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Chen X, Pang L, Yang W, Tian H, Yi Y, Xia B. Enhanced degradation of insoluble chitin: Engineering high-efficiency chitinase fusion enzymes for sustainable applications. BIORESOURCE TECHNOLOGY 2024; 412:131401. [PMID: 39218366 DOI: 10.1016/j.biortech.2024.131401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
N-acetyl-D-glucosamine and its dimer are degradation products of chitin waste with great potential in therapeutic and agricultural applications. However, the hydrolysis of insoluble chitin by chitinases remains a major bottleneck. This study investigated the biochemical properties and catalytic mechanisms of PoChi chitinase obtained from Penicillium oxalicum with a focus on enhancing its efficiency during the degradation of insoluble chitin. Recombinant plasmids were engineered to incorporate chitin-binding (ChBD) and/or fibronectin III (FnIII) domains. Notably, PoChi-FnIII-ChBD exhibited the highest substrate affinity (Km = 2.7 mg/mL) and a specific activity of 15.4 U/mg, which surpasses those of previously reported chitinases. These findings highlight the potential of engineered chitinases in advancing industrial biotechnology applications and offer a promising approach to more sustainable chitin waste management.
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Affiliation(s)
- Xiao Chen
- College of Food Science and Technology, Hunan Agricultural University, East Renmin Road, Changsha, Hunan 410128, China
| | - Li Pang
- College of Horticulture, Hunan Agricultural University, East Renmin Road, Changsha, Hunan 410128, China
| | - Wentao Yang
- College of Food Science and Technology, Hunan Agricultural University, East Renmin Road, Changsha, Hunan 410128, China
| | - Hong Tian
- College of Food Science and Technology, Hunan Agricultural University, East Renmin Road, Changsha, Hunan 410128, China
| | - Youjin Yi
- College of Food Science and Technology, Hunan Agricultural University, East Renmin Road, Changsha, Hunan 410128, China
| | - Bo Xia
- College of Food Science and Technology, Hunan Agricultural University, East Renmin Road, Changsha, Hunan 410128, China.
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2
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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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Røjel N, Kari J, Sørensen TH, Badino SF, Morth JP, Schaller K, Cavaleiro AM, Borch K, Westh P. Substrate binding in the processive cellulase Cel7A: Transition state of complexation and roles of conserved tryptophan residues. J Biol Chem 2020; 295:1454-1463. [PMID: 31848226 PMCID: PMC7008363 DOI: 10.1074/jbc.ra119.011420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/17/2019] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases effectively degrade cellulose and are of biotechnological interest because they can convert lignocellulosic biomass to fermentable sugars. Here, we implemented a fluorescence-based method for real-time measurements of complexation and decomplexation of the processive cellulase Cel7A and its insoluble substrate, cellulose. The method enabled detailed kinetic and thermodynamic analyses of ligand binding in a heterogeneous system. We studied WT Cel7A and several variants in which one or two of four highly conserved Trp residues in the binding tunnel had been replaced with Ala. WT Cel7A had on/off-rate constants of 1 × 105 m-1 s-1 and 5 × 10-3 s-1, respectively, reflecting the slow dynamics of a solid, polymeric ligand. Especially the off-rate constant was many orders of magnitude lower than typical values for small, soluble ligands. Binding rate and strength both were typically lower for the Trp variants, but effects of the substitutions were moderate and sometimes negligible. Hence, we propose that lowering the activation barrier for complexation is not a major driving force for the high conservation of the Trp residues. Using so-called Φ-factor analysis, we analyzed the kinetic and thermodynamic results for the variants. The results of this analysis suggested a transition state for complexation and decomplexation in which the reducing end of the ligand is close to the tunnel entrance (near Trp-40), whereas the rest of the binding tunnel is empty. We propose that this structure defines the highest free-energy barrier of the overall catalytic cycle and hence governs the turnover rate of this industrially important enzyme.
