A coarse-grained model for synergistic action of multiple enzymes on cellulose

Biotechnology for Biofuels

Andrea Asztalos³  Marcus Daniels⁵  Anurag Sethi⁴  Tongye Shen²  Paul Langan¹  Antonio Redondo⁴  Sandrasegaram Gnanakaran⁴ 

[1] Present Address: Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA

[2] Present Address: UT-ORNL, Center for Molecular Biophysics and Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA

[3] Present Address: Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA

[4] Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA

[5] Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA

关键词: Spatial heterogeneity;    Agent-based model;    Endo-cellulase;    Exo-cellulase;    Synergy;    Cellulose degradation;   

Others  :  798252
DOI  :  10.1186/1754-6834-5-55

 received in 2012-03-29, accepted in 2012-06-21,  发布年份 2012

【 摘 要 】

Background

Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, β-glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates.

Results

We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages) and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose.

Conclusions

Our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures the endo-exo synergism of cellulase enzyme cocktails. This model constitutes a critical step towards testing hypotheses and understanding approaches for maximizing synergy and substrate properties with a goal of cost effective enzymatic hydrolysis.

【 授权许可】

   
2012 Asztalos et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Goldemberg J: Ethanol for a sustainable energy future. Science 2007, 315(5813):808-810.
• [2]Himmel ME, Ruth MF, Wyman CE: Cellulase for commodity products from cellulosic biomass. Curr Opin Biotechnol 1999, 10(4):358-364.
• [3]Lynd LR, Cushman JH, Nichols RJ, Wyman CE: Fuel ethanol from cellulosic biomass. Science 1991, 251(4999):1318-1323.
• [4]Klemm D, Heublein B, Fink HP, Bohn A: Cellulose: fascinating biopolymer and sustainable raw material. Angew Chem Int Ed Engl 2005, 44(22):3358-3393.
• [5]Forsberg Z, Vaaje-Kolstad G, Westereng B, Bunaes AC, Stenstrøm Y, MacKenzie A, Sorlie M, Horn SJ, Eijsink VG: Cleavage of cellulose by a CBM33 protein. Protein Sci 2011, 20(9):1479-1483.
• [6]Davies G, Henrissat B: Structures and mechanisms of glycosyl hydrolases. Structure 1995, 3(9):853-859.
• [7]IUBMB: Enzyme Nomenclature. Academic, San Diego; 1992.
• [8]Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS: Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 2002, 66(3):506-577. table of contents
• [9]Teeri TT: Crystalline cellulose degradation: new insight into the function of cellobiohydrolases. Trends Biotechnol 1997, 15(5):160-167.
• [10]Teeri TT, Koivula A, Linder M, Wohlfahrt G, Divne C, Jones TA: Trichoderma reesei cellobiohydrolases: why so efficient on crystalline cellulose? Biochem Soc Trans 1998, 26(2):173-178.
• [11]Zhang YH, Lynd LR: Toward an aggregated understanding of enzymatic hydrolysis of cellulose: noncomplexed cellulase systems. Biotechnol Bioeng 2004, 88(7):797-824.
• [12]Coughlan M, Moloney A, McCrae S, Wood T: Cross-synergistic interactions between components of the cellulase systems of Talaromyces emersonii, Fusarium solani, Penicillium funiculosum and Trichoderma koningii. Biochem Soc Trans 1987, 15:263-264.
• [13]Fägerstam L, Pettersson L: The 1,4-b-glucan cellobiohydrolases of Trichoderma reesei. FEBS Lett 1980, 119:97-100.
• [14]Henrissat B, Driguez H, Viet C, Schulein M: Synergism of Cellulases from Trichoderma reesei in the Degradation of Cellulose. Nat Biotech 1985, 3(8):722-726.
• [15]Kleman-Leyer KM, Siika-Aho M, Teeri TT, Kirk TK: The Cellulases Endoglucanase I and Cellobiohydrolase II of Trichoderma reesei Act Synergistically To Solubilize Native Cotton Cellulose but Not To Decrease Its Molecular Size. Appl Environ Microbiol 1996, 62(8):2883-2887.
• [16]Medve J, Karlsson J, Lee D, Tjerneld F: Hydrolysis of microcrystalline cellulose by cellobiohydrolase I and endoglucanase II from Trichoderma reesei: adsorption, sugar production pattern, and synergism of the enzymes. Biotechnol Bioeng 1998, 59(5):621-634.
