Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates
Journal
Molecular Cell
Journal Volume
81
Journal Issue
4
Pages
870-8830000000000
Date Issued
2021
Author(s)
Abstract
Experimentally guided multi-scale modeling of the cotranscriptional folding pathway of the E. coli signal recognition particle (SRP) RNA reveals that it undergoes an internal toehold-mediated strand-displacement process that requires local structural fluctuations. An intermediate of this pathway is a substrate for RNase P, suggesting concurrent transcription and processing. © 2020 Elsevier Inc.The series of RNA folding events that occur during transcription can critically influence cellular RNA function. Here, we present reconstructing RNA dynamics from data (R2D2), a method to uncover details of cotranscriptional RNA folding. We model the folding of the Escherichia coli signal recognition particle (SRP) RNA and show that it requires specific local structural fluctuations within a key hairpin to engender efficient cotranscriptional conformational rearrangement into the functional structure. All-atom molecular dynamics simulations suggest that this rearrangement proceeds through an internal toehold-mediated strand-displacement mechanism, which can be disrupted with a point mutation that limits local structural fluctuations and rescued with compensating mutations that restore these fluctuations. Moreover, a cotranscriptional folding intermediate could be cleaved in vitro by recombinant E. coli RNase P, suggesting potential cotranscriptional processing. These results from experiment-guided multi-scale modeling demonstrate that even an RNA with a simple functional structure can undergo complex folding and processing during synthesis. © 2020 Elsevier Inc.
Subjects
cotranscriptional RNA folding; molecular dynamics; RNA; RNA fluctuations; RNA folding dynamics; RNA structure; SHAPE-seq; signal recognition particle; toehold strand displacement; transcription
Other Subjects
ribonuclease P; signal recognition particle; bacterial RNA; Escherichia coli protein; ribonuclease P; signal recognition particle; Article; Escherichia coli; gene rearrangement; in vitro study; molecular dynamics; nonhuman; point mutation; RNA cleavage; RNA conformation; RNA folding; RNA processing; RNA sequence; RNA synthesis; RNA transcription; chemistry; metabolism; Escherichia coli; Escherichia coli Proteins; Ribonuclease P; RNA Folding; RNA, Bacterial; Signal Recognition Particle
Type
journal article