DSSR-PyMOL cartoon-block schematics: PDB entry 5kh8

PDB-id

5kh8; DSSR-derived features in text and JSON formats

Class

RNA

Method

NMR

Summary

Solution structures of the apo state fluoride riboswitch

Reference

Zhao B, Guffy SL, Williams B, Zhang Q (2017): "An excited state underlies gene regulation of a transcriptional riboswitch." Nat. Chem. Biol., 13, 968-974. doi: 10.1038/nchembio.2427.

Abstract

Riboswitches control gene expression through ligand-dependent structural rearrangements of the sensing aptamer domain. However, we found that the Bacillus cereus fluoride riboswitch aptamer adopts identical tertiary structures in solution with and without ligand. Using chemical-exchange saturation transfer (CEST) NMR spectroscopy, we revealed that the structured ligand-free aptamer transiently accesses a low-populated (∼1%) and short-lived (∼3 ms) excited conformational state that unravels a conserved 'linchpin' base pair to signal transcription termination. Upon fluoride binding, this highly localized, fleeting process is allosterically suppressed, which activates transcription. We demonstrated that this mechanism confers effective fluoride-dependent gene activation over a wide range of transcription rates, which is essential for robust toxicity responses across diverse cellular conditions. These results unveil a novel switching mechanism that employs ligand-dependent suppression of an aptamer excited state to coordinate regulatory conformational transitions rather than adopting distinct aptamer ground-state tertiary architectures, exemplifying a new mode of ligand-dependent RNA regulation.