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Sogabe M, Kojima S, Kaya T, Tomioka A, Kaji H, Sato T, Chiba Y, Shimizu A, Tanaka N, Suzuki N, Hayashi I, Mikami M, Togayachi A, Narimatsu H. Sensitive New Assay System for Serum Wisteria floribunda Agglutinin-Reactive Ceruloplasmin That Distinguishes Ovarian Clear Cell Carcinoma from Endometrioma. Anal Chem 2022; 94:2476-2484. [PMID: 35044763 DOI: 10.1021/acs.analchem.1c04302] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Wisteria floribunda agglutinin (WFA)-reactive ceruloplasmin (CP) is a candidate marker for ovarian clear cell carcinoma (CCC) reported in our previous paper. Herein, a new measurement system was developed to investigate its potential as a serum marker for CCC. Site-specific glycome analysis using liquid chromatography/mass spectrometry showed that WFA-CP from CCC binds to WFA via the GalNAcβ1,4GlcNAc (LDN) structure. We used mutant recombinant WFA (rWFA), which has a high specificity to the LDN structure, instead of native WFA, to increase the specificity of the serum sample measurement. To improve the sensitivity, we used a surface plasmon field-enhanced fluorescence spectroscopy immunoassay system, which is approximately 100 times more sensitive than the conventional sandwich enzyme-linked immunosorbent assay system. With these two improvements, the specificity and sensitivity of the serum rWFA-CP measurement were dramatically improved, clearly distinguishing CCC from endometrioma, from which CCC originates. This rWFA-CP assay can be used clinically for the serodiagnosis of early-stage CCC, which is difficult to detect with existing serum markers.
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Affiliation(s)
- Maki Sogabe
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central-5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Shun Kojima
- Konica Minolta, Inc., No. 1 Sakura-machi, Hino, Tokyo 191-8511, Japan
| | - Takatoshi Kaya
- Konica Minolta, Inc., No. 1 Sakura-machi, Hino, Tokyo 191-8511, Japan
| | - Azusa Tomioka
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central-5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Hiroyuki Kaji
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central-5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Takashi Sato
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central-5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Yasunori Chiba
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central-5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Akira Shimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central-5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Nana Tanaka
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central-5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Nao Suzuki
- Department of Obstetrics and Gynecology, St. Marianna University of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa 216-8511, Japan
| | - Io Hayashi
- Department of Obstetrics and Gynecology, Tokai University, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Mikio Mikami
- Department of Obstetrics and Gynecology, Tokai University, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Akira Togayachi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central-5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Hisashi Narimatsu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central-5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
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2
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Goumenou A, Delaunay N, Pichon V. Recent Advances in Lectin-Based Affinity Sorbents for Protein Glycosylation Studies. Front Mol Biosci 2021; 8:746822. [PMID: 34778373 PMCID: PMC8585745 DOI: 10.3389/fmolb.2021.746822] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/23/2021] [Indexed: 01/29/2023] Open
Abstract
Glycosylation is one of the most significant post-translational modifications occurring to proteins, since it affects some of their basic properties, such as their half-life or biological activity. The developments in analytical methodologies has greatly contributed to a more comprehensive understanding of the quantitative and qualitative characteristics of the glycosylation state of proteins. Despite those advances, the difficulty of a full characterization of glycosylation still remains, mainly due to the complexity of the glycoprotein and/or glycopeptide mixture especially when they are present in complex biological samples. For this reason, various techniques that allow a prior selective enrichment of exclusively glycosylated proteins or glycopeptides have been developed in the past and are coupled either on- or off- line with separation and detection methods. One of the most commonly implemented enrichment methods includes the use of lectin proteins immobilized on various solid supports. Lectins are a group of different, naturally occurring proteins that share a common characteristic, which concerns their affinity for specific sugar moieties of glycoproteins. This review presents the different formats and conditions for the use of lectins in affinity chromatography and in solid phase extraction, including their use in dispersive mode, along with the recent progress made on either commercial or home-made lectin-based affinity sorbents, which can lead to a fast and automated glycosylation analysis.
