Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes.

Claus O. Wilke,Christopher A. Lavender,Kevin M. Weeks,Robert J. Gorelick

doi:10.1371/journal.pcbi.1004230

Abstract

HIV and related primate lentiviruses possess single-stranded RNA genomes. Multiple regions of these genomes participate in critical steps in the viral replication cycle, and the functions of many RNA elements are dependent on the formation of defined structures. The structures of these elements are still not fully understood, and additional functional elements likely exist that have not been identified. In this work, we compared three full-length HIV-related viral genomes: HIV-1NL4-3, SIVcpz, and SIVmac (the latter two strains are progenitors for all HIV-1 and HIV-2 strains, respectively). Model-free RNA structure comparisons were performed using whole-genome structure information experimentally derived from nucleotide-resolution SHAPE reactivities. Consensus secondary structures were constructed for strongly correlated regions by taking into account both SHAPE probing structural data and nucleotide covariation information from structure-based alignments. In these consensus models, all known functional RNA elements were recapitulated with high accuracy. In addition, we identified multiple previously unannotated structural elements in the HIV-1 genome likely to function in translation, splicing and other replication cycle processes; these are compelling targets for future functional analyses. The structure-informed alignment strategy developed here will be broadly useful for efficient RNA motif discovery.

Highlights

RNA plays a direct role in most biological processes [1], and multiple examples of RNA function are found in the replication cycles of positive-strand RNA lentiviruses [2]
Replication and pathogenesis of human immunodeficiency virus (HIV) is governed by information encoded in its singlestranded RNA genome
In addition to coding for viral proteins, the HIV genomic RNA forms base paired and higher-order structures that are critical for viral replication

Summary

Introduction

RNA plays a direct role in most biological processes [1], and multiple examples of RNA function are found in the replication cycles of positive-strand RNA lentiviruses [2]. Viral RNA genomes function at two distinct levels: in the linear encoding of protein sequences and in functional higher-order RNA structures. RNA elements in the human immunodeficiency virus (HIV) genome play important regulatory roles throughout the replication cycle. During transcription of the integrated viral genome, a stem-loop structure in the 50 untranslated region (UTR), called TAR, binds the Tat protein to recruit proteins involved in transcription [3, 4]. Stem-loop structures in the Psi packaging element are required for efficient packaging of viral genome into nascent virions [8]. It remains difficult to rigorously identify conserved RNA structure motifs when sequence conservation is low without meticulous hand-alignment of annotated sequences

Methods

Results

Discussion

Conclusion