1
|
Improved assay system for acidic peptide: N-glycanase (aPNGase) activity in plant extracts. Anal Biochem 2021; 634:114367. [PMID: 34509445 DOI: 10.1016/j.ab.2021.114367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 08/27/2021] [Accepted: 09/02/2021] [Indexed: 11/24/2022]
Abstract
Plant acidic peptide: N-glycanase (aPNGase) release N-glycans from glycopeptides during the degradation process of glycoproteins in developing or growing plants. We have previously developed a new method to detect the aPNGase activity in crude extracts, which is prerequisite for the construction of aPNGase knockout or overexpression lines. However, this method has the disadvantage of requiring de-sialylation treatment and a lectin chromatography. In this study, therefore, we improved the simple and accurate method for detecting aPNGase activity using anion-exchange HPLC requiring neither the desialylation treatment nor the lectin affinity chromatography.
Collapse
|
2
|
Shirai S, Uemura R, Maeda M, Kajiura H, Misaki R, Fujiyama K, Kimura Y. Direct evidence of cytosolic PNGase activity in Arabidopsis thaliana: in vitro assay system for plant cPNGase activity. Biosci Biotechnol Biochem 2021; 85:1460-1463. [PMID: 33724383 DOI: 10.1093/bbb/zbab047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/02/2021] [Indexed: 11/12/2022]
Abstract
Cytosolic peptide:N-glycanase (cPNGase), which occurs ubiquitously in eukaryotic cells, is involved in the de-N-glycosylation of misfolded glycoproteins in the protein quality control system. In this study, we aimed to provide direct evidence of plant cPNGase activity against a denatured glycoprotein using a crude extract prepared from a mutant line of Arabidopsis thaliana lacking 2 acidic PNGase genes.
Collapse
Affiliation(s)
- Sahoko Shirai
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Ryota Uemura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Megumi Maeda
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Hiroyuki Kajiura
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Ryo Misaki
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Kazuhito Fujiyama
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Yoshinobu Kimura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| |
Collapse
|
3
|
Katsube M, Ebara N, Maeda M, Kimura Y. Cytosolic Free N-Glycans Are Retro-Transported Into the Endoplasmic Reticulum in Plant Cells. FRONTIERS IN PLANT SCIENCE 2021; 11:610124. [PMID: 33537045 PMCID: PMC7847903 DOI: 10.3389/fpls.2020.610124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
During endoplasmic reticulum (ER)-associated degradation, free N-glycans (FNGs) are produced from misfolded nascent glycoproteins via the combination of the cytosolic peptide N-glycanase (cPNGase) and endo-β-N-acetylglucosaminidase (ENGase) in the plant cytosol. The resulting high-mannose type (HMT)-FNGs, which carry one GlcNAc residue at the reducing end (GN1-FNGs), are ubiquitously found in developing plant cells. In a previous study, we found that HMT-FNGs assisted in protein folding and inhibited β-amyloid fibril formation, suggesting a possible biofunction of FNGs involved in the protein folding system. However, whether these HMT-FNGs occur in the ER, an organelle involved in protein folding, remained unclear. On the contrary, we also reported the presence of plant complex type (PCT)-GN1-FNGs, which carry the Lewisa epitope at the non-reducing end, indicating that these FNGs had been fully processed in the Golgi apparatus. Since plant ENGase was active toward HMT-N-glycans but not PCT-N-glycans that carry β1-2xylosyl and/or α1-3 fucosyl residue(s), these PCT-GN1-FNGs did not appear to be produced from fully processed glycoproteins that harbored PCT-N-glycans via ENGase activity. Interestingly, PCT-GN1-FNGs were found in the extracellular space, suggesting that HMT-GN1-FNGs formed in the cytosol might be transported back to the ER and processed in the Golgi apparatus through the protein secretion pathway. As the first step in elucidating the production mechanism of PCT-GN1-FNGs, we analyzed the structures of free oligosaccharides in plant microsomes and proved that HMT-FNGs (Man9-7GlcNAc1 and Man9-8GlcNAc2) could be found in microsomes, which almost consist of the ER compartments.
