Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

被引：690

作者：

Nicolas, Pierre ^{[2
]}

Maeder, Ulrike ^{[3
,4
]}

Dervyn, Etienne ^{[1
]}

Rochat, Tatiana ^{[1
]}

Leduc, Aurelie ^{[2
]}

Pigeonneau, Nathalie ^{[1
]}

Bidnenko, Elena ^{[1
]}

Marchadier, Elodie ^{[1
]}

Hoebeke, Mark ^{[2
]}

Aymerich, Stephane ^{[1
]}

Becher, Doerte ^{[3
]}

Bisicchia, Paola ^{[5
]}

Botella, Eric ^{[5
]}

Delumeau, Olivier ^{[1
]}

Doherty, Geoff ^{[6
]}

Denham, Emma L. ^{[7
,8
]}

Fogg, Mark J. ^{[9
]}

Fromion, Vincent ^{[2
]}

Goelzer, Anne ^{[2
]}

Hansen, Annette ^{[5
]}

Haertig, Elisabeth ^{[10
]}

Harwood, Colin R. ^{[11
]}

Homuth, Georg ^{[4
]}

Jarmer, Hanne ^{[12
]}

Jules, Matthieu ^{[1
]}

Klipp, Edda ^{[13
]}

Le Chat, Ludovic ^{[1
]}

Lecointe, Francois ^{[1
]}

Lewis, Peter ^{[6
]}

Liebermeister, Wolfram

March, Anika

Mars, Ruben A. T.

Nannapaneni, Priyanka ^{[4
]}

Noone, David ^{[5
]}

Pohl, Susanne ^{[11
]}

Rinn, Bernd ^{[14
]}

Ruegheimer, Frank ^{[15
,16
]}

Sappa, Praveen K. ^{[4
]}

Samson, Franck ^{[2
]}

Schaffer, Marc ^{[3
]}

Schwikowski, Benno

Steil, Leif ^{[4
]}

Stuelke, Joerg ^{[17
]}

Wiegert, Thomas ^{[18
]}

Devine, Kevin M.

Wilkinson, Anthony J. ^{[9
]}

van Dijl, Jan Maarten ^{[7
,8
]}

Hecker, Michael ^{[3
]}

Voelker, Uwe ^{[4
]}

Bessieres, Philippe ^{[2
]}

机构：

[1] INRA, Micalis UMR1319, F-78350 Jouy En Josas, France

[2] INRA, Math Informat & Genome UR1077, F-78350 Jouy En Josas, France

[3] Ernst Moritz Arndt Univ Greifswald, Inst Microbiol, D-17489 Greifswald, Germany

[4] Ernst Moritz Arndt Univ Greifswald, Interfac Inst Genet & Funct Genom, Greifswald, Germany

[5] Trinity Coll Dublin, Smurfit Inst Genet, Dublin 2, Ireland

[6] Univ Newcastle, Sch Environm & Life Sci, Callaghan, NSW 2308, Australia

[7] Univ Groningen, Dept Med Microbiol, NL-9700 RB Groningen, Netherlands

[8] Univ Med Ctr Groningen, NL-9700 RB Groningen, Netherlands

[9] Univ York, Dept Chem, York Struct Biol Lab, York YO10 5YW, N Yorkshire, England

[10] Tech Univ Carolo Wilhelmina Braunschweig, Inst Microbiol, D-38106 Braunschweig, Germany

[11] Newcastle Univ, Ctr Bacterial Cell Biol, Newcastle Upon Tyne NE2 4AX, Tyne & Wear, England

[12] Tech Univ Denmark, Ctr Biol Sequence Anal, Dept Syst, DK-2800 Lyngby, Denmark

[13] Humboldt Univ, D-10115 Berlin, Germany

[14] ETH, Ctr Informat Sci & Databases, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland

[15] Inst Pasteur, Syst Biol Lab, F-75724 Paris 15, France

[16] CNRS, URA 2171, F-75724 Paris 15, France

[17] Univ Gottingen, Dept Gen Microbiol, D-37077 Gottingen, Germany

[18] Hsch Zittau Gorlitz, FN Biotechnol, D-02763 Zittau, Germany

来源：

SCIENCE | 2012年 / 335卷 / 6072期

基金：

英国医学研究理事会;

关键词：

ESCHERICHIA-COLI; RNA-POLYMERASE; IDENTIFICATION; GENOME; GENE; SEQUENCES; LANDSCAPE; DNA; RHO;

D O I：

10.1126/science.1206848

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for similar to 66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.

