Comparative Analysis of RNA Structures Reveals an mRNA-mRNA Interaction Controlling Listeria Virulence Factor Expression

To understand physiological processes, it is vital to disclose the conformation of biological molecules inside living cells and correlate their structure with their function. Here, we describe a method, FUSE (5ʹ UTR Structure Elucidation), that we developed to study how the structures of 5ʹ UTRs change in response to different conditions inside the human bacterial pathogen Listeria monocytogenes. We discovered a novel RNA thermoswitch and could calculate the ratio of the two conformations that this thermoswitch assumes at different conditions. FUSE also identified the site of base-pairing between a small RNA and mRNA with a single-nucleotide resolution. Strikingly, FUSE discovered a functional mRNA-mRNA interaction, where the stability of an mRNA encoding the PrsA2 chaperone was increased by the direct binding of an mRNA encoding its substrate, the main virulence factor listeriolysin O. Specifically targeting the 5ʹ UTRs, FUSE can be applied in any living organism or virus.