title: Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
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.
authors.affiliation: INRA, UR1077, Mathématique Informatique et Génome, Jouy-en-Josas, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Nicolas
authors.forename: Ulrike
authors.initials: U
authors.lastname: Mäder
authors.forename: Etienne
authors.initials: E
authors.lastname: Dervyn
authors.forename: Tatiana
authors.initials: T
authors.lastname: Rochat
authors.forename: Aurélie
authors.initials: A
authors.lastname: Leduc
authors.forename: Nathalie
authors.initials: N
authors.lastname: Pigeonneau
authors.forename: Elena
authors.initials: E
authors.lastname: Bidnenko
authors.forename: Elodie
authors.initials: E
authors.lastname: Marchadier
authors.forename: Mark
authors.initials: M
authors.lastname: Hoebeke
authors.forename: Stéphane
authors.initials: S
authors.lastname: Aymerich
authors.forename: Dörte
authors.initials: D
authors.lastname: Becher
authors.forename: Paola
authors.initials: P
authors.lastname: Bisicchia
authors.forename: Eric
authors.initials: E
authors.lastname: Botella
authors.forename: Olivier
authors.initials: O
authors.lastname: Delumeau
authors.forename: Geoff
authors.initials: G
authors.lastname: Doherty
authors.forename: Emma L
authors.initials: EL
authors.lastname: Denham
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Fogg
authors.forename: Vincent
authors.initials: V
authors.lastname: Fromion
authors.forename: Anne
authors.initials: A
authors.lastname: Goelzer
authors.forename: Annette
authors.initials: A
authors.lastname: Hansen
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Härtig
authors.forename: Colin R
authors.initials: CR
authors.lastname: Harwood
authors.forename: Georg
authors.initials: G
authors.lastname: Homuth
authors.forename: Hanne
authors.initials: H
authors.lastname: Jarmer
authors.forename: Matthieu
authors.initials: M
authors.lastname: Jules
authors.forename: Edda
authors.initials: E
authors.lastname: Klipp
authors.forename: Ludovic
authors.initials: L
authors.lastname: Le Chat
authors.forename: François
authors.initials: F
authors.lastname: Lecointe
authors.forename: Peter
authors.initials: P
authors.lastname: Lewis
authors.forename: Wolfram
authors.initials: W
authors.lastname: Liebermeister
authors.forename: Anika
authors.initials: A
authors.lastname: March
authors.forename: Ruben A T
authors.initials: RA
authors.lastname: Mars
authors.forename: Priyanka
authors.initials: P
authors.lastname: Nannapaneni
authors.forename: David
authors.initials: D
authors.lastname: Noone
authors.forename: Susanne
authors.initials: S
authors.lastname: Pohl
authors.forename: Bernd
authors.initials: B
authors.lastname: Rinn
authors.forename: Frank
authors.initials: F
authors.lastname: Rügheimer
authors.forename: Praveen K
authors.initials: PK
authors.lastname: Sappa
authors.forename: Franck
authors.initials: F
authors.lastname: Samson
authors.forename: Marc
authors.initials: M
authors.lastname: Schaffer
authors.forename: Benno
authors.initials: B
authors.lastname: Schwikowski
authors.forename: Leif
authors.initials: L
authors.lastname: Steil
authors.forename: Jörg
authors.initials: J
authors.lastname: Stülke
authors.forename: Thomas
authors.initials: T
authors.lastname: Wiegert
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Devine
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Wilkinson
authors.forename: Jan Maarten
authors.initials: JM
authors.lastname: van Dijl
authors.forename: Michael
authors.initials: M
authors.lastname: Hecker
authors.forename: Uwe
authors.initials: U
authors.lastname: Völker
authors.forename: Philippe
authors.initials: P
authors.lastname: Bessières
authors.forename: Philippe
authors.initials: P
authors.lastname: Noirot
mesh_terms: D000222:Adaptation, Physiological; D000465:Algorithms; D001412:Bacillus subtilis / Q000235:genetics* / Q000502:physiology*; D001665:Binding Sites; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D016372:RNA, Antisense / Q000235:genetics / Q000378:metabolism; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018085:Regulon; D012808:Sigma Factor / Q000378:metabolism; D013728:Terminator Regions, Genetic; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D016372:RNA, Antisense; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012808:Sigma Factor