1
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Kumar R, Bhagia S, Mittal A, Wyman CE. Effect of cellulose reducing ends and primary hydroxyl groups modifications on cellulose-cellulase interactions and cellulose hydrolysis. Biotechnol Bioeng 2024; 121:2793-2807. [PMID: 38853638 DOI: 10.1002/bit.28774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/02/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
Cellulose reducing ends are believed to play a vital role in the cellulose recalcitrance to enzymatic conversion. However, their role in insoluble cellulose accessibility and hydrolysis is not clear. Thus, in this study, reducing ends of insoluble cellulose derived from various sources were modified by applying reducing and/or oxidizing agents. The effects of cellulose reducing ends modification on cellulose reducing ends, cellulose structure, and cellulose accessibility to cellulase were evaluated along with the impact on cellulose hydrolysis with complete as well purified cellulase components. Sodium borohydride (NaBH4) reduction and sodium chlorite-acetic acid (SC/AA) oxidation were able to modify more than 90% and 60% of the reducing ends, respectively, while the bicinchoninic acid (BCA) reagent applied for various cycles oxidized cellulose reducing ends to various extents. X-ray diffractograms of the treated solids showed that these treatments did not change the cellulose crystalline structure and the change in crystallinity index was insignificant. Surprisingly, it was found that the cellulose reducing ends modification, either through selective NaBH4 reduction or BCA oxidation, had a negligible impact on cellulose accessibility as well on cellulose hydrolysis rates or final conversions with complete cellulase at loadings as low as 0.5 mg protein/g cellulose. In fact, in contrast to what is traditionally believed, modifications of cellulose reducing ends by these two methods had no apparent impact on cellulose conversion with purified cellulase components and their synergy. However, SC/AA oxidation resulted in significant drop in cellulose conversion (10%-50%) with complete as well purified cellulase components. Nonetheless, further research revealed that the cause for drop in cellulose conversion for the SC/AA oxidation case was due to primary hydroxyl groups (PHGs) oxidation and not the oxidation of reducing ends. Furthermore, it was found that the PHGs modification affects cellulose accessibility and slows the cellulase uptake as well resulting in significant drop in cellulose conversions.
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Affiliation(s)
- Rajeev Kumar
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California Riverside, Riverside, California, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, Tennessee, USA
| | - Samarthya Bhagia
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California Riverside, Riverside, California, USA
- Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, Tennessee, USA
| | - Ashutosh Mittal
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory (NREL), Golden, Colorado, USA
| | - Charles E Wyman
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California Riverside, Riverside, California, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, Tennessee, USA
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, California, USA
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2
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Li P, Wang X, Zhang C, Xu D. Processive binding mechanism of Cel9G from Clostridium cellulovorans: molecular dynamics and free energy landscape investigations. Phys Chem Chem Phys 2023; 25:646-657. [DOI: 10.1039/d2cp04830b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The processive binding mechanism of cellulose by Cel9G from C. cellulovorans was investigated by MD and metadynamics simulations.
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Affiliation(s)
- Penghui Li
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Chunchun Zhang
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
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3
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Dodda SR, Hossain M, Jain P, Aikat K, Mukhopadhyay SS. Comparative Biochemical and Structural Properties of an Industrially Important Biocatalyst Cellobiohydrolase Cel7A from Thermophilic Aspergillus fumigatus. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822050064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Zajki-Zechmeister K, Eibinger M, Nidetzky B. Enzyme Synergy in Transient Clusters of Endo- and Exocellulase Enables a Multilayer Mode of Processive Depolymerization of Cellulose. ACS Catal 2022; 12:10984-10994. [PMID: 36082050 PMCID: PMC9442579 DOI: 10.1021/acscatal.2c02377] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/12/2022] [Indexed: 11/29/2022]
Abstract
Biological degradation of cellulosic materials relies on the molecular-mechanistic principle that internally chain-cleaving endocellulases work synergistically with chain end-cleaving exocellulases in polysaccharide chain depolymerization. How endo-exo synergy becomes effective in the deconstruction of a solid substrate that presents cellulose chains assembled into crystalline material is an open question of the mechanism, with immediate implications on the bioconversion efficiency of cellulases. Here, based on single-molecule evidence from real-time atomic force microscopy, we discover that endo- and exocellulases engage in the formation of transient clusters of typically three to four enzymes at the cellulose surface. The clusters form specifically at regular domains of crystalline cellulose microfibrils that feature molecular defects in the polysaccharide chain organization. The dynamics of cluster formation correlates with substrate degradation through a multilayer-processive mode of chain depolymerization, overall leading to the directed ablation of single microfibrils from the cellulose surface. Each multilayer-processive step involves the spatiotemporally coordinated and mechanistically concerted activity of the endo- and exocellulases in close proximity. Mechanistically, the cooperativity with the endocellulase enables the exocellulase to pass through its processive cycles ∼100-fold faster than when acting alone. Our results suggest an advanced paradigm of efficient multienzymatic degradation of structurally organized polymer materials by endo-exo synergetic chain depolymerization.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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5
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Schaller KS, Molina GA, Kari J, Schiano-di-Cola C, Sørensen TH, Borch K, Peters GH, Westh P. Virtual Bioprospecting of Interfacial Enzymes: Relating Sequence and Kinetics. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kay S. Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
- Department of Chemistry, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | - Gustavo Avelar Molina
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Corinna Schiano-di-Cola
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | | | - Kim Borch
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
| | - Günther H.J. Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
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6
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Degradation of Lignocelluloses Cocoa Shell (Theobroma cacao L.) by Various Types of Mould Treatments. J FOOD QUALITY 2021. [DOI: 10.1155/2021/6127029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lignocellulose can be degraded by lignocellulolytic microorganisms such as moulds. The purpose of the study was to obtain the right type of moulds in degrading lignocellulose on the cocoa shell powder. The study used a completely randomized design method using four treatments of different types of mould (Trichoderma viride, Neurospora sitophila, Aspergillus niger, and Rhizopus oryzae) towards cocoa shell powder fermentation. Solid fermentation of cocoa shell powder was carried out for 5 days in an incubator with a temperature of 30°C for T. viride, N. sitophila, and R. oryzae, while A. niger of 35°C. The fermented substrate was then dried in a cabinet oven with a temperature of 50°C for 4 days. Tests of lignin, cellulose, and hemicellulose were performed towards the treatments by the Chesson method, while the moisture content test was performed using the AOAC method. Degradation of fermented cocoa shell powder has shown a significant effect on moisture, lignin, cellulose, and hemicellulose contents. Trichoderma viride resulted in the highest lignocellulose degradation compared with the other treatments. The percentage decrease of lignin content is up to 46.69 wt%; while cellulose of 22.59 wt%; and hemicellulose is about 19.41 wt% from the initial lignin weight.
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7
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Zajki-Zechmeister K, Kaira GS, Eibinger M, Seelich K, Nidetzky B. Processive Enzymes Kept on a Leash: How Cellulase Activity in Multienzyme Complexes Directs Nanoscale Deconstruction of Cellulose. ACS Catal 2021; 11:13530-13542. [PMID: 34777910 PMCID: PMC8576811 DOI: 10.1021/acscatal.1c03465] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/11/2021] [Indexed: 12/15/2022]
Abstract
Biological deconstruction of polymer materials gains efficiency from the spatiotemporally coordinated action of enzymes with synergetic function in polymer chain depolymerization. To perpetuate enzyme synergy on a solid substrate undergoing deconstruction, the overall attack must alternate between focusing the individual enzymes locally and dissipating them again to other surface sites. Natural cellulases working as multienzyme complexes assembled on a scaffold protein (the cellulosome) maximize the effect of local concentration yet restrain the dispersion of individual enzymes. Here, with evidence from real-time atomic force microscopy to track nanoscale deconstruction of single cellulose fibers, we show that the cellulosome forces the fiber degradation into the transversal direction, to produce smaller fragments from multiple local attacks ("cuts"). Noncomplexed enzymes, as in fungal cellulases or obtained by dissociating the cellulosome, release the confining force so that fiber degradation proceeds laterally, observed as directed ablation of surface fibrils and leading to whole fiber "thinning". Processive cellulases that are enabled to freely disperse evoke the lateral degradation and determine its efficiency. Our results suggest that among natural cellulases, the dispersed enzymes are more generally and globally effective in depolymerization, while the cellulosome represents a specialized, fiber-fragmenting machinery.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Gaurav Singh Kaira
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Klara Seelich
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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8
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Araújo EA, Dias AHS, Kadowaki MAS, Piyadov V, Pellegrini VOA, Urio MB, Ramos LP, Skaf MS, Polikarpov I. Impact of cellulose properties on enzymatic degradation by bacterial GH48 enzymes: Structural and mechanistic insights from processive Bacillus licheniformis Cel48B cellulase. Carbohydr Polym 2021; 264:118059. [PMID: 33910709 DOI: 10.1016/j.carbpol.2021.118059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 11/29/2022]
Abstract
Processive cellulases are highly efficient molecular engines involved in the cellulose breakdown process. However, the mechanism that processive bacterial enzymes utilize to recruit and retain cellulose strands in the catalytic site remains poorly understood. Here, integrated enzymatic assays, protein crystallography and computational approaches were combined to study the enzymatic properties of the processive BlCel48B cellulase from Bacillus licheniformis. Hydrolytic efficiency, substrate binding affinity, cleavage patterns, and the apparent processivity of bacterial BlCel48B are significantly impacted by the cellulose size and its surface morphology. BlCel48B crystallographic structure was solved with ligands spanning -5 to -2 and +1 to +2 subsites. Statistical coupling analysis and molecular dynamics show that co-evolved residues on active site are critical for stabilizing ligands in the catalytic tunnel. Our results provide mechanistic insights into BlCel48B molecular-level determinants of activity, substrate binding, and processivity on insoluble cellulose, thus shedding light on structure-activity correlations of GH48 family members in general.
