1
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Nousi A, Molina GA, Schiano-di-Cola C, Sørensen TH, Borch K, Pedersen JN, Westh P, Marie R. Impact of Synergy Partner Cel7B on Cel7A Binding Rates: Insights from Single-Molecule Data. J Phys Chem B 2024; 128:635-647. [PMID: 38227769 PMCID: PMC10824242 DOI: 10.1021/acs.jpcb.3c05697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 01/18/2024]
Abstract
Enzymatic degradation of cellulosic biomass is a well-established route for the sustainable production of biofuels, chemicals, and materials. A strategy employed by nature and industry to achieve an efficient degradation of cellulose is that cellobiohydrolases (or exocellulases), such as Cel7A, work synergistically with endoglucanases, such as Cel7B, to achieve the complete degradation of cellulose. However, a complete mechanistic understanding of this exo-endo synergy is still lacking. Here, we used single-molecule fluorescence microscopy to quantify the binding kinetics of Cel7A on cellulose when it is acting alone on the cellulose fibrils and in the presence of its synergy partner, the endoglucanase Cel7B. To this end, we used a fluorescently tagged Cel7A and studied its binding in the presence of the unlabeled Cel7B. This provided the single-molecule data necessary for the estimation of the rate constants of association kON and dissociation kOFF of Cel7A for the substrate. We show that the presence of Cel7B does not impact the dissociation rate constant, kOFF. But, the association rate of Cel7A decreases by a factor of 2 when Cel7B is present at a molar proportion of 10:1. This ratio has previously been shown to lead to synergy. This decrease in association rate is observed in a wide range of total enzyme concentrations, from sub nM to μM concentrations. This decrease in kON is consistent with the formation of cellulase clusters recently observed by others using atomic force microscopy.
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Affiliation(s)
- Aimilia Nousi
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gustavo Avelar Molina
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | | | - Kim Borch
- Novozymes
A/S, Krogshøjvej
36, 2880 Bagsværd, Denmark
| | - Jonas N. Pedersen
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
| | - Peter Westh
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Rodolphe Marie
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
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2
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Angeltveit CF, Jeoh T, Horn SJ. Lytic polysaccharide monooxygenase activity increases productive binding capacity of cellobiohydrolases on cellulose. BIORESOURCE TECHNOLOGY 2023; 389:129806. [PMID: 37769978 DOI: 10.1016/j.biortech.2023.129806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Cellobiohydrolases are crucial for cellulose breakdown, but their efficiency on crystalline cellulose is hampered by limited access to single chain ends to initiate hydrolysis. As a result, they depend on enzymes like lytic polysaccharide monooxygenases (LPMOs), which directly target the crystalline cellulose surface. This study investigated how LPMO pretreatment affected the productive binding capacity of a Trichoderma longibrachiatum cellobiohydrolase, TlCBHI, on crystalline cellulose by applying an amperometric cellobiose dehydrogenase biosensor. After the 24-hour of LPMO pretreatment, the productive binding capacity of TlCBHI significantly increased in all reactions. However, with a shorter 5-hour LPMO pretreatment, minimal to no effect on productive binding capacity was observed. Of note, all LPMO reactions were inactivated around this time point. This delayed LPMO effect suggests that the improved binding capacity for cellulases does not directly result from cellulose chain cleavage by LPMOs but rather from the cellulose decrystallization following the oxidative cleavage.
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Affiliation(s)
- Camilla F Angeltveit
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Tina Jeoh
- Biological and Agricultural Engineering, University of California, Davis, United States
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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3
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Sun C, Meng X, Sun F, Zhang J, Tu M, Chang JS, Reungsang A, Xia A, Ragauskas AJ. Advances and perspectives on mass transfer and enzymatic hydrolysis in the enzyme-mediated lignocellulosic biorefinery: A review. Biotechnol Adv 2023; 62:108059. [PMID: 36402253 DOI: 10.1016/j.biotechadv.2022.108059] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/04/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
Abstract
Enzymatic hydrolysis is a critical process for the cellulase-mediated lignocellulosic biorefinery to produce sugar syrups that can be converted into a whole range of biofuels and biochemicals. Such a process operating at high-solid loadings (i.e., scarcely any free water or roughly ≥ 15% solids, w/w) is considered more economically feasible, as it can generate a high sugar concentration at low operation and capital costs. However, this approach remains restricted and incurs "high-solid effects", ultimately causing the lower hydrolysis yields with increasing solid loadings. The lack of available water leads to a highly viscous system with impaired mixing that exhibits strong transfer resistance and reaction limitation imposed on enzyme action. Evidently, high-solid enzymatic hydrolysis involves multi-scale mass transfer and multi-phase enzyme reaction, and thus requires a synergistic perspective of transfer and biotransformation to assess the interactions among water, biomass components, and cellulase enzymes. Porous particle characteristics of biomass and its interface properties determine the water form and distribution state surrounding the particles, which are summarized in this review aiming to identify the water-driven multi-scale/multi-phase bioprocesses. Further aided by the cognition of rheological behavior of biomass slurry, solute transfer theories, and enzyme kinetics, the coupling effects of flow-transfer-reaction are revealed under high-solid conditions. Based on the above basic features, this review lucidly explains the causes of high-solid hydrolysis hindrances, highlights the mismatched issues between transfer and reaction, and more importantly, presents the advanced strategies for transfer and reaction enhancements from the viewpoint of process optimization, reactor design, as well as enzyme/auxiliary additive customization.
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Affiliation(s)
- Chihe Sun
- Key Laboratory of Industrial Biotechnology of MOE, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xianzhi Meng
- Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Fubao Sun
- Key Laboratory of Industrial Biotechnology of MOE, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Junhua Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Maobing Tu
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Jo-Shu Chang
- Department of Chemical and Materials Engineering, Tunghai University, Taichung 407, Taiwan
| | - Alissara Reungsang
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Ao Xia
- Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Chongqing University, Ministry of Education, Chongqing 400044, China
| | - Arthur J Ragauskas
- Department of Chemical & Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Center for Renewable Carbon, Department of Forestry, Wildlife and Fisheries, The University of Tennessee, Knoxville, TN 37996, USA; Joint Institute of Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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4
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Influence of pork liver drying on ferrochelatase activity for zinc protoporphyrin formation. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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5
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Petrášek Z, Nidetzky B. Model of Processive Catalysis with Site Clustering and Blocking and Its Application to Cellulose Hydrolysis. J Phys Chem B 2022; 126:8472-8485. [PMID: 36251767 PMCID: PMC9623590 DOI: 10.1021/acs.jpcb.2c05956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Interactions between particles moving on a linear track and their possible blocking by obstacles can lead to crowding, impeding the particles' transport kinetics. When the particles are enzymes processively catalyzing a reaction along a linear polymeric substrate, these crowding and blocking effects may substantially reduce the overall catalytic rate. Cellulose hydrolysis by exocellulases processively moving along cellulose chains assembled into insoluble cellulose particles is an example of such a catalytic transport process. The details of the kinetics of cellulose hydrolysis and the causes of the often observed reduction of hydrolysis rate over time are not yet fully understood. Crowding and blocking of enzyme particles are thought to be one of the important factors affecting the cellulose hydrolysis, but its exact role and mechanism are not clear. Here, we introduce a simple model based on an elementary transport process that incorporates the crowding and blocking effects in a straightforward way. This is achieved by making a distinction between binding and non-binding sites on the chain. The model reproduces a range of experimental results, mainly related to the early phase of cellulose hydrolysis. Our results indicate that the combined effects of clustering of binding sites together with the occupancy pattern of these sites by the enzyme molecules play a decisive role in the overall kinetics of cellulose hydrolysis. It is suggested that periodic desorption and rebinding of enzyme molecules could be a basis of a strategy to partially counter the clustering of and blocking by the binding sites and so enhance the rate of cellulose hydrolysis. The general nature of the model means that it could be applicable also to other transport processes that make a distinction between binding and non-binding sites, where crowding and blocking are expected to be relevant.
