Catalytic improvement and evolution of atrazine chlorohydrolase

Applied and Environmental Microbiology

Volumn 75, Issue 7, 2009, Pages 2184-2191

  Scott, Colin ^a,b   Jackson, Colin J ^a   Coppin, Chris W ^a,b   Mourant, Roslyn G ^a,b   Hilton, Margaret E ^a,b   Sutherland, Tara D ^a   Russell, Robyn J ^a,b   Oakeshott, John G ^a,b  

^a CSIRO   (Australia)

^b CRC for Sugar Industry Innovation Through Biotechnology   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ATRAZINE; CATALYTIC ACTIVITIES; CATALYTIC MECHANISMS; COOPERATIVITY; KINETIC PROFILES; STRUCTURAL MODELS; SUBSTRATE BINDINGS; WILD-TYPE ENZYMES;

BIOREMEDIATION; CATALYST ACTIVITY; DECHLORINATION; ELECTROCHEMICAL SENSORS; ENZYMES; MODEL STRUCTURES; SUBSTRATES;

HERBICIDES;

AMIDASE; ATRAZINE; ATRAZINE CHLOROHYDROLASE; DEAMINASE; ENZYME; TRIAZINE DERIVATIVE; UNCLASSIFIED DRUG;

ATRAZINE; BIOREMEDIATION; CATALYSIS; DECHLORINATION; ENZYME ACTIVITY; EVOLUTION; HYDROLYSIS; IDENTIFICATION METHOD;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GROWTH; BIOREMEDIATION; CATALYSIS; DECHLORINATION; ENZYME ACTIVE SITE; ENZYME STRUCTURE; ENZYME SUBSTRATE; EVOLUTION; PROTEIN VARIANT;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ATRAZINE; BINDING SITES; DIRECTED MOLECULAR EVOLUTION; DNA MUTATIONAL ANALYSIS; HYDROLASES; KINETICS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; MUTATION, MISSENSE; POINT MUTATION; SEQUENCE ALIGNMENT;

EID: 63849273993     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02634-08     Document Type: Article

References (59)

