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Song X, Li J, Chang Y, Mei X, Luan J, Jiang X, Xue C. The Discovery of a Multidomain Mannanase Containing Dual-Catalytic Domain of the Same Activity: Biochemical Properties and Synergistic Effect. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10451-10458. [PMID: 38632679 DOI: 10.1021/acs.jafc.3c09611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
In recent years, the wide application of mannan has driven the demand for the exploration of mannanase. As one of the main components of hemicellulose, mannan is an important polysaccharide that ruminants need to degrade and utilize, making rumen a rich source of mannanases. In this study, gene mining of mannanases was performed using bioinformatics, and potential dual-catalytic domain mannanases were heterologously expressed to analyze their properties. The hydrolysis pattern and enzymatic products were identified by liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). A dual-catalytic domain mannanase Man26/5 with the same function as the substrate was successfully mined from the genome of cattle rumen microbiota. Compared to the single-catalytic domain, its higher thermal stability (≤50 °C) and catalytic efficiency confirm the synergistic effect between the two catalytic domains. It exhibited a unique "crab-like" structure where the CBM located in the middle is responsible for binding, and the catalytic domains at both ends are responsible for cutting. The exploration of its multidomain structure and synergistic patterns could provide a reference for the artificial construction and molecular modification of enzymes.
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Affiliation(s)
- Xiao Song
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Jiajing Li
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yaoguang Chang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Xuanwei Mei
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Jiayi Luan
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Xiaoxiao Jiang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Changhu Xue
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
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2
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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: 0] [Impact Index Per Article: 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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3
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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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4
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Zajki-Zechmeister K, Eibinger M, Nidetzky B. Enzyme Synergy in Transient Clusters of Endo- and Exocellulase Enables a Multilayer Mode of Processive Depolymerization of Cellulose. ACS Catal 2022; 12:10984-10994. [PMID: 36082050 PMCID: PMC9442579 DOI: 10.1021/acscatal.2c02377] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/12/2022] [Indexed: 11/29/2022]
Abstract
Biological degradation of cellulosic materials relies on the molecular-mechanistic principle that internally chain-cleaving endocellulases work synergistically with chain end-cleaving exocellulases in polysaccharide chain depolymerization. How endo-exo synergy becomes effective in the deconstruction of a solid substrate that presents cellulose chains assembled into crystalline material is an open question of the mechanism, with immediate implications on the bioconversion efficiency of cellulases. Here, based on single-molecule evidence from real-time atomic force microscopy, we discover that endo- and exocellulases engage in the formation of transient clusters of typically three to four enzymes at the cellulose surface. The clusters form specifically at regular domains of crystalline cellulose microfibrils that feature molecular defects in the polysaccharide chain organization. The dynamics of cluster formation correlates with substrate degradation through a multilayer-processive mode of chain depolymerization, overall leading to the directed ablation of single microfibrils from the cellulose surface. Each multilayer-processive step involves the spatiotemporally coordinated and mechanistically concerted activity of the endo- and exocellulases in close proximity. Mechanistically, the cooperativity with the endocellulase enables the exocellulase to pass through its processive cycles ∼100-fold faster than when acting alone. Our results suggest an advanced paradigm of efficient multienzymatic degradation of structurally organized polymer materials by endo-exo synergetic chain depolymerization.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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5
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Defining the Frontiers of Synergism between Cellulolytic Enzymes for Improved Hydrolysis of Lignocellulosic Feedstocks. Catalysts 2021. [DOI: 10.3390/catal11111343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lignocellulose has economic potential as a bio-resource for the production of value-added products (VAPs) and biofuels. The commercialization of biofuels and VAPs requires efficient enzyme cocktail activities that can lower their costs. However, the basis of the synergism between enzymes that compose cellulolytic enzyme cocktails for depolymerizing lignocellulose is not understood. This review aims to address the degree of synergism (DS) thresholds between the cellulolytic enzymes and how this can be used in the formulation of effective cellulolytic enzyme cocktails. DS is a powerful tool that distinguishes between enzymes’ synergism and anti-synergism during the hydrolysis of biomass. It has been established that cellulases, or cellulases and lytic polysaccharide monooxygenases (LPMOs), always synergize during cellulose hydrolysis. However, recent evidence suggests that this is not always the case, as synergism depends on the specific mechanism of action of each enzyme in the combination. Additionally, expansins, nonenzymatic proteins responsible for loosening cell wall fibers, seem to also synergize with cellulases during biomass depolymerization. This review highlighted the following four key factors linked to DS: (1) a DS threshold at which the enzymes synergize and produce a higher product yield than their theoretical sum, (2) a DS threshold at which the enzymes display synergism, but not a higher product yield, (3) a DS threshold at which enzymes do not synergize, and (4) a DS threshold that displays anti-synergy. This review deconvolutes the DS concept for cellulolytic enzymes, to postulate an experimental design approach for achieving higher synergism and cellulose conversion yields.
