Directed evolution of a beta-galactosidase from Pyrococcus woesei resulting in increased thermostable beta-glucuronidase activity

Applied Microbiology and Biotechnology

Volumn 77, Issue 3, 2007, Pages 569-578

  Xiong, Ai Sheng ^a   Peng, Ri He ^a   Zhuang, Jing ^a   Li, Xian ^a   Xue, Yong ^a   Liu, Jin Ge ^a   Gao, Feng ^a   Cai, Bin ^a   Chen, Jian Min ^b   Yao, Quan Hong ^a  

^a INSTITUTE OF EDIBLE FUNGI   (China)

^b YANGZHOU UNIVERSITY   (China)

Author keywords

Beta galactosidase; Beta glucuronidase; Directed evolution; Enzyme properties; Pyrococcus woesei; Structure function analysis

Indexed keywords

AMINO ACIDS; BACTERIA; ENZYMES; GENES; MUTAGENESIS; SYNTHESIS (CHEMICAL); VECTORS;

BETA-GALACTOSIDASE; PYROCOCCUS WOESEI; STRUCTURE-FUNCTION ANALYSIS; THERMOSTABLE BETA-GLUCURONIDASE ACTIVITY;

BIOTECHNOLOGY;

AMINO ACID; BETA GALACTOSIDASE; BETA GLUCURONIDASE;

AMINO ACID; ENZYME ACTIVITY; EVOLUTION; MUTATION; THERMOPHILIC BACTERIUM;

ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME SYNTHESIS; MOLECULAR EVOLUTION; MUTANT; NONHUMAN; NUCLEOTIDE SEQUENCE; PYROCOCCUS; PYROCOCCUS WOESEI; THERMOSTABILITY; WILD TYPE;

AMINO ACID SUBSTITUTION; BACTERIAL PROTEINS; BETA-GALACTOSIDASE; DIRECTED MOLECULAR EVOLUTION; ENZYME STABILITY; GENE EXPRESSION REGULATION, BACTERIAL; GLUCURONIDASE; MUTAGENESIS, SITE-DIRECTED; MUTATION; PROTEIN ENGINEERING; PYROCOCCUS;

PYROCOCCUS WOESEI;

EID: 36248969576     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-007-1182-7     Document Type: Article

References (54)

