A sequence similar to tRNA3Lys gene is embedded in HIV-1 U3/R and promotes minus strand transfer

Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.
Nature Structural & Molecular Biology (Impact Factor: 13.31). 12/2009; 17(1):83-9. DOI: 10.1038/nsmb.1687
Source: PubMed


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 viral sequences of similar length. 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 9-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 9 nucleotides, further increases transfer efficiency. We propose that a gene encoding tRNA(3)(Lys) was incorporated during HIV-1 evolution and retained, largely intact, because of its roles in transcription and strand transfer.

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Available from: Dorota Piekna-Przybylska,
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    • "The RNA template representing the 5' end of HIV-1 RNA included only the first 199nt, as sequences beyond the PBS in the 3' direction also stimulated transfer (Piekna-Przybylska et al., 2010; Song et al., 2009). Alteration or deletion of motif 9 and segment 1 reduced the efficiency of minus strand transfer from about 70% to just about 10%, supporting their proposed role in transfer (Piekna-Przybylska et al., 2010). "
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