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  Metabolomic and transcriptomic stress response of Escherichia coli

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.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-23E6-2 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0019-0657-1
Genre: Journal Article

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 Creators:
Jozefczuk, S.1, Author              
Klie, S.1, 2, Author              
Catchpole, G.1, Author              
Szymanski, J.1, Author              
Cuadros-Inostroza, A.1, Author              
Steinhauser, D.1, 3, Author              
Selbig, J.2, Author              
Willmitzer, L.1, Author              
Affiliations:
1Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753340              
2BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753315              
3Systems Metabolomics, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, Am Mühlenberg 1, 14476 Potsdam-Golm, DE, ou_1797285              

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Free keywords: escherichia coli metabolomic response to stress time course transcriptomic pyruvate formate-lyase citric-acid cycle gene-expression anaerobic regulation stringent response r-package protein identification starvation system
 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

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Language(s): eng - English
 Dates: 2010-05-112010
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
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 Identifiers: ISI: ISI:000278575700001
DOI: 10.1038/msb.2010.18
ISSN: 1744-4292 (Electronic)1744-4292 (Linking)
URI: ://000278575700001http://www.nature.com/msb/journal/v6/n1/pdf/msb201018.pdf
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Title: Molecular Systems Biology
Source Genre: Journal
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Publ. Info: London : Nature Pub. Group
Pages: - Volume / Issue: 6 Sequence Number: - Start / End Page: 364 Identifier: ISSN: 1744-4292
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000021290