Analysis of a single-stranded DNA-scanning process in which activation-induced deoxycytidine deaminase (AID) deaminates C to U haphazardly and inefficiently to ensure mutational diversity

Journal of Biological Chemistry

Volumn 286, Issue 28, 2011, Pages 24931-24942

  Pham, Phuong ^a   Calabrese, Peter ^a   Park, Soo Jung ^a   Goodman, Myron F ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY DIVERSITY; RANDOM WALK MODELS; REPORTER GENE; SINGLE-STRANDED (SS) DNA; SINGLE-STRANDED DNA;

ACTIVATION ANALYSIS; AMINES; GENES; TRANSCRIPTION;

DNA;

ACTIVATION INDUCED DEOXYCYTIDINE DEAMINASE; BETA GALACTOSIDASE; DEAMINASE; DOUBLE STRANDED DNA; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CATALYSIS; CONTROLLED STUDY; DEAMINATION; DNA SEQUENCE; DNA TRANSCRIPTION; GENE CASSETTE; GENETIC VARIABILITY; INSECT CELL; MUTATIONAL DIVERSITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN MOTIF; REPORTER GENE;

CYTIDINE DEAMINASE; CYTOSINE; DEAMINATION; DNA, SINGLE-STRANDED; ENZYME ACTIVATION; LAC OPERON; MUTAGENESIS; URACIL;

EID: 79960145089     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M111.241208     Document Type: Article

References (48)

