Metabolomic and transcriptomic stress response of Escherichia coli
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...
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| Format: | Article |
| Language: | English |
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Springer Nature
2010-05-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.1038/msb.2010.18 |
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| author | Szymon Jozefczuk Sebastian Klie Gareth Catchpole Jedrzej Szymanski Alvaro Cuadros‐Inostroza Dirk Steinhauser Joachim Selbig Lothar Willmitzer |
| author_facet | Szymon Jozefczuk Sebastian Klie Gareth Catchpole Jedrzej Szymanski Alvaro Cuadros‐Inostroza Dirk Steinhauser Joachim Selbig Lothar Willmitzer |
| author_sort | Szymon Jozefczuk |
| collection | DOAJ |
| description | 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 co‐clustering 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. |
| format | Article |
| id | doaj-art-9cd3c976778a47fd8bb2bfe5dd02c1ab |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2010-05-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-9cd3c976778a47fd8bb2bfe5dd02c1ab2025-08-24T12:00:38ZengSpringer NatureMolecular Systems Biology1744-42922010-05-016111610.1038/msb.2010.18Metabolomic and transcriptomic stress response of Escherichia coliSzymon Jozefczuk0Sebastian Klie1Gareth Catchpole2Jedrzej Szymanski3Alvaro Cuadros‐Inostroza4Dirk Steinhauser5Joachim Selbig6Lothar Willmitzer7Molecular Plant Physiology, Max‐Planck‐Institute for Molecular Plant PhysiologyMolecular Plant Physiology, Max‐Planck‐Institute for Molecular Plant PhysiologyMolecular Plant Physiology, Max‐Planck‐Institute for Molecular Plant PhysiologyMolecular Plant Physiology, Max‐Planck‐Institute for Molecular Plant PhysiologyMolecular Plant Physiology, Max‐Planck‐Institute for Molecular Plant PhysiologyMolecular Plant Physiology, Max‐Planck‐Institute for Molecular Plant PhysiologyMolecular Plant Physiology, Max‐Planck‐Institute for Molecular Plant PhysiologyMolecular Plant Physiology, Max‐Planck‐Institute for Molecular Plant PhysiologyAbstract 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 co‐clustering 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.https://doi.org/10.1038/msb.2010.18Escherichia colimetabolomicresponse to stresstime coursetranscriptomic |
| spellingShingle | Szymon Jozefczuk Sebastian Klie Gareth Catchpole Jedrzej Szymanski Alvaro Cuadros‐Inostroza Dirk Steinhauser Joachim Selbig Lothar Willmitzer Metabolomic and transcriptomic stress response of Escherichia coli Molecular Systems Biology Escherichia coli metabolomic response to stress time course transcriptomic |
| title | Metabolomic and transcriptomic stress response of Escherichia coli |
| title_full | Metabolomic and transcriptomic stress response of Escherichia coli |
| title_fullStr | Metabolomic and transcriptomic stress response of Escherichia coli |
| title_full_unstemmed | Metabolomic and transcriptomic stress response of Escherichia coli |
| title_short | Metabolomic and transcriptomic stress response of Escherichia coli |
| title_sort | metabolomic and transcriptomic stress response of escherichia coli |
| topic | Escherichia coli metabolomic response to stress time course transcriptomic |
| url | https://doi.org/10.1038/msb.2010.18 |
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