Abstract
The semi-rational design of enzymes has become a popular and effective modification method to improve their hydrolytic activity and/or thermal stability toward target substrates. Here, the specific activity of a maltogenic amylase from Lactobacillus rhamnosus YXY412 (LrMA) toward soluble starch was exactly enhanced through hotspot-based research. Based on multiple sequence alignment, three-dimensional structure and existed literature, thirty-eight amino acid residues of LrMA were rationally selected for site-directed mutagenesis. After the screening of the mutants, LrMAD172A, LrMAG260A, LrMAK334A and LrMAM477A were selected with the activity accounted for 144–209% of that in wild-type. Among all the mutants, LrMAG260A possessed the highest activity toward soluble starch, reached 133 U/mg, about twice as high as that in the wild-type. Its temperature for optimum activity still maintained at 60 °C, while had no significant loss of thermal stability occurred. In addition, compared with the wild-type in pH stability, the mutant retained over 80% residual activity at a wider pH range of 4.5–8.5. Furthermore, the kcat/Km of LrMAG260A was two times higher than that of the wild-type, indicating that the mutant had a better affinity and a higher conversion efficiency for soluble starch.
Similar content being viewed by others
Data availability
Not applicable.
References
Bertoldo C, Antranikian G. Starch-hydrolyzing enzymes from thermophilic archaea and bacteria. Curr Opin Chem Biol. 2002;6:151–60. https://doi.org/10.1016/s1367-5931(02)00311-3.
Park KH, Kim TJ, Cheong TK, Kim JW, Oh BH, Svensson B. Structure, specificity and function of cyclomaltodextrinase, a multispecific enzyme of the alpha-amylase family. Biochim Biophys Acta. 2000;1478:165–85. https://doi.org/10.1016/s0167-4838(00)00041-8.
Stam MR, Danchin EG, Rancurel C, Coutinho PM, Henrissat B. Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins. Protein Eng Des Sel. 2006;19:555–62. https://doi.org/10.1093/protein/gzl044.
Saburi W, Morimoto N, Mukai A, Kim DH, Takehana T, Koike S, Matsui H, Mori H. A thermophilic alkalophilic alpha-amylase from Bacillus sp AAH-31 shows a novel domain organization among glycoside hydrolase family 13 enzymes. Biosci Biotechnol Biochem. 2013;77:1867–73. https://doi.org/10.1271/bbb.130284.
Shim JH, Park JT, Hong JS, Kim KW, Kim MJ, Auh JH, Kim YW, Park CS, Boos W, Kim JW, Park KH. Role of maltogenic amylase and pullulanase in maltodextrin and glycogen metabolism of Bacillus subtilis 168. J Bacteriol. 2009;191:4835–44. https://doi.org/10.1128/JB.00176-09.
Kim TJ, Kim MJ, Kim BC, Kim JC, Cheong TK, Kim JW, Park KH. Modes of action of acarbose hydrolysis and transglycosylation catalyzed by a thermostable maltogenic amylase, the gene for which was cloned from a Thermus strain. Appl Environ Microbiol. 1999;65:1644–51. https://doi.org/10.1128/AEM.65.4.1644-1651.1999.
Kim TJ, Shin JH, Oh JH, Kim MJ, Lee SB, Ryu S, Kwon K, Kim JW, Choi EH, Robyt JF, Park KH. Analysis of the gene encoding cyclomaltodextrinase from alkalophilic Bacillus sp I-5 and characterization of enzymatic properties. Arch Biochem Biophys. 1998;353:221–7. https://doi.org/10.1006/abbi.1998.0639.
Hondoh H, Kuriki T, Matsuura Y. Three-dimensional structure and substrate binding of Bacillus stearothermophilus neopullulanase. J Mol Biol. 2003;326:177–88. https://doi.org/10.1016/s0022-2836(02)01402-x.
Kamitori S, Abe A, Ohtaki A, Kaji A, Tonozuka T, Sakano Y. Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 a resolution and alpha-amylase 2 (TVAII) at 2.3 a resolution. J Mol Biol. 2002;318:443–53. https://doi.org/10.1016/S0022-2836(02)00111-0.
Kim JS, Cha SS, Kim HJ, Kim TJ, Ha NC, Oh ST, Cho HS, Cho MJ, Kim MJ, Lee HS, Kim JW, Choi KY, Park KH, Oh BH. Crystal structure of a maltogenic amylase provides insights into a catalytic versatility. J Biol Chem. 1999;274:26279–86. https://doi.org/10.1074/jbc.274.37.26279.
