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Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli
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By exploring global gene expression of Escherichia coli growing on six different carbon sources, we discovered a striking genome transcription pattern: as carbon substrate quality declines, cells systematically increase the number of genes expressed. Gene induction occurs in a hierarchical manner and includes many factors for uptake and metabolism of better but currently unavailable carbon sources. Concomitantly, cells also increase their motility. Thus, as the growth potential of the environment decreases, cells appear to devote progressively more energy on the mere possibility of improving conditions. This adaptation is not what would be predicated by classic regulatory models alone. We also observe an inverse correlation between gene activation and rRNA synthesis suggesting that reapportioning RNA polymerase (RNAP) contributes to the expanded genome activation. Significant differences in RNAP distribution in vivo, monitored using an RNAP-green fluorescent protein fusion, from energy-rich and energy-poor carbon source cultures support this hypothesis. Together, these findings represent the integration of both substrate-specific and global regulatory systems, and may be a bacterial approximation to metazoan risk-prone foraging behavior.
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“As such, ALE studies highlight that duplications and large scale genomic variations, although they can lead to significant issues such as genomic instability [152], play a major role in e.g. yeast evolution; this is also indicated by data on wine yeasts, galactose utilization, comparative genomics and drug resistance [115,153-156].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [152]
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Fu, N., Su, D. G. T., Cort, J., Chen, B., Xiong, Y., Qian, W., Konopka, A. E., Bigelow, D. J., & Squier, T. C. (2013) · Journal of the American Chemical Society · doi:10.1021/ja3117284 · Cited by 28
A Genomic View of the Catabolism of Aromatic Compounds in Pseudomonas
Jiménez, J. I., Nogales, J., García, J. L., & Dı́az, E. (2009) · Springer eBooks · doi:10.1007/978-3-540-77587-4_91 · Cited by 28
Metadata
- Authors
- Liu, M., Durfee, T., Cabrera, J. E., Zhao, K., Jin, D. J., & Blattner, F. R.
- Affiliations
- University of Wisconsin–Madison (US)
- National Institutes of Health (US)
- Corresponding author
- Blattner, Frederick R.
- ORCID
- Liu, Mingzhu
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 2005-04
- Volume
- 280
- Issue
- 16
- Pages
- 15921-15927
- ISSN
- 0021-9258 (ISSN-L)
- OpenAlex
- W2081114359
- Cited by
- 209
- References
- 50
- Citations by year
- 2026: 7 · 2025: 6 · 2024: 7 · 2023: 2 · 2022: 8 · 2021: 11 · 2020: 8 · 2019: 8 · 2018: 13 · 2017: 5 · 2016: 9 · 2015: 11 · 2014: 10 · 2013: 13 · 2012: 16
- FWCI
- 7.94
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (GM35682-17S1, R01GM035682)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- Escherichia coli, global gene expression, ribosomal RNA synthesis, bacterial motility, energy allocation
- MeSH terms
- Alanine, Carbon, Computer Simulation, Escherichia coli, Glucose, Glycerol, Models, Biological, Proline, Promoter Regions, Genetic, RNA, Ribosomal, Transcription, Genetic, Up-Regulation, Acetic Acid, Succinic Acid, Gene Expression Profiling
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