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.

The bifurcated stem loop 4 (SL4) is crucial for efficient packaging of mouse mammary tumor virus (MMTV) genomic RNA

“…This observation lends support to the developing hypothesis that retroviral packaging determinants are dynamic in nature and require structural flexibility to allow successful recognition of the packaging substrate RNA that is most likely recognized as a dimer by the Gag proteins [5–7,49]. Thus, packaging signals may act as ‘structural switches’ that favor either translation or dimerization/packaging of the gRNA, and also help the virus differentiate between spliced and unspliced viral RNAs.…”

“…The specificity for gRNA during packaging, thus, has been ascribed to high-affinity interactions between the NC domain of Gag and the packaging signal [5–13]. We have made a similar observation in the case of MPMV, where genetic and structure-prediction analyses have suggested that either ssPurines (Region A) or its partially repeated but base-paired sequence (Region B) plays a crucial role in gRNA packaging, possibly by functioning as a NC binding site [32,33].…”

“…Interestingly, in almost all retroviruses, sequences augmenting gRNA dimerization and packaging have been mapped nearly to the same 100 to 400 nucleotides in the 5ʹ region of the gRNA [5–13], which also harbors the dimer linkage structure (DLS) [5,7–13]. Based on our findings, it is reasonable to propose that the bifurcated SL4 in MMTV packaging signal RNA that contains phylogenetically-conserved pal II and ssPurines [25] functions as a major dimerization and packaging determinant during MMTV gRNA packaging process, during which pal II initiates gRNA dimerization and ssPurines functions as a potential Gag binding site for specific incorporation of the dimeric RNA into the newly forming virus particles.…”

“…Accordingly, an early study suggested that MMTV harbors sequences responsible for gRNA packaging at the 5ʹ end of its genome [4]. Packaging signals in other retroviruses have been shown to fold into higher order structures comprising of various structural motifs [5–13]. For example, a well-defined 5ʹ region of the murine leukemia virus (MLV) and some other retroviruses has been found to be required as well as sufficient for gRNA packaging, since inclusion of these sequences in heterologous non-retroviral RNAs facilitates the packaging of these ‘foreign’ RNAs into viral particles [14–17].…”

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).…”