Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지

Functional Nucleotides of U5 LTR Determining Substrate Specificity of Prototype Foamy Virus Integrase

  • Kang, Seung-Yi (Department of Biotechnology, Chung-Ang University) ;
  • Ahn, Dog-Gn (Department of Biotechnology, Chung-Ang University) ;
  • Lee, Chan (Department of Food Science and Technology, Chung-Ang University) ;
  • Lee, Yong-Sup (Kyung Hee East-West Pharmaceutical Research Institute, College of Pharmacy, Kyung Hee University) ;
  • Shin, Cha-Gyun (Department of Biotechnology, Chung-Ang University)
  • Published : 2008.06.30
Download PDF
⟨ Previous Next ⟩

Abstract

In order to study functional nucleotides in prototype foamy virus (PFV) DNA on specific recognition by PFV integrase (IN), we designed chimeric U5 long terminal repeat (LTR) DNA substrates by exchanging comparative sequences between human immunodeficiency virus type-1 (HIV-1) and PFV U5 LTRs, and investigated the 3'-end processing reactivity using HIV-1 and PFV INs, respectively. HIV-1 IN recognized the nucleotides present in the fifth and sixth positions at the 3'-end of the substrates more specifically than any other nucleotides in the viral DNA. However, PFV IN recognized the eighth and ninth nucleotides as distinctively as the fifth and sixth nucleotides in the reactions. In addition, none of the nucleotides present in the twelfth, sixteenth, seventeenth, eighteenth, nineteenth, and twentieth positions were not differentially recognized by HIV-1 and PFV INs, respectively. Therefore, our results suggest that the functional nucleotides that are specifically recognized by its own IN in the PFV U5 LTR are different from those in the HIV-1 U5 LTR in aspects of the positions and nucleotide sequences. Furthermore, it is proposed that the functional nucleotides related to the specific recognition by retroviral INs are present inside ten nucleotides from the 3'-end of the U5 LTR.

