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Improving the Thermostability of α-Glucosidase from Xanthomonas campestris through Proline Substitutions Guided by Semi-rational Design

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Abstract

The α-glycosidase from Xanthomonas campestris (XgtA) can specifically catalyze the transglycosylation reactions, thus can be applied for the enzymatic synthesis of α-glycosides. However, the low thermal stability of XgtA has been a bottleneck for its industrial application. In this research, a combined semi-rational design strategy was used based on analysis of the α-helices and β-turns of XgtA, FireProt prediction of thermostable mutants and molecular dynamic simulations for improving the thermostability. The key positions with a significant impact on the thermal stability of XgtA were identified and the effect of proline substitution was tested. Five single-point mutants V167P, A177P, A210P, A220P, T345P, and a combined mutant Mut5 were obtained with improved thermal stability. Mut5 displayed a 3.06-fold increase in time of half-life at 45°C without impairing its initial hydrolytic activity. Molecular dynamics simulations revealed that changes in the flexibility of amino acid residues, newly-forming hydrogen bonding networks and hydrophobic interactions were responsible for the improved thermostability. These results suggest that proline substitution of key flexible positions is an effective strategy for improving enzyme thermostability.

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References

  1. Kimura, A. (2000) Molecular anatomy of α-glucosidase. Trends Glycosci. Glycotechnol. 12: 373–380.

    Article  CAS  Google Scholar 

  2. Desmet, T. W. Soetaert, P. Bojarová, V. Křen, L. Dijkhuizen, V. Eastwick-Field, and A. Schiller (2012) Enzymatic glycosylation of small molecules: challenging substrates require tailored catalysts. Chemistry. 18: 10786–10801.

    Article  CAS  Google Scholar 

  3. Lévêque, E., Š. Janeček, B. Haye, and A. Belarbi (2000) Thermophilic archaeal amylolytic enzymes. Enzyme Microb. Technol. 26: 3–14.

    Article  Google Scholar 

  4. Hung, V. S., Y. Hatada, S. Goda, J. Lu, Y. Hidaka, Z. Li, M. Akita, Y. Ohta, K. Watanabe, H. Matsui, S. Ito, and K. Horikoshi (2005) alpha-Glucosidase from a strain of deep-sea Geobacillus: a potential enzyme for the biosynthesis of complex carbohydrates. Appl. Microbiol. Biotechnol. 68: 757–765.

    Article  CAS  Google Scholar 

  5. Kato, N., S. Suyama, M. Shirokane, M. Kato, T. Kobayashi, and N. Tsukagoshi (2002) Novel alpha-glucosidase from Aspergillus nidulans with strong transglycosylation activity. Appl. Environ. Microbiol. 68: 1250–1256.

    Article  CAS  PubMed Central  Google Scholar 

  6. Malá, S., H. Dvoráková, R. Hrabal, and B. Králová (1999) Towards regioselective synthesis of oligosaccharides by use of alpha-glucosidases with different substrate specificity. Carbohydr. Res. 322: 209–218.

    Article  Google Scholar 

  7. Bissaro, B., P. Monsan, R. Fauré, and M. J. O’Donohue (2015) Glycosynthesis in a waterworld: new insight into the molecular basis of transglycosylation in retaining glycoside hydrolases. Biochem. J. 467: 17–35.

    Article  CAS  Google Scholar 

  8. Chen, L., Y. Zhou, C. Lu, Z. Ma, H. Chen, L. Zhu, Y. Lu, and X. Chen (2021) Efficient production of l-menthyl α-glucopyranoside from l-menthol via whole-cell biotransformation using recombinant Escherichia coli. Biotechnol. Lett. 43: 1757–1764.

    Article  CAS  Google Scholar 

  9. Kurosu, J., T. Sato, K. Yoshida, T. Tsugane, S. Shimura, K. Kirimura, K. Kino, and S. Usami (2002) Enzymatic synthesis of alpha-arbutin by alpha-anomer-selective glucosylation of hydroquinone using lyophilized cells of Xanthomonas campestris WU-9701. J. Biosci. Bioeng. 93: 328–330.

    Article  CAS  Google Scholar 

  10. Sato, T., H. Takeuchi, K. Takahashi, J. Kurosu, K. Yoshida, T. Tsugane, S. Shimura, K. King, and K. Kirimura (2003) Selective alpha-glucosylation of eugenol by alpha-glucosyl transfer enzyme of Xanthomonas campestris WU-9701. J. Biosci. Bioeng. 96: 199–202.

