Divergence and convergence in enzyme evolution: Parallel evolution of paraoxonases from quorum-quenching lactonases

Journal of Biological Chemistry

Volumn 287, Issue 1, 2012, Pages 11-20

  Elias, Mikael ^a   Tawfik, Dan S ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

CONVERGENT EVOLUTION; LACTONASE; ORGANOPHOSPHATE HYDROLASE;

HYDROLASES;

QUENCHING;

ARYLDIALKYLPHOSPHATASE; GLUCONOLACTONASE; GLYCOSIDASE; METALLO BETA LACTAMASE; PARATHION METHYL; PHOSPHOTRIESTERASE LIKE LACTONASE; PROTEIN AIIA; PROTEINASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; CATALYSIS; CONVERGENT EVOLUTION; DIVERGENT EVOLUTION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; EVOLUTION; NONHUMAN; PARALLEL EVOLUTION; PRIORITY JOURNAL; QUORUM SENSING; SEQUENCE HOMOLOGY; SHORT SURVEY;

ANIMALS; ARYLDIALKYLPHOSPHATASE; EVOLUTION, MOLECULAR; HUMANS; QUORUM SENSING; SUBSTRATE SPECIFICITY;

EID: 84855269223     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.R111.257329     Document Type: Short Survey

References (80)

