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

Eiji Aono; Tomoya Baba; Takeshi Ara; Tatsunari Nishi; Tomoko Nakamichi; Eiji Inamoto; Hiromi Toyonaga; Miki Hasegawa; Yuki Takai; Yoshiko Okumura; Miki Baba; Masaru Tomita; Chiaki Kato; Taku Oshima; Kaoru Nakasone; Hirotada Mori

doi:10.1039/C000396D

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Molecular BioSystems

Issue 7, 2010

Research interfacing chemical biology with the -omic sciences and systems biology.

Impact Factor 3.534 12 Issues per Year Indexed in MEDLINE

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

Eiji Aono,^a Tomoya Baba,^b Takeshi Ara,^b Tatsunari Nishi,^c Tomoko Nakamichi,^a Eiji Inamoto,^a Hiromi Toyonaga,^a Miki Hasegawa,^b Yuki Takai,^b Yoshiko Okumura,^b Miki Baba,^b Masaru Tomita,^b Chiaki Kato,^d Taku Oshima,^a Kaoru Nakasone*^e and Hirotada Mori*^a^b

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Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
E-mail: hmori@gtc.naist.jp ;
Fax: +81-743-72-5669 ;
Tel: +81-743-72-5660

Institute of Advanced Biosciences, Keio University, 403-1 Tsuruoka, Yamagata 997-0017, Japan

Genaris, Inc., Leading Venture Plaza 2-308, 75-1 Ono, Tsurumi, Yokohama 230-0046, Japan

Marine Ecosystems Research Program, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan

Department of Biotechnology and Chemistry, School of Engineering, Kinki University, Higashihiroshima, Hiroshima 739-2116, Japan
E-mail: nakasone@hiro.kindai.ac.jp ;
Fax: +81-82-434-7011 ;
Tel: +81-82-439-1110 (ex. 307)

Mol. BioSyst., 2010,6, 1216-1226

DOI: 10.1039/C000396D
Received 07 Jan 2010, Accepted 24 Mar 2010
First published online 11 May 2010

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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 γ-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.

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