• [17]Petterson LG: Symposium on Enzymatic Hydrolysis of Cellulose. SITRA, Helsinski; 1975.
• [18]Xu Q, Adney W: Sing S-Y, Himmel ME: Industrial Enzymes: Structure. Springer Netherlands, Function and Applications; 2007.
• [19]Bansal P, Hall M, Realff MJ, Lee JH, Bommarius AS: Modeling cellulase kinetics on lignocellulosic substrates. Biotechnol Adv 2009, 27(6):833-848.
• [20]Levine SE, Fox JM, Blanch HW, Clark DS: A mechanistic model of the enzymatic hydrolysis of cellulose. Biotechnol Bioeng 2010, 107(1):37-51.
• [21]Okazaki M, Moo-Young M: Kinetics of enzymatic hydrolysis of cellulose: analytical description of a mechanistic model. Biotechnol Bioeng 1978, 20(5):637-663.
• [22]Zhang YH, Lynd LR: A functionally based model for hydrolysis of cellulose by fungal cellulase. Biotechnol Bioeng 2006, 94(5):888-898.
• [23]Zhou W, Hao Z, Xu Y, Schuttler HB: Cellulose hydrolysis in evolving substrate morphologies II: Numerical results and analysis. Biotechnol Bioeng 2009, 104(2):275-289.
• [24]Zhou W, Schuttler HB, Hao Z, Xu Y: Cellulose hydrolysis in evolving substrate morphologies I: A general modeling formalism. Biotechnol Bioeng 2009, 104(2):261-274.
• [25]Zhou W, Xu Y, Schuttler HB: Cellulose hydrolysis in evolving substrate morphologies III: time-scale analysis. Biotechnol Bioeng 2010, 107(2):224-234.
• [26]Griggs AJ, Stickel JJ, Lischeske JJ: A mechanistic model for enzymatic saccharification of cellulose using continuous distribution kinetics I: depolymerization by EGI and CBHI. Biotechnol Bioeng 2012, 109(3):665-675.
• [27]Griggs AJ, Stickel JJ, Lischeske JJ: A mechanistic model for enzymatic saccharification of cellulose using continuous distribution kinetics II: cooperative enzyme action, solution kinetics, and product inhibition. Biotechnol Bioeng 2012, 109(3):676-685.
• [28]Warden AC, Little BA, Haritos VS: fA cellular automaton model of crystalline cellulose hydrolysis by cellulases. Biotechnol Biofuels 2011, 4(1):39. BioMed Central Full Text
• [29]Beckham GT, Bomble YJ, Bayer EA, Himmel ME, Crowley MF: Applications of computational science for understanding enzymatic deconstruction of cellulose. Curr Opin Biotechnol 2011, 22(2):231-238.
• [30]Bu L, Beckham GT, Crowley MF, Chang CH, Matthews JF, Bomble YJ, Adney WS, Himmel ME, Nimlos MR: The energy landscape for the interaction of the family 1 carbohydrate-binding module and the cellulose surface is altered by hydrolyzed glycosidic bonds. J Phys Chem B 2009, 113(31):10994-11002.
• [31]Nimlos MR, Matthews JF, Crowley MF, Walker RC, Chukkapalli G, Brady JW, Adney WS, Cleary JM, Zhong L, Himmel ME: Molecular modeling suggests induced fit of Family I carbohydrate-binding modules with a broken-chain cellulose surface. Protein Eng Des Sel 2007, 20(4):179-187.
• [32]Zhong L, Matthews JF, Crowley MF, Rignall T, Talon C, Cleary JM, Walker RC, Chukkapalli G, McCabe C, Nimlos MR, et al.: Interactions of the complete cellobiohydrolase I from Trichodera reesei with microcrystalline cellulose \beta. Cellulose 2008, 15:261-273.
• [33]Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, et al.: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocreajecorina). Nat Biotechnol 2008, 26(5):553-560.
• [34]Divne C, Stahlberg J, Teeri TT, Jones TA: High-resolution crystal structures reveal how a cellulose chain is bound in the 50Å long tunnel of cellobiohydrolase I from Trichoderma reesei. J Mol Biol 1998, 275(2):309-325.
• [35]Kleywegt GJ, Zou JY, Divne C, Davies GJ, Sinning I, Stahlberg J, Reinikainen T, Srisodsuk M, Teeri TT, Jones TA: The crystal structure of the catalytic core domain of endoglucanase I from Trichoderma reesei at 3.6 A resolution, and a comparison with related enzymes. J Mol Biol 1997, 272(3):383-397.
• [36]Rouvinen J, Bergfors T, Teeri T, Knowles JK, Jones TA: Three-dimensional structure of cellobiohydrolase II from Trichoderma reesei. Science 1990, 249(4967):380-386.
