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Ma Y, Zhang L, Ma X, Bai K, Tian Z, Wang Z, Muratkhan M, Wang X, Lü X, Liu M. Saccharide mapping as an extraordinary method on characterization and identification of plant and fungi polysaccharides: A review. Int J Biol Macromol 2024; 275:133350. [PMID: 38960255 DOI: 10.1016/j.ijbiomac.2024.133350] [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: 12/19/2023] [Revised: 05/26/2024] [Accepted: 06/20/2024] [Indexed: 07/05/2024]
Abstract
Saccharide mapping was a promising scheme to unveil the mystery of polysaccharide structure by analysis of the fragments generated from polysaccharide decomposition process. However, saccharide mapping was not widely applied in the polysaccharide analysis for lacking of systematic introduction. In this review, a detailed description of the establishment process of saccharide mapping, the pros and cons of downstream technologies, an overview of the application of saccharide mapping, and practical strategies were summarized. With the updating of the available downstream technologies, saccharide mapping had been expanding its scope of application to various kinds of polysaccharides. The process of saccharide mapping analysis included polysaccharides degradation and hydrolysates analysis, and the degradation process was no longer limited to acid hydrolysis. Some downstream technologies were convenient for rapid qualitative analysis, while others could achieve quantitative analysis. For the more detailed structure information could be provided by saccharide mapping, it was possible to improve the quality control of polysaccharides during preparation and application. This review filled the blank of basic information about saccharide mapping and was helpful for the establishment of a professional workflow for the saccharide mapping application to promote the deep study of polysaccharide structure.
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Affiliation(s)
- Yuntian Ma
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China; College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lichen Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaoyu Ma
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ke Bai
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhuoer Tian
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhangyang Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Marat Muratkhan
- Department of Food Technology and Processing Products, Technical Faculty, Saken Seifullin Kazakh Agrotechnical University, Nur-Sultan, Kazakhstan
| | - Xin Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Centre of Dairy Products Quality, Safety and Health, Shaanxi, China; Northwest A&F University Shen Zhen Research Institute, Shenzhen, China.
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Centre of Dairy Products Quality, Safety and Health, Shaanxi, China; Northwest A&F University Shen Zhen Research Institute, Shenzhen, China.
| | - Manshun Liu
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China; College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China.
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2
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Ohashi T, Mabira Y, Mitsuyoshi Y, Kajiura H, Misaki R, Ishimizu T, Fujiyama K. Expression of an endo-rhamnogalacturonase from Aspergillus aculeatus enhances release of Arabidopsis transparent mucilage. J Biosci Bioeng 2024; 138:73-82. [PMID: 38643032 DOI: 10.1016/j.jbiosc.2024.03.006] [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: 06/02/2023] [Revised: 03/24/2024] [Accepted: 03/24/2024] [Indexed: 04/22/2024]
Abstract
Mucilage is a gelatinous and sticky hydrophilic polysaccharide released from epidermal cells of seed coat after the hydration of mature seeds and is composed primarily of unbranched rhamnogalacturonan I (RG-I). In this study, we produced a recombinant endo-RG-I hydrolase from Aspergillus aculeatus (AaRhgA) in the fission yeast Schizosaccharomyces pombe and examined its substrate preference for pyridylaminated (PA) RG-I with the various degrees of polymerization (DP). Recombinant AaRhgA requires PA-RG-I with a DP of 10 or higher for its hydrolase activity. We heterologously expressed the AarhgA gene under the strong constitutive promoter, cauliflower mosaic virus 35S promoter, in Arabidopsis thaliana. In a series of biochemical analyses of each mucilage fraction released from the water-imbibed seeds of the transgenic plants, we found the enhanced deposition of the transparent mucilage layer that existed in the peripheral regions of the adherent mucilage and was not stained with ruthenium red. This study demonstrated the feasibility of manipulating the mucilage organization by heterologous expression of the endo-RG-I hydrolase.
