Generation and analysis of mesophilic variants of the thermostable archaeal I-Dmoi homing endonuclease

Journal of Biological Chemistry

Volumn 283, Issue 7, 2008, Pages 4364-4374

  Prieto, Jesús ^a   Epinat, Jean Charles ^b   Redondo, Pilar ^a   Ramos, Elena ^a   Padró, Daniel ^a,c   Cédrone, Frédéric ^b   Montoya, Guillermo ^a   Pâques, Frédéric ^b   Blanco, Francisco J ^a,d  

^a Structural Biology and Biocomputing Programme   (Spain)

^b Arvid Wallgrens Backe 20   (France)

^c CIC BIOMAGUNE   (Spain)

^d Structural Biology Unit   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BINDING SITES; BIOCHEMICAL ENGINEERING; CATALYSTS; DNA; ENZYMES; GENES; OLIGOMERS; ORGANIC ACIDS; PROTEINS;

ACTIVITY PROFILES; ARCHAEAL; CHEMICAL DENATURATIONS; DIRECTED EVOLUTIONS; ENDONUCLEASE; ENDONUCLEASES; FUNCTIONAL ASSAYS; GENOME ENGINEERINGS; HYPERTHERMOPHILIC ARCHAEON; IN VITRO; LOW TEMPERATURES; MESOPHILIC; MUTANT ENZYMES; NOVEL PROTEINS; POWERFUL TOOLS; PROTEIN DYNAMICS; SINGLE CHAINS; STRUCTURAL DISTORTIONS;

NUCLEIC ACIDS;

BACTERIAL PROTEIN; ENDONUCLEASE; HOMING ENDONUCLEASE; PROTEIN I DMOL; UNCLASSIFIED DRUG; PRIMER DNA; RESTRICTION ENDONUCLEASE;

ARTICLE; DESULFUROCOCCUS MOBILIS; DNA BINDING MOTIF; GENE MUTATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; WILD TYPE; CHEMICAL STRUCTURE; CHEMISTRY; DESULFUROCOCCACEAE; ENZYME STABILITY; ENZYMOLOGY; METABOLISM; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION; SPECTROFLUOROMETRY; TEMPERATURE; ULTRACENTRIFUGATION;

ARCHAEA; DESULFUROCOCCUS MOBILIS;

BASE SEQUENCE; DESULFUROCOCCACEAE; DNA PRIMERS; DNA RESTRICTION ENZYMES; ENZYME STABILITY; MODELS, MOLECULAR; PROTEIN CONFORMATION; SPECTROMETRY, FLUORESCENCE; TEMPERATURE; ULTRACENTRIFUGATION;

EID: 42949157474     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M706323200     Document Type: Article

References (70)