    Article  CAS  Google Scholar 

  11. Sato, T., H. Nakagawa, J. Kurosu, K. Yoshida, T. Tsugane, S. Shimura, K. Kirimura, K. Kino, and S. Usami (2000) Alpha-anomer-selective glucosylation of (+)-catechin by the crude enzyme, showing glucosyl transfer activity, of Xanthomonas campestris WU-9701. J. Biosci. Bioeng. 90: 625–630.

    Article  CAS  Google Scholar 

  12. Watanabe, R., Y. Arimura, Y. Ishii, and K. Kirimura (2020) Crystal structure of α-glucosyl transfer enzyme XgtA from Xanthomonas campestris WU-9701. Biochem. Biophys. Res. Commun. 526: 580–585.

    Article  CAS  Google Scholar 

  13. Sato, T., N. Hasegawa, J. Saito, S. Umezawa, Y. Honda, K. Kino, and K. Kirimura (2012) Purification, characterization, and gene identification of an α-glucosyl transfer enzyme, a novel type α-glucosidase from Xanthomonas campestris WU-9701. J. Mol. Catal. B Enzym. 80: 20–27.

    Article  CAS  Google Scholar 

  14. Bommarius, A. S. and M. F. Paye (2013) Stabilizing biocatalysts. Chem. Soc. Rev. 42: 6534–6565.

    Article  CAS  Google Scholar 

  15. Xu, Z., Y. K. Cen, S. P. Zou, Y. P. Xue, and Y. G. Zheng (2020) Recent advances in the improvement of enzyme thermostability by structure modification. Crit. Rev. Biotechnol. 40: 83–98.

    Article  CAS  Google Scholar 

  16. Chen, H., S. Yang, A. Xu, R. Jiang, Z. Tang, J. Wu, L. Zhu, S. Liu, X. Chen, and Y. Lu (2019) Insight into the glycosylation and hydrolysis kinetics of alpha-glucosidase in the synthesis of glycosides. Appl. Microbiol. Biotechnol. 103: 9423–9432.

    Article  CAS  Google Scholar 

  17. Talakad, J. C., P. R. Wilderman, D. R. Davydov, S. Kumar, and J. R. Halpert (2010) Rational engineering of cytochromes P450 2B6 and 2B11 for enhanced stability: insights into structural importance of residue 334. Arch. Biochem. Biophys. 494: 151–158.

    Article  CAS  Google Scholar 

  18. Reetz, M. T., J. D. Carballeira, and A. Vogel (2006) Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angew. Chem. Int. Ed. Engl. 45: 7745–7751.

    Article  CAS  Google Scholar 

  19. Chen, Q., Y. Xiao, W. Zhang, and W. Mu (2020) Current methods and applications in computational protein design for food industry. Crit. Rev. Food Sci. Nutr. 60: 3259–3270.

    Article  CAS  Google Scholar 

  20. Schymkowitz, J., J. Borg, F. Stricher, R. Nys, F. Rousseau, and L. Serrano (2005) The FoldX web server: an online force field. Nucleic Acids Res. 33: W382–W388.

    Article  CAS  PubMed Central  Google Scholar 

  21. Reetz, M. T. and J. D. Carballeira (2007) Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat. Protoc. 2: 891–903.

    Article  CAS  Google Scholar 

  22. Zeiske, T., K. A. Stafford, and A. G. Palmer3rd (2016) Thermostability of enzymes from molecular dynamics simulations. J. Chem. Theory Comput. 12: 2489–2492.

    Article  CAS  PubMed Central  Google Scholar 

  23. Sun, Z., Q. Liu, G. Qu, Y. Feng, and M. T. Reetz (2019) Utility of B-factors in protein science: interpreting rigidity, flexibility, and internal motion and engineering thermostability. Chem. Rev. 119: 1626–1665.

    Article  CAS  Google Scholar 

  24. Ge, L., D. Li, T. Wu, L. Zhao, G. Ding, Z. Wang, and W. Xiao (2018) B-factor-saturation mutagenesis as a strategy to increase the thermostability of α-L-rhamnosidase from Aspergillus terreus. J. Biotechnol. 275: 17–23.

    Article  CAS  Google Scholar 

  25. Parthasarathy, S. and M. R. N. Murthy (2000) Protein thermal stability: insights from atomic displacement parameters (B values). Protein Eng. 13: 9–13.

    Article  CAS  Google Scholar 

  26. Krüger, D. M., P. C. Rathi, C. Pfleger, and H. Gohlke (2013) CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function. Nucleic Acids Res. 41: W340–W348.

    Article  PubMed Central  Google Scholar 

  27. Pfleger, C., P. C. Rathi, D. L. Klein, S. Radestock, and H. Gohlke (2013) Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function. J. Chem. Inf. Model. 53: 1007–1015.

