Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments

Nucleic Acids Research

Volumn 30, Issue 18, 2002, Pages 3927-3935

  Takami, Hideto ^a,c   Takaki, Yoshihiro ^a   Uchiyama, Ikuo ^b  

^a JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

^b National Institutes of Natural Sciences   (Japan)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALKALINITY; ARTICLE; BACILLUS; BACTERIAL GENOME; BACTERIUM ISOLATION; CONTROLLED STUDY; DEEP SEA; EVOLUTIONARY ADAPTATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; GRAM POSITIVE BACTERIUM; HOMEOSTASIS; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; OCEANOBACILLUS IHEYENSIS; OSMOTIC PRESSURE; PH; PRIORITY JOURNAL; REGULATORY MECHANISM; SALINITY; SALT TOLERANCE; SEDIMENT;

BACILLI; BACILLUS; BACTERIA (MICROORGANISMS); OCEANOBACILLUS IHEYENSIS; POSIBACTERIA; PROKARYOTA;

EID: 0037106449     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf526     Document Type: Article

References (32)

1. Takami,H., Inoue,A., Fuji,F. and Horikoshi,K. (1997) Microbial flora in the deepest sea mud of Mariana Trench. FEMS Microbial. Lett., 152, 279-285.
2. Takami,H., Kobata,K., Nagahama,T., Kobayashi,H., Inoue,A. and Horikoshi,K. (1999) Biodiversity in deep-sea sites near the south part of Japan. Extremophiles, 3, 97-102.
3. Priest,F.G. (1993) Systematics and ecology of Bacillus. In Sonenshein,A.L., Hoch,J.A. and Losick,R. (eds), Bacillus subtilis and Other Gram-Positive Bacteria. ASM Press, Washington, DC, pp. 3-16.
4. Takami,H. (1999) Isolation and characterization of microorganisms from deep-sea mud. In Horikoshi,K. and Tsujii,K. (eds), Extremophiles in Deep-Sea Environments. Springer-Verlag, Tokyo, Japan, pp. 3-26.
5. Lu,J., Nogi,Y. and Takami,H. (2001) Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya Ridge. FEMS Microbiol. Lett., 205, 291-297.
6. Takami,H., Nakasone,K., Takaki,Y., Maeno,G., Sasaki,R., Masui,N., Fuji,F., Hirama,C., Nakamura,Y., Ogasawara,N. et al. (2000) Complete genome sequence of alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with B. subtilis. Nucleic Acids Res., 28, 4317-4331.
7. Kunst,F., Ogasawara,N., Mozer,I., Albertini,A.M., Alloni,G., Azevedo,V., Bertero,M.G., Bessieres,P., Bolotin,A., Borchert,S. et al. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature, 390, 249-256.
8. Kuroda,M., Ohta,T., Uchiyama,I., Baba,T., Yuzawa,H., Kobayashi,I., Cui,L., Oguchi,A., Aoki,K., Nagai,Y. et al. (2001) Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet, 357, 1225-1240.
9. Nölling,J., Breton,G., Omelchenko,M.V., Makarova,K.S., Zeng,Q., Gibson,R., Lee,H.M., Dubois,J., Qiu,D., Hitti,J. et al. (2001) Complete sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J. Bacteriol., 183, 4823-4838.
10. Sakiyama,T., Takami,H., Ogasawara,N., Kuhara,S., Kozuki,T., Doga,K., Ohyama,A. and Horikoshi,K. (2000) An automated system for genome analysis to support microbial whole-genome shotgun sequencing. Biosci. Biotech. Biochem., 64, 670-673.
11. Yada,T., Totoki,Y., Takagi,T. and Nakai,K. (2001) A novel bacterial gene-finding system with top-class accuracy in locating start codons. DNA Res., 8, 97-106.
12. Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
13. Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
14. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
15. Jones,D.T., Taylor,W.R. and Thornton,J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci., 8, 275-283.
16. Sokal,R. and Sneath,P.H.A. (1963) Principles of Numerical Taxonomy. W.H. Freeman and Co., San Francisco, CA.
17. Mahillon,J. and Chandler,M. (1998) Insertion sequence. Microbiol. Mol. Biol. Rev., 62, 725-774.
18. Takami,H., Han,C.G., Takaki,Y. and Ohtsubo,E. (2001) Identification and distribution of new insertion sequences in the genome of alkaliphilic Bacillus halodurans C-125. J. Bacteriol., 183, 4345-4356.
19. Horikoshi,K. (1999) Alkaliphiles. Haward Academic, Amsterdam, The Netherlands.
20. Schadewaldt,P., Hummel,W., Wendel,U. and Adelmeyer,F. (1995) Enzymatic method for determination of branched-chain amino acid aminotransferase activity. Anal. Biochem., 230, 199-204.
21. Kagamiyama,H. and Hayashi,H. (2000) Branched-chain amino acid aminotransferase of E. coli. Methods Enzymol., 324, 103-113.
22. +-dependence of alkaliphily in Bacillus. Biochim. Biophys. Acta, 1505, 156-168.
23. Tsujii,K. (2002) Donnan equilibria in microbial cell walls: a pH-homeostatic mechanism in alkaliphiles. Colloids Surf. Biointerfaces, 24, 247-251.
24. Chen,C.M., Ye,Q.Z., Zhu,Z., Wanner,B.L. and Walsh,C.T. (1990) Molecular biology of carbon-phosphorus bond cleavage. J. Biol. Chem., 265, 4461-4471.
25. Murata,K., Higaki,N. and Yimura,A. (1988) Detection of carbon-phosphorus lyase activity in cell free extracts of Enterobacter aerogenes. Biochem. Biophys. Res. Commun., 57, 190-195.
26. Krämer,R. and Palmieri,F. (1992) Metabolite carriers in mitochondria. Molecular. In Ernster,L. (ed.), New Comprehensive Biochemistry: Mechanisms in Bioenergetics. Elsevier Science B.V., Amsterdam, The Netherlands, Vol. 23, pp. 359-384.
27. 4-dicarboxlylate carriers and sensors in bacteria. Biochim. Biophys. Acta, 1553, 39-56.
28. Ventosa,A., Nieto,J. and Oren,A. (1998) Biology of moderately halophilic aerobic bacteria. Microbiol. Mol. Biol. Rev., 62, 504-544.
29. Ren,D., Navarro,B., Xu,H., Yue,L., Shi,Q. and Clapham,D.E. (2001) A prokaryotic voltage-gated sodium channel. Science, 294, 2372-2375.
30. Shioi,J.I., Matsuura,S. and Imae,Y. (1980) Quantitative measurements of proton motive force and motility in Bacillus subtilis. J. Bacteriol., 144, 891-897.
31. Sneath,P.H.A., Mair,N.S., Sharp,M.E. and Holt,J.G. (1986) Bergey's Manual of Systematic Bacteriology, Vol. 2. Wiliams and Wikins, Baltimore, MD.
32. Kempf,B. and Bremer,E. (1998) Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments. Arch. Microbiol., 170, 319-330.