Cited by 209Bacterial Genetics and BiotechnologyGene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli

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Liu, Mingzhu, Durfee, Tim, Cabrera, Julio E., Zhao, Kai, Jin, Ding J., Blattner, Frederick R.·2005·Journal of Biological Chemistry

Abstract

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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Crossref · 10.1074/jbc.m414050200

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  • Duplications and large scale genomic variations, although they can lead to significant issues such as genomic instability, play a major role in yeast evolution.

    “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].”

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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.
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
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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