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Affiliation(s)
- Evandro A Araújo
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil; Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials, Campinas 13083-970, São Paulo, Brazil
| | - Artur Hermano Sampaio Dias
- Institute of Chemistry and Center for Computer in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, São Paulo, Brazil
| | - Marco A S Kadowaki
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil
| | - Vasily Piyadov
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil
| | - Vanessa O A Pellegrini
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil
| | - Mateus B Urio
- Graduate Programs in Bioenergy, Chemistry and Chemical Engineering, Federal University of Paraná (UFPR), Curitiba 81531-980, Paraná, Brazil
| | - Luiz P Ramos
- Graduate Programs in Bioenergy, Chemistry and Chemical Engineering, Federal University of Paraná (UFPR), Curitiba 81531-980, Paraná, Brazil
| | - Munir S Skaf
- Institute of Chemistry and Center for Computer in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, São Paulo, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil.
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9
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Kari J, Molina GA, Schaller KS, Schiano-di-Cola C, Christensen SJ, Badino SF, Sørensen TH, Røjel NS, Keller MB, Sørensen NR, Kolaczkowski B, Olsen JP, Krogh KBRM, Jensen K, Cavaleiro AM, Peters GHJ, Spodsberg N, Borch K, Westh P. Physical constraints and functional plasticity of cellulases. Nat Commun 2021; 12:3847. [PMID: 34158485 PMCID: PMC8219668 DOI: 10.1038/s41467-021-24075-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
Enzyme reactions, both in Nature and technical applications, commonly occur at the interface of immiscible phases. Nevertheless, stringent descriptions of interfacial enzyme catalysis remain sparse, and this is partly due to a shortage of coherent experimental data to guide and assess such work. In this work, we produced and kinetically characterized 83 cellulases, which revealed a conspicuous linear free energy relationship (LFER) between the substrate binding strength and the activation barrier. The scaling occurred despite the investigated enzymes being structurally and mechanistically diverse. We suggest that the scaling reflects basic physical restrictions of the hydrolytic process and that evolutionary selection has condensed cellulase phenotypes near the line. One consequence of the LFER is that the activity of a cellulase can be estimated from its substrate binding strength, irrespectively of structural and mechanistic details, and this appears promising for in silico selection and design within this industrially important group of enzymes.
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Affiliation(s)
- Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gustavo A Molina
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kay S Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Corinna Schiano-di-Cola
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stefan J Christensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Silke F Badino
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Nanna S Røjel
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | - Malene B Keller
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg C, Denmark
| | - Nanna Rolsted Sørensen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | - Bartlomiej Kolaczkowski
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | | | | | | | | | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
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10
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Heise K, Delepierre G, King AWT, Kostiainen MA, Zoppe J, Weder C, Kontturi E. Chemical Modification of Reducing End-Groups in Cellulose Nanocrystals. Angew Chem Int Ed Engl 2021; 60:66-87. [PMID: 32329947 PMCID: PMC7821002 DOI: 10.1002/anie.202002433] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Indexed: 12/31/2022]
Abstract
Native plant cellulose has an intrinsic supramolecular structure. Consequently, it can be isolated as nanocellulose species, which can be utilized as building blocks for renewable nanomaterials. The structure of cellulose also permits its end-wise modification, i.e., chemical reactions exclusively on one end of a cellulose chain or a nanocellulose particle. The premises for end-wise modification have been known for decades. Nevertheless, different approaches for the reactions have emerged only recently, because of formidable synthetic and analytical challenges associated with the issue, including the adverse reactivity of the cellulose reducing end and the low abundance of newly introduced functionalities. This Review gives a full account of the scientific underpinnings and challenges related to end-wise modification of cellulose nanocrystals. Furthermore, we present how the chemical modification of cellulose nanocrystal ends may be applied to directed assembly, resulting in numerous possibilities for the construction of new materials, such as responsive liquid crystal templates and composites with tailored interactions.
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Affiliation(s)
- Katja Heise
- Department of Bioproducts and BiosystemsAalto UniversityP.O. Box 16300FI-00076 AaltoEspooFinland
| | - Gwendoline Delepierre
- Adolphe Merkle InstituteUniversité de FribourgChemin des Verdiers 4CH-1700FribourgSwitzerland
| | - Alistair W. T. King
- Materials Chemistry DivisionChemistry DepartmentUniversity of HelsinkiA.I. Virtasen aukio 1, P.O. Box 55FI-00014HelsinkiFinland
| | - Mauri A. Kostiainen
- Department of Bioproducts and BiosystemsAalto UniversityP.O. Box 16300FI-00076 AaltoEspooFinland
| | - Justin Zoppe
- Omya International AGBaslerstrasse 42CH-4665OftringenSwitzerland
| | - Christoph Weder
- Adolphe Merkle InstituteUniversité de FribourgChemin des Verdiers 4CH-1700FribourgSwitzerland
| | - Eero Kontturi
- Department of Bioproducts and BiosystemsAalto UniversityP.O. Box 16300FI-00076 AaltoEspooFinland
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11
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Ogonda LA, Saumonneau A, Dion M, Muge EK, Wamalwa BM, Mulaa FJ, Tellier C. Characterization and engineering of two new GH9 and GH48 cellulases from a Bacillus pumilus isolated from Lake Bogoria. Biotechnol Lett 2021; 43:691-700. [PMID: 33386499 DOI: 10.1007/s10529-020-03056-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVES To search for new alkaliphilic cellulases and to improve their efficiency on crystalline cellulose through molecular engineering RESULTS: Two novel cellulases, BpGH9 and BpGH48, from a Bacillus pumilus strain were identified, cloned and biochemically characterized. BpGH9 is a modular endocellulase belonging to the glycoside hydrolase 9 family (GH9), which contains a catalytic module (GH) and a carbohydrate-binding module belonging to class 3 and subclass c (CBM3c). This enzyme is extremely tolerant to high alkali pH and remains significantly active at pH 10. BpGH48 is an exocellulase, belonging to the glycoside hydrolase 48 family (GH48) and acts on the reducing end of oligo-β1,4 glucanes. A truncated form of BpGH9 and a chimeric fusion with an additional CBM3a module was constructed. The deletion of the CBM3c module results in a significant decline in the catalytic activity. However, fusion of CBM3a, although in a non native position, enhanced the activity of BpGH9 on crystalline cellulose. CONCLUSIONS A new alkaliphilic endocellulase BpGH9, was cloned and engineered as a fusion protein (CBM3a-BpGH9), which led to an improved activity on crystalline cellulose.
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Affiliation(s)
- Lydia A Ogonda
- Université de Nantes, CNRS, UFIP, UMR6286, 2, rue de la Houssinière, 44322, Nantes, France.,Department of Biochemistry, School of Medicine, College of Health Sciences, University of Nairobi, P.O BOX 30197-00100, Nairobi, Kenya.,Department of Medical Biochemistry, School of Medicine, Masinde Muliro University of Science and Technology, P.O BOX 190-50100, Kakamega, Kenya
| | - Amélie Saumonneau
- Université de Nantes, CNRS, UFIP, UMR6286, 2, rue de la Houssinière, 44322, Nantes, France
| | - Michel Dion
- Université de Nantes, IRS2, 44000, Nantes, France
| | - Edward K Muge
- Department of Biochemistry, School of Medicine, College of Health Sciences, University of Nairobi, P.O BOX 30197-00100, Nairobi, Kenya
| | - Benson M Wamalwa
- Department of Chemistry, School of Physical Sciences, College of Biological and Physical Sciences, University of Nairobi, P.O BOX 30197-00100, Nairobi, Kenya
| | - Francis J Mulaa
- Department of Biochemistry, School of Medicine, College of Health Sciences, University of Nairobi, P.O BOX 30197-00100, Nairobi, Kenya
| | - Charles Tellier
- Université de Nantes, CNRS, UFIP, UMR6286, 2, rue de la Houssinière, 44322, Nantes, France.
