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You Y, Kong H, Li C, Gu Z, Ban X, Li Z. Carbohydrate binding modules: Compact yet potent accessories in the specific substrate binding and performance evolution of carbohydrate-active enzymes. Biotechnol Adv 2024; 73:108365. [PMID: 38677391 DOI: 10.1016/j.biotechadv.2024.108365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
Carbohydrate binding modules (CBMs) are independent non-catalytic domains widely found in carbohydrate-active enzymes (CAZymes), and they play an essential role in the substrate binding process of CAZymes by guiding the appended catalytic modules to the target substrates. Owing to their precise recognition and selective affinity for different substrates, CBMs have received increasing research attention over the past few decades. To date, CBMs from different origins have formed a large number of families that show a variety of substrate types, structural features, and ligand recognition mechanisms. Moreover, through the modification of specific sites of CBMs and the fusion of heterologous CBMs with catalytic domains, improved enzymatic properties and catalytic patterns of numerous CAZymes have been achieved. Based on cutting-edge technologies in computational biology, gene editing, and protein engineering, CBMs as auxiliary components have become portable and efficient tools for the evolution and application of CAZymes. With the aim to provide a theoretical reference for the functional research, rational design, and targeted utilization of novel CBMs in the future, we systematically reviewed the function-related characteristics and potentials of CAZyme-derived CBMs in this review, including substrate recognition and binding mechanisms, non-catalytic contributions to enzyme performances, module modifications, and innovative applications in various fields.
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Affiliation(s)
- Yuxian You
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Haocun Kong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Caiming Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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2
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Liu H, Huang M, Wei S, Wang X, Zhao Y, Han Z, Ye X, Li Z, Ji Y, Cui Z, Huang Y. Characterization of a multi-domain exo-β-1,3-galactanase from Paenibacillus xylanexedens. Int J Biol Macromol 2024; 266:131413. [PMID: 38582482 DOI: 10.1016/j.ijbiomac.2024.131413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
β-1,3-Galactanases selectively degrade β-1,3-galactan, thus it is an attractive enzyme technique to map high-galactan structure and prepare galactooligosaccharides. In this work, a gene encoding exo-β-1,3-galactanase (PxGal43) was screened form Paenibacillus xylanexedens, consisting of a GH43 domain, a CBM32 domain and α-L-arabinofuranosidase B (AbfB) domain. Using β-1,3-galactan (AG-II-P) as substrate, the recombined enzyme expressed in Escherichia coli BL21 (DE3) exhibited an optimal activity at pH 7.0 and 30 °C. The enzyme was thermostable, retaining >70 % activity after incubating at 50 °C for 2 h. In addition, it showed high tolerance to various metal ions, denaturants and detergents. Substrate specificity indicated that PxGal43 hydrolysis only β-1,3-linked galactosyl oligosaccharides and polysaccharides, releasing galactose as an exo-acting manner. The function of the CBM32 and AbfB domain was revealed by their sequential deletion and suggested that their connection to the catalytic domain was crucial for the oligomerization, catalytic activity, substrate binding and thermal stability of PxGal43. The substrate docking and site-directed mutagenesis proposed that Glu191, Gln244, Asp138 and Glu81 served as the catalytic acid, catalytic base, pKa modulator, and substrate identifier in PxGal43, respectively. These results provide a better understanding and optimization of multi-domain bacterial GH43 β-1,3-galactanase for the degradation of arabinogalactan.
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Affiliation(s)
- Hao Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Min Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Shuxin Wei
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiaowen Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yaqin Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhengyang Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yanling Ji
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
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3
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Takahashi M, Yano S, Horaguchi Y, Otsuka Y, Suyotha W, Makabe K, Konno H, Kokeguchi S. α-1,3-Glucanase from the gram-negative bacterium Flavobacterium sp. EK-14 hydrolyzes fungal cell wall α-1,3-glucan. Sci Rep 2023; 13:21420. [PMID: 38049513 PMCID: PMC10696023 DOI: 10.1038/s41598-023-48627-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
The glycoside hydrolase (GH) 87 α-1,3-glucanase (Agl-EK14) gene was cloned from the genomic DNA of the gram-negative bacterium Flavobacterium sp. EK14. The gene consisted of 2940 nucleotides and encoded 980 amino acid residues. The deduced amino acid sequence of Agl-EK14 included a signal peptide, a catalytic domain, a first immunoglobulin-like domain, a second immunoglobulin-like domain, a ricin B-like lectin domain, and a carboxyl-terminal domain (CTD) involved in extracellular secretion. Phylogenetic analysis of the catalytic domain of GH87 enzymes suggested that Agl-EK14 is distinct from known clusters, such as clusters composed of α-1,3-glucanases from bacilli and mycodextranases from actinomycetes. Agl-EK14 without the signal peptide and CTD hydrolyzed α-1,3-glucan, and the reaction residues from 1 and 2% substrates were almost negligible after 1440 min reaction. Agl-EK14 hydrolyzed the cell wall preparation of Aspergillus oryzae and released glucose, nigerose, and nigero-triose from the cell wall preparation. After treatment of A. oryzae live mycelia with Agl-EK14 (at least 0.5 nmol/ml), mycelia were no longer stained by red fluorescent protein-fused α-1,3-glucan binding domains of α-1,3-glucanase Agl-KA from Bacillus circulans KA-304. Results suggested that Agl-EK14 can be applied to a fungal cell wall lytic enzyme.
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Affiliation(s)
- Masaki Takahashi
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Shigekazu Yano
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan.
| | - Yui Horaguchi
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Yuitsu Otsuka
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Wasana Suyotha
- Enzyme Technology Laboratory, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, 90112, Thailand
| | - Koki Makabe
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Hiroyuki Konno
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Susumu Kokeguchi
- Department of Oral Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8525, Japan
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Acebrón I, Campanero-Rhodes MA, Solís D, Menéndez M, García C, Lillo MP, Mancheño JM. Atomic crystal structure and sugar specificity of a β-trefoil lectin domain from the ectomycorrhizal basidiomycete Laccaria bicolor. Int J Biol Macromol 2023; 233:123507. [PMID: 36754262 DOI: 10.1016/j.ijbiomac.2023.123507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/10/2023] [Accepted: 01/29/2023] [Indexed: 02/10/2023]
Abstract
Lectins from fruiting bodies are a diverse group of sugar-binding proteins from mushrooms that face the biologically relevant challenge of discriminating self- from non-self carbohydrate structures, therefore providing a basis for an innate defence system. Such a system entails both detection and destruction of invaders and/or feeders, and in contrast to more complex organisms with immense immune systems, these two functions normally rely on multitasking lectins, namely, lectins with different functional modules. Here, we present a novel fungal lectin, LBL, from the basidiomycete Laccaria bicolor. Using a diverse set of biophysical techniques, we unveil the fine details of the sugar-binding specificity of the N-terminal β-trefoil of LBL (LBL152), whose structure has been determined at the highest resolution so far reported for such a fold. LBL152 binds complex poly-N-Acetyllactosamine polysaccharides and also robust LBL152 binding to Caenorhabditis elegans and Drosophila melanogaster cellular extracts was detected in microarray assays, with a seeming preference for the fruit fly adult and pupa stages over the larva stage. Prediction of the structure of the C-terminal part of LBL with AlphaFold reveals a tandem repeat of two structurally almost identical domains of around 110 amino acids each, despite sharing low sequence conservation.
