Abstract
Endoglucanases are key elements in several industrial applications, such as cellulosic biomass hydrolysis, cellulose fiber modification for the production paper and composite materials, and in nanocellulose production. In all of these applications, the desired function of the endoglucanase is to create nicks in the amorphous regions of the cellulose. However, endoglucanase can be diverted from its activity on the fibers by other substrates—soluble oligosaccharides. This issue was addressed in the current study using enzyme engineering and an enzyme evolution approach. To this end, a hypothetical endoglucanase from a thermostable bacterium Spirochaeta thermophila was for the first time cloned and characterized. The wild-type enzyme was used as a starting point for mutagenesis and molecular evolution toward a preference for the higher molecular weight substrates. The best of the evolved enzymes was more active than the wild-type enzyme toward high molecular weight substrate at temperatures below 45 °C (3-fold more active at 30 °C) and showed little or no activity with low molecular weight substrates. These findings can be instrumental in bioeconomy sectors, such as second-generation biofuels and biomaterials from lignocellulosic biomass.
Key points
• A new thermostable endoglucanase was characterized.
• The substrate specificity of this endoglucanase was changed by means of genetic engineering.
• A mutant with a preference for long molecular weight substrate was obtained and proposed to be beneficial for cellulose fiber modification.
Similar content being viewed by others
Data availability
The datasets generated during and/or analyzed during the current study are available from supplementary information files and from the corresponding author on reasonable request.
References
Barr BK, Hsieh YL, Ganem B, Wilson DB (1996) Identification of two functionally different classes of exocellulases. Biochemistry 35:586–592. https://doi.org/10.1021/bi9520388
Brunecky R, Alahuhta M, Xu Q, Donohoe BS, Crowley MF, Kataeva IA, Yang SJ, Resch MG, Adams MWW, Lunin VV, Himmel ME, Bomble YJ (2013) Revealing nature’s cellulase diversity: The digestion mechanism of Caldicellulosiruptor bescii CelA. Science 342:1513–1516. https://doi.org/10.1126/science.1244273
Brunecky R, Donohoe BS, Yarbrough JM, Mittal A, Scott R, Ding H, LET I, Russell JF, Chung D, Teter SA, Himmel ME, Bomble YJ (2017) The multi domain Caldicellulosiruptor bescii CelA cellulase excels at the hydrolysis of crystalline cellulose. Sci Rep 7:1–17. https://doi.org/10.1038/s41598-017-08985-w
Cadena EM, Iulia Chriac AI, Javier Pastor FI, Diaz P, Vidal T, Torres AL (2010) Use of cellulases and recombinant cellulose binding domains for refining TCF kraft pulp. Biotechnol Prog 26:960–967. https://doi.org/10.1002/btpr.411
Correa A, Pacheco S, Mechaly AE, Obal G, Béhar G, Mouratou B, Oppezzo P, Alzari PM, Pecorari F (2014) Potent and specific inhibition of glycosidases by small artificial binding proteins (Affitins). PLoS One 9:e97438. https://doi.org/10.1371/journal.pone.0097438
Eckert K, Zielinski F, Lo Leggio L, Schneider E (2002) Gene cloning, sequencing, and characterization of a family 9 endoglucanase (CelA) with an unusual pattern of activity from the thermoacidophile Alicyclobacillus acidocaldarius ATCC27009. Appl Microbiol Biotechnol 60:428–436. https://doi.org/10.1007/s00253-002-1131-4
Eckert K, Vigouroux A, Lo Leggio L, Moréra S (2009) Crystal structures of A. acidocaldarius endoglucanase Cel9A in complex with cello-oligosaccharides: strong - 1 and - 2 subsites mimic cellobiohydrolase activity. J Mol Biol 394:61–70. https://doi.org/10.1016/j.jmb.2009.08.060
Ellinghaus TL, Pereira JH, McAndrew RP, Welner DH, DeGiovanni AM, Guenther JM, Tran HM, Feldman T, Simmons BA, Sale KL, Adams PD (2018) Engineering glycoside hydrolase stability by the introduction of zinc binding. Acta Crystallogr D Struct Biol 74:702–710. https://doi.org/10.1107/S2059798318006678
Han SO, Yukawa H, Inui M, Doi RH (2005) Molecular cloning and transcriptional and expression analysis of engO, encoding a new noncellulosomal family 9 enzyme, from Clostridium cellulovorans. J Bacteriol 187:4884–4889. https://doi.org/10.1128/JB.187.14.4884-4889.2005
Haq HI, Akram F, Khan MA, Hussain Z, Nawaz A, Iqbal K, Shah AJ (2015) CenC, a multidomain thermostable GH9 processive endoglucanase from Clostridium thermocellum: cloning, characterization and saccharification studies. World J Microbiol Biotechnol 31:1699–1710. https://doi.org/10.1007/s11274-015-1920-4