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12
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Heise K, Delepierre G, King AWT, Kostiainen MA, Zoppe J, Weder C, Kontturi E. Chemische Modifizierung der reduzierenden Enden von Cellulosenanokristallen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Katja Heise
- Department of Bioproducts and Biosystems Aalto University P.O. Box 16300 FI-00076 Aalto Espoo Finnland
| | - Gwendoline Delepierre
- Adolphe Merkle Institute Université de Fribourg Chemin des Verdiers 4 CH-1700 Fribourg Schweiz
| | - Alistair W. T. King
- Materials Chemistry Division Chemistry Department University of Helsinki A.I. Virtasen aukio 1, P.O. Box 55 FI-00014 Helsinki Finnland
| | - Mauri A. Kostiainen
- Department of Bioproducts and Biosystems Aalto University P.O. Box 16300 FI-00076 Aalto Espoo Finnland
| | - Justin Zoppe
- Omya International AG Baslerstrasse 42 CH-4665 Oftringen Schweiz
| | - Christoph Weder
- Adolphe Merkle Institute Université de Fribourg Chemin des Verdiers 4 CH-1700 Fribourg Schweiz
| | - Eero Kontturi
- Department of Bioproducts and Biosystems Aalto University P.O. Box 16300 FI-00076 Aalto Espoo Finnland
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13
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Yang T, Guo Y, Gao N, Li X, Zhao J. Modification of a cellulase system by engineering Penicillium oxalicum to produce cellulose nanocrystal. Carbohydr Polym 2020; 234:115862. [DOI: 10.1016/j.carbpol.2020.115862] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 12/31/2022]
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14
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Ellis GA, Klein WP, Lasarte-Aragonés G, Thakur M, Walper SA, Medintz IL. Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02413] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - William P. Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20001, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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15
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Abstract
Cellulase enzymes deconstruct recalcitrant cellulose into soluble sugars, making them a biocatalyst of biotechnological interest for use in the nascent lignocellulosic bioeconomy. Cellobiohydrolases (CBHs) are cellulases capable of liberating many sugar molecules in a processive manner without dissociating from the substrate. Within the complete processive cycle of CBHs, dissociation from the cellulose substrate is rate limiting, but the molecular mechanism of this step is unknown. Here, we present a direct comparison of potential molecular mechanisms for dissociation via Hamiltonian replica exchange molecular dynamics of the model fungal CBH, Trichoderma reesei Cel7A. Computational rate estimates indicate that stepwise cellulose dethreading from the binding tunnel is 4 orders of magnitude faster than a clamshell mechanism, in which the substrate-enclosing loops open and release the substrate without reversing. We also present the crystal structure of a disulfide variant that covalently links substrate-enclosing loops on either side of the substrate-binding tunnel, which constitutes a CBH that can only dissociate via stepwise dethreading. Biochemical measurements indicate that this variant has a dissociation rate constant essentially equivalent to the wild type, implying that dethreading is likely the predominant mechanism for dissociation.
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16
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Wang R, Xu D. Molecular dynamics investigations of oligosaccharides recognized by family 16 and 22 carbohydrate binding modules. Phys Chem Chem Phys 2019; 21:21485-21496. [PMID: 31535114 DOI: 10.1039/c9cp04673a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
As a non-catalytic domain, carbohydrate binding modules (CBMs) are often considered to play some key roles in the degradation and recognition of polysaccharides catalyzed by cellulases. In this work, we investigated the recognition dynamics of cello- or xylo-saccharides by two typical CBMs (CBM16-1 and CBM22-2), which are grouped into Type B CBMs. By combining extensive molecular dynamics, principle component analysis, and binding free energy calculations, we constructed several complex models of the two CBMs in both complex cello- and xylo-oligosaccharides. The corresponding substrate recognition affinity and critical residues having significant contributions were systematically investigated. The residues containing aromatic side chain groups were shown to contribute significantly to substrate binding. The calculated binding free energies were in fairly good agreement with the experimental measurements with the absolute mean error of 0.69 kcal mol-1. The overall electrostatic interactions were shown to have negative effects on substrate recognition. Further metadynamics simulations revealed the substrate dissociation process.
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Affiliation(s)
- Ruihan Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China.
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China. and Research Center for Materials Genome Engineering, Sichuan University, Chengdu, Sichuan 610065, P. R. China
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17
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Kari J, Christensen SJ, Andersen M, Baiget SS, Borch K, Westh P. A practical approach to steady-state kinetic analysis of cellulases acting on their natural insoluble substrate. Anal Biochem 2019; 586:113411. [PMID: 31520594 DOI: 10.1016/j.ab.2019.113411] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 10/26/2022]
Abstract
Measurement of steady-state rates (vSS) is straightforward in standard enzymology with soluble substrate, and it has been instrumental for comparative biochemical analyses within this area. For insoluble substrate, however, experimental values of vss remain controversial, and this has strongly limited the amount and quality of comparative analyses for cellulases and other enzymes that act on the surface of an insoluble substrate. In the current work, we have measured progress curves over a wide range of conditions for two cellulases, TrCel6A and TrCel7A from Trichoderma reesei, acting on their natural, insoluble substrate, cellulose. Based on this, we consider practical compromises for the determination of experimental vSS values, and propose a basic protocol that provides representative reaction rates and is experimentally simple so that larger groups of enzymes and conditions can be readily assayed with standard laboratory equipment. We surmise that the suggested experimental approach can be useful in comparative biochemical studies of cellulases; an area that remains poorly developed.
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Affiliation(s)
- Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800, Kgs. Lyngby, Denmark
| | - Stefan Jarl Christensen
- Department of Science and Environment, Roskilde University, Universitetsvej, Build. 28.C, DK-4000, Roskilde, Denmark
| | - Morten Andersen
- Department of Science and Environment, Roskilde University, Universitetsvej, Build. 28.C, DK-4000, Roskilde, Denmark
| | | | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800, Kgs. Lyngby, Denmark.
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18
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Processivity and the Mechanisms of Processive Endoglucanases. Appl Biochem Biotechnol 2019; 190:448-463. [DOI: 10.1007/s12010-019-03096-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/18/2019] [Indexed: 11/26/2022]
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19
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Petrášek Z, Eibinger M, Nidetzky B. Modeling the activity burst in the initial phase of cellulose hydrolysis by the processive cellobiohydrolase Cel7A. Biotechnol Bioeng 2019; 116:515-525. [PMID: 30515756 PMCID: PMC6590443 DOI: 10.1002/bit.26889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/16/2018] [Accepted: 11/29/2018] [Indexed: 01/05/2023]
Abstract
The hydrolysis of cellulose by processive cellulases, such as exocellulase TrCel7A from Trichoderma reesei, is typically characterized by an initial burst of high activity followed by a slowdown, often leading to incomplete hydrolysis of the substrate. The origins of these limitations to cellulose hydrolysis are not yet fully understood. Here, we propose a new model for the initial phase of cellulose hydrolysis by processive cellulases, incorporating a bound but inactive enzyme state. The model, based on ordinary differential equations, accurately reproduces the activity burst and the subsequent slowdown of the cellulose hydrolysis and describes the experimental data equally well or better than the previously suggested model. We also derive steady‐state expressions that can be used to describe the pseudo‐steady state reached after the initial activity burst. Importantly, we show that the new model predicts the existence of an optimal enzyme‐substrate affinity at which the pseudo‐steady state hydrolysis rate is maximized. The model further allows the calculation of glucose production rate from the first cut in the processive run and reproduces the second activity burst commonly observed upon new enzyme addition. These results are expected to be applicable also to other processive enzymes.
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Affiliation(s)
- Zdeneˇk Petrášek
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Manuel Eibinger
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria.,Austrian Centre of Industrial Biotechnology, Graz, Austria
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20
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21
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Rabinovich ML, Melnik MS, Herner ML, Voznyi YV, Vasilchenko LG. Predominant Nonproductive Substrate Binding by Fungal Cellobiohydrolase I and Implications for Activity Improvement. Biotechnol J 2018; 14:e1700712. [PMID: 29781240 DOI: 10.1002/biot.201700712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/08/2018] [Indexed: 12/20/2022]
Abstract
Enzymatic conversion of the most abundant renewable source of organic compounds, cellulose to fermentable sugars is attractive for production of green fuels and chemicals. The major component of industrial enzyme systems, cellobiohydrolase I from Hypocrea jecorina (Trichoderma reesei) (HjCel7A) processively splits disaccharide units from the reducing ends of tightly packed cellulose chains. HjCel7A consists of a catalytic domain (CD) and a carbohydrate-binding module (CBM) separated by a linker peptide. A tunnel-shaped substrate-binding site in the CD includes nine subsites for β-d-glucose units, seven of which (-7 to -1) precede the catalytic center. Low catalytic activity of Cel7A is the bottleneck and the primary target for improvement. Here it is shown for the first time that, in spite of much lower apparent kcat of HjCel7A at the hydrolysis of β-1,4-glucosidic linkages in the fluorogenic cellotetra- and -pentaose compared to the structurally related endoglucanase I (HjCel7B), the specificity constants (catalytic efficiency) kcat /Km for both enzymes are almost equal in these reactions. The observed activity difference appears from strong nonproductive substrate binding by HjCel7A, particularly significant for MU-β-cellotetraose (MUG4 ). Interaction of substrates with the subsites -6 and -5 proximal to the nonconserved Gln101 residue in HjCel7A decreases Km,ap by >1500 times. HjCel7A can be nonproductively bound onto cellulose surface with Kd ≈2-9 nM via CBM and CD that captures six terminal glucose units of cellulose chain. Decomposition of this nonproductive complex can determine the rate of cellulose conversion. MUG4 is a promising substrate to select active cellobiohydrolase I variants with reduced nonproductive substrate binding.
