Heterologous expression, purification and characterization of nitrilase from Aspergillus niger K10

BMC Biotechnology

Volumn 11, Issue , 2011, Pages

  Kaplan, Ondřej ^a   Bezouška, Karel ^a,b   Plíhal, Ondřej ^a   Ettrich, Rüdiger ^c   Kulik, Natallia ^c   Vaněk, Ondřej ^a,b   Kavan, Daniel ^a,b   Benada, Oldřich ^a   Malandra, Anna ^a,d   Šveda, Ondřej ^a   Veselá, Alicja B ^a   Rinágelová, Anna ^a   Slámová, Kristýna ^a   Cantarella, Maria ^d   Felsberg, Jürgen ^a   Dušková, Jarmila ^e   Dohnálek, Jan ^e   Kotik, Michael ^a   Křen, Vladimír ^a   Martínková, Ludmila ^a  

^a INSTITUTE OF MICROBIOLOGY   (Czech Republic)

^b CHARLES UNIVERSITY   (Czech Republic)

^c INSTITUTE OF MATHEMATICS   (Czech Republic)

^d UNIVERSITY OF L'AQUILA   (Italy)

^e INSTITUTE OF MACROMOLECULAR CHEMISTRY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL CENTRIFUGATION; ASPERGILLUS NIGER; C-TERMINAL PEPTIDES; CATALYTIC PROPERTIES; CDNA LIBRARIES; EXPRESSION VECTORS; FILAMENTOUS FUNGI; GEL FILTRATION; GENE SCREENING; GENE SEQUENCING; HELICAL SEGMENTS; HETEROLOGOUS EXPRESSION; IN-VITRO; MASS SPECTROMETRY ANALYSIS; MULTIMERIC; NATIVE ENVIRONMENT; NITRILASE; PCR PRODUCTS; PROTEIN REFOLDING; PROTEIN SPECIES; QUATERNARY STRUCTURE; RECOMBINANT ENZYMES; SAMPLE HOMOGENEITY; SPECIFIC ACTIVITY; STRUCTURAL STUDIES; SUBSTRATE SPECIFICITY;

AMINO ACIDS; BACTERIA; BACTERIOLOGY; BIOLOGY; CENTRIFUGATION; CYANIDES; ESCHERICHIA COLI; GENES; MASS SPECTROMETRY; PEPTIDES; PURIFICATION;

ENZYMES;

ACID; AMIDE; AMINO ACID; ARGININE; ASPARAGINE; ASPARTIC ACID; CARBOXY TERMINAL TELOPEPTIDE; COMPLEMENTARY DNA; ENZYME; NITRILASE; PROTEIN; RECOMBINANT ENZYME; RECOMBINANT NITRILASE; UNCLASSIFIED DRUG; VALINE; BACTERIAL PROTEIN; HYDROLASE; RECOMBINANT PROTEIN;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; ASPERGILLUS NIGER; BACTERIAL STRAIN; CONTROLLED STUDY; DNA LIBRARY; ELECTRON MICROSCOPY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME PURIFICATION; ENZYME SPECIFICITY; ENZYME STABILITY; ESCHERICHIA COLI; FUNGAL STRAIN; GEL FILTRATION; GENE EXPRESSION; GENE VECTOR; HETEROLOGOUS EXPRESSION; LIGHT SCATTERING; MASS SPECTROMETRY; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; POLYMERASE CHAIN REACTION; PROTEIN CLEAVAGE; PROTEIN PROCESSING; PROTEIN QUATERNARY STRUCTURE; WILD TYPE; AMINO ACID SEQUENCE; BIOSYNTHESIS; DNA SEQUENCE; ENZYMOLOGY; GENETICS; ISOLATION AND PURIFICATION; LIGHT; METABOLISM; METHODOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; PROTEIN FOLDING; RADIATION SCATTERING; SEQUENCE ALIGNMENT;

ASPERGILLUS; ASPERGILLUS NIGER; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; FUNGI; PENICILLIUM;

AMINO ACID SEQUENCE; AMINOHYDROLASES; ASPERGILLUS NIGER; BACTERIAL PROTEINS; CLONING, MOLECULAR; DNA, COMPLEMENTARY; ENZYME STABILITY; LIGHT; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; PROTEIN FOLDING; RECOMBINANT PROTEINS; SCATTERING, RADIATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 78650888717     PISSN: None     EISSN: 14726750     Source Type: Journal    
DOI: 10.1186/1472-6750-11-2     Document Type: Article

References (58)

