Browse > Article

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)
Publication Information
Journal of Microbiology and Biotechnology / v.18, no.6, 2008 , pp. 1044-1049 More about this Journal
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
Integrase; foamy; 3'-end processing; retroviral; U5 LTR;
Citations & Related Records
Times Cited By KSCI : 5  (Citation Analysis)
Times Cited By Web Of Science : 2  (Related Records In Web of Science)
연도 인용수 순위
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 Bushman, F. D. and R. Craigie. 1990. Sequence requirements for integration of Moloney murine leukemia virus DNA in vitro. J. Virol. 64: 5645-5648
3 Daniel, R., R. A. Katz, and A. M. Skalka. 1999. A role for DNA-PK in retroviral DNA integration. Science 284: 644-647   DOI
4 Gerton, J. L., D. Herschlag, and P. O. Brown. 1999. Stereospecificity of reactions catalyzed by HIV-1 integrase. J. Biol. Chem. 274: 33480-33487   DOI   ScienceOn
5 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   과학기술학회마을
6 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
7 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
8 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
9 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   DOI   ScienceOn
10 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
11 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
12 Mizuuchi, K. 1992. Polynucleotidyl transfer reaction in transpositional DNA recombination. Annu. Rev. Biochem. 61: 1011-1051   DOI   ScienceOn
13 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
14 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
15 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
16 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
17 Rice, P., R. Craigie, and D. R. Davies. 1996. Retroviral integrases and their cousins. Curr. Opin. Struct. Biol. 6: 76-83   DOI   ScienceOn
18 Bushman, F. and R. Craigie. 1991. Activities of human immunodeficiency virus integration protein in vivo. Proc. Natl. Acad. Sci. USA 88: 1339-1343
19 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   DOI   ScienceOn
20 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
21 Fujiwara, T. and K. Mizuuchi. 1988. Retrovial DNA integration: Structure of an integration intermediate. Cell 54: 497-504   DOI   ScienceOn
22 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
23 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
24 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
25 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   과학기술학회마을
26 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   DOI   ScienceOn
27 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   과학기술학회마을
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   DOI   ScienceOn
29 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   과학기술학회마을
30 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
31 Linial, M. L. 1999. Foamy viruses are unconventional retroviruses. J. Virol. 73: 1747-1755