1887

Abstract

Reverse transcription (RT) is one of the hallmark features of retroviruses. During RT, virus-encoded reverse transcriptase (RTase) must transfer from one end to the other end of the viral genome on two separate occasions to complete RT and move on to the production of proviral DNA. In addition, multiple strand-transfer events between homologous regions of the dimerized viral genome by RTase are also observed, and such recombination events serve as one of the driving forces behind human immunodeficiency virus (HIV) genome sequence diversity. Although retroviral recombination is widely considered to be important, several features of its mechanism are still unclear. We constructed an HIV-1 vector system to examine the target sequences required for virus recombination, and elucidated other necessary prerequisites to harbour recombination, such as the length, homology and the stability of neighbouring structures around the target sequences.

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2015-11-01
2024-10-03
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References

  1. Adachi A., Gendelman H.E., Koenig S., Folks T., Willey R., Rabson A., Martin M.A. 1986; Production of acquired immunodeficiency syndrome-associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone. J Virol 59:284–291[PubMed]
    [Google Scholar]
  2. An W., Telesnitsky A. 2002a; Effects of varying sequence similarity on the frequency of repeat deletion during reverse transcription of a human immunodeficiency virus type 1 vector. J Virol 76:7897–7902 [View Article][PubMed]
    [Google Scholar]
  3. An W., Telesnitsky A. 2002b; HIV-1 genetic recombination: experimental approaches and observations. AIDS Rev 4:195–212[PubMed]
    [Google Scholar]
  4. Coffin J.M. 1979; Structure, replication, and recombination of retrovirus genomes: some unifying hypotheses. J Gen Virol 42:1–26 [View Article][PubMed]
    [Google Scholar]
  5. Delviks-Frankenberry K., Galli A., Nikolaitchik O., Mens H., Pathak V.K., Hu W.S. 2011; Mechanisms and factors that influence high frequency retroviral recombination. Viruses 3:1650–1680 [View Article][PubMed]
    [Google Scholar]
  6. Desrosiers R.C. 1990; HIV-1 origins. A finger on the missing link. Nature 345:288–289 [View Article][PubMed]
    [Google Scholar]
  7. Dilley K.A., Ni N., Nikolaitchik O.A., Chen J., Galli A., Hu W.S. 2011; Determining the frequency and mechanisms of HIV-1 and HIV-2 RNA copackaging by single-virion analysis. J Virol 85:10499–10508 [View Article][PubMed]
    [Google Scholar]
  8. Galetto R., Negroni M. 2005; Mechanistic features of recombination in HIV. AIDS Rev 7:92–102[PubMed]
    [Google Scholar]
  9. Galetto R., Giacomoni V., Véron M., Negroni M. 2006; Dissection of a circumscribed recombination hot spot in HIV-1 after a single infectious cycle. J Biol Chem 281:2711–2720 [View Article][PubMed]
    [Google Scholar]
  10. Gao F., Robertson D.L., Carruthers C.D., Morrison S.G., Jian B., Chen Y., Barré-Sinoussi F., Girard M., Srinivasan A., other authors. 1998; A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. J Virol 72:5680–5698[PubMed]
    [Google Scholar]
  11. Hu W.S., Hughes S.H. 2012; HIV-1 reverse transcription. Cold Spring Harb Perspect Med 2:a006882 [View Article][PubMed]
    [Google Scholar]
  12. Hu W.S., Temin H.M. 1990; Retroviral recombination and reverse transcription. Science 250:1227–1233 [View Article][PubMed]
    [Google Scholar]
  13. Malim M.H., Emerman M. 2001; HIV-1 sequence variation: drift, shift, and attenuation. Cell 104:469–472 [View Article][PubMed]
    [Google Scholar]
