Disruption of the terminal base pairs of retroviral DNA during integration

Genes and Development

Volumn 11, Issue 3, 1997, Pages 371-382

  Scottoline, Brian P ^a   Chow, Samson ^a,c   Ellison, Viola ^a,b   Brown, Patrick O ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Watson School of Biological Sciences   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DNA distortion; end processing; Recombination; retroviral integration

Indexed keywords

INTEGRASE; POLYNUCLEOTIDE; VIRUS DNA;

ARTICLE; BASE MISPAIRING; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PRIORITY JOURNAL; PROVIRUS; RETROVIRUS; VIRUS DNA CELL DNA INTERACTION; VIRUS GENOME;

EID: 0031050297     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.11.3.371     Document Type: Article

References (72)

1. Baker, T.A. and L. Luo. 1994. Identification of residues in the Mu transposase essential for catalysis. Proc. Natl. Acad. Sci. 91: 6654-6658.
2. Brown, P.O. 1990. Integration of retroviral DNA. Curr. Top. Microbiol. Immunol. 157: 19-48.
3. Brown, P.O., B. Bowerman, H.E. Varmus, and J.M. Bishop. 1987. Correct integration of retroviral DNA in vitro. Cell 49: 347-356.
4. Brown, P.O., B. Bowerman, H.E. Varmus, and J.M. Bishop. 1989. Retroviral integration: Structure of the initial covalent product and its precursor, and a role for the viral IN protein. Proc. Natl Acad. Sci. 86: 2525-2529.
5. Bujacz, G., M. Jaskolski, J. Alexandratos, A. Wlodawer, G Merkel, R.A. Katz, and A.M. Skalka. 1995. Catalytic domain of the avian sarcoma virus integrase: High resolution structure defines ordered active site and a hound metal cofactor. J. Mol. Biol. 253: 333-346.
6. 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. 88: 1339-1343.
7. Bushman, F.D., A. Engelman, 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. 90: 3428-3432.
8. Cannon, P.M., W. Wilson, E. Byles, S.M. Kingsman, and A.J. Kingsman. 1994. Human immunodeficiency virus type 1 integrase: Effect on viral replication of mutations at highly conserved residues. J. Virol. 68: 4768-4775.
9. Chow, S.A., K. 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.
10. Colicelli, J. and S.P. Goff. 1985. Mutants and pseudorevertants of Moloney murine leukemia virus with alterations at the integration site. Cell 42: 573-580.
11. _. 1988. Sequence and spacing requirements of a retrovirus integration site. J. Mol Biol. 199: 47-59.
12. 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.
13. Donehower, L.A. and H.E. Varmus. 1984. A mutant murine leukemia virus with a single missense codon in pol is defective in a function affecting integration. Proc. Natl. Acad. Sci. 81: 6461-6465.
14. Dotan, I., B.P. Scottoline, T.S. Heuer and P.O. Brown. 1995. Characterization of recombinant murine leukemia virus integrase. J. Virol. 69: 456-468.
15. 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.
16. 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 polynucleotidyl transferases. Science 266: 1981-1986.
17. Ellison, V. and P.O. Brown. 1994. A stable complex between integrase and viral DNA ends mediates human immunodeficiency virus integration in vitro. Proc. Natl. Acad. Sci. 91: 7316-7320.
18. 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 dimer. J. Biol. Chem. 270: 3320-3326.
19. Engelman, A. and R. Craigie. 1992. Identification of conserved amino acid residues critical for human immunodeficency virus type 1 integrase function in vitro. J. Virol. 66: 6361-6369.
20. 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.
21. 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.
22. Engelman, A.,G. Englund, J.M. Orenstein, M.A. Martin, and R. Craigie. 1995. Multiple effects of mutations in human immunodeficiency virus integrase on viral replication. J. Virol. 69: 2729-2736.
