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Retroviruses

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Book cover Viral Genome Replication

Retroviruses are a large group of enveloped RNA viruses infecting vertebrates. The viral particles are spherical and acquire their envelope during budding from the infected cell. The lipid bilayer therefore contains cellular proteins as well as the viral envelope glycoproteins. These glycoproteins are constituted by a transmembrane subunit (TM) associated to the surface protein (SU), present on the virion. Underneath the membrane is a spherical shell constituted by the matrix (MA) protein. Internally is the viral capsid, whose shape varies in different viruses, constituted by the CA protein. This core contains the retroviral enzymes (the reverse transcriptase, RT, the integrase, IN, and the protease, PR), together with the genomic RNA, coated by the nucleocapsid protein (NC).

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References

  • Archer TK, Lefebvre P, Wolford RG and Hager GL. (1992) Transcription factor loading on the MMTV promoter: a bimodal mechanism for promoter activation. Science, 255, 1573–6.

    Article  PubMed  CAS  Google Scholar 

  • Berkhout B, van Wamel J and Klaver B. (1995) Requirements for DNA strand transfer during reverse transcription in mutant HIV-1 virions. J Mol Biol, 252, 59–69.

    Article  PubMed  CAS  Google Scholar 

  • Berkhout B, Vastenhouw NL, Klasens BI and Huthoff H. (2001) Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription. RNA, 7, 1097–114.

    Article  PubMed  CAS  Google Scholar 

  • Bex F and Gaynor RB. (1998) Regulation of gene expression by HTLV-I Tax protein. Methods, 16, 83–94.

    Article  PubMed  CAS  Google Scholar 

  • Boone LR and Skalka AM. (1981) Viral DNA synthesized in vitro by avian retrovirus particles permeabilized with melittin. I. Kinetics of synthesis and size of minus- and plus-strand transcripts. J Virol, 37, 109–16.

    PubMed  CAS  Google Scholar 

  • Brandt S, Grunwald T, Lucke S, Stang A and Uberla K. (2006) Functional replacement of the R region of simian immunodeficiency virus-based vectors by heterologous elements. J Gen Virol, 87, 2297–307.

    Article  PubMed  CAS  Google Scholar 

  • Brule F, Bec G, Keith G, Le Grice SF, Roques BP, Ehresmann B, Ehresmann C and Marquet R. (2000) In vitro evidence for the interaction of tRNA3 Lys with U3 during the first strand transfer of HIV-1 reverse transcription. Nucleic Acids Res, 28, 634–40.

    Article  PubMed  CAS  Google Scholar 

  • Cen S, Khorchid A, Gabor J, Rong L, Wainberg MA and Kleiman L. (2000) Roles of Pr55(gag) and NCp7 in tRNA3 Lys genomic placement and the initiation step of reverse transcription in human immunodeficiency virus type 1. J Virol, 74, 10796–800.

    Article  PubMed  CAS  Google Scholar 

  • Cheslock SR, Anderson JA, Hwang CK, Pathak VK and Hu WS. (2000) Utilization of nonviral sequences for minus-strand DNA transfer and gene reconstitution during retroviral replication. J Virol, 74, 9571–9.

    Article  PubMed  CAS  Google Scholar 

  • Coffin JM. (1979) Structure, replication, and recombination of retrovirus genomes: some unifying hypotheses. J Gen Virol, 42, 1–26.

    Article  PubMed  CAS  Google Scholar 

  • Dang Q and Hu WS. (2001) Effects of homology length in the repeat region on minus-strand DNA transfer and retroviral replication. J Virol, 75, 809–20.

    Article  PubMed  CAS  Google Scholar 

  • DeStefano JJ, Bambara RA and Fay PJ. (1994) The mechanism of human immunodeficiency virus reverse transcriptase-catalyzed strand transfer from internal regions of heteropolymeric RNA templates. J Biol Chem, 269, 161–8.

    PubMed  CAS  Google Scholar 

  • DeStefano JJ, Mallaber LM, Rodriguez-Rodriguez L, Fay PJ and Bambara RA. (1992) Requirements for strand transfer between internal regions of heteropolymer templates by human immunodeficiency virus reverse transcriptase. J Virol, 66, 6370–8.