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Affiliation(s)
- Mikhail L Rabinovich
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Maria S Melnik
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Mikhail L Herner
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Yakov V Voznyi
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
| | - Lilia G Vasilchenko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
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22
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Zhai R, Hu J, Saddler JN. The inhibition of hemicellulosic sugars on cellulose hydrolysis are highly dependant on the cellulase productive binding, processivity, and substrate surface charges. BIORESOURCE TECHNOLOGY 2018; 258:79-87. [PMID: 29524690 DOI: 10.1016/j.biortech.2017.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 12/02/2017] [Accepted: 12/04/2017] [Indexed: 05/24/2023]
Abstract
In this study, the influence of major hemicellulosic sugars (mannose and xylose) on cellulose hydrolysis and major enzyme activities were evaluated by using both commercial enzyme cocktail and purified cellulase monocomponents over a "library" of cellulosic substrates. Surprisingly, the results showed that unlike glucose, mannose/xylose did not inhibit individual cellulase activities but significantly decreased their hydrolytic performance on cellulose substrates. When various enzyme-substrate interactions (e.g. adsorption/desorption, productive binding, and processive moving) were evaluated, it appeared that these hemicellulosic sugars significantly reduced the productive binding and processivity of Cel7A, which in turn limited cellulase hydrolytic efficacy. Among a range of major cellulose characteristics (e.g. crystallinity, degree of polymerization, accessibility, and surface charges), the acid group content of the cellulosic substrates seemed to be the main driver that determined the extent of hemicellulosic sugar inhibition. Our results provided new insights for better understanding the sugar inhibition mechanisms of cellulose hydrolysis.
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Affiliation(s)
- Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China; Forest Products Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada
| | - Jinguang Hu
- Forest Products Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada.
| | - Jack N Saddler
- Forest Products Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada
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23
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Enzymatic synthesis of fructooligosaccharides from sucrose by endo-inulinase-catalyzed transfructosylation reaction in biphasic systems. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Kari J, Kont R, Borch K, Buskov S, Olsen JP, Cruyz-Bagger N, Väljamäe P, Westh P. Anomeric Selectivity and Product Profile of a Processive Cellulase. Biochemistry 2016; 56:167-178. [PMID: 28026938 DOI: 10.1021/acs.biochem.6b00636] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cellobiohydrolases (CBHs) make up an important group of enzymes for both natural carbon cycling and industrial deconstruction of lignocellulosic biomass. The consecutive hydrolysis of one cellulose strand relies on an intricate pattern of enzyme-substrate interactions in the long, tunnel-shaped binding site of the CBH. In this work, we have investigated the initial complexation mode with cellulose of the most thoroughly studied CBH, Cel7A from Hypocrea jecorina (HjCel7A). We found that HjCel7A predominantly produces glucose when it initiates a processive run on insoluble microcrystalline cellulose, confirming the validity of an even and odd product ratio as an estimate of processivity. Moreover, the glucose released from cellulose was predominantly α-glucose. A link between the initial binding mode of the enzyme and the reducing end configuration was investigated by inhibition studies with the two anomers of cellobiose. A clear preference for β-cellobiose in product binding site +2 was observed for HjCel7A, but not the homologous endoglucanase, HjCe7B. Possible relationships between this anomeric preference in the product site and the prevalence of odd-numbered initial-cut products are discussed, and a correlation between processivity and anomer selectivity is proposed.
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Affiliation(s)
- Jeppe Kari
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
| | - Riin Kont
- Institute of Molecular and Cell Biology, University of Tartu , Tartu, Estonia
| | - Kim Borch
- Novozymes A/S , Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Steen Buskov
- Novozymes A/S , Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Johan Pelck Olsen
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
| | | | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu , Tartu, Estonia
| | - Peter Westh
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
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25
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Kont R, Kari J, Borch K, Westh P, Väljamäe P. Inter-domain Synergism Is Required for Efficient Feeding of Cellulose Chain into Active Site of Cellobiohydrolase Cel7A. J Biol Chem 2016; 291:26013-26023. [PMID: 27780868 DOI: 10.1074/jbc.m116.756007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/21/2016] [Indexed: 01/27/2023] Open
Abstract
Structural polysaccharides like cellulose and chitin are abundant and their enzymatic degradation to soluble sugars is an important route in green chemistry. Processive glycoside hydrolases (GHs), like cellobiohydrolase Cel7A of Trichoderma reesei (TrCel7A) are key components of efficient enzyme systems. TrCel7A consists of a catalytic domain (CD) and a smaller carbohydrate-binding module (CBM) connected through the glycosylated linker peptide. A tunnel-shaped active site rests in the CD and contains 10 glucose unit binding sites. The active site of TrCel7A is lined with four Trp residues with two of them, Trp-40 and Trp-38, in the substrate binding sites near the tunnel entrance. Although addressed in numerous studies the elucidation of the role of CBM and active site aromatics has been obscured by a complex multistep mechanism of processive GHs. Here we studied the role of the CBM-linker and Trp-38 of TrCel7A with respect to binding affinity, on- and off-rates, processivity, and synergism with endoglucanase. The CBM-linker increased the on-rate and substrate affinity of the enzyme. The Trp-38 to Ala substitution resulted in increased off-rates and decreased processivity. The effect of the Trp-38 to Ala substitution on on-rates was strongly dependent on the presence of the CBM-linker. This compensation between CBM-linker and Trp-38 indicates synergism between CBM-linker and CD in feeding the cellulose chain into the active site. The inter-domain synergism was pre-requisite for the efficient degradation of cellulose in the presence of endoglucanase.
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Affiliation(s)
- Riin Kont
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Jeppe Kari
- the Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark, and
| | - Kim Borch
- Novozymes A/S, Bagsværd DK-2880, Denmark
| | - Peter Westh
- the Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark, and
| | - Priit Väljamäe
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia,
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26
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Nakamura A, Tasaki T, Ishiwata D, Yamamoto M, Okuni Y, Visootsat A, Maximilien M, Noji H, Uchiyama T, Samejima M, Igarashi K, Iino R. Single-molecule Imaging Analysis of Binding, Processive Movement, and Dissociation of Cellobiohydrolase Trichoderma reesei Cel6A and Its Domains on Crystalline Cellulose. J Biol Chem 2016; 291:22404-22413. [PMID: 27609516 DOI: 10.1074/jbc.m116.752048] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 08/24/2016] [Indexed: 11/06/2022] Open
Abstract
Trichoderma reesei Cel6A (TrCel6A) is a cellobiohydrolase that hydrolyzes crystalline cellulose into cellobiose. Here we directly observed the reaction cycle (binding, surface movement, and dissociation) of single-molecule intact TrCel6A, isolated catalytic domain (CD), cellulose-binding module (CBM), and CBM and linker (CBM-linker) on crystalline cellulose Iα The CBM-linker showed a binding rate constant almost half that of intact TrCel6A, whereas those of the CD and CBM were only one-tenth of intact TrCel6A. These results indicate that the glycosylated linker region largely contributes to initial binding on crystalline cellulose. After binding, all samples showed slow and fast dissociations, likely caused by the two different bound states due to the heterogeneity of cellulose surface. The CBM showed much higher specificity to the high affinity site than to the low affinity site, whereas the CD did not, suggesting that the CBM leads the CD to the hydrophobic surface of crystalline cellulose. On the cellulose surface, intact molecules showed slow processive movements (8.8 ± 5.5 nm/s) and fast diffusional movements (30-40 nm/s), whereas the CBM-Linker, CD, and a catalytically inactive full-length mutant showed only fast diffusional movements. These results suggest that both direct binding and surface diffusion contribute to searching of the hydrolysable point of cellulose chains. The duration time constant for the processive movement was 7.7 s, and processivity was estimated as 68 ± 42. Our results reveal the role of each domain in the elementary steps of the reaction cycle and provide the first direct evidence of the processive movement of TrCel6A on crystalline cellulose.
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Affiliation(s)
- Akihiko Nakamura
- From the Okazaki Institute for Integrative Bioscience and.,the Department of Functional Molecular Science, School of Physical Sciences, Graduate University for Advanced Studies (SOKENDAI), Kanagawa 240-0193, Japan
| | - Tomoyuki Tasaki
- the Department of Applied Chemistry, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Daiki Ishiwata
- From the Okazaki Institute for Integrative Bioscience and
| | | | - Yasuko Okuni
- From the Okazaki Institute for Integrative Bioscience and
| | - Akasit Visootsat
- the Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Morice Maximilien
- the National Chemical Engineering Institute in Paris, Paris 75005, France
| | - Hiroyuki Noji
- the Department of Applied Chemistry, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Taku Uchiyama
- the Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan, and
| | - Masahiro Samejima
- the Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan, and
| | - Kiyohiko Igarashi
- the Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan, and.,the VTT Technical Research Centre of Finland, Espoo FI-02044 VTT, Finland
| | - Ryota Iino
- From the Okazaki Institute for Integrative Bioscience and .,the Department of Functional Molecular Science, School of Physical Sciences, Graduate University for Advanced Studies (SOKENDAI), Kanagawa 240-0193, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Aichi 444-8787, Japan
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27
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Kurašin M, Kuusk S, Kuusk P, Sørlie M, Väljamäe P. Slow Off-rates and Strong Product Binding Are Required for Processivity and Efficient Degradation of Recalcitrant Chitin by Family 18 Chitinases. J Biol Chem 2015; 290:29074-85. [PMID: 26468285 DOI: 10.1074/jbc.m115.684977] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Indexed: 12/18/2022] Open
Abstract
Processive glycoside hydrolases are the key components of enzymatic machineries that decompose recalcitrant polysaccharides, such as chitin and cellulose. The intrinsic processivity (P(Intr)) of cellulases has been shown to be governed by the rate constant of dissociation from polymer chain (koff). However, the reported koff values of cellulases are strongly dependent on the method used for their measurement. Here, we developed a new method for determining koff, based on measuring the exchange rate of the enzyme between a non-labeled and a (14)C-labeled polymeric substrate. The method was applied to the study of the processive chitinase ChiA from Serratia marcescens. In parallel, ChiA variants with weaker binding of the N-acetylglucosamine unit either in substrate-binding site -3 (ChiA-W167A) or the product-binding site +1 (ChiA-W275A) were studied. Both ChiA variants showed increased off-rates and lower apparent processivity on α-chitin. The rate of the production of insoluble reducing groups on the reduced α-chitin was an order of magnitude higher than koff, suggesting that the enzyme can initiate several processive runs without leaving the substrate. On crystalline chitin, the general activity of the wild type enzyme was higher, and the difference was magnifying with hydrolysis time. On amorphous chitin, the variants clearly outperformed the wild type. A model is proposed whereby strong interactions with polymer in the substrate-binding sites (low off-rates) and strong binding of the product in the product-binding sites (high pushing potential) are required for the removal of obstacles, like disintegration of chitin microfibrils.