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Affiliation(s)
- Iván Acebrón
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - María Asunción Campanero-Rhodes
- Department of Biological Physical Chemistry, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain; CIBER of Respiratory Diseases Enfermedades Respiratorias (CIBERES), ISCIII, Avda. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Dolores Solís
- Department of Biological Physical Chemistry, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain; CIBER of Respiratory Diseases Enfermedades Respiratorias (CIBERES), ISCIII, Avda. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Margarita Menéndez
- Department of Biological Physical Chemistry, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain; CIBER of Respiratory Diseases Enfermedades Respiratorias (CIBERES), ISCIII, Avda. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Carolina García
- Department of Biological Physical Chemistry, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - M Pilar Lillo
- Department of Biological Physical Chemistry, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - José M Mancheño
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain.
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5
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Liu J, Zhu J, Xu Q, Shi R, Liu C, Sun D, Liu W. Functional identification of two novel carbohydrate-binding modules of glucuronoxylanase CrXyl30 and their contribution to the lignocellulose saccharification. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:40. [PMID: 36890582 PMCID: PMC9996879 DOI: 10.1186/s13068-023-02290-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/28/2023] [Indexed: 03/10/2023]
Abstract
BACKGROUND Glycoside hydrolase (GH) family 30 xylanases are a distinct group of xylanases, most of which have a highly specific catalytic activity for glucuronoxylan. Since GH30 xylanases do not normally carry carbohydrate-binding modules (CBMs), our knowledge of the function of their CBMs is lacking. RESULTS In this work, the CBM functions of CrXyl30 were investigated. CrXyl30 was a GH30 glucuronoxylanase containing tandem CBM13 (CrCBM13) and CBM2 (CrCBM2) at its C terminus, which was identified in a lignocellulolytic bacterial consortium previously. Both CBMs could bind insoluble and soluble xylan, with CrCBM13 having binding specificity for the xylan with L-arabinosyl substitutions, whereas CrCBM2 targeted L-arabinosyl side chains themselves. Such binding abilities of these two CBMs were completely different from other CBMs in their respective families. Phylogenetic analysis also suggested that both CrCBM13 and CrCBM2 belong to novel branches. Inspection of the simulated structure of CrCBM13 identified a pocket that just accommodates the side chain of 3(2)-alpha-L-arabinofuranosyl-xylotriose, which forms hydrogen bonds with three of the five amino acid residues involved in ligand interaction. The truncation of either CrCBM13 or CrCBM2 did not alter the substrate specificity and optimal reaction conditions of CrXyl30, whereas truncation of CrCBM2 decreased the kcat/Km value by 83% (± 0%). Moreover, the absence of CrCBM2 and CrCBM13 resulted in a 5% (± 1%) and a 7% (± 0%) decrease, respectively, in the amount of reducing sugar released by the synergistic hydrolysis of delignified corncob whose hemicellulose is arabinoglucuronoxylan, respectively. In addition, fusion of CrCBM2 with a GH10 xylanase enhanced its catalytic activity against the branched xylan and improved the synergistic hydrolysis efficiency by more than fivefold when delignified corncob was used as substrate. Such a strong stimulation of hydrolysis resulted from the enhancement of hemicellulose hydrolysis on the one hand, and the cellulose hydrolysis is also improved according to the lignocellulose conversion rate measured by HPLC. CONCLUSIONS This study identifies the functions of two novel CBMs in CrXyl30 and shows the good potential of such CBMs specific for branched ligands in the development of efficient enzyme preparations.
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Affiliation(s)
- Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China
| | - Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China
| | - Qian Xu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China
| | - Rui Shi
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China
| | - Cong Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China.
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China.
| | - Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China.
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6
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Zhou T, Hu Y, Yan X, Cui J, Wang Y, Luo F, Yuan Y, Yu Z, Zhou Y. Molecular Cloning and Characterization of a Novel Exo-β-1,3-Galactanase from Penicillium oxalicum sp. 68. J Microbiol Biotechnol 2022; 32:1064-1071. [PMID: 35879293 PMCID: PMC9628948 DOI: 10.4014/jmb.2204.04012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Arabinogalactans have diverse biological properties and can be used as pharmaceutical agents. Most arabinogalactans are composed of β-(1→3)-galactan, so it is particularly important to identify β-1,3-galactanases that can selectively degrade them. In this study, a novel exo-β-1,3-galactanase, named PoGal3, was screened from Penicillium oxalicum sp. 68, and hetero-expressed in P. pastoris GS115 as a soluble protein. PoGal3 belongs to glycoside hydrolase family 43 (GH43) and has a 1,356-bp gene length that encodes 451 amino acids residues. To study the enzymatic properties and substrate selectivity of PoGal3, β-1,3-galactan (AG-P-I) from larch wood arabinogalactan (LWAG) was prepared and characterized by HPLC and NMR. Using AG-P-I as substrate, purified PoGal3 exhibited an optimal pH of 5.0 and temperature of 40°C. We also discovered that Zn2+ had the strongest promoting effect on enzyme activity, increasing it by 28.6%. Substrate specificity suggests that PoGal3 functions as an exo-β-1,3-galactanase, with its greatest catalytic activity observed on AG-P-I. Hydrolytic products of AG-P-I are mainly composed of galactose and β-1,6-galactobiose. In addition, PoGal3 can catalyze hydrolysis of LWAG to produce galacto-oligomers. PoGal3 is the first enzyme identified as an exo-β-1,3-galactanase that can be used in building glycan blocks of crucial glycoconjugates to assess their biological functions.
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Affiliation(s)
- Tong Zhou
- Department of Endocrinology and Metabolism, Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun 130021, P.R. China
| | - Yanbo Hu
- School of Food Sciences and Engineering, Chang Chun University, Changchun 130022, P.R. China
| | - Xuecui Yan
- Engineering Research Center of Glycoconjugates, Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, P.R. China
| | - Jing Cui
- Central Laboratory, Changchun Normal University, Changchun Jilin province, P.R. China
| | - Yibing Wang
- Engineering Research Center of Glycoconjugates, Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, P.R. China
| | - Feng Luo
- Engineering Research Center of Glycoconjugates, Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, P.R. China
| | - Ye Yuan
- Engineering Research Center of Glycoconjugates, Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, P.R. China
| | - Zhenxiang Yu
- Department of Endocrinology and Metabolism, Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun 130021, P.R. China,Corresponding authors Y. Zhou Phone/Fax: +86-431-85098212 E-mail:
| | - Yifa Zhou
- Engineering Research Center of Glycoconjugates, Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, P.R. China,
Z. Yu Phone: +86-431-85098212 Fax: +86-431-85098212 E-mail:
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Cao B, Nie Y, Guan Z, Chen C, Wang N, Wang Z, Shu C, Zhang J, Zhang D. The crystal structure of Cry78Aa from Bacillus thuringiensis provides insights into its insecticidal activity. Commun Biol 2022; 5:801. [PMID: 35945427 PMCID: PMC9363482 DOI: 10.1038/s42003-022-03754-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 07/22/2022] [Indexed: 11/09/2022] Open
Abstract
Genetically modified plants with insecticidal proteins from Bacillus thuringiensis (Bt) have been successfully utilized to control various kinds of pests in crop production and reduce the abuse of pesticides. However, a limited number of genes are available for the protection of crops from rice planthopper. Recently, Cry78Aa protein from Bt strain C9F1 has been found to have high insecticidal activity against Laodelphax striatellus and Nilaparvata lugens. It is the first reported single-component protein in the world to combat rice planthoppers, making it very promising for use in transgenic crops. The ambiguous mechanism of Cry78Aa functions prevented further engineering or application. Here, we report the crystal structure of Cry78Aa, which consists of two domains: a C-terminal β-pore forming domain belonging to the aerolysin family and an N-terminal trefoil domain resembling the S-type ricin B lectin. Thus, Cry78Aa could represent a distinctive type of β-pore forming toxin. We also found that Cry78Aa binds carbohydrates such as galactose derivatives and is essential for insecticidal activity against Laodelphax striatellus. Our results suggest a mechanism underlying the function of Cry78Aa against rice planthoppers and pave the way to maximizing the usage of the toxin. The crystal structure of the Bacillus thuringiensis protein Cry78Aa shows it consists of a C-terminal β-pore forming domain and an N-terminal trefoil domain and suggests a mechanism underlying the function of Cry78Aa against rice planthoppers.
