Improving catalytic efficiency of endo-β-1, 4-xylanase from Geobacillus stearothermophilus by directed evolution and H179 saturation mutagenesis

Journal of Biotechnology

Volumn 168, Issue 4, 2013, Pages 341-347

  Wang, Yan ^a   Feng, Shiyu ^a   Zhan, Tao ^a   Huang, Zongqing ^a   Wu, Guojie ^a   Liu, Ziduo ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

Catalytic efficiency; Directed evolution; Error prone PCR; Site saturation mutagenesis; Xylanase

Indexed keywords

CATALYTIC EFFICIENCIES; DIRECTED EVOLUTION; ERROR PRONE PCR; GEOBACILLUS STEAROTHERMOPHILUS; SATURATION MUTAGENESIS; SCREENING SYSTEM; WILD-TYPE ENZYMES; XYLANASES;

AMINO ACIDS; CLONING; ENZYME ACTIVITY; MUTAGENESIS;

EFFICIENCY;

AMINO ACID DERIVATIVE; ARGININE; METHIONINE; PROLINE; TRYPTOPHAN; XYLAN ENDO 1,3 BETA XYLOSIDASE;

ARTICLE; BIOCATALYST; DIRECTED MOLECULAR EVOLUTION; ENZYME ACTIVITY; GEOBACILLUS STEAROTHERMOPHILUS; MOLECULAR CLONING; NONHUMAN; POINT MUTATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PRODUCTIVITY; SITE DIRECTED MUTAGENESIS; WILD TYPE;

GEOBACILLUS STEAROTHERMOPHILUS;

CATALYTIC EFFICIENCY; DIRECTED EVOLUTION; ERROR-PRONE PCR; SITE-SATURATION MUTAGENESIS; XYLANASE;

AMINO ACID SUBSTITUTION; CATALYSIS; CATALYTIC DOMAIN; DIRECTED MOLECULAR EVOLUTION; ENDO-1,4-BETA XYLANASES; GEOBACILLUS STEAROTHERMOPHILUS; HISTIDINE; KINETICS; MUTAGENESIS; OLIGOPEPTIDES;

EID: 84888843511     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2013.09.014     Document Type: Article

References (36)