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Affiliation(s)
| | - Silja Kuusk
- From the Institutes of Molecular and Cell Biology and
| | - Piret Kuusk
- Physics, University of Tartu, 51010 Tartu, Estonia and
| | - Morten Sørlie
- the Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås 1432, Norway
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28
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Hamid SBA, Islam MM, Das R. Cellulase biocatalysis: key influencing factors and mode of action. CELLULOSE 2015; 22:2157-2182. [DOI: 10.1007/s10570-015-0672-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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29
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Sørensen TH, Cruys-Bagger N, Borch K, Westh P. Free Energy Diagram for the Heterogeneous Enzymatic Hydrolysis of Glycosidic Bonds in Cellulose. J Biol Chem 2015; 290:22203-11. [PMID: 26183776 DOI: 10.1074/jbc.m115.659656] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 01/25/2023] Open
Abstract
Kinetic and thermodynamic data have been analyzed according to transition state theory and a simplified reaction scheme for the enzymatic hydrolysis of insoluble cellulose. For the cellobiohydrolase Cel7A from Hypocrea jecorina (Trichoderma reesei), we were able to measure or collect relevant values for all stable and activated complexes defined by the reaction scheme and hence propose a free energy diagram for the full heterogeneous process. For other Cel7A enzymes, including variants with and without carbohydrate binding module (CBM), we obtained activation parameters for the association and dissociation of the enzyme-substrate complex. The results showed that the kinetics of enzyme-substrate association (i.e. formation of the Michaelis complex) was almost entirely entropy-controlled and that the activation entropy corresponded approximately to the loss of translational and rotational degrees of freedom of the dissolved enzyme. This implied that the transition state occurred early in the path where the enzyme has lost these degrees of freedom but not yet established extensive contact interactions in the binding tunnel. For dissociation, a similar analysis suggested that the transition state was late in the path where most enzyme-substrate contacts were broken. Activation enthalpies revealed that the rate of dissociation was far more temperature-sensitive than the rates of both association and the inner catalytic cycle. Comparisons of one- and two-domain variants showed that the CBM had no influence on the transition state for association but increased the free energy barrier for dissociation. Hence, the CBM appeared to promote the stability of the complex by delaying dissociation rather than accelerating association.
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Affiliation(s)
- Trine Holst Sørensen
- From Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and
| | - Nicolaj Cruys-Bagger
- From Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Peter Westh
- From Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and
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30
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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Kari J, Olsen J, Borch K, Cruys-Bagger N, Jensen K, Westh P. Kinetics of cellobiohydrolase (Cel7A) variants with lowered substrate affinity. J Biol Chem 2014; 289:32459-68. [PMID: 25271162 DOI: 10.1074/jbc.m114.604264] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases are exo-active glycosyl hydrolases that processively convert cellulose to soluble sugars, typically cellobiose. They effectively break down crystalline cellulose and make up a major component in industrial enzyme mixtures used for deconstruction of lignocellulosic biomass. Identification of the rate-limiting step for cellobiohydrolases remains controversial, and recent reports have alternately suggested either association (on-rate) or dissociation (off-rate) as the overall bottleneck. Obviously, this uncertainty hampers both fundamental mechanistic understanding and rational design of enzymes with improved industrial applicability. To elucidate the role of on- and off-rates, respectively, on the overall kinetics, we have expressed a variant in which a tryptophan residue (Trp-38) in the middle of the active tunnel has been replaced with an alanine. This mutation weakens complex formation, and the population of substrate-bound W38A was only about half of the wild type. Nevertheless, the maximal, steady-state rate was twice as high for the variant enzyme. It is argued that these opposite effects on binding and activity can be reconciled if the rate-limiting step is after the catalysis (i.e. in the dissociation process).
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Affiliation(s)
- Jeppe Kari
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
| | - Johan Olsen
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, Bagsværd DK-2880, Denmark
| | - Nicolaj Cruys-Bagger
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
| | - Kenneth Jensen
- Novozymes A/S, Krogshøjvej 36, Bagsværd DK-2880, Denmark
| | - Peter Westh
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
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Momeni MH, Goedegebuur F, Hansson H, Karkehabadi S, Askarieh G, Mitchinson C, Larenas EA, Ståhlberg J, Sandgren M. Expression, crystal structure and cellulase activity of the thermostable cellobiohydrolase Cel7A from the fungus Humicola grisea var. thermoidea. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2356-66. [PMID: 25195749 PMCID: PMC4157447 DOI: 10.1107/s1399004714013844] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/13/2014] [Indexed: 11/11/2022]
Abstract
Glycoside hydrolase family 7 (GH7) cellobiohydrolases (CBHs) play a key role in biomass recycling in nature. They are typically the most abundant enzymes expressed by potent cellulolytic fungi, and are also responsible for the majority of hydrolytic potential in enzyme cocktails for industrial processing of plant biomass. The thermostability of the enzyme is an important parameter for industrial utilization. In this study, Cel7 enzymes from different fungi were expressed in a fungal host and assayed for thermostability, including Hypocrea jecorina Cel7A as a reference. The most stable of the homologues, Humicola grisea var. thermoidea Cel7A, exhibits a 10°C higher melting temperature (T(m) of 72.5°C) and showed a 4-5 times higher initial hydrolysis rate than H. jecorina Cel7A on phosphoric acid-swollen cellulose and showed the best performance of the tested enzymes on pretreated corn stover at elevated temperature (65°C, 24 h). The enzyme shares 57% sequence identity with H. jecorina Cel7A and consists of a GH7 catalytic module connected by a linker to a C-terminal CBM1 carbohydrate-binding module. The crystal structure of the H. grisea var. thermoidea Cel7A catalytic module (1.8 Å resolution; R(work) and R(free) of 0.16 and 0.21, respectively) is similar to those of other GH7 CBHs. The deviations of several loops along the cellulose-binding path between the two molecules in the asymmetric unit indicate higher flexibility than in the less thermostable H. jecorina Cel7A.
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Affiliation(s)
- Majid Haddad Momeni
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Frits Goedegebuur
- DuPont, Industrial Biosciences, Archimedesweg 30, 2333 CN Leiden, The Netherlands
| | - Henrik Hansson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Saeid Karkehabadi
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Glareh Askarieh
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Colin Mitchinson
- DuPont, Industrial Biosciences, Page Mill Road, Palo Alto, CA 94304, USA
| | - Edmundo A. Larenas
- DuPont, Industrial Biosciences, Page Mill Road, Palo Alto, CA 94304, USA
| | - Jerry Ståhlberg
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Mats Sandgren
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
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33
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Alasepp K, Borch K, Cruys-Bagger N, Badino S, Jensen K, Sørensen TH, Windahl MS, Westh P. In situ stability of substrate-associated cellulases studied by DSC. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7134-7142. [PMID: 24856176 DOI: 10.1021/la500161e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This work shows that differential scanning calorimetry (DSC) can be used to monitor the stability of substrate-adsorbed cellulases during long-term hydrolysis of insoluble cellulose. Thermal transitions of adsorbed enzyme were measured regularly in subsets of a progressing hydrolysis, and the size of the transition peak was used as a gauge of the population of native enzyme. Analogous measurements were made for enzymes in pure buffer. Investigations of two cellobiohydrolases, Cel6A and Cel7A, from Trichoderma reesei, which is an anamorph of the fungus Hypocrea jerorina, showed that these enzymes were essentially stable at 25 °C. Thus, over a 53 h experiment, Cel6A lost less than 15% of the native population and Cel7A showed no detectable loss for either the free or substrate-adsorbed state. At higher temperatures we found significant losses in the native populations, and at the highest tested temperature (49 °C) about 80% Cel6A and 35% of Cel7A was lost after 53 h of hydrolysis. The data consistently showed that Cel7A was more long-term stable than Cel6A and that substrate-associated enzyme was less long-term stable than enzyme in pure buffer stored under otherwise equal conditions. There was no correlation between the intrinsic stability, specified by the transition temperature in the DSC, and the long-term stability derived from the peak area. The results are discussed with respect to the role of enzyme denaturation for the ubiquitous slowdown observed in the enzymatic hydrolysis of cellulose.
