An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding.

Matan Drory Retwitzer,Danny Barash,Supratim Sengupta,Ilona Kifer,Zohar Yakhini,Tamir Tuller

doi:10.1371/journal.pone.0134262

Abstract

Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is to find additional eukaryotic riboswitches since more than 20 riboswitch classes have been found in prokaryotes but only one class has been found in eukaryotes. Moreover, this single known class of eukaryotic riboswitch, namely the TPP riboswitch class, has been found in bacteria, archaea, fungi and plants but not in animals. The few examples of eukaryotic riboswitches were identified using sequence-based bioinformatics search methods such as a combination of BLAST and pattern matching techniques that incorporate base-pairing considerations. None of these approaches perform energy minimization structure predictions. There is a clear motivation to develop new bioinformatics methods, aside of the ongoing advances in covariance models, that will sample the sequence search space more flexibly using structural guidance while retaining the computational efficiency of sequence-based methods. We present a new energy minimization approach that transforms structure-based search into a sequence-based search, thereby enabling the utilization of well established sequence-based search utilities such as BLAST and FASTA. The transformation to sequence space is obtained by using an extended inverse RNA folding problem solver with sequence and structure constraints, available within RNAfbinv. Examples in applying the new method are presented for the purine and preQ1 riboswitches. The method is described in detail along with its findings in prokaryotes. Potential uses in finding novel eukaryotic riboswitches and optimizing pre-designed synthetic riboswitches based on ligand simulations are discussed. The method components are freely available for use.

Highlights

OverviewGenetic control of fundamental processes such as transcription, translation, and splicing is a complex process, and is in many cases mediated by proteins that monitor the environment and selectively bind to targets
It is an RNA element that responds to concentration changes of thiamin pyrophosphate (TPP) with a conformational rearrangement that affects transcription termination in Bacillus subtilis and translation initiation in Escherichia coli
The structural basis and biochemical properties of several of these riboswitches have been elucidated at high resolution

Summary

Introduction

OverviewGenetic control of fundamental processes such as transcription, translation, and splicing is a complex process, and is in many cases mediated by proteins that monitor the environment and selectively bind to targets. Cis-acting RNA genetic control elements have been discovered that are capable of directly sensing small ligands thereby playing a regulatory role by switching conformational states without the participation of proteins. The first experimental validations were published in 2002 [1,2,3,4], conserved sequence patterns in the 5' UTRs of bacteria were identified several years earlier using comparative analysis of the upstream regions of several genes expected to be co-regulated These studies contributed to the description of the RFN element [5], the S-box [6] and the THI-box [7]. The conserved sequence and structure of the aptamer domain can identify riboswitches with analogy to a fingerprint, a fact that can be utilized by structure-based bioinformatics search methods that involve sequence considerations

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Conclusion