Shared control of gene expression in bacteria by transcription factors and global physiology of the cell
Gene expression is controlled by the joint effect of (i) the global physiological state of the cell, in particular the activity of the gene expression machinery, and (ii) DNA‐binding transcription factors and other specific regulators. We present a model‐based approach to distinguish between these t...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2013-01-01
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| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/msb.2012.70 |
| _version_ | 1797225934529495040 |
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| author | Sara Berthoumieux Hidde de Jong Guillaume Baptist Corinne Pinel Caroline Ranquet Delphine Ropers Johannes Geiselmann |
| author_facet | Sara Berthoumieux Hidde de Jong Guillaume Baptist Corinne Pinel Caroline Ranquet Delphine Ropers Johannes Geiselmann |
| author_sort | Sara Berthoumieux |
| collection | DOAJ |
| description | Gene expression is controlled by the joint effect of (i) the global physiological state of the cell, in particular the activity of the gene expression machinery, and (ii) DNA‐binding transcription factors and other specific regulators. We present a model‐based approach to distinguish between these two effects using time‐resolved measurements of promoter activities. We demonstrate the strength of the approach by analyzing a circuit involved in the regulation of carbon metabolism in E. coli. Our results show that the transcriptional response of the network is controlled by the physiological state of the cell and the signaling metabolite cyclic AMP (cAMP). The absence of a strong regulatory effect of transcription factors suggests that they are not the main coordinators of gene expression changes during growth transitions, but rather that they complement the effect of global physiological control mechanisms. This change of perspective has important consequences for the interpretation of transcriptome data and the design of biological networks in biotechnology and synthetic biology. |
| first_indexed | 2024-03-11T21:49:12Z |
| format | Article |
| id | doaj.art-1c0388982e91404ba98b5cc6dc10915f |
| institution | Directory Open Access Journal |
| issn | 1744-4292 |
| language | English |
| last_indexed | 2024-04-24T14:16:54Z |
| publishDate | 2013-01-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj.art-1c0388982e91404ba98b5cc6dc10915f2024-04-03T08:20:33ZengSpringer NatureMolecular Systems Biology1744-42922013-01-0191n/an/a10.1038/msb.2012.70Shared control of gene expression in bacteria by transcription factors and global physiology of the cellSara Berthoumieux0Hidde de Jong1Guillaume Baptist2Corinne Pinel3Caroline Ranquet4Delphine Ropers5Johannes Geiselmann6INRIA Grenoble—Rhône‐Alpes Saint Ismier Cedex FranceINRIA Grenoble—Rhône‐Alpes Saint Ismier Cedex FranceINRIA Grenoble—Rhône‐Alpes Saint Ismier Cedex FranceINRIA Grenoble—Rhône‐Alpes Saint Ismier Cedex FranceINRIA Grenoble—Rhône‐Alpes Saint Ismier Cedex FranceINRIA Grenoble—Rhône‐Alpes Saint Ismier Cedex FranceINRIA Grenoble—Rhône‐Alpes Saint Ismier Cedex FranceGene expression is controlled by the joint effect of (i) the global physiological state of the cell, in particular the activity of the gene expression machinery, and (ii) DNA‐binding transcription factors and other specific regulators. We present a model‐based approach to distinguish between these two effects using time‐resolved measurements of promoter activities. We demonstrate the strength of the approach by analyzing a circuit involved in the regulation of carbon metabolism in E. coli. Our results show that the transcriptional response of the network is controlled by the physiological state of the cell and the signaling metabolite cyclic AMP (cAMP). The absence of a strong regulatory effect of transcription factors suggests that they are not the main coordinators of gene expression changes during growth transitions, but rather that they complement the effect of global physiological control mechanisms. This change of perspective has important consequences for the interpretation of transcriptome data and the design of biological networks in biotechnology and synthetic biology.https://doi.org/10.1038/msb.2012.70bacterial physiologycarbon metabolismE. coligene regulatory networkssystems biology |
| spellingShingle | Sara Berthoumieux Hidde de Jong Guillaume Baptist Corinne Pinel Caroline Ranquet Delphine Ropers Johannes Geiselmann Shared control of gene expression in bacteria by transcription factors and global physiology of the cell Molecular Systems Biology bacterial physiology carbon metabolism E. coli gene regulatory networks systems biology |
| title | Shared control of gene expression in bacteria by transcription factors and global physiology of the cell |
| title_full | Shared control of gene expression in bacteria by transcription factors and global physiology of the cell |
| title_fullStr | Shared control of gene expression in bacteria by transcription factors and global physiology of the cell |
| title_full_unstemmed | Shared control of gene expression in bacteria by transcription factors and global physiology of the cell |
| title_short | Shared control of gene expression in bacteria by transcription factors and global physiology of the cell |
| title_sort | shared control of gene expression in bacteria by transcription factors and global physiology of the cell |
| topic | bacterial physiology carbon metabolism E. coli gene regulatory networks systems biology |
| url | https://doi.org/10.1038/msb.2012.70 |
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