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. 1992 Apr 15;89(8):3458–3462. doi: 10.1073/pnas.89.8.3458

Integration of human immunodeficiency virus DNA: adduct interference analysis of required DNA sites.

F D Bushman 1, R Craigie 1
PMCID: PMC48887  PMID: 1533044

Abstract

The integration (IN) protein encoded by human immunodeficiency virus directs the integration of viral DNA into host DNA. We have probed the DNA sites required for the function of IN protein by attaching adducts to model DNA substrates and assaying their effects on integration in vitro. These experiments reveal that modifications in a short region on both DNA strands at the ends of the viral DNA block IN protein function. Modification of the target DNA near the point of DNA strand transfer also blocks IN protein function. Further experiments suggest that distinct subsets of the identified interactions are important for separate steps in the integration process.

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Selected References

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  1. Anderson J. E., Ptashne M., Harrison S. C. A phage repressor-operator complex at 7 A resolution. Nature. 1985 Aug 15;316(6029):596–601. doi: 10.1038/316596a0. [DOI] [PubMed] [Google Scholar]
  2. Brown P. O., Bowerman B., Varmus H. E., Bishop J. M. Retroviral integration: structure of the initial covalent product and its precursor, and a role for the viral IN protein. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2525–2529. doi: 10.1073/pnas.86.8.2525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bruckner R. C., Cox M. M. Specific contacts between the FLP protein of the yeast 2-micron plasmid and its recombination site. J Biol Chem. 1986 Sep 5;261(25):11798–11807. [PubMed] [Google Scholar]
  4. Bushman F. D., Anderson J. E., Harrison S. C., Ptashne M. Ethylation interference and X-ray crystallography identify similar interactions between 434 repressor and operator. Nature. 1985 Aug 15;316(6029):651–653. doi: 10.1038/316651a0. [DOI] [PubMed] [Google Scholar]
  5. Bushman F. D., Craigie R. Activities of human immunodeficiency virus (HIV) integration protein in vitro: specific cleavage and integration of HIV DNA. Proc Natl Acad Sci U S A. 1991 Feb 15;88(4):1339–1343. doi: 10.1073/pnas.88.4.1339. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bushman F. D., Craigie R. Sequence requirements for integration of Moloney murine leukemia virus DNA in vitro. J Virol. 1990 Nov;64(11):5645–5648. doi: 10.1128/jvi.64.11.5645-5648.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bushman F. D., Fujiwara T., Craigie R. Retroviral DNA integration directed by HIV integration protein in vitro. Science. 1990 Sep 28;249(4976):1555–1558. doi: 10.1126/science.2171144. [DOI] [PubMed] [Google Scholar]
  8. Clavel F., Hoggan M. D., Willey R. L., Strebel K., Martin M. A., Repaske R. Genetic recombination of human immunodeficiency virus. J Virol. 1989 Mar;63(3):1455–1459. doi: 10.1128/jvi.63.3.1455-1459.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Colicelli J., Goff S. P. Sequence and spacing requirements of a retrovirus integration site. J Mol Biol. 1988 Jan 5;199(1):47–59. doi: 10.1016/0022-2836(88)90378-6. [DOI] [PubMed] [Google Scholar]
  10. Craigie R., Fujiwara T., Bushman F. The IN protein of Moloney murine leukemia virus processes the viral DNA ends and accomplishes their integration in vitro. Cell. 1990 Aug 24;62(4):829–837. doi: 10.1016/0092-8674(90)90126-y. [DOI] [PubMed] [Google Scholar]
  11. Donehower L. A., Varmus H. E. A mutant murine leukemia virus with a single missense codon in pol is defective in a function affecting integration. Proc Natl Acad Sci U S A. 1984 Oct;81(20):6461–6465. doi: 10.1073/pnas.81.20.6461. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ellison V., Abrams H., Roe T., Lifson J., Brown P. Human immunodeficiency virus integration in a cell-free system. J Virol. 1990 Jun;64(6):2711–2715. doi: 10.1128/jvi.64.6.2711-2715.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Engelman A., Mizuuchi K., Craigie R. HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer. Cell. 1991 Dec 20;67(6):1211–1221. doi: 10.1016/0092-8674(91)90297-c. [DOI] [PubMed] [Google Scholar]
  14. Falvey E., Grindley N. D. Contacts between gamma delta resolvase and the gamma delta res site. EMBO J. 1987 Mar;6(3):815–821. doi: 10.1002/j.1460-2075.1987.tb04824.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Farnet C. M., Haseltine W. A. Integration of human immunodeficiency virus type 1 DNA in vitro. Proc Natl Acad Sci U S A. 1990 Jun;87(11):4164–4168. doi: 10.1073/pnas.87.11.4164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Fujiwara T., Mizuuchi K. Retroviral DNA integration: structure of an integration intermediate. Cell. 1988 Aug 12;54(4):497–504. doi: 10.1016/0092-8674(88)90071-2. [DOI] [PubMed] [Google Scholar]
  17. Grandgenett D. P., Mumm S. R. Unraveling retrovirus integration. Cell. 1990 Jan 12;60(1):3–4. doi: 10.1016/0092-8674(90)90707-l. [DOI] [PubMed] [Google Scholar]
