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Improving the catalytic performance of a GH11 xylanase by rational protein engineering

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Abstract

XynCDBFV from Neocallimastix patriciarum is among the most effective xylanases and holds great potentials in a wide variety of industrial applications. In the present study, several active site residues were modified referring to the instrumental information of the complex structure of XynCDBFV and xylooligosaccharides. Among the 12 single active site mutants, W125F and F163W show increased activity comparing to the wild-type protein. The double mutant W125F/F163W was then generated which displayed nearly 20 % increase in the enzyme activity. Although W125F/F163W showed 5 °C reduction in the optimal temperature, it still preserves similar thermostability and is more active than the wild-type enzyme at temperatures lower than 60 °C. These properties make the double mutant a suitable candidate for commercial applications that involve lower operating temperatures. Furthermore, we investigated the effect of N-glycosylation on the thermostability of XynCDBFV when expressed in the yeast strain Pichia pastoris for industrial use. Two potential glycosylation sites (Asn-37 and Asn-88) were examined, and their roles in enzyme performance were validated. We found that the N-glycosylations of XynCDBFV are related to both catalytic activity and heat stability, with Asn-37 motif playing a dominant role. Collectively, the enzymatic properties of XynCDBFV were improved by molecular engineering, and the influences of N-glycosylations on the enzyme have been clearly elucidated herein.

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References

  • Beckham GT, Dai Z, Matthews JF, Momany M, Payne CM, Adney WS, Baker SE, Himmel ME (2012) Harnessing glycosylation to improve cellulase activity. Curr Opin Biotechnol 23:338–345. doi:10.1016/j.copbio.2011.11.030

    Article  CAS  PubMed  Google Scholar 

  • Biely P, Vrsanska M, Tenkanen M, Kluepfel D (1997) Endo-β-1,4-xylanase families: differences in catalytic properties. J Biotechnol 57:151–166

    Article  CAS  PubMed  Google Scholar 

  • Bornscheuer UT, Pohl M (2001) Improved biocatalysts by directed evolution and rational protein design. Curr Opin Chem Biol 5:137–143

    Article  CAS  PubMed  Google Scholar 

  • Böttcher D, Bornscheuer UT (2010) Protein engineering of microbial enzymes. Curr Opin Microbiol 13:274–282. doi:10.1016/j.mib.2010.01.010

    Article  PubMed  Google Scholar 

  • Bretthauer RK, Castellino FJ (1999) Glycosylation of Pichia pastoris-derived proteins. Biotechnol Appl Biochem 30(Pt 3):193–200

    CAS  PubMed  Google Scholar 

  • Chen YL, Tang TY, Cheng KJ (2001) Directed evolution to produce an alkalophilic variant from a Neocallimastix patriciarum xylanase. Can J Microbiol 47:1088–1094

    Article  CAS  PubMed  Google Scholar 

  • Cheng YS, Ko TP, Huang JW, Wu TH, Lin CY, Luo W, Li Q, Ma Y, Huang CH, Wang AH, Liu JR, Guo RT (2012) Enhanced activity of Thermotoga maritima cellulase 12A by mutating a unique surface loop. Appl Microbiol Biotechnol 95:661–669. doi:10.1007/s00253-011-3791-4

    Article  CAS  PubMed  Google Scholar 

  • Cheng YS, Chen CC, Huang CH, Ko TP, Luo W, Huang JW, Liu JR, Guo RT (2014) Structural analysis of a glycoside hydrolase family 11 xylanase from Neocallimastix patriciarum: insights into the molecular basis of a thermophilic enzyme. J Biol Chem 289:11020–11028. doi:10.1074/jbc.M114.550905

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Collins T, Gerday C, Feller G (2005) Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiol Rev 29:3–23. doi:10.1016/j.femsre.2004.06.005

    Article  CAS  PubMed  Google Scholar 

  • De Lemos EF, Gouders T, Lamotte-Brasseur J, Rigali S, Frere JM (2005) Improving the alkalophilic performances of the Xyl1 xylanase from Streptomyces sp. S38: structural comparison and mutational analysis. Protein Sci 14:292–302. doi:10.1110/ps.04978705

