1
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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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2
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Liu Z, Deng B, Yuan H, Zhang B, Liu J, Meng J, Chang M. Transcription factor FfMYB15 regulates the expression of cellulase gene FfCEL6B during mycelial growth of Flammulina filiformis. Microb Cell Fact 2022; 21:216. [PMID: 36253826 PMCID: PMC9578197 DOI: 10.1186/s12934-022-01932-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cellulose degradation can determine mycelial growth rate and affect yield during the growth of Flammulina filiformis. The degradation of cellulose requires the joint action of a variety of cellulases, and some cellulase-related genes have been detected in mushrooms. However, little is known about the transcriptional regulatory mechanisms of cellulose degradation. Results In this study, FfMYB15 that may regulate the expression of cellulase gene FfCEL6B in F. filiformis was identified. RNA interference (RNAi) showed that FfCEL6B positively regulated mycelial growth. Gene expression analyses indicated that the expression patterns of FfCEL6B and FfMYB15 in mycelia cultured on the 0.9% cellulose medium for different times were similar with a correlation coefficient of 0.953. Subcellular localization and transcriptional activity analyses implied that FfMYB15 was located in the nucleus and was a transcriptional activator. Electrophoretic mobility shift assay (EMSA) and dual-luciferase assays demonstrated that FfMYB15 could bind and activate FfCEL6B promoter by recognizing MYB cis-acting element. Conclusions This study indicated that FfCEL6B played an active role in mycelial growth of F. filiformis and was regulated by FfMYB15. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01932-z.
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Affiliation(s)
- Zongqi Liu
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China
| | - Bing Deng
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China.,Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Hui Yuan
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China
| | - Benfeng Zhang
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China
| | - Jingyu Liu
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China.,Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Junlong Meng
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China.,Collaborative Innovation Center of Advancing Quality and Efficiency of Loess Plateau Edible Fungi, Taigu, 030801, Shanxi, China
| | - Mingchang Chang
- College of Food Science and Engineering, Shanxi Agricultural University, 1 Mingxian South Road, Taigu, 030801, Shanxi Province, China. .,Collaborative Innovation Center of Advancing Quality and Efficiency of Loess Plateau Edible Fungi, Taigu, 030801, Shanxi, China.
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Takeda T, Takahashi M, Shimizu M, Sugihara Y, Yamashita T, Saitoh H, Fujisaki K, Ishikawa K, Utsushi H, Kanzaki E, Sakamoto Y, Abe A, Terauchi R. Rice apoplastic CBM1-interacting protein counters blast pathogen invasion by binding conserved carbohydrate binding module 1 motif of fungal proteins. PLoS Pathog 2022; 18:e1010792. [PMID: 36173975 PMCID: PMC9521807 DOI: 10.1371/journal.ppat.1010792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/04/2022] [Indexed: 11/20/2022] Open
Abstract
When infecting plants, fungal pathogens secrete cell wall-degrading enzymes (CWDEs) that break down cellulose and hemicellulose, the primary components of plant cell walls. Some fungal CWDEs contain a unique domain, named the carbohydrate binding module (CBM), that facilitates their access to polysaccharides. However, little is known about how plants counteract pathogen degradation of their cell walls. Here, we show that the rice cysteine-rich repeat secretion protein OsRMC binds to and inhibits xylanase MoCel10A of the blast fungus pathogen Magnaporthe oryzae, interfering with its access to the rice cell wall and degradation of rice xylan. We found binding of OsRMC to various CBM1-containing enzymes, suggesting that it has a general role in inhibiting the action of CBM1. OsRMC is localized to the apoplast, and its expression is strongly induced in leaves infected with M. oryzae. Remarkably, knockdown and overexpression of OsRMC reduced and enhanced rice defense against M. oryzae, respectively, demonstrating that inhibition of CBM1-containing fungal enzymes by OsRMC is crucial for rice defense. We also identified additional CBM-interacting proteins (CBMIPs) from Arabidopsis thaliana and Setaria italica, indicating that a wide range of plants counteract pathogens through this mechanism. Plants have evolved various activity-inhibiting proteins as a defense against fungal cell wall-degrading enzymes (CWDEs), but how plants counteract the function of fungal enzymes containing carbohydrate binding modules (CBMs) remains unknown. Here, we demonstrate that OsRMC, a member of the cysteine-rich repeat secretion protein family, interacts with fungal CBM1. OsRMC binding to CBM1 of a blast fungal xylanase blocks access to cellulose, resulting in the inhibition of xylanase enzymatic activity. Our study provides significant insights into plant countermeasures against CWDEs in the apoplastic space during plant-fungal pathogen interactions. It also reveals a molecular function of the DUF26 domain widely distributed in plant proteins.
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Affiliation(s)
- Takumi Takeda
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
- * E-mail: (TT); (RT)
| | | | - Motoki Shimizu
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Yu Sugihara
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Mozume, Muko, Kyoto, Japan
| | | | - Hiromasa Saitoh
- Department of Molecular Microbiology, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Koki Fujisaki
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | | | - Hiroe Utsushi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Eiko Kanzaki
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | | | - Akira Abe
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Mozume, Muko, Kyoto, Japan
- * E-mail: (TT); (RT)
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4
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Li L, Lin X, Bao J, Xia H, Li F. Two Extracellular Poly(ε-caprolactone)-Degrading Enzymes From Pseudomonas hydrolytica sp. DSWY01T: Purification, Characterization, and Gene Analysis. Front Bioeng Biotechnol 2022; 10:835847. [PMID: 35372294 PMCID: PMC8971842 DOI: 10.3389/fbioe.2022.835847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 11/17/2022] Open
Abstract
Poly(ε-caprolactone) (PCL) is an artificial polyester with commercially promising application. In this study, two novel PCL-degrading enzymes named PCLase I and PCLase II were purified to homogeneity from the culture supernatant of an effective polyester-degrading bacterium, Pseudomonas hydrolytica sp. DSWY01T. The molecular masses of PCLase I and PCLase II were determined to be 27.5 and 30.0 kDa, respectively. The optimum temperatures for the enzyme activities were 50 and 40°C, and the optimum pH values were 9.0 and 10.0, respectively. The two enzymes exhibited different physical and chemical properties, but both enzymes could degrade PCL substrates into monomers and oligomers. Weight loss detection and scanning electron microscopy revealed that PCLase I had more effective degradation ability than PCLase II. The genes of the two enzymes were cloned on the basis of the peptide fingerprint analysis results. The sequence analysis and substrate specificity analysis results showed that PCLase I and PCLase II were cutinase and lipase, respectively. Interface activation experiment also confirmed this conclusion. Structural analysis and modeling were further performed to obtain possible insights on the mechanism.
