Mutational analysis of adeno-associated virus type 2 Rep68 protein endonuclease activity on partially single-stranded substrates

Journal of Virology

Volumn 74, Issue 6, 2000, Pages 2936-2942

  Davis, Michael D ^a,c   Wu, Jianwen ^b,c   Owens, Roland A ^c  

^a Dept Hlth Admin City of Detroit ^*  (United States)

^b LOUISIANA STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; HYBRID PROTEIN; MALTOSE BINDING PROTEIN;

ADENO ASSOCIATED VIRUS; ARTICLE; ENZYME ACTIVE SITE; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL;

BASE SEQUENCE; DEPENDOVIRUS; DNA HELICASES; DNA, SINGLE-STRANDED; DNA, VIRAL; DNA-BINDING PROTEINS; ENDONUCLEASES; GENE EXPRESSION; HUMANS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PHENYLALANINE; RECOMBINANT FUSION PROTEINS; SUBSTRATE SPECIFICITY; TYROSINE; VIRAL PROTEINS;

EID: 0034004021     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.74.6.2936-2942.2000     Document Type: Article

References (56)

1. Balagué, C., M. Kalla, and W. W. Zhang. 1997. Adeno-associated virus Rep78 protein and terminal repeats enhance integration of DNA sequences into the cellular genome. J. Virol. 71:3299-3306.
2. Bordo, D., and P. Argos. 1991. Suggestions for "safe" residue substitutions in site-directed mutagenesis. J. Mol. Biol. 217:721-729.
3. Carter, B. J. 1990. Adeno-associated virus helper functions, p. 255-282. In P. Tijssen (ed.), Handbook of parvoviruses, vol. I. CRC Press, Inc., Boca Raton, Fla.
4. Carter, B. J., E. Mendelson, and J. P. Trempe. 1990. AAV DNA replication, integration, and genetics, p. 169-226. In P. Tijssen (ed.), Handhook of parvoviruses, vol. I. CRC Press, Inc., Boca Raton, Fla.
5. Chejanovsky, N., and B. J. Carter. 1989. Mutagenesis of an AUG codon in the adeno-associated virus rep gene: effects on viral DNA replication. Virology 173:120-128.
6. Chejanovsky, N., and B. J. Carter. 1989. Replication of a human parvovirus nonsense mutant in mammalian cells containing an inducible amber suppressor. Virology 171:239-247.
7. Chiorini, J. A., M. D. Weitzman, R. A. Owens, E. Urcelay, B. Safer, and R. M. Kotin. 1994. Biologically active Rep proteins of adeno-associated virus type 2 produced as fusion proteins in Escherichia coli. J. Virol. 68:797-804.
8. Chiorini, J. A., S. M. Wiener, R. A. Owens, S. R. M. Kyöstiö, R. M. Kotin, and B. Safer. 1994. Sequence requirements for stable binding and function of Rep68 on the adeno-associated virus type 2 inverted terminal repeats. J. Virol. 68:7448-7457.
9. Davis, M. D., R. S. Wonderling, S. L. Walker, and R. A. Owens. 1999. Analysis of the effects of charge cluster mutations in adeno-associated viius Rep68 protein in vitro. J. Virol. 73:2084-2093.
10. Giraud, C., E. Winocour, and K. I. Berns. 1994. Site-specific integration by adeno-associated virus is directed by a cellular DNA sequence. Proc. Natl. Acad. Sci. USA 91:10039-10043.
11. Hauswirth, W. W., and K. I. Berns. 1977. Origin and termination of adeno-associated virus DNA replication. Virology 78:488-499.
12. Ho, S. N., H. D. Hunt, R. M. Horton, J. K. Pullen, and L. R. Pease. 1989. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77:51-59.
13. Im, D. S., and N. Muzyczka. 1990. The AAV origin binding protein Rep68 is an ATP-dependent site-specific endonuclease with DNA helicase activity. Cell 61:447-457.
14. Im, D. S., and N. Muzyczka. 1989. Factors that hind to adeno-associated virus terminal repeats. J. Virol. 63:3095-3104.
15. Im, D. S., and N. Muzyczka. 1992. Partial purification of adeno-associated virus Rcp78, Rep52, and Rep40 and their biochemical characterization. J. Virol. 66:1119-1128.
16. Koonin, E. V. 1993. A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication. Nucleic Acids Res. 21:2541-2547.
17. Koonin, E. V., and T. V. Ilyina. 1993. Computer-assisted dissection of rolling circle DNA replication. BioSystems 30:241-268.
