Systems Glycobiology Research Group

Wako, Japan

Systems Glycobiology Research Group

Wako, Japan
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Yamaguchi Y.,Nagoya City University | Yamaguchi Y.,Systems Glycobiology Research Group | Hanashima S.,Systems Glycobiology Research Group | Yagi H.,Nagoya City University | And 10 more authors.
Biochemical and Biophysical Research Communications | Year: 2010

Osteopontin (OPN) is an integrin-binding protein found in a variety of tissues and physiological fluids and is involved in divergent biological processes such as migration, adhesion and signaling in integrin-independent as well as dependent manners. The adhesive activity of this protein is modulated upon cleavage by thrombin at the central part of the molecule, in the vicinity of the integrin-binding sequences. Although detailed structural characterization is crucial for further understanding of the regulatory mechanisms of the OPN functions, its intrinsically disordered property hampers in-depth conformational analyses. Here we report an NMR study of mouse OPN and its N-terminal thrombin-cleavage product to characterize intramolecular interaction of this molecule. Paramagnetic relaxation enhancement experiment revealed that OPN exhibits a long-range intramolecular interaction between the N- and C-terminal regions. Furthermore, our NMR data showed that anti-OPN antibody OPN1.2, whose reactivity is impaired by deletion or amino acid substitutions of the arginine-aspartate-glycine integrin-binding motif, binds the N-terminal side of the integrin-binding motifs suggesting the existence of intramolecular interaction. These data suggest that functional interactions of OPN with integrins and the other binding partners can be modulated by the intramolecular interactions. © 2010 Elsevier Inc. All rights reserved.


Kizuka Y.,Systems Glycobiology Research Group | Kitazume S.,Systems Glycobiology Research Group | Yoshida M.,RIKEN | Taniguchi N.,Systems Glycobiology Research Group | Taniguchi N.,Osaka University
Journal of Biological Chemistry | Year: 2011

It is well known that biosynthesis of glycans takes place in organ- and tissue-specific manners and glycan expression is controlled by various factors including glycosyltransferases. The expression mechanism of glycosyltransferases, however, is poorly understood. Here we investigated the expression mechanism of a brain-specific glycosyltransferase, GnT-IX (N-acetylglucosaminyltransferase IX, also designated as GnT-Vb), which synthesizes branched O-mannose glycan. Using an epigenetic approach, we revealed that the genomic region around the transcriptional start site of the GnT-IX gene was highly associated with active chromatin histone marks in a neural cell-specific manner, indicating that brain-specific GnT-IX expression is under control of an epigenetic "histone code." By EMSA and ChIP analyses we identified two regulatory proteins, NeuroD1 and CTCF that bind to and activate the GnT-IX promoter. We also revealed that GnT-IX expression was suppressed in CTCFand NeuroD1-depleted cells, indicating that a NeuroD1- and CTCF-dependent epigenetic mechanism governs brain-specific GnT-IX expression. Several other neural glycosyltransferase genes are also found to be regulated by epigenetic histone modifications. This is the first report demonstrating a molecular mechanism at the chromatin level underlying tissue-specific glycan expression. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.


Yamaguchi Y.,Nagoya City University | Yamaguchi Y.,Systems Glycobiology Research Group | Masuda M.,Tokyo Institute of Psychiatry | Masuda M.,Tokyo Metroplitan University | And 9 more authors.
Journal of Molecular Biology | Year: 2010

α-Synuclein is a major component of filamentous inclusions that are histological hallmarks of Parkinson's disease and other α-synucleinopathies. Previous analyses have revealed that several polyphenols inhibit α-synuclein assembly with low micromolar IC50 values, and that SDS-stable, noncytotoxic soluble α-synuclein oligomers are formed in their presence. Structural elucidation of inhibitor-bound α-synuclein oligomers is obviously required for the better understanding of the inhibitory mechanism. In order to characterize inhibitor-bound α-synucleins in detail, we have prepared α-synuclein dimers in the presence of polyphenol inhibitors, exifone, gossypetin, and dopamine, and purified the products. Peptide mapping and mass spectrometric analysis revealed that exifone-treated α-synuclein monomer and dimer were oxidized at all four methionine residues of α-synuclein. Immunoblot analysis and redox-cycling staining of endoproteinase Asp-N-digested products showed that the N-terminal region (1-60) is involved in the dimerization and exifone binding of α-synuclein. Ultra-high-field NMR analysis of inhibitor-bound α-synuclein dimers showed that the signals derived from the N-terminal region of α-synuclein exhibited line broadening, confirming that the N-terminal region is involved in inhibitor-induced dimerization. The C-terminal portion still predominantly exhibited the random-coil character observed in monomeric α-synuclein. We propose that the N-terminal region of α-synuclein plays a key role in the formation of α-synuclein assemblies. © 2009 Elsevier Ltd. All rights reserved.