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Affiliation(s)
- Zdeněk Petrášek
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010Graz, Austria,
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010Graz, Austria,Austrian
Centre of Industrial Biotechnology, Petersgasse 14, A-8010Graz, Austria,. Phone: +43 (0)316 8738409, +43 (0)316 8738400
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6
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Abstract
The depletion of fossil fuel resources and the negative impact of their use on the climate have resulted in the need for alternative sources of clean, sustainable energy. One available alternative, bioethanol, is a potential substitute for, or additive to, petroleum-derived gasoline. In the lignocellulose-to-bioethanol process, the cellulose hydrolysis step represents a major hurdle that hinders commercialization. To achieve economical production of bioethanol from lignocellulosic materials, the rate and yield of the enzymatic hydrolysis of cellulose, which is preferred over other chemically catalyzed processes, must be enhanced. To achieve this, product inhibition and enzyme loss, which are two major challenges, must be overcome. The implementation of membranes, which can permeate molecules selectively based on their size, offers a solution to this problem. Membrane bioreactors (MBRs) can enhance enzymatic hydrolysis yields and lower costs by retaining enzymes for repeated usage while permeating the products. This paper presents a critical discussion of the use of MBRs as a promising approach to the enhanced enzymatic hydrolysis of cellulosic materials. Various MBR configurations and factors that affect their performance are presented.
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7
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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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8
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Yappert R, Peters B. Processive Depolymerization Catalysts: A Population Balance Model for Chemistry’s “While” Loop. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ryan Yappert
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Baron Peters
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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9
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Neis A, da Silva Pinto L. Glycosyl hydrolases family 5, subfamily 5: Relevance and structural insights for designing improved biomass degrading cocktails. Int J Biol Macromol 2021; 193:980-995. [PMID: 34666133 DOI: 10.1016/j.ijbiomac.2021.10.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
Endoglucanases are carbohydrate-degrading enzymes widely used for bioethanol production as part of the enzymatic cocktail. However, family 5 subfamily 5 (GH5_5) endoglucanases are still poorly explored in depth. The Trichoderma reesei representative is the most studied enzyme, presenting catalytic activity in acidic media and mild temperature conditions. Though biochemically similar, its modular structure and synergy with other components vary greatly compared to other GH5_5 members and there is still a lack of specific studies regarding their interaction with other cellulases and application on novel and better mixtures. In this regard, the threedimensional structure elucidation is a highly valuable tool to both uncover basic catalytic mechanisms and implement engineering techniques, proved by the high success rate GH5_5 endoglucanases show. GH5_5 enzymes must be carefully evaluated to fully uncover their potential in biomass-degrading cocktails: the optimal industrial conditions, synergy with other cellulases, structural studies, and enzyme engineering approaches. We aimed to provide the current understanding of these main topics, collecting all available information about characterized GH5_5 endoglucanases function, structure, and bench experiments, in order to suggest future directions to a better application of these enzymes in the industry.
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Affiliation(s)
- Alessandra Neis
- Laboratório de Bioinformática e Proteômica (BioPro Lab), Centro de Desenvolvimento Tecnológico, Campus Universitário, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Caixa Postal 96010-900, Brazil.
| | - Luciano da Silva Pinto
- Laboratório de Bioinformática e Proteômica (BioPro Lab), Centro de Desenvolvimento Tecnológico, Campus Universitário, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Caixa Postal 96010-900, Brazil.
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10
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Abril B, Sanchez-Torres EA, Bou R, Garcia-Perez JV, Benedito J. Ultrasound intensification of Ferrochelatase extraction from pork liver as a strategy to improve ZINC-protoporphyrin formation. ULTRASONICS SONOCHEMISTRY 2021; 78:105703. [PMID: 34388654 PMCID: PMC8363878 DOI: 10.1016/j.ultsonch.2021.105703] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/15/2021] [Accepted: 07/29/2021] [Indexed: 05/06/2023]
Abstract
The enzyme Ferrochelatase (FeCH), which is naturally present in pork liver, catalyses the formation of Zinc-protoporphyrin (ZnPP), a natural pigment responsible for the typical color of dry-cured Italian Parma ham. The aim of this study was to evaluate the feasibility of using high power ultrasound in continuous and pulsed modes to intensify the extraction of the enzyme FeCH from pork liver. US application during FeCH extraction led to an improved enzymatic activity and further increase in the formation of ZnPP. The optimal condition tested was that of 1 min in continuous US application, in which time the enzymatic activity increased by 33.3 % compared to conventional extraction (30 min). Pulsed US application required 5 min treatments to observe a significant intensification effect. Therefore, ultrasound is a potentially feasible technique as it increases the catalytic activity of FeCH and saves time compared to the conventional extraction method.
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Affiliation(s)
- B Abril
- Department of Food Technology, Universitat Politècnica de València, Camí de Vera, s/n, Valencia 46022, Spain
| | - E A Sanchez-Torres
- IRTA, XaRTA, Food Technology, Finca Camps i Armet, Monells, Girona E-17121, Spain
| | - R Bou
- IRTA, XaRTA, Food Technology, Finca Camps i Armet, Monells, Girona E-17121, Spain
| | - J V Garcia-Perez
- Department of Food Technology, Universitat Politècnica de València, Camí de Vera, s/n, Valencia 46022, Spain
| | - J Benedito
- Department of Food Technology, Universitat Politècnica de València, Camí de Vera, s/n, Valencia 46022, Spain.
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11
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Sukumaran RK, Christopher M, Kooloth-Valappil P, Sreeja-Raju A, Mathew RM, Sankar M, Puthiyamadam A, Adarsh VP, Aswathi A, Rebinro V, Abraham A, Pandey A. Addressing challenges in production of cellulases for biomass hydrolysis: Targeted interventions into the genetics of cellulase producing fungi. BIORESOURCE TECHNOLOGY 2021; 329:124746. [PMID: 33610429 DOI: 10.1016/j.biortech.2021.124746] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Lignocellulosic materials are the favoured feedstock for biorefineries due to their abundant availability and non-completion with food. Biobased technologies for refining these materials are limited mainly by the cost of biomass hydrolyzing enzymes, typically sourced from filamentous fungi. Therefore, considerable efforts have been directed at improving the quantity and quality of secreted lignocellulose degrading enzymes from fungi in order to attain overall economic viability. Process improvements and media engineering probably have reached their thresholds and further production enhancements require modifying the fungal metabolism to improve production and secretion of these enzymes. This review focusses on the types and mechanisms of action of known fungal biomass degrading enzymes, our current understanding of the genetic control exerted on their expression, and possible routes for intervention, especially on modulating catabolite repression, transcriptional regulators, signal transduction, secretion pathways etc., in order to improve enzyme productivity, activity and stability.