Keywords

References

  1. Achong, B. G., P. W. Mansell, M. A. Epstein, and P. Clifford. 1971. An unusual virus in cultures from a human nasopharangyl carcinoma. J. Natl. Cancer Inst. 46: 299-307
  2. Appa, R. S., C.-G. Shin, P. Lee, and S. A. Chow. 2001. Role of the nonspecific DNA-binding region and $\alpha$ helices within the core domain of retroviral integrase in selecting target DNA sites for integration. J. Biol. Chem. 276: 45846-45855
  3. 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. USA 86: 2525-2529
  4. Bushman, F. D. and R. Craigie. 1990. Sequence requirements for integration of Moloney murine leukemia virus DNA in vitro. J. Virol. 64: 5645-5648
  5. Bushman, F. and R. Craigie. 1991. Activities of human immunodeficiency virus integration protein in vivo. Proc. Natl. Acad. Sci. USA 88: 1339-1343
  6. Daniel, R., R. A. Katz, and A. M. Skalka. 1999. A role for DNA-PK in retroviral DNA integration. Science 284: 644-647 https://doi.org/10.1126/science.284.5414.644
  7. Du, Z., P. O. Ilyinskii, K. Lally, R. 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
  8. Ellison, V. and P. O. Brown. 1994. A stable complex between integrase and viral DNA ends mediates HIV integration in vitro. Proc. Natl. Acad. Sci. USA 91: 7316-7320
  9. 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 https://doi.org/10.1016/0092-8674(91)90297-C
  10. Fujiwara, T. and K. Mizuuchi. 1988. Retrovial DNA integration: Structure of an integration intermediate. Cell 54: 497-504 https://doi.org/10.1016/0092-8674(88)90071-2
  11. Gerton, J. L., D. Herschlag, and P. O. Brown. 1999. Stereospecificity of reactions catalyzed by HIV-1 integrase. J. Biol. Chem. 274: 33480-33487 https://doi.org/10.1074/jbc.274.47.33480
  12. Kang, C. S., S.-Y. Son, and I. S. Bang. 2006. High-level expression of T4 endonuclease V in insect cells as biologically active form. J. Microbiol. Biotechnol. 16: 1583-1590
  13. 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
  14. Kim, Y. J., H. S. Lee, S. S. Bae, J. H. Jeon, J. K. Lim, Y. Cho, K. H. Nam, S. G. Kang, S.-J. Kim, S.-T. Kwon, and J.-H. Lee. 2007. Cloning, purification, and characterization of a new DNA polymerasefrom a hyperthermophilic archaeon, Thermococcus sp. Nal. J. Microbiol. Biotechnol. 17: 1090-1097
  15. Lafemina, R. L., P. L. Callahan, and M. G. Cordingley. 1991. Substrate specificity of recombinant human immunodeficiency virus integrase protein. J. Virol. 65: 5624-5630
  16. Lee, H. S., S. Y. Kang, and C.-G. Shin. 2005. Characterization of the functional domains of human foamy virus integrase using chimeric integrases. Mol. Cells 19: 246-255
  17. Linial, M. L. 1999. Foamy viruses are unconventional retroviruses. J. Virol. 73: 1747-1755
  18. Masuda, T., M. J. Kuroda, and S. Harada. 1998. Specific and independent recognition of U3 and U5 att sites by human immunodeficiency virus type 1 integrase in vivo. J. Virol. 72: 8396-8402
  19. Mizuuchi, K. 1992. Polynucleotidyl transfer reaction in transpositional DNA recombination. Annu. Rev. Biochem. 61: 1011-1051 https://doi.org/10.1146/annurev.bi.61.070192.005051
  20. Moebes, A., J. Enssle, P. D. Bieniasz, M. Heinkelein, D. Lindermann, M. Bock, M. O. McClure, and A. Rethwilm. 1997. Human foamy virus reverse transcription that occurs late in the viral replication cycle. J. Virol. 71: 7305-7311
  21. Murphy, L. E., T. De Los Santos, and S. P. Goff. 1993. Mutational analysis of the sequences at the termini of the Moloney murine leukemia virus DNA required for integration. Virology 195: 432-440 https://doi.org/10.1006/viro.1993.1393
  22. Oh, Y.-T. and C.-G. Shin. 1999. Comparison of enzymatic activities of the HIV-1 and HFV integrases to their U5 LTR substrate. Biochem. Mol. Biol. Int. 47: 621-629
  23. Pahl, A. and R. M. Flugel. 1993. Endonucleolytic cleavages and DNA-joining activities of the integration protein of human foamy virus. J. Virol. 67: 5426-5434
  24. Park, M.-O., K.-H. Lim, T.-H. Kim, and H.-I. Chang. 2007. Characterization of site-specific recombination by the integrase MJ1 from enterococcal bacteriophage $\varphi$FC1. J. Microbiol. Biotechnol. 17: 342-347
  25. Reicin, A. S., G. Kalpana, S. Paik, S. Marmon, and S. P. Goff. 1995. Sequence in the human immunodeficiency virus type 1 U3 region required for in vivo and in vitro integration. J. Virol. 69: 5904-5907
  26. Rice, P., R. Craigie, and D. R. Davies. 1996. Retroviral integrases and their cousins. Curr. Opin. Struct. Biol. 6: 76-83 https://doi.org/10.1016/S0959-440X(96)80098-4
  27. 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 https://doi.org/10.1016/0092-8674(89)90401-7
  28. Snasel, J., D. Rejman, R. Liboska, Z. Tocik, T. Ruml, I. Rosenberg, and I. Pichova. 2001. Inhibition of HIV-1 integrase by modified oligonucleotides derived from U5 LTR. Eur. J. Biochem. 268: 980-986 https://doi.org/10.1046/j.1432-1327.2001.01956.x
  29. Van, T. K., S.-I. Ryu, K.-J. Lee, E.-J. Kim, and S.-B. Lee. 2007. Cloning and characterization of glycogen-debranching enzyme from hyperthermophilic archaeon Sulfolobus shibatae. J. Microbiol. Biotechnol. 17: 792-799
  30. 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 mutation. J. Virol. 67: 425-437
  31. Vink, C., D. C. van Gent, Y. Elgersma, and R. H. A. Plasterk. 1991. Human immunodeficiency virus integrase protein requires a subterminal position of its viral DNA recognition sequence for efficient cleavage. J. Virol. 65: 4636-4644