Hu J, Tian D, Renneckar S, Saddler JN (2018) Enzyme mediated nanofibrillation of cellulose by the synergistic actions of an endoglucanase, lytic polysaccharide monooxygenase (LPMO) and xylanase. Sci Rep 8:3195. https://doi.org/10.1038/s41598-018-21016-6
Irwin DC, Spezio M, Walker LP, Wilson DB (1993) Activity studies of eight purified cellulases: Specificity, synergism, and binding domain effects. Biotechnol Bioeng 42:1002–1013. https://doi.org/10.1002/bit.260420811
Johnson AD (2010) An extended IUPAC nomenclature code for polymorphic nucleic acids. Bioinformatics 26:1386–1389. https://doi.org/10.1093/bioinformatics/btq098
Johnson WC, Lindsey AJ (1939) An improved universal buffer. Analyst 64:490–492. https://doi.org/10.1039/AN9396400490
Jung ED, Lao G, Irwin D, Barr BK, Benjamin A, Wilson DB (1993) DNA sequences and expression in Streptomyces lividans of an exoglucanase gene and an endoglucanase gene from Thermomonospora fusca. Appl Environ Microbiol 59:3032–3043. https://doi.org/10.1128/aem.59.9.3032-3043.1993
Juy M, Amrt AG, Alzari PM, Poljak RJ, Claeyssens M, Béguin P, Aubert JP (1992) Three-dimensional structure of a thermostable bacterial cellulase. Nature 357:89–91. https://doi.org/10.1038/357089a0
Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685. https://doi.org/10.1038/227680a0
Liang PH, Lin WL, Hsieh HY, Lin TY, Chen CH, Tewary SK, Lee HL, Yuan SF, Yang B, Yao JY, Ho MC (2018) A flexible loop for mannan recognition and activity enhancement in a bifunctional glycoside hydrolase family 5. Biochim Biophys Acta, Gen Subj 1862:513–521. https://doi.org/10.1016/j.bbagen.2017.11.004
Mangan D, Cornaggia C, McKie V, Kargelis T, McCleary BV (2016) A novel automatable enzyme-coupled colorimetric assay for endo-1,4-β-glucanase (cellulase). Anal Bioanal Chem 408:4159–4168. https://doi.org/10.1007/s00216-016-9507-y
McCleary BV, Mangan D, Daly R, Fort S, Ivory R, McCormack N (2014) Novel substrates for the measurement of endo-1,4-β-glucanase (endo-cellulase). Carbohydr Res 385:9–17. https://doi.org/10.1016/j.carres.2013.12.001
Miller GL (1959) Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem 31:426–428. https://doi.org/10.1021/ac60147a030
Nakabayashi M, Kamachi S, Malle D, Yanamoto T, Kishishita S, Fujii T, Inoue H, Ishikawa K (2019) Construction of thermostable cellobiohydrolase I from the fungus Talaromyces cellulolyticus by protein engineering. Protein Eng Des Sel 32:33–40. https://doi.org/10.1093/protein/gzz001
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera - A visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612. https://doi.org/10.1002/jcc.20084
Qian Y, Zhong L, Gao J, Sun N, Wang Y, Sun G, Qu Y, Zhong Y (2017) Production of highly efficient cellulase mixtures by genetically exploiting the potentials of Trichoderma reesei endogenous cellulases for hydrolysis of corncob residues. Microb Cell Factories 16:207. https://doi.org/10.1186/s12934-017-0825-3
Ribeiro RSA, Pohlmann BC, Calado V, Bojorge N, Pereira N (2019) Production of nanocellulose by enzymatic hydrolysis: Trends and challenges. Eng Life Sci 19:279–291. https://doi.org/10.1002/elsc.201800158
Sakon J, Irwin D, Wilson DB, Karplus PA (1997) Structure and mechanism of endo/exocellulase E4 from Thermomonospora fusca. Nat Struct Biol 4:810–818. https://doi.org/10.1038/nsb1097-810
Santos CR, Meza AN, Hoffmam ZB, Silva JC, Alvarez TM, Ruller R, Giesel GM, Verli H, Squina FM, Prade RA, Murakami MT (2010) Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B: Crystal structure, conformational stability and functional characterization of the xylanase 10B from Thermotoga petrophila RKU-1. Biochem Biophys Res Commun 403:214–219. https://doi.org/10.1016/j.bbrc.2010.11.010
Sazci A, Erenler K, Radford A (1986) Detection of cellulolytic fungi by using Congo red as an indicator: a comparative study with the dinitrosalicyclic acid reagent method. J Appl Bacteriol 61:559–562. https://doi.org/10.1111/j.1365-2672.1986.tb01729.x
Schiano-di-Cola C, Røjel N, Jensen K, Kari J, Sørensen TH, Borch K, Westh P (2019) Systematic deletions in the cellobiohydrolase (CBH) Cel7A from the fungus Trichoderma reesei reveal flexible loops critical for CBH activity. J Biol Chem 294:1807–1815. https://doi.org/10.1074/jbc.RA118.006699
Studier FW (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41:207–234. https://doi.org/10.1016/j.pep.2005.01.016