Collapse
|
4
|
Mátyás B, Singer J, Szarka M, Lowy DA, Döncző B, Makleit P, Failoc-Rojas VE, Ramirez A, Martínez P, Sándor Z, Kincses I, Guttman A. Determination of complex type free, non-conjugated oligosaccharide glucose unit values in tomato xylem sap for early detection of nutrient deficiency. Electrophoresis 2020; 42:200-205. [PMID: 33128395 DOI: 10.1002/elps.202000254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/04/2020] [Accepted: 10/27/2020] [Indexed: 11/07/2022]
Abstract
Although knowledge on glycan biosynthesis and processing is continuously maturing, there are still a limited number of studies that examine biological functions of N-glycan structures in plants, which remain virtually unknown. Here, the statistical correlation between nutrient (nitrogen) deficiency symptoms of crops and changes in 8-aminopyrene-1,3,6-trisulfonic acid (APTS)-labeled complex type free oligosaccharides is reported. While deficiency symptoms are predicted by multispectral images and Kjeldahl digestion, APTS-labeled complex type free oligosaccharides are identified by their glucose unit (GU) values in tomato xylem sap, using capillary electrophoresis with laser induced fluorescence detection (CE-LIF). Given the limited number of structures obtained from plants, archived in the literature, in the future, it is intended to create an open access database of promising indicators, namely, glycan structures that are presumably responsible for the nutrient deficiency caused stress in plants (http://glycoplants.org).
Collapse
Affiliation(s)
- Bence Mátyás
- Genesis Sustainable Future Ltd., 33 Rákóczi St., Sárospatak, B-A-Z, H-3950, Hungary.,Research Group of Applied Plant Glycobiology, Dama Research Center limited, Kowloon, Hong Kong
| | | | - Máté Szarka
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, Hungary.,Institute for Nuclear Research (Atomki), Debrecen, Hungary.,Vitrolink Ltd., Debrecen, Hungary
| | - Daniel A Lowy
- Genesis Sustainable Future Ltd., 33 Rákóczi St., Sárospatak, B-A-Z, H-3950, Hungary.,Research Group of Applied Plant Glycobiology, Dama Research Center limited, Kowloon, Hong Kong.,Northern Virginia Community College, Alxandria, VA, USA
| | | | - Péter Makleit
- Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Hungary
| | - Virgilio E Failoc-Rojas
- Unidad de Investigación para la Generación y Síntesis de Evidencias en Salud, Universidad San Ignacio de Loyola, Lima, Peru
| | - Andrés Ramirez
- Centro de Investigación y Transferencia de Tecnología - CIITT, Universidad Católica de Cuenca, Azogues, Ecuador
| | - Pedro Martínez
- Centro de Investigación y Transferencia de Tecnología - CIITT, Universidad Católica de Cuenca, Azogues, Ecuador
| | - Zsolt Sándor
- Research Group of Applied Plant Glycobiology, Dama Research Center limited, Kowloon, Hong Kong.,Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Hungary
| | - Ida Kincses
- Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Hungary
| | - András Guttman
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, Hungary.,Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprém, Hungary
| |
Collapse
|
5
|
Kimura M, Ogura M, Akamatsu M, Sugimoto K, Maeda M, Nitoda T, Nagasawa-Fujimori H, Yamashita H, Kimura Y. Convenient preparation of an antigenic oligosaccharide from white kidney bean powder: A useful plant oligosaccharide for synthesis of immunoactive glycopolymer. Int J Biol Macromol 2020; 153:1016-1023. [PMID: 31747570 DOI: 10.1016/j.ijbiomac.2019.10.231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/08/2019] [Accepted: 10/24/2019] [Indexed: 10/25/2022]
Abstract
Plant glycoproteins, especially allergenic glycoproteins such as pollen allergens, often carry antigenic N-glycans with α1-3 fucose and/or β1-2 xylose residue(s) on the trimannosyl core structure. We previously reported that one of such antigenic free-form N-glycans, Man3Xyl1Fuc1GlcNAc2 (M3FX) suppressed IL-4 production from Th2 cells of pollinosis patients. For the molecular-level analysis of this immunoactivity, an effective and convenient procedure for large scale preparation of the immunoactive free-form N-glycan and a synthesis of glycopolymers bearing multivalent M3FX has been required. During the preparation of prebiotic oligosaccharides from several edible beans, we found that the free-form M3FX accumulates in relatively large amounts in white kidney beans. In this report, we describe a new procedure for preparation of M3FX from white kidney bean powders by a combination of ion-exchange method, gel-filtration, and hydrophilic partitioning. The high-purity of M3FX prepared by this procedure was confirmed by MS-analysis and 1H-NMR, suggesting that the free-form M3FX can be used for the synthesis of neoglycopolymer. Using this new procedure, the immunoactive oligosaccharide can be prepared without the chemical method such as hydrazinolysis and other purification steps required to exclude other type of N-glycans.
