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Nucleic Acids Research 2006 34(8):2206-2218; doi:10.1093/nar/gkl226
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Published online 2 May 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Hairpin-induced tRNA-mediated (HITME) recombination in HIV-1

Pavlina Konstantinova, Peter de Haan1, Atze T. Das and Ben Berkhout*

Department of Human Retrovirology, Academic Medical Center, University of Amsterdam Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands 1 Viruvation B. V. Wassenaarseweg 72 2333 AL Leiden, The Netherlands

*To whom correspondence should be addressed. Tel: +31 20 566 4822; Fax: +31 20 691 6531; Email: b.berkhout{at}amc.uva.nl

Received January 24, 2006. Revised February 23, 2006. Accepted March 27, 2006.

Recombination due to template switching during reverse transcription is a major source of genetic variability in retroviruses. In the present study we forced a recombination event in human immunodeficiency virus type 1 (HIV-1) by electroporation of T cells with DNA from a molecular HIV-1 clone that has a 300 bp long hairpin structure in the Nef gene (HIV-lhNef). HIV-lhNef does not replicate, but replication-competent escape variants emerged in four independent cultures. The major part of the hairpin was deleted in all escape viruses. In three cases, the hairpin deletion was linked to patch insertion of tRNAasp, tRNAglu or tRNAtrp sequences. The tRNAs were inserted in the viral genome in the antisense orientation, indicating that tRNA-mediated recombination occurred during minus-strand DNA synthesis. We here propose a mechanistic model for this hairpin-induced tRNA-mediated (HITME) recombination. The transient role of the cellular tRNA molecule as enhancer of retroviral recombination is illustrated by the eventual removal of inserted tRNA sequences by a subsequent recombination/deletion event.


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