Open AccessGenome sequence of the model sulfate reducer Desulfovibrio gigas : a comparative analysis within the Desulfovibrio genus
Author(s) -
MoraisSilva Fabio O.,
Rezende Antonio Mauro,
Pimentel Catarina,
Santos Catia I.,
Clemente Carla,
Varela–Raposo Ana,
Resende Daniela M.,
Silva Sofia M.,
Oliveira Luciana Márcia,
Matos Marcia,
Costa Daniela A.,
Flores Orfeu,
Ruiz Jerónimo C.,
RodriguesPousada Claudina
Publication year - 2014
Publication title -
microbiologyopen
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.881
H-Index - 36
ISSN - 2045-8827
DOI - 10.1002/mbo3.184
Subject(s) - reducer , desulfovibrio , whole genome sequencing , biology , genome , genetics , genus , computational biology , evolutionary biology , zoology , bacteria , gene , physics , thermodynamics
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 rpo B and gyr B) 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 Min CDE 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, Nfn AB or Mnh.