    PubMed  CAS  Google Scholar 

  • Dingwall C, Ernberg I, Gait MJ, Green SM, Heaphy S, Karn J, Lowe AD, Singh M and Skinner MA. (1990) HIV-1 tat protein stimulates transcription by binding to a U-rich bulge in the stem of the TAR RNA structure. EMBO J, 9, 4145–53.

    PubMed  CAS  Google Scholar 

  • Einfeld D. (1996) Maturation and assembly of retroviral glycoproteins. Curr Top Microbiol Immunol, 214, 133–76.

    Article  PubMed  CAS  Google Scholar 

  • Feinstein SC, Ross SR and Yamamoto KR. (1982) Chromosomal position effects determine transcriptional potential of integrated mammary tumor virus DNA. J Mol Biol, 156, 549–65.

    Article  PubMed  CAS  Google Scholar 

  • Galetto R, Giacomoni V, Veron M and Negroni M. (2006) Dissection of a circumscribed recombination hot spot in HIV-1 after a single infectious cycle. J Biol Chem, 281, 2711–20.

    Article  PubMed  CAS  Google Scholar 

  • Galetto R, Moumen A, Giacomoni V, Veron M, Charneau P and Negroni M. (2004) The structure of HIV-1 genomic RNA in the gp120 gene determines a recombination hot spot in vivo. J Biol Chem, 279, 36625–32.

    Article  PubMed  CAS  Google Scholar 

  • Holman AG and Coffin JM. (2005) Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites. Proc Natl Acad Sci U S A, 102, 6103–7.

    Google Scholar 

  • Isel C, Lanchy JM, Le Grice SF, Ehresmann C, Ehresmann B and Marquet R. (1996) Specific initiation and switch to elongation of human immunodeficiency virus type 1 reverse transcription require the post-transcriptional modifications of primer tRNA3 Lys. EMBO J, 15, 917–24.

    PubMed  CAS  Google Scholar 

  • Isel C, Westhof E, Massire C, Le Grice SF, Ehresmann B, Ehresmann C and Marquet R. (1999) Structural basis for the specificity of the initiation of HIV-1 reverse transcription. EMBO J, 18, 1038–48.

    Article  PubMed  CAS  Google Scholar 

  • Jacks T and Varmus HE. (1985) Expression of the Rous sarcoma virus pol gene by ribosomal frameshifting. Science, 230, 1237–42.

    Article  PubMed  CAS  Google Scholar 

  • Katz RA and Skalka AM. (1990) Control of retroviral RNA splicing through maintenance of suboptimal processing signals. Mol Cell Biol, 10, 696–704.

    PubMed  CAS  Google Scholar 

  • Khorchid A, Javanbakht H, Wise S, Halwani R, Parniak MA, Wainberg MA and Kleiman L. (2000) Sequences within Pr160gag-pol affecting the selective packaging of primer tRNA3 Lys into HIV-1. J Mol Biol, 299, 17–26.

    Article  PubMed  CAS  Google Scholar 

  • Klarmann GJ, Yu H, Chen X, Dougherty JP and Preston BD. (1997) Discontinuous plus-strand DNA synthesis in human immunodeficiency virus type 1-infected cells and in a partially reconstituted cell-free system. J Virol, 71, 9259–69.

    PubMed  CAS  Google Scholar 

  • Klaver B and Berkhout B. (1994) Premature strand transfer by the HIV-1 reverse transcriptase during strong-stop DNA synthesis. Nucleic Acids Res, 22, 137–44.

    Article  PubMed  CAS  Google Scholar 

  • Kulpa D, Topping R and Telesnitsky A. (1997) Determination of the site of first strand transfer during Moloney murine leukemia virus reverse transcription and identification of strand transfer-associated reverse transcriptase errors. EMBO J, 16, 856–65.

    Article  PubMed  CAS  Google Scholar 

  • Kung HJ, Fung YK, Majors JE, Bishop JM and Varmus HE. (1981) Synthesis of plus strands of retroviral DNA in cells infected with avian sarcoma virus and mouse mammary tumor virus. J Virol, 37, 127–38.

    PubMed  CAS  Google Scholar 

  • Levin JG, Guo J, Rouzina I and Musier-Forsyth K. (2005) Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism. Prog Nucleic Acid Res Mol Biol, 80, 217–86.

    Article  PubMed  CAS  Google Scholar 

  • Lewinski MK and Bushman FD. (2005) Retroviral DNA integration – mechanism and consequences. Adv Genet, 55, 147–81.

