1887

Abstract

Many reports describe the characteristics of susceptible viral DNA substrates to various retroviral integrases during reactions in which manganese serves as the divalent cation cofactor for site-specific nicking. However, manganese is known to alter the specificity of some endonucleases and magnesium may be the divalent cation used during retroviral integration . To address these concerns, we identified conditions under which the integrases of human immunodeficiency virus type 1 and visna virus were optimally active with magnesium (the first time such activity was shown for visna virus integrase) and used these conditions to test the susceptibility of a series of oligodeoxynucleotide substrates. The data show that two base pairs immediately internal to the conserved CA dinucleotide near the termini of retroviral DNA are selectively recognized by the two integrases and that the final six base pairs of viral DNA contain sufficient sequence information for specific recognition and cleavage by each enzyme. The results validate the importance of the subterminal viral DNA positions even in the presence of magnesium and identify viral DNA positions that functionally interact with integrase. The data obtained under magnesium-dependent conditions, which were obtained with substrates containing single and multiple base-pair substitutions and two different retroviral integrases, are consistent with those previously obtained with manganese. Thus, the large body of manganese-dependent data identifying terminal viral DNA positions that are important in substrate recognition by various integrases likely reflects interactions that are biologically relevant.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-81-3-839
2000-03-01
2020-10-28
Loading full text...

Full text loading...

/deliver/fulltext/jgv/81/3/0810839a.html?itemId=/content/journal/jgv/10.1099/0022-1317-81-3-839&mimeType=html&fmt=ahah