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Affiliation(s)
- Nanna Røjel
- Institut for Naturvidenskab og Miljo, Roskilde University, DK-4000 Roskilde, Denmark
| | - Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | | - Silke F Badino
- Institut for Naturvidenskab og Miljo, Roskilde University, DK-4000 Roskilde, Denmark
| | - J Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Kay Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | | - Kim Borch
- Novozymes A/S, DK-2800 Kgs. Lyngby Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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Abstract
Extracellular polysaccharides and glycoproteins of pathogenic bacteria assist in adherence, autoaggregation, biofilm formation, and host immune system evasion. As a result, considerable research in the field of glycobiology is dedicated to study the composition and function of glycans associated with virulence, as well as the enzymes involved in their biosynthesis with the aim to identify novel antibiotic targets. Especially, insights into the enzyme mechanism, substrate binding, and transition-state structures are valuable as a starting point for rational inhibitor design. An intriguing aspect of enzymes that generate or process polysaccharides and glycoproteins is the level of processivity. The existence of enzymatic processivity reflects the need for regulation of the final glycan/glycoprotein length and structure, depending on the role they perform. In this Review, we describe the currently reported examples of various processive enzymes involved in polymerization and transfer of sugar moieties, predominantly in bacterial pathogens, with a focus on the biochemical methods, to showcase the importance of studying processivity for understanding the mechanism.
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Affiliation(s)
- Liubov Yakovlieva
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Marthe T. C. Walvoort
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
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Visootsat A, Nakamura A, Vignon P, Watanabe H, Uchihashi T, Iino R. Single-molecule imaging analysis reveals the mechanism of a high-catalytic-activity mutant of chitinase A from Serratia marcescens. J Biol Chem 2020; 295:1915-1925. [PMID: 31924658 PMCID: PMC7029130 DOI: 10.1074/jbc.ra119.012078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/03/2020] [Indexed: 12/17/2022] Open
Abstract
Chitin degradation is important for biomass conversion and has potential applications for agriculture, biotechnology, and the pharmaceutical industry. Chitinase A from the Gram-negative bacterium Serratia marcescens (SmChiA) is a processive enzyme that hydrolyzes crystalline chitin as it moves linearly along the substrate surface. In a previous study, the catalytic activity of SmChiA against crystalline chitin was found to increase after the tryptophan substitution of two phenylalanine residues (F232W and F396W), located at the entrance and exit of the substrate binding cleft of the catalytic domain, respectively. However, the mechanism underlying this high catalytic activity remains elusive. In this study, single-molecule fluorescence imaging and high-speed atomic force microscopy were applied to understand the mechanism of this high-catalytic-activity mutant. A reaction scheme including processive catalysis was used to reproduce the properties of SmChiA WT and F232W/F396W, in which all of the kinetic parameters were experimentally determined. High activity of F232W/F396W mutant was caused by a high processivity and a low dissociation rate constant after productive binding. The turnover numbers for both WT and F232W/F396W, determined by the biochemical analysis, were well-replicated using the kinetic parameters obtained from single-molecule imaging analysis, indicating the validity of the reaction scheme. Furthermore, alignment of amino acid sequences of 258 SmChiA-like proteins revealed that tryptophan, not phenylalanine, is the predominant amino acid at the corresponding positions (Phe-232 and Phe-396 for SmChiA). Our study will be helpful for understanding the kinetic mechanisms and further improvement of crystalline chitin hydrolytic activity of SmChiA mutants.
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Affiliation(s)
- Akasit Visootsat
- Department of Functional Molecular Science, School of Physical Sciences, Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Akihiko Nakamura
- Department of Functional Molecular Science, School of Physical Sciences, Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Paul Vignon
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Chimie ParisTech, Paris 75231, France
| | - Hiroki Watanabe
- Department of Physics, Nagoya University, Nagoya, Aichi 464-8601, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Science, Okazaki, Aichi 444-8787, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya, Aichi 464-8601, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Science, Okazaki, Aichi 444-8787, Japan
| | - Ryota Iino
- Department of Functional Molecular Science, School of Physical Sciences, Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan.
