title: Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis.
abstract: The 4 202 353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066 predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments, 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no match to any protein database. Among the total CDSs, 8.8% match sequences of proteins found only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of various organisms, including B.subtilis. The B. halodurans genome contains 112 transposase genes, indicating that transposases have played an important evolutionary role in horizontal gene transfer and also in internal genetic rearrangement in the genome. Strain C-125 lacks some of the necessary genes for competence, such as comS, srfA and rapC, supporting the fact that competence has not been demonstrated experimentally in C-125. There is no paralog of tupA, encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genome and an ortholog of tupA cannot be found in the B.subtilis genome. Out of 11 sigma factors which belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting that they may have a role in the special mechanism of adaptation to an alkaline environment.
authors.affiliation: Japan Marine Science and Technology Center, Deep-Sea Microorganisms Research Group, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan. takamih@jamstec.go.jp
authors.forename: H
authors.initials: H
authors.lastname: Takami
authors.forename: K
authors.initials: K
authors.lastname: Nakasone
authors.forename: Y
authors.initials: Y
authors.lastname: Takaki
authors.forename: G
authors.initials: G
authors.lastname: Maeno
authors.forename: R
authors.initials: R
authors.lastname: Sasaki
authors.forename: N
authors.initials: N
authors.lastname: Masui
authors.forename: F
authors.initials: F
authors.lastname: Fuji
authors.forename: C
authors.initials: C
authors.lastname: Hirama
authors.forename: Y
authors.initials: Y
authors.lastname: Nakamura
authors.forename: N
authors.initials: N
authors.lastname: Ogasawara
authors.forename: S
authors.initials: S
authors.lastname: Kuhara
authors.forename: K
authors.initials: K
authors.lastname: Horikoshi
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics; D000222:Adaptation, Physiological / Q000235:genetics; D000468:Alkalies / Q000378:metabolism; D001407:Bacillus / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001412:Bacillus subtilis / Q000737:chemistry / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics / Q000502:physiology; D001482:Base Composition; D001692:Biological Transport; D002473:Cell Wall / Q000235:genetics / Q000378:metabolism; D017124:Conserved Sequence / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D019992:Databases as Topic; D004734:Energy Metabolism; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics / Q000502:physiology; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D020161:Physical Chromosome Mapping; D014176:Protein Biosynthesis; D012343:RNA, Transfer / Q000235:genetics; D018741:Replication Origin / Q000235:genetics; D017385:Sequence Homology; D012808:Sigma Factor / Q000235:genetics; D013171:Spores, Bacterial / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics; D019895:Transposases / Q000235:genetics
chemical_list: D018528:ATP-Binding Cassette Transporters; D000468:Alkalies; D001426:Bacterial Proteins; D004251:DNA Transposable Elements; D012808:Sigma Factor; D012343:RNA, Transfer; D019895:Transposases