Context dependence between subdomains in the DNA binding interface of the I-CreI homing endonuclease

Nucleic Acids Research

Volumn 39, Issue 14, 2011, Pages 6124-6136

  Grizot, Sylvestre ^a   Duclert, Aymeric ^a   Thomas, Séverine ^a   Duchateau, Philippe ^a   Pâques, Frédéric ^a  

^a 8 rue de la Croix Jarry   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; I CREL HOMING ENDONUCLEASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; DNA BINDING; DNA SEQUENCE; GENE MUTATION; GENE TARGETING; GENETIC ENGINEERING; MOLECULAR CLONING; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; YEAST;

BINDING SITES; DNA RESTRICTION ENZYMES; DNA-BINDING PROTEINS; MODELS, MOLECULAR; MUTATION; PROTEIN ENGINEERING; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY;

EID: 80051730980     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr186     Document Type: Article

References (48)

1. Stoddard, B.L. (2005) Homing endonuclease structure and function. Q. Rev. Biophys., 38, 49-95. (Pubitemid 43338672)
2. Rouet, P., Smih, F. and Jasin, M. (1994) Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. Proc. Natl Acad. Sci. USA, 91, 6064-6068. (Pubitemid 24188283)
3. Choulika, A., Perrin, A., Dujon, B. and Nicolas, J.F. (1995) Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae. Mol. Cell. Biol., 15, 1968-1973.
4. Paques, F. and Duchateau, P. (2007) Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy. Curr. Gene Ther., 7, 49-66. (Pubitemid 46322288)
5. Galetto, R., Duchateau, P. and Paques, F. (2009) Targeted approaches for gene therapy and the emergence of engineered meganucleases. Expert Opin. Biol. Ther., 9, 1289-1303.
6. Grizot, S., Smith, J., Daboussi, F., Prieto, J., Redondo, P., Merino, N., Villate, M., Thomas, S., Lemaire, L., Montoya, G. et al. (2009) Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease. Nucleic Acids Res., 37, 5405-5419.
7. Redondo, P., Prieto, J., Munoz, I.G., Alibes, A., Stricher, F., Serrano, L., Cabaniols, J.P., Daboussi, F., Arnould, S., Perez, C. et al. (2008) Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature, 456, 107-111.
8. Arnould, S., Perez, C., Cabaniols, J.P., Smith, J., Gouble, A., Grizot, S., Epinat, J.C., Duclert, A., Duchateau, P. and Paques, F. (2007) Engineered I-CreI derivatives cleaving sequences from the human XPC gene can induce highly efficient gene correction in mammalian cells. J. Mol. Biol., 371, 49-65. (Pubitemid 47030453)
9. Smith, J., Grizot, S., Arnould, S., Duclert, A., Epinat, J.-C., Prieto, J., Redondo, P., Blanco, F.J., Bravo, J., Montoya, G. et al. (2006) A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences. Nucleic Acids Res., 34, e149.
10. Ashworth, J., Taylor, G.K., Havranek, J.J., Quadri, S.A., Stoddard, B.L. and Baker, D. (2010) Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Res., 38, 5601-5608.
11. Ashworth, J., Havranek, J.J., Duarte, C.M., Sussman, D., Monnat, R.J. Jr, Stoddard, B.L. and Baker, D. (2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature, 441, 656-659. (Pubitemid 43927299)
12. Gao, H., Smith, J., Yang, M., Jones, S., Djukanovic, V., Nicholson, M.G., West, A., Bidney, D., Falco, S.C., Jantz, D. et al. Heritable targeted mutagenesis in maize using a designed endonuclease. Plant J., 61, 176-187.
13. Porteus, M.H. and Carroll, D. (2005) Gene targeting using zinc finger nucleases. Nat. Biotechnol., 23, 967-973. (Pubitemid 41114030)
14. Carroll, D. (2008) Progress and prospects: zinc-finger nucleases as gene therapy agents. Gene Ther., 15, 1463-1468.