    Article  CAS  Google Scholar 

  28. Matthews, B. W., H. Nicholson, and W. J. Becktel (1987) Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc. Natl. Acad. Sci. U. S. A. 84: 6663–6667.

    Article  CAS  PubMed Central  Google Scholar 

  29. Hardy, F., G. Vriend, O. R. Veltman, B. van der Vinne, G. Venema, and V. G. H. Eijsink (1993) Stabilization of Bacillus stearothermophilus neutral protease by introduction of prolines. FEBS Lett. 317: 89–92.

    Article  CAS  Google Scholar 

  30. Zhu, G. P., C. Xu, M. K. Teng, L. M. Tao, X. Y. Zhu, C. J. Wu, J. Hang, L. W. Niu, and Y. Z. Wang (1999) Increasing the thermostability of D-xylose isomerase by introduction of a proline into the turn of a random coil. Protein Eng. 12: 635–638.

    Article  CAS  Google Scholar 

  31. Watanabe, K., T. Masuda, H. Ohashi, H. Mihara, and Y. Suzuki (1994) Multiple proline substitutions cumulatively thermostabilize Bacillus cereus ATCC7064 oligo-1,6-glucosidase. Irrefragable proof supporting the proline rule. Eur. J. Biochem. 226: 277–283.

    Article  CAS  Google Scholar 

  32. Fuchs, P. F. J. and A. J. P. Alix (2005) High accuracy prediction of beta-turns and their types using propensities and multiple alignments. Proteins. 59: 828–839.

    Article  CAS  Google Scholar 

  33. Anbarasan, S., J. Jänis, M. Paloheimo, M. Laitaoja, M. Vuolanto, J. Karimäki, P. Vainiotalo, M. Leisola, and O. Turunen (2010) Effect of glycosylation and additional domains on the thermostability of a family 10 xylanase produced by Thermopolyspora flexuosa. Appl. Environ. Microbiol. 76: 356–360.

    Article  CAS  Google Scholar 

  34. Goihberg, E., O. Dym, S. Tel-Or, I. Levin, M. Peretz, and Y. Burstein (2007) A single proline substitution is critical for the thermostabilization of Clostridium beijerinckii alcohol dehydrogenase. Proteins. 66: 196–204.

    Article  CAS  Google Scholar 

  35. Dotsenko, A. S., S. Pramanik, A. V. Gusakov, A. M. Rozhkova, I. N. Zorov, A. P. Sinitsyn, M. D. Davari, and U. Schwaneberg (2019) Critical effect of proline on thermostability of endoglucanase II from Penicillium verruculosum. Biochem. Eng. J. 152: 107395.

    Article  CAS  Google Scholar 

  36. Yu, H., Y. Zhao, C. Guo, Y. Gan, and H. Huang (2015) The role of proline substitutions within flexible regions on thermostability of luciferase. Biochim. Biophys. Acta. 1854: 65–72.

    Article  CAS  Google Scholar 

  37. Spassov, V. Z. and L. Yan (2016) A pH-dependent computational approach to the effect of mutations on protein stability. J. Comput. Chem. 37: 2573–2587.

    Article  CAS  Google Scholar 

  38. Musil, M., J. Stourac, J. Bendl, J. Brezovsky, Z. Prokop, J. Zendulka, T. Martinek, D. Bednar, and J. Damborsky (2017) FireProt: web server for automated design of thermostable proteins. Nucleic Acids Res. 45: W393–W399.

    Article  CAS  PubMed Central  Google Scholar 

  39. Pace, C. N., H. Fu, K. L. Fryar, J. Landua, S. R. Trevino, B. A. Shirley, M. M. Hendricks, S. Iimura, K. Gajiwala, J. M. Scholtz, and G. R. Grimsley (2011) Contribution of hydrophobic interactions to protein stability. J. Mol. Biol. 408: 514–528.

    Article  CAS  PubMed Central  Google Scholar 

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Acknowledgements

This research was supported by the National Natural Science Foundation of China (82104322) and the Natural Science Foundation of Zhejiang (LQ22H280012).

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Correspondence to Linjiang Zhu or Xiaolong Chen.

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Chen, L., Jiang, K., Zhou, Y. et al. Improving the Thermostability of α-Glucosidase from Xanthomonas campestris through Proline Substitutions Guided by Semi-rational Design. Biotechnol Bioproc E 27, 631–639 (2022). https://doi.org/10.1007/s12257-022-0129-2

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  • DOI: https://doi.org/10.1007/s12257-022-0129-2

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