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Affiliation(s)
- Takao Ohashi
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan; Department of Life Science, Faculty of Science and Engineering, Setsunan University, Neyagawa, Osaka 572-8508, Japan.
| | - Yurika Mabira
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yutaro Mitsuyoshi
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroyuki Kajiura
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ryo Misaki
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takeshi Ishimizu
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Kazuhito Fujiyama
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
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3
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Makabe K, Ishida N, Kanezaki N, Shiono Y, Koseki T. Aspergillus oryzae α-l-rhamnosidase: Crystal structure and insight into the substrate specificity. Proteins 2024; 92:236-245. [PMID: 37818702 DOI: 10.1002/prot.26608] [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: 07/10/2023] [Revised: 09/16/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
The subsequent biochemical and structural investigations of the purified recombinant α-l-rhamnosidase from Aspergillus oryzae expressed in Pichia pastoris, designated as rAoRhaA, were performed. The specific activity of the rAoRhaA wild-type was higher toward hesperidin and narirutin, where the l-rhamnose residue was α-1,6-linked to β-d-glucoside, than toward neohesperidin and naringin with an α-1,2-linkage to β-d-glucoside. However, no activity was detected toward quercitrin, myricitrin, and epimedin C. rAoRhaA kinetic analysis indicated that Km values for neohesperidin, naringin, and rutin were lower compared to those for hesperidin and narirutin. kcat values for hesperidin and narirutin were higher than those for neohesperidin, naringin, and rutin. High catalytic efficiency (kcat /Km ) toward hesperidin and narirutin was a result of a considerably high kcat value, while Km values for hesperidin and narirutin were higher than those for naringin, neohesperidin, and rutin. The crystal structure of rAoRhaA revealed that the catalytic domain was represented by an (α/α)6 -barrel with the active site located in a deep cleft and two β-sheet domains were also present in the N- and C-terminal sites of the catalytic domain. Additionally, five asparagine-attached N-acetylglucosamine molecules were observed. The catalytic residues of AoRhaA were suggested to be Asp254 and Glu524, and their catalytic roles were confirmed by mutational studies of D254N and E524Q variants, which lost their activity completely. Notably, three aspartic acids (Asp117, Asp249, and Asp261) located at the catalytic pocket were replaced with asparagine. D117N variant showed reduced activity. D249N and D261N variants activities drastically decreased.
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Affiliation(s)
- Koki Makabe
- Graduate School of Science and Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Japan
| | - Naoki Ishida
- Department of Food, Life and Environmental Sciences, Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| | - Nanako Kanezaki
- Department of Food, Life and Environmental Sciences, Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| | - Yoshihito Shiono
- Department of Food, Life and Environmental Sciences, Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| | - Takuya Koseki
- Department of Food, Life and Environmental Sciences, Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
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4
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Chen SK, Wang X, Guo YQ, Song XX, Yin JY, Nie SP. Exploring the partial degradation of polysaccharides: Structure, mechanism, bioactivities, and perspectives. Compr Rev Food Sci Food Saf 2023; 22:4831-4870. [PMID: 37755239 DOI: 10.1111/1541-4337.13244] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/22/2023] [Accepted: 09/04/2023] [Indexed: 09/28/2023]
Abstract
Polysaccharides are promising biomolecules with lowtoxicity and diverse bioactivities in food processing and clinical drug development. However, an essential prerequisite for their applications is the fine structure characterization. Due to the complexity of polysaccharide structure, partial degradation is a powerful tool for fine structure analysis, which can effectively provide valid information on the structure of backbone and branching glycosidic fragments of complex polysaccharides. This review aims to conclude current methods of partial degradation employed for polysaccharide structural characterization, discuss the molecular mechanisms, and describe the molecular structure and solution properties of degraded polysaccharides. In addition, the effects of polysaccharide degradation on the conformational relationships between the molecular structure and bioactivities, such as antioxidant, antitumor, and immunomodulatory activities, are also discussed. Finally, we summarize the prospects and current challenges for the partial degradation of polysaccharides. This review will be of great value for the scientific elucidation of polysaccharide fine structures and potential applications.
