Aspects of HIV-1 Assembly That Promote Primer TRNA(Lys3) Annealing to Viral RNA

The major cellular tRNA(Lys) isoacceptors are tRNA(Lys1,2) and tRNA(Lys3). During the replication of human immunodeficiency virus 1 (HIV-1), tRNA(Lys3) is used to prime reverse transcription of the viral RNA genome into double-stranded DNA, which is then integrated into the host genome. The annealing of tRNA(Lys3) to 5'-terminal sequences of viral RNA is multi-staged, with an initial poor quality, cytoplasmic annealing promoted by the Gag precursor protein, followed by a more effective annealing imposed upon the Gag-annealed tRNA(Lys3) that occurs after viral protein processing, and that is facilitated by mature nucleocapsid (NCp7). The initial annealing by Gag is assisted by the architecture of an early viral assembly intermediate we term the "tRNA(Lys3) annealing complex" whose composition includes Gag, GagPol, viral RNA, lysyl-tRNA synthetase (LysRS), and the tRNA(Lys) isoacceptors. Our model proposes that the reverse transcriptase sequences in GagPol bind all tRNAs non-specifically, and that the cytoplasmic tRNA population to which GagPol is exposed is enriched in tRNA(Lys) isoacceptors due to a specific interaction between Gag and LysRS. We further predict a protein conformation within the annealing complex that not only promotes this tRNA(Lys) enrichment, but that also facilitates the transfer of tRNA(Lys3) from GagPol to the viral RNA where annealing is carried out by nucleocapsid sequences within Gag.