23. Fayet, O., P. Ramond, P. Polard, M.F. Prere, and M. Chandler. 1990. Functional similarities between retroviruses and the IS3 family of bacterial insertion sequences? Mol Microbiol. 4: 1771-1777.
24. Fitzgerald, M.L., A.C. Vora, and D.P. Grandgenett. 1990. Removal of 3′-OH-terminal nucleotides from blunt ended long terminal repeat termini by the avian retrovirus integration protein. J. Virol. 64: 5656-5659.
25. Fujiwara, T. and K. Mizuuchi. 1988. Retroviral DNA integration: Structure of an integration intermediate. Cell 54: 497-504.
26. Goff, S.P. 1992. Genetics of retroviral integration. Annu. Rev. Genet. 26: 527-544.
27. Hippenmeyer, P.J. and D.P. Grandgenett. 1985. Mutants of the Rous sarcoma virus reverse transcriptase gene arc defective in early replication events. J. Biol. Chem 260: 8250-8256.
28. Katz, R.A. and A.M. Skalka. 1994. The retroviral enzymes. Annu. Rev. Biochem. 63: 133-173.
29. 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.
30. Katzman, M. and M. Sudol. 1994. In vitro activities of purified visna virus integrase. J. Virol. 68: 3558-3569.
31. 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.
32. Kulkosky, J., K.S. Jones, R.A. Katz, J.P.G. Mack, and A.M. Skala. 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.
33. LaFemina, R.L., P.L. Callahan, and M.G. Cordingley. 1991. Substrate specificity of recombinant human immunodeficiency virus integrase. J. Virol. 65: 5624-5630.
34. LaFemina, R.L., C.L. Schneider, H.L. Robbins, P.L. Callahan, K. LeGrow, E. Roth, W.A. Schleif, and E.L. 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.
35. Lavoie, B.D., B.S. Chan, R.G. Allison, and G. Chaconas. 1991. Structural aspects of a higher order nucleoprotein complex: Induction of an altered DNA structure at the Mu-host junction in the Mu type 1 transpososome. EMBO J. 10:3051-3059.
36. 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.
37. Leavitt, A.D., L. Shiue, and H.E. Varmus. 1993. Site-directed mutagenesis of HIV-1 integrase demonstrate differential effects on integrase in vitro. J. Biol. Chem. 268: 2113-2119.
38. Leroy, J.L., M. Kochoyan, T. Huynh-Dinh, and M. Geuron. 1988. Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton. J. Mol. Biol. 16: 223-237.
39. Mizuuchi, K. 1992. Polynucleotidyl transfer reactions in transpositional DNA recombination. J. Biol. Chem. 267: 21273-21276.
40. Moe, J.G. and I.M. Russu. 1992. Kinetics and energetics of base-Pair opening in 5′-d(CGCGAATTCGCG)-3′ and a substituted dodecamer containing G-T mismatches. Biochemistry 31: 8421-8428.
41. Muller, H.-P. and H.E. Varmus. 1994. DNA bending creates favored sites for retroviral integration: An explanation for preferred insertion sites in nucleosomes. EMBO J. 13: 4707-4714.
42. Pahl, A. and RM. Flugel. 1993. Endonucleolytic cleavage and DNA-joining activities of the integration protein of human foamy virus. J. Virol. 67: 5426-5434.
43. Panganiban, A.T. and H.M. Temin. 1983. The terminal nucleotides of retrovirus DNA are required for integration but not virus production. Nature 306: 155-160.
44. _. 1984. The retrovirus pol gene encodes a product required for DNA integration: Identification of a retrovirus int locus. Proc. Natl Acad Sci. 81: 7885-7889.
45. Polard, P. and M. Chandler. 1995. Bacterial transposases and retroviral integrases. Mol. Microbiol. 15: 13-23.
46. Pruss, D., F.D. Bushman, and A.P. Wolffe. 1994a. Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core. Proc. Natl Acad. Sci. 91: 5913-5917.
47. Pruss, D., R. Reeves, F.D. Bushman, and A.P. Wolffe. 1994b. The influence of DNA and nucleosome structure on integration events directed by HIV integrase. J. Biol. Chem. 269: 25031-25041.
48. 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.
49. Ramsden, D.A., J.F. McBlane, D.C. van Gent, and M. Gellert. 1996. Distinct DNA sequence and structure requirements for the two sites of V(D)J recombination signal cleavage. EMBO J. 15: 3197-3206.