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Affiliation(s)
- Rajeev K Sukumaran
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Meera Christopher
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Prajeesh Kooloth-Valappil
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - AthiraRaj Sreeja-Raju
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Reshma M Mathew
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Meena Sankar
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Anoop Puthiyamadam
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Velayudhanpillai-Prasannakumari Adarsh
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Aswathi Aswathi
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Valan Rebinro
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Amith Abraham
- Department of Chemical Engineering, Hanyang University, Seoul, Republic of Korea
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
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12
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A comparative biochemical investigation of the impeding effect of C1-oxidizing LPMOs on cellobiohydrolases. J Biol Chem 2021; 296:100504. [PMID: 33675751 PMCID: PMC8047454 DOI: 10.1016/j.jbc.2021.100504] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/17/2021] [Accepted: 03/02/2021] [Indexed: 11/20/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are known to act synergistically with glycoside hydrolases in industrial cellulolytic cocktails. However, a few studies have reported severe impeding effects of C1-oxidizing LPMOs on the activity of reducing-end cellobiohydrolases. The mechanism for this effect remains unknown, but it may have important implications as reducing-end cellobiohydrolases make up a significant part of such cocktails. To elucidate whether the impeding effect is general for different reducing-end cellobiohydrolases and study the underlying mechanism, we conducted a comparative biochemical investigation of the cooperation between a C1-oxidizing LPMO from Thielavia terrestris and three reducing-end cellobiohydrolases; Trichoderma reesei (TrCel7A), T. terrestris (TtCel7A), and Myceliophthora heterothallica (MhCel7A). The enzymes were heterologously expressed in the same organism and thoroughly characterized biochemically. The data showed distinct differences in synergistic effects between the LPMO and the cellobiohydrolases; TrCel7A was severely impeded, TtCel7A was moderately impeded, while MhCel7A was slightly boosted by the LPMO. We investigated effects of C1-oxidations on cellulose chains on the activity of the cellobiohydrolases and found reduced activity against oxidized cellulose in steady-state and pre-steady-state experiments. The oxidations led to reduced maximal velocity of the cellobiohydrolases and reduced rates of substrate complexation. The extent of these effects differed for the cellobiohydrolases and scaled with the extent of the impeding effect observed in the synergy experiments. Based on these results, we suggest that C1-oxidized chain ends are poor attack sites for reducing-end cellobiohydrolases. The severity of the impeding effects varied considerably among the cellobiohydrolases, which may be relevant to consider for optimization of industrial cocktails.
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13
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Østby H, Hansen LD, Horn SJ, Eijsink VGH, Várnai A. Enzymatic processing of lignocellulosic biomass: principles, recent advances and perspectives. J Ind Microbiol Biotechnol 2020; 47:623-657. [PMID: 32840713 PMCID: PMC7658087 DOI: 10.1007/s10295-020-02301-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023]
Abstract
Efficient saccharification of lignocellulosic biomass requires concerted development of a pretreatment method, an enzyme cocktail and an enzymatic process, all of which are adapted to the feedstock. Recent years have shown great progress in most aspects of the overall process. In particular, increased insights into the contributions of a wide variety of cellulolytic and hemicellulolytic enzymes have improved the enzymatic processing step and brought down costs. Here, we review major pretreatment technologies and different enzyme process setups and present an in-depth discussion of the various enzyme types that are currently in use. We pay ample attention to the role of the recently discovered lytic polysaccharide monooxygenases (LPMOs), which have led to renewed interest in the role of redox enzyme systems in lignocellulose processing. Better understanding of the interplay between the various enzyme types, as they may occur in a commercial enzyme cocktail, is likely key to further process improvements.
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Affiliation(s)
- Heidi Østby
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Line Degn Hansen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway.
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14
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Molecular recognition in the product site of cellobiohydrolase Cel7A regulates processive step length. Biochem J 2020; 477:99-110. [PMID: 31816027 DOI: 10.1042/bcj20190770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 11/17/2022]
Abstract
Cellobiohydrolase Cel7A is an industrial important enzyme that breaks down cellulose by a complex processive mechanism. The enzyme threads the reducing end of a cellulose strand into its tunnel-shaped catalytic domain and progresses along the strand while sequentially releasing the disaccharide cellobiose. While some molecular details of this intricate process have emerged, general structure-function relationships for Cel7A remain poorly elucidated. One interesting aspect is the occurrence of particularly strong ligand interactions in the product binding site. In this work, we analyze these interactions in Cel7A from Trichoderma reesei with special emphasis on the Arg251 and Arg394 residues. We made extensive biochemical characterization of enzymes that were mutated in these two positions and showed that the arginine residues contributed strongly to product binding. Specifically, ∼50% of the total standard free energy of product binding could be ascribed to four hydrogen bonds to Arg251 and Arg394, which had previously been identified in crystal structures. Mutation of either Arg251 or Arg394 lowered production inhibition of Cel7A, but at the same time altered the enzyme product profile and resulted in ∼50% reduction in both processivity and hydrolytic activity. The position of the two arginine residues closely matches the two-fold screw axis symmetry of the substrate, and this energetically favors the productive enzyme-substrate complex. Our results indicate that the strong and specific ligand interactions of Arg251 and Arg394 provide a simple proofreading system that controls the step length during consecutive hydrolysis and minimizes dead time associated with transient, non-productive complexes.
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15
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Hamre AG, Sørlie M. Kinetic relationships with processivity in Serratia marcescens family 18 glycoside hydrolases. Biochem Biophys Res Commun 2020; 521:120-124. [PMID: 31629467 DOI: 10.1016/j.bbrc.2019.10.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 10/25/2022]
Abstract
In nature, recalcitrant polysaccharides such as chitin and cellulose are degraded by glycoside hydrolases (GH) that act synergistically through different modes of action including attack from reducing-end and nonreducing-end (exo-mode) and random (endo-mode) on single polysaccharide chains. Both modes can be combined with a processive mechanism where the GH remain bound to the polysaccharide to perform multiple catalytic steps before dissociation into the solution. In this work, we have determined association rate constants and their activation paramaters for three co-evolved GHs from Serratia marcescens (SmChiA, SmChiB, and SmChiC) with an oligomeric substrate. Interestingly, we observe a positive correlation between the association rate constants and processive ability for the GHs. Previously, a positive correlation has been observed between substrate binding affinity and processive ability. SmChiA with highest processive ability of the three GHs bind with a kon of 11.5 ± 0.2 μM-1s-1, which is five-fold and 130-fold faster than SmChiB (less processive) and SmChiC (nonprocessive), respectively.
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Affiliation(s)
- Anne Grethe Hamre
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway.
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16
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Ahamed F, Song HS, Ooi CW, Ho YK. Modelling heterogeneity in cellulose properties predicts the slowdown phenomenon during enzymatic hydrolysis. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2019.05.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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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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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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19
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Schiano-di-Cola C, Røjel N, Jensen K, Kari J, Sørensen TH, Borch K, Westh P. Systematic deletions in the cellobiohydrolase (CBH) Cel7A from the fungus Trichoderma reesei reveal flexible loops critical for CBH activity. J Biol Chem 2018; 294:1807-1815. [PMID: 30538133 DOI: 10.1074/jbc.ra118.006699] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/08/2018] [Indexed: 11/06/2022] Open
Abstract
Glycoside hydrolase family 7 (GH7) cellulases are some of the most efficient degraders of cellulose, making them particularly relevant for industries seeking to produce renewable fuels from lignocellulosic biomass. The secretome of the cellulolytic model fungus Trichoderma reesei contains two GH7s, termed TrCel7A and TrCel7B. Despite having high structural and sequence similarities, the two enzymes are functionally quite different. TrCel7A is an exolytic, processive cellobiohydrolase (CBH), with high activity on crystalline cellulose, whereas TrCel7B is an endoglucanase (EG) with a preference for more amorphous cellulose. At the structural level, these functional differences are usually ascribed to the flexible loops that cover the substrate-binding areas. TrCel7A has an extensive tunnel created by eight peripheral loops, and the absence of four of these loops in TrCel7B makes its catalytic domain a more open cleft. To investigate the structure-function relationships of these loops, here we produced and kinetically characterized several variants in which four loops unique to TrCel7A were individually deleted to resemble the arrangement in the TrCel7B structure. Analysis of a range of kinetic parameters consistently indicated that the B2 loop, covering the substrate-binding subsites -3 and -4 in TrCel7A, was a key determinant for the difference in CBH- or EG-like behavior between TrCel7A and TrCel7B. Conversely, the B3 and B4 loops, located closer to the catalytic site in TrCel7A, were less important for these activities. We surmise that these results could be useful both in further mechanistic investigations and for guiding engineering efforts of this industrially important enzyme family.
