The complete genome sequence of the Gram-positive bacterium Bacillus subtilis
F. Kunst,Naotake Ogasawara,Ivan Moszer,Alessandra M. Albertini,G. Alloni,Vasco Azevedo,M. G. Bertero,M. G. Bertero,Philippe Bessières,Bolotin Ap,S. Borchert,Rainer Borriss,L. Boursier,Alain Brans,M. Braun,S. C. Brignell,Sierd Bron,S. Brouillet,S. Brouillet,Carlo V. Bruschi,B. Caldwell,V. Capuano,Noel Carter,Soo Keun Choi,J.-J. Codani,Ian F. Connerton,Nicola J. Cummings,Richard A. Daniel,François Denizot,Kevin M. Devine,A. Düsterhöft,Stanislav Dusko Ehrlich,P. T. Emmerson,K. D. Entian,Jeff Errington,C. Fabret,Eugenio Ferrari,D. Foulger,C. Fritz,Masaya Fujita,Yasutaro Fujita,S. Fuma,Alessandro Galizzi,Nathalie Galleron,Sa Youl Ghim,Philippe Glaser,André Goffeau,E. J. Golightly,Guido Grandi,G. Guiseppi,BJ Guy,Kazuko Haga,Jacques Haiech,Colin R. Harwood,Alain Hénaut,H. Hilbert,Siger Holsappel,S. Hosono,Marie-Françoise Hullo,Mitsuhiro Itaya,Louis M. Jones,Bernard Joris,Dimitri Karamata,Y. Kasahara,M. Klaerr-Blanchard,Carsten Klein,Y. Kobayashi,P. Koetter,G. Koningstein,Susanne Krogh,Miyuki Kumano,Kanako Kurita,Alla Lapidus,S. Lardinois,J. Lauber,Vladimir Lazarevic,Simon Ming-Yuen Lee,Alain Levine,H. Liu,S. Masuda,Catherine Mauël,Claudine Médigue,Claudine Médigue,N. Medina,Rafael P. Mellado,Motoki Mizuno,D. Moestl,S. Nakai,Michiel A. Noback,David Noone,Mary O'Reilly,K. Ogawa,A. Ogiwara,B. Oudega,S.-H. Park,Victor Parro,Thomas Pohl,Daniel Portetelle,Steffen Porwollik,A. M. Prescott,E. Presecan,Petar Pujic,Bénédicte Purnelle,Georges Rapoport,M. Rey,Stacey Reynolds,Michael A. Rieger,Carlo Rivolta,Eduardo P. C. Rocha,Eduardo P. C. Rocha,B. Roche,Matthias Rose,Yoshito Sadaie,Toshitada Sato,E. Scanlan,S. Schleich,R. Schroeter,F Scoffone,Junichi Sekiguchi,Agnieszka Sekowska,Simone J. Séror,Pascale Serror,B.-S. Shin,Blazenka Soldo,Alexei Sorokin,E. Tacconi,T. Takagi,Hideyuki Takahashi,Ken-Ichi Takemaru,Michio Takeuchi,A. Tamakoshi,Tetsu Tanaka,Peter Terpstra,Angelo Tognoni,Valentina Tosato,Shigeki Uchiyama,Micheline Vandenbol,Françoise Vannier,A. Vassarotti,Alain Viari,R. Wambutt,E. Wedler,H. Wedler,T. Weitzenegger,P. Winters,Anil Wipat,Hiroki Yamamoto,Kunio Yamane,K. Yasumoto,Katsunori Yata,K. Yoshida,Hisashi Yoshikawa,Emmanuelle Zumstein,Hiroshi Yoshikawa,Antoine Danchin +154 more
TLDR
Bacillus subtilis is the best-characterized member of the Gram-positive bacteria, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.Abstract:
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.read more
Citations
More filters
Journal ArticleDOI
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
Stewart T. Cole,Roland Brosch,Julian Parkhill,Thierry Garnier,Carol Churcher,David Harris,Stephen V. Gordon,Karin Eiglmeier,S. Gas,Clifton E. Barry,Fredj Tekaia,K. Badcock,D. Basham,D. Brown,Tracey Chillingworth,R. Connor,Robert L. Davies,K. Devlin,Theresa Feltwell,S. Gentles,N. Hamlin,S. Holroyd,T. Hornsby,Kay Jagels,Anders Krogh,J. McLean,Sharon Moule,Lee Murphy,K. Oliver,J. Osborne,Michael A. Quail,Marie-Adèle Rajandream,Jane Rogers,S. Rutter,K. Seeger,Jason Skelton,Rob Squares,S. Squares,John Sulston,K. Taylor,Sally Whitehead,Bart Barrell +41 more
TL;DR: The complete genome sequence of the best-characterized strain of Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve the understanding of the biology of this slow-growing pathogen and to help the conception of new prophylactic and therapeutic interventions.
Journal ArticleDOI
Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen.
Charles K. Stover,X. Q. Pham,A. L. Erwin,S. D. Mizoguchi,Paul Warrener,Mark J. Hickey,Fiona S. L. Brinkman,W. O. Hufnagle,D. J. Kowalik,Lagrou Mj,R. L. Garber,L. Goltry,E. Tolentino,S. Westbrock-Wadman,Ying Yuan,L. L. Brody,S. N. Coulter,K. R. Folger,Arnold Kas,K. Larbig,R. Lim,Kelly D. Smith,David H. Spencer,Gane Ka-Shu Wong,Z. Wu,Ian T. Paulsen,Ian T. Paulsen,Jonathan Reizer,Milton H. Saier,Robert E. W. Hancock,Stephen Lory,Maynard V. Olson +31 more
TL;DR: It is proposed that the size and complexity of the P. aeruginosa genome reflect an evolutionary adaptation permitting it to thrive in diverse environments and resist the effects of a variety of antimicrobial substances.
