Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.

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

doi:10.1126/science.1206848

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.

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 HansenElisabeth 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

Research output: Contribution to journal › Journal article › Research › peer-review

Abstract

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 ~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.

Original language	English
Journal	Science
Volume	335
Issue number	6072
Pages (from-to)	1103-1106
ISSN	0036-8075
DOIs	https://doi.org/10.1126/science.1206848
Publication status	Published - 2012

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Nicolas, P., Mäder, U., Dervyn, E., Rochat, T., Leduc, A., Pigeonneau, N., Bidnenko, E., Marchadier, E., Hoebeke, M., Aymerich, S., Becher, D., Bisicchia, P., Botella, E., Delumeau, O., Doherty, G., Denham, E. L., Fogg, M. J., Fromion, V., Goelzer, A., ... Noirot, P. (2012). Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science, 335(6072), 1103-1106. https://doi.org/10.1126/science.1206848

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abstract = "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 ~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.",

author = "Pierre Nicolas and Ulrike M{\"a}der and Etienne Dervyn and Tatiana Rochat and Aur{\'e}lie Leduc and Nathalie Pigeonneau and Elena Bidnenko and Elodie Marchadier and Mark Hoebeke and St{\'e}phane Aymerich and D{\"o}rte Becher and Paola Bisicchia and Eric Botella and Olivier Delumeau and Geoff Doherty and Denham, {Emma L} and Fogg, {Mark J} and Vincent Fromion and Anne Goelzer and Annette Hansen and Elisabeth H{\"a}rtig and Harwood, {Colin R} and Georg Homuth and Hanne Jarmer and Matthieu Jules and Edda Klipp and {Le Chat}, Ludovic and Fran{\c c}ois Lecointe and Peter Lewis and Wolfram Liebermeister and Anika March and Mars, {Ruben A T} and Priyanka Nannapaneni and David Noone and Susanne Pohl and Bernd Rinn and Frank R{\"u}gheimer and Sappa, {Praveen K} and Franck Samson and Marc Schaffer and Benno Schwikowski and Leif Steil and J{\"o}rg St{\"u}lke and Thomas Wiegert and Devine, {Kevin M} and Wilkinson, {Anthony J} and {van Dijl}, {Jan Maarten} and Michael Hecker and Uwe V{\"o}lker and Philippe Bessi{\`e}res and Philippe Noirot",

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Nicolas, P, Mäder, U, Dervyn, E, Rochat, T, Leduc, A, Pigeonneau, N, Bidnenko, E, Marchadier, E, Hoebeke, M, Aymerich, S, Becher, D, Bisicchia, P, Botella, E, Delumeau, O, Doherty, G, Denham, EL, Fogg, MJ, Fromion, V, Goelzer, A, Hansen, A, Härtig, E, Harwood, CR, Homuth, G, Jarmer, H, Jules, M, Klipp, E, Le Chat, L, Lecointe, F, Lewis, P, Liebermeister, W, March, A, Mars, RAT, Nannapaneni, P, Noone, D, Pohl, S, Rinn, B, Rügheimer, F, Sappa, PK, Samson, F, Schaffer, M, Schwikowski, B, Steil, L, Stülke, J, Wiegert, T, Devine, KM, Wilkinson, AJ, van Dijl, JM, Hecker, M, Völker, U, Bessières, P & Noirot, P 2012, 'Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.', Science, vol. 335, no. 6072, pp. 1103-1106. https://doi.org/10.1126/science.1206848

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T1 - Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.

AU - Nicolas, Pierre

AU - Mäder, Ulrike

AU - Dervyn, Etienne

AU - Rochat, Tatiana

AU - Leduc, Aurélie

AU - Pigeonneau, Nathalie

AU - Bidnenko, Elena

AU - Marchadier, Elodie

AU - Hoebeke, Mark

AU - Aymerich, Stéphane

AU - Becher, Dörte

AU - Bisicchia, Paola

AU - Botella, Eric

AU - Delumeau, Olivier

AU - Doherty, Geoff

AU - Denham, Emma L

AU - Fogg, Mark J

AU - Fromion, Vincent

AU - Goelzer, Anne

AU - Hansen, Annette

AU - Härtig, Elisabeth

AU - Harwood, Colin R

AU - Homuth, Georg

AU - Jarmer, Hanne

AU - Jules, Matthieu

AU - Klipp, Edda

AU - Le Chat, Ludovic

AU - Lecointe, François

AU - Lewis, Peter

AU - Liebermeister, Wolfram

AU - March, Anika

AU - Mars, Ruben A T

AU - Nannapaneni, Priyanka

AU - Noone, David

AU - Pohl, Susanne

AU - Rinn, Bernd

AU - Rügheimer, Frank

AU - Sappa, Praveen K

AU - Samson, Franck

AU - Schaffer, Marc

AU - Schwikowski, Benno

AU - Steil, Leif

AU - Stülke, Jörg

AU - Wiegert, Thomas

AU - Devine, Kevin M

AU - Wilkinson, Anthony J

AU - van Dijl, Jan Maarten

AU - Hecker, Michael

AU - Völker, Uwe

AU - Bessières, Philippe

AU - Noirot, Philippe

PY - 2012

Y1 - 2012

N2 - 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 ~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.

AB - 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 ~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.

U2 - 10.1126/science.1206848

DO - 10.1126/science.1206848

M3 - Journal article

C2 - 22383849

SN - 0036-8075

VL - 335

SP - 1103

EP - 1106

JO - Science

JF - Science

IS - 6072

ER -

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.

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