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Affiliation(s)
- Anastasia Goumenou
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), UMR 8231 Chemistry, Biology and Innovation (CBI), ESPCI Paris, CNRS, PSL University, Paris, France
| | - Nathalie Delaunay
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), UMR 8231 Chemistry, Biology and Innovation (CBI), ESPCI Paris, CNRS, PSL University, Paris, France
| | - Valérie Pichon
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), UMR 8231 Chemistry, Biology and Innovation (CBI), ESPCI Paris, CNRS, PSL University, Paris, France.,Sorbonne University, Paris, France
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3
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to 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, matrices, derivatization, MALDI imaging, fragmentation and 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. Much of this material is 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 the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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4
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Noro E, Matsuda A, Kyoutou T, Sato T, Tomioka A, Nagai M, Sogabe M, Tsuruno C, Takahama Y, Kuno A, Tanaka Y, Kaji H, Narimatsu H. N-glycan structures of Wisteria floribunda agglutinin-positive Mac2 binding protein in the serum of patients with liver fibrosis†. Glycobiology 2021; 31:1268-1278. [PMID: 34192302 DOI: 10.1093/glycob/cwab060] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/03/2021] [Accepted: 06/17/2021] [Indexed: 12/18/2022] Open
Abstract
The extent of liver fibrosis predicts prognosis and is important for determining treatment strategies for chronic hepatitis. During the fibrosis progression, serum levels of Mac2 binding protein (M2BP) increase and the N-glycan structure changes to enable binding to Wisteria floribunda agglutinin (WFA) lectin. As a novel diagnostic marker, glycosylation isomer of M2BP (M2BPGi) has been developed. However, its glycan structures recognized by WFA are unclear. In this study, we analyzed site-specific N-glycan structures of serum M2BP using Glyco-RIDGE (Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile) method. We evaluated five sample types: 1) M2BP immunoprecipitated from normal healthy sera (NHS-IP(+)), 2) M2BP immunoprecipitated from sera of patients with liver cirrhosis (stage 4; F4-IP(+)), 3) M2BP captured with WFA from serum of patients with liver cirrhosis (stage 4; F4-WFA(+)), 4) recombinant M2BP produced by HEK293 cells (rM2BP), and 5) WFA-captured rM2BP (rM2BP-WFA(+)). In NHS-IP(+) M2BP, bi-antennary N-glycan was the main structure, and LacNAc extended to its branches. In F4-IP(+) M2BP, many branched structures, including tri-antennary and tetra-antennary N-glycans, were found. F4-WFA(+) showed a remarkable increase in branched structures relative to the quantity before enrichment. In recombinant M2BP, both no sialylated-LacdiNAc and -branched LacNAc structures were emerged. The LacdiNAc structure was not found in serum M2BP. Glycosidase-assisted HISCL assays suggest that, reactivity with WFA of both serum and recombinant M2BP depends on unsialylated and branched LacNAc, and in part of recombinant, depends on LacdiNAc. On M2BPGi, the highly branched LacNAc, probably dense cluster of LacNAc, would be recognized by WFA.
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Affiliation(s)
- Erika Noro
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8568, Japan
| | - Atsushi Matsuda
- Department of Biochemistry, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.,Engineering 1, Sysmex Corporation, Kobe, Hyogo 651-0073, Japan
| | - Takuya Kyoutou
- Engineering 1, Sysmex Corporation, Kobe, Hyogo 651-0073, Japan
| | - Takashi Sato
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8568, Japan.,Molecular & Cellular Glycoproteomics Research Group, Cellular & Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Azusa Tomioka
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8568, Japan.,Molecular & Cellular Glycoproteomics Research Group, Cellular & Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Misugi Nagai
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8568, Japan.,Molecular & Cellular Glycoproteomics Research Group, Cellular & Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Maki Sogabe
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8568, Japan.,Molecular & Cellular Glycoproteomics Research Group, Cellular & Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | | | - Yoichi Takahama
- Engineering 1, Sysmex Corporation, Kobe, Hyogo 651-0073, Japan
| | - Atsushi Kuno
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8568, Japan.,Molecular & Cellular Glycoproteomics Research Group, Cellular & Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Yasuhito Tanaka
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan
| | - Hiroyuki Kaji
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8568, Japan.,Molecular & Cellular Glycoproteomics Research Group, Cellular & Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8565, Japan
| | - Hisashi Narimatsu
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki 305-8568, Japan
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5