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Affiliation(s)
- Beibei Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yangfan Nie
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuanyu Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nancong Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zeyu Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Changlong Shu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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8
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Le NG, van Ulsen P, van Spanning R, Brouwer A, van Straalen NM, Roelofs D. A Functional Carbohydrate Degrading Enzyme Potentially Acquired by Horizontal Gene Transfer in the Genome of the Soil Invertebrate Folsomia candida. Genes (Basel) 2022; 13:genes13081402. [PMID: 36011312 PMCID: PMC9460274 DOI: 10.3390/genes13081402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/16/2022] Open
Abstract
Horizontal gene transfer (HGT) is defined as the acquisition by an organism of hereditary material from a phylogenetically unrelated organism. This process is mostly observed among bacteria and archaea, and considered less likely between microbes and multicellular eukaryotes. However, recent studies provide compelling evidence of the evolutionary importance of HGT in eukaryotes, driving functional innovation. Here, we study an HGT event in Folsomia candida (Collembola, Hexapoda) of a carbohydrate-active enzyme homologous to glycosyl hydrase group 43 (GH43). The gene encodes an N-terminal signal peptide, targeting the product for excretion, which suggests that it contributes to the diversity of digestive capacities of the detritivore host. The predicted α-L-arabinofuranosidase shows high similarity to genes in two other Collembola, an insect and a tardigrade. The gene was cloned and expressed in Escherichia coli using a cell-free protein expression system. The expressed protein showed activity against p-nitrophenyl-α-L-arabinofuranoside. Our work provides evidence for functional activity of an HGT gene in a soil-living detritivore, most likely from a bacterial donor, with genuine eukaryotic properties, such as a signal peptide. Co-evolution of metazoan GH43 genes with the Panarthropoda phylogeny suggests the HGT event took place early in the evolution of this ecdysozoan lineage.
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Affiliation(s)
- Ngoc Giang Le
- Department of Ecological Science, Faculty of Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
- Correspondence:
| | - Peter van Ulsen
- Department of Molecular Cell Biology, Faculty of Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Rob van Spanning
- Department of Molecular Cell Biology, Faculty of Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | | | - Nico M. van Straalen
- Department of Ecological Science, Faculty of Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Dick Roelofs
- Department of Ecological Science, Faculty of Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
- Keygene N.V., 6708 PW Wageningen, The Netherlands
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9
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Villa-Rivera MG, Cano-Camacho H, López-Romero E, Zavala-Páramo MG. The Role of Arabinogalactan Type II Degradation in Plant-Microbe Interactions. Front Microbiol 2021; 12:730543. [PMID: 34512607 PMCID: PMC8424115 DOI: 10.3389/fmicb.2021.730543] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
Arabinogalactans (AGs) are structural polysaccharides of the plant cell wall. A small proportion of the AGs are associated with hemicellulose and pectin. Furthermore, AGs are associated with proteins forming the so-called arabinogalactan proteins (AGPs), which can be found in the plant cell wall or attached through a glycosylphosphatidylinositol (GPI) anchor to the plasma membrane. AGPs are a family of highly glycosylated proteins grouped with cell wall proteins rich in hydroxyproline. These glycoproteins have important and diverse functions in plants, such as growth, cellular differentiation, signaling, and microbe-plant interactions, and several reports suggest that carbohydrate components are crucial for AGP functions. In beneficial plant-microbe interactions, AGPs attract symbiotic species of fungi or bacteria, promote the development of infectious structures and the colonization of root tips, and furthermore, these interactions can activate plant defense mechanisms. On the other hand, plants secrete and accumulate AGPs at infection sites, creating cross-links with pectin. As part of the plant cell wall degradation machinery, beneficial and pathogenic fungi and bacteria can produce the enzymes necessary for the complete depolymerization of AGs including endo-β-(1,3), β-(1,4) and β-(1,6)-galactanases, β-(1,3/1,6) galactanases, α-L-arabinofuranosidases, β-L-arabinopyranosidases, and β-D-glucuronidases. These hydrolytic enzymes are secreted during plant-pathogen interactions and could have implications for the function of AGPs. It has been proposed that AGPs could prevent infection by pathogenic microorganisms because their degradation products generated by hydrolytic enzymes of pathogens function as damage-associated molecular patterns (DAMPs) eliciting the plant defense response. In this review, we describe the structure and function of AGs and AGPs as components of the plant cell wall. Additionally, we describe the set of enzymes secreted by microorganisms to degrade AGs from AGPs and its possible implication for plant-microbe interactions.
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Affiliation(s)
- Maria Guadalupe Villa-Rivera
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Horacio Cano-Camacho
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Mexico
| | - Everardo López-Romero
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Mexico
| | - María Guadalupe Zavala-Páramo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Mexico
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10
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Morais MAB, Coines J, Domingues MN, Pirolla RAS, Tonoli CCC, Santos CR, Correa JBL, Gozzo FC, Rovira C, Murakami MT. Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations. Nat Commun 2021; 12:367. [PMID: 33446650 PMCID: PMC7809346 DOI: 10.1038/s41467-020-20620-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Xylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, the second most abundant carbohydrate in plants. Here, we kinetically and mechanistically describe the non-reducing-end xylose-releasing exo-oligoxylanase activity and report the crystal structure of a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations of the active site xylosyl unit are found, suggesting two alternative catalytic routes. These results are confirmed by QM/MM simulations that unveil the complete hydrolysis mechanism and identify two possible reaction pathways, involving different transition state conformations for the cleavage of xylooligosaccharides. Such catalytic conformational promiscuity in glycosidases is related to the open architecture of the active site and thus might be extended to other exo-acting enzymes. These findings expand the current general model of catalytic mechanism of glycosidases, a main reaction in nature, and impact on our understanding about their interaction with substrates and inhibitors.
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Affiliation(s)
- Mariana A B Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Joan Coines
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Celisa C C Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Camila R Santos
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Jessica B L Correa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Fabio C Gozzo
- Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, 13083-970, Brazil
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain.
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil.
