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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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Xia B, Li Z, Wei J, Hu G, Yang J, Zhang H, Hu X. Modification of the Loop Region Near the Substrate Tunnel to Alter the Hydrolytic Process of Dextranase. J Biotechnol 2024; 381:57-66. [PMID: 38185430 DOI: 10.1016/j.jbiotec.2024.01.003] [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: 08/15/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
Dextranases are hydrolases that exclusively catalyze the disruption of α-1,6 glycosidic bonds. A series of variant enzymes were obtained by comparing the sequences of dextranases from different sources and introducing sequence substitutions. A correlation was found between the number of amino acids in the 397-401 region and the hydrolytic process. When there were no more than 5 amino acids in the 397-401 region, the enzyme first hydrolyzed the dextran T70 to a low molecular weight dextran with a molecular weight of about 5000, then IMOs1 appeared in the system if the degradation continued, showing a clear sequential relationship. And when there are more than 5 amino acids in the 397-401 region, IMOs were produced at the beginning of hydrolysis and continue to increase throughout the hydrolytic process. At the same time, we investigated the enzymatic properties of the variants and found that the hydrolytic rate of A-Ca was 11 times higher than that of the original enzyme. The proportion of IMOs produced by A-Ca was 80.68%, which was nearly10% higher than the original enzyme, providing a new enzyme for the industrial preparation of IMOs.
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Affiliation(s)
- Bingbing Xia
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China
| | - Zhiwei Li
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China
| | - Jinao Wei
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China
| | - Ganpeng Hu
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China
| | - Jingwen Yang
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China
| | - Hongbin Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China.
| | - Xueqin Hu
- School of Food and Biological Engineering, Hefei University of Technology, Anhui 230000, China.
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Mir B, Yang J, Li Z, Wang L, Ali V, Hu X, Zhang H. Review on recent advances in the properties, production and applications of microbial dextranases. World J Microbiol Biotechnol 2023; 39:242. [PMID: 37400664 DOI: 10.1007/s11274-023-03691-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
Dextranase is a type of hydrolase that is responsible for catalyzing the breakdown of high-molecular-weight dextran into low-molecular-weight polysaccharides. This process is called dextranolysis. A select group of bacteria and fungi, including yeasts and likely certain complex eukaryotes, produce dextranase enzymes as extracellular enzymes that are released into the environment. These enzymes join dextran's α-1,6 glycosidic bonds to make glucose, exodextranases, or isomalto-oligosaccharides (endodextranases). Dextranase is an enzyme that has a wide variety of applications, some of which include the sugar business, the production of human plasma replacements, the treatment of dental plaque and its protection, and the creation of human plasma replacements. Because of this, the quantity of studies carried out on worldwide has steadily increased over the course of the past couple of decades. The major focus of this study is on the most current advancements in the production, administration, and properties of microbial dextranases. This will be done throughout the entirety of the review.
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Affiliation(s)
- Baiza Mir
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Jingwen Yang
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China.
| | - Zhiwei Li
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Lei Wang
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Vilayat Ali
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Xueqin Hu
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Hongbin Zhang
- College of Food and Biological Engineering, Hefei University of Technology, Hefei, China.
