1
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Tang C, Wang L, Sun J, Chen G, Shen J, Wang L, Han Y, Luo J, Li Z, Zhang P, Zeng S, Qi D, Geng J, Liu J, Dai Z. Degradable living plastics programmed by engineered spores. Nat Chem Biol 2024:10.1038/s41589-024-01713-2. [PMID: 39169270 DOI: 10.1038/s41589-024-01713-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/29/2024] [Indexed: 08/23/2024]
Abstract
Plastics are widely used materials that pose an ecological challenge because their wastes are difficult to degrade. Embedding enzymes and biomachinery within polymers could enable the biodegradation and disposal of plastics. However, enzymes rarely function under conditions suitable for polymer processing. Here, we report degradable living plastics by harnessing synthetic biology and polymer engineering. We engineered Bacillus subtilis spores harboring the gene circuit for the xylose-inducible secretory expression of Burkholderia cepacia lipase (BC-lipase). The spores that were resilient to stresses during material processing were mixed with poly(caprolactone) to produce living plastics in various formats. Spore incorporation did not compromise the physical properties of the materials. Spore recovery was triggered by eroding the plastic surface, after which the BC-lipase released by the germinated cells caused near-complete depolymerization of the polymer matrix. This study showcases a method for fabricating green plastics that can function when the spores are latent and decay when the spores are activated and sheds light on the development of materials for sustainability.
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Affiliation(s)
- Chenwang Tang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage; National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Lin Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jing Sun
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage; National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Guangda Chen
- Department of Mechanical and Energy Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Junfeng Shen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liang Wang
- Center for Polymers in Medicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ying Han
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiren Luo
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhiying Li
- Center for Polymers in Medicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Pei Zhang
- Department of Mechanical and Energy Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Simin Zeng
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Dianpeng Qi
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage; National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Jin Geng
- Center for Polymers in Medicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ji Liu
- Department of Mechanical and Energy Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Zhuojun Dai
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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2
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Díaz RE, Ecker AK, Correy GJ, Asthana P, Young ID, Faust B, Thompson MC, Seiple IB, Van Dyken S, Locksley RM, Fraser JS. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. eLife 2024; 12:RP89918. [PMID: 38884443 PMCID: PMC11182645 DOI: 10.7554/elife.89918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024] Open
Abstract
Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability to function under acidic conditions in the stomach but is also active in tissues with more neutral pHs, such as the lung. Here, we used a combination of biochemical, structural, and computational modeling approaches to examine how the mouse homolog (mAMCase) can act in both acidic and neutral environments. We measured kinetic properties of mAMCase activity across a broad pH range, quantifying its unusual dual activity optima at pH 2 and 7. We also solved high-resolution crystal structures of mAMCase in complex with oligomeric GlcNAcn, the building block of chitin, where we identified extensive conformational ligand heterogeneity. Leveraging these data, we conducted molecular dynamics simulations that suggest how a key catalytic residue could be protonated via distinct mechanisms in each of the two environmental pH ranges. These results integrate structural, biochemical, and computational approaches to deliver a more complete understanding of the catalytic mechanism governing mAMCase activity at different pH. Engineering proteins with tunable pH optima may provide new opportunities to develop improved enzyme variants, including AMCase, for therapeutic purposes in chitin degradation.
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Affiliation(s)
- Roberto Efraín Díaz
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - Andrew K Ecker
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
- Cardiovascular Research Institute, University of California, San FranciscoSan FranciscoUnited States
| | - Galen J Correy
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Pooja Asthana
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Iris D Young
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Bryan Faust
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Biophysics Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - Michael C Thompson
- Chemistry and Chemical Biology Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Chemistry and Chemical Biology, University of California, MercedMercedUnited States
| | - Ian B Seiple
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
- Cardiovascular Research Institute, University of California, San FranciscoSan FranciscoUnited States
| | - Steven Van Dyken
- Department of Pathology and Immunology, Washington University School of Medicine in St LouisSt LouisUnited States
| | - Richard M Locksley
- Department of Medicine, University of California, San FranciscoSan FranciscoUnited States
- Department of Microbiology and Immunology, University of California, San FranciscoSan FranciscoUnited States
- University of California, Howard Hughes Medical Institute, San FranciscoSan FranciscoUnited States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
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3
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Mao M, Ahrens L, Luka J, Contreras F, Kurkina T, Bienstein M, Sárria Pereira de Passos M, Schirinzi G, Mehn D, Valsesia A, Desmet C, Serra MÁ, Gilliland D, Schwaneberg U. Material-specific binding peptides empower sustainable innovations in plant health, biocatalysis, medicine and microplastic quantification. Chem Soc Rev 2024; 53:6445-6510. [PMID: 38747901 DOI: 10.1039/d2cs00991a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Material-binding peptides (MBPs) have emerged as a diverse and innovation-enabling class of peptides in applications such as plant-/human health, immobilization of catalysts, bioactive coatings, accelerated polymer degradation and analytics for micro-/nanoplastics quantification. Progress has been fuelled by recent advancements in protein engineering methodologies and advances in computational and analytical methodologies, which allow the design of, for instance, material-specific MBPs with fine-tuned binding strength for numerous demands in material science applications. A genetic or chemical conjugation of second (biological, chemical or physical property-changing) functionality to MBPs empowers the design of advanced (hybrid) materials, bioactive coatings and analytical tools. In this review, we provide a comprehensive overview comprising naturally occurring MBPs and their function in nature, binding properties of short man-made MBPs (<20 amino acids) mainly obtained from phage-display libraries, and medium-sized binding peptides (20-100 amino acids) that have been reported to bind to metals, polymers or other industrially produced materials. The goal of this review is to provide an in-depth understanding of molecular interactions between materials and material-specific binding peptides, and thereby empower the use of MBPs in material science applications. Protein engineering methodologies and selected examples to tailor MBPs toward applications in agriculture with a focus on plant health, biocatalysis, medicine and environmental monitoring serve as examples of the transformative power of MBPs for various industrial applications. An emphasis will be given to MBPs' role in detecting and quantifying microplastics in high throughput, distinguishing microplastics from other environmental particles, and thereby assisting to close an analytical gap in food safety and monitoring of environmental plastic pollution. In essence, this review aims to provide an overview among researchers from diverse disciplines in respect to material-(specific) binding of MBPs, protein engineering methodologies to tailor their properties to application demands, re-engineering for material science applications using MBPs, and thereby inspire researchers to employ MBPs in their research.
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Affiliation(s)
- Maochao Mao
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Leon Ahrens
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Julian Luka
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Francisca Contreras
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Tetiana Kurkina
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Marian Bienstein
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | | | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Andrea Valsesia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Cloé Desmet
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | | | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
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4
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Díaz RE, Ecker AK, Correy GJ, Asthana P, Young ID, Faust B, Thompson MC, Seiple IB, Van Dyken SJ, Locksley RM, Fraser JS. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.03.542675. [PMID: 37398339 PMCID: PMC10312649 DOI: 10.1101/2023.06.03.542675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability to function under acidic conditions in the stomach but is also active in tissues with more neutral pHs, such as the lung. Here, we used a combination of biochemical, structural, and computational modeling approaches to examine how the mouse homolog (mAMCase) can act in both acidic and neutral environments. We measured kinetic properties of mAMCase activity across a broad pH range, quantifying its unusual dual activity optima at pH 2 and 7. We also solved high resolution crystal structures of mAMCase in complex with oligomeric GlcNAcn, the building block of chitin, where we identified extensive conformational ligand heterogeneity. Leveraging these data, we conducted molecular dynamics simulations that suggest how a key catalytic residue could be protonated via distinct mechanisms in each of the two environmental pH ranges. These results integrate structural, biochemical, and computational approaches to deliver a more complete understanding of the catalytic mechanism governing mAMCase activity at different pH. Engineering proteins with tunable pH optima may provide new opportunities to develop improved enzyme variants, including AMCase, for therapeutic purposes in chitin degradation.