Collapse
Affiliation(s)
- Mariko Kimura
- Faculty of Home Economics, Kobe Women's University, 2-1 Aoyama Higashisuma, Suma-ku, Kobe 654-8585, Japan.
| | - Mikako Ogura
- Faculty of Agriculture, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan
| | - Miyuki Akamatsu
- Faculty of Home Economics, Kobe Women's University, 2-1 Aoyama Higashisuma, Suma-ku, Kobe 654-8585, Japan
| | - Kaede Sugimoto
- Faculty of Agriculture, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan
| | - Megumi Maeda
- Faculty of Agriculture, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan; Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan
| | - Teruhiko Nitoda
- Faculty of Agriculture, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan; Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan
| | - Haruko Nagasawa-Fujimori
- Faculty of Home Economics, Kobe Women's University, 2-1 Aoyama Higashisuma, Suma-ku, Kobe 654-8585, Japan
| | - Hirotaka Yamashita
- Department of Bioactive Molecules, Gifu Pharmaceutical University, Daigakunishi 1-25-4, Gifu 501-1196, Japan
| | - Yoshinobu Kimura
- Faculty of Agriculture, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan; Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan.
| |
Collapse
|
6
|
Rahman MZ, Tsujimori Y, Maeda M, Hossain MA, Ishimizu T, Kimura Y. Molecular characterization of second tomato α1,3/4-fucosidase (α-Fuc'ase Sl-2), a member of glycosyl hydrolase family 29 active toward the core α1,3-fucosyl residue in plant N-glycans. J Biochem 2018; 164:53-63. [PMID: 29444271 DOI: 10.1093/jb/mvy029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 02/04/2018] [Indexed: 01/07/2023] Open
Abstract
In a previous study, we molecular-characterized a tomato (Solanum lycopersicum) α1, 3/4-fucosidase (α-Fuc'ase Sl-1) encoded in a tomato gene (Solyc03g006980), indicating that α-Fuc'ase Sl-1 is involved in the turnover of Lea epitope-containing N-glycans. In this study, we have characterized another tomato gene (Solyc11g069010) encoding α1, 3/4-fucosidase (α-Fuc'ase Sl-2), which is also active toward the complex type N-glycans containing Lea epitope(s). The baculovirus-insect cell expression system was used to express that α-Fuc'ase Sl-2 with anti-FLAG tag, and the expression product (rFuc'ase Sl-2), was found as a 65 kDa protein using SDS-PAGE and has an optimum pH of around 5.0. Similarly to rFuc'ase Sl-1, rFuc'ase Sl-2 hydrolyzed the non-reducing terminal α1, 3-fucose residue on LNFP III and α1, 4-fucose residues of Lea epitopes on plant complex type N-glycans, but not the core α1, 3-fucose residue on Manβ1-4GlcNAcβ1-4(Fucα1-3)GlcNAc or Fucα1-3GlcNAc. However, we found that both α-Fuc'ases Sl-1 and Sl-2 were specifically active toward α1, 3-fucose residue on GlcNAcβ1-4(Fucα1-3)GlcNAc, indicating that the non-substituted β-GlcNAc linked to the proximal GlcNAc residue of the core tri-saccharide moiety of plant specific N-glycans must be a pre-requisite for α-Fuc'ase activity. A 3 D modelled structure of the catalytic sites of α-Fuc'ase Sl-2 suggested that Asp192 and Glu236 may be important for binding to the α1, 3/4 fucose residue.
