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BY 4.0 license Open Access Published by De Gruyter Open Access November 15, 2019

Towards an understanding of RNA structural modalities: a riboswitch case study

Hee Rhang Yoon , Aaztli Coria , Alain Laederach and Christine Heitsch

Abstract

A riboswitch is a type of RNA molecule that regulates important biological functions by changing structure, typically under ligand-binding. We assess the extent that these ligand-bound structural alternatives are present in the Boltzmann sample, a standard RNA secondary structure prediction method, for three riboswitch test cases. We use the cluster analysis tool RNAStructProfiling to characterize the different modalities present among the suboptimal structures sampled. We compare these modalities to the putative base pairing models obtained from independent experiments using NMR or fluorescence spectroscopy. We find, somewhat unexpectedly, that profiling the Boltzmann sample captures evidence of ligand-bound conformations for two of three riboswitches studied. Moreover, this agreement between predicted modalities and experimental models is consistent with the classification of riboswitches into thermodynamic versus kinetic regulatory mechanisms. Our results support cluster analysis of Boltzmann samples by RNAStructProfiling as a possible basis for de novo identification of thermodynamic riboswitches, while highlighting the challenges for kinetic ones.

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Received: 2019-07-22
Accepted: 2019-10-10
Published Online: 2019-11-15

© 2019 Hee Rhang Yoon et al., published by De Gruyter

This work is licensed under the Creative Commons Attribution 4.0 Public License.

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