HIV-1 Viral RNA Is Selected in the Form of Monomers that Dimerize in a Three-step Protease-dependent Process; the DIS of Stem–Loop 1 Initiates Viral RNA Dimerization

We have characterized the viral RNA conformation in wild-type, protease-inactive (PR–) and SL1-defective (ΔDIS) human immunodeficiency virus type 1 (HIV-1), as a function of the age of the viruses, from newly released to grown-up (≥24 h old). We report evidence for packaging HIV-1 genomic RNA (gRNA) in the form of monomers in PR– virions, viral RNA rearrangement (not maturation) within PR– HIV-1, protease-dependent formation of thermolabile dimeric viral RNAs, a new form of immature gRNA dimer at about 5 h post virion release, and slow-acting dimerization signals in SL1-defective viruses. The rates of gRNA dimer formation were ≥3-fold and ≥10-fold slower in ΔDIS and PR– viruses than in wild-type, respectively. Thus, the DIS, i.e. the palindrome in the apical loop of SL1, is a dimerization initiation signal, but its role can be masked by one or several slow-acting dimerization site(s) when grown-up SL1-inactive virions are investigated. Grown-up PR– virions are not flawless models for immature virions because gRNA dimerization increases with the age of PR– virions, indicating that the PR– mutation does not “freeze” gRNA conformation in a nascent primordial state. Our study is the first on gRNA conformation in newly released mutant or primate retroviruses. It shows for the first time that the packaged retroviral gRNA matures in more than one step, and that formation of immature dimeric viral RNA requires viral protein maturation. The monomeric viral RNAs isolated from budding HIV-1, as modeled by newly released PR– virions, may be seen as dimers that are much more fragile than thermolabile dimers.