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11
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Matsuyama K, Kishine N, Fujimoto Z, Sunagawa N, Kotake T, Tsumuraya Y, Samejima M, Igarashi K, Kaneko S. Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-β-1,3-galactanase from Phanerochaete chrysosporium. J Biol Chem 2020; 295:18539-18552. [PMID: 33093171 PMCID: PMC7939473 DOI: 10.1074/jbc.ra120.016149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/20/2020] [Indexed: 12/27/2022] Open
Abstract
Arabinogalactan proteins (AGPs) are plant proteoglycans with functions in growth and development. However, these functions are largely unexplored, mainly because of the complexity of the sugar moieties. These carbohydrate sequences are generally analyzed with the aid of glycoside hydrolases. The exo-β-1,3-galactanase is a glycoside hydrolase from the basidiomycete Phanerochaete chrysosporium (Pc1,3Gal43A), which specifically cleaves AGPs. However, its structure is not known in relation to its mechanism bypassing side chains. In this study, we solved the apo and liganded structures of Pc1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family 35 (CBM35) binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveals that the tautomerized imidic acid group of Gln263 serves as the catalytic base residue instead. Pc1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite -1 contains a space that can accommodate the C-6 methylol of Gal, enabling the enzyme to bypass the β-1,6-linked galactan side chains of AGPs. Furthermore, the galactan-binding domain in CBM35 has a different ligand interaction mechanism from other sugar-binding CBM35s, including those that bind galactomannan. Specifically, we noted a Gly → Trp substitution, which affects pyranose stacking, and an Asp → Asn substitution in the binding pocket, which recognizes β-linked rather than α-linked Gal residues. These findings should facilitate further structural analysis of AGPs and may also be helpful in engineering designer enzymes for efficient biomass utilization.
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Affiliation(s)
- Kaori Matsuyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Naomi Kishine
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Zui Fujimoto
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Toshihisa Kotake
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama, Japan
| | - Yoichi Tsumuraya
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama, Japan
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan; Faculty of Engineering, Shinshu University, Nagano, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan; VTT Technical Research Centre of Finland, Espoo, Finland.
| | - Satoshi Kaneko
- Department of Subtropical Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa, Japan
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12
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Nibbering P, Petersen BL, Motawia MS, Jørgensen B, Ulvskov P, Niittylä T. Golgi-localized exo-β1,3-galactosidases involved in cell expansion and root growth in Arabidopsis. J Biol Chem 2020; 295:10581-10592. [PMID: 32493777 DOI: 10.1074/jbc.ra120.013878] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
Plant arabinogalactan proteins (AGPs) are a diverse group of cell surface- and wall-associated glycoproteins. Functionally important AGP glycans are synthesized in the Golgi apparatus, but the relationships among their glycosylation levels, processing, and functionalities are poorly understood. Here, we report the identification and functional characterization of two Golgi-localized exo-β-1,3-galactosidases from the glycosyl hydrolase 43 (GH43) family in Arabidopsis thaliana GH43 loss-of-function mutants exhibited root cell expansion defects in sugar-containing growth media. This root phenotype was associated with an increase in the extent of AGP cell wall association, as demonstrated by Yariv phenylglycoside dye quantification and comprehensive microarray polymer profiling of sequentially extracted cell walls. Characterization of recombinant GH43 variants revealed that the exo-β-1,3-galactosidase activity of GH43 enzymes is hindered by β-1,6 branches on β-1,3-galactans. In line with this steric hindrance, the recombinant GH43 variants did not release galactose from cell wall-extracted glycoproteins or AGP-rich gum arabic. These results indicate that the lack of exo-β-1,3-galactosidase activity alters cell wall extensibility in roots, a phenotype that could be explained by the involvement of galactosidases in AGP glycan biosynthesis.
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Affiliation(s)
- Pieter Nibbering
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Bent L Petersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Mohammed Saddik Motawia
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Bodil Jørgensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter Ulvskov
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Totte Niittylä
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
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13
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Khan F, Kurre D, Suguna K. Crystal structures of a β-trefoil lectin from Entamoeba histolytica in monomeric and a novel disulfide bond-mediated dimeric forms. Glycobiology 2020; 30:474-488. [DOI: 10.1093/glycob/cwaa001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 01/12/2020] [Accepted: 01/17/2020] [Indexed: 01/02/2023] Open
Abstract
Abstractβ-Trefoil lectins are galactose/N-acetyl galactosamine specific lectins, which are widely distributed across all kingdoms of life and are known to perform several important functions. However, there is no report available on the characterization of these lectins from protozoans. We have performed structural and biophysical studies on a β-trefoil lectin from Entamoeba histolytica (EntTref), which exists as a mixture of monomers and dimers in solution. Further, we have determined the affinities of EntTref for rhamnose, galactose and different galactose-linked sugars. We obtained the crystal structure of EntTref in a sugar-free form (EntTref_apo) and a rhamnose-bound form (EntTref_rham). A novel Cys residue-mediated dimerization was revealed in the crystal structure of EntTref_apo while the structure of EntTref_rham provided the structural basis for the recognition of rhamnose by a β-trefoil lectin for the first time. To the best of our knowledge, this is the only report of the structural, functional and biophysical characterization of a β-trefoil lectin from a protozoan source and the first report of Cys-mediated dimerization in this class of lectins.
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Affiliation(s)
- Farha Khan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, CV Raman Rd, 560012, India
| | - Devanshu Kurre
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, CV Raman Rd, 560012, India
| | - K Suguna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, CV Raman Rd, 560012, India
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14
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Degradative enzymes for type II arabinogalactan side chains in Bifidobacterium longum subsp. longum. Appl Microbiol Biotechnol 2018; 103:1299-1310. [PMID: 30564851 DOI: 10.1007/s00253-018-9566-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 10/27/2022]
Abstract
Type II arabinogalactan (AG) is a soluble prebiotic fiber stimulating the proliferation of bifidobacteria in the human gut. Larch AG, which is comprised of type II AG, is known to be utilized as an energy source for Bifidobacterium longum subsp. longum (B. longum). We have previously characterized GH43_24 exo-β-1,3-galactanase (Bl1,3Gal) for the degradation of type II AG main chains in B. longum JCM1217. In this study, we characterized GH30_5 exo-β-1,6-galactobiohydrolase (Bl1,6Gal) and GH43_22 α-L-arabinofuranosidase (BlArafA), which are degradative enzymes for type II AG side chains in cooperation with exo-β-1,3-galactanase. The recombinant exo-β-1,6-galactobiohydrolase specifically released β-1,6-galactobiose (β-1,6-Gal2) from the nonreducing terminal of β-1,6-galactooligosaccharides, and the recombinant α-L-arabinofuranosidase released arabinofuranose (Araf) from α-1,3-Araf-substituted β-1,6-galactooligosaccharides. β-1,6-Gal2 was additively released from larch AG by the combined use of type II AG degradative enzymes, including Bl1,3Gal, Bl1,6Gal, and BlArafA. The gene cluster encoding the type II AG degradative enzymes is conserved in all B. longum strains, but not in other bifidobacterial species. The degradative enzymes for type II AG side chains are thought to be important for the acquisition of type II AG in B. longum.