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Affiliation(s)
- Corinna Schiano-di-Cola
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Nanna Røjel
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Kenneth Jensen
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark, and
| | - Jeppe Kari
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Trine Holst Sørensen
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark, and
| | - Peter Westh
- the Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, DK-2800 Kgs. Lyngby, Denmark
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20
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21
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Christensen SJ, Kari J, Badino SF, Borch K, Westh P. Rate‐limiting step and substrate accessibility of cellobiohydrolase Cel6A from
Trichoderma reesei. FEBS J 2018; 285:4482-4493. [DOI: 10.1111/febs.14668] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/11/2018] [Accepted: 09/28/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Stefan J. Christensen
- Research Unit for Functional Biomaterials Department of Science and Environment Roskilde University Denmark
| | - Jeppe Kari
- Research Unit for Functional Biomaterials Department of Science and Environment Roskilde University Denmark
| | - Silke F. Badino
- Research Unit for Functional Biomaterials Department of Science and Environment Roskilde University Denmark
| | | | - Peter Westh
- Research Unit for Functional Biomaterials Department of Science and Environment Roskilde University Denmark
- Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark
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22
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Mai VQ, Vo TT, Meere M. Modelling hyaluronan degradation by streptococcus pneumoniae hyaluronate lyase. Math Biosci 2018; 303:126-138. [DOI: 10.1016/j.mbs.2018.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/06/2018] [Accepted: 07/02/2018] [Indexed: 11/26/2022]
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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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Westh P, Borch K, Sørensen T, Tokin R, Kari J, Badino S, Cavaleiro MA, Røjel N, Christensen S, Vesterager CS, Schiano-di-Cola C. Thermoactivation of a cellobiohydrolase. Biotechnol Bioeng 2018; 115:831-838. [PMID: 29240229 DOI: 10.1002/bit.26513] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/21/2017] [Accepted: 12/04/2017] [Indexed: 01/11/2023]
Abstract
We have measured activity and substrate affinity of the thermostable cellobiohydrolase, Cel7A, from Rasamsonia emersonii over a broad range of temperatures. For the wild type enzyme, which does not have a Carbohydrate Binding Module (CBM), higher temperature only led to moderately increased activity against cellulose, and we ascribed this to a pronounced, temperature induced desorption of enzyme from the substrate surface. We also tested a "high affinity" variant of R. emersonii Cel7A with a linker and CBM from a related enzyme. At room temperature, the activity of the variant was similar to the wild type, but the variant was more accelerated by temperature and about two-fold faster around 70 °C. This better thermoactivation of the high-affinity variant could not be linked to differences in stability or the catalytic process, but coincided with less desorption as temperature increased. Based on these observations and earlier reports on moderate thermoactivation of cellulases, we suggest that better cellulolytic activity at industrially relevant temperatures may be attained by engineering improved substrate affinity into enzymes that already possess good thermostability.
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Affiliation(s)
- Peter Westh
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | | | - Trine Sørensen
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | - Radina Tokin
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | - Jeppe Kari
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | - Silke Badino
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | | | - Nanna Røjel
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | - Stefan Christensen
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | - Cynthia S Vesterager
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
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25
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Borisova AS, Eneyskaya EV, Jana S, Badino SF, Kari J, Amore A, Karlsson M, Hansson H, Sandgren M, Himmel ME, Westh P, Payne CM, Kulminskaya AA, Ståhlberg J. Correlation of structure, function and protein dynamics in GH7 cellobiohydrolases from Trichoderma atroviride, T. reesei and T. harzianum. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:5. [PMID: 29344086 PMCID: PMC5766984 DOI: 10.1186/s13068-017-1006-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/23/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND The ascomycete fungus Trichoderma reesei is the predominant source of enzymes for industrial conversion of lignocellulose. Its glycoside hydrolase family 7 cellobiohydrolase (GH7 CBH) TreCel7A constitutes nearly half of the enzyme cocktail by weight and is the major workhorse in the cellulose hydrolysis process. The orthologs from Trichoderma atroviride (TatCel7A) and Trichoderma harzianum (ThaCel7A) show high sequence identity with TreCel7A, ~ 80%, and represent naturally evolved combinations of cellulose-binding tunnel-enclosing loop motifs, which have been suggested to influence intrinsic cellobiohydrolase properties, such as endo-initiation, processivity, and off-rate. RESULTS The TatCel7A, ThaCel7A, and TreCel7A enzymes were characterized for comparison of function. The catalytic domain of TatCel7A was crystallized, and two structures were determined: without ligand and with thio-cellotriose in the active site. Initial hydrolysis of bacterial cellulose was faster with TatCel7A than either ThaCel7A or TreCel7A. In synergistic saccharification of pretreated corn stover, both TatCel7A and ThaCel7A were more efficient than TreCel7A, although TatCel7A was more sensitive to thermal inactivation. Structural analyses and molecular dynamics (MD) simulations were performed to elucidate important structure/function correlations. Moreover, reverse conservation analysis (RCA) of sequence diversity revealed divergent regions of interest located outside the cellulose-binding tunnel of Trichoderma spp. GH7 CBHs. CONCLUSIONS We hypothesize that the combination of loop motifs is the main determinant for the observed differences in Cel7A activity on cellulosic substrates. Fine-tuning of the loop flexibility appears to be an important evolutionary target in Trichoderma spp., a conclusion supported by the RCA data. Our results indicate that, for industrial use, it would be beneficial to combine loop motifs from TatCel7A with the thermostability features of TreCel7A. Furthermore, one region implicated in thermal unfolding is suggested as a primary target for protein engineering.
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Affiliation(s)
- Anna S. Borisova
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre “Kurchatov Institute”, Orlova Roscha, Gatchina, Leningrad Region 188300 Russia
| | - Elena V. Eneyskaya
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre “Kurchatov Institute”, Orlova Roscha, Gatchina, Leningrad Region 188300 Russia
| | - Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, KY 40506-0046 USA
| | - Silke F. Badino
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
| | - Jeppe Kari
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
| | - Antonella Amore
- National Renewable Energy Laboratory, Biosciences Center, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, 750 07 Uppsala, Sweden
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
| | - Michael E. Himmel
- National Renewable Energy Laboratory, Biosciences Center, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Peter Westh
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, KY 40506-0046 USA
- Present Address: Division of Chemical, Bioengineering, Environmental, and Transport Systems, National Science Foundation, Alexandria, VA USA
| | - Anna A. Kulminskaya
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre “Kurchatov Institute”, Orlova Roscha, Gatchina, Leningrad Region 188300 Russia
- Department of Medical Physics, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
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26
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Badino SF, Kari J, Christensen SJ, Borch K, Westh P. Direct kinetic comparison of the two cellobiohydrolases Cel6A and Cel7A from Hypocrea jecorina. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1739-1745. [DOI: 10.1016/j.bbapap.2017.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/25/2017] [Accepted: 08/14/2017] [Indexed: 01/17/2023]
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27
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Kansou K, Rémond C, Paës G, Bonnin E, Tayeb J, Bredeweg B. Testing scientific models using Qualitative Reasoning: Application to cellulose hydrolysis. Sci Rep 2017; 7:14122. [PMID: 29074872 PMCID: PMC5658447 DOI: 10.1038/s41598-017-14281-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/06/2017] [Indexed: 12/17/2022] Open
Abstract
With the accumulation of scientific information in natural science, even experts can find difficult to keep integrating new piece of information. It is critical to explore modelling solutions able to capture information scattered in publications as a computable representation form. Traditional modelling techniques are important in that regard, but relying on numerical information comes with limitations for integrating results from distinct studies, high-level representations can be more suited. We present an approach to stepwise construct mechanistic explanation from selected scientific papers using the Qualitative Reasoning framework. As a proof of concept, we apply the approach to modelling papers about cellulose hydrolysis mechanism, focusing on the causal explanations for the decreasing of hydrolytic rate. Two explanatory QR models are built to capture classical explanations for the phenomenon. Our results show that none of them provides sufficient explanation for a set of basic experimental observations described in the literature. Combining the two explanations into a third one allowed to get a new and sufficient explanation for the experimental results. In domains where numerical data are scarce and strongly related to the experimental conditions, this approach can aid assessing the conceptual validity of an explanation and support integration of knowledge from different sources.