    Article  Google Scholar 

  • Fonseca-Maldonado R, Vieira DS, Alponti JS, Bonneil E, Thibault P, Ward RJ (2013) Engineering the pattern of protein glycosylation modulates the thermostability of a GH11 xylanase. J Biol Chem 288:25522–25534. doi:10.1074/jbc.M113.485953

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao F, Jiang Y, Zhou GH, Han ZK (2007) The effects of xylanase supplementation on growth, digestion, circulating hormone and metabolite levels, immunity and gut microflora in cockerels fed on wheat-based diets. Br Poult Sci 48:480–488. doi:10.1080/00071660701477320

    Article  CAS  PubMed  Google Scholar 

  • Huang JW, Cheng YS, Ko TP, Lin CY, Lai HL, Chen CC, Ma Y, Zheng Y, Huang CH, Zou P, Liu JR, Guo RT (2012) Rational design to improve thermostability and specific activity of the truncated Fibrobacter succinogenes 1,3-1,4-β-D-glucanase. Appl Microbiol Biotechnol 94:111–121. doi:10.1007/s00253-011-3586-7

    Article  CAS  PubMed  Google Scholar 

  • Huang JW, Chen CC, Huang CH, Huang TY, Wu TH, Cheng YS, Ko TP, Lin CY, Liu JR, Guo RT (2014) Improving the specific activity of β-mannanase from Aspergillus niger BK01 by structure-based rational design. Biochim Biophys Acta 1844:663–669. doi:10.1016/j.bbapap.2014.01.011

    Article  CAS  PubMed  Google Scholar 

  • Joshi MD, Sidhu G, Pot I, Brayer GD, Withers SG, McIntosh LP (2000) Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase. J Mol Biol 299:255–279. doi:10.1006/jmbi.2000.3722

    Article  CAS  PubMed  Google Scholar 

  • König J, Grasser R, Pikor H, Vogel K (2002) Determination of xylanase, β-glucanase, and cellulase activity. Anal Bioanal Chem 374:80–87. doi:10.1007/s00216-002-1379-7

    Article  PubMed  Google Scholar 

  • Labrou NE (2010) Random mutagenesis methods for in vitro directed enzyme evolution. Curr Protein Pept Sci 11:91–100

    Article  CAS  PubMed  Google Scholar 

  • Lu D, Yang C, Liu Z (2012) How hydrophobicity and the glycosylation site of glycans affect protein folding and stability: a molecular dynamics simulation. J Phys Chem B 116:390–400. doi:10.1021/jp203926r

    Article  CAS  PubMed  Google Scholar 

  • Miller GL (1959) Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem 31:426–428

    Article  CAS  Google Scholar 

  • Otten LG, Hollmann F, Arends IW (2010) Enzyme engineering for enantioselectivity: from trial-and-error to rational design? Trends Biotechnol 28:46–54. doi:10.1016/j.tibtech.2009.10.001

    Article  CAS  PubMed  Google Scholar 

  • Paes G, O’Donohue MJ (2006) Engineering increased thermostability in the thermostable GH-11 xylanase from Thermobacillus xylanilyticus. J Biotechnol 125:338–350. doi:10.1016/j.jbiotec.2006.03.025

    Article  CAS  PubMed  Google Scholar 

  • Pokhrela S, Joo JC, Lee HS, Yoo YJ (2013) Activity enhancement of a Bacillus circulans xylanase by introducing ion-pair interactions into an α-helix. Process Biochem 48:1495–1501

    Article  Google Scholar 

  • Polizeli ML, Rizzatti AC, Monti R, Terenzi HF, Jorge JA, Amorim DS (2005) Xylanases from fungi: properties and industrial applications. Appl Microbiol Biotechnol 67:577–591. doi:10.1007/s00253-005-1904-7

    Article  CAS  PubMed  Google Scholar 

  • Ramalingam ADHaC (2010) Xylanases and its application in food industry: a review. J Exp Sci 1:1-11

  • Romero PA, Arnold FH (2009) Exploring protein fitness landscapes by directed evolution. Nat Rev Mol Cell Biol 10:866–876. doi:10.1038/nrm2805

