Characterizing RNA Thermometers through Shape-Seq

Whether harvested from nature or designed synthetically, RNA regulators offer synthetic biologists a valuable way to control gene expression and engineer cells that can sense and respond to their environment.  As part of our on-going efforts to expand the toolbox of RNA regulators available for use, we report the functional and structural characterization of a series of RNA thermometers derived from Salmonella.  These thermometers regulate the translation of a downstream gene via a temperature-sensitive hairpin that occludes the RBS at low temperatures but not at high temperatures.  Using a combination of fluorescent reporter gene read-outs and RNA structural probing via SHAPE-Seq, we dissect the underlying mechanism of these thermometers in order to allow for their use and modification in synthetic biology applications.