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Affiliation(s)
- Kamal Kansou
- INRA, Biopolymères Interactions Assemblages, BP 71267, 44316, Nantes, France.
| | - Caroline Rémond
- FARE laboratory, INRA, University of Reims Champagne-Ardenne, 51100, Reims, France
| | - Gabriel Paës
- FARE laboratory, INRA, University of Reims Champagne-Ardenne, 51100, Reims, France
| | - Estelle Bonnin
- INRA, Biopolymères Interactions Assemblages, BP 71267, 44316, Nantes, France
| | - Jean Tayeb
- FARE laboratory, INRA, University of Reims Champagne-Ardenne, 51100, Reims, France
| | - Bert Bredeweg
- Informatics Institute, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
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28
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Badino SF, Bathke JK, Sørensen TH, Windahl MS, Jensen K, Peters GHJ, Borch K, Westh P. The influence of different linker modifications on the catalytic activity and cellulose affinity of cellobiohydrolase Cel7A from Hypocrea jecorina. Protein Eng Des Sel 2017; 30:495-501. [PMID: 28873985 DOI: 10.1093/protein/gzx036] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/04/2017] [Indexed: 12/13/2022] Open
Abstract
Various cellulases consist of a catalytic domain connected to a carbohydrate-binding module (CBM) by a flexible linker peptide. The linker if often strongly O-glycosylated and typically has a length of 20-50 amino acid residues. Functional roles, other than connecting the two folded domains, of the linker and its glycans, have been widely discussed, but experimental evidence remains sparse. One of the most studied cellulose degrading enzymes is the multi-domain cellobiohydrolase Cel7A from Hypocrea jecorina. Here, we designed variants of Cel7A with mutations in the linker region to elucidate the role of the linker. We found that moderate modification of the linker could result in significant changes in substrate affinity and catalytic efficacy. These changes were quite different for different linker variants. Thus, deletion of six residues near the catalytic domain had essentially no effects on enzyme function. Conversely, a substitution of four glycosylation sites near the middle of the linker reduced substrate affinity and increased maximal turnover. The observation of weaker binding provides some support of recent suggestions that linker glycans may be directly involved in substrate interactions. However, a variant with several inserted glycosylation sites near the CBM also showed lower affinity for the substrate compared to the wild-type, and we suggest that substrate interactions of the glycans depend on their exact location as well as other factors such as changes in structure and dynamics of the linker peptide.
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Affiliation(s)
- Silke Flindt Badino
- Research Unit for Functional Biomaterials, Department of Science and Environment, INM, Roskilde University, 1 Universitetsvej, Build. 28 C, DK-4000, Roskilde, Denmark
| | - Jenny Kim Bathke
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Build. 207, DK-2800 Kgs. Lyngby, Denmark
| | - Trine Holst Sørensen
- Research Unit for Functional Biomaterials, Department of Science and Environment, INM, Roskilde University, 1 Universitetsvej, Build. 28 C, DK-4000, Roskilde, Denmark
| | - Michael Skovbo Windahl
- Research Unit for Functional Biomaterials, Department of Science and Environment, INM, Roskilde University, 1 Universitetsvej, Build. 28 C, DK-4000, Roskilde, Denmark
| | - Kenneth Jensen
- Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Build. 207, DK-2800 Kgs. Lyngby, Denmark
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Peter Westh
- Research Unit for Functional Biomaterials, Department of Science and Environment, INM, Roskilde University, 1 Universitetsvej, Build. 28 C, DK-4000, Roskilde, Denmark
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29
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A quenched-flow system for measuring heterogeneous enzyme kinetics with sub-second time resolution. Enzyme Microb Technol 2017; 105:45-50. [DOI: 10.1016/j.enzmictec.2017.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 11/18/2022]
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30
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Kari J, Andersen M, Borch K, Westh P. An Inverse Michaelis–Menten Approach for Interfacial Enzyme Kinetics. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00838] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeppe Kari
- Dept.
of Science and Environment, Roskilde University, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark
| | - Morten Andersen
- Dept.
of Science and Environment, Roskilde University, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark
| | - Kim Borch
- Novozymes A/S, Krogshøjvej
36, DK-2880 Bagsværd, Denmark
| | - Peter Westh
- Dept.
of Science and Environment, Roskilde University, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark
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31
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Cross M, Rajan S, Chekaiban J, Saunders J, Hamilton C, Kim JS, Coster MJ, Gasser RB, Hofmann A. Enzyme characteristics of pathogen-specific trehalose-6-phosphate phosphatases. Sci Rep 2017; 7:2015. [PMID: 28515463 PMCID: PMC5435700 DOI: 10.1038/s41598-017-02220-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/07/2017] [Indexed: 12/21/2022] Open
Abstract
Owing to the key role of trehalose in pathogenic organisms, there has recently been growing interest in trehalose metabolism for therapeutic purposes. Trehalose-6-phosphate phosphatase (TPP) is a pivotal enzyme in the most prominent biosynthesis pathway (OtsAB). Here, we compare the enzyme characteristics of recombinant TPPs from five important nematode and bacterial pathogens, including three novel members of this protein family. Analysis of the kinetics of trehalose-6-phosphate hydrolysis reveals that all five enzymes display a burst-like kinetic behaviour which is characterised by a decrease of the enzymatic rate after the pre-steady state. The observed super-stoichiometric burst amplitudes can be explained by multiple global conformational changes in members of this enzyme family during substrate processing. In the search for specific TPP inhibitors, the trapping of the complex conformational transitions in TPPs during the catalytic cycle may present a worthwhile strategy to explore.
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Affiliation(s)
- Megan Cross
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Siji Rajan
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Janine Chekaiban
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Jake Saunders
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Chloe Hamilton
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Mark J Coster
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Andreas Hofmann
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia.
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
- Queensland Tropical Health Alliance, Smithfield, Queensland, 4878, Australia.
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32
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Hamre AG, Frøberg EE, Eijsink VGH, Sørlie M. Thermodynamics of tunnel formation upon substrate binding in a processive glycoside hydrolase. Arch Biochem Biophys 2017; 620:35-42. [PMID: 28359644 DOI: 10.1016/j.abb.2017.03.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/20/2017] [Accepted: 03/23/2017] [Indexed: 11/18/2022]
Abstract
Glycoside hydrolases (GHs) catalyze the hydrolysis of glycosidic bonds and are key enzymes in carbohydrate metabolism. Efficient degradation of recalcitrant polysaccharides such as chitin and cellulose is accomplished due to synergistic enzyme cocktails consisting of accessory enzymes and mixtures of GHs with different modes of action and active site topologies. The substrate binding sites of chitinases and cellulases often have surface exposed aromatic amino acids and a tunnel or cleft topology. The active site of the exo-processive chitinase B (ChiB) from Serratia marcescens is partially closed, creating a tunnel-like catalytic cleft. To gain insight in the fundamental principles of substrate binding in this enzyme, we have studied the contribution of five key residues involved in substrate binding and tunnel formation to the thermodynamics of substrate binding. Mutation of Trp97, Phe190, Trp220 and Glu221, which are all part of the tunnel walls, resulted in significant less favorable conformational entropy change (ΔS°conf) upon binding (-TΔΔS°conf = ∼5 kcal/mol). This suggest that these residues are important for the structural rigidity and pre-shaping of the tunnel prior to binding. Mutation of Asp316, which, by forming a hydrogen bond to Trp97 is crucial in the active-site tunnel roof, resulted in a more favorable ΔS°conf relative to the wild type (-TΔΔS°conf = -2.2 kcal/mol). This shows that closing the tunnel-roof comes with an entropy cost, as previously suggested based on the crystal structures of GHs with tunnel topologies in complex with their substrates.
