Bacteria use a variety of mechanisms to sense and respond to environmental change. Moderate temperature variation, for example, can be sensed by RNA thermometers, which regulate gene expression through temperature-dependent structural changes. These RNA elements have been found in the 5′-untranslated region (UTR) of prokaryotic genes involved in heat or cold shock responses and in pathogenic virulence. Regulation primarily occurs at the translational level via altered accessibility to the ribosome-binding site. Our goal is to further characterize the molecular determinants controlling the behavior of RNA thermometers involved in the heat shock response. A short RNA thermometer has been previously identified in the 5′-UTR of the <i>htrA </i>gene from <i>Salmonella enterica</i>. We have experimentally determined the secondary structure of this thermometer using SHAPE (Selective 2′-Hydroxyl Acylation analyzed by Primer Extension) assays. We then investigated the structural response of this thermometer to temperature change, using SHAPE assays and thermal denaturation studies to compare the global folding behavior to the response at the single-nucleotide level.

Investigations of an RNA thermometer using SHAPE assays

251st National Meeting (2016)

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