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4
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Glycoside hydrolases active on microbial exopolysaccharide α-glucans: structures and function. Essays Biochem 2023; 67:505-520. [PMID: 36876882 DOI: 10.1042/ebc20220219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 03/07/2023]
Abstract
Glucose is the most abundant monosaccharide in nature and is an important energy source for living organisms. Glucose exists primarily as oligomers or polymers and organisms break it down and consume it. Starch is an important plant-derived α-glucan in the human diet. The enzymes that degrade this α-glucan have been well studied as they are ubiquitous throughout nature. Some bacteria and fungi produce α-glucans with different glucosidic linkages compared with that of starch, and their structures are quite complex and not fully understood. Compared with enzymes that degrade the α-(1→4) and α-(1→6) linkages in starch, biochemical and structural studies of the enzymes that catabolize α-glucans from these microorganisms are limited. This review focuses on glycoside hydrolases that act on microbial exopolysaccharide α-glucans containing α-(1→6), α-(1→3), and α-(1→2) linkages. Recently acquired information regarding microbial genomes has contributed to the discovery of enzymes with new substrate specificities compared with that of previously studied enzymes. The discovery of new microbial α-glucan-hydrolyzing enzymes suggests previously unknown carbohydrate utilization pathways and reveals strategies for microorganisms to obtain energy from external sources. In addition, structural analysis of α-glucan degrading enzymes has revealed their substrate recognition mechanisms and expanded their potential use as tools for understanding complex carbohydrate structures. In this review, the author summarizes the recent progress in the structural biology of microbial α-glucan degrading enzymes, touching on previous studies of microbial α-glucan degrading enzymes.
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Hu X, Xia B, Ru W, Zhang Y, Yang J, Zhang H. Research progress on structure and catalytic mechanism of dextranase. EFOOD 2023. [DOI: 10.1002/efd2.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Xue‐Qin Hu
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Bing‐Bing Xia
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Wei‐Juan Ru
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Yu‐Xin Zhang
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Jing‐Wen Yang
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Hong‐Bin Zhang
- School of Food and Biological Engineering Hefei University of Technology Hefei China
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Wei Z, Chen J, Xu L, Liu N, Yang J, Wang S. Improving the thermostability of GH49 dextranase AoDex by site-directed mutagenesis. AMB Express 2023; 13:7. [PMID: 36656394 PMCID: PMC9852402 DOI: 10.1186/s13568-023-01513-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 01/08/2023] [Indexed: 01/20/2023] Open
Abstract
As an indispensable enzyme for the hydrolysis of dextran, dextranase has been widely used in the fields of food and medicine. It should be noted that the weak thermostability of dextranase has become a restricted factor for industrial applications. This study aims to improve the thermostability of dextranase AoDex in glycoside hydrolase (GH) family 49 that derived from Arthrobacter oxydans KQ11. Some mutants were predicted and constructed based on B-factor analysis, PoPMuSiC and HotMuSiC algorithms, and four mutants exhibited higher heat resistance. Compared with the wild-type, mutant S357P showed the best improved thermostability with a 5.4-fold increase of half-life at 60 °C, and a 2.1-fold increase of half-life at 65 °C. Furthermore, S357V displayed the most obvious increase in enzymatic activity and thermostability simultaneously. Structural modeling analysis indicated that the improved thermostability of mutants might be attributed to the introduction of proline and hydrophobic effects, which generated the rigid optimization of the structural conformation. These results illustrated that it was effective to improve the thermostability of dextranase AoDex by rational design and site-directed mutagenesis. The thermostable mutant of dextranase AoDex has potential application value, and it can also provide references for engineering other thermostable dextranases of the GH49 family.
