The effects of alternate polypurine tracts (PPTs) and mutations of sequences adjacent to the PPT on viral replication and cleavage specificity of the rous sarcoma virus reverse transcriptase

Journal of Virology

Volumn 82, Issue 17, 2008, Pages 8592-8604

  Chang, Kevin W ^a   Oh, Jangsuk ^a,b   Alvord, W Gregory ^a   Hughes, Stephen H ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; RNA DIRECTED DNA POLYMERASE; THYMIDINE; VIRUS RNA;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; EMBRYO; ENZYME DEGRADATION; GENE DELETION; GENE SEQUENCE; GENE STRUCTURE; NONHUMAN; POINT MUTATION; POLYPURINE TRACT; PRIORITY JOURNAL; ROUS SARCOMA ONCOVIRUS; VIRUS REPLICATION; VIRUS TITRATION; WILD TYPE;

ADENINE; ANIMALS; BASE SEQUENCE; CELL LINE; CELLS, CULTURED; CHICK EMBRYO; CONSENSUS SEQUENCE; EMBRYO, NONMAMMALIAN; FIBROBLASTS; GUANINE; MOLECULAR SEQUENCE DATA; MUTATION; PURINES; RIBONUCLEASE H; RNA-DIRECTED DNA POLYMERASE; ROUS SARCOMA VIRUS; SENSITIVITY AND SPECIFICITY; TERMINAL REPEAT SEQUENCES;

RICE STRIPE VIRUS; ROUS SARCOMA VIRUS;

EID: 50149103532     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.00499-08     Document Type: Article

References (35)