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Affiliation(s)
- Roberto Efraín Díaz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrew K Ecker
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Galen J Correy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Pooja Asthana
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Iris D Young
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bryan Faust
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael C Thompson
- Department of Chemistry and Chemical Biology, University of California, Merced, Merced, CA 95343, USA
| | - Ian B Seiple
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven J Van Dyken
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Richard M Locksley
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
- University of California, San Francisco, Howard Hughes Medical Institute, San Francisco, CA 94143, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
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5
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Guan F, Tian X, Zhang R, Zhang Y, Wu N, Sun J, Zhang H, Tu T, Luo H, Yao B, Tian J, Huang H. Enhancing the endo-activity of the thermophilic chitinase to yield chitooligosaccharides with high degrees of polymerization. BIORESOUR BIOPROCESS 2024; 11:29. [PMID: 38647930 PMCID: PMC10991111 DOI: 10.1186/s40643-024-00735-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/21/2024] [Indexed: 04/25/2024] Open
Abstract
Thermophilic endo-chitinases are essential for production of highly polymerized chitooligosaccharides, which are advantageous for plant immunity, animal nutrition and health. However, thermophilic endo-chitinases are scarce and the transformation from exo- to endo-activity of chitinases is still a challenging problem. In this study, to enhance the endo-activity of the thermophilic chitinase Chi304, we proposed two approaches for rational design based on comprehensive structural and evolutionary analyses. Four effective single-point mutants were identified among 28 designed mutations. The ratio of (GlcNAc)3 to (GlcNAc)2 quantity (DP3/2) in the hydrolysates of the four single-point mutants undertaking colloidal chitin degradation were 1.89, 1.65, 1.24, and 1.38 times that of Chi304, respectively. When combining to double-point mutants, the DP3/2 proportions produced by F79A/W140R, F79A/M264L, F79A/W272R, and M264L/W272R were 2.06, 1.67, 1.82, and 1.86 times that of Chi304 and all four double-point mutants exhibited enhanced endo-activity. When applied to produce chitooligosaccharides (DP ≥ 3), F79A/W140R accumulated the most (GlcNAc)4, while M264L/W272R was the best to produce (GlcNAc)3, which was 2.28 times that of Chi304. The two mutants had exposed shallower substrate-binding pockets and stronger binding abilities to shape the substrate. Overall, this research offers a practical approach to altering the cutting pattern of a chitinase to generate functional chitooligosaccharides.
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Affiliation(s)
- Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoqian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Food Science and Technology, Hebei Agricultural University, Hebei Baoding, 071000, China
| | - Ruohan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yan Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Food Science and Technology, Hebei Agricultural University, Hebei Baoding, 071000, China
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jilu Sun
- College of Food Science and Technology, Hebei Agricultural University, Hebei Baoding, 071000, China
| | - Honglian Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tao Tu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huiying Luo
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bin Yao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jian Tian
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Huoqing Huang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Brunecky R, Knott BC, Subramanian V, Linger JG, Beckham GT, Amore A, Taylor LE, Vander Wall TA, Lunin VV, Zheng F, Garrido M, Schuster L, Fulk EM, Farmer S, Himmel ME, Decker SR. Engineering of glycoside hydrolase family 7 cellobiohydrolases directed by natural diversity screening. J Biol Chem 2024; 300:105749. [PMID: 38354778 PMCID: PMC10943489 DOI: 10.1016/j.jbc.2024.105749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
Protein engineering and screening of processive fungal cellobiohydrolases (CBHs) remain challenging due to limited expression hosts, synergy-dependency, and recalcitrant substrates. In particular, glycoside hydrolase family 7 (GH7) CBHs are critically important for the bioeconomy and typically difficult to engineer. Here, we target the discovery of highly active natural GH7 CBHs and engineering of variants with improved activity. Using experimentally assayed activities of genome mined CBHs, we applied sequence and structural alignments to top performers to identify key point mutations linked to improved activity. From ∼1500 known GH7 sequences, an evolutionarily diverse subset of 57 GH7 CBH genes was expressed in Trichoderma reesei and screened using a multiplexed activity screening assay. Ten catalytically enhanced natural variants were identified, produced, purified, and tested for efficacy using industrially relevant conditions and substrates. Three key amino acids in CBHs with performance comparable or superior to Penicillium funiculosum Cel7A were identified and combinatorially engineered into P. funiculosum cel7a, expressed in T. reesei, and assayed on lignocellulosic biomass. The top performer generated using this combined approach of natural diversity genome mining, experimental assays, and computational modeling produced a 41% increase in conversion extent over native P. funiculosum Cel7A, a 55% increase over the current industrial standard T. reesei Cel7A, and 10% improvement over Aspergillus oryzae Cel7C, the best natural GH7 CBH previously identified in our laboratory.
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Affiliation(s)
- Roman Brunecky
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Brandon C Knott
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Venkataramanan Subramanian
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Jeffrey G Linger
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Gregg T Beckham
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Antonella Amore
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Larry E Taylor
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Todd A Vander Wall
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Vladimir V Lunin
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Fei Zheng
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Mercedes Garrido
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Logan Schuster
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Emily M Fulk
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Samuel Farmer
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Michael E Himmel
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA.
| | - Stephen R Decker
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, Golden, Colorado, USA.
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7
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Leadbeater DR, Bruce NC. Functional characterisation of a new halotolerant seawater active glycoside hydrolase family 6 cellobiohydrolase from a salt marsh. Sci Rep 2024; 14:3205. [PMID: 38332324 PMCID: PMC10853513 DOI: 10.1038/s41598-024-53886-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/06/2024] [Indexed: 02/10/2024] Open
Abstract
Realising a fully circular bioeconomy requires the valorisation of lignocellulosic biomass. Cellulose is the most attractive component of lignocellulose but depolymerisation is inefficient, expensive and resource intensive requiring substantial volumes of potable water. Seawater is an attractive prospective replacement, however seawater tolerant enzymes are required for the development of seawater-based biorefineries. Here, we report a halophilic cellobiohydrolase SMECel6A, identified and isolated from a salt marsh meta-exo-proteome dataset with high sequence divergence to previously characterised cellobiohydrolases. SMECel6A contains a glycoside hydrolase family 6 (GH6) domain and a carbohydrate binding module family 2 (CBM2) domain. Characterisation of recombinant SMECel6A revealed SMECel6A to be active upon crystalline and amorphous cellulose. Mono- and oligosaccharide product profiles revealed cellobiose as the major hydrolysis product confirming SMECel6A as a cellobiohydrolase. We show SMECel6A to be halophilic with optimal activity achieved in 0.5X seawater displaying 80.6 ± 6.93% activity in 1 × seawater. Structural predictions revealed similarity to a characterised halophilic cellobiohydrolase despite sharing only 57% sequence identity. Sequential thermocycling revealed SMECel6A had the ability to partially reversibly denature exclusively in seawater retaining significant activity. Our study confirms that salt marsh ecosystems harbour enzymes with attractive traits with biotechnological potential for implementation in ionic solution based bioprocessing systems.
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Affiliation(s)
- Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
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8
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Tanaka Y, Uchihashi T, Nakamura A. Product inhibition slow down the moving velocity of processive chitinase and sliding-intermediate state blocks re-binding of product. Arch Biochem Biophys 2024; 752:109854. [PMID: 38081338 DOI: 10.1016/j.abb.2023.109854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023]
Abstract
Processive movement is the key reaction for crystalline polymer degradation by enzyme. Product release is an important phenomenon in resetting the moving cycle, but how it affects chitinase kinetics was unknown. Therefore, we investigated the effect of diacetyl chitobiose (C2) on the biochemical activity and movement of chitinase A from Serratia marcescens (SmChiA). The apparent inhibition constant of C2 on crystalline chitin degradation of SmChiA was 159 μM. The binding position of C2 obtained by X-ray crystallography was at subsite +1, +2 and Trp275 interact with C2 at subsite +1. This binding state is consistent with the competitive inhibition obtained by biochemical analysis. The apparent inhibition constant of C2 on the moving velocity of high-speed (HS) AFM observations was 330 μM, which is close to the biochemical results, indicating that the main factor in crystalline chitin degradation is also the decrease in degradation activity due to inhibition of processive movement. The Trp275 is a key residue for making a sliding intermediate complex. SmChiA W275A showed weaker activity and affinity than WT against crystalline chitin because it is less processive than WT. In addition, biochemical apparent inhibition constant for C2 of SmChiA W275A was 45.6 μM. W275A mutant showed stronger C2 inhibition than WT even though the C2 binding affinity is weaker than WT. This result indicated that Trp275 is important for the interaction at subsite +1, but also important for making sliding intermediate complex and physically block the rebinding of C2 on the catalytic site for crystalline chitin degradation.
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Affiliation(s)
- Yoshiko Tanaka
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya,Suruga-ku, Shizuoka, 422-8529, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Aichi, 464-8602, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Higashiyama 5-1, Myodaiji, Okazaki, 444-0864, Japan
| | - Akihiko Nakamura
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Shizuoka Institute for the Study of Marine Biology and Chemistry, Shizuoka, Shizuoka, 422-8529, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaijicho, Okazaki, Aichi, 444-8787, Japan.
