Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

Abstract

Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant “downhill” pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design.

Mn2+-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches

“…effective K d ) and kinetic factors (e.g. RNA folding and RNA polymerase rate) within its folding window (Quarta et al, 2012). High concentrations (10 mM) of Mg 2+ could also induce transcription read-through (data not shown), presumably by favoring the bound-like aptamer structure, a typical observation in diverse riboswitch families (Hennelly et al, 2013; Holmstrom et al, 2014; Santner et al, 2012).…”

Single-molecule studies of riboswitch folding

“…Intermediate states expose details of the landscape that are particularly important for understanding those riboswitches that act co-transcriptionally . Because the competition between aptamer-and expression platform in this context is highly sensitive to the presence of kinetic traps, certain folding intermediates can play an outsized role in the regulatory decision, in a manner which cannot be handled satisfactorily by existing theoretical or computational approaches (however, recent work involving the prediction of different possible secondary structures during simulated elongation of nascent riboswitch RNAs shows promise [118, 119]). Studies of folding intermediates can also reveal the roles played by divalent cations (section 5.5 ) and the interplay between secondary and tertiary structure formation (section 5.4 ).…”

Kinetic regulation mechanism of pbuE riboswitch

“…But the post-transcriptional full-length pbuE riboswitch was found to be fixed in the ligand-incompetent structure even when adenine is at saturation level, 32,35,38 which suggested that the regulatory activity should be in the transcription process. During transcription elongation, because the upstream RNA section folds first, this will influence the folding pathway of the downstream RNA section.…”