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Affiliation(s)
- Linying Li
- School of Life Sciences, Northeast Normal University, Changchun, China
- Engineering Research Center of Glycoconjugates, Ministry of Education, Changchun, China
| | - Xiumei Lin
- Changchun GeneScience Pharmaceutical Co., Ltd., Changchun, China
| | - Jianfeng Bao
- School of Life Sciences, Northeast Normal University, Changchun, China
| | - Hongmei Xia
- School of Life Sciences, Northeast Normal University, Changchun, China
- National Demonstration Center for Experimental Biology Education, Northeast Normal University, Changchun, China
| | - Fan Li
- School of Life Sciences, Northeast Normal University, Changchun, China
- Engineering Research Center of Glycoconjugates, Ministry of Education, Changchun, China
- *Correspondence: Fan Li,
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5
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Liu T, Zhang Y, Lu X, Wang P, Zhang X, Tian J, Wang Q, Song J, Jin Y, Xiao H. Binding affinity of family 4 carbohydrate binding module on cellulose films of nanocrystals and nanofibrils. Carbohydr Polym 2021; 251:116725. [PMID: 33142548 DOI: 10.1016/j.carbpol.2020.116725] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 11/26/2022]
Abstract
The binding affinity and thermodynamics of family 4 carbohydrate-binding module (CBM4), belonging to type B CBM, on model surfaces of cellulose nanocrystals (CNC) and nanofibrils (CNF) were investigated by quartz crystal microbalance with dissipation monitoring (QCM-D) technology in real-time at different temperatures. The thermodynamic parameters associated with the interaction, such as Gibbs free energy, enthalpy change, entropy change and heat capacity were obtained using the van't Hoff analysis via a nonlinear parameter estimation. The results demonstrated CBM4 binds preferentially to both CNF and CNC, whereas the driving forces behind them were very different. The former was related to the hydrogen bonds formed in the CBM4 clefts, resulting in a favorable enthalpy but compensated by unfavorable entropy change; on the contrary, the latter was mainly driven by favorable entropy but compensated by unfavorable enthalpic change due to water rearrangement.
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Affiliation(s)
- Tian Liu
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Yu Zhang
- Dinano Tech Co., Ltd., Nanjing Branch, Nanjing, 210046, China
| | - Xiaomin Lu
- Department of Forest Biomaterials, North Carolina State University, Campus Box 8005, Raleigh, NC, 27695-8005, United States
| | - Peipei Wang
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Xinyu Zhang
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Jing Tian
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Qingcheng Wang
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Junlong Song
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China.
| | - Yongcan Jin
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Huining Xiao
- Department of Chemical Engineering, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada
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6
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Tokunaga Y, Nagata T, Kondo K, Katahira M, Watanabe T. NMR elucidation of nonproductive binding sites of lignin models with carbohydrate-binding module of cellobiohydrolase I. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:164. [PMID: 33042221 PMCID: PMC7541279 DOI: 10.1186/s13068-020-01805-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/27/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Highly efficient enzymatic saccharification of pretreated lignocellulose is a key step in achieving lignocellulosic biorefinery. Cellobiohydrolase I (Cel7A) secreted by Trichoderma reesei is an industrially used cellulase that possesses carbohydrate-binding module 1 (TrCBM1) at the C-terminal domain. The nonproductive binding of TrCBM1 to lignin significantly decreases the enzymatic saccharification efficiency and increases the cost of biomass conversion because of the additionally required enzymes. Understanding the interaction mechanism between lignin and TrCBM1 is essential for realizing a cost-effective biofuel production; however, the binding sites in lignin have not been clearly elucidated. RESULTS Three types of 13C-labeled β-O-4 lignin oligomer models were synthesized and characterized. The 2D 1H-13C heteronuclear single-quantum correlation (HSQC) spectra of the 13C-labeled lignin models confirmed that the three types of the 13C labels were correctly incorporated in the (1) aromatic rings and β positions, (2) α positions, and (3) methoxy groups, respectively. The TrCBM1-binding sites in lignin were analyzed by observing NMR chemical shift perturbations (CSPs) using the synthetic 13C-labeled β-O-4 lignin oligomer models. Obvious CSPs were observed in signals from the aromatic regions in oligomers bound to TrCBM1, whereas perturbations in the signals from aliphatic regions and methoxy groups were insignificant. These findings indicated that hydrophobic interactions and π-π stacking were dominating factors in nonproductive binding. The synthetic lignin models have two configurations whose terminal units were differently aligned and donated C(I) and C(II). The C(I) ring showed remarkable perturbation compared with the C(II), which indicated that the binding of TrCBM1 was markedly affected by the configuration of the lignin models. The long-chain lignin models (degree of polymerization (DP) 4.16-4.70) clearly bound to TrCBM1. The interactions of TrCBM1 with the short-chain lignin models (DP 2.64-3.12) were insignificant, indicating that a DP greater than 4 was necessary for TrCBM1 binding. CONCLUSION The CSP analysis using 13C-labeled β-O-4 lignin oligomer models enabled the identification of the TrCBM1 binding sites in lignins at the atomic level. This specific interaction analysis will provide insights for new molecular designs of cellulase having a controlled affinity to cellulose and lignin for a cost-effective biorefinery process.