1. Adair, G. S. 1925. The hemoglobin system. VI. The oxygen dissociation curve of hemoglobin. J. Biol. Chem. 63:529-545.
2. Alcalde, M., M. Ferrer, F. J. Plou, and A. Ballesteros. 2006. Environmental biocatalysis: from remediation with enzymes to novel green processes. Trends Biotechnol. 24:281-287.
3. Arnold, K., L. Bordoli, J. Kopp, and T. Schwede. 2006. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22:195-201.
4. Bell, A. M., and N. C. Duke. 2005. Effects of Photosystem II inhibiting herbicides on mangroves - preliminary toxicology trials. Mar. Pollut. Bull. 51:297-307.
5. Belluck, D. A., S. L. Benjamin, and T. Dawson. 1991. Groundwater contamination by atrazine and its metabolites - risk assessment, policy, and legal implications. ACS Symp. Ser. 459:254-273.
6. Billeter, S. R., and W. F. van Gunsteren. 1997. A modular molecular dynamics quantum dynamics program for non-adiabatic proton transfers in solution. Comput. Physics Commun. 107:61-91.
7. Boundy-Mills, K. L., M. L. deSouza, R. T. Mandelbaum, L. P. Wackett, and M. J. Sadowsky. 1997. The atzB gene of Pseudomonas sp. strain ADP encodes the second enzyme of a novel atrazine degradation pathway. Appl. Environ. Microbiol. 63:916-923.
8. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comp. Chem. 4:187-217.
9. Bustos-Jaimes, I., A. Sosa-Peinado, E. Rudino-Pinera, E. Horjales, and M. L, Calcagno. 2002. On the role of the conformational flexibility of the active-site lid on the allosteric kinetics of glucosamine-6-phosphate deaminase. J. Mol. Biol. 319:183-189.
10. Cheng, G., N. Shapir, M. J. Sadowsky, and L. P. Wackett. 2005. Allophanate hydrolase, not urease, functions in bacterial cyanuric acid metabolism. Appl. Environ. Microbiol. 71:4437-4445.
11. de Souza, M. L., M. J. Sadowsky, and L. P. Wackett. 1996. Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization. J. Bacteriol. 178:4894-4900.
12. de Souza, M. L., L. P. Wackett, K. L. Boundymills, R. T. Mandelbaum, and M. J. Sadowsky. 1995. Cloning, characterization, and expression of a gene region from Pseudomonas sp. strain ADP involved in the dechlorination of atrazine. Appl. Environ. Microbiol. 61:3373-3378.
13. Emsley, P., and K. Cowtan. 2004. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60:2126-2132.
14. Fruchey, I., N. Shapir, M. J. Sadowsky, and L. P. Wackett 2003. On the origins of cyanuric acid hydrolase: purification, substrates, and prevalence of AtzD from Pseudomonas sp. strain ADP. Appl. Environ. Microbiol. 69:3653-3657.
15. Gavrilescu, M. 2005. Fate of pesticides in the environment and its bioremediation. Eng. Life Sci. 5:497-526.
16. Hayes, T., K. Haston, M. Tsui, A. Hoang, C. Haeffele, and A. Vonk. 2003. Atrazine-induced hermaphroditism at 0.1 ppb in American leopard frogs (Rana pipiens): laboratory and field evidence. Environ. Health Perspect. 111:568-575.
17. Hayes, T. B., A. Collins, M. Lee, M. Mendoza, N. Noriega, A. A. Stuart, and A. Vonk. 2002. Hermaphroditic. de masculinized frogs after exposure to the herbicide atrazine at low ecologically relevant doses. Proc. Natl. Acad. Sci. USA 99:5476-5480.
18. Hayes, T. B., A. A. Stuart, M. Mendoza, A. Collins, N. Noriega, A. Vonk, G. Johnston, R. Liu, and D. Kpodzo. 2006. Characterization of atrazine-induced gonadal malformations in African clawed frogs (Xenopus laevis) and comparisons with effects of an androgen antagonist (cyproterone acetate) and exogenous estrogen (17 beta-estradiol): support for the demasculinization/ feminization hypothesis. Environ. Health Perspect. 114:134-141.
19. Higiuchi, R., B. Krummel, and R. Saiki. 1988. Nucleic Acids Res. 16:7351-7367.
20. Holm, L., and C. Sander. 1997. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins 28:72-82.
21. Huff, J. 2002. IARC monographs, industry influence, and upgrading, downgrading, and under-grading chemicals - a personal point of view. Int. J. Occup. Environ. Health 8:249-270.
22. Huff, J., and J. Sass. 2007. Atrazine - a likely human carcinogen? Int. J. Occup. Environ. Health 13:356-358.
23. Ireton, G. C., M. E. Black, and B. L. Stoddard. 2001. Crystallization and preliminary X-ray analysis of bacterial cytosine deaminase. Acta Crystallogr. D 57:1643-1645.
24. Ireton, G. C., G. McDermott, M. E. Black, and B. L. Stoddard. 2002. The structure of Escherichia coli cytosine deaminase. J. Mol. Biol. 315:687-697.
25. Kaplan, W., and T. G. Littlejohn. 2001. Swiss-PDB Viewer (Deep View). Brief. Bioinform. 2:195-197.
26. Kawahigashi, H., S. Hirose, H. Ohkawa, and Y, Ohkawa. 2007. Herbicide resistance of transgenic rice plants expressing human CYP1A1. Biotechnol. Adv. 25:75-84.
27. Kawahigashi, H., S. Hirose, H. Ohkawa, and Y. Ohkawa. 2006. Phytoremediation of the herbicides atrazine and metolachlor by transgenic rice plants expressing human CYP1A1. CYP2B6, and CYP2C19. J. Agric. Eood Chem. 54:2985-2991.
28. Khersonsky, O., C. Roodveldt, and D. S. Tawfik. 2006. Enzyme promiscuity: evolutionary and mechanistic aspects. Curr. Opin. Chem. Biol. 10:498-508.
29. Lei, Z. F., C. M. Ye, and X. J. Wang. 2001. Hydrolysis kinetics of atrazine and influence factors. J. Environ. Sci. (China) 13:99-103.
30. Levy, M., and S. L. Miller. 1998. The stability of the RNA bases: implications for the origin of life. Proc. Natl. Acad. Sci. USA 95:7933-7938.
