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| Status |
Public on May 12, 2020 |
| Title |
Genome-wide stabilization of mRNA during E. coli growth from "feast to famine" (stabilome) |
| Platform organism |
Escherichia coli K-12 |
| Sample organism |
Escherichia coli str. K-12 substr. MG1655 |
| Experiment type |
Expression profiling by array
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| Summary |
Bacteria have to continuously adjust to nutrient fluctuations from favorable to less favorable conditions and carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed by E. coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. It results from both mRNA transcription and degradation controls. However, the contribution of transcript stability regulation in gene expression is poorly characterized. Using combined transcriptome and mRNA decay analyses, we investigated (i) how transcript stability changes in E. coli during the glucose-acetate-starvation transition and (ii) if these changes contribute to gene expression changes. Our work highlights that transcript stability increases along carbon depletion. Most of the stabilization occurs at glucose-acetate transition when glucose is exhausted, then stabilized mRNAs remain stable during acetate consumption and carbon starvation. Meanwhile, expression of most genes is downregulated and we observed three time less gene expression upregulation. Using control analysis theory on 375 genes, we show that most of gene expression regulation is driven by changes in transcription. Although mRNA stabilization is not the controlling phenomenon, it contributes to the emphasis or attenuation of transcription regulation. However, upregulation of 18 genes (33% of our studied upregulated set) is mainly governed by transcript stabilization. Because these genes are associated with response to nutrient changes and stress, this illustrates the importance of post-transcriptional regulations in bacterial response to nutrient starvation.
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| Overall design |
A microarray study was performed to estimate genome wide mRNA half-lives in E. coli K12 MG1655 cultured in M9+glucose (3g/l). In three growth phases, at glucose exhaustion (P2), during acetate consumption (P3) and during carbon starvation (P4), sampling was performed before the addition of rifampicin (500 µg/l) for transcription arrest and over the time after rifampicin addition. Total RNA was then extracted from each sample. Each array measures the expression level of 4,254 genes from Escherichia coli MG1655 with eight 60-mer probes per gene in replicates. Three independent kinetics were performed for each growth condition.
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| Contributor(s) |
Morin M, Enjalbert B, Ropers D, Girbal L, Cocaign-Bousquet M |
| Citation(s) |
32434841 |
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| Submission date |
Jan 27, 2020 |
| Last update date |
Aug 03, 2020 |
| Contact name |
Laurence Girbal |
| E-mail(s) |
girbal@insa-toulouse.fr
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| Phone |
33 5 61 55 97 24
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| Organization name |
TBI
|
| Street address |
135 avenue de rangueil
|
| City |
Toulouse |
| ZIP/Postal code |
31077 |
| Country |
France |
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| Platforms (1) |
| GPL25406 |
NimbleGen E. coli K12 Gene Expression Array [130108_Ecoli_K12_exp] |
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| Samples (35)
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| Relations |
| BioProject |
PRJNA603353 |
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