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Affiliation(s)
- Kadri Alasepp
- Research Unit for Functional Biomaterials, NSM, Roskilde University. 1 Universitetsvej , Build. 18.1, DK-4000 Roskilde Denmark
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34
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Towards a molecular-level theory of carbohydrate processivity in glycoside hydrolases. Curr Opin Biotechnol 2014; 27:96-106. [DOI: 10.1016/j.copbio.2013.12.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
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35
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Anumula KR. Single tag for total carbohydrate analysis. Anal Biochem 2014; 457:31-7. [PMID: 24769375 DOI: 10.1016/j.ab.2014.04.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/14/2014] [Accepted: 04/17/2014] [Indexed: 11/18/2022]
Abstract
Anthranilic acid (2-aminobenzoic acid, 2-AA) has the remarkable property of reacting rapidly with every type of reducing carbohydrate. Reactivity of 2-AA with carbohydrates in aqueous solutions surpasses all other tags reported to date. This unique capability is attributed to the strategically located -COOH which accelerates Schiff base formation. Monosaccharides, oligosaccharides (N-, O-, and lipid linked and glycans in secretory fluids), glycosaminoglycans, and polysaccharides can be easily labeled with 2-AA. With 2-AA, labeling is simple in aqueous solutions containing proteins, peptides, buffer salts, and other ingredients (e.g., PNGase F, glycosidase, and transferase reaction mixtures). In contrast, other tags require relatively pure glycans for labeling in anhydrous dimethyl sulfoxide-acetic acid medium. Acidic conditions are known to cause desialylation, thus requiring a great deal of attention to sample preparation. Simpler labeling is achieved with 2-AA within 30-60 min in mild acetate-borate buffered solution. 2-AA provides the highest sensitivity and resolution in chromatographic methods for carbohydrate analysis in a simple manner. Additionally, 2-AA is uniquely qualified for quantitative analysis by mass spectrometry in the negative mode. Analyses of 2-AA-labeled carbohydrates by electrophoresis and other techniques have been reported. Examples cited here demonstrate that 2-AA is the universal tag for total carbohydrate analysis.
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36
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Boonvitthya N, Bozonnet S, Burapatana V, O'Donohue MJ, Chulalaksananukul W. Comparison of the heterologous expression of Trichoderma reesei endoglucanase II and cellobiohydrolase II in the yeasts Pichia pastoris and Yarrowia lipolytica. Mol Biotechnol 2013; 54:158-69. [PMID: 22638966 DOI: 10.1007/s12033-012-9557-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sequences encoding the genes for endoglucanase II and cellobiohydrolase II from the fungus Trichoderma reesei QM9414 were successfully cloned and expressed in Yarrowia lipolytica under the control of the POX2 or TEF promoters, and using either the native or preproLip2 secretion signals. The expression level of both recombinant enzymes was compared with that obtained using Pichia pastoris, under the control of the AOX1 promoter to evaluate the utility of Y. lipolytica as a host strain for recombinant EGII and CBHII production. Extracellular endoglucanase activity was similar between TEF-preoproLip2-eglII expressed in Y. lipolytica and P. pastoris induced by 0.5 % (v/v) methanol, but when recombinant protein expression in P. pastoris was induced with 3 % (v/v) methanol, the activity was increased by about sevenfold. In contrast, the expression level of cellobiohydrolase from the TEF-preproLip2-cbhII cassette was higher in Y. lipolytica than in P. pastoris. Transformed Y. lipolytica produced up to 15 mg/l endoglucanase and 50 mg/l cellobiohydrolase, with the specific activity of both proteins being greater than their homologs produced by P. pastoris. Partial characterization of recombinant endoglucanase II and cellobiohydrolase II expressed in both yeasts revealed their optimum pH and temperature, and their pH and temperature stabilities were identical and hyperglycosylation had little effect on their enzymatic activity and properties.
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37
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Cruys-Bagger N, Tatsumi H, Ren GR, Borch K, Westh P. Transient kinetics and rate-limiting steps for the processive cellobiohydrolase Cel7A: effects of substrate structure and carbohydrate binding domain. Biochemistry 2013; 52:8938-48. [PMID: 24228828 DOI: 10.1021/bi401210n] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cellobiohydrolases are exoacting, processive enzymes that effectively hydrolyze crystalline cellulose. They have attracted considerable interest because of their role in both natural carbon cycling and industrial enzyme cocktails used for the deconstruction of cellulosic biomass, but many mechanistic and regulatory aspects of their heterogeneous catalysis remain poorly understood. Here, we address this by applying a deterministic model to real-time kinetic data with high temporal resolution. We used two variants of the cellobiohydrolase Cel7A from Hypocrea jecorina , and three types of cellulose as substrate. Analysis of the pre-steady-state regime allowed delineation rate constants for both fast and slow steps in the enzymatic cycle and assessment of how these constants influenced the rate of hydrolysis at quasi-steady state. Processive movement on the cellulose strand advanced with characteristic times of 0.15-0.7 s per step at 25 °C, and the rate was highest on amorphous substrate. The cellulose binding module was found to raise this rate on crystalline, but not on amorphous, substrate. The rapid processive movement signified high intrinsic reactivity, but this parameter had marginal influence on the steady-state rate. This was because dissociation and association were slower and, hence, rate limiting. Specifically, the dissociation from the strand was found to occur with characteristic times of 45-100 s. This meant that dissociation was the bottleneck, except at very low substrate loads (0.5-1 g/L), where association became slower.
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Affiliation(s)
- Nicolaj Cruys-Bagger
- Research Unit for Functional Biomaterials, NSM, Roskilde University , Universitetsvej 1, DK-4000 Roskilde, Denmark
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38
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Kont R, Kurašin M, Teugjas H, Väljamäe P. Strong cellulase inhibitors from the hydrothermal pretreatment of wheat straw. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:135. [PMID: 24053778 PMCID: PMC3849272 DOI: 10.1186/1754-6834-6-135] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 09/13/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND The use of the enzymatic hydrolysis of lignocellulose with subsequent fermentation to ethanol provides a green alternative for the production of transportation fuels. Because of its recalcitrant nature, the lignocellulosic biomass must be pretreated before enzymatic hydrolysis. However, the pretreatment often results in the formation of compounds that are inhibitory for the enzymes or fermenting organism. Although well recognized, little quantitative information on the inhibition of individual cellulase components by identified inhibitors is available. RESULTS Strong cellulase inhibitors were separated from the liquid fraction of the hydrothermal pretreatment of wheat straw. HPLC and mass-spectroscopy analyses confirmed that the inhibitors were oligosaccharides (inhibitory oligosaccharides, IOS) with a degree of polymerization from 7 to 16. The IOS are composed of a mixture of xylo- (XOS) and gluco-oligosaccharides (GOS). We propose that XOS and GOS are the fragments of the xylan backbone and mixed-linkage β-glucans, respectively. The IOS were approximately 100 times stronger inhibitors for Trichoderma reesei cellobiohydrolases (CBHs) than cellobiose, which is one of the strongest inhibitors of these enzymes reported to date. Inhibition of endoglucanases (EGs) by IOS was weaker than that of CBHs. Most of the tested cellulases and hemicellulases were able to slowly degrade IOS and reduce the inhibitory power of the liquid fraction to some extent. The most efficient single enzyme component here was T. reesei EG TrCel7B. Although reduced by the enzyme treatment, the residual inhibitory power of IOS and the liquid fraction was strong enough to silence the major component of the T. reesei cellulase system, CBH TrCel7A. CONCLUSIONS The cellulase inhibitors described here may be responsible for the poor yields from the enzymatic conversion of the whole slurries from lignocellulose pretreatment under conditions that do not favor complete degradation of hemicellulose. Identification of the inhibitory compounds helps to design better enzyme mixtures for their degradation and to optimize the pretreatment regimes to minimize their formation.
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Affiliation(s)
- Riin Kont
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b - 202, 51010 Tartu, Estonia
| | - Mihhail Kurašin
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b - 202, 51010 Tartu, Estonia
| | - Hele Teugjas
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b - 202, 51010 Tartu, Estonia
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b - 202, 51010 Tartu, Estonia
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Kawai T, Nakazawa H, Ida N, Okada H, Ogasawara W, Morikawa Y, Kobayashi Y. A comprehensive analysis of the effects of the main component enzymes of cellulase derived from Trichoderma reesei on biomass saccharification. ACTA ACUST UNITED AC 2013; 40:805-10. [DOI: 10.1007/s10295-013-1290-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 05/10/2013] [Indexed: 10/26/2022]
Abstract
Abstract
The aim of this study was a comprehensive analysis of the effects of the component enzymes of cellulase derived from Trichoderma reesei strain PC-3-7 on biomass saccharification. We used cellulases with deleted CBH I, CBH II, or EG I, which contain all other component enzymes, for saccharification of differently pretreated biomasses of rice straw, Erianthus, eucalyptus, and Japanese cedar. We found that CBH I was the most effective in saccharification of all pretreated cellulosic biomasses, although the effect was weaker in saccharification of sulfuric acid- and hydrothermally pretreated rice straw than of others; CBH II was more effective for rice straw than for eucalyptus, and was the most effective at the early stages of biomass degradation; EG I had little effect on pretreated biomasses, in particular, it had no effect on steam-exploded Japanese cedar. Thus, the effects of the main component enzymes depend on the biomass source and pretreatment. These findings will likely help to improve cellulase for industrial use.
