Mapping viral DNA specificity to the central region of integrase by using functional human immunodeficiency virus type 1/visna virus chimeric proteins

Journal of Virology

Volumn 72, Issue 3, 1998, Pages 1744-1753

  Katzman, Michael ^a,b   Sudol, Malgorzata ^a  

^a PENN STATE COLLEGE OF MEDICINE   (United States)

^b PENN STATE MILTON S HERSHEY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRASE; VIRUS DNA; VIRUS PROTEIN;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CHIMERA; DNA DETERMINATION; DNA INTEGRATION; ENZYME ANALYSIS; ENZYME PURIFICATION; ENZYME SPECIFICITY; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; VISNA VIRUS;

EID: 0031935582     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.72.3.1744-1753.1998     Document Type: Article

References (73)

1. Andrake, M. D., and A. M. Skalka. 1995. Multimerization determinants reside in both the catalytic core and C terminus of avian sarcoma virus integrase. J. Biol. Chem. 270:29299-29306.
2. Andrake, M. D., and A. M. Skalka. 1996. Retroviral integrase, putting the pieces together. J. Biol. Chem. 271:19633-19636.
3. Barsov, E. V., W. E. Huber, J. Marcotrigiano, P. K. Clark, A. D. Clark, E. Arnold, and S. H. Hughes. 1996. Inhibition of human immunodeficiency virus type 1 integrase by the Fab fragment of a specific monoclonal antibody suggests that different multimerization states are required for different enzymatic functions. J. Virol. 70:4484-4494.
4. Bizub-Bender, D., J. Kulkosky, and A. M. Skalka. 1994. Monoclonal antibodies against HIV type 1 integrase: clues to molecular structure. AIDS Res. Hum. Retroviruses 10:1105-1115.
5. Bujacz, C., M. Jaskolski, J. Alexandratos, A. Wlodawer, G. Merkel, R. A. Katz, and A. M. Skalka. 1995. High-resolution structure of the catalytic domain of avian sarcoma virus integrase. J. Mol. Biol. 253:333-346.
6. Burke, C. J., G. Sanyal, M. W. Bruner, J. A. Ryan, R. L. LaFemina, H. L. Robbins, A. S. Zeft, C. R. Middaugh, and M. G. Cordingley. 1992. Structural implications of spectroscopic characterization of a putative zinc finger peptide from HIV-1 integrase. J. Biol. Chem. 267:9639-9644.
7. Bushman, F. D., and R. Craigie. 1991. Activities of human immunodeficiency virus (HIV) integration protein in vitro: specific cleavage and integration of HIV DNA. Proc. Natl. Acad. Sci. USA 88:1339-1343.
8. Bushman, F. D., A. Engelman, I. Palmer, P. Wingfield, and R. Craigie. 1993. Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding. Proc. Natl. Acad. Sci. USA 90:3428-3432.
9. Bushman, F. D., and B. Wang. 1994. Rous sarcoma virus integrase protein: mapping functions for catalysis and substrate binding. J. Virol. 68:2215-2223.
10. Chow, S. A., K. A. Vincent, V. Ellison, and P. O. Brown. 1992. Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. Science 255:723-726.
11. Craigie, R., T. Fujiwara, and F. Bushman. 1990. The IN protein of Moloney murine leukemia virus processes the viral DNA ends and accomplishes their integration in vitro. Cell 62:829-837.
12. Drelich, M., M. Haenggi, and J. Mous. 1993. Conserved residues Pro-109 and Asp-116 are required for interaction of the human immunodeficiency virus type 1 integrase protein with its viral DNA substrate. J. Virol. 67:5041-5044.
13. Drelich, M., R. Wilhelm, and J. Mous. 1992. Identification of amino acid residues critical for endonuclease and integration activities of HIV-1 IN protein in vitro. Virology 188:459-468.
14. Du, Z., P. O. Ilyinskii, K. Lally, R. C. Desrosiers, and A. Engelman. 1997. A mutation in integrase can compensate for mutations in the simian immunodeficiency virus att site. J. Virol. 71:8124-8132.
15. Dyda, F., A. B. Hickman, T. M. Jenkins, A. Engelman, R. Craigie, and D. R. Davies. 1994. Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science 266:1981-1986.
