Life of psi: how full-length HIV-1 RNAs become packaged genomes in the viral particles

Abstract

As a member of the retrovirus family, HIV-1 packages its RNA genome into particles and replicates through a DNA intermediate that integrates into the host cellular genome. The multiple genes encoded by HIV-1 are expressed from the same promoter and their expression is regulated by splicing and ribosomal frameshift. The full-length HIV-1 RNA plays a central role in viral replication as it serves as the genome in the progeny virus and is used as the template for Gag and GagPol translation. In this review, we summarize findings that contribute to our current understanding of how full-length RNA is expressed and transported, cis- and trans-acting elements important for RNA packaging, the locations and timing of RNA:RNA and RNA:Gag interactions, and the processes required for this RNA to be packaged into viral particles.

Keywords: Full-length RNA; Gag; HIV-1; RNA dimerization; RNA export; RNA packaging; RNA transcription and processing; RRE; Retrovirus; Rev; Virus assembly.

Figure 1. HIV-1 generates multiple RNA species through splicing

A single promoter from upstream LTR drives HIV-1 transcription. Along with the unspliced full-length transcript several alternatively spliced transcripts are generated depending on the number of splicing events that occur and which splice sites are selected. The dashed lines connect the major splice donor sites to the appropriate splice acceptor. The proteins expressed by these RNA species are indicated on the left.

Figure 2. Nuclear export mechanism of full-length and partially spliced HIV-1 RNA

Viral protein Rev serves as a bridge that recruits Crm1and RanGTP to intron-containing HIV-1 RNAs by binding to the RRE. The Rev-RRE-Crm1-RanGTP complex moves through the nuclear pore complex (NPC). Once in cytoplasm, RanGap and RanBP1 lead to hydrolysis of Ran-associated GTP into GDP causing the dissociation of the export complex and the release of HIV-1 RNA. Although not shown, other host proteins, such as DDX3, may be involved in the nuclear export process (Figure not drawn to scale).

Figure 3. Cis- and trans- factors of HIV-1 RNA packaging

(A) and (B) Two models of the HIV-1 5’ leader RNA secondary structures favoring translation (left) or RNA dimerization and packaging (right). AUG start codon of gag (green), DIS (red), Ψ (purple), U5 (red). (A) Conformation switch of the HIV-1 5’ leader RNA proposed by the Berkhout group (Abbink and Berkhout, 2003). In the long distance interaction (LDI) structure (left) the DIS sequence is sequestered through base-pair interactions with the Poly(A). However, in the branched multiple hairpin (BMH) structure (right) the AUG start codon of gag binds the U5 region, exposing the DIS sequence and promoting RNA dimerization and packaging. (B) Conformation switch proposed by the Summers group (Lu et al., 2011). Alternative RNA secondary structures of the HIV-1 5’ leader RNA favoring translation (left) in which DIS is base-paired with the U5 region or dimerization and packaging (right) in which the AUG base-pairs with the U5 region the DIS sequence is exposed. (C) Domains of the HIV-1 Gag polyprotein. MA (Matrix), CA (Capsid), SP1 (Spacer 1), NC (Nucleocapsid), SP2 (Spacer 2), p6.