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Affiliation(s)
- Tetsushi Kawai
- Japan Bioindustry Association AIST Tsukuba Central 6, 1-1-1 Higashi 305-8566 Tsukuba Ibaraki Japan
| | - Hikaru Nakazawa
- grid.260427.5 0000000106712234 Department of Bioengineering Nagaoka University of Technology 1603-1 Kamitomioka 940-2188 Nagaoka Japan
| | - Noriko Ida
- Japan Bioindustry Association AIST Tsukuba Central 6, 1-1-1 Higashi 305-8566 Tsukuba Ibaraki Japan
| | - Hirofumi Okada
- grid.260427.5 0000000106712234 Department of Bioengineering Nagaoka University of Technology 1603-1 Kamitomioka 940-2188 Nagaoka Japan
| | - Wataru Ogasawara
- grid.260427.5 0000000106712234 Department of Bioengineering Nagaoka University of Technology 1603-1 Kamitomioka 940-2188 Nagaoka Japan
| | - Yasushi Morikawa
- Japan Bioindustry Association AIST Tsukuba Central 6, 1-1-1 Higashi 305-8566 Tsukuba Ibaraki Japan
| | - Yoshinori Kobayashi
- Japan Bioindustry Association AIST Tsukuba Central 6, 1-1-1 Higashi 305-8566 Tsukuba Ibaraki Japan
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40
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Teugjas H, Väljamäe P. Product inhibition of cellulases studied with 14C-labeled cellulose substrates. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:104. [PMID: 23883520 PMCID: PMC3726336 DOI: 10.1186/1754-6834-6-104] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/11/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND As a green alternative for the production of transportation fuels, the enzymatic hydrolysis of lignocellulose and subsequent fermentation to ethanol are being intensively researched. To be economically feasible, the hydrolysis of lignocellulose must be conducted at a high concentration of solids, which results in high concentrations of hydrolysis end-products, cellobiose and glucose, making the relief of product inhibition of cellulases a major challenge in the process. However, little quantitative information on the product inhibition of individual cellulases acting on cellulose substrates is available because it is experimentally difficult to assess the hydrolysis of the heterogeneous polymeric substrate in the high background of added products. RESULTS The cellobiose and glucose inhibition of thermostable cellulases from Acremonium thermophilum, Thermoascus aurantiacus, and Chaetomium thermophilum acting on uniformly 14C-labeled bacterial cellulose and its derivatives, 14C-bacterial microcrystalline cellulose and 14C-amorphous cellulose, was studied. Cellulases from Trichoderma reesei were used for comparison. The enzymes most sensitive to cellobiose inhibition were glycoside hydrolase (GH) family 7 cellobiohydrolases (CBHs), followed by family 6 CBHs and endoglucanases (EGs). The strength of glucose inhibition followed the same order. The product inhibition of all enzymes was relieved at higher temperatures. The inhibition strength measured for GH7 CBHs with low molecular-weight model substrates did not correlate with that measured with 14C-cellulose substrates. CONCLUSIONS GH7 CBHs are the primary targets for product inhibition of the synergistic hydrolysis of cellulose. The inhibition must be studied on cellulose substrates instead of on low molecular-weight model substrates when selecting enzymes for lignocellulose hydrolysis. The advantages of using higher temperatures are an increase in the catalytic efficiency of enzymes and the relief of product inhibition.
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Affiliation(s)
- Hele Teugjas
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b – 202, Tartu 51010, Estonia
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b – 202, Tartu 51010, Estonia
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41
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Cruys-Bagger N, Elmerdahl J, Praestgaard E, Borch K, Westh P. A steady-state theory for processive cellulases. FEBS J 2013; 280:3952-61. [PMID: 23786663 DOI: 10.1111/febs.12397] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/17/2013] [Accepted: 06/13/2013] [Indexed: 11/28/2022]
Abstract
Processive enzymes perform sequential steps of catalysis without dissociating from their polymeric substrate. This mechanism is considered essential for efficient enzymatic hydrolysis of insoluble cellulose (particularly crystalline cellulose), but a theoretical framework for processive kinetics remains to be fully developed. In this paper, we suggest a deterministic kinetic model that relies on a processive set of enzyme reactions and a quasi steady-state assumption. It is shown that this approach is practicable in the sense that it leads to mathematically simple expressions for the steady-state rate, and only requires data from standard assay techniques as experimental input. Specifically, it is shown that the processive reaction rate at steady state may be expressed by a hyperbolic function related to the conventional Michaelis-Menten equation. The main difference is a 'kinetic processivity coefficient', which represents the probability of the enzyme dissociating from the substrate strand before completing n sequential catalytic steps, where n is the mean processivity number measured experimentally. Typical processive cellulases have high substrate affinity, and therefore this probability is low. This has significant kinetic implications, for example the maximal specific rate (V(max)/E₀) for processive cellulases is much lower than the catalytic rate constant (k(cat)). We discuss how relationships based on this theory may be used in both comparative and mechanistic analyses of cellulases.
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Affiliation(s)
- Nicolaj Cruys-Bagger
- Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, Roskilde, Denmark
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42
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Nakamura A, Tsukada T, Auer S, Furuta T, Wada M, Koivula A, Igarashi K, Samejima M. The tryptophan residue at the active site tunnel entrance of Trichoderma reesei cellobiohydrolase Cel7A is important for initiation of degradation of crystalline cellulose. J Biol Chem 2013; 288:13503-10. [PMID: 23532843 DOI: 10.1074/jbc.m113.452623] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Mutation of Trp-40 in the Cel7A cellobiohydrolase from Trichoderma reesei (TrCel7A) causes a loss of crystalline cellulose-degrading ability. RESULTS Mutant W40A showed reduced specific activity for crystalline cellulose and diffused the cellulose chain from the entrance of the active site tunnel. CONCLUSION Trp-40 is essential for chain end loading to initiate processive hydrolysis of TrCel7A. SIGNIFICANCE The mechanisms of crystalline polysaccharide degradation are clarified. The glycoside hydrolase family 7 cellobiohydrolase Cel7A from Trichoderma reesei is one of the best studied cellulases with the ability to degrade highly crystalline cellulose. The catalytic domain and the cellulose-binding domain (CBD) are both necessary for full activity on crystalline substrates. Our previous high-speed atomic force microscopy studies showed that mutation of Trp-40 at the entrance of the catalytic tunnel drastically decreases the ability to degrade crystalline cellulose. Here, we examined the activities of the WT enzyme and mutant W40A (with and without the CBD) for various substrates. Evaluation and comparison of the specific activities of the enzymes (WT, W40A, and the corresponding catalytic subunits (WTcat and W40Acat)) adsorbed on crystalline cellulose indicated that Trp-40 is involved in recruiting individual substrate chains into the active site tunnel to initiate processive hydrolysis. This was supported by molecular dynamics simulation study, i.e. the reducing end glucose unit was effectively loaded into the active site of WTcat, but not into that of W40Acat, when the simulation was started from subsite -7. However, when similar simulations were carried out starting from subsite -5, both enzymes held the substrate for 50 ns, indicating that the major difference between WTcat and W40Acat is the length of the free chain end of the substrate required to allow initiation of processive movements; this also reflects the difference between crystalline and amorphous celluloses. The CBD is important for enhancing the enzyme population on crystalline substrate, but it also decreases the specific activity of the adsorbed enzyme, possibly by attaching the enzyme to non-optimal places on the cellulose surface and/or hindering processive hydrolysis.
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Affiliation(s)
- Akihiko Nakamura
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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Prates ÉT, Stankovic I, Silveira RL, Liberato MV, Henrique-Silva F, Pereira N, Polikarpov I, Skaf MS. X-ray structure and molecular dynamics simulations of endoglucanase 3 from Trichoderma harzianum: structural organization and substrate recognition by endoglucanases that lack cellulose binding module. PLoS One 2013; 8:e59069. [PMID: 23516599 PMCID: PMC3597598 DOI: 10.1371/journal.pone.0059069] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/11/2013] [Indexed: 11/18/2022] Open
Abstract
Plant biomass holds a promise for the production of second-generation ethanol via enzymatic hydrolysis, but its utilization as a biofuel resource is currently limited to a large extent by the cost and low efficiency of the cellulolytic enzymes. Considerable efforts have been dedicated to elucidate the mechanisms of the enzymatic process. It is well known that most cellulases possess a catalytic core domain and a carbohydrate binding module (CBM), without which the enzymatic activity can be drastically reduced. However, Cel12A members of the glycosyl hydrolases family 12 (GHF12) do not bear a CBM and yet are able to hydrolyze amorphous cellulose quite efficiently. Here, we use X-ray crystallography and molecular dynamics simulations to unravel the molecular basis underlying the catalytic capability of endoglucanase 3 from Trichoderma harzianum (ThEG3), a member of the GHF12 enzymes that lacks a CBM. A comparative analysis with the Cellulomonas fimi CBM identifies important residues mediating interactions of EG3s with amorphous regions of the cellulose. For instance, three aromatic residues constitute a harboring wall of hydrophobic contacts with the substrate in both ThEG3 and CfCBM structures. Moreover, residues at the entrance of the active site cleft of ThEG3 are identified, which might hydrogen bond to the substrate. We advocate that the ThEG3 residues Asn152 and Glu201 interact with the substrate similarly to the corresponding CfCBM residues Asn81 and Arg75. Altogether, these results show that CBM motifs are incorporated within the ThEG3 catalytic domain and suggest that the enzymatic efficiency is associated with the length and position of the substrate chain, being higher when the substrate interact with the aromatic residues at the entrance of the cleft and the catalytic triad. Our results provide guidelines for rational protein engineering aiming to improve interactions of GHF12 enzymes with cellulosic substrates.