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Affiliation(s)
- Shi-Kang Chen
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province, China
| | - Xin Wang
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province, China
| | - Yu-Qing Guo
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province, China
| | - Xiao-Xiao Song
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province, China
| | - Jun-Yi Yin
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province, China
| | - Shao-Ping Nie
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province, China
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5
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Wang J, Liu Z, Li X, Liu G, Zhao J. Elucidating structure of pectin in ramie fiber to customize enzyme cocktail for high-efficiency enzymatic degumming. Carbohydr Polym 2023; 314:120954. [PMID: 37173048 DOI: 10.1016/j.carbpol.2023.120954] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/13/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023]
Abstract
Pectin is one of the main components of bast fiber including ramie fiber, and must be removed before use. Enzymatic degumming is the preferred process as it is an environment-friendly, simple and controllable process for ramie degumming. However, an important problem limiting wide application of this process is the high cost due to the low efficiency of enzymatic degumming. In this study, pectin samples were extracted from raw ramie fiber and degummed ramie fiber, respectively, and their structures were characterized and compared to allow tailoring of an enzyme cocktail for degrading the pectin. It was elucidated that pectin from ramie fiber is composed of low esterified homogalacturonan (HG) and low branched rhamnogalacturonan I (RG-I), and the ratio of HG/RG-I is 1.72:1. Based on the pectin structure, potential enzymes to be used for enzymatic degumming of ramie fiber were proposed and an enzyme cocktail was customized. Degumming experiments confirmed that the customized enzyme cocktail can effectively remove pectin from ramie fiber. To our knowledge, this is the first time the structural characteristics of pectin in ramie fiber have been clarified, and it also provides an example of tailoring a specific enzyme system to achieve high-efficiency degumming for biomass containing pectin.
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Affiliation(s)
- Jincheng Wang
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao 266237, Shandong, China
| | - Zhaoxi Liu
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao 266237, Shandong, China
| | - Xuezhi Li
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao 266237, Shandong, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao 266237, Shandong, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao 266237, Shandong, China.
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6
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Jiao X, Li F, Zhao J, Wei Y, Zhang L, Yu W, Li Q. The Preparation and Potential Bioactivities of Modified Pectins: A Review. Foods 2023; 12:1016. [PMID: 36900531 PMCID: PMC10001417 DOI: 10.3390/foods12051016] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Pectins are complex polysaccharides that are widely found in plant cells and have a variety of bioactivities. However, the high molecular weights (Mw) and complex structures of natural pectins mean that they are difficult for organisms to absorb and utilize, limiting their beneficial effects. The modification of pectins is considered to be an effective method for improving the structural characteristics and promoting the bioactivities of pectins, and even adding new bioactivities to natural pectins. This article reviews the modification methods, including chemical, physical, and enzymatic methods, for natural pectins from the perspective of their basic information, influencing factors, and product identification. Furthermore, the changes caused by modifications to the bioactivities of pectins are elucidated, including their anti-coagulant, anti-oxidant, anti-tumor, immunomodulatory, anti-inflammatory, hypoglycemic, and anti-bacterial activities and the ability to regulate the intestinal environment. Finally, suggestions and perspectives regarding the development of pectin modification are provided.
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Affiliation(s)
- Xu Jiao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- National Engineering Research Center for Fruits and Vegetables Processing, Beijing 100083, China
| | - Fei Li
- College of Life Science, Qingdao University, Qingdao 266071, China
| | - Jing Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- National Engineering Research Center for Fruits and Vegetables Processing, Beijing 100083, China
| | - Yunlu Wei
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Luyao Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- National Engineering Research Center for Fruits and Vegetables Processing, Beijing 100083, China
| | - Wenjun Yu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- National Engineering Research Center for Fruits and Vegetables Processing, Beijing 100083, China
| | - Quanhong Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- National Engineering Research Center for Fruits and Vegetables Processing, Beijing 100083, China
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7
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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8
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Peng M, de Vries RP. Machine learning prediction of novel pectinolytic enzymes in Aspergillus niger through integrating heterogeneous (post-) genomics data. Microb Genom 2021; 7. [PMID: 34874247 PMCID: PMC8767319 DOI: 10.1099/mgen.0.000674] [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] [Indexed: 11/18/2022] Open
Abstract
Pectinolytic enzymes are a variety of enzymes involved in breaking down pectin, a complex and abundant plant cell-wall polysaccharide. In nature, pectinolytic enzymes play an essential role in allowing bacteria and fungi to depolymerize and utilize pectin. In addition, pectinases have been widely applied in various industries, such as the food, wine, textile, paper and pulp industries. Due to their important biological function and increasing industrial potential, discovery of novel pectinolytic enzymes has received global interest. However, traditional enzyme characterization relies heavily on biochemical experiments, which are time consuming, laborious and expensive. To accelerate identification of novel pectinolytic enzymes, an automatic approach is needed. We developed a machine learning (ML) approach for predicting pectinases in the industrial workhorse fungus, Aspergillus niger. The prediction integrated a diverse range of features, including evolutionary profile, gene expression, transcriptional regulation and biochemical characteristics. Results on both the training and the independent testing dataset showed that our method achieved over 90 % accuracy, and recalled over 60 % of pectinolytic genes. Application of the ML model on the A. niger genome led to the identification of 83 pectinases, covering both previously described pectinases and novel pectinases that do not belong to any known pectinolytic enzyme family. Our study demonstrated the tremendous potential of ML in discovery of new industrial enzymes through integrating heterogeneous (post-) genomimcs data.
