Potential thermosensitive riboswitches in the genome of Salmonella

Currently, a number of structurally and functionally different thermosensitive elements, such as structurally and functionally different RNA thermometers, for controlling a variety of biological processes in bacteria, including virulence are known. These well-known RNA thermometers are structures, whether matched or mismatched, which are represented by either a single stretched hairpin structure or a few hairpins. Based on computer and thermodynamic analyses of 25 isolates of Salmonella enterica with complete genome, we have developed an algorithm and criteria to search for potential RNA thermometers, which will enable us to undertake a future search for potential riboswitches in the genomes of other socially significant pathogens. In addition to the well-known 4U RNA thermometer, another four hairpin-loop structures have been identified in S. enterica as new potential RNA thermometers and two of them are localized in 5'-UTR of virulence regulators gltB and yaeQ. They are highly conserved noncanonical structures and correspond to the necessary and sufficient conditions for forming RNA thermometers, since they are found in each of the 25 S. enterica genome isolates. We analyzed the thermosensitive motif in the pXO1 plasmid of Bacillus anthracis-an anthrax-causative pathogen-and visualized matched hairpins that form a cruciform structure in pUC8 supercoiled plasmid by atomic force microscopy.