Dimeric RNA Recognition Regulates HIV-1 Genome Packaging

Abstract

How retroviruses regulate the amount of RNA genome packaged into each virion has remained a long-standing question. Our previous study showed that most HIV-1 particles contain two copies of viral RNA, indicating that the number of genomes packaged is tightly regulated. In this report, we examine the mechanism that controls the number of RNA genomes encapsidated into HIV-1 particles. We hypothesize that HIV-1 regulates genome packaging by either the mass or copy number of the viral RNA. These two distinct mechanisms predict different outcomes when the genome size deviates significantly from that of wild type. Regulation by RNA mass would result in multiple copies of a small genome or one copy of a large genome being packaged, whereas regulation by copy number would result in two copies of a genome being packaged independent of size. To distinguish between these two hypotheses, we examined the packaging of viral RNA that was larger (≈17 kb) or smaller (≈3 kb) than that of wild-type HIV-1 (≈9 kb) and found that most particles packaged two copies of the viral genome regardless of whether they were 17 kb or 3 kb. Therefore, HIV-1 regulates RNA genome encapsidation not by the mass of RNA but by packaging two copies of RNA. To further explore the mechanism that governs this regulation, we examined the packaging of viral RNAs containing two packaging signals that can form intermolecular dimers or intramolecular dimers (self-dimers) and found that one self-dimer is packaged. Therefore, HIV-1 recognizes one dimeric RNA instead of two copies of RNA. Our findings reveal that dimeric RNA recognition is the key mechanism that regulates HIV-1 genome encapsidation and provide insights into a critical step in the generation of infectious viruses.

Deciphering the Role of the Gag-Pol Ribosomal Frameshift Signal in HIV-1 RNA Genome Packaging

“…Recent studies demonstrated that most HIV-1 particles contain RNA genomes (30); furthermore, two copies of viral RNA forming a dimer are packaged even when the RNA size is one-third of the wild-type genome (48). These results support the hypothesis that recognition of one dimeric RNA by Gag is a key point of viral RNA encapsidation.…”

Distinct binding interactions of HIV-1 Gag to Psi and non-Psi RNAs: Implications for viral genomic RNA packaging

“…SL2 contains the splice donor site, critical for splicing of the viral RNA for translation of viral accessory proteins, and SL3 is a sequence shown to contribute to gRNA packaging (Clever and Parslow 1997;McBride and Panganiban 1997;Russell et al 2003) and high-affinity NC binding (De Guzman et al 1998;Athavale et al 2010). In HIV-1, genome packaging and dimerization are hypothesized to be coordinated processes, as virions contain only dimeric gRNA (Moore and Hu 2009;Nikolaitchik et al 2013). A model for the switch between translation and packaging has been proposed based on NMR spectroscopy data showing that the DIS loop of SL1 folds back and interacts with an upstream region in the viral RNA, thereby preventing dimerization of SL1 and promoting translation (Lu et al 2011a).…”

Transcriptional start site heterogeneity modulates the structure and function of the HIV-1 genome

“…These RNAs serve as the viral genome (gRNA) and are used as templates for reverse transcription during an early stage of the replication cycle. gRNAs are selected for packaging as dimers (6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22), enabling strand-transfermediated recombination during reverse transcription and facilitating genetic evolution under environmental and chemotherapeutic pressures (23).…”