Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism
Joerg Martin J. M. Buescher
(1)
,
Wolfram Liebermeister
(2)
,
Matthieu M. Jules
(3)
,
Markus M. Uhr
(4)
,
Jan J. Muntel
(5)
,
Eric E. Botella
(6)
,
Bernd B. Hessling
(5)
,
Roelco Jacobus R. J. Kleijn
(1)
,
Ludovic L. Le Chat
(3)
,
François Lecointe
(3)
,
Ulrike U. Mäder
(5)
,
Pierre P. Nicolas
(7)
,
Sjouke S. Piersma
(8)
,
Frank F. Rügheimer
(9)
,
Dorte D. Becher
(5)
,
Philippe Bessieres Bessières
(7)
,
Elena E. Bidnenko
(3)
,
Emma E. Denham
(8)
,
Etienne Dervyn
(3)
,
Kevin K. Devine
(6)
,
Geoff G. Doherty
(10)
,
Samuel S. Drulhe
(9)
,
Liza L. Felicori
(11)
,
Mark M. Fogg
(12)
,
Anne Goelzer
(7)
,
Annette A. Hansen
(6)
,
Colin C. Harwood
(13)
,
Michael M. Hecker
(5)
,
Sebastian S. Hubner
(14)
,
Claus C. Hultschig
(15)
,
Hanne H. Jarmer
(16)
,
Edda E. Klipp
(2)
,
Aurelie A. Leduc
(7)
,
Peter P. Lewis
(10)
,
Frank F. Molina
(11)
,
Philippe P. Noirot
(3)
,
Sabine S. Peres
(11)
,
Nathalie N. Pigeonneau
(3)
,
Susanne S. Pohl
(17)
,
Simon S. Rasmussen
(16)
,
Bernd B. Rinn
(15)
,
Marc M. Schaffer
(5)
,
Julian J. Schnidder
(18)
,
Benno B. Schwikowski
(9)
,
Jan Maarten J. M. van Dijl
(8)
,
Patrick P. Veiga
(7)
,
Sean S. Walsh
(19)
,
Anthony A. Wilkinson
(12)
,
Jörg J. Stelling
(4)
,
Stephane S. Aymerich
(3)
,
Uwe U. Sauer
(1)
1
Institute of Molecular Systems Biology [Zurich]
2 Theoretical Biophysics [Berlin]
3 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
4 D-BSSE - Department of Biosystems Science and Engineering [ETH Zürich]
5 Institut für Mikrobiologie - Institute for Microbiology
6 Smurfit Institute of Genetics
7 MIG - Unité Mathématique Informatique et Génome
8 Department of Medical Microbiology
9 Biologie systémique - Systems Biology
10 School of Environmental and Life Sciences
11 Sysdiag CNRS Bio-Rad UMR 3145, Cap Delta/Parc Euromédecine
12 York Structural Biology Laboratory, Department of Chemistry
13 Centre for Bacterial Cell Biology, Institute of Cell and Molecular Biosciences
14 Smurfit Institute of Genetics,
15 Center for Information Sciences and Databases - Department of Biosystems Science and Engineering
16 Center for Biological Sequence Analysis, Department of Systems Biology
17 Centre for Bacterial Cell Biology, Institute, of Cell and Molecular Biosciences
18 Institute Molecular Systems Biology
19 Center for Information Sciences and Databases, Department of Biosystems Science and Engineering
2 Theoretical Biophysics [Berlin]
3 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
4 D-BSSE - Department of Biosystems Science and Engineering [ETH Zürich]
5 Institut für Mikrobiologie - Institute for Microbiology
6 Smurfit Institute of Genetics
7 MIG - Unité Mathématique Informatique et Génome
8 Department of Medical Microbiology
9 Biologie systémique - Systems Biology
10 School of Environmental and Life Sciences
11 Sysdiag CNRS Bio-Rad UMR 3145, Cap Delta/Parc Euromédecine
12 York Structural Biology Laboratory, Department of Chemistry
13 Centre for Bacterial Cell Biology, Institute of Cell and Molecular Biosciences
14 Smurfit Institute of Genetics,
15 Center for Information Sciences and Databases - Department of Biosystems Science and Engineering
16 Center for Biological Sequence Analysis, Department of Systems Biology
17 Centre for Bacterial Cell Biology, Institute, of Cell and Molecular Biosciences
18 Institute Molecular Systems Biology
19 Center for Information Sciences and Databases, Department of Biosystems Science and Engineering
Joerg Martin J. M. Buescher
- Function : relator_co_first_author
Wolfram Liebermeister
- Function : relator_co_first_author
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Matthieu M. Jules
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- IdRef : 07968453X
Markus M. Uhr
- Function : relator_co_first_author
Jan J. Muntel
- Function : relator_co_first_author
François Lecointe
- Function : Author
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- IdHAL : francois-lecointe
- ORCID : 0000-0002-9596-2514
- IdRef : 070755973
Etienne Dervyn
- Function : Author
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- IdHAL : etienne-dervyn
Anne Goelzer
- Function : Author
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- IdHAL : anne-goelzer
- ORCID : 0000-0003-2222-6142
- IdRef : 150326866
Philippe P. Noirot
- Function : Author
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- IdHAL : philippe-noirot3
- ORCID : 0000-0003-3446-6987
Sabine S. Peres
- Function : Author
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Jörg J. Stelling
- Function : relator_co_last_author
Stephane S. Aymerich
- Function : relator_co_last_author
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.