Genome-wide analyses

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The genome sequence

Daniel R Reuß, Andrea Thürmer, Rolf Daniel, Wim J Quax, Jörg Stülke
Complete Genome Sequence of Bacillus subtilis subsp. subtilis Strain ∆6.
Genome Announc: 2016, 4(4);
[PubMed:27469946] [WorldCat.org] [DOI] (P e)

Janet L Smith, Jonathan M Goldberg, Alan D Grossman
Complete Genome Sequences of Bacillus subtilis subsp. subtilis Laboratory Strains JH642 (AG174) and AG1839.
Genome Announc: 2014, 2(4);
[PubMed:24994804] [WorldCat.org] [DOI] (P e)

Daniel R Zeigler
The genome sequence of Bacillus subtilis subsp. spizizenii W23: insights into speciation within the B. subtilis complex and into the history of B. subtilis genetics.
Microbiology (Reading, Engl.): 2011, 157(Pt 7);2033-41
[PubMed:21527469] [WorldCat.org] [DOI] (I p)

Valérie Barbe, Stéphane Cruveiller, Frank Kunst, Patricia Lenoble, Guillaume Meurice, Agnieszka Sekowska, David Vallenet, Tingzhang Wang, Ivan Moszer, Claudine Médigue, Antoine Danchin
From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later.
Microbiology (Reading, Engl.): 2009, 155(Pt 6);1758-75
[PubMed:19383706] [WorldCat.org] [DOI] (P p)

Daniel R Zeigler, Zoltán Prágai, Sabrina Rodriguez, Bastien Chevreux, Andrea Muffler, Thomas Albert, Renyuan Bai, Markus Wyss, John B Perkins
The origins of 168, W23, and other Bacillus subtilis legacy strains.
J. Bacteriol.: 2008, 190(21);6983-95
[PubMed:18723616] [WorldCat.org] [DOI] (I p)

Anjana Srivatsan, Yi Han, Jianlan Peng, Ashley K Tehranchi, Richard Gibbs, Jue D Wang, Rui Chen
High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies.
PLoS Genet.: 2008, 4(8);e1000139
[PubMed:18670626] [WorldCat.org] [DOI] (I e)

F Kunst, N Ogasawara, I Moszer, A M Albertini, G Alloni, V Azevedo, M G Bertero, P Bessières, A Bolotin, S Borchert, R Borriss, L Boursier, A Brans, M Braun, S C Brignell, S Bron, S Brouillet, C V Bruschi, B Caldwell, V Capuano, N M Carter, S K Choi, J J Cordani, I F Connerton, N J Cummings, R A Daniel, F Denziot, K M Devine, A Düsterhöft, S D Ehrlich, P T Emmerson, K D Entian, J Errington, C Fabret, E Ferrari, D Foulger, C Fritz, M Fujita, Y Fujita, S Fuma, A Galizzi, N Galleron, S Y Ghim, P Glaser, A Goffeau, E J Golightly, G Grandi, G Guiseppi, B J Guy, K Haga, J Haiech, C R Harwood, A Hènaut, H Hilbert, S Holsappel, S Hosono, M F Hullo, M Itaya, L Jones, B Joris, D Karamata, Y Kasahara, M Klaerr-Blanchard, C Klein, Y Kobayashi, P Koetter, G Koningstein, S Krogh, M Kumano, K Kurita, A Lapidus, S Lardinois, J Lauber, V Lazarevic, S M Lee, A Levine, H Liu, S Masuda, C Mauël, C Médigue, N Medina, R P Mellado, M Mizuno, D Moestl, S Nakai, M Noback, D Noone, M O'Reilly, K Ogawa, A Ogiwara, B Oudega, S H Park, V Parro, T M Pohl, D Portelle, S Porwollik, A M Prescott, E Presecan, P Pujic, B Purnelle, G Rapoport, M Rey, S Reynolds, M Rieger, C Rivolta, E Rocha, B Roche, M Rose, Y Sadaie, T Sato, E Scanlan, S Schleich, R Schroeter, F Scoffone, J Sekiguchi, A Sekowska, S J Seror, P Serror, B S Shin, B Soldo, A Sorokin, E Tacconi, T Takagi, H Takahashi, K Takemaru, M Takeuchi, A Tamakoshi, T Tanaka, P Terpstra, A Togoni, V Tosato, S Uchiyama, M Vandebol, F Vannier, A Vassarotti, A Viari, R Wambutt, H Wedler, T Weitzenegger, P Winters, A Wipat, H Yamamoto, K Yamane, K Yasumoto, K Yata, K Yoshida, H F Yoshikawa, E Zumstein, H Yoshikawa, A Danchin
The complete genome sequence of the gram-positive bacterium Bacillus subtilis.
Nature: 1997, 390(6657);249-56
[PubMed:9384377] [WorldCat.org] [DOI] (P p)


