Knotty is nice: Metabolite binding and RNA-mediated gene regulation by the preQ₁ riboswitch family

Riboswitches sense specific cellular metabolites, leading to messenger RNA conformational changes that regulate downstream genes. Here, we review the three known prequeosine₁ (preQ₁) riboswitch classes, which encompass five gene-regulatory motifs derived from distinct consensus models of folded RNA pseudoknots. Structural and functional analyses reveal multiple gene-regulation strategies ranging from partial occlusion of the ribosome-binding Shine-Dalgarno sequence (SDS), SDS sequestration driven by kinetic or thermodynamic folding pathways, direct preQ₁ recognition by the SDS, and complete SDS burial with in the riboswitch architecture. Family members can also induce elemental transcriptional pausing, which depends on ligand-mediated pseudoknot formation. Accordingly, preQ₁ family members provide insight into a wide range of gene-regulatory tactics as well as a diverse repertoire of chemical approaches used to recognize the preQ₁ metabolite. From a broader perspective, future challenges for the field will include the identification of new riboswitches in mRNAs that do not possess an SDS or those that induce ligand-dependent transcriptional pausing. When choosing an antibacterial target, the field must also consider how well a riboswitch accommodates mutations. Investigation of riboswitches in their natural context will also be critical to elucidate how RNA-mediated gene regulation influences organism fitness, thus providing a firm foundation for antibiotic development.