Two temperature-responsive RNAs act in concert: the small RNA CyaR and the mRNA \(\it ompX\)

Bacterial pathogens, such as \(\textit {Yersinia pseudotuberculosis}\), 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 messenger RNAs, our investigation revealed temperature-driven structural rearrangements in the small RNA CyaR (cyclic AMP-activated RNA). At 25°C, CyaR primarily adopts a conformation that occludes its seed region, but transitions to a liberated state at 37°C. By RNA sequencing and in-line probing experiments, we identified the Shine–Dalgarno sequence of \(\it ompX\) as a direct target of CyaR. Interestingly, the \(\it ompX\) transcript itself exhibits RNA thermometer-like properties, facilitating CyaR base pairing at elevated temperatures. This interaction impedes ribosome binding to \(\it ompX\) and accelerates degradation of the \(\it ompX\) transcript. Furthermore, we observed induced proteolytic turnover of the \(\it ompX\) protein at higher temperatures. Collectively, our study uncovered multilayered post-transcriptional mechanisms governing \(\it ompX\) expression, resulting in lower \(\it ompX\) levels at 37°C compared with 25°C.