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9
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Zhao S, Liu M, Sun X, Jiang X, Li Y, Wu X, Wang L. Engineering the Relatively Conserved Residues in Active Site Architecture of Thermophilic Chitinase SsChi18A Enhanced Catalytic Activity. Biomacromolecules 2024; 25:238-247. [PMID: 38116793 DOI: 10.1021/acs.biomac.3c00936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Chitinase plays a vital role in the efficient biotransformation of the chitin substrate. This study aimed to modify and elucidate the contribution of the relatively conserved residues in the active site architecture of a thermophilic chitinase SsChi18A from Streptomyces sp. F-3 in processive catalysis. The enzymatic activity on colloidal chitin increased to 151%, 135%, and 129% in variants Y286W, E287A, and K186A compared with the wild type (WT). Also, the apparent processive parameter G2/G1 was lower in the variants compared to the WT, indicating the essential role of Tyr-286, Glu-287, and Lys-186 in processive catalysis. Additionally, the enzymatic activity on the crystalline chitin of F48W and double mutants F48W/Y209F and F48W/Y286W increased by 35%, 16%, and 36% compared with that for WT. Molecular dynamics simulations revealed that the driving force of processive catalysis might be related to the changes in interaction energy. This study provided a rational design strategy targeting relatively conserved residues to enhance the catalytic activity of GH18 processive chitinases.
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Affiliation(s)
- Sha Zhao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Mengyu Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Xiaomeng Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, People's Republic of China
| | - Yingjie Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
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10
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Paul M, Banerjee A, Maiti S, Mitra D, DasMohapatra PK, Thatoi H. Evaluation of substrate specificity and catalytic promiscuity of Bacillus albus cellulase: an insight into in silico proteomic study aiming at enhanced production of renewable energy. J Biomol Struct Dyn 2023:1-23. [PMID: 38126200 DOI: 10.1080/07391102.2023.2295971] [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: 05/09/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
Cellulases are enzymes that aid in the hydrolysis of cellulosic fibers and have a wide range of industrial uses. In the present in silico study, sequence alignment between cellulases from different Bacillus species revealed that most of the residues are conserved in those aligned enzymes. Three dimensional structures of cellulase enzymes from 23 different Bacillus species have been predicted and based on the alignment between the modeled structures, those enzymes have been categorized into 7 different groups according to the homology in their conformational folds. There are two structural contents in Gr-I cellulase namely β1-α2 and β3-α5 loops which varies greatly according to their static position. Molecular docking study between the B. albus cellulase and its various cellulosic substrates including xylanoglucan oligosaccharides revealed that residues viz. Phe154, Tyr258, Tyr282, Tyr285, and Tyr376 of B. albus cellulase are significantly involved in formation stacking interaction during enzyme-substrate binding. Residue interaction network and binding energy analysis for the B. albus cellulase with different cellulosic substrates depicted the strong affinity of XylGlc3 substrate with the receptor enzyme. Molecular interaction and molecular dynamics simulation studies exhibited structural stability of enzyme-substrate complexes which are greatly influenced by the presence of catalytic promiscuity in their substrate binding sites. Screening of B. albus in carboxymethylcellulose (CMC) and xylan supplemented agar media revealed the capability of the bacterium in degrading both cellulose and xylan. Overall, the study demonstrated B. albus cellulase as an effective biocatalyst candidate with the potential role of catalytic promiscuity for possible applications in biofuel industries.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, India
- Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Amrita Banerjee
- Oriental Institute of Science and Technology, Midnapore, India
| | - Smarajit Maiti
- Oriental Institute of Science and Technology, Midnapore, India
| | - Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, India
| | - Pradeep K DasMohapatra
- Department of Microbiology, Raiganj University, Raiganj, India
- PAKB Environment Conservation Centre, Raiganj University, Raiganj, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, India
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11
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Jia L, Zhao L, Qin B, Lu F, Liu D, Liu F. Enhancement of rice husks saccharification through hydrolase preparation assisted by lytic polysaccharide monooxygenase. Enzyme Microb Technol 2023; 171:110319. [PMID: 37672961 DOI: 10.1016/j.enzmictec.2023.110319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023]
Abstract
Rice husk is an abundant agricultural waste generated from rice production, but its application is limited. Considering its complex components, the rice husk was hydrolyzed by different enzymes to enhance its saccharification. In this study, saccharification of the rice husk by cellulase, xylosidase, and xylanase was first investigated. The synergistic effect of LPMO on the above hydrolases and different enzyme combinations in the saccharification process was then explored. Thereafter, the formulation of the enzyme cocktail and the degradation conditions were optimized to obtain the highest saccharification efficiency. The results showed that the optimum enzyme cocktail consists of Celluclast 1.5 L (83.3 mg/g substrate), the key enzymes in the saccharification process, worked with BpXyl (20 mg/g substrate), BpXyn11 (24 mg/g substrate), and R17L/N25G (4 mg/g substrate). The highest reducing sugar concentration (1.19 mg/mL) was obtained at pH 6.0 and 60 ℃ for 24 h. Fourier transform infrared spectroscopy and scanning electron microscopy were employed to characterize the structural changes in the rice husk after degradation. The results showed that the key chemical bonds in cellulose and hemicellulose were broken. This study illuminated the concept of saccharifying lignocellulose from rice husk using LPMO synergistically assisted combined-hydrolase including cellulase, xylosidase, and xylanase, and provided a theoretical basis for lignocellulose biodegradation.
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Affiliation(s)
- Li Jia
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin 300457, PR China
| | - Lei Zhao
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin 300457, PR China
| | - Bo Qin
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin 300457, PR China
| | - Fuping Lu
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin 300457, PR China
| | - Dingkuo Liu
- Tianjin Enterprise Key Laboratory of Biological Feed Additives, Tianjin 300111, PR China
| | - Fufeng Liu
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin 300457, PR China.
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12
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Maillard F, Kohler A, Morin E, Hossann C, Miyauchi S, Ziegler-Devin I, Gérant D, Angeli N, Lipzen A, Keymanesh K, Johnson J, Barry K, Grigoriev IV, Martin FM, Buée M. Functional genomics gives new insights into the ectomycorrhizal degradation of chitin. THE NEW PHYTOLOGIST 2023; 238:845-858. [PMID: 36702619 DOI: 10.1111/nph.18773] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Ectomycorrhizal (EcM) fungi play a crucial role in the mineral nitrogen (N) nutrition of their host trees. While it has been proposed that several EcM species also mobilize organic N, studies reporting the EcM ability to degrade N-containing polymers, such as chitin, remain scarce. Here, we assessed the capacity of a representative collection of 16 EcM species to acquire 15 N from 15 N-chitin. In addition, we combined genomics and transcriptomics to identify pathways involved in exogenous chitin degradation between these fungal strains. Boletus edulis, Imleria badia, Suillus luteus, and Hebeloma cylindrosporum efficiently mobilized N from exogenous chitin. EcM genomes primarily contained genes encoding for the direct hydrolysis of chitin. Further, we found a significant relationship between the capacity of EcM fungi to assimilate organic N from chitin and their genomic and transcriptomic potentials for chitin degradation. These findings demonstrate that certain EcM fungal species depolymerize chitin using hydrolytic mechanisms and that endochitinases, but not exochitinases, represent the enzymatic bottleneck of chitin degradation. Finally, this study shows that the degradation of exogenous chitin by EcM fungi might be a key functional trait of nutrient cycling in forests dominated by EcM fungi.
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Affiliation(s)
- François Maillard
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Christian Hossann
- Université de Lorraine, AgroParisTech, INRAE, SILVA, Silvatech, F-54000, Nancy, France
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | | | - Dominique Gérant
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, 54000, Nancy, France
| | - Nicolas Angeli
- Université de Lorraine, AgroParisTech, INRAE, SILVA, Silvatech, F-54000, Nancy, France
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
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13
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The interplay between lytic polysaccharide monooxygenases and glycoside hydrolases. Essays Biochem 2023; 67:551-559. [PMID: 36876880 DOI: 10.1042/ebc20220156] [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: 10/20/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 03/07/2023]
Abstract
In nature, enzymatic degradation of recalcitrant polysaccharides such as chitin and cellulose takes place by a synergistic interaction between glycoside hydrolases (GHs) and lytic polysaccharide monooxygenases (LPMOs). The two different families of carbohydrate-active enzymes use two different mechanisms when breaking glycosidic bonds between sugar moieties. GHs employ a hydrolytic activity and LPMOs are oxidative. Consequently, the topologies of the active sites differ dramatically. GHs have tunnels or clefts lined with a sheet of aromatic amino acid residues accommodating single polymer chains being threaded into the active site. LPMOs are adapted to bind to the flat crystalline surfaces of chitin and cellulose. It is believed that the LPMO oxidative mechanism provides new chain ends that the GHs can attach to and degrade, often in a processive manner. Indeed, there are many reports of synergies as well as rate enhancements when LPMOs are applied in concert with GHs. Still, these enhancements vary in magnitude with respect to the nature of the GH and the LPMO. Moreover, impediment of GH catalysis is also observed. In the present review, we discuss central works where the interplay between LPMOs and GHs has been studied and comment on future challenges to be addressed to fully use the potential of this interplay to improve enzymatic polysaccharide degradation.