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saha BC (2003) Hemicellulose bioconversion. J Ind Microbiol Biotechnol 30:279–291. doi:10.1007/s10295-003-0049-x

    Article  CAS  PubMed  Google Scholar 

  • Sapag A, Wouters J, Lambert C, de Ioannes P, Eyzaguirre J, Depiereux E (2002) The endoxylanases from family 11: computer analysis of protein sequences reveals important structural and phylogenetic relationships. J Biotechnol 95:109–131 doi:10.1016/S0168-1656(02)00002–0

  • Shental-Bechor D, Levy Y (2008) Effect of glycosylation on protein folding: a close look at thermodynamic stabilization. Proc Natl Acad Sci U S A 105:8256–8261. doi:10.1073/pnas.0801340105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song L, Siguier B, Dumon C, Bozonnet S, O’Donohue MJ (2012) Engineering better biomass-degrading ability into a GH11 xylanase using a directed evolution strategy. Biotechnol Biofuels 5:3. doi:10.1186/1754-6834-5-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sriprang R, Asano K, Gobsuk J, Tanapongpipat S, Champreda V, Eurwilaichitr L (2006) Improvement of thermostability of fungal xylanase by using site-directed mutagenesis. J Biotechnol 126:454–462. doi:10.1016/j.jbiotec.2006.04.031

    Article  CAS  PubMed  Google Scholar 

  • Stephens DE, Singh S, Permaul K (2009) Error-prone PCR of a fungal xylanase for improvement of its alkaline and thermal stability. FEMS Microbiol Lett 293:42–47. doi:10.1111/j.1574-6968.2009.01519.x

    Article  CAS  PubMed  Google Scholar 

  • Subramaniyan S, Prema P (2002) Biotechnology of microbial xylanases: enzymology, molecular biology, and application. Crit Rev Biotechnol 22:33–64. doi:10.1080/07388550290789450

    Article  CAS  PubMed  Google Scholar 

  • Umemoto H, Ihsanawati IM, Yatsunami R, Fukui T, Kumasaka T, Tanaka N, Nakamura S (2009) Improvement of alkaliphily of Bacillus alkaline xylanase by introducing amino acid substitutions both on catalytic cleft and protein surface. Biosci Biotechnol Biochem 73:965–967

    Article  CAS  PubMed  Google Scholar 

  • Viikari L, Kantelinen A, Sundquist J, Linko M (1994) Xylanases in bleaching: from an idea to the industry. FEMS Microbiol Rev 13:335–350

    Article  CAS  Google Scholar 

  • Wu TH, Chen CC, Cheng YS, Ko TP, Lin CY, Lai HL, Huang TY, Liu JR, Guo RT (2014) Improving specific activity and thermostability of Escherichia coli phytase by structure-based rational design. J Biotechnol 175:1–6. doi:10.1016/j.jbiotec.2014.01.034

    Article  CAS  PubMed  Google Scholar 

  • You C, Yuan H, Huang Q, Lu H (2010) Substrate molecule enhances the thermostability of a mutant of a family 11 xylanase from Neocallimastix patriciarum. Afr J Biotechnol 9:1288–1294

    CAS  Google Scholar 

  • Zou S, Xie L, Liu Y, Kaleem I, Zhang G, Li C (2012) N-linked glycosylation influences on the catalytic and biochemical properties of Penicillium purpurogenum β-D-glucuronidase. J Biotechnol 157:399–404. doi:10.1016/j.jbiotec.2011.12.017

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by grants from the National Basic Research Program of China (2011CB710800 and 2011CBA00805), the National High Technology Research and Development Program of China (2012AA022200), the National Natural Science Foundation of China (31200053 and 31300615), and the Chinese Academy of Sciences (KSZD-EW-Z-015–2).

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The authors declare that they have no competing interests.

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Correspondence to Rey-Ting Guo.

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Ya-Shan Cheng and Chun-Chi Chen contributed equally to this work.

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Cheng, YS., Chen, CC., Huang, JW. et al. Improving the catalytic performance of a GH11 xylanase by rational protein engineering. Appl Microbiol Biotechnol 99, 9503–9510 (2015). https://doi.org/10.1007/s00253-015-6712-0

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