Applications and biological roles of riboswitch RNAs. Metabolite-sensing riboswitches have been discovered that respond to a variety of metabolites. Most riboswitches are used in feedback loops for negative regulation of biosynthesis or transport genes. However, certain riboswitch classes respond to stress signals or the availability of a key enzymatic cofactor or substrate. A particular riboswitch class responds to the second messenger, cyclic di-GMP, for control of numerous fundamental cellular processes. In addition to these natural roles, riboswitches are also increasingly viewed as useful tools in assisting the functional analyses of riboswitch-associated genes, as drug targets, and as scaffolds for construction of artificial or reengineered riboswitches [44–46].