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Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC
Published on: May 9, 2020
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Two temperature-responsive RNAs act in concert: the small RNA CyaR and the mRNA ompX
David A Guanzon1, Stephan Pienkoß1, Vivian B Brandenburg2
1Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany.
Nucleic Acids Research
|February 5, 2025
Summary
Temperature shifts alter bacterial RNA structures. The small RNA CyaR changes conformation with temperature, regulating ompX gene expression and protein levels through RNA-RNA interactions and mRNA degradation.
Area of Science:
- Microbiology
- Molecular Biology
- RNA Biology
Background:
- Bacterial pathogens experience temperature changes during infection.
- Temperature shifts impact bacterial RNA structures and gene expression.
- Previous studies focused on 5'-UTR RNA thermometers in virulence mRNAs.
Purpose of the Study:
- Investigate temperature-driven structural rearrangements in the small RNA CyaR.
- Identify CyaR's targets and regulatory mechanisms.
- Elucidate multilayered post-transcriptional control of ompX expression.
Main Methods:
- RNA sequencing
- In-line probing experiments
- Analysis of RNA-protein interactions
Main Results:
- CyaR undergoes temperature-dependent conformational changes, liberating its seed region at 37°C.
- CyaR directly targets the Shine-Dalgarno sequence of ompX mRNA.
- ompX mRNA exhibits RNA thermometer properties, facilitating CyaR binding at higher temperatures.
- CyaR binding inhibits ompX translation and promotes mRNA degradation.
- OmpX protein undergoes temperature-induced proteolytic turnover.
Conclusions:
- Multilayered post-transcriptional regulation governs ompX expression in response to temperature.
- Lower OmpX levels are observed at 37°C compared to 25°C due to CyaR-mediated control.
- This study reveals novel temperature-dependent RNA regulatory mechanisms in Yersinia pseudotuberculosis.
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