16. Ellison, V., J. Gerton, K. A. Vincent, and P. O. Brown. 1995. An essential interaction between distinct domains of HIV-1 integrase mediates assembly of the active multimer. J. Biol. Chem. 270:3320-3326.
17. Engelman, A., F. D. Bushman, and R. Craigie. 1993. Identification of discrete functional domains of HIV-1 integrase and their organization within an active multimeric complex. EMBO J. 12:3269-3275.
18. Engelman, A., and R. Craigie. 1992. Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro. J. Virol. 66:6361-6369.
19. Engelman, A., A. B. Hickman, and R. Craigie. 1994. The core and carboxyl-terminal domains of the integrase protein of human immunodeficiency virus type 1 each contribute to nonspecific DNA binding. J. Virol. 68:5911-5917.
20. Engelman, A., Y. Liu, H. Chen, M. Farzan, and F. Dyda. 1997. Structure-based mutagenesis of the catalytic domain of human immunodeficiency virus type 1 integrase. J. Virol. 71:3507-3514.
21. Engelman, A., K. Mizuuchi, and R. Craigie. 1991. HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer. Cell 67:1211-1221.
22. Goulaouic, H., and S. A. Chow. 1996. Directed integration of viral DNA mediated by fusion proteins consisting of human immunodeficiency virus type 1 integrase and Escherichia coli LexA protein. J. Virol. 70:37-46.
23. Hazuda, D. J., A. L. Wolfe, J. C. Hastings, H. L. Robbins, P. L. Graham, R. L. LaFemina, and E. A. Emini. 1994. Viral long terminal repeat substrate binding characteristics of the human immunodeficiency virus type 1 integrase. J. Biol. Chem. 269:3999-4004.
24. Hong, T., E. Murphy, J. Groarke, and K. Drlica. 1993. Human immunodeficiency virus type 1 DNA integration: fine structure target analysis using synthetic oligonucleotides. J. Virol. 67:1127-1131.
25. Horton, R. M., S. N. Ho, J. K. Pullen, H. D. Hunt, Z. Cai, and L. R. Pease. 1993. Gene splicing by overlap extension. Methods Enzymol. 217:270-279.
26. Jenkins, T. M., A. Engelman, R. Ghirlando, and R. Craigie. 1996. A soluble active mutant of HIV-1 integrase: involvement of both the core and carboxyl-terminal domains in multimerization. J. Biol. Chem. 271:7712-7718.
27. Jenkins, T. M., D. Esposito, A. Engelman, and R. Craigie. 1997. Personal communication.
28. Jenkins, T. M., A. B. Hickman, F. Dyda, R. Ghirlando, D. R. Davies, and R. Craigie. 1995. Catalytic domain of human immunodeficiency virus type 1 integrase: identification of a soluble mutant by systematic replacement of hydrophobic residues. Proc. Natl. Acad. Sci. USA 92:6057-6061.
29. Jones, K. S., J. Coleman, G. W. Merkel, T. M. Laue, and A. M. Skalka. 1992. Retroviral integrase functions as a multimer and can turn over catalytically. J. Biol. Chem. 267:16037-16040.
30. Jonsson, C. B., G. A. Donzella, and M. J. Roth. 1993. Characterization of the forward and reverse integration reactions of the Moloney murine leukemia virus integrase protein purified from Escherichia coli. J. Biol. Chem. 268: 1462-1469.
31. Jonsson, C. B., and M. J. Roth. 1993. Role of the His-Cys finger of Moloney murine leukemia virus integrase protein in integration and disintegration. J. Virol. 67:5562-5571.
32. Katz, R. A., G. Merkel, J. Kulkosky, J. Leis, and A. M. Skalka. 1990. The avian retroviral IN protein is both necessary and sufficient for integrative recombination in vitro. Cell 63:87-95.
33. Katzman, M., R. A. Katz, A. M. Skalka, and J. Leis. 1989. The avian retroviral integration protein cleaves the terminal sequences of linear viral DNA at the in vivo sites of integration. J. Virol. 63:5319-5327.
34. Katzman, M., J. P. G. Mack, A. M. Skalka, and J. Leis. 1991. A covalent complex between retroviral integrase and nicked substrate DNA. Proc. Natl. Acad. Sci. USA 88:4695-4699.
