ArticleMicrobial biotechnology2021
Escherichia coli segments its controls on carbon-dependent gene expression into global and specific regulations.
Article in Microbial biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 8 citations in OpenAlex.
- Improving the Annotations of JCVI-Syn3a Proteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Insights into the regulatory mechanisms and application prospects of the transcription factor Cra.Applied and environmental microbiology · 2024Review
- Patterns of Fitness and Gene Expression Epistasis Generated by Beneficial Mutations in the rho and rpoB Genes of Escherichia coli during High-Temperature Adaptation.Molecular biology and evolution · 2024Article
- Revisiting Fur Regulon Leads to a Comprehensive Understanding of Iron and Fur Regulation.International journal of molecular sciences · 2023Article
- Small RNA GcvB Regulates Oxidative Stress Response ofAntioxidants (Basel, Switzerland) · 2021Article
- Escherichia coli segments its controls on carbon-dependent gene expression into global and specific regulations.Microbial biotechnology · 2021Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
How bacteria adjust gene expression to cope with variable environments remains open to question. Here, we investigated the way global gene expression changes in E. coli correlated with the metabolism of seven carbon substrates chosen to trigger a large panel of metabolic pathways. Coarse-grained analysis of gene co-expression identified a novel regulation pattern: we established that the gene expression trend following immediately the reduction of growth rate (GR) was correlated to its initial expression level. Subsequent fine-grained analysis of co-expression demonstrated that the Crp regulator, coupled with a change in GR, governed the response of most GR-dependent genes. By contrast, the Cra, Mlc and Fur regulators governed the expression of genes responding to non-glycolytic substrates, glycolytic substrates or phosphotransferase system transported sugars following an idiosyncratic way. This work allowed us to expand additional genes in the panel of gene complement regulated by each regulator and to elucidate the regulatory functions of each regulator comprehensively. Interestingly, the bulk of genes controlled by Cra and Mlc were, respectively, co-regulated by Crp- or GR-related effect and our quantitative analysis showed that each factor took turns to work as the primary one or contributed equally depending on the conditions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.