1. Kim JS, Tiwari MK, Moon HJ, 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, 83:273-283. 10.1007/s00253-009-1862-6, 19153727.
2. Zhu DM, Mukherjee C, Yang Y, Rios BE, Gallagher DT, Smith NN, Biehl ER, Hua L. A new nitrilase from Bradyrhizobium japonicum USDA 110 - Gene cloning, biochemical characterization and substrate specificity. J Biotechnol 2008, 133:327-333. 10.1016/j.jbiotec.2007.10.001, 18061298.
3. Heinemann U, Engels D, Bürger S, Kiziak C, Mattes R, Stolz A. Cloning of a nitrilase gene from the cyanobacterium Synechocystis sp. strain PCC6803 and heterologous expression and characterization of the encoded protein. Appl Environ Microbiol 2003, 69:4359-4366. 10.1128/AEM.69.8.4359-4366.2003, 169084, 12902216.
4. Mueller P, Egorova K, Vorgias CE, Boutou E, Trauthwein H, Verseck S, Antranikian G. Cloning, overexpression, and characterization of a thermoactive nitrilase from the hyperthermophilic archaeon Pyrococcus abyssi. Protein Expres Purif 2006, 47:672-681.
5. Podar M, Eads JR, Richardson TH. Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study. BMC Evol Biol 2005, 5:42. 10.1186/1471-2148-5-42, 1199592, 16083508.
6. Seffernick JL, Samanta SK, Louie TM, Wackett LP, Subramanian M. Investigative mining of sequence data for novel enzymes: A case study with nitrilases. J Biotechnol 2009, 143:17-26. 10.1016/j.jbiotec.2009.06.004, 19539670.
7. Martínková L, Vejvoda V, Kaplan O, Kubáč D, Malandra A, Cantarella M, Bezouška K, Křen V. Fungal nitrilases as biocatalysts: Recent developments. Biotechnol Adv 2009, 27:661-670.
8. Kaplan O, Vejvoda V, Plíhal O, Pompach P, Kavan D, Bojarová P, Bezouška K, Macková M, Cantarella M, Jirků V, Křen V, Martínková L. Purification and characterization of a nitrilase from Aspergillus niger K10. Appl Microbiol Biotechnol 2006, 73:567-575. 10.1007/s00253-006-0503-6, 17061133.
9. Malandra A, Cantarella M, Kaplan O, Vejvoda V, Uhnáková B, Štěpánkovč D, Martínková L. Continuous hydrolysis of 4-cyanopyridine by nitrilases from Fusarium solani O1 and Aspergillus niger K10. Appl Microbiol Biotechnol 2009, 85:277-284. 10.1007/s00253-009-2073-x, 19554325.
10. Banerjee A, Dubey S, Kaul P, Barse B, Piotrowski M, Banerjee UC. Enantioselective nitrilase from Pseudomonas putida: Cloning, heterologous expression, and bioreactor studies. Mol Biotechnol 2009, 41:35-41. 10.1007/s12033-008-9094-z, 18704770.
11. Kiziak C, Conradt D, Stolz A, Mattes R, Klein J. Nitrilase from Pseudomonas fluorescens EBC 191: cloning and heterologous expression of the gene and biochemical characterization of the recombinant enzyme. Microbiology 2005, 151:3639-3648. 10.1099/mic.0.28246-0, 16272385.
12. Thuku RN, Weber BW, Varsani A, Sewell BT. Post-translational cleavage of recombinantly expressed nitrilase from Rhodococcus rhodochrous J1 yields a stable, active helical form. FEBS J 2007, 274:2099-2108. 10.1111/j.1742-4658.2007.05752.x, 17371547.
13. Wu SJ, Fogiel AJ, Petrillo KL, Hann EC, Mersinger LJ, Di Cosimo R, O'Keefe DP, Ben-Bassat A, Payne MS. Protein engineering of Acidovorax facilis 72W nitrilase for bioprocess development. Biotechnol Bioeng 2007, 97:689-693. 10.1002/bit.21289, 17154311.
14. Bartling D, Seedorf M, Schmidt RC, Weiler EW. Molecular characterization of two cloned nitrilases from Arabidopsis thaliana: Key enzymes in biosynthesis of the plant hormone indole-3-acetic acid. Proc Natl Acad Sci USA 1994, 91:6021-6025. 10.1073/pnas.91.13.6021, 44129, 8016109.
15. Osswald S, Wajant H, Effenberger F. Characterization and synthetic applications of recombinant AtNIT1 from Arabidopsis thaliana. Eur J Biochem 2002, 269:680-687. 10.1046/j.0014-2956.2001.02702.x, 11856328.
16. Basile LJ, Willson RC, Sewell BT, Benedik MJ. Genome mining of cyanide-degrading nitrilases from filamentous fungi. Appl Microbiol Biotechnol 2008, 80:427-435. 10.1007/s00253-008-1559-2, 18587571.
