Gene cloning, expression, and characterization of a nitrilase from Alcaligenes faecalis ZJUTB10

Journal of Agricultural and Food Chemistry

Volumn 59, Issue 21, 2011, Pages 11560-11570

  Liu, Zhi Qiang ^a   Dong, Li Zhu ^a   Cheng, Feng ^a   Xue, Ya Ping ^a   Wang, Yuan Shan ^a   Ding, Jie Nv ^a   Zheng, Yu Guo ^a   Shen, Yin Chu ^a  

^a ZHEJIANG UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Alcaligenes faecalis; characterization; enantioselective hydrolysis; Nitrilase; structure modeling

Indexed keywords

ALCALIGENES FAECALIS; CATALYTIC TRIAD; ENANTIOMERIC EXCESS; ENANTIOSELECTIVE HYDROLYSIS; GENE CLONING; HYDROLYTIC ACTIVITIES; INDUSTRIAL ENZYMES; INHIBITORY EFFECT; MANDELIC ACID; NITRILASE; OPTIMUM PH; SITE DIRECTED MUTAGENESIS; STRUCTURE MODELING; SUBSTRATE SPECIFICITY;

CARBOXYLIC ACIDS; CLONING; CYANIDES; HYDROLYSIS;

GENE EXPRESSION;

BACTERIAL PROTEIN; HYDROLASE; NITRILASE;

ALCALIGENES FAECALIS; AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; CHEMISTRY; ENZYME SPECIFICITY; ENZYME STABILITY; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; SEQUENCE ALIGNMENT;

ALCALIGENES FAECALIS; AMINO ACID SEQUENCE; AMINOHYDROLASES; BACTERIAL PROTEINS; CATALYSIS; CLONING, MOLECULAR; ENZYME STABILITY; KINETICS; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

ALCALIGENES FAECALIS;

EID: 80455134683     PISSN: 00218561     EISSN: 15205118     Source Type: Journal    
DOI: 10.1021/jf202746a     Document Type: Article

References (49)

