New insights into the formation of HIV-1 reverse transcription initiation complex

HIV-1 reverse transcriptase uses the host tRNA3Lys as a primer for the synthesis of the minus DNA strand. The first event in viral replication is thus the annealing of tRNA to the primer binding site (PBS) in the 5′ UTR of the viral RNA. This event requires a major RNA rearrangement which is chaperoned by the viral NC protein. The binding of NC to nucleic acids is essentially non-specific, however, NC is known to bind selectively to hairpins located in the 5′ region of the viral RNA. In a previous study, using an NMR approach in which the reaction is slowed down by controlling temperature, we were able to follow details in this RNA unfolding/refolding process and to uncover an intermediate state. We showed that annealing initiates at the junction between the acceptor and the TΨC stems, and that, at physiological temperature, complete annealing is reached only in the presence of NC, probably when the zinc fingers contact the TΨC/D loops.In the present work, we have refined our model of the formation of the tRNA3Lys/PBS duplex. First, we show that annealing can initiate both from the single-stranded CCA 3′-end bases of the acceptor stem and from the bases in the TΨC stem. Secondly, by NMR and fluorescence spectroscopy, we have studied the complex between the NC protein and RNA hairpins that mimic the D and T arms of the tRNA3Lys. Interestingly, the NC protein shows strong and specific binding to the D arm of tRNA3Lys, which could explain the overall annealing mechanism.