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15
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Fujii Y, Gerdol M, Hasan I, Koide Y, Matsuzaki R, Ikeda M, Rajia S, Ogawa Y, Kawsar SMA, Ozeki Y. Phylogeny and Properties of a Novel Lectin Family with β-Trefoil Folding in Mussels. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1717.1e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yuki Fujii
- Department of Pharmaceutical Sciences, Nagasaki International University
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste
| | - Imtiaj Hasan
- Department of Life and Environmental System Science, Yokohama City University
- Department of Biochemistry and Molecular Biology, University of Rajshahi
| | - Yasuhiro Koide
- Department of Life and Environmental System Science, Yokohama City University
| | - Risa Matsuzaki
- Department of Life and Environmental System Science, Yokohama City University
| | - Mayu Ikeda
- Department of Life and Environmental System Science, Yokohama City University
| | - Sultana Rajia
- Department of Life and Environmental System Science, Yokohama City University
- Department of Pharmacy, Faculty of Pharmacy, Varendra University
| | - Yukiko Ogawa
- Department of Pharmaceutical Sciences, Nagasaki International University
| | - S. M. Abe Kawsar
- Department of Life and Environmental System Science, Yokohama City University
- Department of Chemistry, Faculty of Science, University of Chittagong
| | - Yasuhiro Ozeki
- Department of Life and Environmental System Science, Yokohama City University
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16
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de Camargo BR, Claassens NJ, Quirino BF, Noronha EF, Kengen SW. Heterologous expression and characterization of a putative glycoside hydrolase family 43 arabinofuranosidase from Clostridium thermocellum B8. Enzyme Microb Technol 2018; 109:74-83. [DOI: 10.1016/j.enzmictec.2017.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/28/2017] [Accepted: 09/30/2017] [Indexed: 11/30/2022]
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17
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Jones DR, Thomas D, Alger N, Ghavidel A, Inglis GD, Abbott DW. SACCHARIS: an automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:27. [PMID: 29441125 PMCID: PMC5798181 DOI: 10.1186/s13068-018-1027-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/18/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Deposition of new genetic sequences in online databases is expanding at an unprecedented rate. As a result, sequence identification continues to outpace functional characterization of carbohydrate active enzymes (CAZymes). In this paradigm, the discovery of enzymes with novel functions is often hindered by high volumes of uncharacterized sequences particularly when the enzyme sequence belongs to a family that exhibits diverse functional specificities (i.e., polyspecificity). Therefore, to direct sequence-based discovery and characterization of new enzyme activities we have developed an automated in silico pipeline entitled: Sequence Analysis and Clustering of CarboHydrate Active enzymes for Rapid Informed prediction of Specificity (SACCHARIS). This pipeline streamlines the selection of uncharacterized sequences for discovery of new CAZyme or CBM specificity from families currently maintained on the CAZy website or within user-defined datasets. RESULTS SACCHARIS was used to generate a phylogenetic tree of a GH43, a CAZyme family with defined subfamily designations. This analysis confirmed that large datasets can be organized into sequence clusters of manageable sizes that possess related functions. Seeding this tree with a GH43 sequence from Bacteroides dorei DSM 17855 (BdGH43b, revealed it partitioned as a single sequence within the tree. This pattern was consistent with it possessing a unique enzyme activity for GH43 as BdGH43b is the first described α-glucanase described for this family. The capacity of SACCHARIS to extract and cluster characterized carbohydrate binding module sequences was demonstrated using family 6 CBMs (i.e., CBM6s). This CBM family displays a polyspecific ligand binding profile and contains many structurally determined members. Using SACCHARIS to identify a cluster of divergent sequences, a CBM6 sequence from a unique clade was demonstrated to bind yeast mannan, which represents the first description of an α-mannan binding CBM. Additionally, we have performed a CAZome analysis of an in-house sequenced bacterial genome and a comparative analysis of B. thetaiotaomicron VPI-5482 and B. thetaiotaomicron 7330, to demonstrate that SACCHARIS can generate "CAZome fingerprints", which differentiate between the saccharolytic potential of two related strains in silico. CONCLUSIONS Establishing sequence-function and sequence-structure relationships in polyspecific CAZyme families are promising approaches for streamlining enzyme discovery. SACCHARIS facilitates this process by embedding CAZyme and CBM family trees generated from biochemically to structurally characterized sequences, with protein sequences that have unknown functions. In addition, these trees can be integrated with user-defined datasets (e.g., genomics, metagenomics, and transcriptomics) to inform experimental characterization of new CAZymes or CBMs not currently curated, and for researchers to compare differential sequence patterns between entire CAZomes. In this light, SACCHARIS provides an in silico tool that can be tailored for enzyme bioprospecting in datasets of increasing complexity and for diverse applications in glycobiotechnology.
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Affiliation(s)
- Darryl R. Jones
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1 Canada
| | - Dallas Thomas
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1 Canada
| | - Nicholas Alger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1 Canada
| | - Ata Ghavidel
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1 Canada
| | - G. Douglas Inglis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1 Canada
| | - D. Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1 Canada
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18
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De Schutter K, Tsaneva M, Kulkarni SR, Rougé P, Vandepoele K, Van Damme EJM. Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa). RICE (NEW YORK, N.Y.) 2017; 10:26. [PMID: 28560587 PMCID: PMC5449364 DOI: 10.1186/s12284-017-0164-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/16/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Lectins, defined as 'Proteins that can recognize and bind specific carbohydrate structures', are widespread among all kingdoms of life and play an important role in various biological processes in the cell. Most plant lectins are involved in stress signaling and/or defense. The family of Euonymus-related lectins (EULs) represents a group of stress-related lectins composed of one or two EUL domains. The latter protein domain is unique in that it is ubiquitous in land plants, suggesting an important role for these proteins. RESULTS Despite the availability of multiple completely sequenced rice genomes, little is known on the occurrence of lectins in rice. We identified 329 putative lectin genes in the genome of Oryza sativa subsp. japonica belonging to nine out of 12 plant lectin families. In this paper, an in-depth molecular characterization of the EUL family of rice was performed. In addition, analyses of the promoter sequences and investigation of the transcript levels for these EUL genes enabled retrieval of important information related to the function and stress responsiveness of these lectins. Finally, a comparative analysis between rice cultivars and several monocot and dicot species revealed a high degree of sequence conservation within the EUL domain as well as in the domain organization of these lectins. CONCLUSIONS The presence of EULs throughout the plant kingdom and the high degree of sequence conservation in the EUL domain suggest that these proteins serve an important function in the plant cell. Analysis of the promoter region of the rice EUL genes revealed a diversity of stress responsive elements. Furthermore analysis of the expression profiles of the EUL genes confirmed that they are differentially regulated in response to several types of stress. These data suggest a potential role for the EULs in plant stress signaling and defense.
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Affiliation(s)
- Kristof De Schutter
- Laboratory Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Mariya Tsaneva
- Laboratory Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Shubhada R Kulkarni
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
| | - Pierre Rougé
- UMR 152 PHARMA-DEV, Université de Toulouse, IRD, UPS, Chemin des Maraîchers 35, 31400, Toulouse, France
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
| | - Els J M Van Damme
- Laboratory Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000, Ghent, Belgium.
