Nucleic Acids Research, 2000, Vol. 28, No. 21 4317-4331
© 2000 Oxford University Press
Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis
Japan Marine Science and Technology Center, Deep-Sea Microorganisms Research Group, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan, 1Nara Institute of Science and Technology, Graduate School of Biological Sciences, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan and 2Kyushu University, Graduate School of Genetic Resources Technology, Hakozaki, Higashi-ku, Fukuoka 812-8555, Japan
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 
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.
* To whom correspondence should be addressed. Tel: +81 468 67 3895; Fax: +81 468 66 6364; Email: takamih@jamstec.go.jp +AP001507–AP001520
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T. Shimizu, K. Shima, K.-i. Yoshino, K. Yonezawa, T. Shimizu, and H. Hayashi Proteome and Transcriptome Analysis of the Virulence Genes Regulated by the VirR/VirS System in Clostridium perfringens J. Bacteriol., May 15, 2002; 184(10): 2587 - 2594. [Abstract] [Full Text] [PDF]
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S. Adak, K. S. Aulak, and D. J. Stuehr Direct Evidence for Nitric Oxide Production by a Nitric-oxide Synthase-like Protein from Bacillus subtilis J. Biol. Chem., May 3, 2002; 277(18): 16167 - 16171. [Abstract] [Full Text] [PDF]
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T. Shiba, K. Takeda, M. Yajima, and M. Tadano Genes from Pseudomonas sp. Strain BS Involved in the Conversion of L-2-Amino-{Delta}2-Thiazolin-4-Carbonic Acid to L-Cysteine Appl. Envir. Microbiol., May 1, 2002; 68(5): 2179 - 2187. [Abstract] [Full Text] [PDF]
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V. Briolat and G. Reysset Identification of the Clostridium perfringens Genes Involved in the Adaptive Response to Oxidative Stress J. Bacteriol., May 1, 2002; 184(9): 2333 - 2343. [Abstract] [Full Text] [PDF]
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 Q. Bao, Y. Tian, W. Li, Z. Xu, Z. Xuan, S. Hu, W. Dong, J. Yang, Y. Chen, Y. Xue, et al. A Complete Sequence of the T. tengcongensis Genome Genome Res., May 1, 2002; 12(5): 689 - 700. [Abstract] [Full Text] [PDF]
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Evolutionary Analysis by Whole-Genome Comparisons J. Bacteriol., April 15, 2002; 184(8): 2260 - 2272.
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F. Narberhaus {alpha}-Crystallin-Type Heat Shock Proteins: Socializing Minichaperones in the Context of a Multichaperone Network Microbiol. Mol. Biol. Rev., March 1, 2002; 66(1): 64 - 93. [Abstract] [Full Text] [PDF]
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G. Gouesbet, G. Jan, and P. Boyaval Two-Dimensional Electrophoresis Study of Lactobacillus delbrueckii subsp. bulgaricus Thermotolerance Appl. Envir. Microbiol., March 1, 2002; 68(3): 1055 - 1063. [Abstract] [Full Text] [PDF]
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B.-J. Hwang, H.-J. Yeom, Y. Kim, and H.-S. Lee Corynebacterium glutamicum Utilizes both Transsulfuration and Direct Sulfhydrylation Pathways for Methionine Biosynthesis J. Bacteriol., March 1, 2002; 184(5): 1277 - 1286. [Abstract] [Full Text] [PDF]
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A. U. Kuhlmann and E. Bremer Osmotically Regulated Synthesis of the Compatible Solute Ectoine in Bacillus pasteurii and Related Bacillus spp. Appl. Envir. Microbiol., February 1, 2002; 68(2): 772 - 783. [Abstract] [Full Text] [PDF]
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K. S. Makarova, L. Aravind, N. V. Grishin, I. B. Rogozin, and E. V. Koonin A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis Nucleic Acids Res., January 15, 2002; 30(2): 482 - 496. [Abstract] [Full Text] [PDF]