35. Katzman, M., and M. Sudol. 1994. In vitro activities of purified visna virus integrase. J. Virol. 68:3558-3569.
36. Katzman, M., and M. Sudol. 1995. Mapping domains of retroviral integrase responsible for viral DNA specificity and target site selection by analysis of chimeras between human immunodeficiency virus type 1 and visna virus integrases. J. Virol. 69:5687-5696.
37. Katzman, M., and M. Sudol. 1996. Influence of subterminal viral DNA nucleotides on differential susceptibility to cleavage by human immunodeficiency virus type 1 and visna virus integrases. J. Virol. 70:9069-9073.
38. Katzman, M., and M. Sudol. 1996. Nonspecific alcoholysis, a novel endonuclease activity of human immunodeficiency virus type 1 and other retroviral integrases. J. Virol. 70:2598-2604.
39. Katzman, M., M. Sudol, and J. S. Pufnock. 1997. Unpublished data.
40. Katzman, M., M. Sudol, L. M. Skinner, and A. L. Morgan. 1997. Unpublished data.
41. Khan, E., J. P. G. Mack, R. A. Katz, J. Kulkosky, and A. M. Skalka. 1991. Retroviral integrase domains: DNA binding and the recognition of LTR sequences. Nucleic Acids Res. 19:851-860.
42. Kitamura, Y., Y. M. H. Lee, and J. M. Coffin. 1992. Nonrandom integration of retroviral DNA in vitro: effect of CpG methylation. Proc. Natl. Acad. Sci. USA 89:5532-5536.
43. Kulkosky, J., K. S. Jones, R. A. Katz, J. P. G. Mack, and A. M. Skalka. 1992. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol. Cell. Biol. 12:2331-2338.
44. Kulkosky, J., R. A. Katz, G. Merkel, and A. M. Skalka. 1995. Activities and substrate specificity of the evolutionarily conserved central domain of retroviral integrase. Virology 206:448-456.
45. LaFemina, R. L., C. L. Schneider, H. L. Robbins, P. L. Callahan, K. LeGrow, E. Roth, W. A. Schleif, and E. A. Emini. 1992. Requirement of active human immunodeficiency virus type 1 integrase enzyme for productive infection of human T-lymphoid cells. J. Virol. 66:7414-7419.
46. Leavitt, A. D., R. B. Rose, and H. E. Varmus. 1992. Both substrate and target oligonucleotide sequences affect in vitro integration mediated by human immunodeficiency virus type 1 integrase protein produced in Saccharomyces cerevisiae. J. Virol. 66:2359-2368.
47. Leavitt, A. D., L. Shiue, and H. E. Varmus. 1993. Site-directed mutagenesis of HIV-1 integrase demonstrates differential effects on integrase functions in vitro. J. Biol. Chem. 268:2113-2119.
48. Lodi, P. J., J. A. Ernst, J. Kuszewski, A. B. Hickman, A. Engelman, R. Craigie, G. M. Clore, and A. M. Gronenborn. 1995. Solution structure of the DNA binding domain of HIV-1 integrase. Biochemistry 34:9826-9833.
49. Lutzke, R. A., C. Vink, and R. H. A. Plasterk. 1994. Characterization of the minimal DNA-binding domain of the HIV integrase protein. Nucleic Acids Res. 22:4125-4131.
50. Mazumder, A., A. Engelman, R. Craigie, M. Fesen, and Y. Pommier. 1994. Intermolecular disintegration and intramolecular strand transfer activities of wild-type and mutant HIV-1 integrase. Nucleic Acids Res. 22:1037-1043.
51. Mazumder, A., N. Neamati, A. A. Pilon, S. Sunder, and Y. Pommier. 1996. Chemical trapping of ternary complexes of human immunodeficiency virus type 1 integrase, divalent metal, and DNA substrates containing an abasic site: implications for the role of lysine 136 in DNA binding. J. Biol. Chem. 271:27330-27338.
52. Mizuuchi, K. 1992. Transpositional recombination: mechanistic insights from studies of Mu and other elements. Annu. Rev. Biochem. 61:1011-1051.
53. Pahl, A., and R. M. Flugel. 1995. Characterization of the human spuma retrovirus integrase by site-directed mutagenesis, by complementation analysis, and by swapping the zinc finger domain of HIV-1. J. Biol. Chem. 270:2957-2966.
54. Pemberton, I. K., M. Buckle, and H. Buc. 1996. The metal ion-induced cooperative binding of HIV-1 integrase to DNA exhibits a marked preference for Mn(II) rather than Mg(II). J. Biol. Chem. 271:1498-1506.
