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

ISSN
0036-8075
Date Issued
2012
Author(s)
Nicolas, Pierre
Maeder, Ulrike
Dervyn, Etienne
Rochat, Tatiana
Leduc, Aurelie
Pigeonneau, Nathalie
Bidnenko, Elena
Marchadier, Elodie
Hoebeke, Mark
Aymerich, Stephane
Becher, Doerte
Bisicchia, Paola
Botella, Eric
Delumeau, Olivier
Doherty, Geoff
Denham, Emma L.
Fogg, Mark J.
Fromion, Vincent
Goelzer, Anne
Hansen, Annette
Haertig, Elisabeth
Harwood, Colin R.
Homuth, Georg
Jarmer, Hanne
Jules, Matthieu
Klipp, Edda
Le Chat, Ludovic
Lecointe, Francois
Lewis, Peter
Liebermeister, Wolfram
March, Anika
Mars, Ruben A. T.
Nannapaneni, Priyanka
Noone, David
Pohl, Susanne
Rinn, Bernd
Ruegheimer, Frank
Sappa, Praveen Kumar
Samson, Franck
Schaffer, Marc
Schwikowski, Benno
Steil, Leif
Wiegert, Thomas
Devine, Kevin M.
Wilkinson, Anthony J.
van Dijl, Jan Maarten
Hecker, Michael
Voelker, Uwe
Bessieres, Philippe
Noirot, Philippe
DOI
10.1126/science.1206848
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 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.