References

  1. Asante-Appiah, E. & Skalka, A. M. ( 1997a; ). A metal-induced conformational change and activation of HIV-1 integrase. Journal of Biological Chemistry 272, 16196-16205.[CrossRef]
    [Google Scholar]
  2. Asante-Appiah, E. & Skalka, A. M. (1997b). Molecular mechanisms in retrovirus DNA integration. Antiviral Research 36(3), 139–156.
  3. Balakrishnan, M. & Jonsson, C. B. ( 1997; ). Functional identification of nucleotides conferring substrate specificity to retroviral integrase reactions. Journal of Virology 71, 1025-1035.
    [Google Scholar]
  4. Brown, P. O. ( 1997; ). Integration. In Retroviruses, pp. 161-203. Edited by J. M. Coffin, S. H. Hughes & H. E. Varmus. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  5. Brown, P. O., Bowerman, B., Varmus, H. E. & Bishop, J. M. ( 1987; ). Correct integration of retroviral DNA in vitro. Cell 49, 347-356.[CrossRef]
    [Google Scholar]
  6. Bujacz, G., Alexandratos, J., Wlodawer, A., Merkel, G., Andrake, M., Katz, R. A. & Skalka, A. M. ( 1997; ). Binding of different divalent cations to the active site of avian sarcoma virus integrase and their effects on enzymatic activity. Journal of Biological Chemistry 272, 18161-18168.[CrossRef]
    [Google Scholar]
  7. Bushman, F. D. & Craigie, R. ( 1991; ). Activities of human immunodeficiency virus (HIV) integration protein in vitro: specific cleavage and integration of HIV DNA. Proceedings of the National Academy of Sciences, USA 88, 1339-1343.[CrossRef]
    [Google Scholar]
  8. Carteau, S., Batson, S. C., Poljak, L., Mouscadet, J.-F., de Rocquigny, H., Darlix, J.-L., Roques, B. P., Kas, E. & Auclair, C. ( 1997; ). Human immunodeficiency virus type 1 nucleocapsid protein specifically stimulates Mg2+-dependent DNA integration in vitro. Journal of Virology 71, 6225-6229.
    [Google Scholar]
  9. Cobrinik, D. A., Aiyar, A., Ge, Z., Katzman, M., Huang, H. & Leis, J. ( 1991; ). Overlapping retrovirus U5 sequence elements are required for efficient integration and initiation of reverse transcription. Journal of Virology 65, 3864-3872.
    [Google Scholar]
  10. Craigie, R., Fujiwara, T. & Bushman, F. ( 1990; ). The IN protein of Moloney murine leukemia virus processes the viral DNA ends and accomplishes their integration in vitro. Cell 62, 829-837.[CrossRef]
    [Google Scholar]
  11. Ellison, V., Abrams, H., Roe, T., Lifson, J. & Brown, P. ( 1990; ). Human immunodeficiency virus integration in a cell-free system. Journal of Virology 64, 2711-2715.
    [Google Scholar]
  12. Engelman, A. & Craigie, R. ( 1995; ). Efficient magnesium-dependent human immunodeficiency virus type 1 integrase activity. Journal of Virology 69, 5908-5911.
    [Google Scholar]
  13. Esposito, D. & Craigie, R. ( 1998; ). Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein–DNA interaction. EMBO Journal 17, 5832-5843.[CrossRef]
    [Google Scholar]
  14. Farnet, C. M. & Haseltine, W. A. ( 1990; ). Integration of human immunodeficiency virus type 1 DNA in vitro. Proceedings of the National Academy of Sciences, USA 87, 4164-4168.[CrossRef]
    [Google Scholar]
  15. Fitzgerald, M. L., Vora, A. C., Zeh, W. G. & Grandgenett, D. P. ( 1992; ). Concerted integration of viral DNA termini by purified avian myeloblastosis virus integrase. Journal of Virology 66, 6257-6263.
    [Google Scholar]
  16. Fujiwara, T. & Mizuuchi, K. ( 1988; ). Retroviral DNA integration: structure of an integration intermediate. Cell 54, 497-504.[CrossRef]
    [Google Scholar]
  17. Fujiwara, T. & Craigie, R. ( 1989; ). Integration of mini-retroviral DNA: a cell-free reaction for biochemical analysis of retroviral integration. Proceedings of the National Academy of Sciences, USA 86, 3065-3069.[CrossRef]
    [Google Scholar]
  18. Fulton, A. B. ( 1982; ). How crowded is the cytoplasm? Cell 30, 345-347.[CrossRef]
    [Google Scholar]
  19. Goldgur, Y., Dyda, F., Hickman, A. B., Jenkins, T. M., Craigie, R. & Davies, D. R. ( 1998; ). Three new structures of the core domain of HIV-1 integrase: an active site that binds magnesium. Proceedings of the National Academy of Sciences, USA 95, 9150-9154.[CrossRef]
    [Google Scholar]
  20. Goodarzi, G., Im, G.-J., Brackmann, K. & Grandgenett, D. ( 1995; ). Concerted integration of retrovirus-like DNA by human immunodeficiency virus type 1 integrase. Journal of Virology 69, 6090-6097.
    [Google Scholar]
  21. Hsu, M. & Berg, P. ( 1978; ). Altering the specificity of restriction endonuclease: effect of replacing Mg2+ with Mn2+. Biochemistry 17, 131-138.[CrossRef]
    [Google Scholar]
  22. Huang, P., Dong, A. & Caughey, W. S. ( 1995; ). Effects of dimethyl sulfoxide, glycerol, and ethylene glycol on secondary structure of cytochrome c and lysozyme as observed by infrared spectroscopy. Journal of Pharmaceutical Sciences 84, 387-392.[CrossRef]
    [Google Scholar]
  23. Jackson, M. & Mantsch, H. H. ( 1991; ). Beware of proteins in DMSO. Biochimica et Biophysica Acta 1078, 231-235.[CrossRef]
    [Google Scholar]
  24. Katz, R. A., Merkel, G., Kulkosky, J., Leis, J. & Skalka, A. M. ( 1990; ). The avian retroviral IN protein is both necessary and sufficient for integrative recombination in vitro. Cell 63, 87-95.[CrossRef]
    [Google Scholar]
