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Metabolomic and transcriptomic stress response of Escherichia coli

MPS-Authors
http://pubman.mpdl.mpg.de/cone/persons/resource/persons97210

Jozefczuk,  S.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97232

Klie,  S.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;
BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97101

Catchpole,  G.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97435

Szymanski,  J.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97111

Cuadros-Inostroza,  A.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97425

Steinhauser,  D.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;
Systems Metabolomics, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97409

Selbig,  J.
BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97481

Willmitzer,  L.
Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Jozefczuk, S., Klie, S., Catchpole, G., Szymanski, J., Cuadros-Inostroza, A., Steinhauser, D., et al. (2010). Metabolomic and transcriptomic stress response of Escherichia coli. Molecular Systems Biology, 6, 364. doi:10.1038/msb.2010.18.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0014-23E6-2
Abstract
Environmental fluctuations lead to a rapid adjustment of the physiology of Escherichia coli, necessitating changes on every level of the underlying cellular and molecular network. Thus far, the majority of global analyses of E. coli stress responses have been limited to just one level, gene expression. Here, we incorporate the metabolite composition together with gene expression data to provide a more comprehensive insight on system level stress adjustments by describing detailed time-resolved E. coli response to five different perturbations (cold, heat, oxidative stress, lactose diauxie, and stationary phase). The metabolite response is more specific as compared with the general response observed on the transcript level and is reflected by much higher specificity during the early stress adaptation phase and when comparing the stationary phase response to other perturbations. Despite these differences, the response on both levels still follows the same dynamics and general strategy of energy conservation as reflected by rapid decrease of central carbon metabolism intermediates coinciding with downregulation of genes related to cell growth. Application of coclustering and canonical correlation analysis on combined-metabolite and transcript data identified a number of significant condition-dependent associations between metabolites and transcripts. The results confirm and extend existing models about co-regulation between gene expression and metabolites demonstrating the power of integrated systems oriented analysis. Molecular Systems Biology 6: 364; published online 11 May 2010; doi: 10.1038/msb.2010.18