A Role of Cellulose Binding Module of the Thermophilic Endoglucanase TbCel12A
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Abstract
Endoglucanases are enzymes that play an important role in hydrolysis of lignocellulose by attacking glycosidic linkages in cellulose fibers and other glucans. The cellulose binding module (CBM) is responsible for binding the enzyme to the substrate. However, CBMs in certain enzymes interfere with substrate hydrolysis resulting in moderate or low activity. In a previous study, the processive endoglucanase TbCel12A including its CBM had low activity towards carboxymethyl cellulose (CMC). To assess the effect of the CBM, the catalytic domain of TbCel12A was produced without the CBM. The TbCel12A catalytic domain without the CBM hydrolyzed CMC 23 times more rapidly, while the pH and temperature optima and thermotolerance remained unchanged compared to full-length TbCel12A. Therefore, TbCel12A does not require the CBM for CMC hydrolysis and its application may be improved without it.
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M. Crippa, D. Guizzardi, E. Solazzo, M. Muntean, E. Schaaf, F. Monforti-Ferrario, M. Banja, J. G. J. Olivier, G. Grassi, S. Rossi, E. Vignati, “GHG emissions of all world countries,” 2021. [Online]. Available: https://edgar.jrc.ec.europa.eu/report _2021
IEA, “Outlook for energy demand,” in World Energy Outlook 2022. Paris, France: OECD Publishing, 2022.
F. G. Santeramo, “Circular and green economy: The state-of-the-art,” Heliyon, vol. 8, no. 4, Apr. 2022, doi: 10.1016/j.heliyon.2022.e09297.
T. Ruensodsai and M. Sriariyanun, “Sustainable development and progress of lignocellulose conversion to platform chemicals,” The Journal of King Mongkut's University of Technology North Bangkok, vol. 32, no. 4, pp. 815–818, Oct. 2022, doi: 10.14416/j.kmutnb.2022.03.001
A. P. Saravanan, A. Pugazhendhi, and T. Mathimani, “A comprehensive assessment of biofuel policies in the BRICS nations: Implementation, blending target and gaps,” Fuel, vol. 272, Apr. 2020, Art. no. 117635, doi: 10.1016/j.fuel.2020.117635.
M. Sriariyanun and K. Kitsubthawee, “Trend in lignocellosic biorefinery for production of value-added biochrmicals,” Applied Science and Engineering Progress, vol. 13, no. 4, pp. 283–284, Oct. 2020, doi: 10.14416/j.asep. 2020.02.005.
M. P. Gundupalli and M. Sriariyanun, “Recent trends and updates for chemical pretreatment of lignocellulosic biomass,” Applied Science and Engineering Progress, vol. 16, no. 1, pp. 1–4, Jan. 2023, doi: 10.14416/j.asep.2022.03.002.
G. Brodeur, E. Yau, K. Badal, J. Collier, K. B. Ramachandran, and S. Ramakrishnan, “Chemical and physicochemical pretreatment of lignocellulosic biomass: A review,” Enzyme Research, vol. 2011, no. 1, May 2011, doi: 10.4061/2011/787532.
Y. H. Lee and L. T. Fan, “Properties and mode of action of cellulase,” in Advances in Biochemical Engineering, vol. 17, Berlin, Heidelberg: Springer, pp. 101–129, 1980, doi: 10.1007/3- 540-09955-7_9.
Y. Hu, G. Kang, L. Wang, M. Gao, P. Wang, D. Yang, and H. Huang, “Current status of mining, modification, and application of cellulases in bioactive substance extraction,” Current Issues in Molecular Biology, vol. 43, pp. 687–703, Sep. 2021, doi: 10.3390/cimb43020050.
K. H. Chang, H. S. Jee, N. K. Lee, S. H. Park, N. W. Lee, and H. D. Paik, “Optimization of the enzymatic production of 20(S)-ginsenoside Rg3 from white ginseng extract using response surface methodology,” New Biotechnology, vol. 26, no. 3, pp. 181–186, Oct. 2009, doi: 10.1016/j.nbt.2009.08.011.
