title: A sequence similar to tRNA 3 Lys gene is embedded in HIV-1 U3-R and promotes minus-strand transfer.
abstract: 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.
authors: Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.
authors: Dorota
authors: D
authors: Piekna-Przybylska
authors: Laura
authors: L
authors: DiChiacchio
authors: David H
authors: DH
authors: Mathews
authors: Robert A
authors: RA
authors: Bambara
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000235:genetics; D012357:RNA, Transfer, Lys / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*; D016415:Sequence Alignment; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D009841:Oligonucleotides; D012357:RNA, Transfer, Lys; D012367:RNA, Viral