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Affiliation(s)
- Anne Grethe Hamre
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway
| | - Emil Ebbestad Frøberg
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway.
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33
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Jeoh T, Cardona MJ, Karuna N, Mudinoor AR, Nill J. Mechanistic kinetic models of enzymatic cellulose hydrolysis-A review. Biotechnol Bioeng 2017; 114:1369-1385. [PMID: 28244589 DOI: 10.1002/bit.26277] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/10/2017] [Accepted: 02/22/2017] [Indexed: 01/05/2023]
Abstract
Bioconversion of lignocellulose forms the basis for renewable, advanced biofuels, and bioproducts. Mechanisms of hydrolysis of cellulose by cellulases have been actively studied for nearly 70 years with significant gains in understanding of the cellulolytic enzymes. Yet, a full mechanistic understanding of the hydrolysis reaction has been elusive. We present a review to highlight new insights gained since the most recent comprehensive review of cellulose hydrolysis kinetic models by Bansal et al. (2009) Biotechnol Adv 27:833-848. Recent models have taken a two-pronged approach to tackle the challenge of modeling the complex heterogeneous reaction-an enzyme-centric modeling approach centered on the molecularity of the cellulase-cellulose interactions to examine rate limiting elementary steps and a substrate-centric modeling approach aimed at capturing the limiting property of the insoluble cellulose substrate. Collectively, modeling results suggest that at the molecular-scale, how rapidly cellulases can bind productively (complexation) and release from cellulose (decomplexation) is limiting, while the overall hydrolysis rate is largely insensitive to the catalytic rate constant. The surface area of the insoluble substrate and the degrees of polymerization of the cellulose molecules in the reaction both limit initial hydrolysis rates only. Neither enzyme-centric models nor substrate-centric models can consistently capture hydrolysis time course at extended reaction times. Thus, questions of the true reaction limiting factors at extended reaction times and the role of complexation and decomplexation in rate limitation remain unresolved. Biotechnol. Bioeng. 2017;114: 1369-1385. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Tina Jeoh
- Biological and Agricultural Engineering, University of California, Davis, California
| | - Maria J Cardona
- Chemical Engineering, University of California, Davis, California.,Intel Corporation, Hillsboro, Oregon
| | - Nardrapee Karuna
- Biological and Agricultural Engineering, University of California, Davis, California.,Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Nakhon Pathom, Thailand
| | - Akshata R Mudinoor
- Biological and Agricultural Engineering, University of California, Davis, California
| | - Jennifer Nill
- Chemical Engineering, University of California, Davis, California
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34
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Sanz-Vicente I, Domínguez A, Ferrández C, Galbán J. Enzymatic methods for choline-containing water soluble phospholipids based on fluorescence of choline oxidase: Application to lyso-PAF. Anal Biochem 2017; 519:30-37. [PMID: 27956151 DOI: 10.1016/j.ab.2016.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/01/2016] [Accepted: 12/08/2016] [Indexed: 11/25/2022]
Abstract
In this paper we present methods to determine water soluble phospholipids containing choline (wCh-PL). The analytes were hydrolyzed by the enzyme phospholipase D and the choline formed was oxidized by the enzyme Choline Oxidase (ChOx); the fluorescence changes of the ChOx are followed during the enzymatic reaction, avoiding the necessity of an indicating step. Both reactions (hydrolysis and oxidation) can be combined in two different ways: 1) a two-step process (TSP) in which the hydrolysis reaction takes place during an incubation time and then the oxidation reaction is carried out, the analytical signal being provided by the intrinsic fluorescence of ChOx due to tryptophan; 2) a one-step process (OSP) in which both enzymatic reactions are carried out simultaneously in the same test; in this case the analytical signal is provided by the ChOx extrinsic fluorescence due to a fluorescent probe (Ru (II) chelate) linked to the enzyme (ChOx-RuC). The analytical capabilities of these methods were studied using 1,2-dioctanoyl-sn-glycero-3-phosphocholine (C8PC), a water soluble short alkyl chain Ch-PL as a substrate, and 1-O-hexadecyl-sn-glyceryl-3-phosphorylcholine (lyso-PAF). The analytical features of merit for both analytes using both methods were obtained. The TSP gave a 10-fold sensitivity and lower quantification limit (1.0*10-5 M for lyso-PAF), but OSP reduced the determination time and permitted to use the same enzyme aliquot for several measurements. Both methods gave similar precision (RSD 7%, n = 5). The TSP was applied to the determination of C8PC and lyso-PAF in spiked synthetic serum matrix using the standard addition method. The application of this methodology to PLD activity determination is also discussed.
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Affiliation(s)
- Isabel Sanz-Vicente
- Analytical Biosensors Group, Analytical Chemistry Department, Faculty of Sciences, Aragon Institute of Nanoscience, University of Zaragoza, 50009 Zaragoza, Spain.
| | - Andrés Domínguez
- Analytical Biosensors Group, Analytical Chemistry Department, Faculty of Sciences, Aragon Institute of Nanoscience, University of Zaragoza, 50009 Zaragoza, Spain
| | - Carlos Ferrández
- Analytical Biosensors Group, Analytical Chemistry Department, Faculty of Sciences, Aragon Institute of Nanoscience, University of Zaragoza, 50009 Zaragoza, Spain
| | - Javier Galbán
- Analytical Biosensors Group, Analytical Chemistry Department, Faculty of Sciences, Aragon Institute of Nanoscience, University of Zaragoza, 50009 Zaragoza, Spain
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35
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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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36
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Karuna N, Jeoh T. The productive cellulase binding capacity of cellulosic substrates. Biotechnol Bioeng 2016; 114:533-542. [PMID: 27696345 DOI: 10.1002/bit.26193] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/12/2016] [Accepted: 09/26/2016] [Indexed: 01/18/2023]
Abstract
Cellulosic biomass is the most promising feedstock for renewable biofuel production; however, the mechanisms of the heterogeneous cellulose saccharification reaction are still unsolved. As cellulases need to bind isolated molecules of cellulose at the surface of insoluble cellulose fibrils or larger aggregated cellulose structures in order to hydrolyze glycosidic bonds, the "accessibility of cellulose to cellulases" is considered to be a reaction limiting property of cellulose. We have defined the accessibility of cellulose to cellulases as the productive binding capacity of cellulose, that is, the concentration of productive binding sites on cellulose that are accessible for binding and hydrolysis by cellulases. Productive cellulase binding to cellulose results in hydrolysis and can be quantified by measuring hydrolysis rates. In this study, we measured the productive Trichoderma reesei Cel7A (TrCel7A) binding capacity of five cellulosic substrates from different sources and processing histories. Swollen filter paper and bacterial cellulose had higher productive binding capacities of ∼6 µmol/g while filter paper, microcrystalline cellulose, and algal cellulose had lower productive binding capacities of ∼3 µmol/g. Swelling and regenerating filter paper using phosphoric acid increased the initial accessibility of the reducing ends to TrCel7A from 4 to 6 µmol/g. Moreover, this increase in initial productive binding capacity accounted in large part for the difference in the overall digestibility between filter paper and swollen filter paper. We further demonstrated that an understanding of how the productive binding capacity declines over the course of the hydrolysis reaction has the potential to predict overall saccharification time courses. Biotechnol. Bioeng. 2017;114: 533-542. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nardrapee Karuna
- Department of Biological and Agricultural Engineering, University of California, One Shields Ave., Davis 95616, California
| | - Tina Jeoh
- Department of Biological and Agricultural Engineering, University of California, One Shields Ave., Davis 95616, California