Transcript analysis

Wout Overkamp, Onur Ercan, Martijn Herber, Antonius J A van Maris, Michiel Kleerebezem, Oscar P Kuipers
Physiological and cell morphology adaptation of Bacillus subtilis at near-zero specific growth rates: a transcriptome analysis.
Environ. Microbiol.: 2015, 17(2);346-63
[PubMed:25367190] [WorldCat.org] [DOI] (I p)

Pierre Nicolas, Ulrike Mäder, Etienne Dervyn, Tatiana Rochat, Aurélie Leduc, Nathalie Pigeonneau, Elena Bidnenko, Elodie Marchadier, Mark Hoebeke, Stéphane Aymerich, Dörte Becher, Paola Bisicchia, Eric Botella, Olivier Delumeau, Geoff Doherty, Emma L Denham, Mark J Fogg, Vincent Fromion, Anne Goelzer, Annette Hansen, Elisabeth Härtig, Colin R Harwood, Georg Homuth, Hanne Jarmer, Matthieu Jules, Edda Klipp, Ludovic Le Chat, François Lecointe, Peter Lewis, Wolfram Liebermeister, Anika March, Ruben A T Mars, Priyanka Nannapaneni, David Noone, Susanne Pohl, Bernd Rinn, Frank Rügheimer, Praveen K Sappa, Franck Samson, Marc Schaffer, Benno Schwikowski, Leif Steil, Jörg Stülke, Thomas Wiegert, Kevin M Devine, Anthony J Wilkinson, Jan Maarten van Dijl, Michael Hecker, Uwe Völker, Philippe Bessières, Philippe Noirot
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
Science: 2012, 335(6072);1103-6
[PubMed:22383849] [WorldCat.org] [DOI] (I p)

Evert-Jan Blom, Anja N J A Ridder, Andrzej T Lulko, Jos B T M Roerdink, Oscar P Kuipers
Time-resolved transcriptomics and bioinformatic analyses reveal intrinsic stress responses during batch culture of Bacillus subtilis.
PLoS ONE: 2011, 6(11);e27160
[PubMed:22087258] [WorldCat.org] [DOI] (I p)

Kai Song
Recognition of prokaryotic promoters based on a novel variable-window Z-curve method.
Nucleic Acids Res.: 2012, 40(3);963-71
[PubMed:21954440] [WorldCat.org] [DOI] (I p)

Andreas Otto, Jörg Bernhardt, Hanna Meyer, Marc Schaffer, Florian-A Herbst, Juliane Siebourg, Ulrike Mäder, Michael Lalk, Michael Hecker, Dörte Becher
Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis.
Nat Commun: 2010, 1;137
[PubMed:21266987] [WorldCat.org] [DOI] (I p)

Simon Rasmussen, Henrik Bjørn Nielsen, Hanne Jarmer
The transcriptionally active regions in the genome of Bacillus subtilis.
Mol. Microbiol.: 2009, 73(6);1043-57
[PubMed:19682248] [WorldCat.org] [DOI] (I p)


A database for the time-resolved expression of all B. subtilis genes

Proteome analysis

Sandra Maaβ, Gerhild Wachlin, Jörg Bernhardt, Christine Eymann, Vincent Fromion, Katharina Riedel, Dörte Becher, Michael Hecker
Highly precise quantification of protein molecules per cell during stress and starvation responses in Bacillus subtilis.
Mol. Cell Proteomics: 2014, 13(9);2260-76
[PubMed:24878497] [WorldCat.org] [DOI] (I p)

