Characterization of Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease, reveals a unique mode of DNA binding, helical distortion, and cleavage compared with a canonical LAGLIDADG homing endonuclease

Journal of Biological Chemistry

Volumn 284, Issue 38, 2009, Pages 25912-25928

  Singh, Pawan ^a   Tripathi, Pankaj ^a   Silva, George H ^b   Pingoud, Alfred ^b   Muniyappa, K ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

2-AMINOPURINE; ACTIVE HOMING; AMINO ACID SEQUENCE; BIOLOGICAL STANDPOINT; CLEAVAGE SITES; DIVALENT CATION; DNA BINDING; DNA TARGETS; DOUBLE STRAND BREAKS; ENDONUCLEASE ACTIVITIES; ENDONUCLEASES; ESSENTIAL GENE; FOOTPRINTING; GENE DECAY; INSERTION SITE; MODULAR STRUCTURES; MYCOBACTERIUM LEPRAE; PHENANTHROLINES;

AMINES; AMINO ACIDS; BACTERIOLOGY; DNA; MANGANESE; MANGANESE COMPOUNDS; METAL REFINING; NUCLEIC ACIDS; ORGANIC ACIDS;

GENES;

ENDONUCLEASE; INTEIN; RECA PROTEIN; BACTERIAL DNA; BACTERIAL PROTEIN; MAGNESIUM; MANGANESE;

AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL STRAIN; BINDING SITE; CONTROLLED STUDY; DNA METHYLATION; DOUBLE STRANDED DNA BREAK; ENZYME ACTIVITY; GENE FUNCTION; GENE INSERTION; GENE MAPPING; GENE SEQUENCE; MYCOBACTERIUM LEPRAE; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CLEAVAGE; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; COMPARATIVE STUDY; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR EVOLUTION; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE;

MYCOBACTERIUM LEPRAE;

BACTERIAL PROTEINS; DNA, BACTERIAL; ENDONUCLEASES; EVOLUTION, MOLECULAR; INTEINS; MAGNESIUM; MANGANESE; MYCOBACTERIUM LEPRAE; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; REC A RECOMBINASES;

EID: 70350005163     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.042861     Document Type: Article

References (75)