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Lenza MP, Oyenarte I, Diercks T, Quintana JI, Gimeno A, Coelho H, Diniz A, Peccati F, Delgado S, Bosch A, Valle M, Millet O, Abrescia NGA, Palazón A, Marcelo F, Jiménez‐Osés G, Jiménez‐Barbero J, Ardá A, Ereño‐Orbea J. Structural Characterization of N-Linked Glycans in the Receptor Binding Domain of the SARS-CoV-2 Spike Protein and their Interactions with Human Lectins. Angew Chem Int Ed Engl 2020; 59:23763-23771. [PMID: 32915505 PMCID: PMC7894318 DOI: 10.1002/anie.202011015] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/08/2020] [Indexed: 01/17/2023]
Abstract
The glycan structures of the receptor binding domain of the SARS-CoV2 spike glycoprotein expressed in human HEK293F cells have been studied by using NMR. The different possible interacting epitopes have been deeply analysed and characterized, providing evidence of the presence of glycan structures not found in previous MS-based analyses. The interaction of the RBD 13 C-labelled glycans with different human lectins, which are expressed in different organs and tissues that may be affected during the infection process, has also been evaluated by NMR. In particular, 15 N-labelled galectins (galectins-3, -7 and -8 N-terminal), Siglecs (Siglec-8, Siglec-10), and C-type lectins (DC-SIGN, MGL) have been employed. Complementary experiments from the glycoprotein perspective or from the lectin's point of view have permitted to disentangle the specific interacting epitopes in each case. Based on these findings, 3D models of the interacting complexes have been proposed.
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Affiliation(s)
- Maria Pia Lenza
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Iker Oyenarte
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Tammo Diercks
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Jon Imanol Quintana
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Ana Gimeno
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Helena Coelho
- UCIBIOREQUIMTEDepartamento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516CaparicaPortugal
| | - Ana Diniz
- UCIBIOREQUIMTEDepartamento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516CaparicaPortugal
| | - Francesca Peccati
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Sandra Delgado
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Alexandre Bosch
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Mikel Valle
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Oscar Millet
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Nicola G. A. Abrescia
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
- Ikerbasque, Basque Foundation for Science48013BilbaoSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)Instituto de Salud Carlos IIIMadridSpain
| | - Asís Palazón
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
- Ikerbasque, Basque Foundation for Science48013BilbaoSpain
| | - Filipa Marcelo
- UCIBIOREQUIMTEDepartamento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516CaparicaPortugal
| | - Gonzalo Jiménez‐Osés
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Jesús Jiménez‐Barbero
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
- Ikerbasque, Basque Foundation for Science48013BilbaoSpain
- Department of Organic Chemistry IIUniversity of the Basque CountryUPV/EHU48940LeioaSpain
| | - Ana Ardá
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - June Ereño‐Orbea
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
- Ikerbasque, Basque Foundation for Science48013BilbaoSpain
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6
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Lenza MP, Oyenarte I, Diercks T, Quintana JI, Gimeno A, Coelho H, Diniz A, Peccati F, Delgado S, Bosch A, Valle M, Millet O, Abrescia NGA, Palazón A, Marcelo F, Jiménez‐Osés G, Jiménez‐Barbero J, Ardá A, Ereño‐Orbea J. Structural Characterization of N‐Linked Glycans in the Receptor Binding Domain of the SARS‐CoV‐2 Spike Protein and their Interactions with Human Lectins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Maria Pia Lenza
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Iker Oyenarte
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Tammo Diercks
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Jon Imanol Quintana
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Ana Gimeno
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Helena Coelho
- UCIBIO REQUIMTE Departamento de Química Faculdade de Ciências e Tecnologia Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Ana Diniz
- UCIBIO REQUIMTE Departamento de Química Faculdade de Ciências e Tecnologia Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Francesca Peccati
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Sandra Delgado
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Alexandre Bosch
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Mikel Valle
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Oscar Millet
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Nicola G. A. Abrescia
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) Instituto de Salud Carlos III Madrid Spain
| | - Asís Palazón
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
| | - Filipa Marcelo
- UCIBIO REQUIMTE Departamento de Química Faculdade de Ciências e Tecnologia Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Gonzalo Jiménez‐Osés