Jan Muntel, Vincent Fromion, Anne Goelzer, Sandra Maaβ, Ulrike Mäder, Knut Büttner, Michael Hecker, Dörte Becher
Comprehensive absolute quantification of the cytosolic proteome of Bacillus subtilis by data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS(E)).
Mol. Cell Proteomics: 2014, 13(4);1008-19
[PubMed:24696501] [WorldCat.org] [DOI] (I p)

Dooil Kim, Byung Jo Yu, Jung Ae Kim, Yong-Jik Lee, Soo-Geun Choi, Sunghyun Kang, Jae-Gu Pan
The acetylproteome of Gram-positive model bacterium Bacillus subtilis.
Proteomics: 2013, 13(10-11);1726-36
[PubMed:23468065] [WorldCat.org] [DOI] (I p)

Dörte Becher, Knut Büttner, Martin Moche, Bernd Hessling, Michael Hecker
From the genome sequence to the protein inventory of Bacillus subtilis.
Proteomics: 2011, 11(15);2971-80
[PubMed:21710564] [WorldCat.org] [DOI] (I p)

Andreas Otto, Jörg Bernhardt, Hanna Meyer, Marc Schaffer, Florian-A Herbst, Juliane Siebourg, Ulrike Mäder, Michael Lalk, Michael Hecker, Dörte Becher
Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis.
Nat Commun: 2010, 1;137
[PubMed:21266987] [WorldCat.org] [DOI] (I p)

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

Ulf Gerth, Holger Kock, Ilja Kusters, Stephan Michalik, Robert L Switzer, Michael Hecker
Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis.
J. Bacteriol.: 2008, 190(1);321-31
[PubMed:17981983] [WorldCat.org] [DOI] (I p)

Christine Eymann, Dörte Becher, Jörg Bernhardt, Katrin Gronau, Anja Klutzny, Michael Hecker
Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis.
Proteomics: 2007, 7(19);3509-26
[PubMed:17726680] [WorldCat.org] [DOI] (P p)

Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol. Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307] [WorldCat.org] [DOI] (P p)

Susanne Wolff, Haike Antelmann, Dirk Albrecht, Dörte Becher, Jörg Bernhardt, Sierd Bron, Knut Büttner, Jan Maarten van Dijl, Christine Eymann, Andreas Otto, Le Thi Tam, Michael Hecker
Towards the entire proteome of the model bacterium Bacillus subtilis by gel-based and gel-free approaches.
J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.: 2007, 849(1-2);129-40
[PubMed:17055787] [WorldCat.org] [DOI] (P p)

Susanne Wolff, Andreas Otto, Dirk Albrecht, Jianru Stahl Zeng, Knut Büttner, Matthias Glückmann, Michael Hecker, Dörte Becher
Gel-free and gel-based proteomics in Bacillus subtilis: a comparative study.
Mol. Cell Proteomics: 2006, 5(7);1183-92
[PubMed:16552027] [WorldCat.org] [DOI] (P p)

Christine Eymann, Annette Dreisbach, Dirk Albrecht, Jörg Bernhardt, Dörte Becher, Sandy Gentner, Le Thi Tam, Knut Büttner, Gerrit Buurman, Christian Scharf, Simone Venz, Uwe Völker, Michael Hecker
A comprehensive proteome map of growing Bacillus subtilis cells.
Proteomics: 2004, 4(10);2849-76
[PubMed:15378759] [WorldCat.org] [DOI] (P p)

Harold Tjalsma, Haike Antelmann, Jan D H Jongbloed, Peter G Braun, Elise Darmon, Ronald Dorenbos, Jean-Yves F Dubois, Helga Westers, Geeske Zanen, Wim J Quax, Oscar P Kuipers, Sierd Bron, Michael Hecker, Jan Maarten van Dijl
Proteomics of protein secretion by Bacillus subtilis: separating the "secrets" of the secretome.
Microbiol. Mol. Biol. Rev.: 2004, 68(2);207-33
[PubMed:15187182] [WorldCat.org] [DOI] (P p)


See also: Additional genome projects for Bacillus subtilis and other Bacilli

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