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Affiliation(s)
- Érica T. Prates
- Institute of Chemistry, State University of Campinas–UNICAMP. Cx.P. 6154, Campinas, São Paulo, Brazil
| | - Ivana Stankovic
- Institute of Chemistry, State University of Campinas–UNICAMP. Cx.P. 6154, Campinas, São Paulo, Brazil
| | - Rodrigo L. Silveira
- Institute of Chemistry, State University of Campinas–UNICAMP. Cx.P. 6154, Campinas, São Paulo, Brazil
| | - Marcelo V. Liberato
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Flávio Henrique-Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Nei Pereira
- Centro de Tecnologia, Escola de Química, Laboratório de Desenvolvimento de Bioprocessos (LaDeBio), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Igor Polikarpov
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Munir S. Skaf
- Institute of Chemistry, State University of Campinas–UNICAMP. Cx.P. 6154, Campinas, São Paulo, Brazil
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Maurer S, Brady N, Fajardo N, Radke C. Surface kinetics for cooperative fungal cellulase digestion of cellulose from quartz crystal microgravimetry. J Colloid Interface Sci 2013; 394:498-508. [DOI: 10.1016/j.jcis.2012.12.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 12/07/2012] [Accepted: 12/08/2012] [Indexed: 10/27/2022]
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Murphy L, Bohlin C, Baumann MJ, Olsen SN, Sørensen TH, Anderson L, Borch K, Westh P. Product inhibition of five Hypocrea jecorina cellulases. Enzyme Microb Technol 2013; 52:163-9. [DOI: 10.1016/j.enzmictec.2013.01.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 01/02/2013] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
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Mora S, Banerjee S. Economics of the hydrolysis of cellulosic sludge to glucose. Bioprocess Biosyst Eng 2012; 36:1039-42. [PMID: 23149860 DOI: 10.1007/s00449-012-0856-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 10/25/2012] [Indexed: 10/27/2022]
Abstract
Cellulosic sludge from paper mills making bleached products can be enzymatically converted to glucose. A kinetic model that accounts for product inhibition was used to estimate the cost:benefits of the process. In the proposed scheme, the sludge is enzymatically hydrolyzed in a sequence of CSTRs, the ash separated, and the product glucose concentrated through reverse osmosis. The water recovered is mostly recycled. By far, the most important economic variable is the value of the glucose. However, even if the glucose is assumed to be of no value the avoided cost of sludge disposal approximately offsets the process costs. The approach should generate significant revenue if the glucose is valued at market.
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Affiliation(s)
- Sandeep Mora
- Institute of Paper Science and Technology, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0620, USA
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Luterbacher JS, Parlange JY, Walker LP. A pore-hindered diffusion and reaction model can help explain the importance of pore size distribution in enzymatic hydrolysis of biomass. Biotechnol Bioeng 2012; 110:127-36. [PMID: 22811319 DOI: 10.1002/bit.24614] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 06/08/2012] [Accepted: 07/09/2012] [Indexed: 11/06/2022]
Abstract
Until now, most efforts to improve monosaccharide production from biomass through pretreatment and enzymatic hydrolysis have used empirical optimization rather than employing a rational design process guided by a theory-based modeling framework. For such an approach to be successful a modeling framework that captures the key mechanisms governing the relationship between pretreatment and enzymatic hydrolysis must be developed. In this study, we propose a pore-hindered diffusion and kinetic model for enzymatic hydrolysis of biomass. When compared to data available in the literature, this model accurately predicts the well-known dependence of initial cellulose hydrolysis rates on surface area available to a cellulase-size molecule. Modeling results suggest that, for particles smaller than 5 × 10(-3) cm, a key rate-limiting step is the exposure of previously unexposed cellulose occurring after cellulose on the surface has hydrolyzed, rather than binding or diffusion. However, for larger particles, according to the model, diffusion plays a more significant role. Therefore, the proposed model can be used to design experiments that produce results that are either affected or unaffected by diffusion. Finally, by using pore size distribution data to predict the biomass fraction that is accessible to degradation, this model can be used to predict cellulose hydrolysis with time using only pore size distribution and initial composition data.
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Affiliation(s)
- Jeremy S Luterbacher
- Department of Chemical and Biomolecular Engineering, Olin Hall, Cornell University, Ithaca, New York 14850, USA
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Jalak J, Kurašin M, Teugjas H, Väljamäe P. Endo-exo synergism in cellulose hydrolysis revisited. J Biol Chem 2012; 287:28802-15. [PMID: 22733813 DOI: 10.1074/jbc.m112.381624] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Synergistic cooperation of different enzymes is a prerequisite for efficient degradation of cellulose. The conventional mechanistic interpretation of the synergism between randomly acting endoglucanases (EGs) and chain end-specific processive cellobiohydrolases (CBHs) is that EG-generated new chain ends on cellulose surface serve as starting points for CBHs. Here we studied the hydrolysis of bacterial cellulose (BC) by CBH TrCel7A and EG TrCel5A from Trichoderma reesei under both single-turnover and "steady state" conditions. Unaccountable by conventional interpretation, the presence of EG increased the rate constant of TrCel7A-catalyzed hydrolysis of BC in steady state. At optimal enzyme/substrate ratios, the "steady state" rate of synergistic hydrolysis became limited by the velocity of processive movement of TrCel7A on BC. A processivity value of 66 ± 7 cellobiose units measured for TrCel7A on (14)C-labeled BC was close to the leveling off degree of polymerization of BC, suggesting that TrCel7A cannot pass through the amorphous regions on BC and stalls. We propose a mechanism of endo-exo synergism whereby the degradation of amorphous regions by EG avoids the stalling of TrCel7A and leads to its accelerated recruitment. Hydrolysis of pretreated wheat straw suggested that this mechanism of synergism is operative also in the degradation of lignocellulose. Although both mechanisms of synergism are used in parallel, the contribution of conventional mechanism is significant only at high enzyme/substrate ratios.
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Affiliation(s)
- Jürgen Jalak
- Institute of Molecular and Cell Biology, University of Tartu, Vanemuise 46-138, 51014 Tartu, Estonia
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Sørlie M, Zakariassen H, Norberg AL, Eijsink VGH. Processivity and substrate-binding in family 18 chitinases. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.676282] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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50
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Segato F, Damasio ARL, Gonçalves TA, Murakami MT, Squina FM, Polizeli M, Mort AJ, Prade RA. Two structurally discrete GH7-cellobiohydrolases compete for the same cellulosic substrate fiber. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:21. [PMID: 22494694 PMCID: PMC3431977 DOI: 10.1186/1754-6834-5-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 03/30/2012] [Indexed: 05/14/2023]
Abstract
BACKGROUND Cellulose consisting of arrays of linear beta-1,4 linked glucans, is the most abundant carbon-containing polymer present in biomass. Recalcitrance of crystalline cellulose towards enzymatic degradation is widely reported and is the result of intra- and inter-molecular hydrogen bonds within and among the linear glucans. Cellobiohydrolases are enzymes that attack crystalline cellulose. Here we report on two forms of glycosyl hydrolase family 7 cellobiohydrolases common to all Aspergillii that attack Avicel, cotton cellulose and other forms of crystalline cellulose. RESULTS Cellobiohydrolases Cbh1 and CelD have similar catalytic domains but only Cbh1 contains a carbohydrate-binding domain (CBD) that binds to cellulose. Structural superpositioning of Cbh1 and CelD on the Talaromyces emersonii Cel7A 3-dimensional structure, identifies the typical tunnel-like catalytic active site while Cbh1 shows an additional loop that partially obstructs the substrate-fitting channel. CelD does not have a CBD and shows a four amino acid residue deletion on the tunnel-obstructing loop providing a continuous opening in the absence of a CBD. Cbh1 and CelD are catalytically functional and while specific activity against Avicel is 7.7 and 0.5 U.mg prot-1, respectively specific activity on pNPC is virtually identical. Cbh1 is slightly more stable to thermal inactivation compared to CelD and is much less sensitive to glucose inhibition suggesting that an open tunnel configuration, or absence of a CBD, alters the way the catalytic domain interacts with the substrate. Cbh1 and CelD enzyme mixtures on crystalline cellulosic substrates show a strong combinatorial effort response for mixtures where Cbh1 is present in 2:1 or 4:1 molar excess. When CelD was overrepresented the combinatorial effort could only be partially overcome. CelD appears to bind and hydrolyze only loose cellulosic chains while Cbh1 is capable of opening new cellulosic substrate molecules away from the cellulosic fiber. CONCLUSION Cellobiohydrolases both with and without a CBD occur in most fungal genomes where both enzymes are secreted, and likely participate in cellulose degradation. The fact that only Cbh1 binds to the substrate and in combination with CelD exhibits strong synergy only when Cbh1 is present in excess, suggests that Cbh1 unties enough chains from cellulose fibers, thus enabling processive access of CelD.
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Affiliation(s)
- Fernando Segato
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisas em Energia e Materiais, Campinas, Sao Paulo, Brazil
| | - André R L Damasio
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
- Department of Biochemistry, Ribeirão Preto School of Medicine, Ribeirão Preto, Sao Paulo, Brazil
| | - Thiago Augusto Gonçalves
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisas em Energia e Materiais, Campinas, Sao Paulo, Brazil
| | - Mario T Murakami
- Laboratório Nacional de Biociências (LNBio), Campinas, Sao Paulo, Brazil
| | - Fabio M Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisas em Energia e Materiais, Campinas, Sao Paulo, Brazil
| | | | - Andrew J Mort
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - Rolf A Prade
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisas em Energia e Materiais, Campinas, Sao Paulo, Brazil
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