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Nature 390, 249-256 (20 November 1997) | doi:10.1038/36786; Received 16 July 1997; Accepted 29 September 1997

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The complete genome sequence of the Gram-positive bacterium Bacillus subtilis

F. Kunst1, N. Ogasawara2, I. Moszer3, A. M. Albertini4, G. Alloni4, V. Azevedo5, M. G. Bertero3,4, P. Bessières5, A. Bolotin5, S. Borchert6, R. Borriss7, L. Boursier3, A. Brans8, M. Braun9, S. C. Brignell10, S. Bron11, S. Brouillet3,12, C. V. Bruschi13, B. Caldwell14, V. Capuano5, N. M. Carter10, S.-K. Choi15, J.-J. Codani16, I. F. Connerton17, N. J. Cummings17, R. A. Daniel18, F. Denizot19, K. M. Devine20, A. Düsterhöft9, S. D. Ehrlich5, P. T. Emmerson21, K. D. Entian6, J. Errington18, C. Fabret19, E. Ferrari14, D. Foulger18, C. Fritz9, M. Fujita22, Y. Fujita23, S. Fuma24, A. Galizzi4, N. Galleron5, S.-Y. Ghim15, P. Glaser3, A. Goffeau25, E. J. Golightly26, G. Grandi27, G. Guiseppi19, B. J. Guy10, K. Haga28, J. Haiech19, C. R. Harwood10, A. Hénaut29, H. Hilbert9, S. Holsappel11, S. Hosono30, M.-F. Hullo3, M. Itaya31, L. Jones32, B. Joris8, D. Karamata33, Y. Kasahara2, M. Klaerr-Blanchard3, C. Klein6, Y. Kobayashi30, P. Koetter6, G. Koningstein34, S. Krogh20, M. Kumano24, K. Kurita24, A. Lapidus5, S. Lardinois8, J. Lauber9, V. Lazarevic33, S.-M. Lee35, A. Levine36, H. Liu28, S. Masuda30, C. Mauël33, C. Médigue3,12, N. Medina36, R. P. Mellado37, M. Mizuno30, D. Moestl9, S. Nakai2, M. Noback11, D. Noone20, M. O'Reilly20, K. Ogawa24, A. Ogiwara38, B. Oudega34, S.-H. Park15, V. Parro37, T. M. Pohl39, D. Portetelle40, S. Porwollik7, A. M. Prescott18, E. Presecan3, P. Pujic5, B. Purnelle25, G. Rapoport1, M. Rey26, S. Reynolds33, M. Rieger41, C. Rivolta33, E. Rocha3,12, B. Roche36, M. Rose6, Y. Sadaie22, T. Sato30, E. Scanlan20, S. Schleich3, R. Schroeter7, F. Scoffone4, J. Sekiguchi42, A. Sekowska3, S. J. Seror36, P. Serror5, B.-S. Shin15, B. Soldo33, A. Sorokin5, E. Tacconi4, T. Takagi43, H. Takahashi28, K. Takemaru30, M. Takeuchi30, A. Tamakoshi24, T. Tanaka44, P. Terpstra11, A. Tognoni27, V. Tosato13, S. Uchiyama42, M. Vandenbol40, F. Vannier36, A. Vassarotti45, A. Viari12, R. Wambutt46, E. Wedler46, H. Wedler46, T. Weitzenegger39, P. Winters14, A. Wipat10, H. Yamamoto42, K. Yamane24, K. Yasumoto28, K. Yata22, K. Yoshida23, H.-F. Yoshikawa28, E. Zumstein5, H. Yoshikawa2 & A. Danchin3

