Discovery and Characterization of RNA Thermometers

RNA thermometers are highly structured noncoding RNAs located in the 5′-untranslated regions (UTRs) of genes that regulate expression by undergoing conformational changes in response to temperature. We developed Robo-Therm, a pipeline that combines an adaptive and user-friendly in silico motif search with a well-established reporter system to identify and characterize RNA thermometers.

We have successfully implemented Robo-Therm to discover and characterize eight novel RNA thermometers. All of these annotated RNA thermometers have been found in bacteria genomes, and two of them also occur in phage genomes which infect the bacterial host that also contains the same thermometer. These thermometers have been discovered upstream of a variety of genes, including those that regulate gene expression (σ70), play a role in antibiotic resistance (tetR family regulator), determine phage life cycles (blyA), and five different genes involved in membrane transport (various ATP-binding cassette transporters). Overall, our studies suggest that RNA thermometers may be more common than previously anticipated, and revelation of these RNA thermometers will expand the knowledge of how specific genes are regulated as well as how bacteria respond to heat stress. 

blyA

ABC transporter thermometers