Two temperature-responsive RNAs act in concert: The small RNA CyaR and the mRNA ompX

Bacterial pathogens, such as in Yersinia pseudotuberculosis, encounter temperature fluctuations during host infection and upon return to the environment. These temperature shifts impact RNA structures globally. While previous transcriptome-wide studies have focused on RNA thermometers in the 5-untranslated region of virulence-related mRNAs, our investigation revealed temperature-driven structural rearrangements in the small RNA (sRNA) CyaR. At 25{degrees}C, CyaR primarily adopts a conformation that occludes its seed region, but transitions to a liberated state at 37{degrees}C. By RNA-sequencing and in-line probing experiments, we identified the Shine-Dalgarno sequence of ompX as a direct target of CyaR. Interestingly, the ompX transcript itself exhibits RNA thermometer-like properties, facilitating CyaR base pairing at elevated temperatures. This interaction impedes ribosome binding to ompX and accelerates degradation of the ompX transcript. Furthermore, we observed induced proteolytic turnover of the OmpX protein at higher temperatures. Collectively, our study uncovered multi-layered posttranscriptional mechanisms governing ompX expression, resulting in lower OmpX levels at 37{degrees}C compared to 25{degrees}C. We propose that CyaR remains mostly passive at 25{degrees}C but becomes primed to repress ompX at 37{degrees}C, thereby expediting outer membrane remodelling in anticipation of pathogenesis.