Ninagawa S.,Kyoto University | Ninagawa S.,Japan Institute for Molecular Science | Ninagawa S.,Okazaki Institute for Integrative Bioscience | Okada T.,Kyoto University | And 14 more authors.
Journal of Cell Biology | Year: 2015

Glycoproteins and non-glycoproteins possessing unfolded/misfolded parts in their luminal regions are cleared from the endoplasmic reticulum (ER) by ER-associated degradation (ERAD)-L with distinct mechanisms. Two-step mannose trimming from Man9GlcNAc2 is crucial in the ERAD-L of glycoproteins. We recently showed that this process is initiated by EDEM2 and completed by EDEM3/EDEM1. Here, we constructed chicken and human cells simultaneously deficient in EDEM1/2/3 and analyzed the fates of four ERAD-L substrates containing three potential N-glycosylation sites. We found that native but unstable or somewhat unfolded glycoproteins, such as ATF6α, ATF6α(C), CD3-δ-ΔTM, and EMC1, were stabilized in EDEM1/2/3 triple knockout cells. In marked contrast, degradation of severely misfolded glycoproteins, such as null Hong Kong (NHK) and deletion or insertion mutants of ATF6α(C), CD3-δ-ΔTM, and EMC1, was delayed only at early chase periods, but they were eventually degraded as in wild-type cells. Thus, higher eukaryotes are able to extract severely misfolded glycoproteins from glycoprotein ERAD and target them to the non-glycoprotein ERAD pathway to maintain the homeostasis of the ER. © 2015 Ninagawa et al.


Harada Y.,Systems Glycobiology Research Group | Harada Y.,Kagoshima University | Masahara-Negishi Y.,Systems Glycobiology Research Group | Suzuki T.,Systems Glycobiology Research Group
Glycobiology | Year: 2015

During asparagine (N)-linked protein glycosylation, eukaryotic cells generate considerable amounts of free oligosaccharides (fOSs) in the cytosol. It is generally assumed that such fOSs are produced by the deglycosylation of misfolded N-glycoproteins that are destined for proteasomal degradation or as the result of the degradation of dolichol-linked oligosaccharides (DLOs), which serve as glycan donor substrates in N-glycosylation reactions. The findings reported herein show that the majority of cytosolic fOSs are generated by a peptide:N-glycanase (PNGase) and an endo-β-N-acetylglucosaminidase (ENGase)-independent pathway in mammalian cells. The ablation of the cytosolic deglycosylating enzymes, PNGase and ENGase, in mouse embryonic fibroblasts had little effect on the amount of cytosolic fOSs generated. Quantitative analyses of fOSs using digitonin-permeabilized cells revealed that they are generated by the degradation of fully assembled Glc3Man9GlcNAc2-pyrophosphate-dolichol (PP-Dol) in the lumen of the endoplasmic reticulum. Because the degradation of Glc3Man9GlcNAc2-PP-Dol is greatly inhibited in the presence of an N-glycosylation acceptor peptide that is recognized by the oligosaccharyltransferase (OST), the OST-mediated hydrolysis of DLO is the most likely mechanism responsible for the production of a large fraction of the cytosolic fOSs. © 2015 The Author.


