biostudies-literatureGuanzon DAGerman Research FoundationDFGKatholischer Akademischer Ausländer-Dienstgkaf041https://www.ebi.ac.uk/biostudies/studies/S-EPMC11795201biostudies-literatureUnknown53(3)Bacterial pathogens, such as 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 ompX as a direct target of CyaR. Interestingly, the ompX transcript itself exhibits RNA thermometer-like propNucleic acids researchTwo temperature-responsive RNAs act in concert: the small RNA CyaR and the mRNA ompX.PMC11795201NA 240/14-1GRK 2341Dietze AWimbert ARoder JBrandenburg VBTwittenhoff CNarberhaus FGuanzon DAScheller DPienkoß SfalseTwo temperature-responsive RNAs act in concert: the small RNA CyaR and the mRNA ompX.Bacterial pathogens, such as 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 ompX as a direct target of CyaR. Interestingly, the ompX transcript itself exhibits RNA thermometer-like prop2025-01-01T00:00:00Z2025 Jan2025-04-04T02:09:17.123Z2025-04-04T02:09:17.123ZS-EPMC117952013990711010.1093/nar/gkaf041