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Affiliation(s)
- Yuki Tokunaga
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Uji, Kyoto 611-0011 Japan
| | - Takashi Nagata
- Institute of Advanced Energy (IAE), Kyoto University, Uji, Kyoto 611-0011 Japan
| | - Keiko Kondo
- Institute of Advanced Energy (IAE), Kyoto University, Uji, Kyoto 611-0011 Japan
| | - Masato Katahira
- Institute of Advanced Energy (IAE), Kyoto University, Uji, Kyoto 611-0011 Japan
| | - Takashi Watanabe
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Uji, Kyoto 611-0011 Japan
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7
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Sidar A, Albuquerque ED, Voshol GP, Ram AFJ, Vijgenboom E, Punt PJ. Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms. Front Bioeng Biotechnol 2020; 8:871. [PMID: 32850729 PMCID: PMC7410926 DOI: 10.3389/fbioe.2020.00871] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Enzymatic degradation of abundant renewable polysaccharides such as cellulose and starch is a field that has the attention of both the industrial and scientific community. Most of the polysaccharide degrading enzymes are classified into several glycoside hydrolase families. They are often organized in a modular manner which includes a catalytic domain connected to one or more carbohydrate-binding modules. The carbohydrate-binding modules (CBM) have been shown to increase the proximity of the enzyme to its substrate, especially for insoluble substrates. Therefore, these modules are considered to enhance enzymatic hydrolysis. These properties have played an important role in many biotechnological applications with the aim to improve the efficiency of polysaccharide degradation. The domain organization of glycoside hydrolases (GHs) equipped with one or more CBM does vary within organisms. This review comprehensively highlights the presence of CBM as ancillary modules and explores the diversity of GHs carrying one or more of these modules that actively act either on cellulose or starch. Special emphasis is given to the cellulase and amylase distribution within the filamentous microorganisms from the genera of Streptomyces and Aspergillus that are well known to have a great capacity for secreting a wide range of these polysaccharide degrading enzyme. The potential of the CBM and other ancillary domains for the design of improved polysaccharide decomposing enzymes is discussed.
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Affiliation(s)
- Andika Sidar
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Department of Food Science and Agricultural Product Technology, Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Erica D Albuquerque
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Sun Pharmaceutical Industries Europe BV., Hoofddorp, Netherlands
| | - Gerben P Voshol
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
| | - Arthur F J Ram
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Erik Vijgenboom
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Peter J Punt
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
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8
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Sista Kameshwar AK, Qin W. Systematic review of publicly available non-Dikarya fungal proteomes for understanding their plant biomass-degrading and bioremediation potentials. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0264-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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9
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NMR Analysis on Molecular Interaction of Lignin with Amino Acid Residues of Carbohydrate-Binding Module from Trichoderma reesei Cel7A. Sci Rep 2019; 9:1977. [PMID: 30760856 PMCID: PMC6374431 DOI: 10.1038/s41598-018-38410-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/12/2018] [Indexed: 12/20/2022] Open
Abstract
Lignocellulosic biomass is anticipated to serve as a platform for green chemicals and fuels. Nonproductive binding of lignin to cellulolytic enzymes should be avoided for conversion of lignocellulose through enzymatic saccharification. Although carbohydrate-binding modules (CBMs) of cellulolytic enzymes strongly bind to lignin, the adsorption mechanism at molecular level is still unclear. Here, we report NMR-based analyses of binding sites on CBM1 of cellobiohydrolase I (Cel7A) from a hyper-cellulase-producing fungus, Trichoderma reesei, with cellohexaose and lignins from Japanese cedar (C-MWL) and Eucalyptus globulus (E-MWL). A method was established to obtain properly folded TrCBM1. Only TrCBM1 that was expressed in freshly transformed E. coli had intact conformation. Chemical shift perturbation analyses revealed that TrCBM1 adsorbed cellohexaose in highly specific manner via two subsites, flat plane surface and cleft, which were located on the opposite side of the protein surface. Importantly, MWLs were adsorbed at multiple binding sites, including the subsites, having higher affinity than cellohexaose. G6 and Q7 were involved in lignin binding on the flat plane surface of TrCBM1, while cellohexaose preferentially interacted with N29 and Q34. TrCBM1 used much larger surface area to bind with C-MWL than E-MWL, indicating the mechanisms of adsorption toward hardwood and softwood lignins are different.
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10
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Griffo A, Rooijakkers BJM, Hähl H, Jacobs K, Linder MB, Laaksonen P. Binding Forces of Cellulose Binding Modules on Cellulosic Nanomaterials. Biomacromolecules 2019; 20:769-777. [PMID: 30657665 PMCID: PMC6727214 DOI: 10.1021/acs.biomac.8b01346] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
In
this study, the interaction forces between different cellulosic
nanomaterials and a protein domain belonging to cellulose binding
modules family 1 (CBM1) were investigated at the molecular scale.
Cellulose binding modules are protein domains found in carbohydrate
active enzymes having an affinity toward cellulosic materials. Here,
the binding force of a fusion protein containing a cellulose binding
module (CBM1) produced recombinantly in E. coli was quantified on different cellulose nanocrystals immobilized on
surfaces. Adhesion of the CBM on cellulose with different degrees
of crystallinity as well as on chitin nanocrystals was examined. This
study was carried out by single molecule force spectroscopy using
an atomic force microscope, which enables the detection of binding
force of individual molecules. The study contains a preliminary quantification
of the interactions at the molecular level that sheds light on the
development of new nanocellulose-based nanocomposites with improved
strength and elasticity.
