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

Abstract

Sulfate-reducing bacteria (SRB) are anaerobic prokaryotes found ubiquitously in nature. SRB were the first nonphotosynthetic, anaerobic bacteria shown to generate energy (ATP) through electron transfer-coupled phosphorylation. For this process, the SRB typically use sulfate as the terminal electron acceptor for respiration of hydrogen or various organic acids, which results in the production of sulfide, a highly reactive and toxic end-product. Beyond their obvious function in the sulfur cycle, SRB play an important role in global cycling of numerous other elements 1 . For example, in the carbon cycle, the SRB form part of microbial consortia that completely mineralize organic carbon in anaerobic environments; polymeric materials (e.g., cellulose) are first depolymerized and metabolized by fermentative microorganisms, and the resulting organic acid and reduced gas (that is, CO and H 2 ) end-products are further fermented or oxidized by other microbes, including SRB. The latter are particularly active in sulfate-rich (e.g., marine) environments, where they effectively link the global sulfur and carbon cycles 1,2 .Beyond these ecological roles, SRB also have a major economic impact because of their involvement in biocorrosion of ferrous metals in anaerobic environments 3 , described as "industrial venereal disease-it's expensive, everybody has it, and nobody wants to talk about it" 4 . For example, because SRB are abundant in oil fields, their metabolism has many negative consequences for the petroleum industry (e.g., corrosion of drilling and pumping machinery and storage tanks, souring of oil by sulfide production, plugging of machinery and rock pores with biomass and sulfide precipitates). The SRB also contribute to bioremediation of toxic metal ions 5,6 . Their metabolism increases the pH, causing toxic metal ions like copper (II), nickel (II) and cadmium (II) to precipitate as metal sulfides in acidic aquatic environments (e.g., mine effluents). Additionally, SRB can deliver electrons directly to oxidized toxic metal ions, including uranium (VI), technetium (VII), and chromium (VI), converting these into less soluble, reduced forms. Hence, SRB-mediated reduction represents a potentially useful mechanism for the bioremediation of metal ion contaminants from anaerobic sediments 6 .Most research on the metabolism and biochemistry of SRB has been done on the genus Desulfovibrio, a member of the δ-proteobacteria The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encod...

The mechanism of formate oxidation by metal-dependent formate dehydrogenases

“…The kinetic studies of the enzyme with the isotopically enriched 2 HCOONa clearly indicate that the C-H bond break is involved in the rate-limiting step of the catalytic mechanism. Analyzing the activation energy values for every step of the simulated mechanism, and having in mind that the three initial steps of the mechanism (Scheme 8, steps A-B, B-C, and C-D) do not take part in the enzymatic catalytic cycle, we can note that the highest activation energy barrier involves the transfer of the proton from the substrate to the selenium (21.2 kcal/mol, Scheme 8, step D-E), suggesting that, in agreement with the experimental results, this is the rate-limiting event of the catalytic mechanism.…”

“…Formate oxidation might also be part of a mechanism to form a proton gradient, once small uncharged molecules such as formic acid can cross the cytoplasmic membrane to the periplasmic space and release two protons after oxidation [2,3]. Prokaryote Fdhs are metalloenzymes with different subunit composition containing either molybdenum or tungsten at the active site.…”

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

“…The abundance of detectable dsrB genes in biofilm samples allowed the conclusion that these signatures were derived from bacteria and not from the dominant SM1 Euryarchaeon (three-log difference in archaeal 16S rRNA and dsrB gene abundance). Moreover, the one-log difference of bacterial 16S rRNA and dsrB genes can be attributed to the fact that ribosomal genes can have up to 15 copies per genome (Klappenbach et al, 2001;Lee et al, 2009), whereas dsrB genes generally appear once (Heidelberg et al, 2004).…”

Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

“…Moderately increased expression of DVU3171 (a cytochrome c 3 -encoding gene) was detected in JW9013 and JW9009 (Table 2). Cytochrome c 3 was previously reported to be the major electron carrier for metal ion reduction (19), and the upregulation of this gene may be related to an increased chromate reduction capacity in crp/fnr mutants. The alkyl hydroperoxide reductase C gene ahpC (DVU2247), known for reducing hydrogen peroxide (H 2 O 2 ) into H 2 O (6), was downregulated in JW9007 (Table 2), suggesting the possible role of DVU0379 in oxidative stress response.…”