31. Lockert, C. K., K. D. Hoagland, and B. D. Siegfried. 2006. Comparative sensitivity of freshwater algae to atrazine. Bull. Environ. Contam. Toxicol. 76:73-79.
32. Mandelbaum, R. T., D. L. Allan, and L. P. Wackett. 1995. Isolation and characterization of a Pseudomonas sp. that mineralizes the s-triazine herbicide atrazine. Appl. Environ. Microbiol. 61:1451-1457.
33. Martinez, B., J. Tomkins, L. P. Wackett, R. Wing, and M. J. Sadowsky. 2001. Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J. Bacteriol. 183:5684-5697.
34. Melo, F., and E. Feytmans. 1998. Assessing protein structures with a nonlocal atomic interaction energy. J. Mol. Biol. 277:1141-1152.
35. Merkler, D. J., and V. L. Schramm. 1990. Catalytic and regulatory site composition of yeast amp deaminase by comparative binding and rate studies - resolution of the cooperative mechanism. J. Biol. Chem. 265:4420-4426.
36. Notredame, C., D. G. Higgins, and J. Heringa. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:205-217.
37. Porter, D. J. T., and E. A. Austin. 1993. Cytosine deaminase - the roles of divalent metal-ions in catalysis. J. Biol. Chem. 268:24005- 24011.
38. Raillard, S., A. Krebber, Y. C. Chen, J. E. Ness, E. Bermudez, R. Trinidad, R. Fullem, C. Davis, M. Welch, J. Seffernick, L. P. Wackett, W. P. C. Stemmer, and J. Minshull. 2001. Novel enzyme activities and functional plasticity revealed by recombining highly homologous enzymes. Chem. Biol. 8:891-898.
39. Sadowsky, M. J., Z. K. Tong, M. de Souza, and L. P, Wackett. 1998. AtzC is a new member of the amidohydrolase protein superfamily and is homologous to other atrazine-metabolizing enzymes. J. Bacteriol. 180:152-158.
40. Scott, C., G. Pandey, C. J. Hartley, C. J. Jackson, M. J. Cheesman, M. C. Taylor, R. Pandey, J. L. Khurana, M. Teese, C. W. Coppin, K. M. Weir, R. K. Jain, R. Lal, R. J. Russell, and J. G. Oakeshott. 2008. The enzymatic basis for bioremediation. Indian J. Microbiol. 48:65-79.
41. Seffernick, J. L., M. L. de Souza, M. J. Sadowsky, and L. P. Wackett. 2001. Melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different. J. Bacteriol. 183:2405-2410.
42. Seffernick, J. L., and L. P. Wackett. 2001. Rapid evolution of bacterial catabolic enzymes: a case study with atrazine chlorohydrolase. Biochemistry 40:12747-12753.
43. Seibert, C. M., and F. M. Raushel. 2005. Structural and catalytic diversity within the amidohydrolase superfamily. Biochemistry 44:6383-6391.
44. Shapir, N., E. F. Mongodin, M. J. Sadowsky, S. C. Daugherty, K. E. Nelson, and L. P. Wackett. 2007. Evolution of catabolic pathways: genomic insights into microbial s-triazine metabolism. J. Bacteriol. 189:674-682.
45. Shapir, N., M. J. Sadowsky, and L. P. Wackett. 2005. Purification and characterization of allophanate hydrolase (AtzF) from Pseudomonas sp. strain ADP. J. Bacteriol. 187:3731-3738.
46. Shi, J., T. L. Blundell, and K. Mizuguchi. 2001. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310:243-257.
47. Strong, L. C., H. McTavish, M. J. Sadowsky, and L. P. Wackett. 2000. Field-scale remediation of atrazine-contaminated soil using recombinant Escherichia coli expressing atrazine chlorohydrolase. Environ. Microbiol. 2:91-98.
48. Sutherland, T. D., I. Home, K. M. Weir, C. W. Coppin, M. R. Williams, M. Selleck, R. J. Russell, and J. G. Oakeshott. 2004. Enzymatic bioremediation: from enzyme discovery to applications. Clin. Exp. Pharmacol. Physiol. 31: 817-821.
49. Sutton, W. F., A. E. Brown, and B. Truelove. 1984. Atrazine-resistant and diuron-resistant strains of Rhodopseudomonas sphaeroides. Weed Sci. 32: 664-669.
50. Tawfik, M., H. Ragab, and J. P. McCollum. 1968. Colorimetric methods for the determination of simazime and related chloro-s-triazines. J. Agric. Food Chem. 16:284-289.
51. Thurman, E. M., and M. T. Meyer 1996. Herbicide metabolites in surface water and groundwater: introduction and overview. ACS Symp. Ser. 630: 1-15.
52. Tomlin, C. D. S. 2006. The pesticide manual. 14th ed. British Crop Protection Council, Alton. United Kingdom.
53. van der Meer, J. R. 2006. Environmental pollution promotes selection of microbial degradation pathways. Front. Ecol. Environ. 4:35-42.
54. Wackett, L. P. 1998. Directed evolution of new enzymes and pathways for environmental biocatalysis. Enzyme Eng. 864:142-152.
55. Wackett, L. P. 2004. Evolution of enzymes for the metabolism of new chemical inputs into the environment. J. Biol. Chem. 279:41259-41262.
56. Wackett, L. P. 2004. Evolution of new enzymes and pathways: soil microbes adapt to s-triazine herbicides. Pestic. Decontam. Detox. 863:37-48.
57. Wang, L., D. A. Samac, N. Shapir, L. P. Wackett, C. P. Vance, N. E. Olszewski, and M. J. Sadowsky. 2005. Biodegradation of atrazine in transgenic plants expressing a modified bacterial atrazine chlorohydrolase (atzA) gene. Plant Biotechnol. J. 3:475-486.
58. Yamazaki, K., K. Fujii, A. Iwasaki, K. Takagi, K. Satsuma, N. Harada, and T. Uchimura. 2008. Different substrate specificities of two triazine hydrolases (TrzNs) from Nocardioides species. FEMS Microbiol. Lett. 286:171-177.
59. Young, D. 2001. SPARTAN, p. 330. In Computational chemistry. Wiley-lnterscience, New York, NY.