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Affiliation(s)
- Zhen Wei
- grid.443480.f0000 0004 1800 0658Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005 China ,grid.443480.f0000 0004 1800 0658Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005 China
| | - Jinling Chen
- grid.443480.f0000 0004 1800 0658School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, 222005 China
| | - Linxiang Xu
- grid.443480.f0000 0004 1800 0658Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005 China ,grid.443480.f0000 0004 1800 0658Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005 China
| | - Nannan Liu
- grid.443480.f0000 0004 1800 0658Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005 China ,grid.443480.f0000 0004 1800 0658Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005 China
| | - Jie Yang
- grid.443480.f0000 0004 1800 0658Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005 China ,grid.443480.f0000 0004 1800 0658School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, 222005 China
| | - Shujun Wang
- grid.443480.f0000 0004 1800 0658Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005 China ,grid.443480.f0000 0004 1800 0658School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, 222005 China
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Xu L, Zhang Y, Liu N, Wei Z, Wang Z, Wang Y, Wang S. Purification and characterization of cold-adapted and salt-tolerant dextranase from Cellulosimicrobium sp. THN1 and its potential application for treatment of dental plaque. Front Microbiol 2022; 13:1012957. [PMID: 36439846 PMCID: PMC9691899 DOI: 10.3389/fmicb.2022.1012957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 10/17/2022] [Indexed: 10/28/2023] Open
Abstract
The cold-adapted and/or salt-tolerant enzymes from marine microorganisms were confirmed to be meritorious tools to enhance the efficiency of biocatalysis in industrial biotechnology. We purified and characterized a dextranase CeDex from the marine bacterium Cellulosimicrobium sp. THN1. CeDex acted in alkaline pHs (7.5-8.5) and a broad temperature range (10-50°C) with sufficient pH stability and thermostability. Remarkably, CeDex retained approximately 40% of its maximal activities at 4°C and increased its activity to 150% in 4 M NaCl, displaying prominently cold adaptation and salt tolerance. Moreover, CeDex was greatly stimulated by Mg2+, Na+, Ba2+, Ca2+ and Sr2+, and sugarcane juice always contains K+, Ca2+, Mg2+ and Na+, so CeDex will be suitable for removing dextran in the sugar industry. The main hydrolysate of CeDex was isomaltotriose, accompanied by isomaltotetraose, long-chain IOMs, and a small amount of isomaltose. The amino acid sequence of CeDex was identified from the THN1 genomic sequence by Nano LC-MS/MS and classified into the GH49 family. Notably, CeDex could prevent the formation of Streptococcus mutans biofilm and disassemble existing biofilms at 10 U/ml concentration and would have great potential to defeat biofilm-related dental caries.
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Affiliation(s)
- Linxiang Xu
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
| | - Yan Zhang
- School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, China
| | - Nannan Liu
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
| | - Zhen Wei
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
| | - Zhen Wang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Shujun Wang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
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Kurosawa S, Hasebe F, Okamura H, Yoshida A, Matsuda K, Sone Y, Tomita T, Shinada T, Takikawa H, Kuzuyama T, Kosono S, Nishiyama M. Molecular Basis for Enzymatic Aziridine Formation via Sulfate Elimination. J Am Chem Soc 2022; 144:16164-16170. [PMID: 35998388 DOI: 10.1021/jacs.2c07243] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural products containing an aziridine ring, such as mitomycin C and azinomycin B, exhibit antitumor activities by alkylating DNA via their aziridine rings; however, the biosynthetic mechanisms underlying the formation of these rings have not yet been elucidated. We herein investigated the biosynthesis of vazabitide A, the structure of which is similar to that of azinomycin B, and demonstrated that Vzb10/11, with no similarities to known enzymes, catalyzed the formation of the aziridine ring via sulfate elimination. To elucidate the detailed reaction mechanism, crystallization of Vzb10/11 and the homologous enzyme, AziU3/U2, in the biosynthesis of azinomycin B was attempted, and the structure of AziU3/U2, which had a new protein fold overall, was successfully determined. The structural analysis revealed that these enzymes adjusted the dihedral angle between the amino group and the adjacent sulfate group of the substrate to almost 180° and enhanced the nucleophilicity of the C6-amino group temporarily, facilitating the SN2-like reaction to form the aziridine ring. The present study reports for the first time the molecular basis for aziridine ring formation.
