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

Galetto, Román; Giacomoni, Véronique; Véron, Michel; Negroni, Matteo

doi:10.1074/jbc.m505457200

Cited by 44 publications

(50 citation statements)

References 51 publications

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“…This is in agreement with studies showing that recombination rates depend on a complex set of factors, such as the availability of nucleotide (nt) substrates (25)(26)(27), the RNA template itself (7,12,28), overall sequence similarity (6,7,10,12), and local sequence context of recombining sequences (28)(29)(30). Using both in vitro assays and single-cycle HIV-1 vectors, recombination hot spots have been identified in the untranslated regions (UTRs) (30)(31)(32), in gag (29,33), and in env (28,34). However, only limited information on recombination is available within other regions of the HIV-1 genome (33).…”

supporting

confidence: 65%

“…There have been many studies showing that even in the absence of selection, recombination does not occur randomly on the HIV-1 genome, highlighting the presence of additional factors governing the recombination process (11,19,(28)(29)(30)(31)(32)(33)(34)(35)59). However, many of these studies do not measure recombination rate in their natural genome context, or they measure recombination between highly divergent genomes that may not be most representative of the situation in vivo, where we expect recombination between closely related members of the viral quasispecies.…”

Section: Discussionmentioning

confidence: 99%

“…Interestingly, this hot region, P H 19 to P H 21, corresponds exactly to some of the most highly structured RNA in the HIV-1 genome, as measured by selective 2=-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry (63). Indeed, RNA structures are proposed to favor recombination by causing reverse transcriptase to pause on the template (12,27,(64)(65)(66), and mechanistic studies demonstrate that the presence of RNA structure is often a feature of recombination hot spots (34,67). It has been previously reported that HIV-1 gene junctions are both enriched in RNA structure and thus more recombinogenic than other regions of the HIV-1 genome (61,63).…”

Section: Discussionmentioning

confidence: 99%

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Identifying Recombination Hot Spots in the HIV-1 Genome

Smyth

Schlub

Grimm

et al. 2014

J Virol

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HIV-1 infection is characterized by the rapid generation of genetic diversity that facilitates viral escape from immune selection and antiretroviral therapy. Despite recombination's crucial role in viral diversity and evolution, little is known about the genomic factors that influence recombination between highly similar genomes. In this study, we use a minimally modified fulllength HIV-1 genome and high-throughput sequence analysis to study recombination in gag and pol in T cells. We find that recombination is favored at a number of recombination hot spots, where recombination occurs six times more frequently than at corresponding cold spots. Interestingly, these hot spots occur near important features of the HIV-1 genome but do not occur at sites immediately around protease inhibitor or reverse transcriptase inhibitor drug resistance mutations. We show that the recombination hot and cold spots are consistent across five blood donors and are independent of coreceptor-mediated entry. Finally, we check common experimental confounders and find that these are not driving the location of recombination hot spots. This is the first study to identify the location of recombination hot spots between two similar viral genomes with great statistical power and under conditions that closely reflect natural recombination events among HIV-1 quasispecies. IMPORTANCEThe ability of HIV-1 to evade the immune system and antiretroviral therapy depends on genetic diversity within the viral quasispecies. Retroviral recombination is an important mechanism that helps to generate and maintain this genetic diversity, but little is known about how recombination rates vary within the HIV-1 genome. We measured recombination rates in gag and pol and identified recombination hot and cold spots, demonstrating that recombination is not random but depends on the underlying gene sequence. The strength and location of these recombination hot and cold spots can be used to improve models of viral dynamics and evolution, which will be useful for the design of robust antiretroviral therapies.