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Affiliation(s)
- Alessandra Griffo
- Department of Bioproducts and Biosystems , Aalto University , Espoo, FI-00076 Aalto , Finland
| | - Bart J M Rooijakkers
- Department of Bioproducts and Biosystems , Aalto University , Espoo, FI-00076 Aalto , Finland
| | - Hendrik Hähl
- Department of Experimental Physics , Saarland University , Saarbrücken 66123 , Germany
| | - Karin Jacobs
- Department of Experimental Physics , Saarland University , Saarbrücken 66123 , Germany
| | - Markus B Linder
- Department of Bioproducts and Biosystems , Aalto University , Espoo, FI-00076 Aalto , Finland
| | - Päivi Laaksonen
- Department of Bioproducts and Biosystems , Aalto University , Espoo, FI-00076 Aalto , Finland
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11
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Happs RM, Guan X, Resch MG, Davis MF, Beckham GT, Tan Z, Crowley MF. O-glycosylation effects on family 1 carbohydrate-binding module solution structures. FEBS J 2015; 282:4341-56. [PMID: 26307003 DOI: 10.1111/febs.13500] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/18/2015] [Accepted: 08/21/2015] [Indexed: 01/20/2023]
Abstract
UNLABELLED Family 1 carbohydrate-binding modules (CBMs) are ubiquitous components of multimodular fungal enzymes that degrade plant cell wall polysaccharides and bind specifically to cellulose. Native glycosylation of family 1 CBMs has been shown to substantially impact multiple physical properties, including thermal and proteolytic stability and cellulose binding affinity. To gain molecular insights into the changes in CBM properties upon glycosylation, solution structures of two glycoforms of a Trichoderma reesei family 1 CBM were studied by NMR spectroscopy: a glycosylated family 1 CBM with a mannose group attached to both Thr1 and Ser3 and a second family 1 CBM with single mannose groups attached to Thr1, Ser3 and Ser14. The structures clearly reveal that monosaccharides at both Ser3 and Ser14 on family 1 CBMs present additional cellulose binding platforms, similar to well-characterized aromatic residues at the binding interface, which align to the cellulose surface. These results are in agreement with previous experimental work demonstrating that glycans at Ser3 and Ser14 impart significant improvements in binding affinity. Additionally, detailed analysis of the NMR structures and molecular simulations indicates that the protein backbone of the CBM is not significantly altered by attachment of monosaccharides, and that the mannose attached to Ser14 may be more flexible than the mannose at Ser3. Overall, the present study reveals how family 1 CBM structures are affected by covalent attachment of monosaccharides, which are likely important post-translational modifications of these common subdomains of fungal plant cell wall degrading enzymes. DATABASE Structural data have been deposited in the RCSB Protein Data Bank (PDB codes: 2MWJ and 2MWK) and the BioMagRes Bank (BMRB codes: 25331 and 25332) for CBM_M2 and CBM_M3, respectively.
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Affiliation(s)
- Renee M Happs
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO, USA
| | - Xiaoyang Guan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Michael G Resch
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO, USA
| | - Mark F Davis
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO, USA
| | - Gregg T Beckham
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO, USA
| | - Zhongping Tan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Michael F Crowley
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, USA
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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13
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Colussi F, Sørensen TH, Alasepp K, Kari J, Cruys-Bagger N, Windahl MS, Olsen JP, Borch K, Westh P. Probing substrate interactions in the active tunnel of a catalytically deficient cellobiohydrolase (Cel7). J Biol Chem 2014; 290:2444-54. [PMID: 25477511 DOI: 10.1074/jbc.m114.624163] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases break down cellulose sequentially by sliding along the crystal surface with a single cellulose strand threaded through the catalytic tunnel of the enzyme. This so-called processive mechanism relies on a complex pattern of enzyme-substrate interactions, which need to be addressed in molecular descriptions of processivity and its driving forces. Here, we have used titration calorimetry to study interactions of cellooligosaccharides (COS) and a catalytically deficient variant (E212Q) of the enzyme Cel7A from Trichoderma reesei. This enzyme has ∼10 glucopyranose subsites in the catalytic tunnel, and using COS ligands with a degree of polymerization (DP) from 2 to 8, different regions of the tunnel could be probed. For COS ligands with a DP of 2-3 the binding constants were around 10(5) m(-1), and for longer ligands (DP 5-8) this value was ∼10(7) m(-1). Within each of these groups we did not find increased affinity as the ligands got longer and potentially filled more subsites. On the contrary, we found a small but consistent affinity loss as DP rose from 6 to 8, particularly at the higher investigated temperatures. Other thermodynamic functions (ΔH, ΔS, and ΔCp) decreased monotonously with both temperature and DP. Combined interpretation of these thermodynamic results and previously published structural data allowed assessment of an affinity profile along the length axis of the active tunnel.
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Affiliation(s)
- Francieli Colussi
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Trine H Sørensen
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Kadri Alasepp
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Jeppe Kari
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Nicolaj Cruys-Bagger
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Michael S Windahl
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Johan P Olsen
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Peter Westh
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
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14
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Zhao J, Chen H. Stimulation of Cellulases by Small Phenolic Compounds in Pretreated Stover. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:3223-3229. [PMID: 24564197 DOI: 10.1021/jf405046m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The effect of small phenolic compounds in pretreated stover on celluase activity is crucial but has not yet been fully elucidated. This work investigated the effects of both phenolic acid and phenolic aldehyde on cellulase activity. The model substances of small phenolic compounds identified in steam exploded corn stover were used to examine their individual effects on cellulase activity. It was found that phenolic aldehyde significantly inhibited cellulase activity at 0.05-8 g/L. However, phenolic acids might have a concentration-dependent effect on cellulase activity: significant inhibition at 0.05 g/L and slight stimulation at 2-4 g/L. Small phenolic compounds mixture might also have a concentration-dependent effect on cellulase activity: significant stimulation at 2-8 g/L and slight inhibition at 0.05-1 g/L. The small phenolic compounds in pretreated stover were proven to be able to significantly stimulate enzymatic hydrolysis of stover. On the basis of these results, it is proposed that the concentration-dependent effects of small phenolic compounds on cellulase activity should be considered while removing them after pretreatment.
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Affiliation(s)
- Junying Zhao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190, China
- Graduate University of Chinese Academy of Sciences , Beijing 100049, China
| | - Hongzhang Chen
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190, China
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15
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Cellulolytic Enzyme Production and Enzymatic Hydrolysis for Second-Generation Bioethanol Production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 128:1-24. [DOI: 10.1007/10_2011_131] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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16
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Nozaki K, Nishijima H, Arai T, Mizuno M, Sato N, Amano Y. Regulation of Adsorption Behavior of Carbohydrate-Binding Module Family 1 and Endo-β-1,4-Glucanase onto Crystalline Cellulose. J Appl Glycosci (1999) 2011. [DOI: 10.5458/jag.jag.jag-2011_007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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17
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Abstract
Bioactive paper includes a range of potential paper-based materials that can perform analytical functions normally reserved for multi-well plates in the laboratory or for portable electronic devices. Pathogen detection is the most compelling application. Simple paper-based detection, not requiring hardware, has the potential to have impacts in society, ranging from the kitchen to disasters in the developing world. Bioactive-paper research is an emerging field with significant efforts in Canada, USA (Harvard), Finland and Australia. Following a brief introduction to the material and surface properties of paper, I review the literature. Some of the early work exploits the porosity of paper to generate paper-based microfluidics ("paperfluidics") devices. I exclude from this review printed electronic devices and plastics-supported devices.