17. Vejvoda V, Kaplan O, Bezouška K, Pompach P, Šulc M, Cantarella M, Benada O, Uhnáková B, Rinágelová A, Lutz-Wahl S, Fischer L, Křen V, Martínková L. Purification and characterization of a nitrilase from Fusarium solani O1. J Mol Catal B-Enz 2008, 50:99-106.
18. Wang P, Van Etten HD. Cloning and properties of a cyanide hydratase gene from the phytopathogenic fungus Gloeocercospora sorghi. Biochem Biophys Res Commun 1992, 187:1048-1054. 10.1016/0006-291X(92)91303-8, 1382413.
19. Dent KC, Weber BW, Benedik MJ, Sewell BT. The cyanide hydratase from Neurospora crassa forms a helix which has a dimeric repeat. Appl Microbiol Biotechnol 2009, 82:271-278. 10.1007/s00253-008-1735-4, 18946669.
20. Yeom SJ, Kim HJ, Lee JK, Kim DE, Oh DK. An amino acid at position 142 in nitrilase from Rhodococcus rhodochrous ATCC 33278 determines the substrate specificity for aliphatic and aromatic nitriles. Biochem J 2008, 415:401-407. 10.1042/BJ20080440, 2570083, 18412544.
21. Pace HC, Hodawadekar SC, Draganescu A, Huang J, Bieganowski P, Pekarsky Y, Croce CM, Brenner C. Crystal structure of the worm NitFhit Rosetta Stone protein reveals a Nit tetramer binding two Fhit dimers. Curr Biol 2000, 10:907-917. 10.1016/S0960-9822(00)00621-7, 10959838.
22. Sakai N, Tajika Y, Yao M, Watanabe N, Tanaka I. Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6 A ° resolution. Proteins 2004, 57:869-873. 10.1002/prot.20259, 15390259.
23. Kumaran D, Eswaramoorthy S, Gerchman SE, Kycia H, Studier FW, Swaminathan S. Crystal structure of a putative CN hydrolase from yeast. Proteins 2003, 52:283-291. 10.1002/prot.10417, 12833551.
24. Lundgren S, Lohkamp B, Andersen B, Piškur J, Dobritzsch D. The crystal structure of β-alanine synthase from Drosophila melanogaster reveals a homooctameric helical turn-like assembly. J Mol Biol 2008, 377:1544-1559. 10.1016/j.jmb.2008.02.011, 18336837.
25. Barglow KT, Saikatendu KS, Bracey MH, Huey R, Morris GM, Olson AJ, Stevens RC, Cravatt BF. Functional proteomic and structural insights into molecular recognition in the nitrilase family enzymes. Biochemistry 2008, 47:13514-13523. 10.1021/bi801786y, 2665915, 19053248.
26. Kozielski F, Schönbrunn E, Sack S, Müller J, Brady ST, Mandelkow E. Crystallization and preliminary x-ray analysis of the single-headed and double-headed motor protein kinesin. J Struct Biol 1997, 119:28-34. 10.1006/jsbi.1997.3872, 9216086.
27. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK - a program to check the stereochemical quality of protein structures. J Appl Cryst 1993, 26:283-291.
28. Kobayashi M, Yanaka N, Nagasawa T, Yamada H. Primary structure of an aliphatic nitrile-degrading enzyme, aliphatic nitrilase, from Rhodococcus rhodochrous K22 and expression of its gene and identification of the active site residue. Biochemistry 1992, 31:9000-9007. 10.1021/bi00152a042, 1390687.
29. Harper DB. Fungal degradation of aromatic nitriles. Enzymology of C-N cleavage by Fusarium solani. Biochem J 1977, 167:685-692. 1183715, 23761.
30. Goldlust A, Bohak Z. Induction, purification, and characterization of the nitrilase of Fusarium oxysporum f. sp. melonis. Biotechnol Appl Biochem 1989, 11:581-601.
31. Vejvoda V, Kubáč D, Davidová A, Kaplan O, Šulc M, Šveda O, Chaloupková R, Martínková L. Purification and characterization of nitrilase from Fusarium solani IMI196840. Proc Biochem 2010, 45:1115-1120.
32. O'Reilly C, Turner PD. The nitrilase family of CN hydrolysing enzymes - a comparative study. J Appl Microbiol 2003, 95:1161-1174.
33. Almatawah QA, Cramp R, Cowan DA. Characterization of an inducible nitrilase from a thermophilic bacillus. Extremophiles 1999, 3:283-291. 10.1007/s007920050129, 10591020.