  18. Hippenmeyer P. J., Grandgenett D. P. Requirement of the avian retrovirus pp32 DNA binding protein domain for replication. Virology. 1984 Sep;137(2):358–370. doi: 10.1016/0042-6822(84)90228-9. [DOI] [PubMed] [Google Scholar]
  19. Hong T., Drlica K., Pinter A., Murphy E. Circular DNA of human immunodeficiency virus: analysis of circle junction nucleotide sequences. J Virol. 1991 Jan;65(1):551–555. doi: 10.1128/jvi.65.1.551-555.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Katz R. A., Merkel G., Kulkosky J., Leis J., Skalka A. M. The avian retroviral IN protein is both necessary and sufficient for integrative recombination in vitro. Cell. 1990 Oct 5;63(1):87–95. doi: 10.1016/0092-8674(90)90290-u. [DOI] [PubMed] [Google Scholar]
  21. Katzman M., Katz R. A., Skalka A. M., Leis J. The avian retroviral integration protein cleaves the terminal sequences of linear viral DNA at the in vivo sites of integration. J Virol. 1989 Dec;63(12):5319–5327. doi: 10.1128/jvi.63.12.5319-5327.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. LaFemina R. L., Callahan P. L., Cordingley M. G. Substrate specificity of recombinant human immunodeficiency virus integrase protein. J Virol. 1991 Oct;65(10):5624–5630. doi: 10.1128/jvi.65.10.5624-5630.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lu A. L., Jack W. E., Modrich P. DNA determinants important in sequence recognition by Eco RI endonuclease. J Biol Chem. 1981 Dec 25;256(24):13200–13206. [PubMed] [Google Scholar]
  24. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. McClarin J. A., Frederick C. A., Wang B. C., Greene P., Boyer H. W., Grable J., Rosenberg J. M. Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution. Science. 1986 Dec 19;234(4783):1526–1541. doi: 10.1126/science.3024321. [DOI] [PubMed] [Google Scholar]
  26. Panganiban A. T., Temin H. M. The retrovirus pol gene encodes a product required for DNA integration: identification of a retrovirus int locus. Proc Natl Acad Sci U S A. 1984 Dec;81(24):7885–7889. doi: 10.1073/pnas.81.24.7885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Pauza C. D. Two bases are deleted from the termini of HIV-1 linear DNA during integrative recombination. Virology. 1990 Dec;179(2):886–889. doi: 10.1016/0042-6822(90)90161-j. [DOI] [PubMed] [Google Scholar]
  28. Pullen K. A., Champoux J. J. Plus-strand origin for human immunodeficiency virus type 1: implications for integration. J Virol. 1990 Dec;64(12):6274–6277. doi: 10.1128/jvi.64.12.6274-6277.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Qian X. H., Inman R. B., Cox M. M. Protein-based asymmetry and protein-protein interactions in FLP recombinase-mediated site-specific recombination. J Biol Chem. 1990 Dec 15;265(35):21779–21788. [PubMed] [Google Scholar]
  30. Roth M. J., Schwartzberg P. L., Goff S. P. Structure of the termini of DNA intermediates in the integration of retroviral DNA: dependence on IN function and terminal DNA sequence. Cell. 1989 Jul 14;58(1):47–54. doi: 10.1016/0092-8674(89)90401-7. [DOI] [PubMed] [Google Scholar]
  31. Schwartzberg P., Colicelli J., Goff S. P. Construction and analysis of deletion mutations in the pol gene of Moloney murine leukemia virus: a new viral function required for productive infection. Cell. 1984 Jul;37(3):1043–1052. doi: 10.1016/0092-8674(84)90439-2. [DOI] [PubMed] [Google Scholar]
  32. Sherman P. A., Fyfe J. A. Human immunodeficiency virus integration protein expressed in Escherichia coli possesses selective DNA cleaving activity. Proc Natl Acad Sci U S A. 1990 Jul;87(13):5119–5123. doi: 10.1073/pnas.87.13.5119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Siebenlist U., Gilbert W. Contacts between Escherichia coli RNA polymerase and an early promoter of phage T7. Proc Natl Acad Sci U S A. 1980 Jan;77(1):122–126. doi: 10.1073/pnas.77.1.122. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Smith J. S., Kim S. Y., Roth M. J. Analysis of long terminal repeat circle junctions of human immunodeficiency virus type 1. J Virol. 1990 Dec;64(12):6286–6290. doi: 10.1128/jvi.64.12.6286-6290.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sun L., Singer B. The specificity of different classes of ethylating agents toward various sites of HeLa cell DNA in vitro and in vivo. Biochemistry. 1975 Apr 22;14(8):1795–1802. doi: 10.1021/bi00679a036. [DOI] [PubMed] [Google Scholar]
  36. Taylor J. D., Badcoe I. G., Clarke A. R., Halford S. E. EcoRV restriction endonuclease binds all DNA sequences with equal affinity. Biochemistry. 1991 Sep 10;30(36):8743–8753. doi: 10.1021/bi00100a005. [DOI] [PubMed] [Google Scholar]
  37. Whitcomb J. M., Kumar R., Hughes S. H. Sequence of the circle junction of human immunodeficiency virus type 1: implications for reverse transcription and integration. J Virol. 1990 Oct;64(10):4903–4906. doi: 10.1128/jvi.64.10.4903-4906.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. van Gent D. C., Elgersma Y., Bolk M. W., Vink C., Plasterk R. H. DNA binding properties of the integrase proteins of human immunodeficiency viruses types 1 and 2. Nucleic Acids Res. 1991 Jul 25;19(14):3821–3827. doi: 10.1093/nar/19.14.3821. [DOI] [PMC free article] [PubMed] [Google Scholar]

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