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Dolatmoradi M, Sándor Z, Vágó I, Lowy DA, Vertes A, Kincses I. Nutrient supplementation-induced metabolic profile changes and early appearance of free N-glycans in nutrient deficient tomato plants revealed by mass spectrometry. Analyst 2024; 149:2709-2718. [PMID: 38525956 DOI: 10.1039/d4an00024b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Inorganic fertilizers are routinely used in large scale crop production for the supplementation of nitrogen, phosphorus, and potassium in nutrient poor soil. To explore metabolic changes in tomato plants grown on humic sand under different nutritional conditions, matrix-assisted laser desorption ionization (MALDI) mass spectrometry was utilized for the analysis of xylem sap. Variations in the abundances of metabolites and oligosaccharides, including free N-glycans (FNGs), were determined. Statistical analysis of the sample-related peaks revealed significant differences in the abundance ratios of multiple metabolites, including oligosaccharides, between the control plants, grown with no fertilizers, and plants raised under "ideal" and "nitrogen deficient" nutritional conditions, i.e., under the three treatment types. Among the 36 spectral features tentatively identified as oligosaccharides, the potential molecular structures for 18 species were predicted based on their accurate masses and isotope distribution patterns. To find the spectral features that account for most of the differences between the spectra corresponding to the three different treatments, multivariate statistical analysis was carried out by orthogonal partial least squares-discriminant analysis (OPLS-DA). They included both FNGs and non-FNG compounds that can be considered as early indicators of nutrient deficiency. Our results reveal that the potential nutrient deficiency indicators can be expanded to other metabolites beyond FNGs. The m/z values for 20 spectral features with the highest variable influence on projection (VIP) scores were ranked in the order of their influence on the statistical model.
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Affiliation(s)
- Marjan Dolatmoradi
- Department of Chemistry, George Washington University, Washington, DC, USA.
| | - Zsolt Sándor
- Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Hungary.
| | - Imre Vágó
- Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Hungary.
| | | | - Akos Vertes
- Department of Chemistry, George Washington University, Washington, DC, USA.
| | - Ida Kincses
- Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Hungary.
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Takata S, Hayashi M, Maeda M, Ishimizu T, Kimura Y. Structural features of free N-glycans in α1,3/4-fucosidase-deficient Arabidopsis thaliana: Deletion of α1,3/4-fucosidase activity induced accumulation of plant complex type GN1 free N-glycans. Biosci Biotechnol Biochem 2022; 86:1413-1416. [PMID: 35867865 DOI: 10.1093/bbb/zbac120] [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: 06/11/2022] [Accepted: 07/12/2022] [Indexed: 11/14/2022]
Abstract
Deletion of α-1,3/4-fucosidase activity in Arabidopsis thaliana resulted in the accumulation of GN1-type free N-glycans with the Lewis a epitope (GN1-FNG). This suggests that the release of α-fucose residue(s) may trigger rapid degradation of the plant complex-type (PCT) GN1-FNG. The fact that PCT-GN1-FNG has rarely been detected to date is probably due to its easier degradation compared to PCT-GN2-FNG.
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Affiliation(s)
- Shun Takata
- Faculty of Agriculture, Division of Agricultural Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, Japan
| | - Megumi Hayashi
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Megumi Maeda
- Faculty of Agriculture, Division of Agricultural Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, Japan.,Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Okayama, Japan
| | - Takeshi Ishimizu
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Yoshinobu Kimura
- Faculty of Agriculture, Division of Agricultural Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama, Japan.,Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Okayama, Japan
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Kosaka S, Katsube M, Maeda M, Kimura Y. Improved method for preparation and purification of recombinant α-synuclein: high-mannose-type free N-glycan prepared from an edible bean (Vigna angulari, Azuki bean) inhibits α-synuclein aggregation. Biosci Biotechnol Biochem 2022; 86:770-774. [PMID: 35293991 DOI: 10.1093/bbb/zbac040] [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: 01/12/2022] [Accepted: 03/08/2022] [Indexed: 11/14/2022]
Abstract
Parkinson's disease is characterized by the accumulation of amyloid, which consists of α-synuclein (α-Syn). To screen compounds with amyloid aggregation inhibitory activity, an effective method for the preparation of α-Syn is a prerequisite. We established a simpler method for α-Syn preparation using freeze-thaw treatment of transformed Escherichia coli. Furthermore, we found that the high-mannose type free N-glycans could prevent α-Syn aggregation.