  25. Katzman, M. & Katz, R. A. ( 1999; ). Substrate recognition by retroviral integrases. Advances in Virus Research 52, 371-395.
    [Google Scholar]
  26. Katzman, M. & Sudol, M. ( 1994; ). In vitro activities of purified visna virus integrase. Journal of Virology 68, 3558-3569.
    [Google Scholar]
  27. Katzman, M. & Sudol, M. ( 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. Journal of Virology 69, 5687-5696.
    [Google Scholar]
  28. Katzman, M. & Sudol, M. ( 1996; ). Influence of subterminal viral DNA nucleotides on differential susceptibility to cleavage by human immunodeficiency virus type 1 and visna virus integrases. Journal of Virology 70, 9069-9073.
    [Google Scholar]
  29. Katzman, M. & Sudol, M. ( 1998; ). 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 72, 1744-1753.
    [Google Scholar]
  30. Katzman, M., Katz, R. A., Skalka, A. M. & Leis, J. ( 1989; ). The avian retroviral integration protein cleaves the terminal sequences of linear viral DNA at the in vivo sites of integration. Journal of Virology 63, 5319-5327.
    [Google Scholar]
  31. Knull, H. & Minton, A. P. ( 1996; ). Structure within eukaryotic cytoplasm and its relationship to glycolytic metabolism. Cell Biochemistry and Function 14, 237-248.[CrossRef]
    [Google Scholar]
  32. Kukolj, G. & Skalka, A. M. ( 1995; ). Enhanced and coordinated processing of synapsed viral DNA ends by retroviral integrases in vitro. Genes & Development 9, 2556-2567.[CrossRef]
    [Google Scholar]
  33. LaFemina, R. L., Callahan, P. L. & Cordingly, M. G. ( 1991; ). Substrate specificity of recombinant human immunodeficiency virus integrase protein. Journal of Virology 65, 5624-5630.
    [Google Scholar]
  34. Lee, S. P. & Han, M. K. ( 1996; ). Zinc stimulates Mg2+-dependent 3′-processing activity of human immunodeficiency virus type 1 integrase in vitro. Biochemistry 35, 3837-3844.[CrossRef]
    [Google Scholar]
  35. Lee, S. P., Kin, H. G., Censullo, M. L. & Han, M. K. ( 1995a; ). Characterization of Mg2+-dependent 3′-processing activity for human immunodeficiency virus type 1 integrase in vitro: Real-time kinetic studies using fluorescence resonance energy transfer. Biochemistry 34, 10205-10214.[CrossRef]
    [Google Scholar]
  36. Lee, S. P., Censullo, M. L., Kim, H. G. & Han, M. K. ( 1995b; ). Substrate-length-dependent activities of human immunodeficiency virus type 1 integrase in vitro: differential DNA binding affinities associated with different lengths of substrates. Biochemistry 34, 10215-10223.[CrossRef]
    [Google Scholar]
  37. Lee, S. P., Xiao, J., Knutson, J. R., Lewis, M. S. & Han, M. K. ( 1997; ). Zn2+ promotes the self-association of human immunodeficiency virus type-1 integrase in vitro. Biochemistry 36, 173-180.[CrossRef]
    [Google Scholar]
  38. Maignan, S., Guilloteau, J.-P., Zhou-Liu, Q., Clément-Mella, C. & Mikol, V. ( 1998; ). Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases. Journal of Molecular Biology 282, 359-368.[CrossRef]
    [Google Scholar]
  39. Miller, M. D., Bor, Y.-C. & Bushman, F. ( 1995; ). Target DNA capture by HIV-1 integration complexes. Current Biology 5, 1047-1055.[CrossRef]
    [Google Scholar]
  40. Minton, A. P. ( 1998; ). Molecular crowding: analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion. Methods in Enzymology 295, 127-149.
    [Google Scholar]
  41. Pemberton, I. K., Buckle, M. & Buc, H. ( 1996; ). The metal ion-induced cooperative binding of HIV-1 integrase to DNA exhibits a marked preference for Mn(II) rather than Mg(II). Journal of Biological Chemistry 271, 1498-1506.[CrossRef]
    [Google Scholar]
  42. Sherman, P. A., Dickson, M. L. & Fyfe, J. A. ( 1992; ). Human immunodeficiency virus type 1 integration protein: DNA sequence requirements for cleaving and joining reactions. Journal of Virology 66, 3593-3601.
    [Google Scholar]
  43. Shibagaki, Y., Holmes, M. L., Appa, R. S. & Chow, S. A. ( 1997; ). Characterization of feline immunodeficiency virus integrase and analysis of functional domains. Virology 230, 1-10.[CrossRef]
    [Google Scholar]
  44. Vermote, C. L. M. & Halford, S. E. ( 1992; ). EcoRV restriction endonuclease: communication between catalytic metal ions and DNA recognition. Biochemistry 31, 6082-6089.[CrossRef]
    [Google Scholar]
  45. Vora, A. C. & Grandgenett, D. P. ( 1995; ). Assembly and catalytic properties of retrovirus integrase-DNA complexes capable of efficiently performing concerted integration. Journal of Virology 69, 7483-7488.
    [Google Scholar]
  46. Wolfe, A. L., Felock, P. J., Hastings, J. C., Uncapher Blau, C. & Hazuda, D. J. ( 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. Journal of Virology 70, 1424-1432.
    [Google Scholar]
  47. Zheng, R., Jenkins, T. M. & Craigie, R. ( 1996; ). Zinc folds the N-terminal domain of HIV-1 integrase, promotes multimerization, and enhances catalytic activity. Proceedings of the National Academy of Sciences, USA 93, 13659-13664.[CrossRef]
    [Google Scholar]
  48. Zimmerman, S. B. & Minton, A. P. ( 1993; ). Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annual Review of Biophysics and Biomolecular Structure 22, 27-65.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-81-3-839
Loading
/content/journal/jgv/10.1099/0022-1317-81-3-839
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error