ArticleBMC genomics2015
Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.Nature biotechnology · 2026Article
- Diverse intrinsic properties shape transcript stability and stabilization inNAR genomics and bioinformatics · 2024Article
- 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
- Assessing the Role of Cold-Shock Protein C: a Novel Regulator of Acinetobacter baumannii Biofilm Formation and Virulence.Infection and immunity · 2022Article
- Article
- Temperature-Dependent Influence of FliA Overexpression on PHL628Frontiers in cellular and infection microbiology · 2021Article
- Regulation of mRNA Stability During Bacterial Stress Responses.Frontiers in microbiology · 2020Review
- Chemical and Metabolic Controls on Dihydroxyacetone Metabolism Lead to Suboptimal Growth of Escherichia coli.Applied and environmental microbiology · 2019Article
- Article
- Allergic sensitization increases the amount of extracellular ATP hydrolyzed by guinea pig leukocytes.Purinergic signalling · 2019Article
- Structural Basis of the Subcellular Topology Landscape ofFrontiers in microbiology · 2019Article
- Role of CsrA in stress responses and metabolism important for Salmonella virulence revealed by integrated transcriptomics.PloS one · 2019Article
- PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli.BMC genomics · 2018Article
- Natural environmental water sources in endemic regions of northeastern Brazil are potential reservoirs of viable Mycobacterium leprae.Memorias do Instituto Oswaldo Cruz · 2017Article
- Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans.BMC genomics · 2016Article
- The Csr system regulates genome-wide mRNA stability and transcription and thus gene expression in Escherichia coli.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundChanges to mRNA lifetime adjust mRNA concentration, facilitating the adaptation of growth rate to changes in growth conditions. However, the mechanisms regulating mRNA lifetime are poorly understood at the genome-wide scale and have not been investigated in bacteria growing at different rates.
resultsWe used linear covariance models and the best model selected according to the Akaike information criterion to identify and rank intrinsic and extrinsic general transcript parameters correlated with mRNA lifetime, using mRNA half-life datasets for E. coli, obtained at four growth rates. The principal parameter correlated with mRNA stability was mRNA concentration, the mRNAs most concentrated in the cells being the least stable. However, sequence-related features (codon adaptation index (CAI), ORF length, GC content, polycistronic mRNA), gene function and essentiality also affected mRNA lifetime at all growth rates. We also identified sequence motifs within the 5'UTRs potentially related to mRNA stability. Growth rate-dependent effects were confined to particular functional categories (e.g. carbohydrate and nucleotide metabolism). Finally, mRNA stability was less strongly correlated with the amount of protein produced than mRNA concentration and CAI.
conclusionsThis study provides the most complete genome-wide analysis to date of the general factors correlated with mRNA lifetime in E. coli. We have generalized for the entire population of transcripts or excluded determinants previously defined as regulators of stability for some particular mRNAs and identified new, unexpected general indicators. These results will pave the way for discussions of the underlying mechanisms and their interaction with the growth physiology of bacteria.
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