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. 1996 Dec;70(12):9069–9073. doi: 10.1128/jvi.70.12.9069-9073.1996

Influence of subterminal viral DNA nucleotides on differential susceptibility to cleavage by human immunodeficiency virus type 1 and visna virus integrases.

M Katzman 1, M Sudol 1
PMCID: PMC191014  PMID: 8971046

Abstract

A comparison of the extents of site-specific cleavage of U5 and U3 viral DNA termini by the integrases of human immunodeficiency virus type 1 and visna virus guided the quantitative testing of oligonucleotide substrates containing specific base substitutions. The simultaneous exchange of positions 5 and 6 between U3 substrates switched the patterns of differential susceptibility to the two integrases. The activity of visna virus integrase was more dependent on the identity of position 5 adjacent to the invariant CA bases than on position 6, whereas human immunodeficiency virus type 1 integrase appeared to interact even more critically with position 6. Although the paired natural substrates of most lentiviral integrases match at positions 7 and 8, these bases were not important for susceptibility of U5 substrates. In fact, the final six U5 positions contained all of the sequence information necessary for susceptibility. These results suggest that constraints other than integration influence the terminal inverted repeats of retroviral DNA.

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Selected References

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  1. 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]
  2. Bushman F. D., Craigie R. Integration of human immunodeficiency virus DNA: adduct interference analysis of required DNA sites. Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3458–3462. doi: 10.1073/pnas.89.8.3458. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cannon P. M., Byles E. D., Kingsman S. M., Kingsman A. J. Conserved sequences in the carboxyl terminus of integrase that are essential for human immunodeficiency virus type 1 replication. J Virol. 1996 Jan;70(1):651–657. doi: 10.1128/jvi.70.1.651-657.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cannon P. M., Wilson W., Byles E., Kingsman S. M., Kingsman A. J. Human immunodeficiency virus type 1 integrase: effect on viral replication of mutations at highly conserved residues. J Virol. 1994 Aug;68(8):4768–4775. doi: 10.1128/jvi.68.8.4768-4775.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cobrinik D., Aiyar A., Ge Z., Katzman M., Huang H., Leis J. Overlapping retrovirus U5 sequence elements are required for efficient integration and initiation of reverse transcription. J Virol. 1991 Jul;65(7):3864–3872. doi: 10.1128/jvi.65.7.3864-3872.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. 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]
  7. Goff S. P. Genetics of retroviral integration. Annu Rev Genet. 1992;26:527–544. doi: 10.1146/annurev.ge.26.120192.002523. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. 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]
  10. Katzman M., Sudol M. In vitro activities of purified visna virus integrase. J Virol. 1994 Jun;68(6):3558–3569. doi: 10.1128/jvi.68.6.3558-3569.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Katzman M., Sudol M. 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. 1995 Sep;69(9):5687–5696. doi: 10.1128/jvi.69.9.5687-5696.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Katzman M., Sudol M. Nonspecific alcoholysis, a novel endonuclease activity of human immunodeficiency virus type 1 and other retroviral integrases. J Virol. 1996 Apr;70(4):2598–2604. doi: 10.1128/jvi.70.4.2598-2604.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kitamura Y., Ayukawa T., Ishikawa T., Kanda T., Yoshiike K. Human endogenous retrovirus K10 encodes a functional integrase. J Virol. 1996 May;70(5):3302–3306. doi: 10.1128/jvi.70.5.3302-3306.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kukolj G., Skalka A. M. Enhanced and coordinated processing of synapsed viral DNA ends by retroviral integrases in vitro. Genes Dev. 1995 Oct 15;9(20):2556–2567. doi: 10.1101/gad.9.20.2556. [DOI] [PubMed] [Google Scholar]
