The Structure of HIV-1 Genomic RNA in the gp120 Gene Determines a Recombination Hot Spot in Vivo

Abstract

By frequently rearranging large regions of the genome, genetic recombination is a major determinant in the plasticity of the human immunodeficiency virus type I (HIV-1) population. In retroviruses, recombination mostly occurs by template switching during reverse transcription. The generation of retroviral vectors provides a means to study this process after a single cycle of infection of cells in culture. Using HIV-1-derived vectors, we present here the first characterization and estimate of the strength of a recombination hot spot in HIV-1 in vivo. In the hot spot region, located within the C2 portion of the gp120 envelope gene, the rate of recombination is up to ten times higher than in the surrounding regions. The hot region corresponds to a previously identified RNA hairpin structure. Although recombination breakpoints in vivo cluster in the top portion of the hairpin, the bias for template switching in this same region appears less marked in a cell-free system. By modulating the stability of this hairpin we were able to affect the local recombination rate both in vitro and in infected cells, indicating that the local folding of the genomic RNA is a major parameter in the recombination process. This characterization of reverse transcription products generated after a single cycle of infection provides insights in the understanding of the mechanism of recombination in vivo and suggests that specific regions of the genome might be prompted to yield different rates of evolution due to the presence of circumscribed recombination hot spots.

Evidence of a novel RNA secondary structurein the coding region of HIV-1 pol gene

“…One possibility in the literature is that it might assist recombination. The predicted structure is similar to a secondary structure whose role in recombination in HIV has been well studied (Galetto et al 2004). They both contain an z20-bp-long stem at the base (Fig.…”

“…They all have been found to play important roles in HIV transcription. In addition, it has been reported that an RNA secondary structure in the gp120 gene facilitated recombination, creating a recombination hot spot in HIV (Moumen et al 2001;Galetto et al 2004). All these studies suggest that RNA secondary structure in HIV plays important roles in the viral life cycle.…”

Identification of a major restriction in HIV-1 intersubtype recombination

“…Therefore, in order for HIV-1 intersubtype recombination to occur, the RNAs of the two subtypes of viruses must be copackaged into the same virion and recombination must occur during reverse transcription. We and others (13)(14)(15)(21)(22)(23)(24)(25) have examined HIV-1 recombination with subtype B-based vectors. Although there is ample evidence among the circulating variants (1) and cell culture experiments (26,27) to indicate that intersubtype recombination could occur, very little is known about the rates and limitations of recombination between different HIV-1 subtypes.…”

Phylogenetic Mapping of Recombination Hotspots in Human Immunodeficiency Virus via Spatially Smoothed Change-Point Processes

“…Since local sequence motifs have been long suspected to promote HIV recombination (Balakrishnan et al 2001;Moumen et al 2001Moumen et al , 2003Negroni and Buc 2001;Galetto et al 2004), we examine this part of the HIV genome for the presence of known motifs. One of the HIV instability elements, denoted as INS2-M6 by Schneider et al (1997), covers sites [564,609] of our master alignment (see Figure 3).…”

“…Following Bernardinelli et al (1995) we express our prior belief about v in terms of a ratio of recombination probabilities p i =p j % e g i Àg j . On the basis of in vitro HIV recombination detection experiments (Moumen et al 2001;Dykes et al 2004;Galetto et al 2004) we expect that site recombination probabilities should not vary more than sevenfold or equivalently that recombination log odds should not differ by .2. Since our smoothing prior implies that …”