15. Elrod-Erickson, M., Rould, M.A., Nekludova, L. and Pabo, C.O. (1996) Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure, 4, 1171-1180. (Pubitemid 27005385)
16. Ramirez, C.L., Foley, J.E., Wright, D.A., Muller-Lerch, F., Rahman, S.H., Cornu, T.I., Winfrey, R.J., Sander, J.D., Fu, F., Townsend, J.A. et al. (2008) Unexpected failure rates for modular assembly of engineered zinc fingers. Nat. Methods, 5, 374-375. (Pubitemid 351619087)
17. Greisman, H.A. and Pabo, C.O. (1997) A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science, 275, 657-661. (Pubitemid 27061331)
18. Isalan, M., Klug, A. and Choo, Y. (2001) A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter. Nat. Biotechnol., 19, 656-660. (Pubitemid 32625437)
19. Maeder, M.L., Thibodeau-Beganny, S., Osiak, A., Wright, D.A., Anthony, R.M., Eichtinger, M., Jiang, T., Foley, J.E., Winfrey, R.J., Townsend, J.A. et al. (2008) Rapid 'open-source' engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol. Cell, 31, 294-301. (Pubitemid 352001401)
20. Maeder, M.L., Thibodeau-Beganny, S., Sander, J.D., Voytas, D.F. and Joung, J.K. (2009) Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays. Nat. Protoc., 4, 1471-1501.
21. Chevalier, B.S., Monnat, R.J. Jr and Stoddard, B.L. (2001) The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites. Nat. Struct. Biol., 8, 312-316. (Pubitemid 32275014)
22. Chevalier, B., Turmel, M., Lemieux, C., Monnat, R.J. Jr and Stoddard, B.L. (2003) Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI. J. Mol. Biol., 329, 253-269. (Pubitemid 36561582)
23. Bolduc, J.M., Spiegel, P.C., Chatterjee, P., Brady, K.L., Downing, M.E., Caprara, M.G., Waring, R.B. and Stoddard, B.L. (2003) Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor. Genes Dev., 17, 2875-2888. (Pubitemid 37523153)
24. Moure, C.M., Gimble, F.S. and Quiocho, F.A. (2003) The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity. J. Mol. Biol., 334, 685-695. (Pubitemid 37433885)
25. Marcaida, M.J., Prieto, J., Redondo, P., Nadra, A.D., Alibes, A., Serrano, L., Grizot, S., Duchateau, P., Paques, F., Blanco, F.J. et al. (2008) Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. Proc. Natl Acad. Sci. USA, 105, 16888-16893.
26. Silva, G.H., Dalgaard, J.Z., Belfort, M. and Van Roey, P. (1999) Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI. J. Mol. Biol., 286, 1123-1136. (Pubitemid 29116680)
27. Arnould, S., Chames, P., Perez, C., Lacroix, E., Duclert, A., Epinat, J.C., Stricher, F., Petit, A.S., Patin, A., Guillier, S. et al. (2006) Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J. Mol. Biol., 355, 443-458. (Pubitemid 41785749)
28. Doyon, J.B., Pattanayak, V., Meyer, C.B. and Liu, D.R. (2006) Directed evolution and substrate specificity profile of homing endonuclease I-SceI. J. Am. Chem. Soc., 128, 2477-2484.
29. Seligman, L.M., Chisholm, K.M., Chevalier, B.S., Chadsey, M.S., Edwards, S.T., Savage, J.H. and Veillet, A.L. (2002) Mutations altering the cleavage specificity of a homing endonuclease. Nucleic Acids Res., 30, 3870-3879. (Pubitemid 35012459)
30. Sussman, D., Chadsey, M., Fauce, S., Engel, A., Bruett, A., Monnat, R. Jr, Stoddard, B.L. and Seligman, L.M. (2004) Isolation and characterization of new homing endonuclease specificities at individual target site positions. J. Mol. Biol., 342, 31-41. (Pubitemid 39094503)
31. Grizot, S., Epinat, J.C., Thomas, S., Duclert, A., Rolland, S., Paques, F. and Duchateau, P. (2010) Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds. Nucleic Acids Res., 38, 2006-2018.