  15. Kulkosky J., Skalka A. M. Molecular mechanism of retroviral DNA integration. Pharmacol Ther. 1994;61(1-2):185–203. doi: 10.1016/0163-7258(94)90062-0. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Leavitt A. D., Rose R. B., Varmus H. E. 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. 1992 Apr;66(4):2359–2368. doi: 10.1128/jvi.66.4.2359-2368.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lee S. P., Censullo M. L., Kim H. G., Han M. K. Substrate-length-dependent activities of human immunodeficiency virus type 1 integrase in vitro: differential DNA binding affinities associated with different lengths of substrates. Biochemistry. 1995 Aug 15;34(32):10215–10223. doi: 10.1021/bi00032a015. [DOI] [PubMed] [Google Scholar]
  19. Masuda T., Planelles V., Krogstad P., Chen I. S. Genetic analysis of human immunodeficiency virus type 1 integrase and the U3 att site: unusual phenotype of mutants in the zinc finger-like domain. J Virol. 1995 Nov;69(11):6687–6696. doi: 10.1128/jvi.69.11.6687-6696.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Mazumder A., Gupta M., Pommier Y. Methylphosphonodiester substitution near the conserved CA dinucleotide in the HIV LTR alters both extent of 3'-processing and choice of nucleophile by HIV-1 integrase. Nucleic Acids Res. 1994 Oct 25;22(21):4441–4448. doi: 10.1093/nar/22.21.4441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Mazumder A., Pommier Y. Processing of deoxyuridine mismatches and abasic sites by human immunodeficiency virus type-1 integrase. Nucleic Acids Res. 1995 Aug 11;23(15):2865–2871. doi: 10.1093/nar/23.15.2865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Moore S. P., Powers M., Garfinkel D. J. Substrate specificity of Ty1 integrase. J Virol. 1995 Aug;69(8):4683–4692. doi: 10.1128/jvi.69.8.4683-4692.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Pahl A., Flügel R. M. Endonucleolytic cleavages and DNA-joining activities of the integration protein of human foamy virus. J Virol. 1993 Sep;67(9):5426–5434. doi: 10.1128/jvi.67.9.5426-5434.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Reicin A. S., Kalpana G., Paik S., Marmon S., Goff S. Sequences in the human immunodeficiency virus type 1 U3 region required for in vivo and in vitro integration. J Virol. 1995 Sep;69(9):5904–5907. doi: 10.1128/jvi.69.9.5904-5907.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Sherman P. A., Dickson M. L., Fyfe J. A. Human immunodeficiency virus type 1 integration protein: DNA sequence requirements for cleaving and joining reactions. J Virol. 1992 Jun;66(6):3593–3601. doi: 10.1128/jvi.66.6.3593-3601.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. Störmann K. D., Schlecht M. C., Pfaff E. Comparative studies of bacterially expressed integrase proteins of caprine arthritis-encephalitis virus, maedi-visna virus and human immunodeficiency virus type 1. J Gen Virol. 1995 Jul;76(Pt 7):1651–1663. doi: 10.1099/0022-1317-76-7-1651. [DOI] [PubMed] [Google Scholar]
  28. Vink C., van Gent D. C., Elgersma Y., Plasterk R. H. Human immunodeficiency virus integrase protein requires a subterminal position of its viral DNA recognition sequence for efficient cleavage. J Virol. 1991 Sep;65(9):4636–4644. doi: 10.1128/jvi.65.9.4636-4644.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Vink C., van der Linden K. H., Plasterk R. H. Activities of the feline immunodeficiency virus integrase protein produced in Escherichia coli. J Virol. 1994 Mar;68(3):1468–1474. doi: 10.1128/jvi.68.3.1468-1474.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Whitcomb J. M., Hughes S. H. Retroviral reverse transcription and integration: progress and problems. Annu Rev Cell Biol. 1992;8:275–306. doi: 10.1146/annurev.cb.08.110192.001423. [DOI] [PubMed] [Google Scholar]
  31. Yoshinaga T., Fujiwara T. Different roles of bases within the integration signal sequence of human immunodeficiency virus type 1 in vitro. J Virol. 1995 May;69(5):3233–3236. doi: 10.1128/jvi.69.5.3233-3236.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Yoshinaga T., Kimura-Ohtani Y., Fujiwara T. Detection and characterization of a functional complex of human immunodeficiency virus type 1 integrase and its DNA substrate by UV cross-linking. J Virol. 1994 Sep;68(9):5690–5697. doi: 10.1128/jvi.68.9.5690-5697.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. van den Ent F. M., Vink C., Plasterk R. H. DNA substrate requirements for different activities of the human immunodeficiency virus type 1 integrase protein. J Virol. 1994 Dec;68(12):7825–7832. doi: 10.1128/jvi.68.12.7825-7832.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]

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