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19
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Terada D, Voet ARD, Noguchi H, Kamata K, Ohki M, Addy C, Fujii Y, Yamamoto D, Ozeki Y, Tame JRH, Zhang KYJ. Computational design of a symmetrical β-trefoil lectin with cancer cell binding activity. Sci Rep 2017; 7:5943. [PMID: 28724971 PMCID: PMC5517649 DOI: 10.1038/s41598-017-06332-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/12/2017] [Indexed: 01/24/2023] Open
Abstract
Computational protein design has advanced very rapidly over the last decade, but there remain few examples of artificial proteins with direct medical applications. This study describes a new artificial β-trefoil lectin that recognises Burkitt’s lymphoma cells, and which was designed with the intention of finding a basis for novel cancer treatments or diagnostics. The new protein, called “Mitsuba”, is based on the structure of the natural shellfish lectin MytiLec-1, a member of a small lectin family that uses unique sequence motifs to bind α-D-galactose. The three subdomains of MytiLec-1 each carry one galactose binding site, and the 149-residue protein forms a tight dimer in solution. Mitsuba (meaning “three-leaf” in Japanese) was created by symmetry constraining the structure of a MytiLec-1 subunit, resulting in a 150-residue sequence that contains three identical tandem repeats. Mitsuba-1 was expressed and crystallised to confirm the X-ray structure matches the predicted model. Mitsuba-1 recognises cancer cells that express globotriose (Galα(1,4)Galβ(1,4)Glc) on the surface, but the cytotoxicity is abolished.
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Affiliation(s)
- Daiki Terada
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan.,Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Arnout R D Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001, Heverlee, Belgium
| | - Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001, Heverlee, Belgium
| | - Kenichi Kamata
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
| | - Mio Ohki
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
| | - Christine Addy
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuki Fujii
- Department of Pharmacy, Graduate School of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298, Japan
| | - Daiki Yamamoto
- Laboratory of Glycobiology and Marine Biochemistry, Graduate School of NanoBio Sciences, Yokohama City University, 22-2, Seto, Yokohama, Kanagawa, 236-0027, Japan
| | - Yasuhiro Ozeki
- Laboratory of Glycobiology and Marine Biochemistry, Graduate School of NanoBio Sciences, Yokohama City University, 22-2, Seto, Yokohama, Kanagawa, 236-0027, Japan
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan.
| | - Kam Y J Zhang
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
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20
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Unusual active site location and catalytic apparatus in a glycoside hydrolase family. Proc Natl Acad Sci U S A 2017; 114:4936-4941. [PMID: 28396425 DOI: 10.1073/pnas.1701130114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The human gut microbiota use complex carbohydrates as major nutrients. The requirement for an efficient glycan degrading systems exerts a major selection pressure on this microbial community. Thus, we propose that these bacteria represent a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis, we focused on enzymes that hydrolyze rhamnosidic bonds, as cleavage of these linkages is chemically challenging and there is a paucity of information on l-rhamnosidases. Here we screened the activity of enzymes derived from the human gut microbiota bacterium Bacteroides thetaiotaomicron, which are up-regulated in response to rhamnose-containing glycans. We identified an α-l-rhamnosidase, BT3686, which is the founding member of a glycoside hydrolase (GH) family, GH145. In contrast to other rhamnosidases, BT3686 cleaved l-Rha-α1,4-d-GlcA linkages through a retaining double-displacement mechanism. The crystal structure of BT3686 showed that the enzyme displayed a type A seven-bladed β-propeller fold. Mutagenesis and crystallographic studies, including the structure of BT3686 in complex with the reaction product GlcA, revealed a location for the active site among β-propeller enzymes cited on the posterior surface of the rhamnosidase. In contrast to the vast majority of GH, the catalytic apparatus of BT3686 does not comprise a pair of carboxylic acid residues but, uniquely, a single histidine functions as the only discernable catalytic amino acid. Intriguingly, the histidine, His48, is not invariant in GH145; however, when engineered into structural homologs lacking the imidazole residue, α-l-rhamnosidase activity was established. The potential contribution of His48 to the catalytic activity of BT3686 is discussed.
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21
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Hehemann JH, Truong LV, Unfried F, Welsch N, Kabisch J, Heiden SE, Junker S, Becher D, Thürmer A, Daniel R, Amann R, Schweder T. Aquatic adaptation of a laterally acquired pectin degradation pathway in marine gammaproteobacteria. Environ Microbiol 2017; 19:2320-2333. [PMID: 28276126 DOI: 10.1111/1462-2920.13726] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 03/03/2017] [Accepted: 03/05/2017] [Indexed: 01/09/2023]
Abstract
Mobile genomic islands distribute functional traits between microbes and habitats, yet it remains unclear how their proteins adapt to new environments. Here we used a comparative phylogenomic and proteomic approach to show that the marine bacterium Pseudoalteromonas haloplanktis ANT/505 acquired a genomic island with a functional pathway for pectin catabolism. Bioinformatics and biochemical experiments revealed that this pathway encodes a series of carbohydrate-active enzymes including two multi-modular pectate lyases, PelA and PelB. PelA is a large enzyme with a polysaccharide lyase family 1 (PL1) domain and a carbohydrate esterase family 8 domain, and PelB contains a PL1 domain and two carbohydrate-binding domains of family 13. Comparative phylogenomic analyses indicate that the pathway was most likely acquired from terrestrial microbes, yet we observed multi-modular orthologues only in marine bacteria. Proteomic experiments showed that P. haloplanktis ANT/505 secretes both pectate lyases into the environment in the presence of pectin. These multi-modular enzymes may therefore represent a marine innovation that enhances physical interaction with pectins to reduce loss of substrate and enzymes by diffusion. Our results revealed that marine bacteria can catabolize pectin, and highlight enzyme fusion as a potential adaptation that may facilitate microbial consumption of polymeric substrates in aquatic environments.
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Affiliation(s)
- Jan-Hendrik Hehemann
- MARUM, Center for Marine Environmental Sciences at the University of Bremen, Leobener Strasse, Bremen, D-28359, Germany.,Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Le Van Truong
- Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Institute of Biotechnology, Vietnamese Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Frank Unfried
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany.,Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Norma Welsch
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Johannes Kabisch
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany.,Department of Biology, Computer-aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 10, Darmstadt, D-64287, Germany
| | - Stefan E Heiden
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Sabryna Junker
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, D-17487, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, D-17487, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory (G2L), Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory (G2L), Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Thomas Schweder
- Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
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22
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Labourel A, Crouch LI, Brás JLA, Jackson A, Rogowski A, Gray J, Yadav MP, Henrissat B, Fontes CMGA, Gilbert HJ, Najmudin S, Baslé A, Cuskin F. The Mechanism by Which Arabinoxylanases Can Recognize Highly Decorated Xylans. J Biol Chem 2016; 291:22149-22159. [PMID: 27531750 PMCID: PMC5063996 DOI: 10.1074/jbc.m116.743948] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Indexed: 12/15/2022] Open
Abstract
The enzymatic degradation of plant cell walls is an important biological process of increasing environmental and industrial significance. Xylan, a major component of the plant cell wall, consists of a backbone of β-1,4-xylose (Xylp) units that are often decorated with arabinofuranose (Araf) side chains. A large penta-modular enzyme, CtXyl5A, was shown previously to specifically target arabinoxylans. The mechanism of substrate recognition displayed by the enzyme, however, remains unclear. Here we report the crystal structure of the arabinoxylanase and the enzyme in complex with ligands. The data showed that four of the protein modules adopt a rigid structure, which stabilizes the catalytic domain. The C-terminal non-catalytic carbohydrate binding module could not be observed in the crystal structure, suggesting positional flexibility. The structure of the enzyme in complex with Xylp-β-1,4-Xylp-β-1,4-Xylp-[α-1,3-Araf]-β-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (−2* subsite) that abuts onto the catalytic center. The −2* subsite can also bind to Xylp and Arap, explaining why the enzyme can utilize xylose and arabinose as specificity determinants. Alanine substitution of Glu68, Tyr92, or Asn139, which interact with arabinose and xylose side chains at the −2* subsite, abrogates catalytic activity. Distal to the active site, the xylan backbone makes limited apolar contacts with the enzyme, and the hydroxyls are solvent-exposed. This explains why CtXyl5A is capable of hydrolyzing xylans that are extensively decorated and that are recalcitrant to classic endo-xylanase attack.