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Affiliation(s)
- Robert Pelton
- Department of Chemical Engineering, JHE-136, McMaster University, Hamilton, Ontario, Canada L8S 4L7
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18
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Igarashi K, Wada M, Samejima M. Kinetic Analysis of Cellobiohydrolase: Quantification of Enzymatic Reaction at a Solid/Liquid Interface Applying the Concept of Surface Density. TRENDS GLYCOSCI GLYC 2009. [DOI: 10.4052/tigg.21.13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Gierlinger N, Goswami L, Schmidt M, Burgert I, Coutand C, Rogge T, Schwanninger M. In Situ FT-IR Microscopic Study on Enzymatic Treatment of Poplar Wood Cross-Sections. Biomacromolecules 2008; 9:2194-201. [DOI: 10.1021/bm800300b] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Notburga Gierlinger
- Department of Biomaterials, Max-Planck Institute of Colloids and Interfaces, Potsdam, Germany, Institut National de la Recherche Agronomique (INRA), umr Physiologie Intégrative de l’Arbre Fruitier et Forestier (PIAF), 234 av. du Brézet, 63100 Clermont-Ferrand, France, Forschungszentrum Karlsruhe GmbH, Institut für Mikrostrukturtechnik, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, and Department of Chemistry, Boku - University of Natural Resources and Applied Life Sciences,
| | - Luna Goswami
- Department of Biomaterials, Max-Planck Institute of Colloids and Interfaces, Potsdam, Germany, Institut National de la Recherche Agronomique (INRA), umr Physiologie Intégrative de l’Arbre Fruitier et Forestier (PIAF), 234 av. du Brézet, 63100 Clermont-Ferrand, France, Forschungszentrum Karlsruhe GmbH, Institut für Mikrostrukturtechnik, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, and Department of Chemistry, Boku - University of Natural Resources and Applied Life Sciences,
| | - Martin Schmidt
- Department of Biomaterials, Max-Planck Institute of Colloids and Interfaces, Potsdam, Germany, Institut National de la Recherche Agronomique (INRA), umr Physiologie Intégrative de l’Arbre Fruitier et Forestier (PIAF), 234 av. du Brézet, 63100 Clermont-Ferrand, France, Forschungszentrum Karlsruhe GmbH, Institut für Mikrostrukturtechnik, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, and Department of Chemistry, Boku - University of Natural Resources and Applied Life Sciences,
| | - Ingo Burgert
- Department of Biomaterials, Max-Planck Institute of Colloids and Interfaces, Potsdam, Germany, Institut National de la Recherche Agronomique (INRA), umr Physiologie Intégrative de l’Arbre Fruitier et Forestier (PIAF), 234 av. du Brézet, 63100 Clermont-Ferrand, France, Forschungszentrum Karlsruhe GmbH, Institut für Mikrostrukturtechnik, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, and Department of Chemistry, Boku - University of Natural Resources and Applied Life Sciences,
| | - Catherine Coutand
- Department of Biomaterials, Max-Planck Institute of Colloids and Interfaces, Potsdam, Germany, Institut National de la Recherche Agronomique (INRA), umr Physiologie Intégrative de l’Arbre Fruitier et Forestier (PIAF), 234 av. du Brézet, 63100 Clermont-Ferrand, France, Forschungszentrum Karlsruhe GmbH, Institut für Mikrostrukturtechnik, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, and Department of Chemistry, Boku - University of Natural Resources and Applied Life Sciences,
| | - Tilmann Rogge
- Department of Biomaterials, Max-Planck Institute of Colloids and Interfaces, Potsdam, Germany, Institut National de la Recherche Agronomique (INRA), umr Physiologie Intégrative de l’Arbre Fruitier et Forestier (PIAF), 234 av. du Brézet, 63100 Clermont-Ferrand, France, Forschungszentrum Karlsruhe GmbH, Institut für Mikrostrukturtechnik, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, and Department of Chemistry, Boku - University of Natural Resources and Applied Life Sciences,
| | - Manfred Schwanninger
- Department of Biomaterials, Max-Planck Institute of Colloids and Interfaces, Potsdam, Germany, Institut National de la Recherche Agronomique (INRA), umr Physiologie Intégrative de l’Arbre Fruitier et Forestier (PIAF), 234 av. du Brézet, 63100 Clermont-Ferrand, France, Forschungszentrum Karlsruhe GmbH, Institut für Mikrostrukturtechnik, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, and Department of Chemistry, Boku - University of Natural Resources and Applied Life Sciences,
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20
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Wang L, Zhang Y, Gao P. A novel function for the cellulose binding module of cellobiohydrolase I. ACTA ACUST UNITED AC 2008; 51:620-9. [PMID: 18622745 DOI: 10.1007/s11427-008-0088-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 05/21/2008] [Indexed: 11/29/2022]
Abstract
A homogeneous cellulose-binding module (CBM) of cellobiohydrolase I (CBHI) from Trichoderma pseudokoningii S-38 was obtained by the limited proteolysis with papain and a series of chromatographs filtration. Analysis of FT-IR spectra demonstrated that the structural changes result from a weakening and splitting of the hydrogen bond network in cellulose by the action of CBM(CBHI) at 40 degrees C for 24 h. The results of molecular dynamic simulations are consistent with the experimental conclusions, and provide a nanoscopic view of the mechanism that strong and medium H-bonds decreased dramatically when CBM was bound to the cellulose surface. The function of CBM(CBHI) is not only limited to locating intact CBHI in close proximity with cellulose fibrils, but also is involved in the structural disruption at the fibre surface. The present studies provided considerable evidence for the model of the intramolecular synergy between the catalytic domain and their CBMs.
