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Shi Q, Abdel-Hamid AM, Sun Z, Cheng Y, Tu T, Cann I, Yao B, Zhu W. Carbohydrate-binding modules facilitate the enzymatic hydrolysis of lignocellulosic biomass: Releasing reducing sugars and dissociative lignin available for producing biofuels and chemicals. Biotechnol Adv 2023; 65:108126. [PMID: 36921877 DOI: 10.1016/j.biotechadv.2023.108126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/05/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023]
Abstract
The microbial decomposition and utilization of lignocellulosic biomass present in the plant tissues are driven by a series of carbohydrate active enzymes (CAZymes) acting in concert. As the non-catalytic domains widely found in the modular CAZymes, carbohydrate-binding modules (CBMs) are intimately associated with catalytic domains (CDs) that effect the diverse hydrolytic reactions. The CBMs function as auxiliary components for the recognition, adhesion, and depolymerization of the complex substrate mediated by the associated CDs. Therefore, CBMs are deemed as significant biotools available for enzyme engineering, especially to facilitate the enzymatic hydrolysis of dense and insoluble plant tissues to acquire more fermentable sugars. This review aims at presenting the taxonomies and biological properties of the CBMs currently curated in the CAZy database. The molecular mechanisms that CBMs use in assisting the enzymatic hydrolysis of plant polysaccharides and the regulatory factors of CBM-substrate interactions are outlined in detail. In addition, guidelines for the rational designs of CBM-fused CAZymes are proposed. Furthermore, the potential to harness CBMs for industrial applications, especially in enzymatic pretreatment of the recalcitrant lignocellulose, is evaluated. It is envisaged that the ideas outlined herein will aid in the engineering and production of novel CBM-fused enzymes to facilitate efficient degradation of lignocellulosic biomass to easily fermentable sugars for production of value-added products, including biofuels.
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Affiliation(s)
- Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Ahmed M Abdel-Hamid
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Zhanying Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Isaac Cann
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL 61801, USA; Department of Animal Science, University of Illinois at Urbana-Champaign, IL 61801, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, IL 61801, USA; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, IL 61801, USA; Center for East Asian and Pacific Studies, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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DeVree BT, Steiner LM, Głazowska S, Ruhnow F, Herburger K, Persson S, Mravec J. Current and future advances in fluorescence-based visualization of plant cell wall components and cell wall biosynthetic machineries. Biotechnol Biofuels 2021; 14:78. [PMID: 33781321 PMCID: PMC8008654 DOI: 10.1186/s13068-021-01922-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/05/2021] [Indexed: 05/18/2023]
Abstract
Plant cell wall-derived biomass serves as a renewable source of energy and materials with increasing importance. The cell walls are biomacromolecular assemblies defined by a fine arrangement of different classes of polysaccharides, proteoglycans, and aromatic polymers and are one of the most complex structures in Nature. One of the most challenging tasks of cell biology and biomass biotechnology research is to image the structure and organization of this complex matrix, as well as to visualize the compartmentalized, multiplayer biosynthetic machineries that build the elaborate cell wall architecture. Better knowledge of the plant cells, cell walls, and whole tissue is essential for bioengineering efforts and for designing efficient strategies of industrial deconstruction of the cell wall-derived biomass and its saccharification. Cell wall-directed molecular probes and analysis by light microscopy, which is capable of imaging with a high level of specificity, little sample processing, and often in real time, are important tools to understand cell wall assemblies. This review provides a comprehensive overview about the possibilities for fluorescence label-based imaging techniques and a variety of probing methods, discussing both well-established and emerging tools. Examples of applications of these tools are provided. We also list and discuss the advantages and limitations of the methods. Specifically, we elaborate on what are the most important considerations when applying a particular technique for plants, the potential for future development, and how the plant cell wall field might be inspired by advances in the biomedical and general cell biology fields.
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Affiliation(s)
- Brian T DeVree
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Lisa M Steiner
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Sylwia Głazowska
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Felix Ruhnow
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Klaus Herburger
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Staffan Persson
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
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Gatt E, Khatri V, Bley J, Barnabé S, Vandenbossche V, Beauregard M. Enzymatic hydrolysis of corn crop residues with high solid loadings: New insights into the impact of bioextrusion on biomass deconstruction using carbohydrate-binding modules. Bioresour Technol 2019; 282:398-406. [PMID: 30884460 DOI: 10.1016/j.biortech.2019.03.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Lignocellulosic biomass is a sustainable source of renewable substrate to produce low carbon footprint energy and materials. Biomass conversion is usually performed in two steps: a biomass pretreatment for improving cellulose accessibility followed by enzymatic hydrolysis of cellulose. In this study we investigated the efficiency of a bioextrusion pretreatment (extrusion in the presence of cellulase enzyme) for production of reducing sugars from corn crop agricultural residues. Our results demonstrate that bioextrusion increased the reducing sugar conversion yield by at least 94% at high solid/liquid ratio (14%-40%). Monitoring biomass surface with carbohydrate-binding modules (FTCM-depletion assay) revealed that well known negative impact of high solid/liquid ratio on conversion yield is not due to the lack of exposed cellulose which was abundant under such conditions. Bioextrusion was found to be less efficient on alkaline pretreated biomass but being a mild and solvent limiting pretreatment, it might help to minimize the waste stream.