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37
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Sørensen TH, Windahl MS, McBrayer B, Kari J, Olsen JP, Borch K, Westh P. Loop variants of the thermophileRasamsonia emersoniiCel7A with improved activity against cellulose. Biotechnol Bioeng 2016; 114:53-62. [DOI: 10.1002/bit.26050] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Trine Holst Sørensen
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1; Building 28, DK-4000 Roskilde Denmark
| | | | | | - Jeppe Kari
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1; Building 28, DK-4000 Roskilde Denmark
| | - Johan Pelck Olsen
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1; Building 28, DK-4000 Roskilde Denmark
| | | | - Peter Westh
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1; Building 28, DK-4000 Roskilde Denmark
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38
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Cruys-Bagger N, Alasepp K, Andersen M, Ottesen J, Borch K, Westh P. Rate of Threading a Cellulose Chain into the Binding Tunnel of a Cellulase. J Phys Chem B 2016; 120:5591-600. [DOI: 10.1021/acs.jpcb.6b01877] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolaj Cruys-Bagger
- Department
of Science and Environment, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark
- Novozymes A/S, Krogshøjvej
36, DK-2880 Bagsværd, Denmark
| | - Kadri Alasepp
- Department
of Science and Environment, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark
| | - Morten Andersen
- Department
of Science and Environment, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark
| | - Johnny Ottesen
- Department
of Science and Environment, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark
| | - Kim Borch
- Novozymes A/S, Krogshøjvej
36, DK-2880 Bagsværd, Denmark
| | - Peter Westh
- Department
of Science and Environment, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark
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39
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Olsen JP, Alasepp K, Kari J, Cruys-Bagger N, Borch K, Westh P. Mechanism of product inhibition for cellobiohydrolase Cel7A during hydrolysis of insoluble cellulose. Biotechnol Bioeng 2016; 113:1178-86. [DOI: 10.1002/bit.25900] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/23/2015] [Accepted: 11/29/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Johan P. Olsen
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
| | - Kadri Alasepp
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
| | - Jeppe Kari
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
| | - Nicolaj Cruys-Bagger
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
- Novozymes A/S; Bagsvaerd Denmark
| | | | - Peter Westh
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
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40
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Wallace J, Brienzo M, García-Aparicio MP, Görgens JF. Lignin enrichment and enzyme deactivation as the root cause of enzymatic hydrolysis slowdown of steam pretreated sugarcane bagasse. N Biotechnol 2016; 33:361-71. [PMID: 26820122 DOI: 10.1016/j.nbt.2016.01.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 11/25/2015] [Accepted: 01/14/2016] [Indexed: 01/21/2023]
Abstract
The enzymatic hydrolysis (EH) rate normally decreases during the hydrolysis, leaving unhydrolyzed material as residue. This phenomenon occurs during the hydrolysis of both cellulose (avicel) and lignocellulosic material, in nature or even pretreated. The progression of EH of steam pretreated sugarcane bagasse was associated with an initial (fast), intermediate (slower) and recalcitrant (slowest) phases, at glucan to glucose conversion yields of 61.7, 81.6 and 86%, respectively. Even though the EH of avicel as a simpler material than steam pretreated sugarcane bagasse, EH slowdown was present. The less thermo-stable endo-xylanase lost 58% of initial enzyme activity, followed by β-glucosidase that lost 16%, culminating in FPase activity loss of 30% in the first 24hours. After 72hours of EH the total loss of FPase activity was 40% compared to the initial activity. Analysis of the solid residue from EH showed that lignin content, phenolic compounds and ash increased while glucan decreased as hydrolysis progressed. During the initial fast phase of EH, the total solid residue surface area consisted predominantly of internal surface area. Thereafter, in the intermediate and recalcitrant phases of EH, the ratio of external:internal surface area increased. The proposed fiber damage and decrease in internal surface area, probably by EH action, was visualized by scanning electron microscopy imagery. The higher lignin/glucan ratio as EH progressed and enzyme deactivation by thermo instability were the main effects observed, respectively to substrate and enzyme.
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Affiliation(s)
- Joshua Wallace
- Department of Process Engineering, University of Stellenbosch, Private Bag X1, Stellenbosch 7602, South Africa
| | - Michel Brienzo
- Department of Process Engineering, University of Stellenbosch, Private Bag X1, Stellenbosch 7602, South Africa.
| | - María P García-Aparicio
- Department of Process Engineering, University of Stellenbosch, Private Bag X1, Stellenbosch 7602, South Africa; Department of Microbiology, University of Stellenbosch, Private Bag X1, Stellenbosch 7602, South Africa
| | - Johann F Görgens
- Department of Process Engineering, University of Stellenbosch, Private Bag X1, Stellenbosch 7602, South Africa
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41
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Eibinger M, Zahel T, Ganner T, Plank H, Nidetzky B. Cellular automata modeling depicts degradation of cellulosic material by a cellulase system with single-molecule resolution. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:56. [PMID: 26962329 PMCID: PMC4784381 DOI: 10.1186/s13068-016-0463-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/19/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Enzymatic hydrolysis of cellulose involves the spatiotemporally correlated action of distinct polysaccharide chain cleaving activities confined to the surface of an insoluble substrate. Because cellulases differ in preference for attacking crystalline compared to amorphous cellulose, the spatial distribution of structural order across the cellulose surface imposes additional constraints on the dynamic interplay between the enzymes. Reconstruction of total system behavior from single-molecule activity parameters is a longstanding key goal in the field. RESULTS We have developed a stochastic, cellular automata-based modeling approach to describe degradation of cellulosic material by a cellulase system at single-molecule resolution. Substrate morphology was modeled to represent the amorphous and crystalline phases as well as the different spatial orientations of the polysaccharide chains. The enzyme system model consisted of an internally chain-cleaving endoglucanase (EG) as well as two processively acting, reducing and non-reducing chain end-cleaving cellobiohydrolases (CBHs). Substrate preference (amorphous: EG, CBH II; crystalline: CBH I) and characteristic frequencies for chain cleavage, processive movement, and dissociation were assigned from biochemical data. Once adsorbed, enzymes were allowed to reach surface-exposed substrate sites through "random-walk" lateral diffusion or processive motion. Simulations revealed that slow dissociation of processive enzymes at obstacles obstructing further movement resulted in local jamming of the cellulases, with consequent delay in the degradation of the surface area affected. Exploiting validation against evidence from atomic force microscopy imaging as a unique opportunity opened up by the modeling approach, we show that spatiotemporal characteristics of cellulose surface degradation by the system of synergizing cellulases were reproduced quantitatively at the nanometer resolution of the experimental data. This in turn gave useful prediction of the soluble sugar release rate. CONCLUSIONS Salient dynamic features of cellulose surface degradation by different cellulases acting in synergy were reproduced in simulations in good agreement with evidence from high-resolution visualization experiments. Due to the single-molecule resolution of the modeling approach, the utility of the presented model lies not only in predicting system behavior but also in elucidating inherently complex (e.g., stochastic) phenomena involved in enzymatic cellulose degradation. Thus, it creates synergy with experiment to advance the mechanistic understanding for improved application.