Collapse
Affiliation(s)
- Md Ziaur Rahman
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.,Institute of Food and Radiation Biology, Atomic Energy Research Establishment, Bangladesh Atomic Energy Commission, Ganakbari, Savar, Dhaka 1340, Bangladesh
| | - Yuta Tsujimori
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Megumi Maeda
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Md Anowar Hossain
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Takeshi Ishimizu
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yoshinobu Kimura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| |
Collapse
|
7
|
Uemura R, Ogura M, Matsumaru C, Akiyama T, Maeda M, Kimura Y. Novel assay system for acidic Peptide:N-glycanase (aPNGase) activity in crude plant extract. Biosci Biotechnol Biochem 2018; 82:1172-1175. [DOI: 10.1080/09168451.2018.1459464] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Abstract
Acidic peptide:N-glycanase (aPNGase) plays a pivotal role in plant glycoprotein turnover. For the construction of aPNGase-knockout or -overexpressing plants, a new method to detect the activity in crude plant extracts is required because endogenous peptidases present in the extract hamper enzyme assays using fluorescence-labeled N-glycopeptides as a substrate. In this study, we developed a new method for measuring aPNGase activity in crude extracts from plant materials.
Collapse
Affiliation(s)
- Ryota Uemura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University , Okayama, Japan
| | - Mikako Ogura
- Faculty of Agriculture, Okayama University , Okayama, Japan
| | - Chihiro Matsumaru
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University , Okayama, Japan
| | - Tsuyoshi Akiyama
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University , Okayama, Japan
| | - Megumi Maeda
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University , Okayama, Japan
- Faculty of Agriculture, Okayama University , Okayama, Japan
| | - Yoshinobu Kimura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University , Okayama, Japan
- Faculty of Agriculture, Okayama University , Okayama, Japan
| |
Collapse
|
8
|
Signaling through plant lectins: modulation of plant immunity and beyond. Biochem Soc Trans 2018; 46:217-233. [PMID: 29472368 DOI: 10.1042/bst20170371] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 12/12/2022]
Abstract
Lectins constitute an abundant group of proteins that are present throughout the plant kingdom. Only recently, genome-wide screenings have unraveled the multitude of different lectin sequences within one plant species. It appears that plants employ a plurality of lectins, though relatively few lectins have already been studied and functionally characterized. Therefore, it is very likely that the full potential of lectin genes in plants is underrated. This review summarizes the knowledge of plasma membrane-bound lectins in different biological processes (such as recognition of pathogen-derived molecules and symbiosis) and illustrates the significance of soluble intracellular lectins and how they can contribute to plant signaling. Altogether, the family of plant lectins is highly complex with an enormous diversity in biochemical properties and activities.
Collapse
|
9
|
Effects of silver nanocolloids on plant complex type N-glycans in Oryza sativa roots. Sci Rep 2018; 8:1000. [PMID: 29343819 PMCID: PMC5772479 DOI: 10.1038/s41598-018-19474-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/03/2018] [Indexed: 02/05/2023] Open
Abstract
Silver nanomaterials have been mainly developed as antibacterial healthcare products worldwide, because of their antibacterial activity. However, there is little data regarding the potential risks and effects of large amounts of silver nanomaterials on plants. In contrast, N-glycans play important roles in various biological phenomena, and their structures and expressions are sensitive to ambient environmental changes. Therefore, to assesse the effects of silver nanomaterials, we focused on the correlation between N-glycans and the effects of silver nanomaterials in plants and analyzed N-glycan structures in Oryza sativa seedlings exposed to silver nanocolloids (SNCs). The phenotype analysis showed that the shoot was not affected by any SNC concentrations, whereas the high SNC exposed root was seriously damaged. Therefore, we performed comparative N-glycan analysis of roots. As a result, five of total N-glycans were significantly increased in SNC exposed roots, of which one was a free-N-glycan with one beta-N-acetylglucosamine residue at the reducing end. Our results suggest that the transition of plant complex type N-glycans, including free-N-glycans, was caused by abnormalities in O. sativa development, and free-N-glycan itself has an important role in plant development. This study originally adapted glycome transition analysis to environmental toxicology and proposed a new category called “Environmental glycobiology”.
Collapse
|