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Affiliation(s)
- Aurore Labourel
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Lucy I Crouch
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Joana L A Brás
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal, NZYTech Genes & Enzymes, 1649-038 Lisboa, Portugal
| | - Adam Jackson
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Artur Rogowski
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Joseph Gray
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Madhav P Yadav
- the Eastern Regional Research Center, United States Department of Agriculture-Agricultural Research Service, Wyndmoor, Pennsylvania 19038
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7857 CNRS, Aix-Marseille University, F-13288 Marseille, France, USC1408 Architecture et Fonction des Macromolécules Biologiques, INRA, F-13288 Marseille, France, and the Department of Biological Sciences, King Abdulaziz University, Jedda 21589, Saudi Arabia
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal, NZYTech Genes & Enzymes, 1649-038 Lisboa, Portugal
| | - Harry J Gilbert
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal,
| | - Arnaud Baslé
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom,
| | - Fiona Cuskin
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom,
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23
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Crystal structure of MytiLec, a galactose-binding lectin from the mussel Mytilus galloprovincialis with cytotoxicity against certain cancer cell types. Sci Rep 2016; 6:28344. [PMID: 27321048 PMCID: PMC4913266 DOI: 10.1038/srep28344] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/31/2016] [Indexed: 01/07/2023] Open
Abstract
MytiLec is a lectin, isolated from bivalves, with cytotoxic activity against cancer cell lines that express globotriaosyl ceramide, Galα(1,4)Galβ(1,4)Glcα1-Cer, on the cell surface. Functional analysis shows that the protein binds to the disaccharide melibiose, Galα(1,6)Glc, and the trisaccharide globotriose, Galα(1,4)Galβ(1,4)Glc. Recombinant MytiLec expressed in bacteria showed the same haemagglutinating and cytotoxic activity against Burkitt's lymphoma (Raji) cells as the native form. The crystal structure has been determined to atomic resolution, in the presence and absence of ligands, showing the protein to be a member of the β-trefoil family, but with a mode of ligand binding unique to a small group of related trefoil lectins. Each of the three pseudo-equivalent binding sites within the monomer shows ligand binding, and the protein forms a tight dimer in solution. An engineered monomer mutant lost all cytotoxic activity against Raji cells, but retained some haemagglutination activity, showing that the quaternary structure of the protein is important for its cellular effects.
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24
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Liao JH, Chien CTH, Wu HY, Huang KF, Wang I, Ho MR, Tu IF, Lee IM, Li W, Shih YL, Wu CY, Lukyanov PA, Hsu STD, Wu SH. A Multivalent Marine Lectin from Crenomytilus grayanus Possesses Anti-cancer Activity through Recognizing Globotriose Gb3. J Am Chem Soc 2016; 138:4787-95. [PMID: 27010847 DOI: 10.1021/jacs.6b00111] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this study, we report the structure and function of a lectin from the sea mollusk Crenomytilus grayanus collected from the sublittoral zone of Peter the Great Bay of the Sea of Japan. The crystal structure of C. grayanus lectin (CGL) was solved to a resolution of 1.08 Å, revealing a β-trefoil fold that dimerizes into a dumbbell-shaped quaternary structure. Analysis of the crystal CGL structures bound to galactose, galactosamine, and globotriose Gb3 indicated that each CGL can bind three ligands through a carbohydrate-binding motif involving an extensive histidine- and water-mediated hydrogen bond network. CGL binding to Gb3 is further enhanced by additional side-chain-mediated hydrogen bonds in each of the three ligand-binding sites. NMR titrations revealed that the three binding sites have distinct microscopic affinities toward galactose and galactosamine. Cell viability assays showed that CGL recognizes Gb3 on the surface of breast cancer cells, leading to cell death. Our findings suggest the use of this lectin in cancer diagnosis and treatment.
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Affiliation(s)
- Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - Chih-Ta Henry Chien
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University , Taipei 106, Taiwan
| | - Han-Ying Wu
- Institute of Biological Chemistry, Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 30043, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - Iren Wang
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - I-Fan Tu
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - I-Ming Lee
- Institute of Biochemical Science, National Taiwan University , Taipei 106, Taiwan
| | - Wei Li
- Key Laboratory of Aquatic Products Processing and Utilization of Liaoning Province, Dalian Ocean University , Dalian 116023, P.R. China
| | - Yu-Ling Shih
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica , Taipei 11529, Taiwan
| | - Pavel A Lukyanov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences , Vladivostok 690022, Russian Federation
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan.,Institute of Biological Chemistry, Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Science, National Taiwan University , Taipei 106, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University , Taipei 106, Taiwan.,Institute of Biological Chemistry, Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Science, National Taiwan University , Taipei 106, Taiwan
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25
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Godoy AS, de Lima MZT, Camilo CM, Polikarpov I. Crystal structure of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17. Acta Crystallogr F Struct Biol Commun 2016; 72:288-93. [PMID: 27050262 PMCID: PMC4822985 DOI: 10.1107/s2053230x16003617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/01/2016] [Indexed: 11/10/2022] Open
Abstract
Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, crystallization and structure determination of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17 (BbGal43A) are described. BbGal43A was successfully produced and showed activity towards synthetic galactosides. BbGal43A was subsequently crystallized and data were collected to 1.4 Å resolution. The structure shows a single-domain molecule, differing from known homologues, and crystal contact analysis predicts the formation of a dimer in solution. Further biochemical studies are necessary to elucidate the differences between BbGal43A and its characterized homologues.
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Affiliation(s)
- Andre S. Godoy
- Departamento de Física em São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13560-970 São Carlos-SP, Brazil
| | - Mariana Z. T. de Lima
- Departamento de Física em São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13560-970 São Carlos-SP, Brazil
| | - Cesar M. Camilo
- Centro de Tecnologia Canavieira, Fazenda Santo Antonio, PO Box 162, 13400-970 Piracicaba-SP, Brazil
| | - Igor Polikarpov
- Departamento de Física em São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13560-970 São Carlos-SP, Brazil
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26
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Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization. Appl Environ Microbiol 2016; 82:1686-1692. [PMID: 26729713 DOI: 10.1128/aem.03453-15] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 12/27/2015] [Indexed: 01/15/2023] Open
Abstract
The rapid rise in DNA sequencing has led to an expansion in the number of glycoside hydrolase (GH) families. The GH43 family currently contains α-l-arabinofuranosidase, β-d-xylosidase, α-l-arabinanase, and β-d-galactosidase enzymes for the debranching and degradation of hemicellulose and pectin polymers. Many studies have revealed finer details about members of GH43 that necessitate the division of GH43 into subfamilies, as was done previously for the GH5 and GH13 families. The work presented here is a robust subfamily classification that assigns over 91% of all complete GH43 domains into 37 subfamilies that correlate with conserved sequence residues and results of biochemical assays and structural studies. Furthermore, cooccurrence analysis of these subfamilies and other functional modules revealed strong associations between some GH43 subfamilies and CBM6 and CBM13 domains. Cooccurrence analysis also revealed the presence of proteins containing up to three GH43 domains and belonging to different subfamilies, suggesting significant functional differences for each subfamily. Overall, the subfamily analysis suggests that the GH43 enzymes probably display a hitherto underestimated variety of subtle specificity features that are not apparent when the enzymes are assayed with simple synthetic substrates, such as pNP-glycosides.
