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Nucleic Acids Research 2004 32(21):6292-6303; doi:10.1093/nar/gkh970
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Published online 1 December 2004

Nucleic Acids Research, Vol. 32 No. 21 © Oxford University Press 2004; all rights reserved

Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus

Hideto Takami*, Yoshihiro Takaki, Gab-Joo Chee, Shinro Nishi, Shigeru Shimamura, Hiroko Suzuki, Satomi Matsui and Ikuo Uchiyama1

Microbial Genome Research Group, Japan Agency of Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan and 1 Research Center for Computational Science, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan

* To whom correspondence should be addressed. Tel: +81 46 867 9643; Fax: +81 46 867 9645; Email: takamih{at}jamstec.go.jp
+AP006508–AP006519

Received August 20, 2004; Revised October 7, 2004; Accepted November 10, 2004

We present herein the first complete genome sequence of a thermophilic Bacillus-related species, Geobacillus kaustophilus HTA426, which is composed of a 3.54 Mb chromosome and a 47.9 kb plasmid, along with a comparative analysis with five other mesophilic bacillar genomes. Upon orthologous grouping of the six bacillar sequenced genomes, it was found that 1257 common orthologous groups composed of 1308 genes (37%) are shared by all the bacilli, whereas 839 genes (24%) in the G.kaustophilus genome were found to be unique to that species. We were able to find the first prokaryotic sperm protamine P1 homolog, polyamine synthase, polyamine ABC transporter and RNA methylase in the 839 unique genes; these may contribute to thermophily by stabilizing the nucleic acids. Contrasting results were obtained from the principal component analysis (PCA) of the amino acid composition and synonymous codon usage for highlighting the thermophilic signature of the G.kaustophilus genome. Only in the PCA of the amino acid composition were the Bacillus-related species located near, but were distinguishable from, the borderline distinguishing thermophiles from mesophiles on the second principal axis. Further analysis revealed some asymmetric amino acid substitutions between the thermophiles and the mesophiles, which are possibly associated with the thermoadaptation of the organism.


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