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6
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Anuganti M, Fu H, Ekatan S, Kumar CV, Lin Y. Kinetic Study on Enzymatic Hydrolysis of Cellulose in an Open, Inhibition-Free System. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5180-5192. [PMID: 33872034 DOI: 10.1021/acs.langmuir.1c00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Due to the complexity of cellulases and the requirement of enzyme adsorption on cellulose prior to reactions, it is difficult to evaluate their reaction with a general mechanistic scheme. Nevertheless, it is of great interest to come up with an approximate analytic description of a valid model for the purpose of developing an intuitive understanding of these complex enzyme systems. Herein, we used the surface plasmonic resonance method to monitor the action of a cellobiohydrolase by itself, as well as its mixture with a synergetic endoglucanase, on the surface of a regenerated model cellulose film, under continuous flow conditions. We found a phenomenological approach by taking advantage of the long steady state of cellulose hydrolysis in the open, inhibition-free system. This provided a direct and reliable way to analyze the adsorption and reaction processes with a minimum number of fitting parameters. We investigated a generalized Langmuir-Michaelis-Menten model to describe a full set of kinetic results across a range of enzyme concentrations, compositions, and temperatures. The overall form of the equations describing the pseudo-steady-state kinetics of the flow-system shares some interesting similarities with the Michaelis-Menten equation. The use of familiar Michaelis-Menten parameters in the analysis provides a unifying framework to study cellulase kinetics. The strategy may provide a shortcut for approaching a quantitative while intuitive understanding of enzymatic degradation of cellulose from top to bottom. The open system approach and the kinetic analysis should be applicable to a variety of cellulases and reaction systems to accelerate the progress in the field.
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Affiliation(s)
- Murali Anuganti
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Hailin Fu
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Stephen Ekatan
- Polymer Program, Institute of Material Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Challa V Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Yao Lin
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
- Polymer Program, Institute of Material Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
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7
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Mitchell DA, Moreira I, Krieger N. Potential of time-stepping stochastic models as tools for guiding the design and operation of processes for the enzymatic hydrolysis of polysaccharides - A review. BIORESOURCE TECHNOLOGY 2021; 323:124559. [PMID: 33388211 DOI: 10.1016/j.biortech.2020.124559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 06/12/2023]
Abstract
Processes for the enzymatic hydrolysis of polysaccharides in biorefineries are becoming increasingly important. The complex network of reactions involved in polysaccharide hydrolysis can be described by stochastic models that advance in steps of time. Such models have the potential to be important tools for guiding process design and operation, and several have been developed over the last two decades. We evaluate these models. Many of the current stochastic models for the hydrolysis of colloidal polysaccharides use empirical parameters that have no recognized biological meaning. Only one model uses classical parameters of enzyme kinetics, namely specificity constants and saturation constants. Recent stochastic models for the hydrolysis of insoluble cellulose give valuable insights into the molecular-level phenomenon that limit hydrolysis rates. We conclude that, if stochastic models of enzymatic polysaccharide hydrolysis are to become widely used tools for guiding process development, then further improvements are required.
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Affiliation(s)
- David Alexander Mitchell
- Postgraduate Program in Chemical Engineering, Federal University of Paraná, P.O. Box 19011, Central Polytechnic, Curitiba 81531-980, Paraná, Brazil; Department of Biochemistry and Molecular Biology, Federal University of Paraná, P.O. Box 19046, Central Polytechnic, Curitiba 81531-980, Paraná, Brazil
| | - Isabelle Moreira
- Postgraduate Program in Chemical Engineering, Federal University of Paraná, P.O. Box 19011, Central Polytechnic, Curitiba 81531-980, Paraná, Brazil
| | - Nadia Krieger
- Postgraduate Program in Chemical Engineering, Federal University of Paraná, P.O. Box 19011, Central Polytechnic, Curitiba 81531-980, Paraná, Brazil; Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Central Polytechnic, Curitiba 81531-980, Paraná, Brazil.
