Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis
Pierre P. Nicolas
(1)
,
Ulrike U. Mäder
(2, 3)
,
Etienne Dervyn
(4)
,
Tatiana Rochat
(4)
,
Aurelie A. Leduc
(1)
,
Nathalie N. Pigeonneau
(4)
,
Elena E. Bidnenko
(4)
,
Elodie E. Marchandier
(4)
,
Mark M. Hoebeke
(1)
,
Stephane S. Aymerich
(4)
,
Dorte D. Becher
(2)
,
Paola P. Bisicchia
(5)
,
Eric E. Botella
(5)
,
Olivier O. Delumeau
(4)
,
Geoff G. Doherty
(6)
,
Emma L. E. L. Denham
(7)
,
Mark J. M. J. Fogg
(8)
,
Vincent V. Fromion
(1)
,
Anne Goelzer
(1)
,
Annette A. Hansen
(5)
,
Elisabeth E. Härtig
(9)
,
Colin R. C. R. Harwood
(10)
,
Georg G. Homuth
(3)
,
Hanne H. Jarmer
(11)
,
Matthieu M. Jules
(4)
,
Edda E. Klipp
(12)
,
Ludovic L. Le Chat
(4)
,
François Lecointe
(4)
,
Peter P. Lewis
(6)
,
Wolfram Liebermeister
(12)
,
Anika A. March
(9)
,
Rubens A. T. R. A. T. Mars
(7)
,
Priyanka P. Nannapaneni
(3)
,
David D. Noone
(5)
,
Susanne S. Pohl
(10)
,
Bernd B. Rinn
(13)
,
Frank F. Rügheimer
(14)
,
Praveen K. P. K. Sappa
(3)
,
Franck F. Samson
(1)
,
Marc M. Schaeffer
(2)
,
Benno B. Schwikowski
(14)
,
Leif L. Steil
(3)
,
Jörg J. Stülke
(15)
,
Thomas T. Wiegert
(16)
,
Kevin M. K. M. Devine
(5)
,
Anthony J. A. J. Wilkinson
(8)
,
Jan Maarten J. M. van Dijl
(7)
,
Michael M. Hecker
(2)
,
Uwe U. Völker
(3)
,
Philippe Bessieres Bessières
(1)
,
Philippe P. Noirot
(4)
1
MIG -
Unité Mathématique Informatique et Génome
2 Institut für Mikrobiologie - Institute for Microbiology
3 Interfaculty Institute for Genetics and Functional Genomics
4 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
5 Smurfit Institute of Genetics
6 School of Environmental and Life Sciences
7 Department of Medical Microbiology
8 York Structural Biology Laboratory, Department of Chemistry
9 Institute of Microbiology
10 Centre for Bacterial Cell Biology, Institute, of Cell and Molecular Biosciences
11 Center for Biological Sequence Analysis, Department of Systems Biology
12 Theoretical Biophysics [Berlin]
13 Center for Information Sciences and Databases - Department of Biosystems Science and Engineering
14 Biologie systémique - Systems Biology
15 Department of General Microbiology Georg-Augus
16 FN Biotechnologie
2 Institut für Mikrobiologie - Institute for Microbiology
3 Interfaculty Institute for Genetics and Functional Genomics
4 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
5 Smurfit Institute of Genetics
6 School of Environmental and Life Sciences
7 Department of Medical Microbiology
8 York Structural Biology Laboratory, Department of Chemistry
9 Institute of Microbiology
10 Centre for Bacterial Cell Biology, Institute, of Cell and Molecular Biosciences
11 Center for Biological Sequence Analysis, Department of Systems Biology
12 Theoretical Biophysics [Berlin]
13 Center for Information Sciences and Databases - Department of Biosystems Science and Engineering
14 Biologie systémique - Systems Biology
15 Department of General Microbiology Georg-Augus
16 FN Biotechnologie
Etienne Dervyn
- Fonction : co premier-auteur
- PersonId : 748698
- IdHAL : etienne-dervyn
- ORCID : 0000-0002-7732-9491
Tatiana Rochat
- Fonction : Auteur
- PersonId : 748902
- IdHAL : tatiana-rochat
- ORCID : 0000-0002-4533-1220
- IdRef : 110152298
Vincent V. Fromion
- Fonction : Auteur
- PersonId : 15608
- IdHAL : vincent-fromion
- ORCID : 0000-0002-9194-5426
- IdRef : 13548023X
Anne Goelzer
- Fonction : Auteur
- PersonId : 171865
- IdHAL : anne-goelzer
- ORCID : 0000-0003-2222-6142
- IdRef : 150326866
Matthieu M. Jules
- Fonction : Auteur
- PersonId : 15020
- IdHAL : matthieu-jules
- ORCID : 0000-0003-0817-8949
- IdRef : 07968453X
François Lecointe
- Fonction : Auteur
- PersonId : 747863
- IdHAL : francois-lecointe
- ORCID : 0000-0002-9596-2514
- IdRef : 070755973
Franck F. Samson
- Fonction : Auteur
- PersonId : 737362
- IdHAL : franck-samson
- ORCID : 0009-0007-0902-792X
Philippe P. Noirot
Connectez-vous pour contacter l'auteur
- Fonction : Auteur correspondant
- PersonId : 1145189
- IdHAL : philippe-noirot3
- ORCID : 0000-0003-3446-6987
Connectez-vous pour contacter l'auteur
Résumé
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.