1. Belfort, M., and Roberts, R. J. (1997) Nucleic Acids Res. 25, 3379-3388
2. Rouet, P., Smih, F., and Jasin, M. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 6064-6068
3. Choulika, A., Perrin, A., Dujon, B., and Nicolas, J. F. (1994) C. R. Acad. Sci. III 317, 1013-1019
4. Choulika, A., Perrin, A., Dujon, B., and Nicolas, J. F. (1995) Mol. Cell. Biol. 15, 1968-1973
5. Chevalier, B. S., and Stoddard, B. L. (2001) Nucleic Acids Res. 29, 3757-3774
6. Wang, J., Kim, H. H., Yuan, X., and Herrin, D. L. (1997) Nucleic Acids Res. 25, 3767-3776
7. Jacquier, A., and Dujon, B. (1985) Cell 41, 383-394
8. Dalgaard, J. Z., Garrett, R. A., and Belfort, M. (1993) Proc. Natl. Acad. Sci. U. S. A. 90, 5414-5417
9. Flick, K. E., McHugh, D., Heath, J. D., Stephens, K. M., Monnat, R. J., Jr., and Stoddard, B. L. (1997) Protein Sci. 6, 2677-2680
10. Silva, G. H., Dalgaard, J. Z., Belfort, M., and Van Roey, P. (1999) J. Mol. Biol. 286, 1123-1136
11. Jurica, M. S., Monnat, R. J., Jr., and Stoddard, B. L. (1998) Mol. Cell 2, 469-476
12. Poland, B. W., Xu, M. Q., and Quiocho, F. A. (2000) J. Biol. Chem. 275, 16408-16413
13. Chevalier, B. S., Monnat, R. J., Jr., and Stoddard, B. L. (2001) Nat. Struct. Biol. 8, 312-316
14. Duan, X., Gimble, F. S., and Quiocho, F. A. (1997) Cell 89, 555-564
15. Werner, E., Wende, W., Pingoud, A., and Heinemann, U. (2002) Nucleic Acids Res. 30, 3962-3971
16. Ichiyanagi, K., Ishino, Y., Ariyoshi, M., Komori, K., and Morikawa, K. (2000) J. Mol. Biol. 300, 889-901
17. Moure, C. M., Gimble, F. S., and Quiocho, F. A. (2003) J. Mol. Biol. 334, 685-695
18. Spiegel, P. C., Chevalier, B., Sussman, D., Turmel, M., Lemieux, C., and Stoddard, B. L. (2006) Structure (Lond.) 14, 869-880
19. Nakayama, H., Shimamura, T., Imagawa, T., Shirai, N., Itoh, T., Sako, Y., Miyano, M., Sakuraba, H., Ohshima, T., Nomura, N., and Tsuge, H. (2006) J. Mol. Biol. 365, 362-378
20. Ashworth, J., Havranek, J. J., Duarte, C. M., Sussman, D., Monnat, R. J., Jr., Stoddard, B. L., and Baker, D. (2006) Nature 441, 656-659
21. Gimble, F. S., Moure, C. M., and Posey, K. L. (2003) J. Mol. Biol. 334, 993-1008
22. Arnould, S., Chames, P., Perez, C., Lacroix, E., Duclert, A., Epinat, J. C., Stricher, F., Petit, A. S., Patin, A., Guillier, S., Rolland, S., Prieto, J., Blanco, F. J., Bravo, J., Montoya, G., Serrano, L., Duchateau, P., and Paques, F. (2006) J. Mol. Biol. 355, 443-458
23. Doyon, J. B., Pattanayak, V., Meyer, C. B., and Liu, D. R. (2006) J. Am. Chem. Soc. 128, 2477-2484
24. Steuer, S., Pingoud, V., Pingoud, A., and Wende, W. (2004) ChemBioChem. 5, 206-213
25. Seligman, L. M., Chisholm, K. M., Chevalier, B. S., Chadsey, M. S., Edwards, S. T., Savage, J. H., and Veillet, A. L. (2002) Nucleic Acids Res. 30, 3870-3879
26. Smith, J., Grizot, S., Arnould, S., Duclert, A., Epinat, J. C., Chames, P., Prieto, J., Redondo, P., Blanco, F. J., Bravo, J., Montoya, G., Paques, F., and Duchateau, P. (2006) Nucleic Acids Res. 34, e149
27. Arnould, S., Perez, C., Cabaniols, J. P., Smith, J., Gouble, A., Grizot, S., Epinat, J. C., Duclert, A., Duchateau, P., and Paques, F. (2007) J. Mol. Biol. 371, 49-65
28. Bibikova, M., Golic, M., Golic, K. G., and Carroll, D. (2002) Genetics 161, 1169-1175
29. Epinat, J. C., Arnould, S., Chames, P., Rochaix, P., Desfontaines, D., Puzin, C., Patin, A., Zanghellini, A., Paques, F., and Lacroix, E. (2003) Nucleic Acids Res. 31, 2952-2962
30. Chevalier, B. S., Kortemme, T., Chadsey, M. S., Baker, D., Monnat, R. J., and Stoddard, B. L. (2002) Mol. Cell 10, 895-905
31. Argast, G. M., Stephens, K. M., Emond, M. J., and Monnat, R. J., Jr. (1998) J. Mol. Biol. 280, 345-353
32. Sussman, D., Chadsey, M., Fauce, S., Engel, A., Bruett, A., Monnat, R., Jr., Stoddard, B. L., and Seligman, L. M. (2004) J. Mol. Biol. 342, 31-41