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K. Kanamaru, S. Stephenson, and M. Perego Overexpression of the PepF Oligopeptidase Inhibits Sporulation Initiation in Bacillus subtilis J. Bacteriol., January 1, 2002; 184(1): 43 - 50. [Abstract] [Full Text] [PDF]
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J. J. Polderman-Tijmes, P. A. Jekel, E. J. de Vries, A. E. J. van Merode, R. Floris, J.-M. van der Laan, T. Sonke, and D. B. Janssen Cloning, Sequence Analysis, and Expression in Escherichia coli of the Gene Encoding an {alpha}-Amino Acid Ester Hydrolase from Acetobacter turbidans Appl. Envir. Microbiol., January 1, 2002; 68(1): 211 - 218. [Abstract] [Full Text] [PDF]
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C. O. Bramer, L. F. Silva, J. G. C. Gomez, H. Priefert, and A. Steinbuchel Identification of the 2-Methylcitrate Pathway Involved in the Catabolism of Propionate in the Polyhydroxyalkanoate-Producing Strain Burkholderia sacchari IPT101T and Analysis of a Mutant Accumulating a Copolyester with Higher 3-Hydroxyvalerate Content Appl. Envir. Microbiol., January 1, 2002; 68(1): 271 - 279. [Abstract] [Full Text] [PDF]
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M. Gobel, K. Kassel-Cati, E. Schmidt, and W. Reineke Degradation of Aromatics and Chloroaromatics by Pseudomonas sp. Strain B13: Cloning, Characterization, and Analysis of Sequences Encoding 3-Oxoadipate:Succinyl-Coenzyme A (CoA) Transferase and 3-Oxoadipyl-CoA Thiolase J. Bacteriol., January 1, 2002; 184(1): 216 - 223. [Abstract] [Full Text] [PDF]
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E. Diaz, A. Ferrandez, M. A. Prieto, and J. L. Garcia Biodegradation of Aromatic Compounds by Escherichia coli Microbiol. Mol. Biol. Rev., December 1, 2001; 65(4): 523 - 569. [Abstract] [Full Text] [PDF]
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E. P. C. Rocha and A. Danchin Ongoing Evolution of Strand Composition in Bacterial Genomes Mol. Biol. Evol., September 1, 2001; 18(9): 1789 - 1799. [Abstract] [Full Text] [PDF]
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H. Takami, C.-G. Han, Y. Takaki, and E. Ohtsubo Identification and Distribution of New Insertion Sequences in the Genome of Alkaliphilic Bacillus halodurans C-125 J. Bacteriol., July 15, 2001; 183(14): 4345 - 4356. [Abstract] [Full Text] [PDF]
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B. R. Belitsky, J. Brill, E. Bremer, and A. L. Sonenshein Multiple Genes for the Last Step of Proline Biosynthesis in Bacillus subtilis J. Bacteriol., July 15, 2001; 183(14): 4389 - 4392. [Abstract] [Full Text] [PDF]
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M. De Angelis, L. Bini, V. Pallini, P. S. Cocconcelli, and M. Gobbetti The acid-stress response in Lactobacillus sanfranciscensis CB1 Microbiology, July 1, 2001; 147(7): 1863 - 1873. [Abstract] [Full Text] [PDF]
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I. Podglajen, J. Breuil, A. Rohaut, C. Monsempes, and E. Collatz Multiple Mobile Promoter Regions for the Rare Carbapenem Resistance Gene of Bacteroides fragilis J. Bacteriol., June 1, 2001; 183(11): 3531 - 3535. [Abstract] [Full Text]
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 S.-i. Makino, M. Suzuki, Y. Zivanovic, H. Myllykallio, and P. Forterre Bacterial Genomic Reorganization upon DNA Replication Science, May 4, 2001; 292(5518): 803a - 803. [Full Text] [PDF]
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T. Ishii, K.-i. Yoshida, G. Terai, Y. Fujita, and K. Nakai DBTBS: a database of Bacillus subtilis promoters and transcription factors Nucleic Acids Res., January 1, 2001; 29(1): 278 - 280. [Abstract] [Full Text] [PDF]
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