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J. Biol. Chem., Vol. 281, Issue 5, 2711-2720, February 3, 2006

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Dissection of a Circumscribed Recombination Hot Spot in HIV-1 after a Single Infectious Cycle^*

From the Unité de Régulation Enzymatique des Activités Cellulaires, CNRS-URA 2185, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France

Recombination is a major source of genetic heterogeneity in the human immunodeficiency virus type 1 (HIV-1) population. The main mechanism responsible for the generation of recombinant viruses is a process of copy choice between the two copies of genomic RNA during reverse transcription. We previously identified, after a single cycle of infection of cells in culture, a recombination hot spot within the gp120 gene, corresponding to the top portion of a RNA hairpin. Here, we determine that the hot region is circumscribed to 18 nucleotides located in the descending strand of the stem, following the sense of reverse transcription. Three factors appeared to be important, albeit at different extents, for the high rate of recombination observed in this region. The position of the hot sequence in the context of the RNA structure appears crucial, because changing its location within this structure triggered differences in recombination up to 20-fold. Another pivotal factor is the presence of a perfectly identical sequence between donor and acceptor RNA in the region of transfer, because single or double nucleotide differences in the hot spot were sufficient to almost completely abolish recombination in the region. Last, the primary structure of the hot region also influenced recombination, although with effects only in the 2-3-fold range. Altogether, these results provide the first molecular dissection of a hot spot in infected cells and indicate that several factors contribute to the generation of a site of preferential copy choice.

Received for publication, May 18, 2005 , and in revised form, November 14, 2005.

^* This work was supported by Grant ANRS 02172 from the French National Agency for AIDS Research (to M. N.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains a supplemental Figure.

¹ Recipient of a fellowship from Sidaction.

² To whom correspondence should be addressed. Tel.: 33-145-688-505; Fax: 33-145-688-399; E-mail: matteo{at}pasteur.fr.

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