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14
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Chaudhari YB, Várnai A, Sørlie M, Horn SJ, Eijsink VGH. Engineering cellulases for conversion of lignocellulosic biomass. Protein Eng Des Sel 2023; 36:gzad002. [PMID: 36892404 PMCID: PMC10394125 DOI: 10.1093/protein/gzad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023] Open
Abstract
Lignocellulosic biomass is a renewable source of energy, chemicals and materials. Many applications of this resource require the depolymerization of one or more of its polymeric constituents. Efficient enzymatic depolymerization of cellulose to glucose by cellulases and accessory enzymes such as lytic polysaccharide monooxygenases is a prerequisite for economically viable exploitation of this biomass. Microbes produce a remarkably diverse range of cellulases, which consist of glycoside hydrolase (GH) catalytic domains and, although not in all cases, substrate-binding carbohydrate-binding modules (CBMs). As enzymes are a considerable cost factor, there is great interest in finding or engineering improved and robust cellulases, with higher activity and stability, easy expression, and minimal product inhibition. This review addresses relevant engineering targets for cellulases, discusses a few notable cellulase engineering studies of the past decades and provides an overview of recent work in the field.
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Affiliation(s)
- Yogesh B Chaudhari
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
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15
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Li P, Wang X, Zhang C, Xu D. Processive binding mechanism of Cel9G from Clostridium cellulovorans: molecular dynamics and free energy landscape investigations. Phys Chem Chem Phys 2023; 25:646-657. [DOI: 10.1039/d2cp04830b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The processive binding mechanism of cellulose by Cel9G from C. cellulovorans was investigated by MD and metadynamics simulations.
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Affiliation(s)
- Penghui Li
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Chunchun Zhang
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
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16
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Penneru SK, Saharay M, Krishnan M. CelS-Catalyzed Processive Cellulose Degradation and Cellobiose Extraction for the Production of Bioethanol. J Chem Inf Model 2022; 62:6628-6638. [PMID: 35649216 DOI: 10.1021/acs.jcim.2c00239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bacterial cellulase enzymes are potent candidates for the efficient production of bioethanol, a promising alternative to fossil fuels, from cellulosic biomass. These enzymes catalyze the breakdown of cellulose in plant biomass into simple sugars and then to bioethanol. In the absence of the enzyme, the cellulosic biomass is recalcitrant to decomposition due to fermentation-resistant lignin and pectin coatings on the cellulose surface, which make them inaccessible for hydrolysis. Cellobiohydrolase CelS is a microbial enzyme that binds to cellulose fiber and efficiently cleaves it into a simple sugar (cellobiose) by a repeated processive chopping mechanism. The two contributing factors to the catalytic reaction rate and the yield of cellobiose are the efficient product expulsion from the product binding site of CelS and the movement of the substrate or cellulose chain into the active site. Despite progress in understanding product expulsion in other cellulases, much remains to be understood about the molecular mechanism of processive action of these enzymes. Here, nonequilibrium molecular dynamics simulations using suitable reaction coordinates are carried out to investigate the energetics and mechanism of the substrate dynamics and product expulsion in CelS. The calculated free energy barrier for the product expulsion is three times lower than that for the processive action indicating that product removal is relatively easier and faster than the sliding of the substrate to the catalytic active site. The water traffic near the active site in response to the product expulsion and the processive action is also explored.
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Affiliation(s)
- Sree Kavya Penneru
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996-1939, United States
| | - Moumita Saharay
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad 500046, Telangana, India
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad 500032, India
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17
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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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18
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The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases. Nat Commun 2022; 13:5577. [PMID: 36151080 PMCID: PMC9508125 DOI: 10.1038/s41467-022-33180-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/03/2022] [Indexed: 11/08/2022] Open
Abstract
In the barley β-D-glucan glucohydrolase, a glycoside hydrolase family 3 (GH3) enzyme, the Trp286/Trp434 clamp ensures β-D-glucosides binding, which is fundamental for substrate hydrolysis during plant growth and development. We employ mutagenesis, high-resolution X-ray crystallography, and multi-scale molecular modelling methods to examine the binding and conformational behaviour of isomeric β-D-glucosides during substrate-product assisted processive catalysis that operates in GH3 hydrolases. Enzyme kinetics reveals that the W434H mutant retains broad specificity, while W434A behaves as a strict (1,3)-β-D-glucosidase. Investigations of reactant movements on the nanoscale reveal that processivity is sensitive to mutation-specific alterations of the tryptophan clamp. While wild-type and W434H utilise a lateral cavity for glucose displacement and sliding of (1,3)-linked hydrolytic products through the catalytic site without dissociation, consistent with their high hydrolytic rates, W434A does not adopt processive catalysis. Phylogenomic analyses of GH3 hydrolases disclose the evolutionary advantage of the tryptophan clamp that confers broad specificity, high catalytic efficiency, and processivity.
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19
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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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20
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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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21
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Liu J, Xu Q, Wu Y, Sun D, Zhu J, Liu C, Liu W. Carbohydrate-binding modules of ChiB and ChiC promote the chitinolytic system of Serratia marcescens BWL1001. Enzyme Microb Technol 2022; 162:110118. [DOI: 10.1016/j.enzmictec.2022.110118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022]
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22
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Li P, Shi M, Wang X, Xu D. QM/MM investigation of the catalytic mechanism of processive endoglucanase Cel9G from Clostridium cellulovorans. Phys Chem Chem Phys 2022; 24:11919-11930. [PMID: 35514276 DOI: 10.1039/d2cp00593j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Carbohydrate degradation catalyzed by glucoside hydrolases (GHs) is a major mechanism in biomass conversion. GH family 9 endoglucanase (Cel9G) from Clostridium cellulovorans, a typical multimodular enzyme, contains a catalytic domain closely linked to a family 3c carbohydrate-binding module (CBM3c). Unlike the conventional behavior proposed for other carbohydrate-binding modules, CBM3c has a direct impact on catalytic activity. In this work, extensive molecular dynamics (MD) simulations were employed to clarify the functional role of CBM3c. Furthermore, the detailed catalytic mechanism of Cel9G was investigated at the atomistic level using the combined quantum mechanical and molecular mechanical (QM/MM) method. Based on these simulations, owing to the rigidity of the peptide linker, CBM3c may affect the enzymatic activity via direct interactions with alpha helix 4 of GH9, especially with the K123 and H125 residues. In addition, using cellohexaose as a substrate, the QM/MM MD simulations confirmed that this enzyme can cleave the β-1,4-glycosidic linkage via an inverting mechanism. An oxocarbenium ion-like transition state was located with a barrier height of 19.6 kcal mol-1. Furthermore, the G(-1) pyranose unit preferentially adopted a distorted 1S5/4H5 conformer in the enzyme-substrate complex. For the cleavage of the glycosidic bond, we were able to identify a plausible route (1S5/4H5 → [4H5/4E]# → 4C1) from the reactant to the product at the G(-1) site.
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Affiliation(s)
- Penghui Li
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, 610064, P. R. China.
| | - Mingsong Shi
- State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, 610064, P. R. China.
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, 610064, P. R. China.
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23
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Cord-Landwehr S, Moerschbacher BM. Deciphering the ChitoCode: fungal chitins and chitosans as functional biopolymers. Fungal Biol Biotechnol 2021; 8:19. [PMID: 34893090 PMCID: PMC8665597 DOI: 10.1186/s40694-021-00127-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022] Open
Abstract
Chitins and chitosans are among the most widespread and versatile functional biopolymers, with interesting biological activities and superior material properties. While chitins are evolutionary ancient and present in many eukaryotes except for higher plants and mammals, the natural distribution of chitosans, i.e. extensively deacetylated derivatives of chitin, is more limited. Unequivocal evidence for its presence is only available for fungi where chitosans are produced from chitin by the action of chitin deacetylases. However, neither the structural details such as fraction and pattern of acetylation nor the physiological roles of natural chitosans are known at present. We hypothesise that the chitin deacetylases are generating chitins and chitosans with specific acetylation patterns and that these provide information for the interaction with specific chitin- and chitosan-binding proteins. These may be structural proteins involved in the assembly of the complex chitin- and chitosan-containing matrices such as fungal cell walls and insect cuticles, chitin- and chitosan-modifying and -degrading enzymes such as chitin deacetylases, chitinases, and chitosanases, but also chitin- and chitosan-recognising receptors of the innate immune systems of plants, animals, and humans. The acetylation pattern, thus, may constitute a kind of 'ChitoCode', and we are convinced that new in silico, in vitro, and in situ analytical tools as well as new synthetic methods of enzyme biotechnology and organic synthesis are currently offering an unprecedented opportunity to decipher this code. We anticipate a deeper understanding of the biology of chitin- and chitosan-containing matrices, including their synthesis, assembly, mineralisation, degradation, and perception. This in turn will improve chitin and chitosan biotechnology and the development of reliable chitin- and chitosan-based products and applications, e.g. in medicine and agriculture, food and feed sciences, as well as cosmetics and material sciences.
