Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches

• Published in: Journal of molecular biology Vol. 434; no. 18; p. 167585
• Main Authors: Lennon, Shelby R., Batey, Robert T.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Ltd 30-09-2022
• Subjects: co-transcriptional folding; cobalamin; gene regulation; riboswitch; RNA structure; riboswitch; cobalamin; gene regulation; RNA structure; co-transcriptional folding
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2022.167585

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•Riboswitches are ideal model systems for studying complex RNA folding and regulation mediated by RNA conformation switching.•Coupling effector binding to a conformational switch while under temporal constraint is essential to riboswitch function.•Cobalamin riboswitches are a robust and widespread solution in bacteria for regulation of an essential metabolite, cobalamin.•Cobalamin binding has a direct role in mediating the cobalamin riboswitch’s conformational and regulatory switch.•Unique aspects of cobalamin riboswitch folding are only accessible during co-transcriptional folding.
Riboswitches are an outstanding example of genetic regulation mediated by RNA conformational switching. In these non-coding RNA elements, the occupancy status of a ligand-binding domain governs the mRNA’s decision to form one of two mutually exclusive structures in the downstream expression platform. Temporal constraints upon the function of many riboswitches, requiring folding of complex architectures and conformational switching in a limited co-transcriptional timeframe, make them ideal model systems for studying these processes. In this review, we focus on the mechanism of ligand-directed conformational changes in one of the most widely distributed riboswitches in bacteria: the cobalamin family. We describe the architectural features of cobalamin riboswitches whose structures have been determined by x-ray crystallography, which suggest a direct physical role of cobalamin in effecting the regulatory switch. Next, we discuss a series of experimental approaches applied to several model cobalamin riboswitches that interrogate these structural models. As folding is central to riboswitch function, we consider the differences in folding landscapes experienced by RNAs that are produced in vitro and those that are allowed to fold co-transcriptionally. Finally, we highlight a set of studies that reveal the difficulties of studying cobalamin riboswitches outside the context of transcription and that co-transcriptional approaches are essential for developing a more accurate picture of their structure–function relationships in these switches. This understanding will be essential for future advancements in the use of small-molecule guided RNA switches in a range of applications such as biosensors, RNA imaging tools, and nucleic acid-based therapies.