Preferences for the selection of unique tRNA primers revealed from analysis of HIV-1 replication in peripheral blood mononuclear cells

Background: All human immunodeficiency virus (HIV-1) uses a host tRNA(Lys, 3) as the primer for reverse transcription. The tRNA(Lys, 3) is bound to a region on the HIV-1 genome, the primer-binding site (PBS), that is complementary to the 18 terminal nucleotides of tRNA(Lys, 3). How HIV-1 selects the tRNA from the intracellular milieu is unresolved. Results: HIV-1 tRNA primer selection has been investigated using viruses in which the primer-binding site ( PBS) and a sequence within U5 were altered so as to be complementary to tRNA(Met), tRNA(Pro) or tRNA(Ile). Analysis of the replication of these viruses in human peripheral blood mononuclear cells (PBMC) revealed preferences for the selection of certain tRNAs. HIV-1 with the PBS altered to be complementary to tRNA(Met), with and without the additional mutation in U5 to be complementary to the anticodon of tRNA(Met), stably maintains the PBS complementary to tRNA(Met) following extended in vitro culture in PBMC. In contrast, viruses with either the PBS or PBS and U5 mutated to be complementary to tRNA(Ile) were unstable during in vitro replication in PBMC and reverted to utilize tRNA(Lys, 3). Viruses with the PBS altered to be complementary to tRNA(Pro) replicated in PBMC but reverted to use tRNA(Lys, 3); viruses with mutations in both the U5 and PBS complementary to tRNA(Pro) maintained this PBS, yet replicated poorly in PBMC. Conclusion: The results of these studies demonstrate that HIV-1 has preferences for selection of certain tRNAs for high-level replication in PBMC.