50. Rice, P.A. and K. Mizuuchi. 1995. Structure of the bacteriophage Mu transposase core: A common structural motif for DNA transposition and retroviral integration. Cell 82: 209-220.
51. 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
52. Rowland, S.J. and K.G.H. Dyke. 1990. Tn552, a novel transposable element from Staphylococcus aureus. Mol Microbiol. 4: 961-975.
53. Sambrook, J., E.F. Fritsch, and T. Maniatis. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
54. Savilahti, H., P.A. Rice, and K. Mizuuchi. 1995. The phage Mu transpososome core: DNA requirements for assembly and funcion. EMBO J. 14: 4893-4903.
55. Schwartzberg, P.J., J. Colicelli, and S.P. Goff. 1984. Construction and analysis of deletion mutations in the pol gene of Moloney murine leukemia virus: A new viral function required for productive infection. Cell 37: 1043-1052.
56. Shapiro, J. 1979. Molecular model for the transposition of bacteriophage Mu and other transposable elements. Proc. Natl. Acad. Sci. 76: 1933-1937.
57. Sherman, P.A. and J.A. Fyfe. 1990. Human immunodeficiency virus integration protein expressed in Escherichia coli possesses selective DNA cleaving activity. J. Virol. 87: 5119-5123.
58. Sherman, P.A., M.L. Dickenson, and J.A. Fyfe. 1992. Human immunodeficiency virus type 1 integration protein: DNA cleaving activity. J. Virol. 66: 3593-3601.
59. Taddeo, B., W.A. Haseltine, and C.M. Farnet. 1994. Integrase mutants of human immmunodeficiency virus type 1 wth a specific defect in integration. J. Virol. 68: 8401-8405.
60. van den Ent, F.M., C. Vink, and R.H. Plasterk. 1994. DNA substrate requirements for different activities of the human immunodeficiency virus type 1 integrase protein. J. Virol. 68: 7825-7832.
61. van Gent, D.C., Y. Elgersma, M.W.J. Bolk, C. Vink, and R.H.A. Plasterk. 1991. DNA binding properties of the integrase of human immunodeficiency viruses types 1 and 2. Nucleic Acids Res. 19: 3821-3827.
62. van Gent, D.C., A.A.M. Oude Groeneger, and R.H.A. Plasterk 1992. Mutational analyis of the integrase protein of human immunodeficiency virus type 2. Proc. Natl. Acad. Sci. 89: 9598-9602.
63. 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: 3261-3268.
64. van Gent, D.C., K. Mizuuchi, and M. Gellert. 1996. Initiation of V(D)J recombination: similarities to transposition and retroviral integration. Science 271: 1592-1594.
65. 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.
66. Vink, C. and R.H.A. Plasterk. 1993. The human immunodeficiency virus integrase protein. Trends Genet. 9: 433-437.
67. Vink, C., D.C. van Gent, Y. Elgersma, and R.H.A. Plasterk. 1991a. Human immunodeficiency virus integrase protein requires a subterminal position of its viral DNA recognition sequence for efficient cleavage. J. Virol. 65: 4636-4644.
68. Vink, C., E. Yeheskiely, G.A. van der Marcl, J.H. van Bloom, and R.H.A. Plasterk. 1991b. Site-specific hydrolysis and alcoholysis of human immunodeficiency virus DNA termini mediated by the viral integrase protein. Nucleic Acids Res. 19: 6691-6698.
69. 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.
70. Vink, C., K.H. van der Linden, and R.H.A. Plasterk. 1994. Activities of the feline imunodeficiency virus integrase protein produced in Escherichia coli. J. Virol. 68: 1468-1474.
71. Whitcomb, J.M. and S.H. Hughes. 1992. Retroviral reverse transcription and integration: Progress and problems. Annu. Rev. Cell Biol. 8: 275-306.
72. Wiskerchen, M. and M.A. Muesing. 1995. Human immunodeficiency virus type 1 integrase: Effects of mutations on viral ability to integrate, direct viral gene expression from unintegrated viral DNA templates, and sustain viral propagation in primary cells. J. Virol. 69: 376-386.