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27
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Abhinav KV, Samuel E, Vijayan M. Archeal lectins: An identification through a genomic search. Proteins 2015; 84:21-30. [DOI: 10.1002/prot.24949] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/13/2015] [Accepted: 10/19/2015] [Indexed: 11/09/2022]
Affiliation(s)
- K. V. Abhinav
- Molecular Biophysics Unit, Indian Institute of Science; Bangalore 560 012 India
| | - Ebenezer Samuel
- Molecular Biophysics Unit, Indian Institute of Science; Bangalore 560 012 India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science; Bangalore 560 012 India
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28
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Bifidobacterium longum subsp. longum Exo-β-1,3-Galactanase, an enzyme for the degradation of type II arabinogalactan. Appl Environ Microbiol 2015; 80:4577-84. [PMID: 24837371 DOI: 10.1128/aem.00802-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Type II arabinogalactan (AG-II) is a suitable carbohydrate source for Bifidobacterium longum subsp. longum, but the degradative enzymes have never been characterized. In this study, we characterized an exo-β-1,3-galactanase, BLLJ_1840, belonging to glycoside hydrolase family 43 from B. longum subsp. longum JCM1217. The recombinant BLLJ_1840 expressed in Escherichia coli hydrolyzed β-1,3-linked galactooligosaccharides but not β-1,4- and β-1,6-linked galactooligosaccharides. The enzyme also hydrolyzed larch wood arabinogalactan (LWAG), which comprises a β-1,3-linked galactan backbone with β-1,6-linked galactan side chains. The kcat/Km ratio of dearabinosylated LWAG was 24-fold higher than that of β-1,3-galactan. BLLJ_1840 is a novel type of exo-β-1,3-galactanase with a higher affinity for the β-1,6-substituted β-1,3-galactan than for nonsubstituted β-1,3-galactan. BLLJ_1840 has 27% to 28% identities with other characterized exo--1,3-galactanases from bacteria and fungi. The homologous genes are conserved in several strains of B. longum subsp. longum and B. longum subsp. infantis but not in other bifidobacteria. Transcriptional analysis revealed that BLLJ_1840 is intensively induced with BLLJ_1841, an endo-β-1,6-galactanase candidate, in the presence of LWAG. This is the first report of exo-β-1,3-galactanase in bifidobacteria, which is an enzyme used for the acquisition of AG-II in B. longum subsp. longum.
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29
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Santos CR, Polo CC, Costa MCMF, Nascimento AFZ, Meza AN, Cota J, Hoffmam ZB, Honorato RV, Oliveira PSL, Goldman GH, Gilbert HJ, Prade RA, Ruller R, Squina FM, Wong DWS, Murakami MT. Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases. J Biol Chem 2014; 289:7362-73. [PMID: 24469445 DOI: 10.1074/jbc.m113.537167] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Arabinanases (ABNs, EC 3.2.1.99) are promising catalysts for environmentally friendly biomass conversion into energy and chemicals. These enzymes catalyze the hydrolysis of the α-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans releasing arabino-oligosaccharides and arabinose, the second most abundant pentose in nature. In this work, new findings about the molecular mechanisms governing activation, functional differentiation, and catalysis of GH43 ABNs are presented. Biophysical, mutational, and biochemical studies with the hyperthermostable two-domain endo-acting ABN from Thermotoga petrophila (TpABN) revealed how some GH43 ABNs are activated by calcium ions via hyperpolarization of the catalytically relevant histidine and the importance of the ancillary domain for catalysis and conformational stability. On the other hand, the two GH43 ABNs from rumen metagenome, ARN2 and ARN3, presented a calcium-independent mechanism in which sodium is the most likely substituent for calcium ions. The crystal structure of the two-domain endo-acting ARN2 showed that its ability to efficiently degrade branched substrates is due to a larger catalytic interface with higher accessibility than that observed in other ABNs with preference for linear arabinan. Moreover, crystallographic characterization of the single-domain exo-acting ARN3 indicated that its cleavage pattern producing arabinose is associated with the chemical recognition of the reducing end of the substrate imposed by steric impediments at the aglycone-binding site. By structure-guided rational design, ARN3 was converted into a classical endo enzyme, confirming the role of the extended Arg(203)-Ala(230) loop in determining its action mode. These results reveal novel molecular aspects concerning the functioning of GH43 ABNs and provide new strategies for arabinan degradation.
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30
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Okawa M, Fukamachi K, Tanaka H, Sakamoto T. Identification of an exo-ß-1,3-D-galactanase from Fusarium oxysporum and the synergistic effect with related enzymes on degradation of type II arabinogalactan. Appl Microbiol Biotechnol 2013; 97:9685-94. [PMID: 23429923 DOI: 10.1007/s00253-013-4759-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 02/04/2013] [Accepted: 02/06/2013] [Indexed: 11/28/2022]
Abstract
An exo-ß-1,3-D-galactanase (Fo/1,3Gal) was purified from the culture filtrate of Fusarium oxysporum 12S. A cDNA encoding Fo/1,3Gal was isolated by in vitro cloning. Module sequence analysis revealed a "GH43_6" domain and a "CBM35_galactosidase-like" domain in Fo/1,3Gal. The recombinant enzyme (rFo/1,3Gal) expressed in Pichia pastoris degraded ß-1,3-galactan and ß-1,3-galactobiose (Gal2), and released only galactose (Gal). In contrast, the enzyme did not hydrolyze p-nitrophenyl ß-D-galactopyranoside, ß-1,4-Gal2, or ß-1,6-Gal2. The enzyme also showed low activity towards native type II arabinogalactans such as larchwood arabinogalactan (LWAG) and gum arabic. Using LWAG as substrate, rFo/1,3Gal released Gal, ß-1,6-Gal2, ß-1,6-galactotriose (Gal3), and ß-1,6-Gal3 substituted with a single arabinofuranose residue accompanied with unidentified oligosaccharides, indicating that the enzyme can by-pass the branching points of ß-1,3-galactan backbones. A time course analysis of products released by rFo/1,3Gal on LWAG revealed that ß-1,6-Gal2 is the main side chain in LWAG and that the activity of rFo/1,3Gal was decreased when degrees of polymerization of side chains increase. rFo/1,3Gal worked synergistically with three other recombinant F. oxysporum enzymes (ß-1,6-galactanase, ß-L-arabinopyranosidase, and α-L-arabinofuranosidase) that degrade side chains, on the degradation of LWAG. However, the synergism was much lower than anticipated, probably because LWAG have longer side chains than the three enzymes used are able to remove or ß-1,3-galactan main chain is interrupted with glycosidic linkages that are different from the ß-1,3-galactosyl linkage. Affinity gel electrophoresis revealed that rFo/1,3Gal specifically bound to ß-1,3-galactan.
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Affiliation(s)
- Mizuho Okawa
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, 599-8531, Osaka, Japan
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