Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus

Abstract

Desulfovibrio gigas is a model organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic context of this organism was however, not yet available. The sequencing of the D. gigas genome provides insights into the integrated network of energy conserving complexes and structures present in this bacterium. Comparison with genomes of other Desulfovibrio spp. reveals the presence of two different CRISPR/Cas systems in D. gigas. Phylogenetic analysis using conserved protein sequences (encoded by rpoB and gyrB) indicates two main groups of Desulfovibrio spp, being D. gigas more closely related to D. vulgaris and D. desulfuricans strains. Gene duplications were found such as those encoding fumarate reductase, formate dehydrogenase, and superoxide dismutase. Complexes not yet described within Desulfovibrio genus were identified: Mnh complex, a v-type ATP-synthase as well as genes encoding the MinCDE system that could be responsible for the larger size of D. gigas when compared to other members of the genus. A low number of hydrogenases and the absence of the codh/acs and pfl genes, both present in D. vulgaris strains, indicate that intermediate cycling mechanisms may contribute substantially less to the energy gain in D. gigas compared to other Desulfovibrio spp. This might be compensated by the presence of other unique genomic arrangements of complexes such as the Rnf and the Hdr/Flox, or by the presence of NAD(P)H related complexes, like the Nuo, NfnAB or Mnh.

An HcpR paralog ofDesulfovibrio gigas provides protection against nitrosative stress

“…Recent evidence suggests that Desulfovibrio magneticus , Desulfovibrio salexigens and Desulfovibrio desufuricans possess a second HcpR related sequence in their genome that was predicted to bind an 18-bp pseudopalindromic DNA sequence similar to the HcpR binding motif [23] . Interestingly, a search of the D. gigas genome [20] revealed the presence of two HcpR sequences that share 48.9% of similarity at the amino acid level, here designated by HcpR1 and HcpR2 ( Fig. 1 ).…”

“…After a search in the genome of D. gigas [20] for genes that may be regulated by HcpR1, fifteen putative targets were found to contain the described consensus binding site within the respective promoter regions. Among the fifteen candidate targets, those annotated in the D. gigas genome as hypothetical proteins were disregarded, as well as those whose consensus binding site was located more than 250 bp upstream of the initiation codon.…”

“…The aim of this work was to clarify whether Desulfovibrio gigas HcpR provides protection against nitrosative stress. To this end, we searched its genome for HcpR-related sequences and identified two HcpR paralogous genes [20] . Phylogenetic analyses on sequences of the HcpR and related regulators found in the Desulfovibrio genus indicate that several species possess two or more HcpR paralogs.…”

Genome Sequence of the Piezophilic, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio indicus J2 T

“…Previous study indicated that energy metabolism of SRB is far more versatile than we considered, so that SRB can use different alternative strategies for energy conservation (5, 6). The genome sequence analysis will allow comprehensive comparisons with other SRB and pave the way for further understanding of SRB lifestyle in anaerobic deep sea environments.…”

Analysis of membrane–protein complexes of the marine sulfate reducer Desulfobacula toluolica Tol2 by 1D blue native‐PAGE complexome profiling and 2D blue native‐/SDS‐PAGE

“…The MnhABCDEFG proteins are also encoded in the genomes of Dv. gigas [61] and D. toluolica Tol2 [20], though its function in SRB is unclear at present.…”