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Affiliation(s)
- Etienne Gatt
- Laboratoire de Chimie Agro-industrielle, LCA, Université de Toulouse, INRA, Toulouse, France.
| | - Vinay Khatri
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; PROTEO, Université Laval, Québec G1V 4G2, Canada.
| | - Julien Bley
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, Canada; Innofibre, 3351 Boulevard des Forges, Québec G9A 5E6, Canada
| | - Simon Barnabé
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, Canada
| | - Virginie Vandenbossche
- Laboratoire de Chimie Agro-industrielle, LCA, Université de Toulouse, INRA, Toulouse, France.
| | - Marc Beauregard
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, Canada; PROTEO, Université Laval, Québec G1V 4G2, Canada
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Weber J, Petrović D, Strodel B, Smits SHJ, Kolkenbrock S, Leggewie C, Jaeger KE. Interaction of carbohydrate-binding modules with poly(ethylene terephthalate). Appl Microbiol Biotechnol 2019; 103:4801-4812. [PMID: 30993383 PMCID: PMC6536475 DOI: 10.1007/s00253-019-09760-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 01/26/2023]
Abstract
Poly(ethylene terephthalate) (PET) is one of the most widely applied synthetic polymers, but its hydrophobicity is challenging for many industrial applications. Biotechnological modification of PET surface can be achieved by PET hydrolyzing cutinases. In order to increase the adsorption towards their unnatural substrate, the enzymes are fused to carbohydrate-binding modules (CBMs) leading to enhanced activity. In this study, we identified novel PET binding CBMs and characterized the CBM-PET interplay. We developed a semi-quantitative method to detect CBMs bound to PET films. Screening of eight CBMs from diverse families for PET binding revealed one CBM that possesses a high affinity towards PET. Molecular dynamics (MD) simulations of the CBM-PET interface revealed tryptophan residues forming an aromatic triad on the peptide surface. Their interaction with phenyl rings of PET is stabilized by additional hydrogen bonds formed between amino acids close to the aromatic triad. Furthermore, the ratio of hydrophobic to polar contacts at the interface was identified as an important feature determining the strength of PET binding of CBMs. The interaction of CBM tryptophan residues with PET was confirmed experimentally by tryptophan quenching measurements after addition of PET nanoparticles to CBM. Our findings are useful for engineering PET hydrolyzing enzymes and may also find applications in functionalization of PET.
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Affiliation(s)
- Joanna Weber
- evoxx technologies GmbH, Alfred-Nobel-Str. 10, D-40789, Monheim am Rhein, Germany
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany
- Bayer AG, Friedrich-Ebert-Straße 475, 42117, Wuppertal, Germany
| | - Dušan Petrović
- Institute of Complex Systems ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstraße 1, D-40225, Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, D-40225, Düsseldorf, Germany
| | - Stephan Kolkenbrock
- evoxx technologies GmbH, Alfred-Nobel-Str. 10, D-40789, Monheim am Rhein, Germany
- Altona Diagnostics GmbH, Mörkenstr. 12, 22767, Hamburg, Germany
| | - Christian Leggewie
- evoxx technologies GmbH, Alfred-Nobel-Str. 10, D-40789, Monheim am Rhein, Germany.
- Erber Enzymes GmbH, Otto-Hahn-Straße 15, 44227, Dortmund, Germany.
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, D-52425, Jülich, Germany.
- Institute of Molecular Enzyme Technology, Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany.
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Oliveira C, Carvalho V, Domingues L, Gama FM. Recombinant CBM-fusion technology - Applications overview. Biotechnol Adv 2015; 33:358-69. [PMID: 25689072 DOI: 10.1016/j.biotechadv.2015.02.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 02/04/2023]
Abstract
Carbohydrate-binding modules (CBMs) are small components of several enzymes, which present an independent fold and function, and specific carbohydrate-binding activity. Their major function is to bind the enzyme to the substrate enhancing its catalytic activity, especially in the case of insoluble substrates. The immense diversity of CBMs, together with their unique properties, has long raised their attention for many biotechnological applications. Recombinant DNA technology has been used for cloning and characterizing new CBMs. In addition, it has been employed to improve the purity and availability of many CBMs, but mainly, to construct bi-functional CBM-fused proteins for specific applications. This review presents a comprehensive summary of the uses of CBMs recombinantly produced from heterologous organisms, or by the original host, along with the latest advances. Emphasis is given particularly to the applications of recombinant CBM-fusions in: (a) modification of fibers, (b) production, purification and immobilization of recombinant proteins, (c) functionalization of biomaterials and (d) development of microarrays and probes.
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Várnai A, Mäkelä MR, Djajadi DT, Rahikainen J, Hatakka A, Viikari L. Carbohydrate-binding modules of fungal cellulases: occurrence in nature, function, and relevance in industrial biomass conversion. Adv Appl Microbiol 2014; 88:103-65. [PMID: 24767427 DOI: 10.1016/B978-0-12-800260-5.00004-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this review, the present knowledge on the occurrence of cellulases, with a special emphasis on the presence of carbohydrate-binding modules (CBMs) in various fungal strains, has been summarized. The importance of efficient fungal cellulases is growing due to their potential uses in biorefinery processes where lignocellulosic biomasses are converted to platform sugars and further to biofuels and chemicals. Most secreted cellulases studied in detail have a bimodular structure containing an active core domain attached to a CBM. CBMs are traditionally been considered as essential parts in cellulases, especially in cellobiohydrolases. However, presently available genome data indicate that many cellulases lack the binding domains in cellulose-degrading organisms. Recent data also demonstrate that CBMs are not necessary for the action of cellulases and they solely increase the concentration of enzymes on the substrate surfaces. On the other hand, in practical industrial processes where high substrate concentrations with low amounts of water are employed, the enzymes have been shown to act equally efficiently with and without CBM. Furthermore, available kinetic data show that enzymes without CBMs can desorb more readily from the often lignaceous substrates, that is, they are not stuck on the substrates and are thus available for new actions. In this review, the available data on the natural habitats of different wood-degrading organisms (with emphasis on the amount of water present during wood degradation) and occurrence of cellulose-binding domains in their genome have been assessed in order to identify evolutionary advantages for the development of CBM-less cellulases in nature.
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