W. Winotapun, P. Opanasopit, T. Ngawhirunpat, and T. Rojanarata, “One-enzyme catalyzed simultaneous plant cell disruption and conversion of released glycoside to aglycone combined with in situ product separation as green one-pot production of genipin from gardenia fruit,” Enzyme and Microbial Technology, vol. 53, no. 2, pp. 92–96, Jul. 2013, doi: 10.1016/j.enzmictec. 2013.05.001.
S. Wu and S. Wu, “Processivity and the mechanisms of processive endoglucanases,” Applied Biochemistry and Biotechnology, vol. 190, no. 2, pp. 448–463, Feb. 2020, doi: 10.1007/s12010-019-03096-w.
Z. Wang, T. Zhang, L. Long, and S. Ding, “Altering the linker in processive GH5 endoglucanase 1 modulates lignin binding and catalytic properties,” Biotechnology for Biofuels, vol. 11, no. 1, pp. 1–11, Dec. 2018, doi: 10.1186/ s13068-018-1333-3.
M. Sandgren, J. Ståhlberg, and C. Mitchinson, “Structural and biochemical studies of GH family 12 cellulases: improved thermal stability, and ligand complexes,” Progress in Biophysics and Molecular Biology, vol. 89, no. 3, pp. 246– 291, doi: 10.1016/j.pbiomolbio.2004.11.002.
E. Drula, M.-L. Garron, S. Dogan, V. Lombard, B. Henrissat, and N. Terrapon, “The carbohydrate-active enzyme database: Functions and literature” Nucleic Acids Research, vol. 50, no. D1, pp. D571–D577, Nov. 2021, doi: 10.1093/nar/ gkab1045.
G. Carrard, A. Koivula, H. Söderlund, and P. Béguin, “Cellulose-binding domains promote hydrolysis of different sites on crystalline cellulose,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 19, pp. 10342–10347, Sep. 2000, doi: 10.1073/pnas.160216697.
A. B. Boraston, D. N. Bolam, H. J. Gilbert, and G. J. Davies, “Carbohydrate-binding modules: Fine-tuning polysaccharide recognition,” Biochemical Journal, vol. 382, no. Pt 3, pp. 769–781, Sep. 2004, doi: 10.1042/BJ20040892.
B. Wu, S. Zheng, M. M. Pedroso, L. W. Guddat, S. Chang, B. He, and G. Schenk, “Processivity and enzymatic mechanism of a multifunctional family 5 endoglucanase from Bacillus subtilis BS-5 with potential applications in the saccharification of cellulosic substrates,” Biotechnology for Biofuels and Bioproducts, vol. 11, no. 1, Jan. 2018, doi: 10.1186/s13068-018-1022-2.
M. H. Wu, M. R. Kao, C. W. Li, S. M. Yu, and T. H. D. Ho, “A unique self-truncation of bacterial GH5 endoglucanases leads to enhanced activity and thermostability” BMC Biology, vol. 20, no.1, Dec. 2022, doi: 10.1186/s12915- 022-01334-y.
J. P. Lee, E. S. Shin, M. Y. Cho, K. D. Lee, and H. Kim, “Roles of Carbohydrate-Binding Module (CBM) of an Endo-β-1,4-Glucanase (Cel5L) from Bacillus sp. KD1014 in Thermostability and Small-Substrate Hydrolyzing Activity,” Journal of Microbiology and Biotechnology, vol. 28, no. 12, pp. 2036–2045, Dec. 2018, doi: 10.4014/ JMB.1810.10001.
T. Kuntothom and J. K. Cairns, “Expression and characterization of TbCel12A, a thermophilic endoglucanase with potential in biomass hydrolysis,” Biocatalysis and Agricultural Biotechnology, vol. 30, Nov. 2020, doi: 10.1016/j. bcab.2020.101835.
F. Sievers, A. Wilm, D. G. Dineen, T. J. Gibson, K. Karplus, W. Li, R. Lopez, H. McWilliam, M. Remmert, J. Söding, J. D. Thompson, and D. Higgins, “Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega,” Molecular Systems Biology, vol. 7, Oct. 2011, doi: 10.1038/msb.2011.75.
M. Goujon, H. McWilliam, W. Li, F. Valentin, S. Squizzato, J. Paern, and R. Lopez, “A new bioinformatics analysis tools framework at EMBL-EBI,” Nucleic Acids Research, vol. 38, pp. W695–W699, May 2010, doi: 10.1093/nar/ gkq313.