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supporting

confidence: 65%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Identifying Recombination Hot Spots in the HIV-1 Genome

Smyth

Schlub

Grimm

et al. 2014

J Virol

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“…In the present study, data from acceptor cleavage provide evidence that at least a portion of transfers occur as a consequence of acceptor invasion early in the region of homology. Single-stranded regions within the acceptor are proposed to favor the acceptor-cDNA interaction or "docking" step (42,46,60,66). In our template system, the absence of strong secondary structures within the proposed invasion site in the acceptor template correlated with efficient transfers compared with the poor transfers when the invasion site in the acceptor was part of a stable secondary structure (42).…”

Section: Discussionmentioning

confidence: 92%

Insights into the Multiple Roles of Pausing in HIV-1 Reverse Transcriptase-promoted Strand Transfers

Gao¹,

Balakrishnan²,

Roques

et al. 2007

Journal of Biological Chemistry

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We previously analyzed the role of pausing induced by hairpin structures within RNA templates in facilitating strand transfer by HIV-1 RT (reverse transcriptase). We proposed a multistep transfer mechanism in which pause-induced RNase H cuts within the initial RNA template (donor) expose regions of cDNA. A second homologous RNA template (acceptor) can interact with the cDNA at such sites, initiating transfer. The acceptor-cDNA hybrid is thought to then propagate by branchmigration, eventually catching up with the primer terminus and completing the transfer. The prominent pause site in the template system facilitated acceptor invasion; however, very few of the transfers terminated at this pause. To examine the effects of homology on pause-promoted transfer, we increased template homology before the pause site, from 19 nucleotides (nt) in the initial template system to 52 nt in the new system. Significantly, the increased homology enhanced transfers 3-fold, with 32% of the transfers now terminating at the pause site. Additionally, the acceptor cleavage profile indicated the creation of a new invasion site in the added region of homology. NC (nucleocapsid) increased the strand transfer throughout the whole template. However, the prominent hot spot for internal transfer remained, which was still at the pause site. We interpret the new results to mean that pause sites can also serve to stall DNA synthesis, allowing acceptor invasions initiated earlier in the template to catch up with the primer terminus.

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“…Based on the example of the S1/S2 structure (Galetto et al 2004), one might predict that a recombination hot spot could be found within our proposed structure (Galetto et al 2006). Recombination breakpoints have been found in nucleotide region 230-330, i.e., in the sequence that folds to the predicted structure, between the pol gene sequences from different subtypes, such as between subtypes A and B, A and D, and B and D, as well as between B and F (Quarleri et al 2004;Yang et al 2004;Sa Filho et al 2005).…”

Section: Role Of the Rna Secondary Structurementioning

confidence: 99%

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

Wang

Barr²,

Guo³

et al. 2008

RNA

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RNA secondary structures play several important roles in the human immunodeficiency virus (HIV) life cycle. To assess whether RNA secondary structure might affect the function of the HIV protease and reverse transcriptase genes, which are the main targets of anti-HIV drugs, we applied a series of different computational approaches to detect RNA secondary structures, including thermodynamic RNA folding predictions, synonymous variability analysis, and covariance analysis. Each method independently revealed strong evidence of a novel RNA secondary structure at the junction of the protease and reverse transcriptase genes, consisting of a 107-nucleotide region containing three stems, A, B, and C. First, RNA folding calculations by mfold and RNAfold both predicted the secondary structure with high confidence. Moreover, the same structure was predicted in a diverse set of reference sequences in HIV-1 group M, indicating that it is conserved across this group. Second, the predicted base-pairing regions displayed markedly reduced synonymous variation (approximately threefold lower than average) in a data set of 20,000 HIV-1 subtype B sequences from clinical samples. Third, independent analysis of covariation between synonymous mutations in this data set identified 10 covariant mutation pairs forming two diagonals that corresponded exactly to the sites predicted to base-pair in stems A and B. Finally, this structure was validated experimentally using selective 29-hydroxyl acylation and primer extension (SHAPE). Discovery of this novel secondary structure suggests many directions for further functional investigation.

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

Cited by 44 publications

References 51 publications

Identifying Recombination Hot Spots in the HIV-1 Genome

Identifying Recombination Hot Spots in the HIV-1 Genome

Insights into the Multiple Roles of Pausing in HIV-1 Reverse Transcriptase-promoted Strand Transfers

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

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