1. Peled, J. U., Kuang, F. L., Iglesias-Ussel, M. D., Roa, S., Kalis, S. L., Goodman, M. F., and Scharff, M. D. (2008) Annu. Rev. Immunol. 26, 481-511
2. Stavnezer, J., Guikema, J. E., and Schrader, C. E. (2008) Annu. Rev. Immunol. 26, 261-292
3. Di Noia, J. M., and Neuberger, M. S. (2007) Annu. Rev. Biochem. 76, 1-22
4. MacDuff, D. A., Demorest, Z. L., and Harris, R. S. (2009) Nucleic Acids Res. 37, 1854-1867
5. Vartanian, J. P., Henry, M., Marchio, A., Suspène, R., Aynaud, M. M., Guétard, D., Cervantes-Gonzalez, M., Battiston, C., Mazzaferro, V., Pineau, P., Dejean, A., and Wain-Hobson, S. (2010) PLoS Pathog. 6, e1000928
6. Bhutani, N., Brady, J. J., Damian, M., Sacco, A., Corbel, S. Y., and Blau, H. M. (2010) Nature 463, 1042-1047
7. Popp, C., Dean, W., Feng, S., Cokus, S. J., Andrews, S., Pellegrini, M., Jacobsen, S. E., and Reik, W. (2010) Nature 463, 1101-1105
8. Rai, K., Huggins, I. J., James, S. R., Karpf, A. R., Jones, D. A., and Cairns, B. R. (2008) Cell 135, 1201-1212
9. Guo, J. U., Su, Y., Zhong, C., Ming, G. L., and Song, H. (2011) Cell 145, 423-434
10. Jiricny, J., and Menigatti, M. (2008) Cell 135, 1167-1169
11. Chelico, L., Pham, P., Petruska, J., and Goodman, M. F. (2009) J. Biol. Chem. 284, 27761-27765
12. Chahwan, R., Wontakal, S. N., and Roa, S. (2010) Trends Genet. 26, 443-448
13. Fritz, E. L., and Papavasiliou, F. N. (2010) Genes Dev. 24, 2107-2114
14. Pham, P., Bransteitter, R., Petruska, J., and Goodman, M. F. (2003) Nature 424, 103-107
15. Bransteitter, R., Pham, P., Calabrese, P., and Goodman, M. F. (2004) J. Biol. Chem. 279, 51612-51621
16. Yu, K., Huang, F. T., and Lieber, M. R. (2004) J. Biol. Chem. 279, 6496-6500
17. Wang, M., Rada, C., and Neuberger, M. S. (2010) J. Exp. Med. 207, 141-153
18. Basu, U., Meng, F. L., Keim, C., Grinstein, V., Pefanis, E., Eccleston, J., Zhang, T., Myers, D., Wasserman, C. R., Wesemann, D. R., Januszyk, K., Gregory, R. I., Deng, H., Lima, C. D., and Alt, F. W. (2011) Cell 144, 353-363
19. Pavri, R., Gazumyan, A., Jankovic, M., Di Virgilio, M., Klein, I., Ansarah- Sobrinho, C., Resch, W., Yamane, A., Reina San-Martin, B., Barreto, V., Nieland, T. J., Root, D. E., Casellas, R., and Nussenzweig, M. C. (2010) Cell 143, 122-133
20. Gorman, J., Chowdhury, A., Surtees, J. A., Shimada, J., Reichman, D. R., Alani, E., and Greene, E. C. (2007) Mol. Cell 28, 359-370
21. Gorman, J., and Greene, E. C. (2008) Nat. Struct. Mol. Biol. 15, 768-774
22. Komazin-Meredith, G., Mirchev, R., Golan, D. E., van Oijen, A. M., and Coen, D. M. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 10721-10726
23. Blainey, P. C., van Oijen, A. M., Banerjee, A., Verdine, G. L., and Xie, X. S. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 5752-5757
24. Kochaniak, A. B., Habuchi, S., Loparo, J. J., Chang, D. J., Cimprich, K. A., Walter, J. C., and van Oijen, A. M. (2009) J. Biol. Chem. 284, 17700-17710
25. Bonnet, I., Biebricher, A., Porté, P. L., Loverdo, C., Bénichou, O., Voituriez, R., Escudé, C., Wende, W., Pingoud, A., and Desbiolles, P. (2008) Nucleic Acids Res. 36, 4118-4127
26. Blainey, P. C., Luo, G., Kou, S. C., Mangel, W. F., Verdine, G. L., Bagchi, B., and Xie, X. S. (2009) Nat. Struct. Mol. Biol. 16, 1224-1229
27. Terry, B. J., Jack, W. E., and Modrich, P. (1985) J. Biol. Chem. 260, 13130-13137
28. Gowers, D. M., Wilson, G. G., and Halford, S. E. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 15883-15888
29. Porecha, R. H., and Stivers, J. T. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 10791-10796
30. Bransteitter, R., Pham, P., Scharff, M. D., and Goodman, M. F. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 4102-4107
31. Ross, S. M. (1994) A First Course in Probability, 4th Ed, pp. 167-169 MacMillan Publishing Co., New York
32. Larijani, M., and Martin, A. (2007) Mol. Cell. Biol. 27, 8038-8048
33. Berg, O. G., Winter, R. B., and von Hippel, P. H. (1981) Biochemistry 20, 6929-6948
34. Halford, S. E. (2001) Biochem. Soc. Trans. 29, 363-374
35. Bennett, S. E., Sanderson, R. J., and Mosbaugh, D. W. (1995) Biochemistry 34, 6109-6119
36. Chelico, L., Pham, P., Calabrese, P., and Goodman, M. F. (2006) Nat. Struct. Mol. Biol. 13, 392-399
37. Sohail, A., Klapacz, J., Samaranayake, M., Ullah, A., and Bhagwat, A. S. (2003) Nucleic Acids Res. 31, 2990-2994
38. Chaudhuri, J., Tian, M., Khuong, C., Chua, K., Pinaud, E., and Alt, F. W. (2003) Nature 422, 726-730
39. Landick, R. (2006) Biochem. Soc. Trans. 34, 1062-1066
40. Liu, C., and Martin, C. T. (2001) J. Mol. Biol. 308, 465-475
41. Sohn, Y., and Kang, C. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 75-80
42. Canugovi, C., Samaranayake, M., and Bhagwat, A. S. (2009) FASEB J. 23, 34-44
43. Shen, H. M., Ratnam, S., and Storb, U. (2005) Mol. Cell. Biol. 25, 10815-10821
44. Carey, D. C., and Strauss, P. R. (1999) Biochemistry 38, 16553-16560
45. Dowd, D. R., and Lloyd, R. S. (1990) J. Biol. Chem. 265, 3424-3431
46. Lindahl, T., and Barnes, D. E. (2000) Cold Spring Harbor Symp. Quant. Biol. 65, 127-133
47. Chelico, L., Prochnow, C., Erie, D. A., Chen, X. S., and Goodman, M. F. (2010) J. Biol. Chem. 285, 16195-16205
48. MacCarthy, T., Kalis, S. L., Roa, S., Pham, P., Goodman, M. F., Scharff, M. D., and Bergman, A. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 8629-8634