Von Ossowski I, Ståhlberg J, Koivula A, Piens K, Becker D, Boer H, Harle R, Harris M, Divne C, Mahdi S, Zhao Y, Driguez H, Claeyssens M, Sinnott ML, Teeri TT (2003) Engineering the exo-loop of Trichoderma reesei cellobiohydrolase, Cel7A. A comparison with Phanerochaete chrysosporium Cel7D. J Mol Biol 333:817–829. https://doi.org/10.1016/S0022-2836(03)00881-7
Wang HJ, Hsiao YY, Chen YP, Ma TY, Tseng CP (2016) Polarity alteration of a calcium site induces a hydrophobic interaction network and enhances Cel9A endoglucanase thermostability. Appl Environ Microbiol 82:1662–1674. https://doi.org/10.1128/AEM.03326-15
Wang M, Du J, Zhang D, Li X, Zhao J (2017) Modification of different pulps by homologous overexpression alkali-tolerant endoglucanase in Bacillus subtilis Y106. Sci Rep 7:3321. https://doi.org/10.1038/s41598-017-03215-9
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, De Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T (2018) SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Res 46:W296–W303. https://doi.org/10.1093/nar/gky427
Watson DL, Wilson DB, Walker LP (2002) Synergism in binary mixtures of Thermobifida fusca cellulases Cel6b, Cel9a, and Cel5a on BMCC and Avicel. Appl Biochem Biotechnol 101:97–111. https://doi.org/10.1385/ABAB:101:2:097
Xu Z, Cen YK, Zou SP, Xue YP, Zheng YG (2020) Recent advances in the improvement of enzyme thermostability by structure modification. Crit Rev Biotechnol 40:83–98 https://www.tandfonline.com/doi/full/10.1080/07388551.2019.1682963
Yang M, Zhang K-D, Zhang P-Y, Zhou X, Ma X-Q, Li F-L (2016) Synergistic cellulose hydrolysis dominated by a multi-modular processive endoglucanase from Clostridium cellulosi. Front Microbiol 7:932. https://doi.org/10.3389/fmicb.2016.00932
Yang H, Shi P, Liu Y, Xia W, Wang X, Cao H, Ma R, Luo H, Bai Y, Yao B (2017) Loop 3 of fungal endoglucanases of glycoside hydrolase family 12 modulates catalytic efficiency. Appl Environ Microbiol 83:e03123–e03116. https://doi.org/10.1128/AEM.03123-16
Younesi FS, Pazhang M, Najavand S, Rahimizadeh P, Akbarian M, Mohammadian M, Khajeh K (2016) Deleting the Ig-Like domain of Alicyclobacillus acidocaldarius endoglucanase Cel9A causes a simultaneous increase in the activity and stability. Mol Biotechnol 58:12–21. https://doi.org/10.1007/s12033-015-9900-3
Zhang F, Chen J-J, Ren W-Z, Nie G-X, Ming H, Tang S-K, Li W-J (2011) Cloning, expression and characterization of an alkaline thermostable GH9 endoglucanase from Thermobifida halotolerans YIM 90462T. Bioresour Technol 102:10143–10146. https://doi.org/10.1016/j.biortech.2011.08.019
Zhang ZK, Li W, Wang YF, Zheng YL, Tan FC, Ma XQ, Yao LS, Bayer EA, Wang LS, Li FL (2018) Processive degradation of crystalline cellulose by a multimodular endoglucanase via a wirewalking mode. Biomacromolecules 19:1686–1696. https://doi.org/10.1021/acs.biomac.8b00340
Zheng F, Tu T, Wang X, Wang Y, Ma R, Su X, Xie X, Yao B, Luo H (2018) Enhancing the catalytic activity of a novel GH5 cellulase GtCel5 from Gloeophyllum trabeum CBS 900.73 by site-directed mutagenesis on loop 6. Biotechnol Biofuels 11:76. https://doi.org/10.1186/s13068-018-1080-5
Zverlov V, Mahr S, Riedel K, Bronnenmeier K (1998) Properties and gene structure of a bifunctional cellulolytic enzyme (CelA) from the extreme thermophile “Anaerocellum thermophilum” with separate glycosyl hydrolase family 9 and 48 catalytic domains. Microbiology 144:457–465. https://doi.org/10.1099/00221287-144-2-457
Funding
This study was funded by the Bio Based Industries Joint Undertaking under the European Union’s Horizon 2020 research and innovation program, project SWEETWOODS, grant number 792061.
Author information
Authors and Affiliations
Contributions
VH planned and performed experiments, performed computer modeling, analyzed data; JDDBL planned and performed experiments, analyzed data; YB and RAR performed experiments, analyzed data; and KB supervised the project, planned and performed experiments, analyzed data, wrote the paper. All authors contributed to discussing and revising the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Ethical approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
ESM 1
(PDF 4361 kb)
Rights and permissions
About this article
Cite this article
Hämäläinen, V., Barajas-López, J.D.D., Berlina, Y. et al. New thermostable endoglucanase from Spirochaeta thermophila and its mutants with altered substrate preferences. Appl Microbiol Biotechnol 105, 1133–1145 (2021). https://doi.org/10.1007/s00253-020-11077-x
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-020-11077-x