Lee HS, Kim MS, Cho HS, Kim JI, Kim TJ, Choi JH, Park C, Lee HS, Oh BH, Park KH. Cyclomaltodextrinase, neopullulanase, and maltogenic amylase are nearly indistinguishable from each other. J Biol Chem. 2002;277:21891–7. https://doi.org/10.1074/jbc.M201623200.
Kolcuoğlu Y, Colak A, Faiz O, Belduz AO. Cloning, expression and characterization of highly thermo- and pH-stable maltogenic amylase from a thermophilic bacterium Geobacillus caldoxylosilyticus TK4. Process Biochem. 2010;45:821–8. https://doi.org/10.1016/j.procbio.2010.02.001.
Nawawi NN, Hashim Z, Manas NHA, Azelee NIW, Illias RM. A porous-cross linked enzyme aggregates of maltogenic amylase from Bacillus lehensis G1: robust biocatalyst with improved stability and substrate diffusion. Int J Biol Macromol. 2020;148:1222–31. https://doi.org/10.1016/j.ijbiomac.2019.10.101.
Kuriki T, Imanaka T. The concept of the alpha-amylase family: structural similarity and common catalytic mechanism. J Biosci Bioeng. 1999;87:557–65. https://doi.org/10.1016/s1389-1723(99)80114-5.
Liu P, Ma L, Duan W, Gao W, Fang Y, Guo L, Yuan C, Wu Z, Cui B. Maltogenic amylase: its structure, molecular modification, and effects on starch and starch-based products. Carbohydr Polym. 2023;319:121183. https://doi.org/10.1016/j.carbpol.2023.121183.
van der Maarel MJ, van der Veen B, Uitdehaag JC, Leemhuis H, Dijkhuizen L. Properties and applications of starch-converting enzymes of the alpha-amylase family. J Biotechnol. 2002;94:137–55. https://doi.org/10.1016/s0168-1656(01)00407-2.
Zhou J, Li Z, Zhang H, Wu J, Ye X, Dong W, Jiang M, Huang Y, Cui Z. Novel maltogenic amylase CoMA from Corallococcus sp strain EGB catalyzes the Conversion of Maltooligosaccharides and Soluble Starch to Maltose. Appl Environ Microbiol. 2018;84:e00152–00118. https://doi.org/10.1128/AEM.00152-18.
Li X, Wang Y, Park JT, Gu L, Li D. An extremely thermostable maltogenic amylase from Staphylothermus marinus: Bacillus expression of the gene and its application in genistin glycosylation. Int J Biol Macromol. 2018;107:413–7. https://doi.org/10.1016/j.ijbiomac.2017.09.007.
Ben Mabrouk S, Aghajari N, Ben Ali M, Ben Messaoud E, Juy M, Haser R, Bejar S. Enhancement of the thermostability of the maltogenic amylase MAUS149 by Gly312Ala and Lys436Arg substitutions. Bioresour Technol. 2011;102:1740–6. https://doi.org/10.1016/j.biortech.2010.08.082.
Oh KW, Kim MJ, Kim HY, Kim BY, Baik MY, Auh JH, Park CS. Enzymatic characterization of a maltogenic amylase from Lactobacillus gasseri ATCC 33323 expressed in Escherichia coli. FEMS Microbiol Lett. 2005;252:175–81. https://doi.org/10.1016/j.femsle.2005.08.050.
Kanpiengjai A, Nguyen TH, Haltrich D, Khanongnuch C. Expression and comparative characterization of complete and C-terminally truncated forms of saccharifying α-amylase from Lactobacillus plantarum S21. Int J Biol Macromol. 2017;103:1294–301. https://doi.org/10.1016/j.ijbiomac.2017.05.168.
Jeon HY, Kim NR, Lee HW, Choi HJ, Choung WJ, Koo YS, Ko DS, Shim JH. Characterization of a Novel maltose-forming α-Amylase from Lactobacillus plantarum subsp. plantarum ST-III. J Agric Food Chem. 2016;64:2307–14. https://doi.org/10.1021/acs.jafc.5b05892.
Vera A, Rigobello V, Demarigny Y. Comparative study of culture media used for sourdough lactobacilli. Food Microbiol. 2009;26:728–33. https://doi.org/10.1016/j.fm.2009.07.010.
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. https://doi.org/10.1006/abio.1976.9999.