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Affiliation(s)
- Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
- *Correspondence: Mao Peng,
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
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9
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Ahmed J, Thakur A, Goyal A. Emerging trends on the role of recombinant pectinolytic enzymes in industries- an overview. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Tang XD, Dong FY, Zhang QH, Lin L, Wang P, Xu XY, Wei W, Wei DZ. Protein engineering of a cold-adapted rhamnogalacturonan acetylesterase: In vivo functional expression and cinnamyl acetate synthesis. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Kondo T, Kichijo M, Maruta A, Nakaya M, Takenaka S, Arakawa T, Fushinobu S, Sakamoto T. Structural and functional analysis of gum arabic l-rhamnose-α-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family. J Biol Chem 2021; 297:101001. [PMID: 34303708 PMCID: PMC8377490 DOI: 10.1016/j.jbc.2021.101001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/24/2022] Open
Abstract
Gum arabic (GA) is widely used as an emulsion stabilizer and coating in several industrial applications, such as foods and pharmaceuticals. GA contains a complex carbohydrate moiety, and the nonreducing ends of the side chains are often capped with l-rhamnose; thus, enzymes that can remove these caps are promising tools for the structural analysis of the carbohydrates comprising GA. In this study, GA-specific l-rhamnose-α-1,4-d-glucuronate lyase from the fungus Fusarium oxysporum 12S (FoRham1) was cloned and characterized. FoRham1 showed the highest amino acid sequence similarity with enzymes belonging to the glycoside hydrolase family 145; however, the catalytic residue on the posterior pocket of the β-propeller fold protein was not conserved. The catalytic residues of FoRham1 were instead conserved with ulvan lyases belonging to polysaccharide lyase family 24. Kinetic analysis showed that FoRham1 has the highest catalytic efficiency for the substrate α-l-rhamnose-(1→4)-d-glucuronic acid. The crystal structures of ligand-free and α-l-rhamnose-(1→4)-d-glucuronic acid –bound FoRham1 were determined, and the active site was identified on the anterior side of the β-propeller. The three-dimensional structure of the active site and mutagenesis analysis revealed the detailed catalytic mechanism of FoRham1. Our findings offer a new enzymatic tool for the further analysis of the GA carbohydrate structure and for elucidating its physiological functions in plants. Based on these results, we renamed glycoside hydrolase family 145 as a new polysaccharide lyase family 42, in which FoRham1 is included.
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Affiliation(s)
- Tatsuya Kondo
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Miyu Kichijo
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Akiho Maruta
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Makoto Nakaya
- Center for Research and Development of Bioresources, Organization for Research Promotion, Osaka Prefecture University, Osaka, Japan
- Department of Nutrition, Otemae College of Nutrition and Confectionery, Osaka, Japan
| | - Shigeo Takenaka
- Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University, Osaka, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Tatsuji Sakamoto
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
- For correspondence: Tatsuji Sakamoto
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12
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Kondo T, Nishimura Y, Matsuyama K, Ishimaru M, Nakazawa M, Ueda M, Sakamoto T. Characterization of three GH35 β-galactosidases, enzymes able to shave galactosyl residues linked to rhamnogalacturonan in pectin, from Penicillium chrysogenum 31B. Appl Microbiol Biotechnol 2019; 104:1135-1148. [DOI: 10.1007/s00253-019-10299-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/24/2019] [Accepted: 12/03/2019] [Indexed: 11/29/2022]
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13
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Pachl P, Škerlová J, Šimčíková D, Kotik M, Křenková A, Mader P, Brynda J, Kapešová J, Křen V, Otwinowski Z, Řezáčová P. Crystal structure of native α-L-rhamnosidase from Aspergillus terreus. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1078-1084. [DOI: 10.1107/s2059798318013049] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/14/2018] [Indexed: 11/10/2022]
Abstract
α-L-Rhamnosidases cleave terminal nonreducing α-L-rhamnosyl residues from many natural rhamnoglycosides. This makes them catalysts of interest for various biotechnological applications. The X-ray structure of the GH78 family α-L-rhamnosidase from Aspergillus terreus has been determined at 1.38 Å resolution using the sulfur single-wavelength anomalous dispersion phasing method. The protein was isolated from its natural source in the native glycosylated form, and the active site contained a glucose molecule, probably from the growth medium. In addition to its catalytic domain, the α-L-rhamnosidase from A. terreus contains four accessory domains of unknown function. The structural data suggest that two of these accessory domains, E and F, might play a role in stabilizing the aglycon portion of the bound substrate.