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Affiliation(s)
- Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
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21
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Viegas A, Brás NF, Cerqueira NMFSA, Fernandes PA, Prates JAM, Fontes CMGA, Bruix M, Romão MJ, Carvalho AL, Ramos MJ, Macedo AL, Cabrita EJ. Molecular determinants of ligand specificity in family 11 carbohydrate binding modules - an NMR, X-ray crystallography and computational chemistry approach. FEBS J 2008; 275:2524-35. [DOI: 10.1111/j.1742-4658.2008.06401.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Pinto R, Amaral AL, Ferreira EC, Mota M, Vilanova M, Ruel K, Gama M. Quantification of the CBD-FITC conjugates surface coating on cellulose fibres. BMC Biotechnol 2008; 8:1. [PMID: 18184429 PMCID: PMC2254392 DOI: 10.1186/1472-6750-8-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Accepted: 01/09/2008] [Indexed: 11/24/2022] Open
Abstract
Background Cellulose Binding Domains (CBD) were conjugated with fluorescein isothiocyanate (FITC). The surface concentration of the Binding Domains adsorbed on cellulose fibres was determined by fluorescence image analysis. Results For a CBD-FITC concentration of 60 mg/L, a coating fraction of 78% and 110% was estimated for Portucel and Whatman fibres, respectively. For a saturating CBD concentration, using Whatman CF11 fibres, a surface concentration of 25.2 × 10-13 mol/mm2 was estimated, the equivalent to 4 protein monolayers. This result does not imply the existence of several adsorbed protein layers. Conclusion It was verified that CBDs were able to penetrate the fibres, according to confocal microscopy and TEM-immunolabelling analysis. The surface concentration of adsorbed CBDs was greater on amorphous fibres (phosphoric acid swollen) than on more crystalline ones (Whatman CF11 and Sigmacell 20).
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Affiliation(s)
- Ricardo Pinto
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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23
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Josefsson P, Henriksson G, Wågberg L. The Physical Action of Cellulases Revealed by a Quartz Crystal Microbalance Study Using Ultrathin Cellulose Films and Pure Cellulases. Biomacromolecules 2007; 9:249-54. [PMID: 18163575 DOI: 10.1021/bm700980b] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Josefsson
- Royal Institute of Technology, Fibre and Polymer Technology, Teknikringen 56, 100 44 Stockholm, Sweden
| | - Gunnar Henriksson
- Royal Institute of Technology, Fibre and Polymer Technology, Teknikringen 56, 100 44 Stockholm, Sweden
| | - Lars Wågberg
- Royal Institute of Technology, Fibre and Polymer Technology, Teknikringen 56, 100 44 Stockholm, Sweden
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24
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Ding S, Cao J, Zhou R, Zheng F. Molecular cloning, and characterization of a modular acetyl xylan esterase from the edible straw mushroomVolvariella volvacea. FEMS Microbiol Lett 2007; 274:304-10. [PMID: 17623028 DOI: 10.1111/j.1574-6968.2007.00844.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A new Volvariella volvacea gene encoding an acetyl xylan esterase (designated as Vvaxe1) was cloned and expressed in Pichia pastoris. The cDNA contained an ORF of 1047 bp encoding 349 amino acids with a calculated mass of 39 990 Da. VvAXE1 is a modular enzyme consisting of an N-terminal signal peptide, a catalytic domain, and a cellulose-binding domain. The amino acid sequence of the enzyme exhibited a high degree of similarity to cinnamoyl esterase B from Penicillium funiculosum, and acetyl xylan esterases from Aspergillus oryzae, Penicillium purpurogenum, and Aspergillus ficuum. Recombinant acetyl xylan esterase released acetate from several acetylated substrates including beta-d-xylose tetraacetate and acetylated xylan. No activity was detectable on p-nitrophenyl acetate. Enzyme-catalyzed hydrolysis of 4-methylumbelliferyl acetate was maximal at pH 8.0 and 60 degrees C, and reciprocal plots revealed an apparent K(m) value of 307.7 microM and a V(max) value of 24 733 IU micromol(-1) protein. ReAXE1 also exhibited a capacity to bind to Avicel and H(3)PO(4) acid-swollen cellulose.
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Affiliation(s)
- Shaojun Ding
- Department of Biological Engineering, Nanjing Forestry University, Nanjing, Jiangsu, China.
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25
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Itoh Y, Watanabe J, Fukada H, Mizuno R, Kezuka Y, Nonaka T, Watanabe T. Importance of Trp59 and Trp60 in chitin-binding, hydrolytic, and antifungal activities of Streptomyces griseus chitinase C. Appl Microbiol Biotechnol 2006; 72:1176-84. [PMID: 16598448 DOI: 10.1007/s00253-006-0405-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2006] [Revised: 02/27/2006] [Accepted: 03/05/2006] [Indexed: 10/24/2022]
Abstract
The chitin-binding domain of Streptomyces griseus chitinase C (ChBD(ChiC)) belongs to CBM family 5. Only two exposed aromatic residues, W59 and W60, were observed in ChBD(ChiC), in contrast to three such residues on CBD(Cel5) in the same CBM family. To study importance of these residues in binding activity and other functions of ChBD(ChiC), site-directed mutagenesis was carried out. Single (W59A and W60A) and double (W59A/W60A) mutations abolished the binding activity of ChiC to colloidal chitin and decreased the hydrolytic activity toward not only colloidal chitin but also a soluble high Mr substrate, glycol chitin. Interaction of ChBD(ChiC) with oligosaccharide was eliminated by these mutations. The hydrolytic activity toward oligosaccharide was increased by deletion of ChBD but not affected by these mutations, indicating that ChBD interferes with oligosaccharide hydrolysis but not through its binding activity. The antifungal activity was drastically decreased by all mutations and significant difference was observed between single and double mutants. Taken together with the structural information, these results suggest that ChBD(ChiC) binds to chitin via a mechanism significantly different from CBD(Cel5), where two aromatic residues play major role, and contributes to various functions of ChiC. Sequence comparison indicated that ChBD(ChiC)-type CBMs are dominant in CBM family 5.