1. Alexeeva M, Carr R, Turner NJ (2003) Directed evolution of enzymes: new biocatalysts for asymmetric synthesis. Org Biomol Chem 1:4133-4137
2. Castle LA, Siehl DL, Gorton R, Patten PA, Chen YH, Bertain S, Cho HJ, Duck N, Wong J, Liu D, Lassner MW (2004) Discovery and directed evolution of a glyphosate tolerance gene. Science 304:1151-1154
3. Coker JA, Sheridan PP, Loveland-Curtze J, Gutshall KR, Auman AJ, Brenchley JE (2003) Biochemical characterization of a beta-galactosidase with a low temperature optimum obtained from an Antarctic Arthrobacter isolate. J Bacteriol 185:5473-5482
4. Coombs JM, Brenchley JE (1999) Biochemical and phylogenetic analyses of a cold-active beta-galactosidase from the lactic acid bacterium Carnobacterium piscicola BA. Appl Environ Microbiol 65:5443-5450
5. Crameri A, Whitehorn EA, Tate E, Stemmer WP (1996) Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat Biotechnol 14:315-319
6. Dabrowski S, Maciunska J, Synowiecki J (1998) Cloning and nucleotide sequence of the thermostable β-galactosidase gene from Pyrococcus woesei in Escherichia coli and some properties of the isolated enzyme. Mol Biotechnol 10:217-222
7. Dabrowski S, Sobiewska G, Maciunska J, Synowiecki J, Kur J (2000) Cloning, expression, and purification of the His(6)-tagged thermostable beta-galactosidase from Pyrococcus woesei in Escherichia coli and some properties of the isolated enzyme. Protein Expr Purif 19:107-112
8. Demir V, Dincturk HB (2006) Semi-anaerobic growth conditions are favoured by some Escherichia coli strains during heterologous expression of some archaeal proteins. Mol Biol Rep 33:59-63
9. Flores H, Ellington AD (2002) Increasing the thermal stability of an oligomeric protein, beta-glucuronidase. J Mol Biol 315:325-337
10. Fradkov AF, Chen Y, Ding L, Barsova EV, Matz MV, Lukyanov SA (2000) Novel fluorescent protein from Discosoma coral and its mutants possesses a unique far-red fluorescence. FEBS Lett 479:127-130
11. Geddie ML, Matsumura I (2004) Rapid evolution of beta-glucuronidase specificity by saturation mutagenesis of an active site loop. J Biol Chem 279:26462-26468
12. Gilissen LJ, Metz PL, Stiekema WJ, Nap JP (1998) Biosafety of E. coli beta-glucuronidase (GUS) in plants. Transgenic Res 7:157-163
13. Helmer G, Casadaban M, Bevan M, Kayes L, Chilton ML (1984) A new chimeric gene as a marker for plant transformation: the expression of Escherichia coli β-galactosidase in sunflower and tobacco cells. Biotechnology 2:520-527
14. Hibbert EG, Baganz F, Hailes HC, Ward JM, Lye GJ, Woodley JM, Dalby PA (2005) Directed evolution of biocatalytic processes. Biomol Eng 22:11-19
15. Holmes ML, Scopes RK, Moritz RL, Simpson RJ, Englert C, Pfeifer F, Dyall-Smith ML (1997) Purification and analysis of an extremely halophilic β-galactosidase from Haloferax alicantei. Biochim Biophys Acta 1337:276-286
16. Hu C, Chee PP, Chee KPP, Chesney RH, Zhou JH, Miller PD, O'brien WT (1990) Intrinsic GUS-like activities in seed plants. Plant Cell Rep 9:1-5
17. Jacobson RH, Zhang XJ, DuBose RF, Matthews BW (1994) Three-dimensional structure of beta-galactosidase from E. coli. Nature 369:761-766
18. Jefferson RA, Kavanaugh TA, Bevan MW (1987) GUS fusions: β-glucuronidase as a sensitive and versatile gene fusion marker for higher plants. EMBO J 6:3901-3907
19. Kosugi S, Ohashi Y, Nakajima K, Arai Y (1990) An improved assay for β-glucuronidase in transformed cells: methanol almost completely suppresses a putative endogenous β-glucuronidase activity. Plant Sci 70:133-140
20. Lassner M, Bedbrook J (2001) Directed molecular evolution in plant improvement. Curr Opin Plant Biol 4:152-156
21. Locher CP, Soong NW, Whalen RG, Punnonen J (2004) Development of novel vaccines using DNA shuffling and screening strategies. Curr Opin Mol Ther 6:34-39
22. Locher CP, Paidhungat M, Whalen RG, Punnonen J (2005) DNA shuffling and screening strategies for improving vaccine efficacy. DNA Cell Biol 24:256-263
23. Matsumura I, Wallingford JB, Surana NK, Vize PD, Ellington AD (1999) Directed evolution of the surface chemistry of the reporter enzyme beta-glucuronidase. Nat Biotechnol 17:696-701
24. Matthews BW (2005) The structure of E. coli beta-galactosidase. C R Biol 328:549-556
25. Miki B, McHugh S (2004) Selectable marker genes in transgenic plants: applications, alternatives and biosafety. J Biotechnol 107:193-232
26. Morley KL, Kazlauskas RJ (2005) Improving enzyme properties: when are closer mutations better. Trends Biotechnol 23:231-237
27. Murray EE, Lotzer J, Eberle M (1989) Codon usage in plant genes. Nucleic Acids Res 17:477-498
28. Nam SH, Oh KH, Kim GJ, Kim HS (2003) Functional tuning of a salvaged green fluorescent protein variant with a new sequence space by directed evolution. Protein Eng 16:1099-1105