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Sun X, Li Y, Tian Z, Qian Y, Zhang H, Wang L. A novel thermostable chitinolytic machinery of Streptomyces sp. F-3 consisting of chitinases with different action modes. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:136. [PMID: 31171937 PMCID: PMC6545677 DOI: 10.1186/s13068-019-1472-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/20/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The biodegradation of chitin is an important part of the carbon and nitrogen cycles in nature. Speeding up the biotransformation of chitin substrates can not only reduce pollution, but also produce high value-added products. However, this process is strictly regulated by the catalytic efficiency of the chitinolytic machinery. Therefore, it is necessary to study the mode of action and compound mechanisms of different chitin-degrading enzymes in depth to improve the catalytic efficiency of the chitinolytic machinery. RESULTS The thermophilic bacterium Streptomyces sp. F-3 showed comparatively high chitin degradation activities. To elucidate the mechanism underlying chitin hydrolysis, six chitin degradation-related enzymes were identified in the extracellular proteome of Streptomyces sp. F-3, including three chitinases (SsChi18A, SsChi18B, and SsChi18C) from the GH18 family, one GH19 chitinase (SsChi19A), one GH20 β-N-acetylhexosaminidase (SsGH20A), and one lytic polysaccharide monooxygenase (SsLPMO10A) from the AA10 family. All were upregulated by chitin. The heterologously expressed hydrolases could withstand temperatures up to 70 °C and were stable at pH values of 4 to 11. Biochemical analyses displayed that these chitin degradation-related enzymes had different functions and thus showed synergistic effects during chitin degradation. Furthermore, based on structural bioinformatics data, we speculated that the different action modes among the three GH18 chitinases may be caused by loop differences in their active site architectures. Among them, SsChi18A is probably processive and mainly acts on polysaccharides, while SsChi18B and SsChi18C are likely endo-non-processive and displayed higher activity on the degradation of chitin oligosaccharides. In addition, proteomic data and synergy experiments also indicated the importance of SsLPMO10A, which could promote the activities of the hydrolases and increase the monosaccharide content in the reaction system, respectively. CONCLUSIONS In this article, the chitinolytic machinery of a thermophilic Streptomyces species was studied to explore the structural basis for the synergistic actions of chitinases from different GH18 subfamilies. The elucidation of the degradation mechanisms of these thermophilic chitinases will lay a theoretical foundation for the efficient industrialized transformation of natural chitin.
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Affiliation(s)
- Xiaomeng Sun
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Yingjie Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Zhennan Tian
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Yuanchao Qian
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Huaiqiang Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
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Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site. Nat Commun 2019; 10:2222. [PMID: 31110237 PMCID: PMC6527550 DOI: 10.1038/s41467-019-09691-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/22/2019] [Indexed: 11/08/2022] Open
Abstract
Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl β-d-glucoside and methyl 6-thio-β-gentiobioside substrate analogues perfused in crystalline HvExoI bind across the catalytic site after they displace glucose, while methyl 2-thio-β-sophoroside attaches nearby. Structural analyses and multi-scale molecular modelling of nanoscale reactant movements in HvExoI reveal that upon productive binding of incoming substrates, the glucose product modifies its binding patterns and evokes the formation of a transient lateral cavity, which serves as a conduit for glucose departure to allow for the next catalytic round. This path enables substrate-product assisted processive catalysis through multiple hydrolytic events without HvExoI losing contact with oligo- or polymeric substrates. We anticipate that such enzyme plasticity could be prevalent among exo-hydrolases. Enzyme substrates and products often diffuse too rapidly to assess the catalytic implications of these movements. Here, the authors characterise the structural basis of product and substrate diffusion for an exo-hydrolase and discover a substrate-product assisted processive catalytic mechanism.
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8
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Nakamura A, Okazaki KI, Furuta T, Sakurai M, Iino R. Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin. Nat Commun 2018; 9:3814. [PMID: 30232340 PMCID: PMC6145945 DOI: 10.1038/s41467-018-06362-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/29/2018] [Indexed: 12/02/2022] Open
Abstract
Processive chitinase is a linear molecular motor which moves on the surface of crystalline chitin driven by processive hydrolysis of single chitin chain. Here, we analyse the mechanism underlying unidirectional movement of Serratia marcescens chitinase A (SmChiA) using high-precision single-molecule imaging, X-ray crystallography, and all-atom molecular dynamics simulation. SmChiA shows fast unidirectional movement of ~50 nm s-1 with 1 nm forward and backward steps, consistent with the length of reaction product chitobiose. Analysis of the kinetic isotope effect reveals fast substrate-assisted catalysis with time constant of ~3 ms. Decrystallization of the single chitin chain from crystal surface is the rate-limiting step of movement with time constant of ~17 ms, achieved by binding free energy at the product-binding site of SmChiA. Our results demonstrate that SmChiA operates as a burnt-bridge Brownian ratchet wherein the Brownian motion along the single chitin chain is rectified forward by substrate-assisted catalysis.
