RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex.

Bhargavi Jayaraman,Isabel Ribeiro,David Mavor,Christina Homer,Alan D Frankel,David C Crosby

doi:10.7554/elife.04120

Bhargavi Jayaraman, Isabel Ribeiro + Show 4 more

Open Access

https://doi.org/10.7554/elife.04120

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Journal: eLife	Publication Date: Dec 8, 2014
Citations: 64	License type: CC BY 4.0

Affiliation: University of California, San Francisco

Abstract

The HIV-1 protein Rev controls a critical step in viral replication by mediating the nuclear export of unspliced and singly-spliced viral mRNAs. Multiple Rev subunits assemble on the Rev Response Element (RRE), a structured region present in these RNAs, and direct their export through the Crm1 pathway. Rev-RRE assembly occurs via several Rev oligomerization and RNA-binding steps, but how these steps are coordinated to form an export-competent complex is unclear. Here, we report the first crystal structure of a Rev dimer-RRE complex, revealing a dramatic rearrangement of the Rev-dimer upon RRE binding through re-packing of its hydrophobic protein-protein interface. Rev-RNA recognition relies on sequence-specific contacts at the well-characterized IIB site and local RNA architecture at the second site. The structure supports a model in which the RRE utilizes the inherent plasticity of Rev subunit interfaces to guide the formation of a functional complex.

Highlights

Retroviruses such as HIV have small genomes and utilize multiple strategies such as overlapping reading frames and alternative splicing, to encode their repertoire of proteins
For the RNA, we utilized variants of Rev Response Element (RRE) IIB40, which has the high-affinity IIB site positioned adjacent to a second site that mimics the stem II junction (Daugherty et al, 2008) (Figure 1C, Figure 1—figure supplement 1), and variants of a 68-nucleotide fragment comprising stems IIA, IIB and IIC
Our structure of the RevRRE complex illustrates a direct physical coupling between RNA binding and protein oligomerization, where RNA binding drastically alters the conformational state of the Rev dimer

Summary

Introduction

Retroviruses such as HIV have small genomes and utilize multiple strategies such as overlapping reading frames and alternative splicing, to encode their repertoire of proteins. The ∼9 kb HIV-1 genome codes for 15 proteins expressed from a set of unspliced and singly-spliced mRNAs in addition to the fully spliced messages (Frankel and Young, 1998) These unspliced and singly-spliced species encode the viral structural and accessory proteins and genomic RNA needed to assemble new virions, but because they contain introns are typically retained in the nucleus for splicing. To export these RNAs to the cytoplasm, the viral protein Rev (Figure 1A), expressed from a fully spliced message, translocates into the nucleus, forms an oligomeric complex on a ∼350 nucleotide, highly structured intronic RNA element, the Rev Response Element (RRE) (Figure 1B), and directs their export through the Crm nuclear export pathway (Fornerod et al, 1997; Pollard and Malim, 1998).

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Conclusion