I. Letunic, S. Khedkar, and P. Bork, “SMART: recent updates, new developments and status in 2020,” Nucleic Acids Research, vol. 49, no. D1, pp. D458–D460, Jan. 2021, doi.org/10.1093/nar/ gkaa937.
J. Jumper, R. Evans, A. Pritzel, T. Green, M. Figurnov, O. Ronneberger, K. Tunyasuvunakool, R. Bates, A. Žídek, A. Potapenko, A. Bridgland, C. Meyer, S. A. A. Kohl, A. J. Ballard, A. Cowie, B. Romera-Paredes, S. Nikolov, R. Jain, J. Adler, T. Back, S. Petersen, D. Reiman, E. Clancy, M. Zielinski, M. Steinegger, M. Pacholska, T. Berghammer, S. Bodenstein, D. Silver, O. Vinyals, A. W. Senior, K. Kavukcuoglu, P. Kohli and D. Hassabis , “Highly accurate protein structure prediction with AlphaFold,” Nature, vol. 596, no. 7873, pp. 583–589, Aug. 2021, doi: 10.1038/ S41586-021-03819-2.
M. Mirdita, K. Schütze, Y. Moriwaki, L. Heo, S. Ovchinnikov, and M. Steinegger, “ColabFold: Making protein folding accessible to all,” Nature Methods, vol. 19, no. 6, pp. 679–682, Jun. 2022, doi: 10.1038/S41592-022-01488-1.
L. Schrödinger and W. DeLanoz, “PyMOL,” 2020. [Online]. Available: http://www.pymol. org/pymol
T. Kuntothom, S. Luang, A.J. Harvey, G.B. Fincher, R. Opassiri, M. Hrmova, and J. K. Cairns, “Rice family GH1 glycoside hydrolases with β-d-glucosidase and β-d-mannosidase activities,” Archives of Biochemistry and Biophysics, vol. 491, pp. 85–95, Nov. 2009, doi: 10.1016/j.abb.2009.09.004.
T. C. McIlvaine, “A buffer solution for colorimetric comparison,” Journal of Biological Chemistry, vol. 49, no. 1, pp. 183–186, Nov. 1921, doi: 10.1016/S0021-9258(18)86000-8.
G. L. Miller, “Use of dinitrosalicylic acid reagent for determination of reducing sugar,” Analytical Chemistry, vol. 31, pp. 426–428, Mar. 1959, doi: 10.1021/ac60147a030.
G. Y. Xu, E. Ong, N. R. Gilkes, D. G. Kilburn, D. R. Muhandiram, M. Harris-Brandts, J. P. Carver, L. E. Kay, and T. S. Harvey, “Solution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy,” Biochemistry, vol. 34, no. 21, pp. 6993–7009, May 1995, doi: 10.1021/bi00021a011.
C. M. Bianchetti, P. Brumm, R. W. Smith, K. Dyer, G. L. Hura, T. J. Rutkoski, and G. N. Phillips Jr, “Structure, dynamics, and specificity of endoglucanase D from Clostridium cellulovorans,” Journal of Molecular Biology, vol. 425, no. 22, pp. 4267–4285, Nov. 2013, doi: 10.1016/J.JMB.2013.05.030.
P. J. Simpson, H. Xie, D. N. Bolam, H. J. Gilbert, and M. P. Williamson, “The structural basis for the ligand specificity of family 2 carbohydrate-binding modules,” Journal of Biological Chemistry, vol. 275, no. 52, pp. 41137–41142, Dec. 2000, doi: 10.1074/JBC.M006948200.
