Nucleic Acids Research, Vol 25, Issue 20 4013-4017, Copyright © 1997 by Oxford University Press
B Berkhout
Reverse transcription of retroviral genomes is primed by a tRNA molecule
that anneals to an 18 nt primer binding site (PBS) on the viral RNA genome.
Additional base pair interactions between the tRNA primer and the viral RNA
have been proposed. In particular, base pairing was proposed between the
anticodon loop of tRNALys3 and the 'A- rich' loop of a hairpin located
immediately upstream of the PBS site in HIV-1 RNA. In order to judge the
importance of this sequence/structure motif, we performed an extensive
phylogenetic analysis of this genomic region in a variety of simian and
human immunodeficiency viruses (SIV and HIV). Both the phylogeny of natural
HIV/SIV sequences and the behaviour of U5-PBS mutant/revertant viruses
support the idea that this RNA structure is critical for virus replication.
Although this hairpin may play a role in tRNA annealing and/or initiation
of reverse transcription, the proposed base pairing interaction between the
A-rich loop of the HIV-1 hairpin and the anticodon of the initiator tRNA is
not directly supported by this analysis.
ARTICLES
The primer binding site on the RNA genome of human and simian immunodeficiency viruses is flanked by an upstream hairpin structure
Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, PO Box 22700, 1100 DE Amsterdam, The Netherlands. b.berkhout@amc.uva.nl
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