1. Lynd, L. R.; Wyman, C. E.; Gerngross, T. U. Biocommodity engineering Biotechnol. Prog. 1999, 15 (5) 777-793
2. Feng, X. W.; Li, C.; Wang, N.; Li, K.; Zhang, W. W.; Wang, Z.; Yu, X. Q. Lipase-catalysed decarboxylative aldol reaction and decarboxylative Knoevenagel reaction Green Chem. 2009, 11 (12) 1933-1936
3. Guebitz, G. M.; Cavaco-Paulo, A. Enzymes go big: surface hydrolysis and functionalisation of synthetic polymers Trends Biotechnol. 2008, 26 (1) 32-38
4. Nagasawa, T.; Yamada, H. Microbial transformations of nitriles Trends Biotechnol. 1989, 7 (6) 153-158
5. Kobayashi, M.; Shimizu, S. Nitrile hydrolases Curr. Opin. Chem. Biol. 2000, 4 (1) 95-102
6. Thuku, R. N.; Brady, D.; Benedik, M. J.; Sewell, B. T. Microbial nitrilases: versatile, spiral forming, industrial enzymes J. Appl. Microbiol. 2009, 106 (3) 703-727
7. Jandhyala, D. M.; Willson, R. C.; Sewell, B. T.; Benedik, M. J. Comparison of cyanide-degrading nitrilases Appl. Microbiol. Biotechnol. 2005, 68 (3) 327-335
8. Zheng, Y. G.; Chen, J.; Liu, Z. Q.; Wu, M. H.; Xing, L. Y.; Shen, Y. C. Isolation, identification and characterization of Bacillus subtilis ZJB-063, a versatile nitrile-converting bacterium Appl. Microbiol. Biotechnol. 2008, 77 (5) 985-993
9. Liu, Z. Q.; Li, F. F.; Cheng, F.; Zhang, T.; You, Z. Y.; Xu, J. M.; Xue, Y. P.; Zheng, Y. G.; Shen, Y. C. A Novel synthesis of iminodiacetic acid: Biocatalysis by whole Alcaligenes faecalis ZJB-09133 cells from iminodiacetonitrile Biotechnol. Prog. 2011, 27 (3) 698-705
10. Fernandes, B. C. M.; Mateo, C.; Kiziak, C.; Chmura, A.; Wacker, J.; van Rantwijk, F.; Stolz, A.; Sheldon, R. A. Nitrile hydratase activity of a recombinant nitrilase Adv. Synth. Catal. 2006, 348 (18) 2597-2603
11. Pace, H. C.; Brenner, C. The nitrilase superfamily: classification, structure and function. Genome Biol. 2001, 2 (1), REVIEWS0001.1-0001.9.
12. Banerjee, A.; Sharma, R.; Banerjee, U. C. The nitrile-degrading enzymes: current status and future prospects Appl. Microbiol. Biotechnol. 2002, 60 (1-2) 33-44
13. Brenner, C. Catalysis in the nitrilase superfamily Curr. Opin. Struct. Biol. 2002, 12 (6) 775-782
14. O'Reilly, C.; Turner, P. D. The nitrilase family of CN hydrolysing enzymes-a comparative study J. Appl. Microbiol. 2003, 95 (6) 1161-1174
15. Williamson, D. S.; Dent, K. C.; Weber, B. W.; Varsani, A.; Frederick, J.; Thuku, R. N.; Cameron, R. A.; van Heerden, J. H.; Cowan, D. A.; Sewell, B. T. Structural and biochemical characterization of a nitrilase from the thermophilic bacterium, Geobacillus pallidus RAPc8 Appl. Microbiol. Biotechnol. 2010, 88 (1) 143-153
16. Xue, Y. P.; Xu, S. Z.; Liu, Z. Q.; Zheng, Y. G.; Shen, Y. C. Enantioselective biocatalytic hydrolysis of (R, S)-mandelonitrile for production of (R)-(-)-mandelic acid by a newly isolated mutant strain J. Ind. Microbiol. Biotechnol. 2011, 38 (2) 337-345
17. Sambrook, J.; Russell, D. W. Molecular cloning: A laboratory manual. In Molecular cloning: A laboratory manual; Cold Spring Harbor Laboratory Press: Woodbury, NY, 2001.
18. Laemmli, U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Nature 1970, 227 (5259) 680-685
19. Bradford, M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal. Biochem. 1976, 72, 248-254
20. Fasman, G. D. Circular Dichroism and the Conformational Analysis of Biomolecules; Plenum Press: New York, 1996.
21. Liu, Z. Q.; Gosser, Y.; Baker, P. J.; Ravee, Y.; Lu, Z. Y.; Alemu, G.; Li, H. G.; Butterfoss, G. L.; Kong, X. P.; Gross, R.; Montclare, J. K. Structural and functional studies of Aspergillus oryzae cutinase: Enhanced thermostability and hydrolytic activity of synthetic ester and polyester degradation J. Am. Chem. Soc. 2009, 131 (43) 15711-15716
22. Greenfield, N. J. Using circular dichroism spectra to estimate protein secondary structure Nat. Protoc. 2006, 1 (6) 2876-2890
23. Pace, C. N.; Grimsley, G. R.; Thomson, J. A.; Barnett, B. J. Conformational stability and activity of ribonuclease T1 with zero, one, and two intact disulfide bonds J. Biol. Chem. 1988, 263 (24) 11820-11825
24. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J. Comput. Chem. 1998, 19 (14) 1639-1662
25. Thompson, J. D.; Gibson, T. J.; Plewniak, F.; Jeanmougin, F.; Higgins, D. G. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 1997, 25 (24) 4876-4882
26. Gouet, P.; Courcelle, E.; Stuart, D. I.; Metoz, F. ESPript: analysis of multiple sequence alignments in PostScript Bioinformatics 1999, 15 (4) 305-308
27. Kaplan, O.; Vejvoda, V.; Plihal, O.; Pompach, P.; Kavan, D.; Bojarova, P.; Bezouska, K.; Mackova, M.; Cantarella, M.; Jirku, V.; Kren, V.; Martinkova, L. Purification and characterization of a nitrilase from Aspergillus niger K10 Appl. Microbiol. Biotechnol. 2006, 73 (3) 567-575
