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| Status |
Public on Dec 10, 2018 |
| Title |
Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase [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 |
Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide approach to determine how RNase R and PNPase affect the mRNA half-lives compared to wild type (stabilome) in the stationary phase. The stabilome is an original dynamic transcriptome-based analysis to measure the rates of mRNA degradation at the genome scale. We have combined the analysis of stabilome with the steady state concentrations of mRNAs (transcriptome) to provide an integrated overview of the in vivo activity of these exoribonucleases at the genome-scale. The stabilome demonstrated that the mRNAs are very stable in the stationary phase and that the deletion of RNase R or PNPase caused only a limited mRNA stabilization. Intriguingly the absence of PNPase provoked also the destabilization of many mRNAs. These changes in mRNA half-lives in the PNPase deletion strain were associated with a massive reorganization of mRNA levels and also variation in several ncRNA concentrations. Finally, the in vivo activity of the degradation machinery was found frequently saturated by mRNAs in the PNPase mutant unlike in the RNase R mutant, suggesting that the degradation activity is limited by the deletion of PNPase but not by the deletion of RNase R. This work allowed the roles of RNase R and PNPase in coordinating E. coli RNA metabolism to be discussed and PNPase to be identified as a central player of the degradation machinery in stationary phase.
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| Overall design |
A microarray study was performed to estimate genome wide mRNA half-lives in three E. coli K12 strains MG1655, MG1655(Δrnr) and MG1655(Δpnp), cultured in LB. Three hours after the entry in stationary phase, sampling was before the addition of rifampcin (500 µg/l) for transcrption arrrest and over the time after rifampcin 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 duplicates. Three independent repetitions were performed for each strain.
Please note that there are variations between the samples of a given strain because there were sampled over the time (between Time 0 and Time 30 minutes) after transcription arrest. So there are repetitions of three kinetics rep1, rep2 and rep3 but these kinetics correspond to different time points except for time 0 which is in common in the three kinetics.
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| Contributor(s) |
Dressaire C, Pobre V, Laguerre S, Girbal L, Arraiano CM, Cocaign-Bousquet M |
| Citation(s) |
30486791 |
| |
| Submission date |
Jul 03, 2018 |
| Last update date |
Dec 10, 2018 |
| 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
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| City |
Toulouse |
| ZIP/Postal code |
31077 |
| Country |
France |
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| Platforms (1) |
| GPL14649 |
NimbleGen E. coli K12 Gene Expression Array [071112_Ecoli_K12_EXP] |
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| Samples (35)
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| This SubSeries is part of SuperSeries: |
| GSE116652 |
Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase |
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| Relations |
| BioProject |
PRJNA479437 |
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