Reverse transcription of the HIV-1 RNA genome is primed by
the cellular tRNAlys3 molecule that anneals to a
complementary sequence in the viral genome, the primer-binding
site (PBS). Additional interactions between the tRNA primer
and the viral RNA were proposed to play a role in reverse
transcription. We recently identified an 8-nt element in the
U5 region upstream of the PBS that is critical for initiation
and processive elongation of reverse transcription. This motif
was termed the primer activation signal (PAS), and is proposed
to interact with the “antiPAS sequence” in the TΨC
arm of tRNAlys3. In this study, we demonstrate that
the efficiency of initiation of reverse transcription can be
modulated by PAS mutations that strengthen or weaken the
interaction with antiPAS. These results provide further evidence
for a direct base-pairing interaction between the PAS in the
viral RNA and the antiPAS in the tRNAlys3 molecule.
A broad phylogenetic survey indicated that a PAS element is
present in all retroviral RNA genomes, suggesting that the process
of reverse transcription is regulated by a common mechanism
in all retroviridae. It has proven very difficult to change
the identity of the tRNA primer for HIV-1 reverse transcription
by changing the PBS sequence. Using in vitro reverse transcription
assays, we demonstrate that the identity of the priming tRNA
species can be switched by simultaneous alteration of the PBS
and PAS motifs to accommodate a new tRNA primer. These results
indicate that the PAS–antiPAS interaction is important
for both primer selection and efficient reverse transcription.