Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level

TW Liao, L Huang, TJ Wilson, LR Ganser… - Nucleic acids …, 2023 - academic.oup.com
Nucleic acids research, 2023academic.oup.com
Riboswitches are regulatory elements found in bacterial mRNAs that control downstream
gene expression through ligand-induced conformational changes. Here, we used single-
molecule FRET to map the conformational landscape of the translational SAM/SAH
riboswitch and probe how co-transcriptional ligand-induced conformational changes affect
its translation regulation function. Riboswitch folding is highly heterogeneous, suggesting a
rugged conformational landscape that allows for sampling of the ligand-bound conformation …
Abstract
Riboswitches are regulatory elements found in bacterial mRNAs that control downstream gene expression through ligand-induced conformational changes. Here, we used single-molecule FRET to map the conformational landscape of the translational SAM/SAH riboswitch and probe how co-transcriptional ligand-induced conformational changes affect its translation regulation function. Riboswitch folding is highly heterogeneous, suggesting a rugged conformational landscape that allows for sampling of the ligand-bound conformation even in the absence of ligand. The addition of ligand shifts the landscape, favoring the ligand-bound conformation. Mutation studies identified a key structural element, the pseudoknot helix, that is crucial for determining ligand-free conformations and their ligand responsiveness. We also investigated ribosomal binding site accessibility under two scenarios: pre-folding and co-transcriptional folding. The regulatory function of the SAM/SAH riboswitch involves kinetically favoring ligand binding, but co-transcriptional folding reduces this preference with a less compact initial conformation that exposes the Shine–Dalgarno sequence and takes min to redistribute to more compact conformations of the pre-folded riboswitch. Such slow equilibration decreases the effective ligand affinity. Overall, our study provides a deeper understanding of the complex folding process and how the riboswitch adapts its folding pattern in response to ligand, modulates ribosome accessibility and the role of co-transcriptional folding in these processes.
Oxford University Press
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