One of the interesting aspects of RNA biology is the functioning of structured RNAs as regulatory elements, in particular as sensors that detect changes in environment and transduce the information into a change in gene expression. One interesting class of such RNAs are the so-called riboswitches. These are RNAs that typically bind to a ligand, much as an in vitro-selected RNA may bind to a chemical (such as an amino acid). Binding changes the structure of the RNA, leading to changes in transcription, stability of the RNA, or translatability of the RNA.
Riboswitches may bind small molecule ligands. Alternatively, they may sense temperature. This occurs because many RNA structures can be rather sensitive to changes in temperature, owing to the tendency of some secondary structures to become disrupted at physiologically meaningful temperatures. A recent study extends the realm of RNA thermometers to include the sensing of cold temperatures, and adds a new twist to the nature of the riboswitch. In this study, the authors studied the regulatory motif of the E. coli cspA gene; this gene is a cold-shock gene, whose expression increases with lower temperature. This regulation may be attributed to in part to the 5′-untranslated part of the cspA mRNA. This work showed that low temperature promotes an RNA fold that enhances translation and RNA stability. Interestingly, this fold requires much (most) of the cspA mRNA; in other words, the whole mRNA is a sort of RNA thermometer that senses low temperature. The authors propose that the structural variations reflect co-transcriptional folding of the RNA, and that two different pathways (and end products) are traversed in cells growing at normal and low temperatures.