    Article  PubMed  CAS  Google Scholar 

  • Lobel LI and Goff SP. (1985) Reverse transcription of retroviral genomes: mutations in the terminal repeat sequences. J Virol, 53, 447–55.

    PubMed  CAS  Google Scholar 

  • Loh TP, Sievert LL and Scott RW. (1990) Evidence for a stem cell-specific repressor of Moloney murine leukemia virus expression in embryonal carcinoma cells. Mol Cell Biol, 10, 4045–57.

    PubMed  CAS  Google Scholar 

  • Malim MH, Hauber J, Le SY, Maizel JV and Cullen BR. (1989) The HIV-1 rev trans-activator acts through a structured target sequence to activate nuclear export of unspliced viral mRNA. Nature, 338, 254–7.

    Article  PubMed  CAS  Google Scholar 

  • Marquet R, Isel C, Ehresmann C and Ehresmann B. (1995) tRNAs as primer of reverse transcriptases. Biochimie, 77, 113–24.

    Article  PubMed  CAS  Google Scholar 

  • Miller MD, Wang B and Bushman FD. (1995) Human immunodeficiency virus type 1 preintegration complexes containing discontinuous plus strands are competent to integrate in vitro. J Virol, 69, 3938–44.

    PubMed  CAS  Google Scholar 

  • Mitchell RS, Beitzel BF, Schroder AR, Shinn P, Chen H, Berry CC, Ecker JR and Bushman FD. (2004) Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol, 2, E234.

    Article  PubMed  Google Scholar 

  • Moumen A, Polomack L, Roques B, Buc H and Negroni M. (2001) The HIV-1 repeated sequence R as a robust hot-spot for copy-choice recombination. Nucleic Acids Res, 29, 3814–21.

    Article  PubMed  CAS  Google Scholar 

  • Moumen A, Polomack L, Unge T, Veron M, Buc H and Negroni M. (2003) Evidence for a mechanism of recombination during reverse transcription dependent on the structure of the acceptor RNA. J Biol Chem, 278, 15973–82.

    Article  PubMed  CAS  Google Scholar 

  • Nabel G and Baltimore D. (1987) An inducible transcription factor activates expression of human immunodeficiency virus in T cells. Nature, 326, 711–3.

    Article  PubMed  CAS  Google Scholar 

  • Negroni M and Buc H. (1999) Recombination during reverse transcription: an evaluation of the role of the nucleocapsid protein. J Mol Biol, 286, 15–31.

    Article  PubMed  CAS  Google Scholar 

  • Negroni M and Buc H. (2001) Mechanisms of retroviral recombination. Annu Rev Genet, 35, 275–302.

    Article  PubMed  CAS  Google Scholar 

  • Nisole S and Saib A. (2004) Early steps of retrovirus replicative cycle. Retrovirology, 1, 9.

    Article  PubMed  Google Scholar 

  • O′Brien WA, Namazi A, Kalhor H, Mao SH, Zack JA and Chen IS. (1994) Kinetics of human immunodeficiency virus type 1 reverse transcription in blood mononuclear phagocytes are slowed by limitations of nucleotide precursors. J Virol, 68, 1258–63.

    PubMed  Google Scholar 

  • Omer CA and Faras AJ. (1982) Mechanism of release of the avian retrovirus tRNATrp primer molecule from viral DNA by ribonuclease H during reverse transcription. Cell, 30, 797–805.

    Article  PubMed  CAS  Google Scholar 

  • Onafuwa A, An W, Robson ND and 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, 4577–87.

    Article  PubMed  CAS  Google Scholar 

  • Paillart JC, Shehu-Xhilaga M, Marquet R and Mak J. (2004) Dimerization of retroviral RNA genomes: an inseparable pair. Nat Rev Microbiol, 2, 461–72.

    Article  PubMed  CAS  Google Scholar 

  • Peters GG and Hu J. (1980) Reverse transcriptase as the major determinant for selective packaging of tRNA′s into Avian sarcoma virus particles. J Virol, 36, 692–700.

    PubMed  CAS  Google Scholar 

  • Petersen R, Kempler G and Barklis E. (1991) A stem cell-specific silencer in the primer-binding site of a retrovirus. Mol Cell Biol, 11, 1214–21.