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Affiliation(s)
- Stefan Cord-Landwehr
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Bruno M Moerschbacher
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany.
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24
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DelRe C, Chang B, Jayapurna I, Hall A, Wang A, Zolkin K, Xu T. Synergistic Enzyme Mixtures to Realize Near-Complete Depolymerization in Biodegradable Polymer/Additive Blends. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2105707. [PMID: 34623716 DOI: 10.1002/adma.202105707] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Embedding catalysts inside of plastics affords accelerated chemical modification with programmable latency and pathways. Nanoscopically embedded enzymes can lead to near-complete degradation of polyesters via chain-end mediated processive depolymerization. The overall degradation rate and pathways have a strong dependence on the morphology of semicrystalline polyesters. Yet, most studies to date focus on pristine polymers instead of mixtures that contain additives and other components despite their nearly universal use in plastic production. Here, additives are introduced to purposely change the morphology of polycaprolactone (PCL) by increasing the bending and twisting of crystalline lamellae. These morphological changes immobilize chain ends preferentially at the crystalline/amorphous interfaces and limit chain-end accessibility by the embedded processive enzyme. This chain-end redistribution reduces the polymer-to-monomer conversion from >95% to less than 50%, causing formation of highly crystalline plastic pieces, including microplastics. By synergizing both random chain scission and processive depolymerization, it is feasible to navigate morphological changes in polymer/additive blends and to achieve near-complete depolymerization. The random scission enzymes in the amorphous domains create new chain ends that are subsequently bound and depolymerized by processive enzymes. Present studies further highlight the importance to consider how the host polymer's morphologies affect the reactions catalyzed by embedded catalytic species.
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Affiliation(s)
- Christopher DelRe
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Boyce Chang
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Ivan Jayapurna
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Aaron Hall
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Ariel Wang
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Kyle Zolkin
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Ting Xu
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA
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25
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Jiménez-Ortega E, Kidibule PE, Fernández-Lobato M, Sanz-Aparicio J. Structural inspection and protein motions modelling of a fungal glycoside hydrolase family 18 chitinase by crystallography depicts a dynamic enzymatic mechanism. Comput Struct Biotechnol J 2021; 19:5466-5478. [PMID: 34712392 PMCID: PMC8515301 DOI: 10.1016/j.csbj.2021.09.027] [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: 07/22/2021] [Revised: 09/21/2021] [Accepted: 09/26/2021] [Indexed: 12/01/2022] Open
Abstract
Chitinases degrade chitin into low molecular weight chitooligomers, which have a broad range of industrial, agricultural, and medical functions. Understanding the relationship between the diverse characteristics of chitinases and their functions is necessary for the improvement of functional enzymes that meet specific requirements. We report here a full crystallographic analysis of three complexes obtained from the chitinase Chit42 from Trichoderma harzianum, which represent different states along the enzymatic mechanism. The inactive double mutant D169A/E171A was submitted to soaking/crystallization experiments with hexa-N-acetyl-glucosamine (NAG6) or tetra-N-acetyl-glucosamine (NAG4), trapping the enzyme-substrate complex (Chit42-NAG6), the enzyme-products complex (Chit42-NAG4-NAG2) and a someway intermediate state. Structural comparison among the different complexes depicts the determinants defining the different subsites and revealed a previously unobserved dynamic on-off ligand binding process associated with a motion of its insertion domain, which might be accompanying the role or aromatics in processivity. An ensemble refinement performed to extract dynamic details from the diffraction data elucidates the implication of some highly flexible residues in the productive sliding of the substrate and the product release event. These positions were submitted to mutagenesis and the activity of the variants was investigated in the hydrolysis of NAG6, colloidal chitin and two chitosans with different polymerization and acetylation degree. All the changes affected the Chit42 hydrolytic activity therefore confirming the involvement of these positions in catalysis. Furthermore, we found the variants R295S and E316S improving the apparent catalytic efficiency of chitin and NAG6 and, together with E316A, enhancing the specific activity on chitosan. Therefore, our results provide novel insight into the molecular mechanisms underlying the hydrolysis of chitinous material by fungal chitinases, and suggest new targets to address engineering of these biotechnologically important enzymes.
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Affiliation(s)
- Elena Jiménez-Ortega
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, 28006 Madrid, Spain
| | - Peter Elias Kidibule
- Department of Molecular Biology, Centre of Molecular Biology Severo Ochoa, CSIC-UAM, 28049 Madrid, Spain
| | - María Fernández-Lobato
- Department of Molecular Biology, Centre of Molecular Biology Severo Ochoa, CSIC-UAM, 28049 Madrid, Spain
| | - Julia Sanz-Aparicio
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, 28006 Madrid, Spain
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26
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Araújo EA, Dias AHS, Kadowaki MAS, Piyadov V, Pellegrini VOA, Urio MB, Ramos LP, Skaf MS, Polikarpov I. Impact of cellulose properties on enzymatic degradation by bacterial GH48 enzymes: Structural and mechanistic insights from processive Bacillus licheniformis Cel48B cellulase. Carbohydr Polym 2021; 264:118059. [PMID: 33910709 DOI: 10.1016/j.carbpol.2021.118059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 11/29/2022]
Abstract
Processive cellulases are highly efficient molecular engines involved in the cellulose breakdown process. However, the mechanism that processive bacterial enzymes utilize to recruit and retain cellulose strands in the catalytic site remains poorly understood. Here, integrated enzymatic assays, protein crystallography and computational approaches were combined to study the enzymatic properties of the processive BlCel48B cellulase from Bacillus licheniformis. Hydrolytic efficiency, substrate binding affinity, cleavage patterns, and the apparent processivity of bacterial BlCel48B are significantly impacted by the cellulose size and its surface morphology. BlCel48B crystallographic structure was solved with ligands spanning -5 to -2 and +1 to +2 subsites. Statistical coupling analysis and molecular dynamics show that co-evolved residues on active site are critical for stabilizing ligands in the catalytic tunnel. Our results provide mechanistic insights into BlCel48B molecular-level determinants of activity, substrate binding, and processivity on insoluble cellulose, thus shedding light on structure-activity correlations of GH48 family members in general.
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Affiliation(s)
- Evandro A Araújo
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil; Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials, Campinas 13083-970, São Paulo, Brazil
| | - Artur Hermano Sampaio Dias
- Institute of Chemistry and Center for Computer in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, São Paulo, Brazil
| | - Marco A S Kadowaki
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil
| | - Vasily Piyadov
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil
| | - Vanessa O A Pellegrini
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil
| | - Mateus B Urio
- Graduate Programs in Bioenergy, Chemistry and Chemical Engineering, Federal University of Paraná (UFPR), Curitiba 81531-980, Paraná, Brazil
| | - Luiz P Ramos
- Graduate Programs in Bioenergy, Chemistry and Chemical Engineering, Federal University of Paraná (UFPR), Curitiba 81531-980, Paraná, Brazil
| | - Munir S Skaf
- Institute of Chemistry and Center for Computer in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, São Paulo, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos 13560-970, São Paulo, Brazil.
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27
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Kari J, Molina GA, Schaller KS, Schiano-di-Cola C, Christensen SJ, Badino SF, Sørensen TH, Røjel NS, Keller MB, Sørensen NR, Kolaczkowski B, Olsen JP, Krogh KBRM, Jensen K, Cavaleiro AM, Peters GHJ, Spodsberg N, Borch K, Westh P. Physical constraints and functional plasticity of cellulases. Nat Commun 2021; 12:3847. [PMID: 34158485 PMCID: PMC8219668 DOI: 10.1038/s41467-021-24075-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
Enzyme reactions, both in Nature and technical applications, commonly occur at the interface of immiscible phases. Nevertheless, stringent descriptions of interfacial enzyme catalysis remain sparse, and this is partly due to a shortage of coherent experimental data to guide and assess such work. In this work, we produced and kinetically characterized 83 cellulases, which revealed a conspicuous linear free energy relationship (LFER) between the substrate binding strength and the activation barrier. The scaling occurred despite the investigated enzymes being structurally and mechanistically diverse. We suggest that the scaling reflects basic physical restrictions of the hydrolytic process and that evolutionary selection has condensed cellulase phenotypes near the line. One consequence of the LFER is that the activity of a cellulase can be estimated from its substrate binding strength, irrespectively of structural and mechanistic details, and this appears promising for in silico selection and design within this industrially important group of enzymes.