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Affiliation(s)
- Yoshikane Itoh
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
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26
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27
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Umemura M, Yuguchi Y, Hirotsu T. Interaction between Cellooligosaccharides in Aqueous Solution from Molecular Dynamics Simulation: Comparison of Cellotetraose, Cellopentaose, and Cellohexaose. J Phys Chem A 2004. [DOI: 10.1021/jp049044a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Myco Umemura
- National Institute of Advanced Industrial Science & Technology, AIST, 2217-14 Hayashi-cho, Takamatsu-shi, Kagawa 761-0395, Japan
| | - Yoshiaki Yuguchi
- National Institute of Advanced Industrial Science & Technology, AIST, 2217-14 Hayashi-cho, Takamatsu-shi, Kagawa 761-0395, Japan
| | - Takahiro Hirotsu
- National Institute of Advanced Industrial Science & Technology, AIST, 2217-14 Hayashi-cho, Takamatsu-shi, Kagawa 761-0395, Japan
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28
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Lehtiö J, Sugiyama J, Gustavsson M, Fransson L, Linder M, Teeri TT. The binding specificity and affinity determinants of family 1 and family 3 cellulose binding modules. Proc Natl Acad Sci U S A 2003; 100:484-9. [PMID: 12522267 PMCID: PMC141021 DOI: 10.1073/pnas.212651999] [Citation(s) in RCA: 226] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2002] [Accepted: 10/26/2002] [Indexed: 11/18/2022] Open
Abstract
Cellulose binding modules (CBMs) potentiate the action of cellulolytic enzymes on insoluble substrates. Numerous studies have established that three aromatic residues on a CBM surface are needed for binding onto cellulose crystals and that tryptophans contribute to higher binding affinity than tyrosines. However, studies addressing the nature of CBM-cellulose interactions have so far failed to establish the binding site on cellulose crystals targeted by CBMs. In this study, the binding sites of CBMs on Valonia cellulose crystals have been visualized by transmission electron microscopy. Fusion of the CBMs with a modified staphylococcal protein A (ZZ-domain) allowed direct immuno-gold labeling at close proximity of the actual CBM binding site. The transmission electron microscopy images provide unequivocal evidence that the fungal family 1 CBMs as well as the family 3 CBM from Clostridium thermocellum CipA have defined binding sites on two opposite corners of Valonia cellulose crystals. In most samples these corners are worn to display significant area of the hydrophobic (110) plane, which thus constitutes the binding site for these CBMs.
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Affiliation(s)
- Janne Lehtiö
- Department of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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29
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Kataeva IA, Seidel RD, Li XL, Ljungdahl LG. Properties and mutation analysis of the CelK cellulose-binding domain from the Clostridium thermocellum cellulosome. J Bacteriol 2001; 183:1552-9. [PMID: 11160085 PMCID: PMC95039 DOI: 10.1128/jb.183.5.1552-1559.2001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The family IV cellulose-binding domain of Clostridium thermocellum CelK (CBD(CelK)) was expressed in Escherichia coli and purified. It binds to acid-swollen cellulose (ASC) and bacterial microcrystalline cellulose (BMCC) with capacities of 16.03 and 3.95 micromol/g of cellulose and relative affinities (K(r)) of 2.33 and 9.87 liters/g, respectively. The CBD(CelK) is the first representative of family IV CBDs to exhibit an affinity for BMCC. The CBD(CelK) also binds to the soluble polysaccharides lichenin, glucomannan, and barley beta-glucan, which are substrates for CelK. It does not bind to xylan, galactomannan, and carboxymethyl cellulose. The CBD(CelK) contains 1 mol of calcium per mol. The CBD(CelK) has three thiol groups and one disulfide, reduction of which results in total loss of cellulose-binding ability. To reveal amino acid residues important for biological function of the domain and to investigate the role of calcium in the CBD(CelK) four highly conserved aromatic residues (Trp(56), Trp(94), Tyr(111), and Tyr(136)) and Asp(192) were mutated into alanines, giving the mutants W56A, W94A, Y111A, Y136A, and D192A. In addition 14 N-terminal amino acids were deleted, giving the CBD-N(CelK). The CBD-N(CelK) and D192A retained binding parameters close to that of the intact CBD(CelK), W56A and W94A totally lost the ability to bind to cellulose, Y136A bound to both ASC and BMCC but with significantly reduced binding capacity and K(r) and Y111A bound weakly to ASC and did not bind to BMCC. Mutations of the aromatic residues in the CBD(CelK) led to structural changes revealed by studying solubility, circular-dichroism spectra, dimer formation, and aggregation. Calcium content was drastically decreased in D192A. The results suggest that Asp192 is in the calcium-binding site of the CBD(CelK) and that calcium does not affect binding to cellulose. The 14 amino acids from the N terminus of the CBD(CelK) are not important for binding. Tyr136, corresponding to Cellulomonas fimi CenC CBD(N1) Y85, located near the binding cleft, might be involved in the formation of the binding surface, while Y111, W56A, and W94A are essential for the binding process by keeping the CBD(CelK) correctly folded.
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Affiliation(s)
- I A Kataeva
- Department of Biochemistry and Molecular Biology and Center for Biological Resources Recovery, The University of Georgia, Athens, Georgia 30602-7229, USA
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McLean BW, Bray MR, Boraston AB, Gilkes NR, Haynes CA, Kilburn DG. Analysis of binding of the family 2a carbohydrate-binding module from Cellulomonas fimi xylanase 10A to cellulose: specificity and identification of functionally important amino acid residues. PROTEIN ENGINEERING 2000; 13:801-9. [PMID: 11161112 DOI: 10.1093/protein/13.11.801] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The family 2a carbohydrate-binding module (CBM2a) of xylanase 10A from Cellulomonas fimi binds to the crystalline regions of cellulose. It does not share binding sites with the N-terminal family 4 binding module (CBM4-1) from the cellulase 9B from C.fimi, a module that binds strictly to soluble sugars and amorphous cellulose. The binding of CBM2a to crystalline matrices is mediated by several residues on the binding face, including three prominent, solvent-exposed tryptophan residues. Binding to crystalline cellulose was analyzed by making a series of conservative (phenylalanine and tyrosine) and non-conservative substitutions (alanine) of each solvent-exposed tryptophan (W17, W54 and W72). Other residues on the binding face with hydrogen bonding potential were substituted with alanine. Each tryptophan plays a different role in binding; a tryptophan is essential at position 54, a tyrosine or tryptophan at position 17 and any aromatic residue at position 72. Other residues on the binding face, with the exception of N15, are not essential determinants of binding affinity. Given the specificity of CBM2a, the structure of crystalline cellulose and the dynamic nature of the binding of CBM2a, we propose a model for the interaction between the polypeptide and the crystalline surface.
