A new cell-based assay for measuring the forward mutation rate of HIV-1

Journal of Virological Methods

Volumn 124, Issue 1-2, 2005, Pages 95-104

  Huang, K J ^a   Wooley, D P ^a,b  

^a WRIGHT STATE UNIVERSITY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

HIV 1; Mutation rate; Retroviridae; Reverse transcription; Thymidine kinase; Variation

Indexed keywords

RECOMBINANT DNA; THYMIDINE KINASE; VIRUS VECTOR;

ARTICLE; BIOASSAY; CALCULATION; CONTROLLED STUDY; GENETIC TRANSFECTION; GENETIC VARIABILITY; HERPES SIMPLEX VIRUS 1; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; MUTATION RATE; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; VIRAL GENETICS; VIRUS MUTANT; VIRUS MUTATION; VIRUS REPLICATION; VIRUS STRAIN;

CELL LINE; GENETIC VECTORS; HIV-1; MUTATION;

HERPESVIRIDAE; HUMAN IMMUNODEFICIENCY VIRUS 1; RETROVIRIDAE;

EID: 12344288031     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2004.11.010     Document Type: Article

References (40)

1. A. Adachi, H.E. Gendelman, S. Koenig, T. Folks, R. Willey, A. Rabson, and M.A. Martin Production of acquired immunodeficiency syndrome-associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone J. Virol. 59 1986 284 291
2. F.M. Ausubel R. Brent R.E. Kingston D.D. Moore J.G. Seidman J.A. Smith K. Struhl Current Protocols in Molecular Biology 1995 John Wiley & Sons Inc. USA
3. S. Bacchetti, and F.L. Graham Transfer of the gene for thymidine kinase to thymidine kinase-deficient human cells by purified herpes simplex viral DNA Proc. Natl. Acad. Sci. U.S.A. 74 1977 1590 1594
4. K. Bebenek, J. Abbotts, J.D. Roberts, S.H. Wilson, and T.A. Kunkel Specificity and mechanism of error-prone replication by human immunodeficiency virus-1 reverse transcriptase J. Biol. Chem. 264 1989 16948 16956
5. K. Bebenek, J. Abbotts, S.H. Wilson, and T.A. Kunkel Error-prone polymerization by HIV-1 reverse transcriptase. Contribution of template-primer misalignment, miscoding, and termination probability to mutational hot spots J. Biol. Chem. 268 1993 10324 10334
6. K.N. Bishop, R.K. Holmes, A.M. Sheehy, N.O. Davidson, S.J. Cho, and M.H. Malim Cytidine deamination of retroviral DNA by diverse APOBEC proteins Curr. Biol. 14 2004 1392 1396
7. U. Blomer, L. Naldini, T. Kafri, D. Trono, I.M. Verma, and F.H. Gage Highly efficient and sustained gene transfer in adult neurons with a lentivirus vector J. Virol. 71 1997 6641 6649
8. A.D. Bolzan, and M.S. Bianchi Genotoxicity of streptonigrin: a review Mutat. Res. 488 2001 25 37
9. K.A. Butner, and C.W. Lo High frequency DNA rearrangements associated with mouse centromeric satellite DNA J. Mol. Biol. 187 1986 547 556
10. D. Chen, and J.T. Patton Reverse transcriptase adds nontemplated nucleotides to cDNAs during 5′-RACE and primer extension Biotechniques 30 574-580 2001 582
11. S.K. Das, E.P. Benditt, and L.A. Loeb Rapid changes in deoxynucleoside triphosphate pools in mammalian cells treated with mutagens Biochem. Biophys. Res. Commun. 114 1983 458 464
12. J.J. DeStefano, A. Raja, and J.V. Cristofaro In vitro strand transfer from broken RNAs results in mismatch but not frameshift mutations Virology 276 2000 7 15
13. F. Gao, Y. Chen, D.N. Levy, J.A. Conway, T.B. Kepler, and H. Hui Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious J. Virol. 78 2004 2426 2433
14. J.S. Gibbs, D.A. Regier, and R.C. Desrosiers Construction and in vitro properties of HIV-1 mutants with deletions in the "nonessential" genes AIDS Res. Hum. Retrov. 10 1994 343 350
15. M.W. Heartlein, J.H. Knoll, and S.A. Latt Chromosome instability associated with human alphoid DNA transfected into the Chinese hamster genome Mol. Cell. Biol. 8 1988 3611 3618
16. J. Ji, and L.A. Loeb Fidelity of HIV-1 reverse transcriptase copying a hypervariable region of the HIV-1 env gene Virology 199 1994 323 330
17. S. Kawai, and M. Nishizawa New procedure for DNA transfection with polycation and dimethyl sulfoxide Mol. Cell. Biol. 4 1984 1172 1174
18. D. Lecossier, F. Bouchonnet, F. Clavel, and A.J. Hance Hypermutation of HIV-1 DNA in the absence of the Vif protein Science 300 2003 1112
