title: 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.
authors: Instituto de Tecnologia Quómica e Biológica - Antonio Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República - Estação Agronómica Nacional, 2780-157, Oeiras, Portugal.
authors: Fabio O
authors: FO
authors: Morais-Silva
authors: Antonio Mauro
authors: AM
authors: Rezende
authors: Catarina
authors: C
authors: Pimentel
authors: Catia I
authors: CI
authors: Santos
authors: Carla
authors: C
authors: Clemente
authors: Ana
authors: A
authors: Varela-Raposo
authors: Daniela M
authors: DM
authors: Resende
authors: Sofia M
authors: SM
authors: da Silva
authors: Luciana Márcia
authors: LM
authors: de Oliveira
authors: Marcia
authors: M
authors: Matos
authors: Daniela A
authors: DA
authors: Costa
authors: Orfeu
authors: O
authors: Flores
authors: Jerónimo C
authors: JC
authors: Ruiz
authors: Claudina
authors: C
authors: Rodrigues-Pousada
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D016000:Cluster Analysis; D017124:Conserved Sequence; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D045286:Desulfovibrio gigas / Q000235:genetics*; D014644:Genetic Variation; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial
keywords: Analysis; Desulfovibrio gigas; comparative genomics; genome