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8
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Qu M, Watanabe-Nakayama T, Sun S, Umeda K, Guo X, Liu Y, Ando T, Yang Q. High-Speed Atomic Force Microscopy Reveals Factors Affecting the Processivity of Chitinases during Interfacial Enzymatic Hydrolysis of Crystalline Chitin. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02751] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mingbo Qu
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China
| | | | - Shaopeng Sun
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
| | - Kenichi Umeda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Xiaoxi Guo
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
| | - Yuansheng Liu
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Qing Yang
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7 Pengfei Road, Shenzhen 518120, China
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9
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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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10
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Abstract
Cooperative enzyme catalysis in nature has long inspired the application of engineered multi-enzyme assemblies for industrial biocatalysis. Despite considerable interest, efforts to harness the activity of cell-surface displayed multi-enzyme assemblies have been based on trial and error rather than rational design due to a lack of quantitative tools. In this study, we developed a quantitative approach to whole-cell biocatalyst characterization enabling a comprehensive study of how yeast-surface displayed multi-enzyme assemblies form. Here we show that the multi-enzyme assembly efficiency is limited by molecular crowding on the yeast cell surface, and that maximizing enzyme density is the most important parameter for enhancing cellulose hydrolytic performance. Interestingly, we also observed that proximity effects are only synergistic when the average inter-enzyme distance is > ~130 nm. The findings and the quantitative approach developed in this work should help to advance the field of biocatalyst engineering from trial and error to rational design.
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11
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Tan L, Tan Z, Feng H, Qiu J. Cellulose as a template to fabricate a cellulase-immobilized composite with high bioactivity and reusability. NEW J CHEM 2018. [DOI: 10.1039/c7nj03271d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, a new strategy was developed to fabricate an oriented cellulase/chitosan/Fe3O4composite, which possesses extremely high activity, reusability, and stability.
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Affiliation(s)
- Lin Tan
- State Key Laboratory of Advanced Processing and Recycling of Nonferrous Metals
- Lanzhou University of Technology
- Lanzhou 730050
- P. R. China
- College of Petrochemical Technology
| | - Zhaojun Tan
- College of Petrochemical Technology
- Lanzhou University of Technology
- Lanzhou
- P. R. China
| | - Huixia Feng
- State Key Laboratory of Advanced Processing and Recycling of Nonferrous Metals
- Lanzhou University of Technology
- Lanzhou 730050
- P. R. China
- College of Petrochemical Technology
| | - Jianhui Qiu
- Department of Machine Intelligence and Systems Engineering
- Faculty of System Science and Technology
- Akita Prefectural University
- Yurihonjo
- Akita 015-0055
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12
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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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13
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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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14
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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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15
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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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16
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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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17
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Zhang H, Chingin K, Zhu L, Chen H. Molecular Characterization of Ongoing Enzymatic Reactions in Raw Garlic Cloves Using Extractive Electrospray Ionization Mass Spectrometry. Anal Chem 2015; 87:2878-83. [DOI: 10.1021/ac504371z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hua Zhang
- Jiangxi Key Laboratory for
Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang 330013 P.R. China
| | - Konstantin Chingin
- Jiangxi Key Laboratory for
Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang 330013 P.R. China
| | - Liang Zhu
- Jiangxi Key Laboratory for
Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang 330013 P.R. China
| | - Huanwen Chen
- Jiangxi Key Laboratory for
Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang 330013 P.R. China
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18
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Greene ER, Himmel ME, Beckham GT, Tan Z. Glycosylation of Cellulases: Engineering Better Enzymes for Biofuels. Adv Carbohydr Chem Biochem 2015; 72:63-112. [PMID: 26613815 DOI: 10.1016/bs.accb.2015.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cellulose in plant cell walls is the largest reservoir of renewable carbon on Earth. The saccharification of cellulose from plant biomass into soluble sugars can be achieved using fungal and bacterial cellulolytic enzymes, cellulases, and further converted into fuels and chemicals. Most fungal cellulases are both N- and O-glycosylated in their native form, yet the consequences of glycosylation on activity and structure are not fully understood. Studying protein glycosylation is challenging as glycans are extremely heterogeneous, stereochemically complex, and glycosylation is not under direct genetic control. Despite these limitations, many studies have begun to unveil the role of cellulase glycosylation, especially in the industrially relevant cellobiohydrolase from Trichoderma reesei, Cel7A. Glycosylation confers many beneficial properties to cellulases including enhanced activity, thermal and proteolytic stability, and structural stabilization. However, glycosylation must be controlled carefully as such positive effects can be dampened or reversed. Encouragingly, methods for the manipulation of glycan structures have been recently reported that employ genetic tuning of glycan-active enzymes expressed from homogeneous and heterologous fungal hosts. Taken together, these studies have enabled new strategies for the exploitation of protein glycosylation for the production of enhanced cellulases for biofuel production.
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