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Affiliation(s)
- Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gustavo A Molina
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kay S Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Corinna Schiano-di-Cola
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stefan J Christensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Silke F Badino
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Nanna S Røjel
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | - Malene B Keller
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg C, Denmark
| | - Nanna Rolsted Sørensen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | - Bartlomiej Kolaczkowski
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | | | | | | | | | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
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28
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Mekasha S, Tuveng TR, Vaaje-Kolstad G, Eijsink VGH. Chromatographic Assays for the Enzymatic Degradation of Chitin. Bio Protoc 2021; 11:e4014. [PMID: 34124313 DOI: 10.21769/bioprotoc.4014] [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: 12/06/2020] [Revised: 02/28/2021] [Accepted: 03/03/2021] [Indexed: 01/14/2023] Open
Abstract
Chitin is an insoluble linear polymer of β(1→4)-linked N-acetylglucosamine. Enzymatic cleavage of chitin chains can be achieved using hydrolytic enzymes, called chitinases, and/or oxidative enzymes, called lytic polysaccharide monooxygenases (LPMOs). These two groups of enzymes have different modes of action and yield different product types that require different analytical methods for detection and quantitation. While soluble chromogenic substrates are readily available for chitinases, proper insight into the activity of these enzymes can only be obtained by measuring activity toward their polymeric, insoluble substrate, chitin. For LPMOs, only assays using insoluble chitin are possible and relevant. Working with insoluble substrates complicates enzyme assays from substrate preparation to product analysis. Here, we describe typical set-ups for chitin degradation reactions and the chromatographic methods used for product analysis. Graphical abstract: Overview of chromatographic methods for assessing the enzymatic degradation of chitin.
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Affiliation(s)
- Sophanit Mekasha
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Tina R Tuveng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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29
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DelRe C, Jiang Y, Kang P, Kwon J, Hall A, Jayapurna I, Ruan Z, Ma L, Zolkin K, Li T, Scown CD, Ritchie RO, Russell TP, Xu T. Near-complete depolymerization of polyesters with nano-dispersed enzymes. Nature 2021; 592:558-563. [DOI: 10.1038/s41586-021-03408-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/01/2021] [Indexed: 02/08/2023]
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30
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Heymann D, Mohanram H, Kumar A, Verma CS, Lescar J, Miserez A. Structure of a consensus chitin-binding domain revealed by solution NMR. J Struct Biol 2021; 213:107725. [PMID: 33744410 DOI: 10.1016/j.jsb.2021.107725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/10/2021] [Accepted: 03/14/2021] [Indexed: 11/29/2022]
Abstract
Chitin-binding proteins (CBPs) are a versatile group of proteins found in almost every organism on earth. CBPs are involved in enzymatic carbohydrate degradation and also serve as templating scaffolds in the exoskeleton of crustaceans and insects. One specific chitin-binding motif found across a wide range of arthropods' exoskeletons is the "extended Rebers and Riddiford" consensus (R&R), whose mechanism of chitin binding remains unclear. Here, we report the 3D structure and molecular level interactions of a chitin-binding domain (CBD-γ) located in a CBP from the beak of the jumbo squid Dosidicus gigas. This CBP is one of four chitin-binding proteins identified in the beak mouthpart of D. gigas and is believed to interact with chitin to form a scaffold network that is infiltrated with a second set of structural proteins during beak maturation. We used solution state NMR spectroscopy to elucidate the molecular interactions between CBD-γ and the soluble chitin derivative pentaacetyl-chitopentaose (PCP), and find that folding of CBD-γ is triggered upon its interaction with PCP. To our knowledge, this is the first experimental 3D structure of a CBP containing the R&R consensus motif, which can be used as a template to understand in more details the role of the R&R motif found in a wide range of CBP-chitin complexes. The present structure also provides molecular information for biomimetic synthesis of graded biomaterials using aqueous-based chemistry and biopolymers.
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Affiliation(s)
- Dario Heymann
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), 59 Nanyang Drive, Level 06-01, Singapore 636921, Singapore
| | - Harini Mohanram
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553, Singapore
| | - Akshita Kumar
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553, Singapore; Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Chandra S Verma
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore 637551, Singapore; Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; Department of Biological Sciences, National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore
| | - Julien Lescar
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), 59 Nanyang Drive, Level 06-01, Singapore 636921, Singapore.
| | - Ali Miserez
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553, Singapore; School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), 59 Nanyang Drive, Level 06-01, Singapore 636921, Singapore.
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31
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Li Y, Gou Y, Liu Z, Xie T, Wang G. Structure-based rational design of chitosanase CsnMY002 for high yields of chitobiose. Colloids Surf B Biointerfaces 2021; 202:111692. [PMID: 33744813 DOI: 10.1016/j.colsurfb.2021.111692] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 10/21/2022]
Abstract
Chitosan oligosaccharides (COS) are attractive active molecules for biomedical applications. Currently, the prohibitively high cost of producing fully defined COS hampers extensive studies on their biological activity and restricts their use in various industries. Thus, cost-effective production of pure COS is of major importance. In this report, chitosanase from Bacillus subtilis MY002 (CsnMY002) was prepared for COS production. The structure of apo CsnMY002 displayed an unexpected tunnel-like substrate-binding site and the structure of the CsnMY002_E19A/(GlcN)6 complex highlighted the "4 + 2″ splitting of hexaglucosamine even though the "3 + 3″ splitting is also observed in the TLC analysis of the enzyme products for hexaglucosamine. Structure based rational design was performed to generate mutants for chitobiose production. The CsnMY002_G21 K mutant produced chitobiose with a relative content > 87 % from chitosan with a low degree of acetylation, and 50.65 mg chitobiose with a purity > 98 % was prepared from 100 mg chitosan. The results provide insight on the catalytic mechanism of chitosanase and underpin future biomedical applications of pure chitobiose.
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Affiliation(s)
- Yubin Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, 610041, China; College of Life Sciences, Sichuan University, Chengdu, 610064, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Gou
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongchuan Liu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, 610041, China
| | - Tian Xie
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, 610041, China
| | - Ganggang Wang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, 610041, China; The Innovative Academy of Seed Design (INASEED), Chinese Academy of Sciences, Beijing, 100101, China.
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32
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Chemical Proprieties of Biopolymers (Chitin/Chitosan) and Their Synergic Effects with Endophytic Bacillus Species: Unlimited Applications in Agriculture. Molecules 2021; 26:molecules26041117. [PMID: 33672446 PMCID: PMC7923285 DOI: 10.3390/molecules26041117] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 11/17/2022] Open
Abstract
Over the past decade, reckless usage of synthetic pesticides and fertilizers in agriculture has made the environment and human health progressively vulnerable. This setting leads to the pursuit of other environmentally friendly interventions. Amongst the suggested solutions, the use of chitin and chitosan came about, whether alone or in combination with endophytic bacterial strains. In the framework of this research, we reported an assortment of studies on the physico-chemical properties and potential applications in the agricultural field of two biopolymers extracted from shrimp shells (chitin and chitosan), in addition to their uses as biofertilizers and biostimulators in combination with bacterial strains of the genus Bacillus sp. (having biochemical and enzymatic properties).
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33
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Singh RV, Sambyal K, Negi A, Sonwani S, Mahajan R. Chitinases production: A robust enzyme and its industrial applications. BIOCATAL BIOTRANSFOR 2021. [DOI: 10.1080/10242422.2021.1883004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Krishika Sambyal
- University Institute of Biotechnology, Chandigarh University, Gharuan, India
| | - Anjali Negi
- University Institute of Biotechnology, Chandigarh University, Gharuan, India
| | - Shubham Sonwani
- Department of Biosciences, Christian Eminent College, Indore, India
| | - Ritika Mahajan
- Department of Microbiology, School of Sciences, JAIN (Deemed-to-be University), Bengaluru, India
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34
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Cheng C, Haider J, Liu P, Yang J, Tan Z, Huang T, Lin J, Jiang M, Liu H, Zhu L. Engineered LPMO Significantly Boosting Cellulase-Catalyzed Depolymerization of Cellulose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:15257-15266. [PMID: 33290065 DOI: 10.1021/acs.jafc.0c05979] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) play a crucial role in the enzymatic depolymerization of cellulose through oxidative cleavage of the glycosidic bond in the highly recalcitrant crystalline cellulose region. Improving the activity of LPMOs is of considerable importance for second-generation biorefinery. In this study, we identified a beneficial amino acid substitution (N526S) located in the cellulose binding module (CBM) of HcLPMO10 (LPMO of Hahella chejuensis) using directed evolution. The improved variant HcLPMO10 M1 (N526S) exhibits 2.1-fold higher activity for the H2O2 production, 2.7-fold higher oxidation activity, and 1.9-fold higher binding capacity toward cellulose compared with those of the wild type (WT). Furthermore, M1 shows 2.1-fold higher activity for degradation of crystalline cellulose in synergy with cellulase, compared to the WT. Structural analysis through molecular modeling and molecular dynamics (MD) simulation revealed that the substitution N526S located in the CBM likely stabilizes the cellulose binding surface and enhances the binding capacity of HcLPMO10 to cellulose, thereby enhancing enzyme activity. These findings demonstrate the important role of the CBM in the catalytic function of LPMO.