Structural Genomics Consortium, China Structural Genomics Consortium, Northeast Structural Genomics Consortium, S. Gräslund, P. Nordlund, J. Weigelt, B. M. Hallberg, J. Bray, O. Gileadi, S. Knapp, U. Oppermann, C. Arrowsmith, R. Hui, J. Ming, S. dhe-Paganon, H. W. Park, A. Savchenko, A. Yee, A. Edwards, R. Vincentelli, C. Cambillau, R. Kim, S. H. Kim, Z. Rao, Y. Shi, T. C. Terwilliger, C. Y. Kim, L. W. Hung, G. S. Waldo, Y. Peleg, S. Albeck, T. Unger, O. Dym, J. Prilusky, J. L. Sussman, R. C. Stevens, S. A. Lesley, I. A. Wilson, A. Joachimiak, F. Collart, I. Dementieva, M. I. Donnelly, W. H. Eschenfeldt, Y. Kim, L. Stols, R. Wu, M. Zhou, S. K. Burley, J. S. Emtage, J. M. Sauder, D. Thompson, K. Bain, J. Luz, T. Gheyi, F. Zhang, S. Atwell, S. C. Almo, J. B. Bonanno, A. Fiser, S. Swaminathan, F. W. Studier, M. R. Chance, A. Sali, T. B. Acton, R. Xiao, L. Zhao, L. C. Ma, J. F. Hunt, L. Tong, K. Cunningham, M. Inouye, S. Anderson, H. Janjua, R. Shastry, C. K. Ho, D. Wang, H. Wang, M. Jiang, G. T. Montelione, D. I. Stuart, R. J. Owens, S. Daenke, A. Schütz, U. Heinemann, S. Yokoyama, K. Büssow, and K. C. Gunsalus, “Protein production and purification,” Nature Methods, vol. 5, no. 2, pp. 135–146, Feb. 2008, doi: 10.1038/nmeth.f.202.
N. N. Hengge, S. J. B. Mallinson, P. Pason, V. V. Lunin, M. Alahuhta, D. Chung, M. E. Himmel, J. Westpheling, and Y. J. Bomble, “Characterization of the biomass degrading enzyme GuxA from Acidothermus cellulolyticus,” International Journal of Molecular Sciences, vol. 23, no. 11, Jun. 2022, doi: 10.3390/IJMS23116070.
S. A. Mahadevan, S. G. Wi, D. S. Lee, and H. J. Bae, “Site-directed mutagenesis and CBM engineering of Cel5A (Thermotoga maritima),” FEMS Microbiology Letters, vol. 287, no. 2, pp. 205–211, Oct. 2008, doi: 10.1111/J.1574- 6968.2008.01324.X.
G. Geiger, G. Furrer, F. Funk, H. Brandl, and R. Schulin, “Heavy metal effects on β-glucosidase activity influenced by pH and buffer systems,” Journal of Enzyme Inhibition, vol. 14, no. 5, pp. 365–379, 1999, doi: 10.3109/ 14756369909030329.
J. de C. Pereira, E. C. Giese, M. M. de S. Moretti, A. C. dos S. Gomes, O. M. Perrone, M. Boscolo, R. da Silva, E. Gomes, and D. A. B. Martins, “Effect of metal ions, chemical agents and organic compounds on lignocellulolytic enzymes activities,” in Enzyme Inhibitors and Activators, M. Senturk, Ed., Rijeka: IntechOpen, 2017, doi: 10.5772/65934.
M. Hans, S. Kumar, A. K. Chandel, and I. Polikarpov, “A review on bioprocessing of paddy straw to ethanol using simultaneous saccharification and fermentation,” Process Biochemistry, vol. 85, pp. 125–134, 2019, doi: 10.1016/j.procbio.2019.06.019.
D. S. Xue, X. Zeng, D. Lin, and S. Yao, “Ethanol tolerant endoglucanase from Aspergillus niger isolated from wine fermentation cellar”, Biocatalysis and Agricultural Biotechnology, vol. 15, pp. 19–24, 2018, doi: 10.1016/j.bcab. 2018.04.016.
H. Yoshikawa, A. Hirano, T. Arakawa, and K. Shiraki, “Mechanistic insights into protein precipitation by alcohol,” International Journal of Biological Macromolecules, vol. 50, no. 3, pp. 865–871, Apr. 2012, doi: 10.1016/J.IJBIO MAC.2011.11.005.
Z. Zhu, J. Qu, L. Yu, X. Jiang, G. Liu, L. Wang, Y. Qu, and Y. Qin, “Three glycoside hydrolase family 12 enzymes display diversity in substrate specificities and synergistic action between each other,” Molecular Biology Reports, vol. 46, no. 5, pp. 5443–5454, Oct. 2019, doi: 10.1007/s11033- 019-04999-x.