1. Cole, S. T., Eiglmeier, K., Parkhill, J., James, K. D., Thomson, N. R., Wheeler, P. R., Honoré, N., Garnier, T., Churcher, C., Harris, D., Mungall, K., Basham, D., Brown, D., Chillingworth, T., Connor, R., Davies, R. M., Devlin, K., Duthoy, S., Feltwell, T., Fraser, A., Hamlin, N., Holroyd, S., Hornsby, T., Jagels, K., Lacroix, C., Maclean, J., Moule, S., Murphy, L., Oliver, K., Quail, M. A., Rajandream, M. A., Rutherford, K. M., Rutter, S., Seeger, K., Simon, S., Simmonds, M., Skelton, J., Squares, R., Squares, S., Stevens, K., Taylor, K., Whitehead, S., Woodward, J. R., and Barrell, B. G. (2001) Nature 409, 1007-1011
2. Brosch, R., Gordon, S. V., Eiglmeier, K., Garnier, T., and Cole, S. T. (2000) Res. Microbiol. 151, 135-142
3. Cole, S. T. (2002) Eur. Respir. J. 36, S78-S86
4. Kowalczykowski, S. C., Dixon, D. A., Eggleston, A. K., Lauder, S. D., and Rehrauer, W. M. (1994) Microbiol. Rev. 58, 401-465
5. Lusetti, S. L., and Cox, M. M. (2002) Annu. Rev. Biochem. 71, 71-100
6. Schlacher, K., Pham, P., Cox, M. M., and Goodman, M. F. (2006) Chem. Rev. 106, 406-419
7. Chen, Z., Yang, H., and Pavletich, N. P. (2008) Nature 453, 489-504
8. Davis, E. O., Sedgwick, S. G., and Colston, M. J. (1991) J. Bacteriol. 173, 5653-5662
9. Davis, E. O., Thangaraj, H. S., Brooks, P. C., and Colston, M. J. (1994) EMBO J. 13, 699-703
10. Davis, E. O., Jenner, P. J., Brooks, P. C., Colston, M. J., and Sedgwick, S. G. (1992) Cell 71, 201-210
11. Frischkorn, K., Springer, B., Böttger, E. C., Davis, E. O., Colston, M. J., and Sander, P. (2000) J. Bacteriol. 182, 3590-3592
12. Guhan, N., and Muniyappa, K. (2002) J. Biol. Chem. 277, 16257-16264
13. Guhan, N., and Muniyappa, K. (2002) J. Biol. Chem. 277, 40352-40361
14. Kane, P. M., Yamashiro, C. T., Wolczyk, D. F., Neff, N., Goebl, M., and Stevens, T. H. (1990) Science 250, 651-657
15. Hirata, R., Ohsumk, Y., Nakano, A., Kawasaki, H., Suzuki, K., and Anraku, Y. (1990) J. Biol. Chem. 265, 6726-6733
16. Pietrokovski, S. (2001) Trends Genet. 17, 465-472
17. Perler, F. B. (2002) Nucleic Acids Res. 30, 383-384
18. Belfort, M., Derbyshire, V., Stoddard, B. L., and Wood, D. W. (eds) (2005) Homing Endonucleases and Inteins (Nucleic Acids and Molecular Biology), Vol. 16, pp. 1-377, Springer-Verlag, Berlin Heidelberg, Germany
19. Guhan, N., and Muniyappa, K. (2003) Crit. Rev. Biochem. Mol. Biol. 38, 199-248
20. Belfort, M., and Roberts, R. J. (1997) Nucleic Acids Res. 25, 3379-3388
21. Jurica, M. S., and Stoddard, B. L. (1999) Cell. Mol. Life Sci. 55, 1304-1326
22. Chevalier, B. S., and Stoddard, B. L. (2001) Nucleic Acids Res. 29, 3757-3774
23. Stoddard, B. L. (2005) Q. Rev. Biophys. 38, 49-95
24. Zhao, L., Bonocora, R. P., Shub, D. A., and Stoddard, B. L. (2007) EMBO J. 26, 2432-2442
25. Perler, F. B., Olsen, G. J., and Adam, E. (1997) Nucleic Acids Res. 25, 1087-1093
26. Dalgaard, J. Z., Klar, A. J., Moser, M. J., Holley, W. R., Chatterjee, A., and Mian, I. S. (1997) Nucleic Acids Res. 25, 4626-4638
27. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
28. Heckman, K. L., and Pease L. R. (2007) Nat. Protoc. 2, 924-932
29. Cunningham, R. P., DasGupta, C., Shibata, T., and Radding, C. M. (1980) Cell 20, 223-235
30. Southworth, M. W., Amaya, K., Evans, T. C., Xu, M. Q., and Perler, F. B. (1999) BioTechniques 27, 110-114, 116, 118-120
31. Bakshi, R. P., Galande, S., Bali, P., Dighe, R., and Muniyappa, K. (2001) J. Mol. Endocrinol. 26, 193-206
32. Bradford, M. M. (1976) Anal. Biochem. 72, 248-254
33. Southern, E. (2006) Nat. Protoc. 1, 518-525
34. Galas, D. J., and Schmitz, A. (1978) Nucleic Acids Res. 5, 3157-3170
35. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K. (eds) (1987) Current Protocols in Molecular Biology, Greene Publishing Associates and Wiley-Interscience, John Wiley & Sons, Inc., New York
36. Maxam, A. M., and Gilbert, W. (1980) Methods Enzymol. 65, 499-560
37. Carey, J. (1991) Methods Enzymol. 208, 103-117