19. M.T. Liddament, W.L. Brown, A.J. Schumacher, and R.S. Harris APOBEC3F properties and hypermutation preferences indicate activity against HIV-1 in vivo Curr. Biol. 14 2004 1385 1391
20. B. Mangeat, P. Turelli, G. Caron, M. Friedli, L. Perrin, and D. Trono Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts Nature 424 2003 99 103
21. L.M. Mansky The mutation rate of human immunodeficiency virus type 1 is influenced by the vpr gene Virology 222 1996 391 400
22. L.M. Mansky, E. Le Rouzic, S. Benichou, and L.C. Gajary Influence of reverse transcriptase variants, drugs, and Vpr on human immunodeficiency virus type 1 mutant frequencies J. Virol. 77 2003 2071 2080
23. L.M. Mansky, and H.M. Temin Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase J. Virol. 69 1995 5087 5094
24. M.A. Martinez, M. Sala, J.P. Vartanian, and S. Wain-Hobson Reverse transcriptase and substrate dependence of the RNA hypermutagenesis reaction Nucleic Acids Res. 23 1995 2573 2578
25. J.P. Murnane, M.J. Yezzi, and B.R. Young Recombination events during integration of transfected DNA into normal human cells Nucleic Acids Res. 18 1990 2733 2738
26. L. Naldini, U. Blomer, P. Gallay, D. Ory, R. Mulligan, F.H. Gage, I.M. Verma, and D. Trono In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector Science 272 1996 263 267
27. S. Parthasarathi, A. Varela-Echavarria, Y. Ron, B.D. Preston, and J.P. Dougherty Genetic rearrangements occurring during a single cycle of murine leukemia virus vector replication: characterization and implications J. Virol. 69 1995 7991 8000
28. P.H. Patel, and B.D. Preston Marked infidelity of human immunodeficiency virus type 1 reverse transcriptase at RNA and DNA template ends Proc. Natl. Acad. Sci. U.S.A. 91 1994 549 553
29. J.A. Peliska, and S.J. Benkovic Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase Science 258 1992 1112 1118
30. F.W. Perrino, B.D. Preston, L.L. Sandell, and L.A. Loeb Extension of mismatched 3′ termini of DNA is a major determinant of the infidelity of human immunodeficiency virus type 1 reverse transcriptase Proc. Natl. Acad. Sci. U.S.A. 86 1989 8343 8347
31. B.D. Preston, B.J. Poiesz, and L.A. Loeb Fidelity of HIV-1 reverse transcriptase Science 242 1988 1168 1171
32. L. Ratner, W. Haseltine, R. Patarca, K.J. Livak, B. Starcich, S.F. Josephs, E.R. Doran, J.A. Rafalski, E.A. Whitehorn, K. Baumeister, L. Ivanoff, S.R. Petteway Jr., M.L. Pearson, J.A. Lautenberger, T.S. Papas, J. Ghrayeb, N.T. Chang, R.C. Gallo, and F. Wong-Staal Complete nucleotide sequence of the AIDS virus, HTLV-III Nature 313 1985 277 284
33. J.D. Roberts, K. Bebenek, and T.A. Kunkel The accuracy of reverse transcriptase from HIV-1 Science 242 1988 1171 1173
34. J. Sambrook, E.F. Fritsch, and T. Maniatis Molecular Cloning: A Laboratory Manual 1989 Cold Spring Harbor Laboratory Cold Spring Harbor, NY
35. R. Swanstrom, H.E. Varmus, and J.M. Bishop The terminal redundancy of the retrovirus genome facilitates chain elongation by reverse transcriptase J. Biol. Chem. 256 1981 1115 1121
36. A. Varela-Echavarría, N. Garvey, B.D. Preston, and J.P. Dougherty Comparison of Moloney murine leukemia virus mutation rate with the fidelity of its reverse transcriptase in vitro J. Biol. Chem. 267 1992 24681 24688
37. J.P. Vartanian, A. Meyerhans, B. Asjo, and S. Wain-Hobson Selection, recombination, and G → A hypermutation of human immunodeficiency virus type 1 genomes J. Virol. 65 1991 1779 1788
38. J.P. Vartanian, A. Meyerhans, M. Sala, and S. Wain-Hobson G → A hypermutation of the human immunodeficiency virus type 1 genome: evidence for dCTP pool imbalance during reverse transcription Proc. Natl. Acad. Sci. U.S.A. 91 1994 3092 3096
39. K.K. Weiss, R. Chen, M. Skasko, H.M. Reynolds, K. Lee, R.A. Bambara, L.M. Mansky, and B. Kim A role for dNTP binding of human immunodeficiency virus type 1 reverse transcriptase in viral mutagenesis Biochemistry 43 2004 4490 4500
40. H. Zhang, B. Yang, R.J. Pomerantz, C. Zhang, S.C. Arunachalam, and L. Gao The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA Nature 424 2003 94 98