1. Theobald, D. L. (2010) Nature 465, 219-222
2. Koonin, E. V., and Galperin, M. Y. (2002) Sequence-Evolution-Function: Computational Approaches in Comparative Genomics, 1st Ed., Springer, New York
3. Kim, K. M., and Caetano-Anollés, G. (2010) Mol. Biol. Evol. 27, 1710-1733
4. Ouzounis, C. A., Kunin, V., Darzentas, N., and Goldovsky, L. (2006) Res. Microbiol. 157, 57-68
5. Koonin, E. V. (2003) Nat. Rev. Microbiol. 1, 127-136
6. Bolton, D. P., and Marsh, J. (1984) J. Physiol. 351, 451-459
7. Tuller, T., Birin, H., Gophna, U., Kupiec, M., and Ruppin, E. (2010) Genome Res. 20, 122-132
8. Kun, Á., Pongor, S., Jordán, F., and Szathmáry, E. (2008) in The Codes of Life (Barbieri, M., and Hoffmeyer, J. eds) pp. 39-58, Springer-Verlag, Amsterdam
9. Lupas, A. N., Ponting, C. P., and Russell, R. B. (2001) J. Struct. Biol. 134, 191-203
10. Trifonov, E. N., and Frenkel, Z. M. (2009) Curr. Opin. Struct. Biol. 19, 335-340
11. Babbitt, P. C., Mrachko, G. T., Hasson, M. S., Huisman, G. W., Kolter, R., Ringe, D., Petsko, G. A., Kenyon, G. L., and Gerlt, J. A. (1995) Science 267, 1159-1161
12. Glasner, M. E., Gerlt, J. A., and Babbitt, P. C. (2006) Curr. Opin. Chem. Biol. 10, 492-497
13. Leipe, D. D., Wolf, Y. I., Koonin, E. V., and Aravind, L. (2002) J. Mol. Biol. 317, 41-72
14. Aravind, L., Anantharaman, V., and Koonin, E. V. (2002) Proteins 48, 1-14
15. Iyer, L. M., Leipe, D. D., Koonin, E. V., and Aravind, L. (2004) J. Struct. Biol. 146, 11-31
16. Burroughs, A. M., Allen, K. N., Dunaway-Mariano, D., and Aravind, L. (2006) J. Mol. Biol. 361, 1003-1034
17. Iyer, L. M., Abhiman, S., de Souza, R. F., and Aravind, L. (2010) Nucleic Acids Res. 38, 5261-5279
18. Khersonsky, O., and Tawfik, D. S. (2010) Annu. Rev. Biochem. 79, 471-505
19. Davies, G., and Henrissat, B. (1995) Structure 3, 853-859
20. Erez, E., Fass, D., and Bibi, E. (2009) Nature 459, 371-378
21. Engelman, D. M., and Zaccai, G. (1980) Proc. Natl. Acad. Sci. U.S.A. 77, 5894-5898
22. Blobel, G. (1980) Proc. Natl. Acad. Sci. U.S.A. 77, 1496-1500
23. Fuqua, W. C., Winans, S. C., and Greenberg, E. P. (1994) J. Bacteriol. 176, 269-275
24. Estin, M. L., Stoltz, D. A., and Zabner, J. (2010) Adv. Exp. Med. Biol. 660, 183-193
25. Jayaraman, A., and Wood, T. K. (2008) Annu. Rev. Biomed. Eng. 10, 145-167
26. Schaefer, A. L., Greenberg, E. P., Oliver, C. M., Oda, Y., Huang, J. J., Bittan- Banin, G., Peres, C. M., Schmidt, S., Juhaszova, K., Sufrin, J. R., and Harwood, C. S. (2008) Nature 454, 595-599
27. Bokhove, M., Nadal Jimenez, P., Quax, W. J., and Dijkstra, B. W. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 686-691
28. Afriat, L., Roodveldt, C., Manco, G., and Tawfik, D. S. (2006) Biochemistry 45, 13677-13686
29. Wang, W. Z., Morohoshi, T., Ikenoya, M., Someya, N., and Ikeda, T. (2010) Appl. Environ. Microbiol. 76, 2524-2530
30. Liu, D., Lepore, B. W., Petsko, G. A., Thomas, P. W., Stone, E. M., Fast, W., and Ringe, D. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 11882-11887
31. Kim, M. H., Choi, W. C., Kang, H. O., Lee, J. S., Kang, B. S., Kim, K. J., Derewenda, Z. S., Oh, T. K., Lee, C. H., and Lee, J. K. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 17606-17611
32. Liu, D., Momb, J., Thomas, P. W., Moulin, A., Petsko, G. A., Fast, W., and Ringe, D. (2008) Biochemistry 47, 7706-7714
33. Momb, J., Wang, C., Liu, D., Thomas, P. W., Petsko, G. A., Guo, H., Ringe, D., and Fast, W. (2008) Biochemistry 47, 7715-7725
34. Liu, D., Thomas, P. W., Momb, J., Hoang, Q. Q., Petsko, G. A., Ringe, D., and Fast, W. (2007) Biochemistry 46, 11789-11799
35. Daiyasu, H., Osaka, K., Ishino, Y., and Toh, H. (2001) FEBS Lett. 503, 1-6
36. Bebrone, C. (2007) Biochem. Pharmacol. 74, 1686-1701
37. Seibert, C. M., and Raushel, F. M. (2005) Biochemistry 44, 6383-6391
38. Wierenga, R. K. (2001) FEBS Lett. 492, 193-198
39. Gerlt, J. A., and Raushel, F. M. (2003) Curr. Opin. Chem. Biol. 7, 252-264
40. Merone, L., Mandrich, L., Rossi, M., and Manco, G. (2005) Extremophiles 9, 297-305
41. Chow, J. Y., Wu, L., and Yew, W. S. (2009) Biochemistry 48, 4344-4353
42. Chow, J. Y., Xue, B., Lee, K. H., Tung, A., Wu, L., Robinson, R. C., and Yew, W. S. (2010) J. Biol. Chem. 285, 40911-40920
43. Hawwa, R., Larsen, S. D., Ratia, K., and Mesecar, A. D. (2009) J. Mol. Biol. 393, 36-57
44. Xiang, D. F., Kolb, P., Fedorov, A. A., Meier, M. M., Fedorov, L. V., Nguyen, T. T., Sterner, R., Almo, S. C., Shoichet, B. K., and Raushel, F. M. (2009) Biochemistry 48, 2237-2247