  1. Institut Pasteur, Unité de Biochimie Microbienne, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
  2. Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara 630-01, Japan
  3. Institut Pasteur, Unité de Régulation de l'Expression Génétique, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
  4. Dipartimento di Genetica e Microbiologia, Universita di Pavia, Via Abbiategrasso 207, 27100 Pavia, Italy
  5. INRA, Génétique Microbienne, Domaine de Vilvert, 78352 Jouy-en-Josas Cedex, France
  6. Institut für Mikrobiologie, J. W. Goethe-Universität, Marie Curie Strasse 9, 60439 Frankfurt/Maine, Germany
  7. Institut für Genetik und Mikrobiologie, Humboldt Universität, Chausseestrasse 17, D-10115 Berlin, Germany
  8. Centre d'Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, Sart Tilman, B-4000 Liège, Belgium
  9. QIAGEN GmbH, Max-Volmer-Strasse 4, D-40724 Hilden, Germany
  10. Department of Microbiological, Immunological and Virological Sciences, The Medical School, University of Newcastle, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
  11. Department of Genetics, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
  12. Atelier de BioInformatique, Université Paris VI, 12 rue Cuvier, 75005 Paris, France
  13. ICGEB, AREA Science Park, Padriciano 99, I-34012 Trieste, Italy
  14. Genencor International, 925 Page Mill Road, Palo Alto, California 94304-1013, USA
  15. Bacterial Molecular Genetics Research Unit, Applied Microbiology Research Division, KRIBB, PO Box 115, Yusong, Taejon 305-600, Korea
  16. INRIA, Domaine de Voluceau, PB 105, 78153 Le Chesnay Cedex, France
  17. Institute of Food Research, Department of Food Macromolecular Science, Reading Laboratory, Earley Gate, Whiteknights Road, Reading RG6 6BZ, UK
  18. Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
  19. Laboratoire de Chimie Bactérienne, CNRS BP 71, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
  20. Department of Genetics, Trinity College, Lincoln Place Gate, Dublin 2, Republic of Ireland
  21. Department of Biochemistry and Genetics, The Medical School, University of Newcastle, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
  22. Radioisotope Center, National Insitute of Genetics, Mishima, Shizuoka-ken 411, Japan
  23. Department of Biotechnology, Faculty of Engineering, Fukuyama University, Higashimura-cho, Fukuyama-shi, Hiroshima 729-02, Japan
  24. Institute of Biological Sciences, Tsukuba University, Tsuiuba-shi, Ibaraki 305, Japan
  25. Faculté des Sciences Agronomiques, Unité de Biochimie Physiologique, Université Catholique de Louvain, Place Croix du Sud, 2-20 B-1348 Louvain-la-Neuve, Belgium
  26. Novo Nordisk Biotech, 1445 Drew Avenue, Davis, California 95616-4880, USA
  27. Eniricerche, Via Maritano 26, San Donato Milanese, 20097 Milan, Italy
  28. Institute of Molecular and Cellular Biology, The University of Tokyo, Bunkyo-ku, Tokyo 113, Japan
  29. Laboratoire Génome et Informatique, Université de Versailles, Bâtiment Buffon, 45 Avenue des États-Unis, 78035 Versailles Cedex, France
  30. Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183, Japan
  31. Mitsubishi Kasei Institute of Life Sciences, 11 Minamyiooa, Machida-shi, Tokyo 194, Japan
  32. Institut Pasteur, Service d'Informatique Scientifique, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
  33. Institut de Génétique et Biologie Microbiennes, Université de Lausanne, 19 rue César Roux, 1005 Lausanne, Switzerland
  34. Department of Molecular Microbiology, MBW/BCA, Faculty of Biology, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
  35. Chongju University College of Science and Engineering, Chongju City, Korea
  36. Institut de Génétique et Microbiologie, Université Paris Sud, URA CNRS 2225, Université Paris XI–Bâtiment 409, 91405 Orsay Cedex, France
  37. Centro Nacional de Biotecnologia (CSIC), Campus Universidad Autonoma, Cantoblanco, 28049 Madrid, Spain
  38. National Institute of Basic Biology, 38 Nishigounaka, Myoudaiji-chou, Okazaki 444, Japan
  39. Gesellschaft für Analyse-Technik und Consulting mbH, Fritz-Arnold Strabetae 23, D-78467 Konstanz, Germany
  40. Department of Microbiology, Faculty of Agronomy, 6 Avenue du Maréchal Juin, B-5030 Gembloux, Belgium
  41. Biotech Research, BMF, Wilhelmsfeld, Klingelstrasse 35, D-69434 Hirschhorn, Germany
  42. Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University 3-15-1, Tokida, Ueda-shi, Nagano 386, Japan
  43. Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108, Japan
  44. Department of Marine Science, School of Marine Science and Technology, Tokai University, 3-20-1 Orido Shimizu, Shizuoka 424, Japan
  45. European Commission, DG XII-E-1, SDME 8/78, Rue de la Loi 200, B-1049 Brussels, Belgium
  46. AGOWAmbH, Glienicker Weg 185, 12489 Berlin, Germany

Correspondence to: F. Kunst1N. Ogasawara2 Correspondence and requests for materials should be addressed to F.K. (e-mail: Email: fkunst@pasteur.fr), N.O. (Email: nogasawa@bs.aist-nara.ac.jp,H.Y jp)

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Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.