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Grants
- JP15H06898 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP17K18429 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP17H05899 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP16H00789 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP16H00858 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP17K19213 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP18H05424 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- JP15H04366 Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 01311805 MEXT | National Institutes of Natural Sciences (NINS)
- J281002 MEXT | National Institutes of Natural Sciences (NINS)
- Advanced Technology Institute Research Grants (RG2709)
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Affiliation(s)
- Akihiko Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, 444-8787, Okazaki, Aichi, Japan.
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama, 240-0193, Japan.
| | - Kei-Ichi Okazaki
- Institute for Molecular Science, National Institutes of Natural Sciences, 444-8787, Okazaki, Aichi, Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Ryota Iino
- Institute for Molecular Science, National Institutes of Natural Sciences, 444-8787, Okazaki, Aichi, Japan.
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama, 240-0193, Japan.
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Reaction specificity of keratanase II in the transglycosylation using the sugar oxazolines having keratan sulfate repeating units. Carbohydr Res 2018; 456:61-68. [DOI: 10.1016/j.carres.2017.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/06/2017] [Accepted: 12/10/2017] [Indexed: 01/18/2023]
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10
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Thimoteo SS, Glogauer A, Faoro H, de Souza EM, Huergo LF, Moerschbacher BM, Pedrosa FO. A broad pH range and processive chitinase from a metagenome library. ACTA ACUST UNITED AC 2017; 50:e5658. [PMID: 28076454 PMCID: PMC5264535 DOI: 10.1590/1414-431x20165658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/25/2016] [Indexed: 01/14/2023]
Abstract
Chitinases are hydrolases that degrade chitin, a polymer of N-acetylglucosamine
linked β(1-4) present in the exoskeleton of crustaceans, insects, nematodes and
fungal cell walls. A metagenome fosmid library from a wastewater-contaminated soil
was functionally screened for chitinase activity leading to the isolation and
identification of a chitinase gene named metachi18A. The
metachi18A gene was subcloned and overexpressed in
Escherichia coli BL21 and the MetaChi18A chitinase was purified
by affinity chromatography as a 6xHis-tagged fusion protein. The MetaChi18A enzyme is
a 92-kDa protein with a conserved active site domain of glycosyl hydrolases family
18. It hydrolyses colloidal chitin with an optimum pH of 5 and temperature of 50°C.
Moreover, the enzyme retained at least 80% of its activity in the pH range from 4 to
9 and 98% at 600 mM NaCl. Thin layer chromatography analyses identified chitobiose as
the main product of MetaChi18A on chitin polymers as substrate. Kinetic analysis
showed inhibition of MetaChi18A activity at high concentrations of colloidal chitin
and 4-methylumbelliferyl N,N′-diacetylchitobiose and sigmoid kinetics at low
concentrations of colloidal chitin, indicating a possible conformational change to
lead the chitin chain from the chitin-binding to the catalytic domain. The observed
stability and activity of MetaChi18A over a wide range of conditions suggest that
this chitinase, now characterized, may be suitable for application in the industrial
processing of chitin.