34. Singh LR, Dar TA, Rahman S, Jamal S, Ahmad F. Glycine betaine may have opposite effect on protein stability at high and low pH values. Biochim Biophys Acta 2009, 1794:929-935.
35. Santoro MM, Liu YF, Khan SMA, Hou L-X, Bolen DW. Increased thermal stability of proteins in the presence of naturally occurring osmolytes. Biochemistry 1992, 31:5278-5283. 10.1021/bi00138a006, 1376620.
36. Sewell BT, Thuku RN, Zhang X, Benedik MJ. Oligomeric structure of nitrilases. Effect of mutating interfacial residues on activity. Ann N Y Acad Sci 2005, 1056:153-159. 10.1196/annals.1352.025, 16387684.
37. Woodward JD, Weber BW, Scheffer MP, Benedik MJ, Hoenger A, Sewell BT. Helical structure of unidirectionally shadowed metal replicas of cyanide hydratase from Gloeocercospora sorghi. J Struct Biol 2008, 161:111-119. 10.1016/j.jsb.2007.09.019, 17997328.
38. Jandhyala D, Berman M, Meyers PR, Sewell BT, Willson RC, Benedik MJ. Cyn D, the cyanide dihydratase from Bacillus pumilus: gene cloning and structural studies. Appl Environ Microbiol 2003, 69:4794-4805. 10.1128/AEM.69.8.4794-4805.2003, 169136, 12902273.
39. Kiziak C, Klein J, Stolz A. Influence of different carboxy-terminal mutations on the substrate-, reaction- and enantiospecificity of the arylacetonitrilase from Pseudomonas fluorescens EBC191. Protein Eng Des Sel 2007, 20:385-396. 10.1093/protein/gzm032, 17693456.
40. Layh N, Parratt J, Willetts A. Characterization and partial purification of an enantioselective arylacetonitrilase from Pseudomonas fluorescens DSM 7155. J Mol Catal B-Enz 1998, 5:467-474.
41. Sareen D, Sharma R, Vohra RM. Chaperone-assisted overexpression of an active D-carbamoylase from Agrobacterium tumefaciens AM 10. Protein Expres Purif 2001, 23:374-379.
42. Kobayashi M, Nagasawa T, Yamada H. Nitrilase of Rhodococcus rhodochrous J1 -Purification and characterization. Eur J Biochem 1989, 182:349-356. 10.1111/j.1432-1033.1989.tb14837.x, 2737207.
43. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
44. NCBI/BLAST. , http://blast.ncbi.nlm.nih.gov/Blast.cgi
45. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
46. Laemmli UK. Cleavage of the structural proteins during assembly of the head of bacteriophage T4. Nature 1970, 227:680-685. 10.1038/227680a0, 5432063.
47. Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976, 72:248-54. 10.1016/0003-2697(76)90527-3, 942051.
48. John Philo's Software Home Page. , http://www.jphilo.mailway.com
49. Schuck P. Size distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modelling. Biophys J 2000, 78:1606-1619. 10.1016/S0006-3495(00)76713-0, 1300758, 10692345.
50. SEDFIT. , http://www.analyticalultracentrifugation.com
51. Schuck P. On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation. Anal Biochem 2003, 320:104-124. 10.1016/S0003-2697(03)00289-6, 12895474.
52. Benada O, Pokorný V. Modification of the polaron sputter-coater unit for glow-discharge activation of carbon support films. J Electron Microsc Tech 1990, 16:235-239. 10.1002/jemt.1060160304, 2243279.
53. Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignments. J Mol Biol 2000, 302:205-217. 10.1006/jmbi.2000.4042, 10964570.
54. Consensus secondary structure prediction. , http://www.bioinf.manchester.ac.uk/dbbrowser/bioactivity/NPS2.html
55. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993, 234:779-815. 10.1006/jmbi.1993.1626, 8254673.
56. Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 2007, 35:W407-W410. 10.1093/nar/gkm290, 1933241, 17517781.
57. Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G. Making optimal use of empirical energy functions: force-field parameterization in crystal space. Proteins 2004, 57:678-683. 10.1002/prot.20251, 15390263.
58. Morris GM, Goodsell DS, Huey R, Olson AJ. Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4. J Comput-Aided Mol Des 1996, 10:293-304. 10.1007/BF00124499, 8877701.