55. Pryciak, P. M., and H. E. Varmus. 1992. Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection. Cell 69:769-780.
56. Roth, M. J., P. L. Schwartzberg, and S. P. Goff. 1989. Structure of the termini of DNA intermediates in the integration of retroviral DNA: dependence on IN function and terminal DNA sequence. Cell 58:47-54.
57. Schauer, M., and A. Billich. 1992. The N-terminal region of HIV-1 integrase is required for integration activity, but not for DNA binding. Biochem. Biophys. Res. Commun. 185:874-880.
58. Scottoline, B. P., S. Chow, V. Ellison, and P. O. Brown. 1997. Disruption of the terminal base pairs of retroviral DNA during integration. Genes Dev. 11:371-382.
59. Sherman, P. A., M. L. Dickson, and J. A. Fyfe. 1992. Human immunodeficiency virus type 1 integration protein: DNA sequence requirements for cleaving and joining reactions. J. Virol. 66:3593-3601.
60. Shibagaki, Y., and S. A. Chow. 1997. Central core domain of retroviral integrase is responsible for target site selection. J. Biol. Chem. 272:8361-8369.
61. Shibagaki, Y., M. L. Holmes, R. S. Appa, and S. A. Chow. 1997. Characterization of feline immunodeficiency virus integrase and analysis of functional domains. Virology 230:1-10.
62. Smith, K. D., A. Valenzuela, J. L. Vigna, K. Aalbers, and C. T. Lutz. 1985. Unwanted mutations in PCR mutagenesis: avoiding the predictable. PCR Methods Applic. 2:253-257.
63. van Gent, D. C., Y. Elgersma, M. W. J. Bolk, C. Vink, and R. H. A. Plasterk. 1991. DNA binding properties of the integrase proteins of human immunodeficiency virus types 1 and 2. Nucleic Acids Res. 19:3821-3827.
64. van Gent, D. C., A. A. M. Oude Groeneger, and R. H. A. Plasterk. 1992. Mutational analysis of the integrase protein of human immunodeficiency virus type 2. Proc. Natl. Acad. Sci. USA 89:9598-9602.
65. van Gent, D. C., A. A. M. Oude Groeneger, and R. H. A. Plasterk. 1993. Identification of amino acids in HIV-2 integrase involved in site-specific hydrolysis and alcoholysis of viral DNA termini. Nucleic Acids Res. 21:3373-3377.
66. van Gent, D. C., C. Vink, A. A. M. Oude Groeneger, and R. H. A. Plasterk. 1993. Complementation between HIV integrase proteins mutated in different domains. EMBO J. 12:3261-3267.
67. Vincent, K. A., V. Ellison, S. A. Chow, and P. O. Brown. 1993. Characterization of human immunodeficiency virus type 1 integrase expressed in Escherichia coli and analysis of variants with amino-terminal mutations. J. Virol. 67:425-437.
68. Vink, C., A. A. M. Oude Groeneger, and R. H. A. Plasterk. 1993. Identification of the catalytic and DNA-binding region of the human immunodeficiency virus type 1 integrase protein. Nucleic Acids Res. 21:1419-1425.
69. Vink, C., and R. H. A. Plasterk. 1993. The human immunodeficiency virus integrase protein. Trends Genet. 9:433-437.
70. Vink, C., K. H. van der Linden, and R. H. A. Plasterk. 1994. Activities of the feline immunodeficiency virus integrase protein produced in Escherichia coli. J. Virol. 68:1468-1474.
71. Woerner, A. M., M. Klutch, J. G. Levin, and C. J. Marcus-Sekura. 1992. Localization of DNA binding activity of HIV-1 integrase to the C-terminal half of the protein. AIDS Res. Hum. Retroviruses 8:297-304.
72. Woerner, A. M., and C. J. Marcus-Sekura. 1993. Characterization of a DNA binding domain in the C-terminus of HIV-1 integrase by deletion mutagenesis. Nucleic Acids Res. 21:3507-3511.
73. Wolfe, A. L., P. J. Felock, J. C. Hastings, C. Uncapher Blau, and D. J. Hazuda. 1996. The role of manganese in promoting multimerization and assembly of human immunodeficiency virus type 1 integrase as a catalytically active complex on immobilized long terminal repeat substrates. J. Virol. 70:1424-1432.