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Affiliation(s)
- Chao Cheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Junaid Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jianhua Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Zijian Tan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Tianchen Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Department of Biological Engineering, College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, P. R. China
| | - Jianping Lin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Haifeng Liu
- Institute of Chemistry, NAWI Graz, BioTechMed Graz, University of Graz, Heinrichstrasse 28, Graz 8010, Austria
| | - Leilei Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
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Selection and mutational analyses of the substrate interacting residues of a chitinase from Enterobacter cloacae subsp. cloacae (EcChi2) to improve transglycosylation. Int J Biol Macromol 2020; 165:2432-2441. [PMID: 33096170 DOI: 10.1016/j.ijbiomac.2020.10.125] [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: 09/15/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 01/05/2023]
Abstract
Transglycosylation (TG) by Enterobacter cloacae subsp. cloacae chitinase 2 (EcChi2) has been deciphered by site-directed mutagenesis. EcChi2 originally displayed feeble TG with chitin oligomer with a degree of polymerization (DP4), for a short duration. Based on the 3D modelling and molecular docking analyses, we altered the substrate interactions at the substrate-binding cleft, catalytic center, and catalytic groove of EcChi2 by mutational approach to improve TG. The mutation of W166A and T277A increased TG by EcChi2 and also affected its catalytic efficiency on the polymeric substrates. Whereas, R171A had a drastically decreased hydrolytic activity but, retained TG activity. In the increased hydrolytic activity of the T277A, altered interactions with the substrates played an indirect role in the catalysis. Mutation of the central Asp, in the conserved DxDxE motif, to Ala (D314A) and Asn (D314N) conversion yielded DP5-DP8 TG products. The quantifiable TG products (DP5 and DP6) increased to 8% (D314A) and 7% (D314N), resulting in a hyper-transglycosylating mutant. Mutation of W276A and W398A resulted in the loss of TG activity, indicating that the aromatic residues (W276 and W398) at +1 and +2 subsites are essential for the TG activity of EcChi2.
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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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Mallakuntla MK, Podile AR. Catalytic efficiency of a multi-domain transglycosylating chitinase from Enterobacter cloacae subsp. cloacae (EcChi2) is influenced by polycystic kidney disease domains. Enzyme Microb Technol 2020; 143:109702. [PMID: 33375970 DOI: 10.1016/j.enzmictec.2020.109702] [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: 06/27/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 11/24/2022]
Abstract
Bacterial chitinases recruited multiple accessory domains for the conversion of recalcitrant polysaccharides to simple soluble sugars/amino sugars. Here, we report detailed properties of a multi-domain GH18 chitinase from Enterobacter cloacae subsp. cloacae (EcChi2) that preferred β-chitin as substrate. EcChi2 exhibited transglycosylation (TG) activity on oligomeric substrates from DP4-DP6. The high amount of DP2 is indicative of exo mode activity of EcChi2. We generated EcChi2 variants (truncated and fusion chimeras) and elucidated the role of catalytic and accessory domains. The catalytic efficiency of truncated GH18 and fusion chimera of GH18+ChBD1-ChBD2 decreased to 22 and 17-fold, respectively, than EcChi2, and lost the hydrolytic activity on polymeric substrates, except colloidal chitin. On the other hand, the catalytic activity of truncated PKD1-GH18-PKD2 on polymeric and oligomeric substrates was similar to EcChi2, suggesting that PKD domains are essential for increasing the rate of hydrolysis. Moreover, the truncated ChBD1-ChBD2 and fusion PKD1 + PKD2 participated in chitin-binding.
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Affiliation(s)
- Mohan Krishna Mallakuntla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 50046, Telangana, India
| | - Appa Rao Podile
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 50046, Telangana, India.
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Rani TS, Madhuprakash J, Podile AR. Chitinase-E from Chitiniphilus shinanonensis generates chitobiose from chitin flakes. Int J Biol Macromol 2020; 163:1037-1043. [DOI: 10.1016/j.ijbiomac.2020.07.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
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Glycoside hydrolase family 18 chitinases: The known and the unknown. Biotechnol Adv 2020; 43:107553. [DOI: 10.1016/j.biotechadv.2020.107553] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/09/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
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40
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Forsberg Z, Stepnov AA, Nærdal GK, Klinkenberg G, Eijsink VGH. Engineering lytic polysaccharide monooxygenases (LPMOs). Methods Enzymol 2020; 644:1-34. [PMID: 32943141 DOI: 10.1016/bs.mie.2020.04.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are mono-copper enzymes that catalyze the hydroxylation of glycosidic bonds found in the most abundant and recalcitrant polysaccharides on Earth. Since their discovery in 2010, these enzymes have received extensive attention in both fundamental and applied research due to their remarkable oxidative power and synergistic interplay with hydrolytic enzymes. The harsh and unnatural conditions used in industrial enzymatic saccharification processes and the sensitivity of LPMOs for damage induced by reactive oxygen species call for enzyme engineering to develop LPMOs to become robust industrial biocatalysts. Other engineering targets include improved catalytic activity, adjusted substrate specificity and the introduction of completely new activities. Reaching these targets not only requires appropriate methods for measuring enzyme activity, but also requires in-depth knowledge of the active site and the reaction mechanism, which is yet to be achieved in the LPMO field. Here we describe what has been done in the LPMO engineering field so far. Furthermore, we address the difficulties involved in properly assessing LPMO functionality, which are due to common side reactions taking place in LPMO reactions and which complicate screening methods.
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Affiliation(s)
- Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Guro Kruge Nærdal
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Geir Klinkenberg
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway.
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41
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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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Mohamad Zabidi NA, Foo HL, Loh TC, Mohamad R, Abdul Rahim R. Enhancement of Versatile Extracellular Cellulolytic and Hemicellulolytic Enzyme Productions by Lactobacillus plantarum RI 11 Isolated from Malaysian Food Using Renewable Natural Polymers. Molecules 2020; 25:molecules25112607. [PMID: 32503356 PMCID: PMC7321320 DOI: 10.3390/molecules25112607] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 02/02/2023] Open
Abstract
Lactobacillus plantarum RI 11 was reported recently to be a potential lignocellulosic biomass degrader since it has the capability of producing versatile extracellular cellulolytic and hemicellulolytic enzymes. Thus, this study was conducted to evaluate further the effects of various renewable natural polymers on the growth and production of extracellular cellulolytic and hemicellulolytic enzymes by this novel isolate. Basal medium supplemented with molasses and yeast extract produced the highest cell biomass (log 10.51 CFU/mL) and extracellular endoglucanase (11.70 µg/min/mg), exoglucanase (9.99 µg/min/mg), β-glucosidase (10.43 nmol/min/mg), and mannanase (8.03 µg/min/mg), respectively. Subsequently, a statistical optimization approach was employed for the enhancement of cell biomass, and cellulolytic and hemicellulolytic enzyme productions. Basal medium that supplemented with glucose, molasses and soybean pulp (F5 medium) or with rice straw, yeast extract and soybean pulp (F6 medium) produced the highest cell population of log 11.76 CFU/mL, respectively. However, formulated F12 medium supplemented with glucose, molasses and palm kernel cake enhanced extracellular endoglucanase (4 folds), exoglucanase (2.6 folds) and mannanase (2.6 folds) specific activities significantly, indicating that the F12 medium could induce the highest production of extracellular cellulolytic and hemicellulolytic enzymes concomitantly. In conclusion, L. plantarum RI 11 is a promising and versatile bio-transformation agent for lignocellulolytic biomass.
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Affiliation(s)
- Nursyafiqah A. Mohamad Zabidi
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; (N.A.M.Z.); (R.M.)
| | - Hooi Ling Foo
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; (N.A.M.Z.); (R.M.)
- Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia;
- Correspondence: (H.L.F.); (T.C.L.); Tel.: +60-3-9769-7476 (H.L.F.); +60-3-97694814 (T.C.L.)
| | - Teck Chwen Loh
- Department of Animal Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia
- Correspondence: (H.L.F.); (T.C.L.); Tel.: +60-3-9769-7476 (H.L.F.); +60-3-97694814 (T.C.L.)
| | - Rosfarizan Mohamad
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; (N.A.M.Z.); (R.M.)
- Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia;
- Institute of Tropical Forestry and Forest Products, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia
| | - Raha Abdul Rahim
- Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia;
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia
- Office of Vice Chancellor, Universiti Teknikal Malaysia Melaka, Jalan Hang Tuah Jaya, Durian Tunggal 76100, Melaka, Malaysia
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Cord-Landwehr S, Richter C, Wattjes J, Sreekumar S, Singh R, Basa S, El Gueddari NE, Moerschbacher BM. Patterns matter part 2: Chitosan oligomers with defined patterns of acetylation. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104577] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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44
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Sørlie M, Horn SJ, Vaaje-Kolstad G, Eijsink VG. Using chitosan to understand chitinases and the role of processivity in the degradation of recalcitrant polysaccharides. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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45
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Barad BA, Liu L, Diaz RE, Basilio R, Van Dyken SJ, Locksley RM, Fraser JS. Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates. Protein Sci 2020; 29:966-977. [PMID: 31930591 PMCID: PMC7096708 DOI: 10.1002/pro.3822] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 12/24/2022]
Abstract
Chitin is an abundant polysaccharide used by many organisms for structural rigidity and water repulsion. As such, the insoluble crystalline structure of chitin poses significant challenges for enzymatic degradation. Acidic mammalian chitinase, a processive glycosyl hydrolase, is the primary enzyme involved in the degradation of environmental chitin in mammalian lungs. Mutations to acidic mammalian chitinase have been associated with asthma, and genetic deletion in mice increases morbidity and mortality with age. We initially set out to reverse this phenotype by engineering hyperactive acidic mammalian chitinase variants. Using a screening approach with commercial fluorogenic substrates, we identified mutations with consistent increases in activity. To determine whether the activity increases observed were consistent with more biologically relevant chitin substrates, we developed new assays to quantify chitinase activity with insoluble chitin, and identified a one-pot fluorogenic assay that is sufficiently sensitive to quantify changes to activity due to the addition or removal of a carbohydrate-binding domain. We show that the activity increases from our directed evolution screen were lost when insoluble substrates were used. In contrast, naturally occurring gain-of-function mutations gave similar results with oligomeric and insoluble substrates. We also show that activity differences between acidic mammalian chitinase and chitotriosidase are reduced with insoluble substrate, suggesting that previously reported activity differences with oligomeric substrates may have been driven by differential substrate specificity. These results highlight the need for assays against physiological substrates when engineering metabolic enzymes, and provide a new one-pot assay that may prove to be broadly applicable to engineering glycosyl hydrolases.
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Affiliation(s)
- Benjamin A. Barad
- Department of Bioengineering and Therapeutic SciencesUniversity of CaliforniaSan FranciscoCalifornia
- Biophysics Graduate ProgramUniversity of CaliforniaSan FranciscoCalifornia
| | - Lin Liu
- Department of Bioengineering and Therapeutic SciencesUniversity of CaliforniaSan FranciscoCalifornia
| | - Roberto E. Diaz
- Department of Bioengineering and Therapeutic SciencesUniversity of CaliforniaSan FranciscoCalifornia
- Tetrad Graduate ProgramUniversity of CaliforniaSan FranciscoCalifornia
| | - Ralp Basilio
- Department of Bioengineering and Therapeutic SciencesUniversity of CaliforniaSan FranciscoCalifornia
- Science Education Partnership High School Intern Program, University of CaliforniaSan FranciscoCalifornia
| | - Steven J. Van Dyken
- Department of Pathology and ImmunologyWashington University School of Medicine in St. LouisSt. LouisMissouri
| | - Richard M. Locksley
- Department of MedicineUniversity of CaliforniaSan FranciscoCalifornia
- Department of Microbiology and ImmunologyUniversity of CaliforniaSan FranciscoCalifornia
- Howard Hughes Medical InstituteSan FranciscoCalifornia
| | - James S. Fraser
- Department of Bioengineering and Therapeutic SciencesUniversity of CaliforniaSan FranciscoCalifornia
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46
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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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47
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Abstract
Cellulase enzymes deconstruct recalcitrant cellulose into soluble sugars, making them a biocatalyst of biotechnological interest for use in the nascent lignocellulosic bioeconomy. Cellobiohydrolases (CBHs) are cellulases capable of liberating many sugar molecules in a processive manner without dissociating from the substrate. Within the complete processive cycle of CBHs, dissociation from the cellulose substrate is rate limiting, but the molecular mechanism of this step is unknown. Here, we present a direct comparison of potential molecular mechanisms for dissociation via Hamiltonian replica exchange molecular dynamics of the model fungal CBH, Trichoderma reesei Cel7A. Computational rate estimates indicate that stepwise cellulose dethreading from the binding tunnel is 4 orders of magnitude faster than a clamshell mechanism, in which the substrate-enclosing loops open and release the substrate without reversing. We also present the crystal structure of a disulfide variant that covalently links substrate-enclosing loops on either side of the substrate-binding tunnel, which constitutes a CBH that can only dissociate via stepwise dethreading. Biochemical measurements indicate that this variant has a dissociation rate constant essentially equivalent to the wild type, implying that dethreading is likely the predominant mechanism for dissociation.
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48
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Wang W, Archbold T, Lam JS, Kimber MS, Fan MZ. A processive endoglucanase with multi-substrate specificity is characterized from porcine gut microbiota. Sci Rep 2019; 9:13630. [PMID: 31541154 PMCID: PMC6754456 DOI: 10.1038/s41598-019-50050-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 09/05/2019] [Indexed: 02/08/2023] Open
Abstract
Cellulases play important roles in the dietary fibre digestion in pigs, and have multiple industrial applications. The porcine intestinal microbiota display a unique feature in rapid cellulose digestion. Herein, we have expressed a cellulase gene, p4818Cel5_2A, which singly encoded a catalytic domain belonging to glycoside hydrolase family 5 subfamily 2, and was previously identified from a metagenomic expression library constructed from porcine gut microbiome after feeding grower pigs with a cellulose-supplemented diet. The activity of purified p4818Cel5_2A was maximal at pH 6.0 and 50 °C and displayed resistance to trypsin digestion. This enzyme exhibited activities towards a wide variety of plant polysaccharides, including cellulosic substrates of avicel and solka-Floc®, and the hemicelluloses of β-(1 → 4)/(1 → 3)-glucans, xyloglucan, glucomannan and galactomannan. Viscosity, reducing sugar distribution and hydrolysis product analyses further revealed that this enzyme was a processive endo-β-(1 → 4)-glucanase capable of hydrolyzing cellulose into cellobiose and cellotriose as the primary end products. These catalytic features of p4818Cel5_2A were further explored in the context of a three-dimensional homology model. Altogether, results of this study report a microbial processive endoglucanase identified from the porcine gut microbiome, and it may be tailored as an efficient biocatalyst candidate for potential industrial applications.
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Affiliation(s)
- Weijun Wang
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Tania Archbold
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Joseph S Lam
- Department of Cellular and Molecular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Matthew S Kimber
- Department of Cellular and Molecular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Ming Z Fan
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
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Jana S, Hamre AG, Eijsink VGH, Sørlie M, Payne CM. Polar residues lining the binding cleft of a Serratia marcescens family 18 chitinase position the substrate for attack and stabilize associative interactions. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1657600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - Anne Grethe Hamre
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Morten Sørlie
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
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Hefferon KL, Cantero‐Tubilla B, Brady J, Wilson D. Aromatic residues surrounding the active site tunnel of TfCel48A influence activity, processivity, and synergistic interactions with other cellulases. Biotechnol Bioeng 2019; 116:2463-2472. [DOI: 10.1002/bit.27086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/29/2019] [Accepted: 06/02/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Kathleen L. Hefferon
- Department of Cellular and Molecular GeneticsCornell University Ithaca New York
- Department of Food Science and TechnologyCornell University Ithaca New York
| | - Borja Cantero‐Tubilla
- Robert Frederick Smith School of Chemical and Biomolecular EngineeringCornell University Ithaca New York
| | - John Brady
- Department of Food Science and TechnologyCornell University Ithaca New York
| | - David Wilson
- Department of Cellular and Molecular GeneticsCornell University Ithaca New York
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