Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments

Abstract

Remineralization of organic matter in deep-sea sediments is important in oceanic biogeochemical cycles, and bacteria play a major role in this process. Shewanella violacea DSS12 is a psychrophilic and piezophilic gamma-proteobacterium that was isolated from the surface layer of deep sea sediment at a depth of 5110 m. Here, we report the complete genome sequence of S. violacea and comparative analysis with the genome of S. oneidensis MR-1, isolated from sediments of a freshwater lake. Unlike S. oneidensis, this deep-sea Shewanella possesses very few terminal reductases for anaerobic respiration and no c-type cytochromes or outer membrane proteins involved in respiratory Fe(iii) reduction, which is characteristic of most Shewanella species. Instead, the S. violacea genome contains more terminal oxidases for aerobic respiration and a much greater number of putative secreted proteases and polysaccharases, in particular, for hydrolysis of collagen, cellulose and chitin, than are encoded in S. oneidensis. Transporters and assimilatory reductases for nitrate and nitrite, and nitric oxide-detoxifying mechanisms (flavohemoglobin and flavorubredoxin) are found in S. violacea. Comparative analysis of the S. violacea genome revealed the respiratory adaptation of this bacterium to aerobiosis, leading to predominantly aerobic oxidation of organic matter in surface sediments, as well as its ability to efficiently use diverse organic matter and to assimilate inorganic nitrogen as a survival strategy in the nutrient-poor deep-sea floor.

Increases of heat shock proteins and their mRNAs at high hydrostatic pressure in a deep-sea piezophilic bacterium, Shewanella violacea

“…While the rpoH gene and putative σ 32 binding sites (RpoH promoters) were found in the S. violacea genome (Figs. 5b, 6b, 7b;Aono et al 2010), neither the repressor protein σ 43 , inverted repeats, nor the corresponding cis-element located in the promoter region of the CIRCE were identified in this genome. This suggests that the transcription of HSP genes is regulated by the σ 32 promoter-dependent mechanism in S. violacea.…”

“…We searched for similar sequences for the binding sites in S. violacea in the genome sequence (Aono et al 2010). We found potential σ 70 and σ 32 binding sites for the groE operon in S. violacea (RpoD and RpoH promoters in Fig.…”

“…Plasmids isolated from several strong positive clones were sequenced with an ABI PRISM dye terminator cycle sequencing kit and a model 377 DNA sequencer (Perkin Elmer/Applied Biosystems). The obtained sequences of the HSP genes and sigma factor were compared with the genome sequences retrieved from DDBJ/GenBank/EMBL (Aono et al 2010).…”

“…It also grows at atmospheric pressure (0.1 MPa) and 8 °C. It is useful as a model piezophile for studying bacterial physiology under different pressure conditions and its genome sequence has been reported (Aono et al 2010).…”

“…The TSSs are shown by bold arrows. The bold ATG, the first ATG codon of grpE acid sequence of the protein and comparison with genome information(Aono et al 2010)…”