1. Baba T., Shinke R., Nanmori T. Identification and characterization of clustered genes for thermostable xylan-degrading enzymes, beta-xylosidase and xylanase, of bacillus stearothermophilus 21. Appl. Environ. Microbiol. 1994, 60(7):2252-2258. Available from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8074507.
2. Bailey M.J., Biely P., Poutanen K. Interlaboratory testing of methods for assay of xylanase activity. J. Biotechnol. 1992, 23(3):257-270.
3. Beg Q.K., Kapoor M., Mahajan L., Hoondal G.S. Microbial xylanases and their industrial applications: a review. Appl. Microbiol. Biotechnol. 2001, 56(3-4):326-338. Available from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11548999.
4. Bhardwaj A., Leelavathi S., Mazumdar-Leighton S., Ghosh A., Ramakumar S., Reddy V.S. The critical role of n- and c-terminal contact in protein stability and folding of a family 10 xylanase under extreme conditions. PLoS One 2010, 5(6):e11347. Available from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20596542, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2893209/pdf/pone.0011347.pdf.
5. Bordoli L., Kiefer F., Arnold K., Benkert P., Battey J., Schwede T. Protein structure homology modeling using swiss-model workspace. Nat. Protoc. 2008, 4(1):1-13.
6. Chávez R., Bull P., Eyzaguirre J. The xylanolytic enzyme system from the genus penicillium. J. Biotechnol. 2006, 123(4):413-433.
7. Chen Y.L., Tang T.Y., Cheng K.J. Directed evolution to produce an alkalophilic variant from a neocallimastix patriciarum xylanase. Can. J. Microbiol. 2001, 47(12):1088-1094.
8. Collins T., Gerday C., Feller G. Xylanases, xylanase families and extremophilic xylanases. FEMS. Microbiol. Rev. 2005, 29(1):3-23.
9. Funahashi J., Takano K., Yamagata Y., Yutani K. Role of surface hydrophobic residues in the conformational stability of human lysozyme at three different positions. Biochemistry 2000, 39(47):14448-14456.
10. Gallardo O., Pastor F.I., Polaina J., Diaz P., Lysek R., Vogel P., Isorna P., Gonzalez B., Sanz-Aparicio J. Structural insights into the specificity of xyn10b from paenibacillus barcinonensis and its improved stability by forced protein evolution. J. Biol. Chem. 2010, 285(4):2721-2733. Available from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19940147.
11. Henrissat B. A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 1991, 280(Pt 2):309.
12. Jain A.N. Surflex-dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J. Comput.-Aided Mol. Des. 2007, 21(5):281-306.
13. Johannes T.W., Zhao H. Directed evolution of enzymes and biosynthetic pathways. Curr. Opin. Microbiol. 2006, 9(3):261-267.
14. Kulkarni N., Shendye A., Rao M. Molecular and biotechnological aspects of xylanases. FEMS Microbiol. Rev. 2006, 23(4):411-456.
15. Leisola M., Turunen O. Protein engineering: opportunities and challenges. Appl. Microbiol. Biotechnol. 2007, 75(6):1225-1232.
16. Lin L., Meng X., Liu P., Hong Y., Wu G., Huang X., Li C., Dong J., Xiao L., Liu Z. Improved catalytic efficiency of endo-β-1, 4-glucanase from bacillus subtilis bme-15 by directed evolution. Appl. Microbiol. Biotechnol. 2009, 82(4):671-679.
17. Liu H., Naismith J.H. An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol. BMC Biotechnol. 2008, 8(1):91.
18. Mamo G., Thunnissen M., Hatti-Kaul R., Mattiasson B. An alkaline active xylanase: insights into mechanisms of high ph catalytic adaptation. Biochimie 2009, 91(9):1187-1196.
19. Manikandan K., Bhardwaj A., Gupta N., Lokanath N.K., Ghosh A., Reddy V.S., Ramakumar S. Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic bacillus sp Ng-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions. Protein Sci. 2009, 15(8):1951-1960.
20. Miller G.L. Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal. Chem. 1959, 31(3):426-428.
21. Miyazaki K., Takenouchi M., Kondo H., Noro N., Suzuki M., Tsuda S. Thermal stabilization of bacillus subtilis family-11 xylanase by directed evolution. J. Biol. Chem. 2006, 281(15):10236-10242.
22. Palackal N., Brennan Y., Callen W.N., Dupree P., Frey G., Goubet F., Hazlewood G.P., Healey S., Kang Y.E., Kretz K.A. An evolutionary route to xylanase process fitness. Protein. Sci. 2009, 13(2):494-503.
23. Perl D., Mueller U., Heinemann U., Schmid F.X. Two exposed amino acid residues confer thermostability on a cold shock protein. Nat. Struct. Mol. Biol. 2000, 7(5):380-383.
24. Polizeli M.L., Rizzatti A.C., Monti R., Terenzi H.F., Jorge J.A., Amorim D.S. Xylanases from fungi: properties and industrial applications. Appl. Microbiol. Biotechnol. 2005, 67(5):577-591. Available from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15944805.
25. Solomon V., Teplitsky A., Shulami S., Zolotnitsky G., Shoham Y., Shoham G. Structure-specificity relationships of an intracellular xylanase from geobacillus stearothermophilus. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2007, 63(Pt 8):845-859. Available from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17642511.
26. Stemmer W.P. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. PNAS 1994, 91(22):10747-10751.
27. Stephens D.E., Singh S., Permaul K. Error-prone pcr of a fungal xylanase for improvement of its alkaline and thermal stability. FEMS Microbiol. Lett. 2009, 293(1):42-47.
28. Tarahovsky Y., Ivanitsky G., Khusainov A. Lysis of escherichia coli cells induced by bacteriophage t4. FEMS Microbiol. Lett. 1994, 122(1):195-199.
29. Teplitsky A., Mechaly A., Stojanoff V., Sainz G., Golan G., Feinberg H., Gilboa R., Reiland V., Zolotnitsky G., Shallom D. Structure determination of the extracellular xylanase from geobacillus stearothermophilus by selenomethionyl mad phasing. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60(5):836-848.
30. Teplitsky A., Shulami S., Moryles S., Shoham Y., Shoham G. Crystallization and preliminary x-ray analysis of an intracellular xylanase from bacillus stearothermophilus t-6. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2000, 56(2):181-184.
31. Turunen O., Vuorio M., Fenel F., Leisola M. Engineering of multiple arginines into the ser/thr surface of trichoderma reesei endo-1, 4-β-xylanase ii increases the thermotolerance and shifts the ph optimum towards alkaline ph. Protein Eng. 2002, 15(2):141-145.
32. Vieira D.S., Degrève L. An insight into the thermostability of a pair of xylanases: the role of hydrogen bonds. Mol. Phys. 2009, 107(1):59-69.
33. Wilson K. Preparation of genomic DNA from bacteria. Curr. Protoc. Mol. Biol. 1987, 241-245.
34. Wong T.S., Tee K.L., Hauer B., Schwaneberg U. Sequence saturation mutagenesis (sesam): a novel method for directed evolution. Nucleic Acids Res. 2004, 32(3). e26-e26.
35. Wu S., Liu B., Zhang X. Characterization of a recombinant thermostable xylanase from deep-sea thermophilic geobacillus sp Mt-1 in east pacific. Appl. Microbiol. Biotechnol. 2006, 72(6):1210-1216.
36. Zhang Z.G., Yi Z.L., Pei X.Q., Wu Z.L. Improving the thermostability of geobacillus stearothermophilus xylanase xt6 by directed evolution and site-directed mutagenesis. Bioresour. Technol. 2010, 101(23):9272-9278. Available from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20691586.