引用

页码：1103 / 1106

页数：4

共 25 条

[1] A NusE:NusG Complex Links Transcription and Translation [J].

Burmann, Bjoern M. ;

Schweimer, Kristian ;

Luo, Xiao ;

Wahl, Markus C. ;

Stitt, Barbara L. ;

Gottesman, Max E. ;

Roesch, Paul .

SCIENCE, 2010, 328 (5977) :501-504

[2] Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E-coli [J].

Cardinale, Christopher J. ;

Washburn, Robert S. ;

Tadigotla, Vasisht R. ;

Brown, Lewis M. ;

Gottesman, Max E. ;

Nudler, Evgeny .

SCIENCE, 2008, 320 (5878) :935-938

[3] The transcription unit architecture of the Escherichia coli genome [J].

Cho, Byung-Kwan ;

Zengler, Karsten ;

Qiu, Yu ;

Park, Young Seoub ;

Knight, Eric M. ;

Barrett, Christian L. ;

Gao, Yuan ;

Palsson, Bernhard O. .

NATURE BIOTECHNOLOGY, 2009, 27 (11) :1043-U115

[4] The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis [J].

Eichenberger, P ;

Fujita, M ;

Jensen, ST ;

Conlon, EM ;

Rudner, DZ ;

Wang, ST ;

Ferguson, C ;

Haga, K ;

Sato, T ;

Liu, JS ;

Losick, R .

PLOS BIOLOGY, 2004, 2 (10) :1664-1683

[5] Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis [J].

Goelzer, Anne ;

Brikci, Fadia Bekkal ;

Martin-Verstraete, Isabelle ;

Noirot, Philippe ;

Bessieres, Philippe ;

Aymerich, Stephane ;

Fromion, Vincent .

BMC SYSTEMS BIOLOGY, 2008, 2

[6] Transcriptome Complexity in a Genome-Reduced Bacterium [J].

Gueell, Marc ;

van Noort, Vera ;

Yus, Eva ;

Chen, Wei-Hua ;

Leigh-Bell, Justine ;

Michalodimitrakis, Konstantinos ;

Yamada, Takuji ;

Arumugam, Manimozhiyan ;

Doerks, Tobias ;

Kuehner, Sebastian ;

Rode, Michaela ;

Suyama, Mikita ;

Schmidt, Sabine ;

Gavin, Anne-Claude ;

Bork, Peer ;

Serrano, Luis .

SCIENCE, 2009, 326 (5957) :1268-1271

[7]

Helmann JD, 2002, ADV MICROB PHYSIOL, V46, P47

[8] COMPILATION AND ANALYSIS OF BACILLUS-SUBTILIS SIGMA(A)-DEPENDENT PROMOTER SEQUENCES - EVIDENCE FOR EXTENDED CONTACT BETWEEN RNA-POLYMERASE AND UPSTREAM PROMOTER DNA [J].

HELMANN, JD .

NUCLEIC ACIDS RESEARCH, 1995, 23 (13) :2351-2360

[9] MuGeN:: simultaneous exploration of multiple genomes and computer analysis results [J].

Hoebeke, M ;

Nicolas, P ;

Bessières, P .

BIOINFORMATICS, 2003, 19 (07) :859-864

[10] A genome-wide survey of short coding sequences in streptococci [J].

Ibrahim, Mariam ;

Nicolas, Pierre ;

Bessieres, Philippe ;

Bolotin, Alexander ;

Monnet, Veronique ;

Gardan, Rozenn .

MICROBIOLOGY-SGM, 2007, 153 :3631-3644

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