1. Barsov, E. V., W. S. Payne, and S. H. Hughes. 2001. Adaptation of chimeric retroviruses in vitro and in vivo: isolation of avian retroviral vectors with extended host range. J. Virol. 75:4973-4983.
2. Chang, K. W., J. G. Julias, W. G. Alvord, J. Oh, and S. H. Hughes. 2005. Alternate polypurine tracts (PPTs) affect the Rous sarcoma virus RNase H cleavage specificity and reveal a preferential cleavage following a GA dinucleotide sequence at the PPT-U3 junction. J. Virol. 79:13694-13704.
3. Dash, C., J. W. Rausch, and S. F. Le Grice. 2004. Using pyrrolo-deoxycytosine to probe RNA/DNA hybrids containing the human immunodeficiency virus type-1 3′ polypurine tract. Nucleic Acids Res. 32:1539-1547.
4. Furfine, E. S., and J. E. Reardon. 1991. Human immunodeficiency virus reverse transcriptase ribonuclease H: specificity of tRNA(Lys3)-primer excision. Biochemistry 30:7041-7046.
5. Himly, M., D. N. Foster, I. Bottoli, J. S. Iacovoni, and P. K. Vogt. 1998. The DF-1 chicken fibroblast cell line: transformation induced by diverse oncogenes and cell death resulting from infection by avian leukosis viruses. Virology 248:295-304.
6. Ilyinskii, P. O., and R. C. Desrosiers. 1998. Identification of a sequence element immediately upstream of the polypurine tract that is essential for replication of simian immunodeficiency virus. EMBO J. 17:3766-3774.
7. Jacobo-Molina, A., J. Ding, R. G. Nanni, A. D. Clark, Jr., X. Lu, C. Tantillo, R. L. Williams, G. Kamer, A. L. Ferris, P. Clark, et al. 1993. Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 Å resolution shows bent DNA. Proc. Natl. Acad. Sci. USA 90:6320-6324.
8. Jones, F. D., and S. H. Hughes. 2007. In vitro analysis of the effects of mutations in the G-tract of the human immunodeficiency virus type 1 polypurine tract on RNase H cleavage specificity. Virology 360:341-349.
9. Julias, J. G., M. J. McWilliams, S. G. Sarafianos, W. G. Alvord, E. Arnold, and S. H. Hughes. 2004. Effects of mutations in the G tract of the human immunodeficiency virus type 1 polypurine tract on virus replication and RNase H cleavage. J. Virol. 78:13315-13324.
10. Julias, J. G., M. J. McWilliams, S. G. Sarafianos, E. Arnold, and S. H. Hughes. 2002. Mutations in the RNase H domain of HIV-1 reverse transcriptase affect the initiation of DNA synthesis and the specificity of RNase H cleavage in vivo. Proc. Natl. Acad. Sci. USA 99:9515-9520.
11. Kopka, M. L., L. Lavelle, G. W. Han, H. L. Ng, and R. E. Dickerson. 2003. An unusual sugar conformation in the structure of an RNA/DNA decamer of the polypurine tract may affect recognition by RNase H. J. Mol. Biol. 334:653-665.
12. Kulkosky, J., R. A. Katz, and A. M. Skalka. 1990. Terminal nucleotides of the preintegrative linear form of HIV-1 DNA deduced from the sequence of circular DNA junctions. J. Acquir. Immune Defic. Syndr. 3:852-858.
13. Kvaratskhelia, M., S. R. Budihas, and S. F. Le Grice. 2002. Pre-existing distortions in nucleic acid structure aid polypurine tract selection by HIV-1 reverse transcriptase. J. Biol. Chem. 277:16689-16696.
14. Li, L., J. M. Olvera, K. E. Yoder, R. S. Mitchell, S. L. Butler, M. Lieber, S. L. Martin, and F. D. Bushman. 2001. Role of the non-homologous DNA end joining pathway in the early steps of retroviral infection. EMBO J. 20:3272-3281.
15. McWilliams, M. J., J. G. Julias, S. G. Sarafianos, W. G. Alvord, E. Arnold, and S. H. Hughes. 2003. Mutations in the 5′ end of the human immunodeficiency virus type 1 polypurine tract affect RNase H cleavage specificity and virus titer. J. Virol. 77:11150-11157.
16. Miles, L. R., B. E. Agresta, M. B. Khan, S. Tang, J. G. Levin, and M. D. Powell. 2005. Effect of polypurine tract (PPT) mutations on human immunodeficiency virus type 1 replication: a virus with a completely randomized PPT retains low infectivity. J. Virol. 79:6859-6867.
17. Oh, J., K. W. Chang, and S. H. Hughes. 2006. Mutations in the U5 sequences adjacent to the primer binding site do not affect tRNA cleavage by Rous sarcoma virus RNase H but do cause aberrant integrations in vivo. J. Virol. 80:451-459.
18. Oh, J., K. W. Chang, R. Wierzchoslawski, W. G. Alvord, and S. H. Hughes. 2008. Rous sarcoma virus (RSV) integration in vivo: a CA dinucleotide is not required in U3, and RSV linear DNA does not autointegrate. J. Virol. 82:503-512.
19. Oh, J., M. J. McWilliams, J. G. Julias, and S. H. Hughes. 2008. Mutations in the U5 region adjacent to the primer binding site affect tRNA cleavage by human immunodeficiency virus type 1 reverse transcriptase in vivo. J. Virol. 82:719-727.
20. Pullen, K. A., L. K. Ishimoto, and J. J. Champoux. 1992. Incomplete removal of the RNA primer for minus-strand DNA synthesis by human immunodeficiency virus type 1 reverse transcriptase. J. Virol. 66:367-373.
21. Rausch, J. W., and S. F. Le Grice. 2004. 'Binding, bending and bonding': polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus. Int. J. Biochem. Cell Biol. 36:1752-1766.
22. Rausch, J. W., and S. F. Le Grice. 2007. Purine analog substitution of the HIV-1 polypurine tract primer defines regions controlling initiation of plus-strand DNA synthesis. Nucleic Acids Res. 35:256-268.
23. Rausch, J. W., D. Lener, J. T. Miller, J. G. Julias, S. H. Hughes, and S. F. Le Grice. 2002. Altering the RNase H primer grip of human immunodeficiency virus reverse transcriptase modifies cleavage specificity. Biochemistry 41:4856-4865.
24. Robson, N. D., and A. Telesnitsky. 1999. Effects of 3′ untranslated region mutations on plus-strand priming during Moloney murine leukemia virus replication. J. Virol. 73:948-957.
25. Robson, N. D., and A. Telesnitsky. 2000. Selection of optimal polypurine tract region sequences during Moloney murine leukemia virus replication. J. Virol. 74:10293-10303.
26. Sarafianos, S. G., K. Das, C. Tantillo, A. D. Clark, Jr., J. Ding, J. M. Whitcomb, P. L. Boyer, S. H. Hughes, and E. Arnold. 2001. Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA: DNA. EMBO J. 20:1449-1461.
27. Schaefer-Klein, J., I. Givol, E. V. Barsov, J. M. Whitcomb, M. VanBrocklin, D. N. Foster, M. J. Federspiel, and S. H. Hughes. 1998. The EV-O-derived cell line DF-1 supports the efficient replication of avian leukosis-sarcoma viruses and vectors. Virology 248:305-311.
28. Schatz, O., J. Mous, and S. F. Le Grice. 1990. HIV-1 RT-associated ribonuclease H displays both endonuclease and 3′-5′ exonuclease activity. EMBO J. 9:1171-1176.
29. Schultz, S. J., M. Zhang, and J. J. Champoux. 2006. Sequence, distance, and accessibility are determinants of 5′-end-directed cleavages by retroviral RNases H. J. Biol. Chem. 281:1943-1955.
30. Smith, J. S., and M. J. Roth. 1992. Specificity of human immunodeficiency virus-1 reverse transcriptase-associated ribonuclease H in removal of the minus-strand primer, tRNA(Lys3). J. Biol. Chem. 267:15071-15079.
31. Telesnitsky, A., and S. P. Goff. 1997. Reverse transcriptase and the generation of retroviral DNA, p. 121-160. In J. M. Coffin, S. H. Hughes, and H. E. Varmus (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
32. Whitcomb, J. M., and S. H. Hughes. 1992. Retroviral reverse transcription and integration: progress and problems. Annu. Rev. Cell Biol. 8:275-306.
33. Whitcomb, J. M., R. Kumar, and S. H. Hughes. 1990. Sequence of the circle junction of human immunodeficiency virus type 1: implications for reverse transcription and integration. J. Virol. 64:4903-4906.
34. Wöhrl, B. M., and K. Moelling. 1990. Interaction of HIV-1 ribonuclease H with polypurine tract containing RNA-DNA hybrids. Biochemistry 29:10141-10147.
35. Yi-Brunozzi, H. Y., and S. F. Le Grice. 2005. Investigating HIV-1 polypurine tract geometry via targeted insertion of abasic lesions in the (-)-DNA template and (+)-RNA primer. J. Biol. Chem. 280:20154-20162.