Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops.

Luigi D'Ascenzo,Quentin Vicens,Pascal Auffinger,Filip Leonarski

doi:10.1261/rna.059097.116

Abstract

When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops that do not fold as expected. We noticed that when a GNRA does not assume its “natural” fold, it adopts the one we typically associate with a UNCG sequence. The same folding interconversion may occur for loops with UNCG sequences, for instance within tRNA anticodon loops. Hence, we show that some structured tetranucleotide sequences starting with G or U can adopt either of these folds. The underlying structural basis that defines these two fold types is the mutually exclusive stacking of a backbone oxygen on either the first (in GNRA) or the last nucleobase (in UNCG), generating an oxygen–π contact. We thereby propose to refrain from using sequences to distinguish between loop conformations. Instead, we suggest using descriptors such as U-turn (for “GNRA-type” folds) and a newly described Z-turn (for “UNCG-type” folds). Because tetraloops adopt for the largest part only two (inter)convertible turns, we are better able to interpret from a structural perspective loop interchangeability occurring in ribosomes and viral RNA. In this respect, we propose a general view on the inclination for a given sequence to adopt (or not) a specific fold. We also suggest how long-noncoding RNAs may adopt discrete but transient structures, which are therefore hard to predict.

Highlights

RNA architecture is modular and hierarchical, which implies that secondary structural elements such as double stranded helices, hairpins, and single-stranded loops are linked by tertiary interactions that guide the assembly process (Hendrix et al 2005; Cruz and Westhof 2009; Butcher and Pyle 2011)
We present structural evidence that challenges these expectations by identifying GNRA sequences that adopt a UNCG fold and vice versa, both in tetraloops closed by a Watson–Crick base pair and in tetraloop-like motifs embedded in larger ribosomal and tRNA loops (Auffinger and Westhof 2001)
This loop dimorphism remains rare within the pool of RNAs for which we currently possess 3D data, it led us to question some basic assumptions we make about RNA folding and structure prediction. To better characterize these interconversions, we propose a more general structure-based tetraloop and tetraloop-like identification scheme that involves on one side the classical and well-described U-turn (Gutell et al 2000) and, on the other, a newly defined “Z-turn,” which is based on the UNCG tetraloop fold and the Z-RNA CpG step it encompasses (D’Ascenzo et al 2016)

Summary

Introduction

RNA architecture is modular and hierarchical, which implies that secondary structural elements such as double stranded helices, hairpins, and single-stranded loops are linked by tertiary interactions that guide the assembly process (Hendrix et al 2005; Cruz and Westhof 2009; Butcher and Pyle 2011). These tetranucleotide loops adopt distinctive folds that involve extensive and well-described networks of hydrogen bonds and stacking interactions (Cheong et al 1990; Heus and Pardi 1991; Allain and Varani 1995; Jucker and Pardi 1995a; Jucker et al 1996; Ennifar et al 2000; Correll and Swinger 2003; Nozinovic et al 2010).

Results

Conclusion