Retroviral RNA Dimerization and Packaging: The What, How, When, Where, and Why

Retroviral genomic RNAs (gRNAs) are packaged as dimers, joined near their 59 ends in non-covalent linkages that withstand modest heat treatment but dissociate at ,65uC. Determinants of gRNA dimerization and recruitment for packaging map to the same ,100 to ,300 base regions and are, for the most part, physically and genetically inseparable [1]. Synthetic RNAs containing these sequences dimerize in vitro. Because transplanting these sequences onto a cell mRNA confers selective packaging, and ablating them greatly reduces gRNA packaging, these sequences are known as Y (psi), for ‘‘packaging signal’’ (Figure 1A) [2]. Within virions, gRNAs are coated with a basic viral protein called nucleocapsid (NC) at a density of about one NC per five to eight RNA bases [3]. This nucleoprotein complex resides within the mature virion core. Total gRNA length, were it in an A-helix, exceeds the core inner diameter by more than 30-fold [4]. Thus, encapsidated gRNA is highly condensed. The co-packaged gRNAs likely are not aligned along their lengths because they are identical and cannot basepair in register, but the nature of their compaction is unknown. If Y is experimentally removed from gRNA but viral proteins are still expressed, morphologically normal virions can form, which are devoid of gRNA. These contain random samples of host mRNA [5]. Each Y+ or Y2 virion also contains several copies of certain host RNAs such as 7SL, the RNA scaffold of signal recognition particles. Other than the primer tRNA, any roles of these host non-coding RNAs in retroviruses are unknown. Usually, a virion’s two gRNAs are identical. However, if a producer cell contains two distinct dimer-compatible proviruses, virions can contain gRNA heterdimers. Both gRNAs are genetically complete but not intact, as they appear to contain nicks and run as smears on denaturing gels. Accordingly, it has been speculated that retroviruses’ dimeric genome organization may serve in part as defense against antiviral nucleases that would otherwise restrict replication [4]. RNA degradation during reverse transcription further limits provirus synthesis to one or fewer per virion [6]. Transmission of no more than one allele at each locus explains why, although they package two gRNAs, retroviruses are not truly diploid.