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Affiliation(s)
- Manuel Eibinger
- />Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Thomas Zahel
- />Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Thomas Ganner
- />Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Harald Plank
- />Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- />Graz Centre for Electron Microscopy, Steyrergasse 17, 8010 Graz, Austria
| | - Bernd Nidetzky
- />Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
- />Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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42
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Wang J, Gao G, Li Y, Yang L, Liang Y, Jin H, Han W, Feng Y, Zhang Z. Cloning, Expression, and Characterization of a Thermophilic Endoglucanase, AcCel12B from Acidothermus cellulolyticus 11B. Int J Mol Sci 2015; 16:25080-95. [PMID: 26506341 PMCID: PMC4632791 DOI: 10.3390/ijms161025080] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/29/2015] [Accepted: 10/13/2015] [Indexed: 12/23/2022] Open
Abstract
The gene ABK52392 from the thermophilic bacterium Acidothermus cellulolyticus 11B was predicted to be endoglucanase and classified into glycoside hydrolase family 12. ABK52392 encodes a protein containing a catalytic domain and a carbohydrate binding module. ABK52392 was cloned and functionally expressed in Escherichia coli. After purification by Ni-NTA agarose affinity chromatography and Q-Sepharose® Fast Flow chromatography, the properties of the recombinant protein (AcCel12B) were characterized. AcCel12B exhibited optimal activity at pH 4.5 and 75 °C. The half-lives of AcCel12B at 60 and 70 °C were about 90 and 2 h, respectively, under acidic conditions. The specific hydrolytic activities of AcCel12B at 70 °C and pH 4.5 for sodium carboxymethylcellulose (CMC) and regenerated amorphous cellulose (RAC) were 118.3 and 104.0 U·mg−1, respectively. The Km and Vmax of AcCel12B for CMC were 25.47 mg·mL−1 and 131.75 U·mg−1, respectively. The time course of hydrolysis for RAC was investigated by measuring reducing ends in the soluble and insoluble phases. The total hydrolysis rate rapidly decreased after the early stage of incubation and the generation of insoluble reducing ends decreased earlier than that of soluble reducing ends. High thermostability of the cellulase indicates its potential commercial significance and it could be exploited for industrial application in the future.
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Affiliation(s)
- Junling Wang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
- Department of Biotechnology, Jilin Agricultural Science and Technology College, Jilin 132101, China.
| | - Gui Gao
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Yuwei Li
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - Liangzhen Yang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Yanli Liang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Hanyong Jin
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Yan Feng
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Zuoming Zhang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
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43
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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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44
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Sørensen TH, Cruys-Bagger N, Windahl MS, Badino SF, Borch K, Westh P. Temperature Effects on Kinetic Parameters and Substrate Affinity of Cel7A Cellobiohydrolases. J Biol Chem 2015; 290:22193-202. [PMID: 26183777 DOI: 10.1074/jbc.m115.658930] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 11/06/2022] Open
Abstract
We measured hydrolytic rates of four purified cellulases in small increments of temperature (10-50 °C) and substrate loads (0-100 g/liter) and analyzed the data by a steady state kinetic model that accounts for the processive mechanism. We used wild type cellobiohydrolases (Cel7A) from mesophilic Hypocrea jecorina and thermophilic Rasamsonia emersonii and two variants of these enzymes designed to elucidate the role of the carbohydrate binding module (CBM). We consistently found that the maximal rate increased strongly with temperature, whereas the affinity for the insoluble substrate decreased, and as a result, the effect of temperature depended strongly on the substrate load. Thus, temperature had little or no effect on the hydrolytic rate in dilute substrate suspensions, whereas strong temperature activation (Q10 values up to 2.6) was observed at saturating substrate loads. The CBM had a dual effect on the activity. On one hand, it diminished the tendency of heat-induced desorption, but on the other hand, it had a pronounced negative effect on the maximal rate, which was 2-fold larger in variants without CBM throughout the investigated temperature range. We conclude that although the CBM is beneficial for affinity it slows down the catalytic process. Cel7A from the thermophilic organism was moderately more activated by temperature than the mesophilic analog. This is in accord with general theories on enzyme temperature adaptation and possibly relevant information for the selection of technical cellulases.
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Affiliation(s)
- Trine Holst Sørensen
- From Roskilde University, Nature, Systems, and Models, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and
| | - Nicolaj Cruys-Bagger
- From Roskilde University, Nature, Systems, and Models, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and
| | - Michael Skovbo Windahl
- From Roskilde University, Nature, Systems, and Models, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Silke Flindt Badino
- From Roskilde University, Nature, Systems, and Models, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Peter Westh
- From Roskilde University, Nature, Systems, and Models, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and
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45
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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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46
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Kuusk S, Sørlie M, Väljamäe P. The predominant molecular state of bound enzyme determines the strength and type of product inhibition in the hydrolysis of recalcitrant polysaccharides by processive enzymes. J Biol Chem 2015; 290:11678-91. [PMID: 25767120 DOI: 10.1074/jbc.m114.635631] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Indexed: 11/06/2022] Open
Abstract
Processive enzymes are major components of the efficient enzyme systems that are responsible for the degradation of the recalcitrant polysaccharides cellulose and chitin. Despite intensive research, there is no consensus on which step is rate-limiting for these enzymes. Here, we performed a comparative study of two well characterized enzymes, the cellobiohydrolase Cel7A from Hypocrea jecorina and the chitinase ChiA from Serratia marcescens. Both enzymes were inhibited by their disaccharide product, namely chitobiose for ChiA and cellobiose for Cel7A. The products behaved as noncompetitive inhibitors according to studies using the (14)C-labeled crystalline polymeric substrates (14)C chitin nanowhiskers and (14)C-labeled bacterial microcrystalline cellulose for ChiA and Cel7A, respectively. The resulting observed Ki (obs) values were 0.45 ± 0.08 mm for ChiA and 0.17 ± 0.02 mm for Cel7A. However, in contrast to ChiA, the Ki (obs) of Cel7A was an order of magnitude higher than the true Ki value governed by the thermodynamic stability of the enzyme-inhibitor complex. Theoretical analysis of product inhibition suggested that the inhibition strength and pattern can be accounted for by assuming different rate-limiting steps for ChiA and Cel7A. Measuring the population of enzymes whose active site was occupied by a polymer chain revealed that Cel7A was bound predominantly via its active site. Conversely, the active-site-mediated binding of ChiA was slow, and most ChiA exhibited a free active site, even when the substrate concentration was saturating for the activity. Collectively, our data suggest that complexation with the polymer chain is rate-limiting for ChiA, whereas Cel7A is limited by dissociation.
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Affiliation(s)
- Silja Kuusk
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia and
| | - Morten Sørlie
- the Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Priit Väljamäe
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia and
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47
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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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48
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Pellegrini VOA, Lei N, Kyasaram M, Olsen JP, Badino SF, Windahl MS, Colussi F, Cruys-Bagger N, Borch K, Westh P. Reversibility of substrate adsorption for the cellulases Cel7A, Cel6A, and Cel7B from Hypocrea jecorina. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:12602-12609. [PMID: 25322452 DOI: 10.1021/la5024423] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Adsorption of cellulases on the cellulose surface is an integral part of the catalytic mechanism, and a detailed description of the adsorption process is therefore required for a fundamental understanding of this industrially important class of enzymes. However, the mode of adsorption has proven intricate, and several key questions remain open. Perhaps most notably it is not clear whether the adsorbed enzyme is in dynamic equilibrium with the free population or irreversibly associated with no or slow dissociation. To address this, we have systematically investigated adsorption reversibility for two cellobiohydrolases (Cel7A and Cel6A) and one endoglucanase (Cel7B) on four types of pure cellulose substrates. Specifically, we monitored dilution-induced release of adsorbed enzyme in samples that had previously been brought to a steady state (constant concentration of free enzyme). In simple dilution experiments (without centrifugation), the results consistently showed full reversibility. In contrast to this, resuspension of enzyme-substrate pellets separated by centrifugation showed extensive irreversibility. We conclude that these enzymes are in a dynamic equilibrium between free and adsorbed states but suggest that changes in the physical properties of cellulose caused by compaction of the pellet hampers subsequent release of adsorbed enzyme. This latter effect may be pertinent to both previous controversies in the literature on adsorption reversibility and the development of enzyme recycling protocols in the biomass industry.
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Affiliation(s)
- Vanessa O A Pellegrini
- Research Unit for Functional Biomaterials, NSM, Roskilde University , 1 Universitetsvej, Build. 18.1, DK-4000 Roskilde, Denmark
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49
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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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50
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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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