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Affiliation(s)
- Sumire Kurosawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Fumihito Hasebe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hironori Okamura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ayako Yoshida
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kenichi Matsuda
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yusuke Sone
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takeo Tomita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tetsuro Shinada
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Hirosato Takikawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Saori Kosono
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Nishiyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Schistosoma mansoni α-N-acetylgalactosaminidase (SmNAGAL) regulates coordinated parasite movement and egg production. PLoS Pathog 2022; 18:e1009828. [PMID: 35025955 PMCID: PMC8791529 DOI: 10.1371/journal.ppat.1009828] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 01/26/2022] [Accepted: 12/13/2021] [Indexed: 12/24/2022] Open
Abstract
α-galactosidase (α-GAL) and α-N-acetylgalactosaminidase (α-NAGAL) are two glycosyl hydrolases responsible for maintaining cellular homeostasis by regulating glycan substrates on proteins and lipids. Mutations in the human genes encoding either enzyme lead to neurological and neuromuscular impairments seen in both Fabry- and Schindler/Kanzaki- diseases. Here, we investigate whether the parasitic blood fluke Schistosoma mansoni, responsible for the neglected tropical disease schistosomiasis, also contains functionally important α-GAL and α-NAGAL proteins. As infection, parasite maturation and host interactions are all governed by carefully-regulated glycosylation processes, inhibiting S. mansoni's α-GAL and α-NAGAL activities could lead to the development of novel chemotherapeutics. Sequence and phylogenetic analyses of putative α-GAL/α-NAGAL protein types showed Smp_089290 to be the only S. mansoni protein to contain the functional amino acid residues necessary for α-GAL/α-NAGAL substrate cleavage. Both α-GAL and α-NAGAL enzymatic activities were higher in females compared to males (p<0.05; α-NAGAL > α-GAL), which was consistent with smp_089290's female biased expression. Spatial localisation of smp_089290 revealed accumulation in parenchymal cells, neuronal cells, and the vitellaria and mature vitellocytes of the adult schistosome. siRNA-mediated knockdown (>90%) of smp_089290 in adult worms significantly inhibited α-NAGAL activity when compared to control worms (siLuc treated males, p<0.01; siLuc treated females, p<0.05). No significant reductions in α-GAL activities were observed in the same extracts. Despite this, decreases in α-NAGAL activities correlated with a significant inhibition in adult worm motility as well as in egg production. Programmed CRISPR/Cas9 editing of smp_089290 in adult worms confirmed the egg reduction phenotype. Based on these results, Smp_089290 was determined to act predominantly as an α-NAGAL (hereafter termed SmNAGAL) in schistosome parasites where it participates in coordinating movement and oviposition processes. Further characterisation of SmNAGAL and other functionally important glycosyl hydrolases may lead to the development of a novel anthelmintic class of compounds.
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Xue N, Svensson B, Bai Y. Structure, function and enzymatic synthesis of glucosaccharides assembled mainly by α1 → 6 linkages - A review. Carbohydr Polym 2022; 275:118705. [PMID: 34742430 DOI: 10.1016/j.carbpol.2021.118705] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 11/02/2022]
Abstract
A variety of glucosaccharides composed of glucosyl residues can be classified into α- and β-type and have wide application in food and medicine areas. Among these glucosaccharides, β-type, such as cellulose and α-type, such as starch and starch derivatives, both contain 1 → 4 linkages and are well studied. Notably, in past decades also α1 → 6 glucosaccharides obtained increasing attention for unique physiochemical and biological properties. Especially in recent years, α1 → 6 glucosaccharides of different molecular weight distribution have been created and proved to be functional. However, compared to β- type and α1 → 4 glucosaccharides, only few articles provide a systematic overview of α1 → 6 glucosaccharides. This motivated, the present first comprehensive review on structure, function and synthesis of these α1 → 6 glucosaccharides, aiming both at improving understanding of traditional α1 → 6 glucosaccharides, such as isomaltose, isomaltooligosaccharides and dextrans, and to draw the attention to newly explored α1 → 6 glucosaccharides and their derivatives, such as cycloisomaltooligosaccharides, isomaltomegalosaccharides, and isomalto/malto-polysaccharides.
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Affiliation(s)
- Naixiang Xue
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Birte Svensson
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China; Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Denmark
| | - Yuxiang Bai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China.