18. Kotin, R. M., R. M. Linden, and K. I. Berns. 1992. Characterization of a preferred site on human chromosome 19q for integration of adeno-associated virus DNA by non-homologous recombination. EMBO J. 11:5071-5078.
19. Kotin, R. M., J. C. Menninger, D. C. Ward, and K. I. Berns. 1991. Mapping and direct visualization of a region-specific viral DNA integration site on chromosome 19q13-qter. Genomics 10:831-834.
20. Kotin, R. M., M. Siniscalco, R. J. Samulski, X. Zhu, L. Hunter, C. A. Laughlin, S. McLaughlin, N. Muzyczka, M. Rocchi, and K. I. Berns. 1990. Site-specific integration by adeno-associated virus. Proc. Natl. Acad. Sci. USA 87:2211-2215.
21. Kube, D. M., S. Ponnazhagan, and A. Srivastava. 1997. Encapsidation of adeno-associated virus type 2 Rep proteins in wild-type and recombinant progeny virions: Rep-mediated growth inhibition of primary human cells. J. Virol. 71:7361-7371.
22. Kyöstiö, S. R. M., and R. A. Owens. 1996. Identification of mutant adenoassociated virus Rep proteins which are dominant-negative for DNA helicase activity. Biochem. Biophys. Res. Commun. 220:294-299.
23. Linden, R. M., E. Winocour, and K. I. Berns. 1996. The recombination signals for adeno-associated virus site-specific integration. Proc. Natl. Acad. Sci. USA 93:7966-7972.
24. McCarty, D. M., T. H. Ni, and N. Muzyczka. 1992. Analysis of mutations in adeno-associated virus Rep protein in vivo and in vitro. J. Virol. 66:4050-4057.
25. McCarty, D. M., J. H. Ryan, S. Zolotukhin, X. Zhou, and N. Muzyczka. 1994. Interaction of the adeno-associated virus Rep protein with a sequence within the A palindrome of the viral terminal repeat. J. Virol. 68:4998-5006.
26. Mendelson, E., J. P. Trempe, and B. J. Carter. 1986. Identification of the trans-acting Rep proteins of adeno-associated virus by antibodies to a synthelic oligopeptide. J. Virol. 60:823-832.
27. Nüesch, J. P. F., S. F. Cotmore, and P. Tattersall. 1995. Sequence motifs in the replicator protein of parvovirus MVM essential for nicking and covalent attachment to the viral origin: identification of the linking tyrosine. Virology 209:122-135.
28. Owens, R. A., M. D. Weitzman, S. R. M. Kyöstiö, and B. J. Carter. 1993. Identification of a DNA-binding domain in the amino terminus of adeno-associated virus Rep proteins. S. Virol. 67:997-1005.
29. Prasad, K. M. R., and J. P. Trempe. 1995. The adeno-associated virus Rep78 protein is covalently linked to viral DNA in a preformed virion. Virology 214:360-370.
30. Ryan, J. H., S. Zolotukhin, and N. Muzyczka. 1996. Sequence requirements for binding of Rep68 to the adeno-associated virus terminal repeats. J. Virol. 70:1542-1553.
31. Samulski, R. J., L. S. Chang, and T. Shenk. 1987. A recombinant plasmid from which an infectious adeno-associated virus genome can be excised in vitro and its use to study viral replication. J. Virol. 61:3096-3101.
32. Samulski, R. J., A. Srivastava, K. I. Berns, and N. Muzyczka. 1983. Rescue of adeno-associated virus from recombinant plasmids: gene correction within the terminal repeats of AAV. Cell 33:135-143.
33. - mutant and correction of terminal palindrome deletions. J. Mol. Biol. 179:1-20.
34. Shelling, A. N., and M. G. Smith. 1994. Targeted integration of transfected and infected adeno-associated virus vectors containing the neomycin resistance gene. Gene Ther. 1:165-169.
35. Skiadopoulos, M. H., and E. A. Faust. 1993. Mutational analysis of conserved tyrosines in the NS-1 protein of the parvovirus minute virus of mice. Virology 194:509-517.
36. Smith, R. H., and R. M. Kotin. 1998. The Rep52 gene product of adeno-associated virus is a DNA helicase with 3′-to-5′ polarity. J. Virol. 72:4874-4881.
37. Snyder, R. O., D. S. Im, and N. Muzyczka. 1991. Evidence for covalent attachment of the adeno-associated virus (AAV) Rep protein to the ends of the AAV genome. J. Virol. 64:6204-6213.
