Ribosome-induced RNA conformational changes in a viral 3\u2032-UTR sense and regulate translation levels

Siqi Tian,Andrea MacFadden,David A. Costantino,Jay C. Nix,Erik W. Hartwick,Rhiju Das,Jeffrey S. Kieft

doi:10.1038/s41467-018-07542-x

Abstract

Structured RNA elements, programmed RNA conformational changes, and interactions between different RNA domains underlie many modes of regulating gene expression, mandating studies to understand the foundational principles that govern these phenomena. Exploring the structured 3′ untranslated region (UTR) of a viral RNA, we discovered that different contexts of the 3′-UTR confer different abilities to enhance translation of an associated open reading frame. In one context, ribosome-induced conformational changes in a ‘sensor’ RNA domain affect a separate RNA ‘functional’ domain, altering translation efficiency. The structure of the entire 3′-UTR reveals that structurally distinct domains use a spine of continuously stacked bases and a strut-like linker to create a conduit for communication within the higher-order architecture. Thus, this 3′-UTR RNA illustrates how RNA can use programmed conformational changes to sense the translation status of an upstream open reading frame, then create a tuned functional response by communicating that information to other RNA elements.

Highlights

Structured RNA elements, programmed RNA conformational changes, and interactions between different RNA domains underlie many modes of regulating gene expression, mandating studies to understand the foundational principles that govern these phenomena
With a 39-nucleotide-long spacer, translation was enhanced relative to a reporter with the stop codon placed as the first three nucleotides in the upstream pseudoknot domain (UPD) (0-nucleotide-long) as in the subgenomic RNA (sgRNA) (Fig. 2b; all mutants used in this study are shown in Supplementary Fig. 2)
We propose that one domain acts as a ribosome sensor, communicating information to the other domain, which results in subtle changes in stability and subsequent changes in the ability of the 3′-untranslated region (UTR) to enhance translation

Summary

Introduction

Structured RNA elements, programmed RNA conformational changes, and interactions between different RNA domains underlie many modes of regulating gene expression, mandating studies to understand the foundational principles that govern these phenomena. The structure of the entire 3′-UTR reveals that structurally distinct domains use a spine of continuously stacked bases and a strut-like linker to create a conduit for communication within the higher-order architecture This 3′-UTR RNA illustrates how RNA can use programmed conformational changes to sense the translation status of an upstream open reading frame, create a tuned functional response by communicating that information to other RNA elements. The CP open reading frame (ORF) is translationally silent on the gRNA, and the sgRNA is generated from the negative-strand gRNA using the “tymobox” promoter[10,11,12] Both RNAs are 5′ capped, but rather than a 3′-poly(A) tail they end in the same two-folded RNA domains separated by a short unpaired linker[9,13] (Fig. 1b). The only direct three-dimensional structural analysis of the complete TYMV 3′-UTR is a smallangle x-ray scattering study that yielded low-resolution envelopes of its global structure[20], but an atomic-resolution structure of the intact 3′-UTR that could reveal the details of interdomain communication had not been previously solved

Objectives

Methods

Results

Conclusion