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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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Zhang X, Chen F, He C, Fang W, Fang Z, Zhang X, Wang X, Xiao Y. Improving the thermostability of a GH97 dextran glucosidase by rational design. Biotechnol Lett 2020; 42:2211-2221. [DOI: 10.1007/s10529-020-02928-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/29/2020] [Indexed: 11/24/2022]
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13
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Tsutsumi K, Gozu Y, Nishikawa A, Tonozuka T. Structural insights into polysaccharide recognition by
Flavobacterium johnsoniae
dextranase, a member of glycoside hydrolase family 31. FEBS J 2019; 287:1195-1207. [DOI: 10.1111/febs.15074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/25/2019] [Accepted: 09/20/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Kenta Tsutsumi
- Department of Applied Biological Science Tokyo University of Agriculture and Technology Japan
| | - Yoshifumi Gozu
- Department of Applied Biological Science Tokyo University of Agriculture and Technology Japan
| | - Atsushi Nishikawa
- Department of Applied Biological Science Tokyo University of Agriculture and Technology Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science Tokyo University of Agriculture and Technology Japan
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14
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Liu H, Ren W, Ly M, Li H, Wang S. Characterization of an Alkaline GH49 Dextranase from Marine Bacterium Arthrobacter oxydans KQ11 and Its Application in the Preparation of Isomalto-Oligosaccharide. Mar Drugs 2019; 17:md17080479. [PMID: 31430863 PMCID: PMC6723167 DOI: 10.3390/md17080479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 11/16/2022] Open
Abstract
A GH49 dextranase gene DexKQ was cloned from marine bacteria Arthrobacter oxydans KQ11. It was recombinantly expressed using an Escherichia coli system. Recombinant DexKQ dextranase of 66 kDa exhibited the highest catalytic activity at pH 9.0 and 55 °C. kcat/Km of recombinant DexKQ at the optimum condition reached 3.03 s−1 μM−1, which was six times that of commercial dextranase (0.5 s−1 μM−1). DexKQ possessed a Km value of 67.99 µM against dextran T70 substrate with 70 kDa molecular weight. Thin-layer chromatography (TLC) analysis showed that main hydrolysis end products were isomalto-oligosaccharide (IMO) including isomaltotetraose, isomaltopantose, and isomaltohexaose. When compared with glucose, IMO could significantly improve growth of Bifidobacterium longum and Lactobacillus rhamnosus and inhibit growth of Escherichia coli and Staphylococcus aureus. This is the first report of dextranase from marine bacteria concerning recombinant expression and application in isomalto-oligosaccharide preparation.
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Affiliation(s)
- Hongfei Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Wei Ren
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- Collaborative Innovation Center of Modern Bio-Manufacture, Anhui University, Hefei 230039, China
| | - Mingsheng Ly
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Haifeng Li
- Medical College, Hangzhou Normal University, Hangzhou 311121, China.
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
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15
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NMR solution geometry of saccharides containing the 6-O-(α-D-glucopyranosyl)-α/β-D-glucopyranose (isomaltose) or 6-O-(α-D-galactopyranosyl)-α/β-D-glucopyranose (melibiose) core. Carbohydr Res 2019; 473:18-35. [DOI: 10.1016/j.carres.2018.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 12/26/2022]
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16
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Nagaya M, Kimura M, Gozu Y, Sato S, Hirano K, Tochio T, Nishikawa A, Tonozuka T. Crystal structure of a β-fructofuranosidase with high transfructosylation activity from Aspergillus kawachii. Biosci Biotechnol Biochem 2017; 81:1786-1795. [DOI: 10.1080/09168451.2017.1353405] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Abstract
β-Fructofuranosidases belonging to glycoside hydrolase family (GH) 32 are enzymes that hydrolyze sucrose. Some GH32 enzymes also catalyze transfructosylation to produce fructooligosaccharides. We found that Aspergillus kawachii IFO 4308 β-fructofuranosidase (AkFFase) produces fructooligosaccharides, mainly 1-kestose, from sucrose. We determined the crystal structure of AkFFase. AkFFase is composed of an N-terminal small component, a β-propeller catalytic domain, an α-helical linker, and a C-terminal β-sandwich, similar to other GH32 enzymes. AkFFase forms a dimer, and the dimerization pattern is different from those of other oligomeric GH32 enzymes. The complex structure of AkFFase with fructose unexpectedly showed that fructose binds both subsites −1 and +1, despite the fact that the catalytic residues were not mutated. Fructose at subsite +1 interacts with Ile146 and Glu296 of AkFFase via direct hydrogen bonds.