• [37]Nieves RA, Ehrman CI, Adney WS, Elander RT, Himmel ME: Technical communication: survey and analysis of commercial cellulase preparations suitable for biomass conversion to ethanol. World J Microbiol Biotechnol 1998, 14:301-304.
• [38]Percival Zhang YH, Himmel ME, Mielenz JR: Outlook for cellulase improvement: screening and selection strategies. Biotechnol Adv 2006, 24(5):452-481.
• [39]Koyama M, Helbert W, Imai T, Sugiyama J, Henrissat B: Parallel-up structure evidences the molecular directionality during biosynthesis of bacterial cellulose. Proc Natl Acad Sci U S A 1997, 94(17):9091-9095.
• [40]Gillespie DT: A rigorous derivation of the chemical master equation. Physica A 1992, 188:404-425.
• [41]Claeyssens M, van Tilbeurgh H, Kamerling JP, Berg J, Vrsanska M, Biely P: Studies of the cellulolytic system of the filamentous fungus Trichoderma reesei QM 9414. Substrate specificity and transfer activity of endoglucanase I. Biochem J 1990, 270(1):251-256.
• [42]Biely P, VršAnskÁ M, Claeyssens M: The endo-1,4-β-glucanase I from Trichoderma reesei. Eur J Biochem 1991, 200(1):157-163.
• [43]Divne C, Stahlberg J, Reinikainen T, Ruohonen L, Pettersson G, Knowles JK, Teeri TT, Jones TA: The three-dimensional crystal structure of the catalytic core of cellobiohydrolase I from Trichoderma reesei. Science 1994, 265(5171):524-528.
• [44]Barr BK, Hsieh YL, Ganem B, Wilson DB: Identification of two functionally different classes of exocellulases. Biochemistry 1996, 35(2):586-592.
• [45]Igarashi K, Koivula A, Wada M, Kimura S, Penttila M, Samejima M: High speed atomic force microscopy visualizes processive movement of Trichoderma reesei cellobiohydrolase I on crystalline cellulose. J Biol Chem 2009, 284(52):36186-36190.
• [46]Gillespie DT: A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions. J Comput Phys 1976, 22:403-434.
• [47]Gillespie DT: Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977, 81(25):2340-2361.
• [48]Tomme P, Van Tilbeurgh H, Pettersson G, Van Damme J, Vandekerckhove J, Knowles J, Teeri T, Claeyssens M: Studies of the cellulolytic system of Trichoderma reesei QM 9414. Analysis of domain function in two cellobiohydrolases by limited proteolysis. Eur J Biochem 1988, 170(3):575-581.
• [49]Gaffney KJ, Davis PH, Piletic IR, Levinger NE, Fayer MD: Hydrogen Bond Dissociation and Reformation in Methanol Oligomers Following Hydroxyl Stretch Relaxation. J Phys Chem A 2002, 106(50):12012-12023.
• [50]Eriksson T, Karlsson J, Tjerneld F: A model explaining declining rate in hydrolysis of lignocellulose substrates with cellobiohydrolase I (cel7A) and endoglucanase I (cel7B) of Trichoderma reesei. Appl Biochem Biotechnol 2002, 101(1):41-60.
• [51]Valjamae P, Sild V, Nutt A, Pettersson G, Johansson G: Acid hydrolysis of bacterial cellulose reveals different modes of synergistic action between cellobiohydrolase I and endoglucanase I. Eur J Biochem 1999, 266(2):327-334.
• [52]Sizova MV, Izquierdo JA, Panikov NS, Lynd LR: Cellulose- and xylan-degrading thermophilic anaerobic bacteria from biocompost. Appl Environ Microbiol 2011, 77(7):2282-2291.
• [53]Jervis EJ, Haynes CA, Kilburn DG: Surface diffusion of cellulases and their isolated binding domains on cellulose. J Biol Chem 1997, 272(38):24016-24023.
• [54]Nidetzky B, Steiner W, Claeyssens M: Cellulose hydrolysis by the cellulases from Trichoderma reesei: adsorptions of two cellobiohydrolases, two endocellulases and their core proteins on filter paper and their relation to hydrolysis. Biochem J 1994, 303(Pt 3):817-823.
• [55]Linder M, Teeri TT: The cellulose-binding domain of the major cellobiohydrolase of Trichoderma reesei exhibits true reversibility and a high exchange rate on crystalline cellulose. Proc Natl Acad Sci U S A 1996, 93(22):12251-12255.
• [56]Boraston A: The interaction of carbohydrate-binding modules with insoluble non-crystalline cellulose is enthalpically driven. Biochem J 2005, 385:479-484.
• [57]Nidetzky B, Steiner W, Hayn M, Claeyssens M: Cellulose hydrolysis by the cellulases from Trichoderma reesei: a new model for synergistic interaction. Biochem J 1994, 298(Pt 3):705-710.