33. Lykke-Andersen, J., Thi-Ngoc, H. P., and Garrett, R. A. (1994) Nucleic Acids Res. 22, 4583-4590
34. Silva, G. H., and Belfort, M. (2004) Nucleic Acids Res. 32, 3156-3168
35. Aagaard, C., Awayez, M. J., and Garrett, R. A. (1997) Nucleic Acids Res. 25, 1523-1530
36. Cadwell, R. C., and Joyce, G. F. (1992) PCR Methods Applications 2, 28-33
37. Cadwell, R. C., and Joyce, G. F. (1994) PCR Methods Applications 3, S136-S140
38. Dalgaard, J. Z., Garrett, R. A., and Belfort, M. (1994) J. Biol. Chem. 269, 28885-28892
39. Chames, P., Epinat, J. C., Guillier, S., Patin, A., Lacroix, E., and Paques, F. (2005) Nucleic Acids Res. 33, e178
40. Hicks, J. B., Hinnen, A., and Fink, G. R. (1979) Cold Spring Harbor Symp. Quant. Biol. 43, 1305-1313
41. Dalgaard, J. Z., Silva, G. H., Belfort, M., and Van Roey, P. (1998) Acta Crystallogr. Sect. D Biol. Crystallogr. 54, 1435-1436
42. Prieto, J., Redondo, P., Padro, D., Arnould, S., Epinat, J. C., Paques, F., Blanco, F. J., and Montoya, G. (2007) Nucleic Acids Res. 35, 3262-3271
43. Viguera, A. R., Martinez, J. C., Filimonov, V. V., Mateo, P. L., and Serrano, L. (1994) Biochemistry 33, 2142-2150
44. Chodorge, M., Fourage, L., Ullmann, C., Duvivier, V., Masson, J., and Lefèvre, F. (2005) Adv. Synth. Catal. 347, 1022-1026
45. Myers, J. K., Pace, C. N., and Scholtz, J. M. (1995) Protein Sci. 4, 2138-2148
46. Serrano, L., Kellis, J. T., Jr., Cann, P., Matouschek, A., and Fersht, A. R. (1992) J. Mol. Biol. 224, 783-804
47. Pace, C. N., and Shaw, K. L. (2000) Proteins 41, Suppl. 4, 1-7
48. Marshall, P., Davis, T. B., and Lemieux, C. (1994) Eur. J. Biochem. 220, 855-859
49. Robertson, A. D., and Murphy, K. P. (1997) Chem. Rev. 97, 1251-1268
50. Rubin-Pitel, S. B., and Zhao, H. (2006) Comb. Chem. High Throughput. Screen. 9, 247-257
51. Pantoliano, M. W., Ladner, R. C., Bryan, P. N., Rollence, M. L., Wood, J. F., and Poulos, T. L. (1987) Biochemistry 26, 2077-2082
52. Sriprapundh, D., Vieille, C., and Zeikus, J. (2003) Protein Eng. 16, 683-690
53. Lebbink, J. H., Kaper, T., Bron, P., van der Oost, J., and de Vos, W. M. (2000) Biochemistry 39, 3656-3665
54. Taguchi, S. O. A., and Momose, H. (1998) Appl. Environ. Microbiol. 64, 492-495
55. Tindbaek, N., Svendsen, A., Oestergaard, P. R., and Draborg, H. (2004) Protein Eng. Des. Sel. 17, 149-156
56. Wintrode, P. L., Miyazaki, K., and Arnold, F. H. (2000) J. Biol. Chem. 275, 31635-31640
57. Makhatadze, G. I., and Privalov, P. L. (1995) Adv. Protein Chem. 47, 307-425
58. Perl, D., and Schmid, F. X. (2002) ChemBioChem. 3, 39-44
59. Wintrode, P. L., and Arnold, F. H. (2000) Adv. Protein Chem. 55, 161-225
60. Chen, K., and Arnold, F. (1993) Proc. Natl. Acad. Sci. U. S. A. 90, 5618-5622
61. Stemmer, W. P. (1994) Nature 370, 389-391
62. Perry, L. J., and Wetzel, R. (1984) Science 226, 555-557
63. Wells, J. A., and Powers, D. (1986) J. Biol. Chem. 261, 6564-6570
64. Adekoya, O. A., Helland, R., Willassen, N. P., and Sylte, I. (2006) Proteins 62, 435-449
65. Arnold, F. H., Wintrode, P. L., Miyazaki, K., and Gershenson, A. (2001) Trends Biochem. Sci. 26, 100-106
66. Serrano, L., Day, A. G., and Fersht, A. R. (1993) J. Mol. Biol. 233, 305-312
67. Lehmann, M., Kostrewa, D., Wyss, M., Brugger, R., D'Arcy, A., Pasamontes, L., and van Loon, A. P. (2000) Protein Eng. 13, 49-57
68. Lehmann, M., Loch, C., Middendorf, A., Studer, D., Lassen, S. F., Pasamontes, L., van Loon, A. P., and Wyss, M. (2002) Protein Eng. 15, 403-411
69. Lucas, P., Otis, C., Mercier, J. P., Turmel, M., and Lemieux, C. (2001) Nucleic Acids Res. 29, 960-969
70. Korkegian, A., Black, M., Baker, D., and Stoddard, B. L. (2005) Science 308, 857-860