45. Del Vecchio, P., Elias, M., Merone, L., Graziano, G., Dupuy, J., Mandrich, L., Carullo, P., Fournier, B., Rochu, D., Rossi, M., Masson, P., Chabriere, E., and Manco, G. (2009) Extremophiles 13, 461-470
46. Elias, M., Dupuy, J., Merone, L., Mandrich, L., Porzio, E., Moniot, S., Rochu, D., Lecomte, C., Rossi, M., Masson, P., Manco, G., and Chabriere, E. (2008) J. Mol. Biol. 379, 1017-1028
47. Draganov, D. I., and La Du, B. N. (2004) Naunyn-Schmiedebergs Arch. Pharmacol. 369, 78-88
48. Roth, R. H., Levy, R., and Giarman, N. J. (1967) Biochem. Pharmacol. 16, 596-598
49. Draganov, D. I., Teiber, J. F., Speelman, A., Osawa, Y., Sunahara, R., and La Du, B. N. (2005) J. Lipid Res. 46, 1239-1247
50. Khersonsky, O., and Tawfik, D. S. (2005) Biochemistry 44, 6371-6382
51. Yang, F., Wang, L. H., Wang, J., Dong, Y. H., Hu, J. Y., and Zhang, L. H. (2005) FEBS Lett. 579, 3713-3717
52. Draganov, D. I. (2010) Chem. Biol. Interact. 187, 370-372
53. Teiber, J. F., and Draganov, D. I. (2011) Methods Mol. Biol. 692, 291-298
54. Teiber, J. F., Horke, S., Haines, D. C., Chowdhary, P. K., Xiao, J., Kramer, G. L., Haley, R. W., and Draganov, D. I. (2008) Infect. Immun. 76, 2512-2519
55. Connelly, P. W., Picardo, C. M., Potter, P. M., Teiber, J. F., Maguire, G. F., and Ng, D. S. (2011) Biochim. Biophys. Acta 1811, 39-45
56. Harel, M., Aharoni, A., Gaidukov, L., Brumshtein, B., Khersonsky, O., Meged, R., Dvir, H., Ravelli, R. B., McCarthy, A., Toker, L., Silman, I., Sussman, J. L., and Tawfik, D. S. (2004) Nat. Struct. Mol. Biol. 11, 412-419
57. Khersonsky, O., and Tawfik, D. S. (2006) J. Biol. Chem. 281, 7649-7656
58. O'Brien, P. J., and Herschlag, D. (1999) Chem. Biol. 6, R91-R105
59. Dyhrman, S. T., Chappell, P. D., Haley, S. T., Moffett, J. W., Orchard, E. D., Waterbury, J. B., and Webb, E. A. (2006) Nature 439, 68-71
60. Munnecke, D. M., and Hsieh, D. P. (1974) Appl. Microbiol. 28, 212-217
61. Yang, K., and Metcalf, W. W. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 7919-7924
62. Serdar, C. M., Gibson, D. T., Munnecke, D. M., and Lancaster, J. H. (1982) Appl. Environ. Microbiol. 44, 246-249
63. Horne, I., Qiu, X., Russell, R. J., and Oakeshott, J. G. (2003) FEMS Microbiol. Lett. 222, 1-8
64. Siddavattam, D., Khajamohiddin, S., Manavathi, B., Pakala, S. B., and Merrick, M. (2003) Appl. Environ. Microbiol. 69, 2533-2539
65. Mulbry, W., Ahrens, E., and Karns, J. (1998) Pesticide Sci. 52, 268-274
66. Yang, H., Carr, P. D., McLoughlin, S. Y., Liu, J. W., Horne, I., Qiu, X., Jeffries, C. M., Russell, R. J., Oakeshott, J. G., and Ollis, D. L. (2003) Protein Eng. 16, 135-145
67. Omburo, G. A., Kuo, J. M., Mullins, L. S., and Raushel, F. M. (1992) J. Biol. Chem. 267, 13278-13283
68. Roodveldt, C., and Tawfik, D. S. (2005) Biochemistry 44, 12728-12736
69. Dong, Y. J., Bartlam, M., Sun, L., Zhou, Y. F., Zhang, Z. P., Zhang, C. G., Rao, Z., and Zhang, X. E. (2005) J. Mol. Biol. 353, 655-663
70. Wang, Y., Addess, K. J., Chen, J., Geer, L. Y., He, J., He, S., Lu, S., Madej, T., Marchler-Bauer, A., Thiessen, P. A., Zhang, N., and Bryant, S. H. (2007) Nucleic Acids Res. 35, D298-D300
71. Aharoni, A., Gaidukov, L., Yagur, S., Toker, L., Silman, I., and Tawfik, D. S. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 482-487
72. Gupta, R. D., Goldsmith, M., Ashani, Y., Simo, Y., Mullokandov, G., Bar, H., Ben-David, M., Leader, H., Margalit, R., Silman, I., Sussman, J. L., andTawfik, D. S. (2011) Nat. Chem. Biol. 7, 120-125
73. Schmidt, D. M., Mundorff, E. C., Dojka, M., Bermudez, E., Ness, J. E., Govindarajan, S., Babbitt, P. C., Minshull, J., and Gerlt, J. A. (2003) Biochemistry 42, 8387-8393
74. Taylor Ringia, E. A., Garrett, J. B., Thoden, J. B., Holden, H. M., Rayment, I., and Gerlt, J. A. (2004) Biochemistry 43, 224-229
75. Poelarends, G. J., Serrano, H., Johnson, W. H., Jr., Hoffman, D. W., and Whitman, C. P. (2004) J. Am. Chem. Soc. 126, 15658-15659
76. Wang, S. C., Johnson, W. H., Jr., and Whitman, C. P. (2003) J. Am. Chem. Soc. 125, 14282-14283
77. Huey, R., Morris, G. M., Olson, A. J., and Goodsell, D. S. (2007) J. Comput. Chem. 28, 1145-1152
78. Galperin, M. Y., and Koonin, E. V. (2012) J. Biol. Chem. 287, 21-28
79. Copley, S. D. (2012) J. Biol. Chem. 287, 3-10
80. Gerlt, J. A., Babbitt, P. C., Jacobson, M. P., and Almo, S. C. (2012) J. Biol. Chem. 287, 29-34