    PubMed  CAS  Google Scholar 

  • Ramsey CA and Panganiban AT. (1993) Replication of the retroviral terminal repeat sequence during in vivo reverse transcription. J Virol, 67, 4114–21.

    PubMed  CAS  Google Scholar 

  • Rothenberg E and Baltimore D. (1977) Increased length of DNA made by virions of murine leukemia virus at limiting magnesium ion concentration. J Virol, 21, 168–78.

    PubMed  CAS  Google Scholar 

  • Schroder AR, Shinn P, Chen H, Berry C, Ecker JR and Bushman F. (2002) HIV-1 integration in the human genome favors active genes and local hotspots. Cell, 110, 521–9.

    Article  PubMed  CAS  Google Scholar 

  • Schultz SJ, Whiting SH and Champoux JJ. (1995) Cleavage specificities of Moloney murine leukemia virus RNase H implicated in the second strand transfer during reverse transcription. J Biol Chem, 270, 24135–45.

    Article  PubMed  CAS  Google Scholar 

  • Sharp PA and Marciniak RA. (1989) HIV TAR: an RNA enhancer? Cell, 59, 229–30.

    Article  PubMed  CAS  Google Scholar 

  • Smith CM, Potts WB, 3rd, Smith JS and Roth MJ. (1997) RNase H cleavage of tRNAPro mediated by M-MuLV and HIV-1 reverse transcriptases. Virology, 229, 437–46.

    Article  PubMed  CAS  Google Scholar 

  • Strebel K. (2003) Virus-host interactions: role of HIV proteins Vif, Tat, and Rev. Aids, 17 Suppl 4, S25–34.

    Article  PubMed  Google Scholar 

  • Telesnitsky A and Goff SP. (1993) Two defective forms of reverse transcriptase can complement to restore retroviral infectivity. EMBO J, 12, 4433–8.

    PubMed  CAS  Google Scholar 

  • Thomas DC, Voronin YA, Nikolenko GN, Chen J, Hu WS and Pathak VK. (2007) Determination of the ex vivo rates of human immunodeficiency virus type 1 reverse transcription by using novel strand-specific amplification analysis. J Virol, 81, 4798–807.

    Article  PubMed  CAS  Google Scholar 

  • Tsukiyama T, Niwa O and Yokoro K. (1990) Characterization of the negative regulatory element of the 5′ noncoding region of Moloney murine leukemia virus in mouse embryonal carcinoma cells. Virology, 177, 772–6.

    Article  PubMed  CAS  Google Scholar 

  • Vogt VM. (1996) Proteolytic processing and particle maturation. Curr Top Microbiol Immunol, 214, 95–131.

    Article  PubMed  CAS  Google Scholar 

  • Wu X, Li Y, Crise B and Burgess SM. (2003) Transcription start regions in the human genome are favored targets for MLV integration. Science, 300, 1749–51.

    Article  PubMed  CAS  Google Scholar 

  • Wu X, Li Y, Crise B, Burgess SM and Munroe DJ. (2005) Weak palindromic consensus sequences are a common feature found at the integration target sites of many retroviruses. J Virol, 79, 5211–4.

    Article  PubMed  CAS  Google Scholar 

  • Yamashita M and Emerman M (2006) Retroviral infection of non-dividing cells: old and new perspectives. Virology, 344, 88–93.

    Article  PubMed  CAS  Google Scholar 

  • Yoshida M. (1994) Mechanism of transcriptional activation of viral and cellular genes by oncogenic protein of HTLV-1. Leukemia, 8 Suppl 1, S51–3.

    PubMed  CAS  Google Scholar 

  • Yoshinaka Y, Katoh I, Copeland TD and Oroszlan S. (1985) Murine leukemia virus protease is encoded by the gag-pol gene and is synthesized through suppression of an amber termination codon. Proc Natl Acad Sci U S A, 82, 1618–22.

    Google Scholar 

  • Zennou V, Petit C, Guetard D, Nerhbass U, Montagnier L and Charneau P. (2000) HIV-1 genome nuclear import is mediated by a central DNA flap. Cell, 101, 173–85.

    Article  PubMed  CAS  Google Scholar 

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Galetto, R., Negroni, M. (2009). Retroviruses. In: Raney, K., Gotte, M., Cameron, C. (eds) Viral Genome Replication. Springer, Boston, MA. https://doi.org/10.1007/b135974_6

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