ArticleNucleic acids research2014
Dual role of transcription and transcript stability in the regulation of gene expression in Escherichia coli cells cultured on glucose at different growth rates.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 84 citations in OpenAlex.
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- Resolving emergent transient oscillations in gene circuits with a growth-coupled model.Science advances · 2026Article
- Gene Expression Across Growth Stages (GEAGS): Modeling Circuit Dynamics in Batch Cultures.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Stress changes the material state of a bacterial biomolecular condensate and shifts its function from mRNA decay to storage.Nature communications · 2025Article
- rRNA loss induced by rifampicin addition in Escherichia coli reflects extraction artifacts rather than in vivo degradation.Scientific reports · 2025Article
- Excess A-subunits of Shiga toxin 2a are produced in enterohemorrhagic Escherichia coli.Scientific reports · 2025Article
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- Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning.Nature communications · 2024Article
- Diverse intrinsic properties shape transcript stability and stabilization inNAR genomics and bioinformatics · 2024Article
- Improved RNA stability estimation through Bayesian modeling reveals mostProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Methodologies for bacterial ribonuclease characterization using RNA-seq.FEMS microbiology reviews · 2023Review
- Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains.eLife · 2023Article
- When translation elongation is impaired, the mRNA is uniformly destabilized by the RNA degradosome, while the concentration of mRNA is altered along the molecule.Nucleic acids research · 2023Article
- RNA-seq Sample Preparation Kits Strongly Affect Transcriptome Profiles of a Gas-Fermenting Bacterium.Microbiology spectrum · 2022Article
- Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli.Nucleic acids research · 2022Article
- Synergistic Regulation of Transcription and Translation in Escherichia coli Revealed by Codirectional Increases in mRNA Concentration and Translation Efficiency.Microbiology spectrum · 2022Article
- 5'UTR sequences influence protein levels inFrontiers in microbiology · 2022Article
- Inactivation of RNase P in Escherichia coli significantly changes post-transcriptional RNA metabolism.Molecular microbiology · 2022Article
- In-Depth Sequence Analysis of Bread WheatInternational journal of molecular sciences · 2021Article
- Control and regulation of acetate overflow ineLife · 2021Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microorganisms extensively reorganize gene expression to adjust growth rate to changes in growth conditions. At the genomic scale, we measured the contribution of both transcription and transcript stability to regulating messenger RNA (mRNA) concentration in Escherichia coli. Transcriptional control was the dominant regulatory process. Between growth rates of 0.10 and 0.63 h(-1), there was a generic increase in the bulk mRNA transcription. However, many transcripts became less stable and the median mRNA half-life decreased from 4.2 to 2.8 min. This is the first evidence that mRNA turnover is slower at extremely low-growth rates. The destabilization of many, but not all, transcripts at high-growth rate correlated with transcriptional upregulation of genes encoding the mRNA degradation machinery. We identified five classes of growth-rate regulation ranging from mainly transcriptional to mainly degradational. In general, differential stability within polycistronic messages encoded by operons does not appear to be affected by growth rate. We show here that the substantial reorganization of gene expression involving downregulation of tricarboxylic acid cycle genes and acetyl-CoA synthetase at high-growth rates is controlled mainly by transcript stability. Overall, our results demonstrate that the control of transcript stability has an important role in fine-tuning mRNA concentration during changes in growth rate.
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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.