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14
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Mensitieri F, De Lise F, Strazzulli A, Moracci M, Notomista E, Cafaro V, Bedini E, Sazinsky MH, Trifuoggi M, Di Donato A, Izzo V. Structural and functional insights into RHA-P, a bacterial GH106 α-L-rhamnosidase from Novosphingobium sp. PP1Y. Arch Biochem Biophys 2018; 648:1-11. [PMID: 29678627 DOI: 10.1016/j.abb.2018.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 11/29/2022]
Abstract
α-L-Rhamnosidases (α-RHAs, EC 3.2.1.40) are glycosyl hydrolases (GHs) hydrolyzing terminal α-l-rhamnose residues from different substrates such as heteropolysaccharides, glycosylated proteins and natural flavonoids. Although the possibility to hydrolyze rhamnose from natural flavonoids has boosted the use of these enzymes in several biotechnological applications over the past decades, to date only few bacterial rhamnosidases have been fully characterized and only one crystal structure of a rhamnosidase of the GH106 family has been described. In our previous work, an α-l-rhamnosidase belonging to this family, named RHA-P, was isolated from the marine microorganism Novosphingobium sp. PP1Y. The initial biochemical characterization highlighted the biotechnological potential of RHA-P for bioconversion applications. In this work, further functional and structural characterization of the enzyme is provided. The recombinant protein was obtained fused to a C-terminal His-tag and, starting from the periplasmic fractions of induced recombinant cells of E. coli strain BL21(DE3), was purified through a single step purification protocol. Homology modeling of RHA-P in combination with a site directed mutagenesis analysis confirmed the function of residues D503, E506, E644, likely located at the catalytic site of RHA-P. In addition, a kinetic characterization of the enzyme on natural flavonoids such as naringin, rutin, hesperidin and quercitrin was performed. RHA-P showed activity on all flavonoids tested, with a catalytic efficiency comparable or even higher than other bacterial α-RHAs described in literature. The results confirm that RHA-P is able to hydrolyze both α-1,2 and α-1,6 glycosidic linkages, and suggest that the enzyme may locate different polyphenolic aromatic moities in the active site.
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Affiliation(s)
- Francesca Mensitieri
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Federica De Lise
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Andrea Strazzulli
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Marco Moracci
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy; Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131, Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Valeria Cafaro
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Emiliano Bedini
- Department of Chemical Sciences, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Matthew Howard Sazinsky
- Department of Chemistry, Pomona College, Sumner Hall, 333 N College Way, Claremont, CA, 91711, United States
| | - Marco Trifuoggi
- Department of Chemical Sciences, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Alberto Di Donato
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Viviana Izzo
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Via S. Allende 2, 84131, Salerno, Italy.
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15
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Kunishige Y, Iwai M, Nakazawa M, Ueda M, Tada T, Nishimura S, Sakamoto T. Crystal structure of exo‐rhamnogalacturonan lyase fromPenicillium chrysogenumas a member of polysaccharide lyase family 26. FEBS Lett 2018; 592:1378-1388. [DOI: 10.1002/1873-3468.13034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/02/2018] [Accepted: 03/07/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Yuika Kunishige
- Division of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
| | - Marin Iwai
- Division of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
| | - Masami Nakazawa
- Division of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
| | - Mitsuhiro Ueda
- Division of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
| | - Toshiji Tada
- Department of Biological Science Graduate School of Science Osaka Prefecture University Sakai Japan
| | - Shigenori Nishimura
- Division of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
| | - Tatsuji Sakamoto
- Division of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
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