28. Almatawah, Q. A.; Cramp, R.; Cowan, D. A. Characterization of an inducible nitrilase from a thermophilic bacillus Extremophiles 1999, 3 (4) 283-291
29. Harper, D. B. Microbial metabolism of aromatic nitriles. Enzymology of C-N cleavage by Nocardia sp. (Rhodochrous group) N.C.I.B. 11216 Biochem. J. 1977, 165 (2) 309-319
30. Hoyle, A. J.; Bunch, A. W.; Knowles, C. J. The nitrilases of Rhodococcus rhodochrous NCIMB 11216 Enzyme Microb. Technol. 1998, 23 (7-8) 475-482
31. Kobayashi, M.; Nagasawa, T.; Yamada, H. Nitrilase of Rhodococcus rhodochrous J1. Purification and characterization Eur. J. Biochem. 1989, 182 (2) 349-356
32. Nagasawa, T.; Wieser, M.; Nakamura, T.; Iwahara, N.; Yoshida, T.; Gekko, K. Nitrilase of Rhodococcus rhodochrous J1-Conversion into the active form by subunit association Eur. J. Biochem. 2000, 267 (1) 138-144
33. Gavagan, J. E.; DiCosimo, R.; Eisenberg, A.; Fager, S. K.; Folsom, P. W.; Hann, E. C.; Schneider, K. J.; Fallon, R. D. A Gram-negative bacterium producing a heat-stable nitrilase highly active on aliphatic dinitriles Appl. Microbiol. Biotechnol. 1999, 52 (5) 654-659
34. Chauhan, S.; Wu, S.; Blumerman, S.; Fallon, R. D.; Gavagan, J. E.; DiCosimo, R.; Payne, M. S. Purification, cloning, sequencing and over-expression in Escherichia coli of a regioselective aliphatic nitrilase from Acidovorax facilis 72W Appl. Microbiol. Biotechnol. 2003, 61 (2) 118-122
35. Zhu, D. M.; Mukherjee, C.; Yang, Y.; Rios, B. E.; Gallagher, D. T.; Smith, N. N.; Biehl, E. R.; Hua, L. A new nitrilase from Bradyrhizobium japonicum USDA 110-Gene cloning, biochemical characterization and substrate specificity J. Biotechnol. 2008, 133 (3) 327-333
36. Kobayashi, M.; Yanaka, N.; Nagasawa, T.; Yamada, H. Purification and Characterization of a Novel Nitrilase of Rhodococcus-Rhodochrous K22 That Acts on Aliphatic Nitriles J. Bacteriol. 1990, 172 (9) 4807-4815
37. Yamamoto, K.; Oishi, K.; Fujimatsu, I.; Komatsu, K. I. Production of R -(-)-Mandelic Acid from Mandelonitrile by Alcaligenes-Faecalis Atcc-8750 Appl. Environ. Microbiol. 1991, 57 (10) 3028-3032
38. Nagasawa, T.; Mauger, J.; Yamada, H. A Novel Nitrilase, Arylacetonitrilase, of Alcaligenes-Faecalis Jm3-Purification and Characterization Eur. J. Biochem. 1990, 194 (3) 765-772
39. Kobayashi, M.; Izui, H.; Nagasawa, T.; Yamada, H. Nitrilase in biosynthesis of the plant hormone indole-3-acetic-acid from indole-3- acetonitrile-cloning of the Alcaligenes gene and site-directed mutagenesis of cysteine residues Proc. Natl. Acad. Sci. U.S.A. 1993, 90 (1) 247-251
40. Zhu, D. M.; Mukherjee, C.; Biehl, E. R.; Hua, L. Discovery of a mandelonitrile hydrolase from Bradyrhizobium japonicum USDA110 by rational genome mining J. Biotechnol. 2007, 129 (4) 645-650
41. Watanabe, A.; Yano, K.; Ikebukuro, K.; Karube, I. Cloning and expression of a gene encoding cyanidase from Pseudomonas stutzeri AK61 Appl. Microbiol. Biotechnol. 1998, 50 (1) 93-97
42. Barclay, M.; Day, J. C.; Thompson, I. P.; Knowles, C. J.; Bailey, M. J. Substrate-regulated cyanide hydratase (chy) gene expression in Fusarium solani: the potential of a transcription-based assay for monitoring the biotransformation of cyanide complexes Environ. Microbiol. 2002, 4 (3) 183-189
43. Banerjee, A.; Kaul, P.; Banerjee, U. C. Purification and characterization of an enantioselective arylacetonitrilase from Pseudomonas putida Arch. Microbiol. 2006, 184 (6) 407-418
44. DeSantis, G.; Wong, K.; Farwell, B.; Chatman, K.; Zhu, Z. L.; Tomlinson, G.; Huang, H. J.; Tan, X. Q.; Bibbs, L.; Chen, P.; Kretz, K.; Burk, M. J. Creation of a productive, highly enantioselective nitrilase through gene site saturation mutagenesis (GSSM) J. Am. Chem. Soc. 2003, 125 (38) 11476-11477
45. Kiziak, C.; Conradt, D.; Stolz, A.; Mattes, R.; Klein, J. Nitrilase from Pseudomonas fluorescens EBC191: cloning and heterologous expression of the gene and biochemical characterization of the recombinant enzyme Microbiology 2005, 151, 3639-3648
46. Sakai, N.; Tajika, Y.; Yao, M.; Watanabe, N.; Tanaka, I. Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6 angstrom resolution Proteins 2004, 57 (4) 869-873
47. Rypniewski, W.; Raczynska, J. E.; Vorgias, C. E.; Antranikian, G. Crystallographic analysis of a thermoactive nitrilase J. Struct. Biol. 2011, 173 (2) 294-302
48. Kim, J. S.; Tiwari, M. K.; Moon, H. J.; Jeya, M.; Ramu, T.; Oh, D. K.; Kim, I. W.; Lee, J. K. Identification and characterization of a novel nitrilase from Pseudomonas fluorescens Pf-5 Appl. Microbiol. Biotechnol. 2009, 83 (2) 273-283
49. Liu, Z. Q.; Leng, Y.; Sun, Z. H. Directed evolution and characterization of a novel d -pantonohydrolase from Fusarium moniliforme J. Agric. Food Chem. 2006, 54 (16) 5823-5830