Okada T.,Saga University | Okada T.,Japan Science and Technology Agency | Okada T.,Musashino University | Ihara H.,Saga University | And 8 more authors.
Glycobiology | Year: 2010

The baculovirus-insect cell expression system is in widespread use for expressing post-translationally modified proteins. As a result, it is potentially applicable for the production of glycoproteins for therapeutic and diagnostic purposes. For practical use, however, remodeling of the biosynthetic pathway of host-cell N-glycosylation is required because insect cells produce paucimannosidic glycoforms, which are different from the typical mammalian glycoform, due to trimming of the non-reducing terminal β1,2-GlcNAc residue of the core structure by a specific β-N-acetylglucosaminidase. In order to establish a cell line which could be used as a host for the baculovirus-based production of glycoproteins with mammalian-type N-glycosylation, we prepared and characterized Spodoptera frugiperda Sf21 cells that had been transfected with the rat cDNA for β1,4-N-acetylglucosaminyltransferase III (GnT-III), which catalyzes the addition of a bisecting GlcNAc. As evidenced by structural analyses of N-glycans prepared from whole cells and the expressed recombinant glycoproteins, the introduction of GnT-III led to the production of bisected hybrid-type N-glycans in which the β1,2-GlcNAc residue at the α1,3-mannosyl branch is completely retained and which has the potential to be present in mammalian cells. These results and other related findings suggest that bisected oligosaccharides are highly resistant to β-N- acetylglucosaminidase activity of the S. frugiperda fused lobes gene product, or other related enzymes, which was confirmed in Sf21 cells. Our present study demonstrates that GnT-III transfection has the potential to be an effective approach in humanizing the N-glycosylation of lepidopteran insect cells, thereby providing a possible preliminary step for the generation of complex-type glycoforms if the presence of a bisecting GlcNAc can be tolerated. © 2010 The Author.


Kato K.,Japan Institute for Molecular Science | Kato K.,Nagoya City University | Kato K.,Ochanomizu University | Kato K.,GLYENCE Co. | And 2 more authors.
Progress in Nuclear Magnetic Resonance Spectroscopy | Year: 2010

A paper published in Progress in Nuclear Magnetic Resonance Spectroscopy informs about stable-isotope-assisted NMR approaches to glycoproteins using immunoglobulin G (IgG) as a model system. The paper describes about the application of the stable-isotope-assisted NMR approach to structural analyses of glycoprotein glycans using IgG as a model system. IgG is described as a multi-domain glycoprotein with a molecular mass of 150 kDa, functioning as the major class of antibodies in the immune system. Three-dimensional structures have been determined by X-ray crystallographic analyses and are available for intact IgG molecules and for a proteolytic fragment Fc. Two methods are employed for stable-isotope-labeling of IgG-Fc glycans. These two methods include metabolic labeling through biosynthetic pathways of production vehicles and in vitro enzymatic attachment of isotopically labeled monosaccharide(s) onto the non-reducing end of the Fc glycans.


PubMed | Nippon Medical School, Systems Glycobiology Research Group and Academia Sinica, Taiwan
Type: Journal Article | Journal: Physiological reports | Year: 2014

We have previously demonstrated that chronic obstructive pulmonary disease (COPD) patients who do not have Siglec-14 are less prone to exacerbation of the disease. Siglec-14 is a myeloid cell protein that recognizes bacteria and triggers inflammatory responses. Therefore, soluble mediators secreted by myeloid cells responding to Siglec-14 engagement could be involved in the pathogenesis of exacerbation and could potentially be utilized as biomarkers of exacerbation. To find out, we sought genes specifically induced in Siglec-14(+) myeloid cells and evaluated their utility as biomarkers of COPD exacerbation. Using DNA microarray, we compared gene expression levels in Siglec-14(+) and control myeloid cell lines stimulated with or without nontypeable Haemophilus influenzae to select genes that were specifically induced in Siglec-14(+) cells. The expressions of several cytokine and chemokine genes were specifically induced in Siglec-14(+) cells. The concentrations of seven gene products were analyzed by multiplex bead array assays in paired COPD patient sera (n = 39) collected during exacerbation and stable disease states. Those gene products that increased during exacerbation were further tested using an independent set (n = 32) of paired patient sera. Serum concentration of interleukin-27 (IL-27) was elevated during exacerbation (discovery set: P = 0.0472; verification set: P = 0.0428; combined: P = 0.0104; one-sided Wilcoxon matched-pairs signed-rank test), particularly in exacerbations accompanied with sputum purulence and in exacerbations lasting more than a week. We concluded that IL-27 might be mechanistically involved in the exacerbation of COPD and could potentially serve as a systemic biomarker of exacerbation.

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