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Affiliation(s)
- B W McLean
- Department of Microbiology and Immunology, University of British Columbia, 300-6174 University Boulevard, Vancouver, BC, Canada V6T 1Z3
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Abstract
Adsorption kinetics and surfactant-mediated elution of Trichoderma reesei CBHI cellulase were recorded in situ, at hydrophobic, silanized silica. Experiments were performed at different solution concentrations, ranging from 0.001 to 0.98 mg/mL. Adsorbed enzyme was partially elutable upon rinsing, with the amount of adsorbed mass remaining being highest at intermediate concentrations. In addition, the resistance to elution with buffer was generally lower at higher concentrations, and the resistance to elution with surfactant was generally lower at intermediate concentrations. These observations are tentatively explained with reference to a mechanism allowing for adsorption of associated monomers of CBHI as well as free monomers.
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Affiliation(s)
- W Suvajittanont
- Department of Bioengineering, Oregon State University, 116 Gilmore Hall, Corvallis, Oregon, USA
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Hashimoto M, Ikegami T, Seino S, Ohuchi N, Fukada H, Sugiyama J, Shirakawa M, Watanabe T. Expression and characterization of the chitin-binding domain of chitinase A1 from Bacillus circulans WL-12. J Bacteriol 2000; 182:3045-54. [PMID: 10809681 PMCID: PMC94488 DOI: 10.1128/jb.182.11.3045-3054.2000] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chitinase A1 from Bacillus circulans WL-12 comprises an N-terminal catalytic domain, two fibronectin type III-like domains, and a C-terminal chitin-binding domain (ChBD). In order to study the biochemical properties and structure of the ChBD, ChBD(ChiA1) was produced in Escherichia coli using a pET expression system and purified by chitin affinity column chromatography. Purified ChBD(ChiA1) specifically bound to various forms of insoluble chitin but not to other polysaccharides, including chitosan, cellulose, and starch. Interaction of soluble chitinous substrates with ChBD(ChiA1) was not detected by means of nuclear magnetic resonance and isothermal titration calorimetry. In addition, the presence of soluble substrates did not interfere with the binding of ChBD(ChiA1) to regenerated chitin. These observations suggest that ChBD(ChiA1) recognizes a structure which is present in insoluble or crystalline chitin but not in chito-oligosaccharides or in soluble derivatives of chitin. ChBD(ChiA1) exhibited binding activity over a wide range of pHs, and the binding activity was enhanced at pHs near its pI and by the presence of NaCl, suggesting that the binding of ChBD(ChiA1) is mediated mainly by hydrophobic interactions. Hydrolysis of beta-chitin microcrystals by intact chitinase A1 and by a deletion derivative lacking the ChBD suggested that the ChBD is not absolutely required for hydrolysis of beta-chitin microcrystals but greatly enhances the efficiency of degradation.
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Affiliation(s)
- M Hashimoto
- Department of Biosystem Science, Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
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Ikegami T, Okada T, Hashimoto M, Seino S, Watanabe T, Shirakawa M. Solution structure of the chitin-binding domain of Bacillus circulans WL-12 chitinase A1. J Biol Chem 2000; 275:13654-61. [PMID: 10788483 DOI: 10.1074/jbc.275.18.13654] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The three-dimensional structure of the chitin-binding domain (ChBD) of chitinase A1 (ChiA1) from a Gram-positive bacterium, Bacillus circulans WL-12, was determined by means of multidimensional heteronuclear NMR methods. ChiA1 is a glycosidase that hydrolyzes chitin and is composed of an N-terminal catalytic domain, two fibronectin type III-like domains, and C-terminal ChBD(ChiA1) (45 residues, Ala(655)-Gln(699)), which binds specifically to insoluble chitin. ChBD(ChiA1) has a compact and globular structure with the topology of a twisted beta-sandwich. This domain contains two antiparallel beta-sheets, one composed of three strands and the other of two strands. The core region formed by the hydrophobic and aromatic residues makes the overall structure rigid and compact. The overall topology of ChBD(ChiA1) is similar to that of the cellulose-binding domain (CBD) of Erwinia chrysanthemi endoglucanase Z (CBD(EGZ)). However, ChBD(ChiA1) lacks the three aromatic residues aligned linearly and exposed to the solvent, which probably interact with cellulose in CBDs. Therefore, the binding mechanism of a group of ChBDs including ChBD(ChiA1) may be different from that proposed for CBDs.
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Affiliation(s)
- T Ikegami
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
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Abstract
Protein-carbohydrate interactions typically rely on aromatic stacking interactions of tyrosine, phenylalanine and tryptophan side chains with the sugar rings whereas histidine residues are rarely involved. The small cellulose-binding domain of the Cel7A cellobiohydrolase (formerly CBHI) from Trichoderma reesei binds to crystalline cellulose primarily using a planar strip of three tyrosine side chains. Binding of the wild-type Cel7A CBD is practically insensitive to pH. Here we have investigated how histidine residues mediate the binding interaction and whether the protonation of a histidine side chain makes the binding sensitive to pH. Protein engineering of the Cel7A CBD was thus used to replace the tyrosine residues in two different positions with histidine residues. All of the mutants exhibited a clear pH-dependency of the binding, in clear contrast to the wild-type. Although the binding of the mutants at optimal pH was less than for the wild-type, in one case, Y31H, this binding almost reached the wild-type level.
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Affiliation(s)
- M Linder
- VTT Biotechnology and Food Research, Finland.
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