38. Hellman, L. M., and Fried, M. G. (2007) Nat. Protoc. 2, 1849-1861
39. Eastberg, J. H., McConnell, Smith, A., Zhao, L., Ashworth, J., Shen, B. W., and Stoddard, B. L. (2007) Nucleic Acids Res. 35, 7209-7221
40. Komori, K., Ichiyanagi, K., Morikawa, K., and Ishino, Y. (1999) Nucleic Acids Res. 27, 4175-4182
41. Wang, J., Kim, H. H., Yuan, X., and Herrin, D. L. (1997) Nucleic Acids Res. 25, 3767-3776
42. Komori, K., Fujita, N., Ichiyanagi, K., Shinagawa, H., Morikawa, K., and Ishino, Y. (1999) Nucleic Acids Res. 27, 4167-4174
43. Saves, I., Ozanne, V., Dietrich, J., and Masson, J. M. (2000) J. Biol. Chem. 275, 2335-2341
44. Gimble, F. S., and Thorner, J. (1992) Nature 357, 301-306
45. Guhan, N., and Muniyappa, K. (2003) Nucleic Acids Res. 31, 4184-4191
46. Richey, B., Cayley, D. S., Mossing, M. C., Kolka, C., Anderson, C. F., Farrar, T. C., and Record, M. T., Jr. (1987) J. Biol. Chem. 262, 7157-7164
47. Perrin, A., Buckle, M., and Dujon, B. (1993) EMBO J. 12, 2939-2947
48. Saves, I., Westrelin, F., Daffé, M., and Masson, J. M. (2001) Nucleic Acids Res. 29, 4310-4318
49. Saves, I., Morlot, C., Thion, L., Rolland, J. L., Diétrich, J., and Masson, J. M. (2002) Nucleic Acids Res. 30, 4158-4165
50. Hampshire, A. J., Rusling, D. A., Broughton-Head, V. J., and Fox, K. R. (2007) Methods 42, 128-140
51. Papavassiliou, A. G., and Heumann, H. (1994) Methods in Molecular Biology, DNA-Protein Interactions, Principles and Protocols (Kneale, G. G., ed) Vol. 30, pp. 43-78, Humana Press Inc., Totowa, NJ
52. Beylot, B., and Spassky, A. (2001) J. Biol. Chem. 276, 25243-25253
53. Wende, W., Grindl, W., Christ, F., Pingoud, A., and Pingoud, V. (1996) Nucleic Acids Res. 24, 4123-4132
54. Hayatsu, H. (1996) J. Biochem. 119, 391-395
55. Rhodes, D., and Fairall, L. (1997) in Protein Function: A Practical Approach (Creighton, T. E., ed) 2nd Ed., pp. 215-244, IRL Press at Oxford University Press, Oxford
56. Shaw, P. E., and Stewart, A. F. (2001) Methods Mol. Biol. 148, 221-227
57. Millar, D. P. (1996) Curr. Opin. Struct. Biol. 6, 322-326
58. Tripathi, P., Anuradha, S., Ghosal, G., and Muniyappa, K. (2006) J. Mol. Biol. 364, 599-611
59. Lenz, T., Bonnist, E. Y., Pljevaljciæ, G., Neely, R. K., Dryden, D. T., Scheidig, A. J., Jones, A. C., and Weinhold, E. (2007) J. Am. Chem. Soc. 129, 6240-6248
60. Tamulaitis, G., Zaremba, M., Szczepanowski, R. H., Bochtler, M., and Siksnys, V. (2007) Nucleic Acids Res. 35, 4792-4799
61. Malta, E., Verhagen, C. P., Moolenaar, G. F., Filippov, D. V., van der Marel, G. A., and Goosen, N. (2008) DNA Repair 7, 1647-1658
62. Saves, I., Lanéelle, M. A., Daffé, M., and Masson, J. M. (2000) FEBS Lett. 480, 221-225
63. Bakhrat, A., Jurica, M. S., Stoddard, B. L., and Raveh, D. (2004) Genetics 166, 721-728
64. Bell-Pedersen, D., Quirk, S., Clyman, J., and Belfort, M. (1990) Nucleic Acids Res. 18, 3763-3770
65. Bryk, M., Belisle, M., Mueller, J. E., and Belfort, M. (1995) J. Mol. Biol. 247, 197-210
66. Jurica, M. S., Monnat, R. J., Jr., and Stoddard, B. L. (1998) Mol. Cell 2, 469-476
67. Moure, C. M., Gimble, F. S., and Quiocho, F. A. (2002) Nat. Struct. Biol. 9, 764-770
68. Moure, C. M., Gimble, F. S., and Quiocho, F. A. (2003) J. Mol. Biol. 334, 685-695
69. Harshey, R. M., and Ramakrishnan, T. (1977) J. Bacteriol. 129, 616-622
70. Hiriyanna, K. T., and Ramakrishnan, T. (1986) Arch. Microbiol. 144, 105-109
71. Duan, X., Gimble, F. S., and Quiocho, F. A. (1997) Cell 89, 555-564
72. Silva, G. H., Dalgaard, J. Z., Belfort, M., and Van Roey, P. (1999) J. Mol. Biol. 286, 1123-1136
73. Ichiyanagi, K., Ishino, Y., Ariyoshi, M., Komori, K., and Morikawa, K. (2000) J. Mol. Biol. 300, 889-901
74. Edgell, D. R., Derbyshire, V., Van Roey, P., LaBonne, S., Stanger, M. J., Li, Z., Boyd, T. M., Shub, D. A., and Belfort, M. (2004) Nat. Struct. Mol. Biol. 11, 936-944
75. Påques, F., and Duchateau, P. (2007) Curr. Gene Ther. 7, 49-66