38. Snyder, R. O., D. S. Im, T. Ni, X. Xiao, R. J. Samulski, and N. Muzyczka. 1993. Features of the adeno-associated virus origin involved in substrate recognition by the viral Rep protein. J. Virol. 67:6096-6104.
39. Snyder, R. O., R. J. Samulski, and N. Muzyczka. 1990. In vitro resolution of covalently joined AAV chromosome ends. Cell 60:105-113.
40. Srivastava, A., E. W. Lusby, and K. I. Berns. 1983. Nucleotide sequence and organization of the adeno-associated virus 2 genome. J. Virol. 45:555-564.
41. Straus, S. E., E. D. Sebring, and J. A. Rose. 1976. Concatemers of alternating plus and minus strands are intermediates in adenovirus-associated virus DNA synthesis. Proc. Natl. Acad. Sci. USA 73:742-746.
42. Thomson, B. J., S. Efstathiou, and R. W. Honess. 1991. Acquisition of the human adeno-associated virus type-2 rep gene by human herpesvirus type-6. Nature (London) 351:78-80.
43. Thomson, B. J., F. W. Weindler, D. Gray, V. Schwaab, and R. Heilbronn. 1994. Human herpesvirus 6 (HHV-6) is a helper virus for adeno-associated virus type 2 (AAV-2) and the AAV-2 rep gene homologue in HHV-6 can mediate AAV-2 DNA replication and regulate gene expression. Virology 204:304-311.
44. Trempe, J. P., E. Mendelson, and B. J. Carter. 1987. Characterization of adeno-associated virus rep proteins in human cells by antibodies raised against rep expressed in Escherichia coli. Virology 161:18-28.
45. Urabe, M., Y. Hasumi, A. Kume, R. T. Surosky, G. J. Kurtzman, K. Tobita, and K. Ozawa. 1999. Charged-to-alanine scanning mutagenesis of the N-terminal half of adeno-associated virus type 2 Rep78 protein. J. Virol. 73: 2682-2693.
46. Urcelay, E., P. Ward, S. M. Wiener, B. Safer, and R. M. Kotin. 1995. Asymmetric replication in vitro from a human sequence element is dependent on adeno-associated virus Rep protein. J. Virol. 69:2038-2046.
47. van Mansfeld, A. D. M., H. A. A. M. van Teeffelen, P. D. Baas, and H. S. Jansz. 1986. Two juxtaposed tyrosyl-OH groups participate φinX174 gene A protein catalysed cleavage and ligation of DNA. Nucleic Acids Res. 14:4229-4238.
48. Walker, S. L., R. S. Wonderling, and R. A. Owens. 1997. Mutational analysis of the adeno-associated virus Rep68 protein: identification of critical residues necessary for site-specific endonuclease activity. J. Virol. 71:2722-2730.
49. Walker, S. L., R. S. Wonderling, and R. A. Owens. 1997. Mutational analysis of the adeno-associated virus type 2 Rep68 protein helicase motifs. J. Virol. 71:6996-7004.
50. Ward, P., E. Urcelay, R. Kotin, B. Safer, and K. I. Berns. 1994 Adeno-associated virus DNA replication in vitro: activation by a maltose binding protein/Rep 68 fusion protein. J. Virol. 68:6029-6037.
51. Weitzman, M. D., S. R. M. Kyöstiö, B. J. Carter, and R. A. Owens. 1996. Interaction of wild-type and mutant adeno-associated virus (AAV) Rep proteins on AAV hairpin DNA. J. Virol. 70:2440-2448.
52. Weitzman, M. D., S. R. M. Kyöstiö, R. M. Kotin, and R. A. Owens. 1994. Adeno-associated virus (AAV) Rep proteins mediate complex formation between AAV DNA and its integration site in human DNA. Proc. Natl. Acad. Sci. USA 91:5808-5812.
53. Wonderling, R. S., S. R. M. Kyöstiö, and R. A. Owens. 1995. A maltose-binding protein/adeno-associated virus Rep68 fusion protein has DNA-RNA helicase and ATPase activities. J. Virol. 69:3542-3548.
54. Wonderling, R. S., and R. A. Owens. 1997. Binding sites for adeno-associated virus Rep proteins within the human genome. J. Virol. 71:2528-2534.
55. Wu, J., M. D. Davis, and R. A, Owens. 1999. Factors affecting the terminal resolution site endonuclease, helicase and ATPase activities of adeno-associated virus type 2 Rep proteins. J. Virol. 73:8235-8244.
56. Zhou, X., I. Zolotukhin, D. S. Im, and N. Muzyczka. 1999. Biochemical characterization of adeno-associated virus Rep68 DNA helicase and ATPase activities. J. Virol. 73:1580-1590.