteriology ◽

10.1128/jb.184.3.679-686.2002 ◽

2002 ◽

Vol 184 (3) ◽

pp. 679-686 ◽

Cited By ~ 59

Author(s):

Brant K. J. Pohorelic ◽

Johanna K. Voordouw ◽

Elisabeth Lojou ◽

Alain Dolla ◽

Jens Harder ◽

...

Keyword(s):

Sulfate Reduction ◽

Electron Donor ◽

Type Strain ◽

Wild Type Strain ◽

Physiological Role ◽

Hydrogen Uptake ◽

Desulfovibrio Vulgaris ◽

Lactate Metabolism ◽

Wild Type ◽

Genes Encoding

ABSTRACT 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 H2 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 H2 was also present, growth in lactate- and sulfate-containing media lacking H2 was less efficient. The hyd mutant produced, transiently, significant amounts of H2 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.

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Desulfovibrio vulgaris Hildenborough prefers lactate over hydrogen as electron donor

Annals of Microbiology ◽

10.1007/s13213-013-0675-0 ◽

2013 ◽

Vol 64 (2) ◽

pp. 451-457 ◽

Cited By ~ 6

Author(s):

Xuanyu Tao ◽

Yabo Li ◽

Haiying Huang ◽

Yong Chen ◽

Pu Liu ◽

...

Keyword(s):

Electron Donor ◽

Desulfovibrio Vulgaris ◽

Desulfovibrio Vulgaris Hildenborough

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Gene Expression by the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough Grown on an Iron Electrode under Cathodic Protection Conditions

Applied and Environmental Microbiology ◽

10.1128/aem.02469-07 ◽

2008 ◽

Vol 74 (8) ◽

pp. 2404-2413 ◽

Cited By ~ 23

Author(s):

Sean M. Caffrey ◽

Hyung Soo Park ◽

Jenny Been ◽

Paul Gordon ◽

Christoph W. Sensen ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Profile ◽

Expression Profile ◽

Cathodic Protection ◽

Gaseous Hydrogen ◽

Iron Electrode ◽

Desulfovibrio Vulgaris ◽

Wild Type ◽

Sulfate Reducing ◽

Genes Encoding

ABSTRACT The genome sequence of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough was reanalyzed to design unique 70-mer oligonucleotide probes against 2,824 probable protein-coding regions. These included three genes not previously annotated, including one that encodes a c-type cytochrome. Using microarrays printed with these 70-mer probes, we analyzed the gene expression profile of wild-type D. vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed negative potential of −1.1 V (cathodic protection conditions). The gene expression profile of cells grown on cathodic hydrogen was compared to that of cells grown with gaseous hydrogen bubbling through the culture. Relative to the latter, the electrode-grown cells overexpressed two hydrogenases, the hyn-1 genes for [NiFe] hydrogenase 1 and the hyd genes, encoding [Fe] hydrogenase. The hmc genes for the high-molecular-weight cytochrome complex, which allows electron flow from the hydrogenases across the cytoplasmic membrane, were also overexpressed. In contrast, cells grown on gaseous hydrogen overexpressed the hys genes for [NiFeSe] hydrogenase. Cells growing on the electrode also overexpressed genes encoding proteins which promote biofilm formation. Although the gene expression profiles for these two modes of growth were distinct, they were more closely related to each other than to that for cells grown in a lactate- and sulfate-containing medium. Electrochemically measured corrosion rates were lower for iron electrodes covered with hyn-1, hyd, and hmc mutant biofilms than for wild-type biofilms. This confirms the importance, suggested by the gene expression studies, of the corresponding gene products in D. vulgaris-mediated iron corrosion.

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Gene Expression Analysis of Energy Metabolism Mutants of Desulfovibrio vulgaris Hildenborough Indicates an Important Role for Alcohol Dehydrogenase

Journal of Bacteriology ◽

10.1128/jb.185.15.4345-4353.2003 ◽

2003 ◽

Vol 185 (15) ◽

pp. 4345-4353 ◽

Cited By ~ 45

Author(s):

Shelley A. Haveman ◽

Véronique Brunelle ◽

Johanna K. Voordouw ◽

Gerrit Voordouw ◽

John F. Heidelberg ◽

...

Keyword(s):

Gene Expression ◽

Energy Metabolism ◽

Carbon Source ◽

Alcohol Dehydrogenase ◽

Sulfate Reduction ◽

Electron Donor ◽

Desulfovibrio Vulgaris ◽

Wild Type ◽

Reading Frame ◽

Metabolic Conditions

ABSTRACT Comparison of the proteomes of the wild-type and Fe-only hydrogenase mutant strains of Desulfovibrio vulgaris Hildenborough, grown in lactate-sulfate (LS) medium, indicated the near absence of open reading frame 2977 (ORF2977)-coded alcohol dehydrogenase in the hyd mutant. Hybridization of labeled cDNA to a macroarray of 145 PCR-amplified D. vulgaris genes encoding proteins active in energy metabolism indicated that the adh gene was among the most highly expressed in wild-type cells grown in LS medium. Relative to the wild type, expression of the adh gene was strongly downregulated in the hyd mutant, in agreement with the proteomic data. Expression was upregulated in ethanol-grown wild-type cells. An adh mutant was constructed and found to be incapable of growth in media in which ethanol was both the carbon source and electron donor for sulfate reduction or was only the carbon source, with hydrogen serving as electron donor. The hyd mutant also grew poorly on ethanol, in agreement with its low level of adh gene expression. The adh mutant grew to a lower final cell density on LS medium than the wild type. These results, as well as the high level of expression of adh in wild-type cells on media in which lactate, pyruvate, formate, or hydrogen served as the sole electron donor for sulfate reduction, indicate that ORF2977 Adh contributes to the energy metabolism of D. vulgaris under a wide variety of metabolic conditions. A hydrogen cycling mechanism is proposed in which protons and electrons originating from cytoplasmic ethanol oxidation by ORF2977 Adh are converted to hydrogen or hydrogen equivalents, possibly by a putative H2-heterodisulfide oxidoreductase complex, which is then oxidized by periplasmic Fe-only hydrogenase to generate a proton gradient.

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