32. Chevalier, B.S., Kortemme, T., Chadsey, M.S., Baker, D., Monnat, R.J. and Stoddard, B.L. (2002) Design, activity, and structure of a highly specific artificial endonuclease. Mol. Cell, 10, 895-905. (Pubitemid 35335643)
33. Epinat, J.C., Arnould, S., Chames, P., Rochaix, P., Desfontaines, D., Puzin, C., Patin, A., Zanghellini, A., Paques, F. and Lacroix, E. (2003) A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells. Nucleic Acids Res., 31, 2952-2962. (Pubitemid 37442138)
34. Silva, G.H., Belfort, M., Wende, W. and Pingoud, A. (2006) From monomeric to homodimeric endonucleases and back: engineering novel specificity of LAGLIDADG enzymes. J. Mol. Biol., 361, 744-754. (Pubitemid 44175386)
35. Ashworth, J., Taylor, G.K., Havranek, J.J., Quadri, S.A., Stoddard, B.L. and Baker, D. (2010) Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Res., 38, 5601-5608.
36. Lanio, T., Jeltsch, A. and Pingoud, A. (2000) On the possibilities and limitations of rational protein design to expand the specificity of restriction enzymes: a case study employing EcoRV as the target. Protein Eng., 13, 275-281. (Pubitemid 30258962)
37. Rimseliene, R., Maneliene, Z., Lubys, A. and Janulaitis, A. (2003) Engineering of restriction endonucleases: using methylation activity of the bifunctional endonuclease Eco57I to select the mutant with a novel sequence specificity. J. Mol. Biol., 327, 383-391. (Pubitemid 36298709)
38. Samuelson, J.C. and Xu, S.Y. (2002) Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity. J. Mol. Biol., 319, 673-683. (Pubitemid 34729442)
39. Schottler, S., Wenz, C., Lanio, T., Jeltsch, A. and Pingoud, A. (1998) Protein engineering of the restriction endonuclease EcoRV-structure-guided design of enzyme variants that recognize the base pairs flanking the recognition site. Eur. J. Biochem., 258, 184-191. (Pubitemid 28538324)
40. Wenz, C., Selent, U., Wende, W., Jeltsch, A., Wolfes, H. and Pingoud, A. (1994) Protein engineering of the restriction endonuclease EcoRV: replacement of an amino acid residue in the DNA binding site leads to an altered selectivity towards unmodified and modified substrates. Biochim. Biophys. Acta, 1219, 73-80. (Pubitemid 24283795)
41. Pabo, C.O., Peisach, E. and Grant, R.A. (2001) Design and selection of novel Cys2His2 zinc finger proteins. Annu. Rev. Biochem., 70, 313-340. (Pubitemid 32662213)
42. Wolfe, S.A., Greisman, H.A., Ramm, E.I. and Pabo, C.O. (1999) Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J. Mol. Biol., 285, 1917-1934. (Pubitemid 29078161)
43. Sarkar, I., Hauber, I., Hauber, J. and Buchholz, F. (2007) HIV-1 proviral DNA excision using an evolved recombinase. Science, 316, 1912-1915. (Pubitemid 47025793)
44. Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., Lahaye, T., Nickstadt, A. and Bonas, U. (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science, 326, 1509-1512.
45. Moscou, M.J. and Bogdanove, A.J. (2009) A simple cipher governs DNA recognition by TAL effectors. Science, 326, 1501.
46. Miller, J.C., Tan, S., Qiao, G., Barlow, K.A., Wang, J., Xia, D.F., Meng, X., Paschon, D.E., Leung, E., Hinkley, S.J. et al. (2011) A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol., 29, 143-148.
47. Li, T., Huang, S., Jiang, W.Z., Wright, D., Spalding, M.H., Weeks, D.P. and Yang, B. (2011) TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res., 39, 359-372.
48. Christian, M., Cermak, T., Doyle, E.L., Schmidt, C., Zhang, F., Hummel, A., Bogdanove, A.J. and Voytas, D.F. (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics, 186, 757-761.