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Affiliation(s)
- S S Thimoteo
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - A Glogauer
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil.,Agência de Inovação, Instituto de Tecnologia do Paraná - Tecpar, Curitiba, PR, Brasil
| | - H Faoro
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil.,Instituto Carlos Chagas, Fiocruz, Curitiba, PR, Brasil
| | - E M de Souza
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - L F Huergo
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - B M Moerschbacher
- Institute for Biology and Biotechnology of Plants, WWU Münster University, Münster, Germany
| | - F O Pedrosa
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
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11
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Wang Y, Zhang S, Song X, Yao L. Cellulose chain binding free energy drives the processive move of cellulases on the cellulose surface. Biotechnol Bioeng 2016; 113:1873-80. [DOI: 10.1002/bit.25970] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/17/2016] [Accepted: 02/21/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Yefei Wang
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
| | - Shujun Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
| | - Xiangfei Song
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
| | - Lishan Yao
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
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12
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Kari J, Olsen J, Borch K, Cruys-Bagger N, Jensen K, Westh P. Kinetics of cellobiohydrolase (Cel7A) variants with lowered substrate affinity. J Biol Chem 2014; 289:32459-68. [PMID: 25271162 DOI: 10.1074/jbc.m114.604264] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases are exo-active glycosyl hydrolases that processively convert cellulose to soluble sugars, typically cellobiose. They effectively break down crystalline cellulose and make up a major component in industrial enzyme mixtures used for deconstruction of lignocellulosic biomass. Identification of the rate-limiting step for cellobiohydrolases remains controversial, and recent reports have alternately suggested either association (on-rate) or dissociation (off-rate) as the overall bottleneck. Obviously, this uncertainty hampers both fundamental mechanistic understanding and rational design of enzymes with improved industrial applicability. To elucidate the role of on- and off-rates, respectively, on the overall kinetics, we have expressed a variant in which a tryptophan residue (Trp-38) in the middle of the active tunnel has been replaced with an alanine. This mutation weakens complex formation, and the population of substrate-bound W38A was only about half of the wild type. Nevertheless, the maximal, steady-state rate was twice as high for the variant enzyme. It is argued that these opposite effects on binding and activity can be reconciled if the rate-limiting step is after the catalysis (i.e. in the dissociation process).
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Affiliation(s)
- Jeppe Kari
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
| | - Johan Olsen
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, Bagsværd DK-2880, Denmark
| | - Nicolaj Cruys-Bagger
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
| | - Kenneth Jensen
- Novozymes A/S, Krogshøjvej 36, Bagsværd DK-2880, Denmark
| | - Peter Westh
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
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van Dongen SFM, Elemans JAAW, Rowan AE, Nolte RJM. Processive catalysis. Angew Chem Int Ed Engl 2014; 53:11420-8. [PMID: 25244684 DOI: 10.1002/anie.201404848] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Indexed: 02/02/2023]
Abstract
Nature's enzymes are an ongoing source of inspiration for scientists. The complex processes behind their selectivity and efficiency is slowly being unraveled, and these findings have spawned many biomimetic catalysts. However, nearly all focus on the conversion of small molecular substrates. Nature itself is replete with inventive catalytic systems which modify, replicate, or decompose entire polymers, often in a processive fashion. Such processivity can, for example, enhance the rate of catalysis by clamping to the polymer substrate, which imparts a large effective molarity. Reviewed herein are the various strategies for processivity in nature's arsenal and their properties. An overview of what has been achieved by chemists aiming to mimic one of nature's greatest tricks is also included.
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Affiliation(s)
- Stijn F M van Dongen
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen (The Netherlands).
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Towards a molecular-level theory of carbohydrate processivity in glycoside hydrolases. Curr Opin Biotechnol 2014; 27:96-106. [DOI: 10.1016/j.copbio.2013.12.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
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Payne CM, Jiang W, Shirts MR, Himmel ME, Crowley MF, Beckham GT. Glycoside Hydrolase Processivity Is Directly Related to Oligosaccharide Binding Free Energy. J Am Chem Soc 2013; 135:18831-9. [DOI: 10.1021/ja407287f] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Wei Jiang
- Argonne
Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Michael R. Shirts
- Department
of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
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Abstract
Natural cellulolytic enzyme systems as well as leading commercial cellulase cocktails are dominated by enzymes that degrade cellulose chains in a processive manner. Despite the abundance of processivity among natural cellulases, the molecular basis as well as the biotechnological implications of this mechanism are only partly understood. One of the major limitations lies in the fact that it is not straightforward to measure and quantify processivity in what essentially are biphasic experimental systems. Here, we describe and discuss both well-established methods and newer methods for measuring cellulase processivity. In addition, we discuss recent insights from studies on chitinases that may help direct further studies on processivity in cellulases.
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Affiliation(s)
- Svein J Horn
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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