29. Ow DW, Wood KV, DeLuca M, Wet JRD, Helinski DR, Howell SH (1986) Transient and stable expression of the firefly luciferase gene in plant cells and transgenic plants. Science 234:856-859
30. Panesar PS, Panesar R, Singh RS, Kennedy JF, Kumar H (2006) Microbial production, immobilization and applications of β-d-galactosidase. J Chem Technol Biotechnol 81:530-543
31. Parikh MR, Matsumura I (2005) Site-saturation mutagenesis is more efficient than DNA shuffling for the directed evolution of beta-fucosidase from beta-galactosidase. J Mol Biol 352:621-628
32. Rogers HJ, Maund SL, Johnson LH (2001) A beta-galactosidase-like gene is expressed during tobacco pollen development. J Exp Bot 52:67-75
33. Rowe LA, Geddie ML, Alexander OB, Matsumura I (2003) A comparison of directed evolution approaches using the beta-glucuronidase model system. J Mol Biol 332:851-860
34. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory mannual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
35. Sharp PM, Tuohy TMF, Mosurski KR (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expression genes. Nucleic Acids Res 14:5125-5143
36. Sheridan PP, Brenchley JE (2000) Characterization of a salt-tolerant family 42 beta-galactosidase from a psychrophilic Antarctic Planococcus isolate. Appl Environ Microbiol 66:2438-2444
37. Shipkowski S, Brenchley JE (2005) Characterization of an unusual cold-active beta-glucosidase belonging to family 3 of the glycoside hydrolases from the psychrophilic isolate Paenibacillus sp. strain C7. Appl Environ Microbiol 71:4225-4232
38. Simmonds J, Cass L, Routly E, Hubbard K, Donaldson P, Bancroft B, Davidson A, Hubbard S, Simmonds D (2004) Oxalate oxidase: a novel reporter gene for monocot and dicot transformations. Mol Breeding 13:79-91
39. Smith DL, Gross KC (2000) A family of at least seven beta-galactosidase genes is expressed during tomato fruit development. Plant Physiol 123:1173-1183
40. Smith PK, Krohn RI, Hermanson GT, Mallia AK, Gartner FH, Provenzano MD, Fujimoto EK, Goeke NM, Olson BJ, Klenk DC (1985) Measurement of protein using bicinchoninic acid. Anal Biochem 150:76-85
41. Smith HO, Hutchison 3rd CA, Pfannkoch C, Venter JC (2003) Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci U S A 100:15440-15445
42. Stefan A, Radeghieri A, Gonzalez A, Hochkoeppler A (2001) Directed evolution of beta-galactosidase from Escherichia coli by mutator strains defective in the 3′->5′ exonuclease activity of DNA polymerase III. FEBS Lett 493:139-143
43. Stewart CN (2001) The utility of green fluorescent protein in transgenic plants. Plant Cell Rep 20:376-382
44. Trimbur DE, Gutshall KR, Prema P, Brenchley JE (1994) Characterization of a psychrotrophic Arthrobacter gene and its cold-active beta-galactosidase. Appl Environ Microbiol 60:4544-4552
45. Xiong AS, Yao QH, Peng RH, Li X, Fan HQ, Guo MJ, Zhang SL (2004a) Isolation, characterization, molecular cloning of the cDNA encoding a novel phytase from Aspergillus niger 113 and high expression in Pichia pastoris. J Biochem Mol Biol 37:282-291
46. Xiong AS, Yao QH, Peng RH, Li X, Fan HQ, Cheng ZM, Li Y (2004b) A simple, rapid, high-fidelity and cost-effective PCR-based two-step DNA synthesis method for long gene sequences. Nucleic Acids Res 32:e98
47. Xiong AS, Yao QH, Peng RH, Han PL, Cheng ZM, Li Y (2005) High level expression of a recombinant acid phytase gene in Pichia pastoris. J Appl Microbiol 98:418-428
48. Xiong AS, Yao QH, Peng RH, Zhang Z, Xu F, Liu JG, Han PL, Chen JM (2006a) High level expression of a synthetic gene encoding Peniophora lycii phytase in methylotrophic yeast Pichia pastoris. Appl Microbiol Biotechnol 72:1039-1047
49. Xiong AS, Yao QH, Peng RH, Duan H, Li X, Fan HQ, Cheng ZM, Li Y (2006b) PCR-based accurate synthesis of long DNA sequences. Nat Protoc 1:791-797
50. Xiong AS, Peng RH, Zhuang J, Liu JG, Xu F, Cai B, Guo ZK, Qiao YS, Chen JM, Zhang Z, Yao QH (2007a) Directed evolution of beta-galactosidase from Escherichia coli into beta-glucuronidase. J Biochem Mol Biol 40:419-425
51. Xiong AS, Peng RH, Liu JG, Zhuang J, Qiao YS, Xu F, Cai B, Zhang Z, Chen JM, Yao QH (2007b) High efficiency and throughput system in directed evolution in vitro of reporter gene. Appl Microbiol Biotechnol 74:160-168
52. Xiong AS, Peng RH, Cheng ZM, Li Y, Liu JG, Zhuang J, Feng G, Xu F, Qiao YS, Zhang Z, Chen JM, Yao QH (2007c) Concurrent mutations in six amino acids in β-glucuronidase improves its thermostability. Protein Eng Des Sel 20:319-325
53. Zhang JH, Dawes G, Stemmer WP (1997) Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening. Proc Natl Acad Sci U S A 94:4504-4509
54. Zillig W, Holz I, Klenk HP, Trent J, Wunderl S, Janekovic D, Imsel E, Haas B (1987) Pyrococcus woesei, sp. nov., an ultrathermophilic marine archaebacterium, representing a novel order. Thermococcales Syst Appl Microbiol 9:62-70