Journal ArticleDOI
Whole genome sequencing of meticillin-resistant Staphylococcus aureus
Makoto Kuroda,Toshiko Ohta,Ikuo Uchiyama,Tadashi Baba,Harumi Yuzawa,Ichizo Kobayashi,Longzhu Cui,Akio Oguchi,Ken-ichi Aoki,Yoshimi Nagai,JianQi Lian,Teruyo Ito,Mutsumi Kanamori,Hiroyuki Matsumaru,Atsushi Maruyama,Hiroyuki Murakami,Akira Hosoyama,Yoko Mizutani-Ui,Noriko K. Takahashi,Toshihiko Sawano,Ryu-ichi Inoue,Chikara Kaito,Kazuhisa Sekimizu,Hideki Hirakawa,Satoru Kuhara,Susumu Goto,Junko Yabuzaki,Minoru Kanehisa,Atsushi Yamashita,Kenshiro Oshima,Keiko Furuya,Chie Yoshino,Tadayoshi Shiba,Masahira Hattori,Naotake Ogasawara,Hideo Hayashi,Keiichi Hiramatsu +36 more
TL;DR: Investigation of many newly identified gene products, including the 70 putative virulence factors, will greatly improve the understanding of the biology of staphylococci and the processes of infectious diseases caused by S aureus.
Journal ArticleDOI
Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments.
TL;DR: The molecular laboratory model of spore resistance mechanisms is summarized and attempts to use the model as a basis for exploration of the resistance of spores to environmental extremes both on Earth and during postulated interplanetary transfer through space as a result of natural impact processes.
Journal ArticleDOI
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
TL;DR: It is shown that the accuracy of gene start prediction can be improved by combining models of protein-coding and non-Coding regions and models of regulatory sites near gene start within an iterative Hidden Markov model based algorithm.
References
More filters
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
The Complete Genome Sequence of Escherichia coli K-12
Frederick R. Blattner,Guy Plunkett,Craig A. Bloch,Nicole T. Perna,Valerie Burland,Monica Riley,Julio Collado-Vides,Jeremy D. Glasner,Christopher K. Rode,George F. Mayhew,Jason Gregor,Nelson Wayne Davis,Heather A. Kirkpatrick,Michael A. Goeden,Debra J. Rose,Bob Mau,Ying Shao +16 more
TL;DR: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented and reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident.
Journal ArticleDOI
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
Fleischmann Rd,Adams,Owen White,Rebecca A. Clayton,Ewen F. Kirkness,Anthony R. Kerlavage,Carol J. Bult,J F Tomb,Brian Dougherty,Merrick Jm +9 more
TL;DR: An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence of the genome from the bacterium Haemophilus influenzae Rd.
Book
Escherichia coli and Salmonella :cellular and molecular biology
TL;DR: The Enteric Bacterial Cell and the Age of Bacteria Variations on a Theme by Escherichia is described.
Journal ArticleDOI
The complete genome sequence of the gastric pathogen Helicobacter pylori
Jean-F. Tomb,Owen White,Anthony R. Kerlavage,Rebecca A. Clayton,Granger G. Sutton,Robert D. Fleischmann,Karen A. Ketchum,Hans-Peter Klenk,Steven R. Gill,Brian Dougherty,Karen E. Nelson,John Quackenbush,Lixin Zhou,Ewen F. Kirkness,Scott N. Peterson,Brendan J. Loftus,Delwood Richardson,Robert J. Dodson,Hanif Khalak,Anna Glodek,Keith McKenney,Lisa M. Fitzegerald,Norman H. Lee,Mark Raymond Adams,Erin Hickey,Douglas E. Berg,Jeanine D. Gocayne,Teresa Utterback,Jeremy Peterson,Jenny M. Kelley,Matthew D. Cotton,J. Weidman,Claire Fujii,Cheryl Bowman,Larry Watthey,Erik Wallin,William S. Hayes,Mark Borodovsky,Peter D. Karp,Hamilton O. Smith,Claire M. Fraser,J. Craig Venter +41 more
TL;DR: Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification, and consistent with its restricted niche, it has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity.
Related Papers (5)
The Complete Genome Sequence of Escherichia coli K-12
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
Stewart T. Cole,Roland Brosch,Julian Parkhill,Thierry Garnier,Carol Churcher,David Harris,Stephen V. Gordon,Karin Eiglmeier,S. Gas,Clifton E. Barry,Fredj Tekaia,K. Badcock,D. Basham,D. Brown,Tracey Chillingworth,R. Connor,Robert L. Davies,K. Devlin,Theresa Feltwell,S. Gentles,N. Hamlin,S. Holroyd,T. Hornsby,Kay Jagels,Anders Krogh,J. McLean,Sharon Moule,Lee Murphy,K. Oliver,J. Osborne,Michael A. Quail,Marie-Adèle Rajandream,Jane Rogers,S. Rutter,K. Seeger,Jason Skelton,Rob Squares,S. Squares,John Sulston,K. Taylor,Sally Whitehead,Bart Barrell +41 more