  14. Moore M.D., Fu W., Nikolaitchik O., Chen J., Ptak R.G., Hu W.S. 2007; Dimer initiation signal of human immunodeficiency virus type 1: its role in partner selection during RNA copackaging and its effects on recombination. J Virol 81:4002–4011 [View Article][PubMed]
    [Google Scholar]
  15. Moore M.D., Chin M.P., Hu W.S. 2009; HIV-1 recombination: an experimental assay and a phylogenetic approach. Methods Mol Biol 485:87–105 [View Article][PubMed]
    [Google Scholar]
  16. Moumen A., Polomack L., Unge T., Véron M., Buc H., Negroni M. 2003; Evidence for a mechanism of recombination during reverse transcription dependent on the structure of the acceptor RNA. J Biol Chem 278:15973–15982 [View Article][PubMed]
    [Google Scholar]
  17. Ni N., Nikolaitchik O.A., Dilley K.A., Chen J., Galli A., Fu W., Prasad V.V., Ptak R.G., Pathak V.K., Hu W.S. 2011; Mechanisms of human immunodeficiency virus type 2 RNA packaging: efficient trans packaging and selection of RNA copackaging partners. J Virol 85:7603–7612 [View Article][PubMed]
    [Google Scholar]
  18. Nikolenko G.N., Svarovskaia E.S., Delviks K.A., Pathak V.K. 2004; Antiretroviral drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase increase template-switching frequency. J Virol 78:8761–8770 [View Article][PubMed]
    [Google Scholar]
  19. Nikolenko G.N., Palmer S., Maldarelli F., Mellors J.W., Coffin J.M., Pathak V.K. 2005; Mechanism for nucleoside analog-mediated abrogation of HIV-1 replication: balance between RNase H activity and nucleotide excision. Proc Natl Acad Sci U S A 102:2093–2098 [View Article][PubMed]
    [Google Scholar]
  20. Onafuwa A., An W., Robson N.D., Telesnitsky A. 2003; Human immunodeficiency virus type 1 genetic recombination is more frequent than that of Moloney murine leukemia virus despite similar template switching rates. J Virol 77:4577–4587 [View Article][PubMed]
    [Google Scholar]
  21. Onafuwa-Nuga A., Telesnitsky A. 2009; The remarkable frequency of human immunodeficiency virus type 1 genetic recombination. Microbiol Mol Biol Rev 73:451–480 [View Article][PubMed]
    [Google Scholar]
  22. Pfeiffer J.K., Telesnitsky A. 2001; Effects of limiting homology at the site of intermolecular recombinogenic template switching during Moloney murine leukemia virus replication. J Virol 75:11263–11274 [View Article][PubMed]
    [Google Scholar]
  23. Sakuragi J., Sakuragi S., Ohishi M., Shioda T. 2008; A rapid recombination assay of HIV-1 using murine CD52 as a novel biomarker. Microbes Infect 10:396–404 [View Article][PubMed]
    [Google Scholar]
  24. Sakuragi J., Sakuragi S., Ohishi M., Shioda T. 2010; Direct correlation between genome dimerization and recombination efficiency of HIV-1. Microbes Infect 12:1002–1011 [View Article][PubMed]
    [Google Scholar]
  25. Simon-Loriere E., Galetto R., Hamoudi M., Archer J., Lefeuvre P., Martin D.P., Robertson D.L., Negroni M. 2009; Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus. PLoS Pathog 5:e1000418 [View Article][PubMed]
    [Google Scholar]
  26. Svarovskaia E.S., Delviks K.A., Hwang C.K., Pathak V.K. 2000; Structural determinants of murine leukemia virus reverse transcriptase that affect the frequency of template switching. J Virol 74:7171–7178 [View Article][PubMed]
    [Google Scholar]
  27. Tristem M., Marshall C., Karpas A., Hill F. 1992; Evolution of the primate lentiviruses: evidence from vpx and vpr. EMBO J 11:3405–3412[PubMed]
    [Google Scholar]
  28. Vuilleumier S., Bonhoeffer S. 2015; Contribution of recombination to the evolutionary history of HIV. Curr Opin HIV AIDS 10:84–89 [View Article][PubMed]
    [Google Scholar]
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