Miller GL. Use of Dinitrosalicylic Acid Reagent for determination of reducing Sugar. Anal Chem. 1959;31:426–8. https://doi.org/10.1021/ac60147a030.
Ruan Y, Xu Y, Zhang W, Zhang R. A new maltogenic amylase from Bacillus licheniformis R-53 significantly improves bread quality and extends shelf life. Food Chem. 2021;344:128599. https://doi.org/10.1016/j.foodchem.2020.128599.
Roy A, Messaoud EB, Bejar S. Isolation and purification of an acidic pullulanase type II from newly isolated Bacillus sp US149. Enzym Microb Technol. 2003;33:720–4. https://doi.org/10.1016/S0141-0229(03)00212-6.
Kim JW, Kim YH, Lee HS, Yang SJ, Kim YW, Lee MH, Kim JW, Seo NS, Park CS, Park KH. Molecular cloning and biochemical characterization of the first archaeal maltogenic amylase from the hyperthermophilic archaeon Thermoplasma volcanium GSS1. Biochim Biophys Acta. 2007;1774:661–9. https://doi.org/10.1016/j.bbapap.2007.03.010.
Liu B, Wang Y, Zhang X. Characterization of a recombinant maltogenic amylase from deep sea thermophilic Bacillus sp WPD616. Enzym Microb Technol. 2006;39:805–10. https://doi.org/10.1016/j.enzmictec.2006.01.003.
Kim YW, Choi JH, Kim JW, Park C, Kim JW, Cha H, Lee SB, Oh BH, Moon TW, Park KH. Directed evolution of Thermus maltogenic amylase toward enhanced thermal resistance. Appl Environ Microbiol. 2003;69:4866–74. https://doi.org/10.1128/AEM.69.8.4866-4874.2003.
Cai X, Shi X, Liu SQ, Qiang Y, Shen JD, Zhang B, Liu ZQ, Zheng YG. Hot spot-based engineering of ketopantoate hydroxymethyltransferase for the improvement of D-pantothenic acid production in Escherichia coli. J Biotechnol. 2023;364:40–9. https://doi.org/10.1016/j.jbiotec.2023.01.010.
Ruan Y, Zhang R, Xu Y. Directed evolution of maltogenic amylase from Bacillus licheniformis R-53: enhancing activity and thermostability improves bread quality and extends shelf life. Food Chem. 2022;381:132222. https://doi.org/10.1016/j.foodchem.2022.132222.
Salentin S, Schreiber S, Haupt VJ, Adasme MF, Schroeder M. PLIP: fully automated protein-ligand interaction profiler. Nucleic Acids Res. 2015;43:W443–447. https://doi.org/10.1093/nar/gkv315.
Seeliger D, de Groot BL. Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J Comput Aided Mol Des. 2010;24:417–22. https://doi.org/10.1007/s10822-010-9352-6.
Tatko CD, Waters ML. Selective aromatic interactions in beta-hairpin peptides. J Am Chem Soc. 2002;124:9372–3. https://doi.org/10.1021/ja0262481.
Nezhad NG, Rahman R, Normi YM, Oslan SN, Shariff FM, Leow TC. Recent advances in simultaneous thermostability-activity improvement of industrial enzymes through structure modification. Int J Biol Macromol. 2023;232:123440. https://doi.org/10.1016/j.ijbiomac.2023.123440.
Acknowledgements
This work was financially supported by the Postdoctoral Science Foundation of China (2021M691278) and the National Key Special Project for the 13th National 5-Year Plan Program of China (2016YFD0400500).
Funding
This work was financially supported by the Postdoctoral Science Foundation of China (2021M691278) and the National Key Special Project for the 13th National 5-Year Plan Program of China (2016YFD0400500).
Author information
Authors and Affiliations
Contributions
Experimental design was done by SXY, WMC and HWN; experiments conducted and analyzed by SXY, ZD, HJ and LYQ; SXY wrote and edited the manuscript. All authors finally approved the manuscript.
Corresponding authors
Ethics declarations
Ethics approval and consent to participate
Not applicable.
Consent for publication
All authors agreed to submit the manuscript for publication in SMAB.
Competing interests
The authors declare that there are no conflicts of interest.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Su, X., Zhang, D., Huang, J. et al. Hotspot-based mutation engineering of MAase from Lactobacillus rhamnosus YXY412 for the improvement of hydrolytic activity. Syst Microbiol and Biomanuf (2024). https://doi.org/10.1007/s43393-024-00261-z
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s43393-024-00261-z