Discovery of Thermoregulatory RNAs - Abstract Temperature variation is a critical environmental factor that influences microbial survival, pathogenesis, and symbiosis, particularly during transitions from external environments into warm-blooded hosts. For pathogens and members of the human gut microbiota, the ability to sense and adapt to host temperature fluctuations is essential for survival. The study of thermoregulatory RNAs is an emerging field with great potential for discovery and innovation. Thermoregulatory RNAs are structured elements that respond to heat stress, with most identified examples known as RNA thermometers (RNATs) residing in the 5′ untranslated regions (UTRs) of mRNAs, where they regulate translation. Despite their importance, the diversity of thermoregulatory RNAs, their natural abundance, and the genes they regulate remain largely unexplored, and their potential roles in transcriptional regulation are not yet understood. Our central goals for the next five years are to expand the discovery and characterization of thermoregulatory RNA elements in bacteria, phages, chloroplasts, and mitochondria, while also engineering synthetic RNATs with improved regulatory properties. A major focus will be on bacterial pathogens, where RNATs regulate virulence genes that drive infection and disease. By uncovering these elements, this work will reveal new RNA-based targets for antibiotic development. In addition, we will identify novel RNAT classes, uncover transcriptional thermoregulatory elements known as thermoterms, and test RNAT activity across prokaryotic and organelle genomes to establish a broader framework for understanding how RNA structures mediate microbial and organelle responses to heat stress. In parallel, synthetic RNATs will be developed as versatile genetic tools that provide precise, modular, temperature-dependent control of gene expression. These foundational advances are essential to achieve before broader ambitions can be realized, and they are strategically designed to lay the groundwork for our long-term vision of building a comprehensive field of thermoregulatory RNA biology that spans both fundamental discovery and applied innovation. This vision includes exploring dual functional RNAs such as ribozymes and riboswitches that incorporate temperature sensitivity into other regulatory mechanisms, extending RNAT discovery into eukaryotic nuclear genes and viral RNAs, advancing RNA-targeted therapeutics, and applying RNATs in chloroplast engineering to enhance crop resilience. Ultimately, this research will reveal how organisms use RNA to adapt to temperature stress, deepen our understanding of gene regulation in response to heat stress, translate that knowledge into new strategies for antibiotic development, and expand the toolkit of thermoregulatory RNAs for synthetic biology.
