Cotranscriptional Folding of a 5' Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution.

Autor: Hien EDM; Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada., St-Pierre P; Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada., Penedo JC; Centre of Biophotonics, Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. Andrews, St Andrews, UK; Centre of Biophotonics, Laboratory for Biophysics and Biomolecular Dynamics, Biomedical Sciences Research Complex, School of Biology, University of St. Andrews, St. Andrews, UK., Lafontaine DA; Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada. Electronic address: daniel.lafontaine@usherbrooke.ca.
Jazyk: angličtina
Zdroj: Journal of molecular biology [J Mol Biol] 2024 Nov 15; Vol. 436 (22), pp. 168771. Date of Electronic Publication: 2024 Aug 30.
DOI: 10.1016/j.jmb.2024.168771
Abstrakt: Transcription elongation is one of the most important processes in the cell. During RNA polymerase elongation, the folding of nascent transcripts plays crucial roles in the genetic decision. Bacterial riboswitches are prime examples of RNA regulators that control gene expression by altering their structure upon metabolite sensing. It was previously revealed that the thiamin pyrophosphate-sensing tbpA riboswitch in Escherichia coli cotranscriptionally adopts three main structures leading to metabolite sensing. Here, using single-molecule FRET, we characterize the transition in which the first nascent structure, a 5' stem-loop, is unfolded during transcription elongation to form the ligand-binding competent structure. Our results suggest that the structural transition occurs in a relatively abrupt manner, i.e., within a 1-2 nucleotide window. Furthermore, a highly dynamic structural exchange is observed, indicating that riboswitch transcripts perform rapid sampling of nascent co-occurring structures. We also observe that the presence of the RNAP stabilizes the 5' stem-loop along the elongation process, consistent with RNAP interacting with the 5' stem-loop. Our study emphasizes the role of early folding stem-loop structures in the cotranscriptional formation of complex RNA molecules involved in genetic regulation.
Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
Databáze: MEDLINE
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