A sequence similar to tRNA(3)(Lys) gene is embedded in HIV-1 U3/R and promotes minus strand transfer

We identified a sequence embedded in the U3/R region of HIV-1 RNA that is highly complementary to human tRNA(3)(Lys). The free energy of annealing to tRNA(3)(Lys) is significantly lower for this sequence and the primer-binding site than for other similar length viral sequences. The only interruption in complementarity is a 29-nucleotide segment inserted where a tRNA intron would be expected. The insert contains the TATA box for viral RNA transcription. The embedded sequence includes a nine-nucleotide segment previously reported to aid minus strand transfer by binding the primer tRNA(3)(Lys). Reconstituting transfer in vitro, we show that including segments from the embedded sequence in the acceptor template, beyond the nine nucleotides, further increases transfer efficiency. We propose that a tRNA(3)(Lys) gene was incorporated during HIV-1 evolution and retained largely intact because of its roles in transcription and strand transfer.