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Affiliation(s)
- Mika Nagaya
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Miyoko Kimura
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Yoshifumi Gozu
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Shona Sato
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Katsuaki Hirano
- Research & Development Center, B Food Science Co., Ltd., Chita, Japan
| | - Takumi Tochio
- Research & Development Center, B Food Science Co., Ltd., Chita, Japan
| | - Atsushi Nishikawa
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
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17
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Purification, expression and characterization of a novel α-l-fucosidase from a marine bacteria Wenyingzhuangia fucanilytica. Protein Expr Purif 2016; 129:9-17. [PMID: 27576198 DOI: 10.1016/j.pep.2016.08.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/23/2016] [Accepted: 08/25/2016] [Indexed: 11/22/2022]
Abstract
α-l-Fucosyl residues are frequently found in oligosaccharides, polysaccharides and glycoconjugates which play fundamental roles in various biological processes. α-l-Fucosidases, glycoside hydrolases for catalyzing the removal of α-l-fucose, can serve as desirable tools in the study and the modification of fucose-containing biomolecules. In this study, an α-l-fucosidase named as Alf1_Wf was purified from a marine bacterium Wenyingzhuangia fucanilytica by using a combination of chromatographic procedures. The sequence of Alf1_Wf was identified via proteomics analysis against the predicted proteome of the bacterium. Recombinant Alf1_Wf with 6×His tag was expressed in E. coli and showed α-l-fucosidase activity. Sequence annotation revealed that Alf1_Wf contained a combination of GH29 catalytic domain and CBM35 accessory domain. Alf1_Wf was confirmed as a member of GH29-A subfamily based on the phylogenetic analysis. Furthermore, biochemical properties and kinetic characteristics of the enzyme were also determined. Substrate specificity determination showed that Alf1_Wf was capable in hydrolyzing α1,4-fucosidic linkage and synthetic substrate pNP-fucose. Besides, Alf1_Wf could act on partially degraded fucoidan. This study successfully purified, identified, cloned, expressed and characterized a novel α-l-fucosidase, and meanwhile revealed a new multidomain structure of glycoside hydrolase. The knowledge gained from this study should facilitate the further research and application of α-l-fucosidases.
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18
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Gozu Y, Ishizaki Y, Hosoyama Y, Miyazaki T, Nishikawa A, Tonozuka T. A glycoside hydrolase family 31 dextranase with high transglucosylation activity from Flavobacterium johnsoniae. Biosci Biotechnol Biochem 2016; 80:1562-7. [DOI: 10.1080/09168451.2016.1182852] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
Glycoside hydrolase family (GH) 31 enzymes exhibit various substrate specificities, although the majority of members are α-glucosidases. Here, we constructed a heterologous expression system of a GH31 enzyme, Fjoh_4430, from Flavobacterium johnsoniae NBRC 14942, using Escherichia coli, and characterized its enzymatic properties. The enzyme hydrolyzed dextran and pullulan to produce isomaltooligosaccharides and isopanose, respectively. When isomaltose was used as a substrate, the enzyme catalyzed disproportionation to form isomaltooligosaccharides. The enzyme also acted, albeit inefficiently, on p-nitrophenyl α-D-glucopyranoside, and p-nitrophenyl α-isomaltoside was the main product of the reaction. In contrast, Fjoh_4430 did not act on trehalose, kojibiose, nigerose, maltose, maltotriose, or soluble starch. The optimal pH and temperature were pH 6.0 and 60 °C, respectively. Our results indicate that Fjoh_4430 is a novel GH31 dextranase with high transglucosylation activity.
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Affiliation(s)
- Yoshifumi Gozu
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Yuichi Ishizaki
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Yuhei Hosoyama
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Takatsugu Miyazaki
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Atsushi Nishikawa
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
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