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Affiliation(s)
- Shota Kosaka
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Okayama, Japan
| | - Makoto Katsube
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Okayama, Japan
| | - Megumi Maeda
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Okayama, Japan
| | - Yoshinobu Kimura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Okayama, Japan
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Hirayama H, Suzuki T. Assay for the peptide:N-glycanase/NGLY1 and disease-specific biomarkers for diagnosing NGLY1 deficiency. J Biochem 2021; 171:169-176. [PMID: 34791337 DOI: 10.1093/jb/mvab127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Cytosolic peptide:N-glycanase (NGLY1 in mammals), a highly conserved enzyme in eukaryotes, catalyzes the deglycosylation of N-glycans that are attached to glycopeptide/glycoproteins. In 2012, an autosomal recessive disorder related to the NGLY1 gene, which was referred to as NGLY1 deficiency, was reported. Since then, more than 100 patients have been identified. Patients with this disease exhibit various symptoms, including various motor deficits and other neurological problems. Effective therapeutic treatments for this disease, however, have not been established. Most recently, it was demonstrated that the intracerebroventricular administration of an adeno-associated virus 9 vector expressing human NGLY1 during the weaning period allowed some motor functions to be recovered in Ngly1-/- rats. This observation led us to hypothesize that a therapeutic intervention for improving these motor deficits or other neurological symptoms found in the patients might be possible. To achieve this, it is critical to establish robust and facile methods for assaying NGLY1 activity in biological samples, for the early diagnosis and evaluation of the therapeutic efficacy for the treatment of NGLY1 deficiency. In this mini-review, we summarize progress made in the development of various assay methods for NGLY1 activity, as well as a recent progress in the identification of NGLY1 deficiency-specific biomarkers.
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Affiliation(s)
- Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
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Maeda M, Okamoto N, Araki N, Kimura Y. Purification, Characterization, and Gene Expression of Rice Endo-β- N-Acetylglucosaminidase, Endo-Os. FRONTIERS IN PLANT SCIENCE 2021; 12:647684. [PMID: 34447396 PMCID: PMC8382983 DOI: 10.3389/fpls.2021.647684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
In the endoplasmic reticulum-associated degradation system of plant and animal cells, high-mannose type free N-glycans (HMT-FNGs) are produced from misfolded glycoproteins prior to proteasomal degradation, and two enzymes, cytosolic peptide:N-glycanase (cPNGase) and endo-β-N-acetylglucosaminidase (endo-β-GlcNAc-ase), are involved in the deglycosylation. Although the physiological functions of these FNGs in plant growth and development remain to be elucidated, detailed characterization of cPNGase and endo-β-GlcNAc-ase is required. In our previous work, we described the purification, characterization, and subcellular distribution of some plant endo-β-GlcNAc-ases and preliminarily reported the gene information of rice endo-β-GlcNAc-ase (Endo-Os). Furthermore, we analyzed the changes in gene expression of endo-β-GlcNAc-ase during tomato fruit maturation and constructed a mutant line of Arabidopsis thaliana, in which the two endo-β-GlcNAc-ase genes were knocked-out based on the Endo-Os gene. In this report, we describe the purification, characterization, amino acid sequence, and gene cloning of Endo-Os in detail. Purified Endo-Os, with an optimal pH of 6.5, showed high activity for high-mannose type N-glycans bearing the Manα1-2Manα1-3Manβ1 unit; this substrate specificity was almost the same as that of other plant endo-β-GlcNAc-ases, suggesting that Endo-Os plays a critical role in the production of HTM-FNGs in the cytosol. Electrospray ionization-mass spectrometry analysis of the tryptic peptides revealed 17 internal amino acid sequences, including the C terminus; the N-terminal sequence could not be identified due to chemical modification. These internal amino acid sequences were consistent with the amino acid sequence (UniProt ID: Q5W6R1) deduced from the Oryza sativa cDNA clone AK112067 (gene ID: Os05g0346500). Recombinant Endo-Os expressed in Escherichia coli using cDNA showed the same enzymatic properties as those of native Endo-Os.
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Affiliation(s)
- Megumi Maeda
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Naoko Okamoto
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Norie Araki
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshinobu Kimura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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De Coninck T, Gistelinck K, Janse van Rensburg HC, Van den Ende W, Van Damme EJM. Sweet Modifications Modulate Plant Development. Biomolecules 2021; 11:756. [PMID: 34070047 PMCID: PMC8158104 DOI: 10.3390/biom11050756] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/28/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Plant development represents a continuous process in which the plant undergoes morphological, (epi)genetic and metabolic changes. Starting from pollination, seed maturation and germination, the plant continues to grow and develops specialized organs to survive, thrive and generate offspring. The development of plants and the interplay with its environment are highly linked to glycosylation of proteins and lipids as well as metabolism and signaling of sugars. Although the involvement of these protein modifications and sugars is well-studied, there is still a long road ahead to profoundly comprehend their nature, significance, importance for plant development and the interplay with stress responses. This review, approached from the plants' perspective, aims to focus on some key findings highlighting the importance of glycosylation and sugar signaling for plant development.
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Affiliation(s)
- Tibo De Coninck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Koen Gistelinck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Henry C. Janse van Rensburg
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Els J. M. Van Damme
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
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