title: Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.
abstract: Adaptation of cells to environmental changes requires dynamic interactions between metabolic and regulatory networks, but studies typically address only one or a few layers of regulation. For nutritional shifts between two preferred carbon sources of Bacillus subtilis, we combined statistical and model-based data analyses of dynamic transcript, protein, and metabolite abundances and promoter activities. Adaptation to malate was rapid and primarily controlled posttranscriptionally compared with the slow, mainly transcriptionally controlled adaptation to glucose that entailed nearly half of the known transcription regulation network. Interactions across multiple levels of regulation were involved in adaptive changes that could also be achieved by controlling single genes. Our analysis suggests that global trade-offs and evolutionary constraints provide incentives to favor complex control programs.
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Joerg Martin
authors.initials: JM
authors.lastname: Buescher
authors.forename: Wolfram
authors.initials: W
authors.lastname: Liebermeister
authors.forename: Matthieu
authors.initials: M
authors.lastname: Jules
authors.forename: Markus
authors.initials: M
authors.lastname: Uhr
authors.forename: Jan
authors.initials: J
authors.lastname: Muntel
authors.forename: Eric
authors.initials: E
authors.lastname: Botella
authors.forename: Bernd
authors.initials: B
authors.lastname: Hessling
authors.forename: Roelco Jacobus
authors.initials: RJ
authors.lastname: Kleijn
authors.forename: Ludovic
authors.initials: L
authors.lastname: Le Chat
authors.forename: François
authors.initials: F
authors.lastname: Lecointe
authors.forename: Ulrike
authors.initials: U
authors.lastname: Mäder
authors.forename: Pierre
authors.initials: P
authors.lastname: Nicolas
authors.forename: Sjouke
authors.initials: S
authors.lastname: Piersma
authors.forename: Frank
authors.initials: F
authors.lastname: Rügheimer
authors.forename: Dörte
authors.initials: D
authors.lastname: Becher
authors.forename: Philippe
authors.initials: P
authors.lastname: Bessieres
authors.forename: Elena
authors.initials: E
authors.lastname: Bidnenko
authors.forename: Emma L
authors.initials: EL
authors.lastname: Denham
authors.forename: Etienne
authors.initials: E
authors.lastname: Dervyn
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Devine
authors.forename: Geoff
authors.initials: G
authors.lastname: Doherty
authors.forename: Samuel
authors.initials: S
authors.lastname: Drulhe
authors.forename: Liza
authors.initials: L
authors.lastname: Felicori
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Fogg
authors.forename: Anne
authors.initials: A
authors.lastname: Goelzer
authors.forename: Annette
authors.initials: A
authors.lastname: Hansen
authors.forename: Colin R
authors.initials: CR
authors.lastname: Harwood
authors.forename: Michael
authors.initials: M
authors.lastname: Hecker
authors.forename: Sebastian
authors.initials: S
authors.lastname: Hubner
authors.forename: Claus
authors.initials: C
authors.lastname: Hultschig
authors.forename: Hanne
authors.initials: H
authors.lastname: Jarmer
authors.forename: Edda
authors.initials: E
authors.lastname: Klipp
authors.forename: Aurélie
authors.initials: A
authors.lastname: Leduc
authors.forename: Peter
authors.initials: P
authors.lastname: Lewis
authors.forename: Frank
authors.initials: F
authors.lastname: Molina
authors.forename: Philippe
authors.initials: P
authors.lastname: Noirot
authors.forename: Sabine
authors.initials: S
authors.lastname: Peres
authors.forename: Nathalie
authors.initials: N
authors.lastname: Pigeonneau
authors.forename: Susanne
authors.initials: S
authors.lastname: Pohl
authors.forename: Simon
authors.initials: S
authors.lastname: Rasmussen
authors.forename: Bernd
authors.initials: B
authors.lastname: Rinn
authors.forename: Marc
authors.initials: M
authors.lastname: Schaffer
authors.forename: Julian
authors.initials: J
authors.lastname: Schnidder
authors.forename: Benno
authors.initials: B
authors.lastname: Schwikowski
authors.forename: Jan Maarten
authors.initials: JM
authors.lastname: Van Dijl
authors.forename: Patrick
authors.initials: P
authors.lastname: Veiga
authors.forename: Sean
authors.initials: S
authors.lastname: Walsh
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Wilkinson
authors.forename: Jörg
authors.initials: J
authors.lastname: Stelling
authors.forename: Stéphane
authors.initials: S
authors.lastname: Aymerich
authors.forename: Uwe
authors.initials: U
authors.lastname: Sauer
mesh_terms: D000222:Adaptation, Physiological; D000465:Algorithms; D001412:Bacillus subtilis / Q000235:genetics* / Q000378:metabolism*; D001426:Bacterial Proteins / Q000378:metabolism; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D016680:Genome, Bacterial; D005947:Glucose / Q000378:metabolism*; D008293:Malates / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D055442:Metabolome; D055432:Metabolomics; D008954:Models, Biological; D009876:Operon; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D008293:Malates; D014157:Transcription Factors; C030298:malic acid; D005947:Glucose