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Jesús Jiménez‐Barbero
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
- Department of Organic Chemistry II University of the Basque Country UPV/EHU 48940 Leioa Spain
| | - Ana Ardá
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - June Ereño‐Orbea
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
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7
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Hosomi A, Iida K, Cho T, Iida H, Kaneko M, Suzuki T. The ER-associated protease Ste24 prevents N-terminal signal peptide-independent translocation into the endoplasmic reticulum in Saccharomyces cerevisiae. J Biol Chem 2020; 295:10406-10419. [PMID: 32513868 DOI: 10.1074/jbc.ra120.012575] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
Soluble proteins destined for the secretory pathway contain an N-terminal signal peptide that induces their translocation into the endoplasmic reticulum (ER). The importance of N-terminal signal peptides for ER translocation has been extensively examined over the past few decades. However, in the budding yeast Saccharomyces cerevisiae, a few proteins devoid of a signal peptide are still translocated into the ER and then N-glycosyl-ated. Using signal peptide-truncated reporter proteins, here we report the detection of significant translocation of N-terminal signal peptide-truncated proteins in a yeast mutant strain (ste24Δ) that lacks the endopeptidase Ste24 at the ER membrane. Furthermore, several ER/cytosolic proteins, including Sec61, Sec66, and Sec72, were identified as being involved in the translocation process. On the basis of screening for 20 soluble proteins that may be N-glycosylated in the ER in the ste24Δ strain, we identified the transcription factor Rme1 as a protein that is partially N-glycosylated despite the lack of a signal peptide. These results clearly indicate that some proteins lacking a signal peptide can be translocated into the ER and that Ste24 typically suppresses this process.
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Affiliation(s)
- Akira Hosomi
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Kamiina, Nagano, Japan
| | - Kazuko Iida
- Laboratory of Biomembrane, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Toshihiko Cho
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Hidetoshi Iida
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Masashi Kaneko
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, Kamiina, Nagano, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
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8
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Nagai-Okatani C, Nishigori M, Sato T, Minamino N, Kaji H, Kuno A. Wisteria floribunda agglutinin staining for the quantitative assessment of cardiac fibrogenic activity in a mouse model of dilated cardiomyopathy. J Transl Med 2019; 99:1749-1765. [PMID: 31253865 DOI: 10.1038/s41374-019-0279-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/24/2019] [Accepted: 05/10/2019] [Indexed: 12/17/2022] Open
Abstract
Cardiac fibrosis is a typical phenomenon in failing hearts for most cardiac diseases, including dilated cardiomyopathy (DCM), and its specific detection and quantification are crucial for the analysis of cardiac remodeling. Since cardiac fibrosis is characterized by extensive remodeling of the myocardial extracellular matrix (ECM), in which glycoproteins are the major components, we assumed that fibrosis-related alterations in the cardiac glycome and glycoproteome would be suitable targets for the detection of cardiac fibrosis. Here, we compared protein glycosylation between heart tissues of normal and DCM model mice by laser microdissection-assisted lectin microarray. Among 45 lectins, Wisteria floribunda agglutinin (WFA) was selected as the most suitable lectin for staining cardiac fibrotic tissues. Although the extent of WFA staining was highly correlated (r > 0.98) with that of picrosirius red staining, a common collagen staining method, WFA did not bind to collagen fibers. Further histochemical analysis with N-glycosidase revealed that WFA staining of fibrotic tissues was attributable to the binding of WFA to N-glycoproteins. Using a mass spectrometry-based approach, we identified WFA-binding N-glycoproteins expressed in DCM hearts, many of which were fibrogenesis-related ECM proteins, as expected. In addition, the identified glycoproteins carrying WFA-binding N-glycans were detected only in DCM hearts, suggesting their cooperative glycosylation alterations with disease progression. Among these WFA-binding ECM N-glycoproteins, co-localization of the collagen α6(VI) chain protein and WFA staining in cardiac tissue sections was confirmed with a double-staining analysis. Collectively, these results indicate that WFA staining is more suitable for the quantitative assessment of cardiac fibrogenic activity than current collagen staining methods. Furthermore, given that plasma WFA-binding glycoprotein levels were significantly correlated with the echocardiographic parameters for left ventricular remodeling, cardiac WFA-binding glycoproteins are candidate circulating glyco-biomarkers for the quantification and monitoring of cardiac fibrogenesis.
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Affiliation(s)
- Chiaki Nagai-Okatani
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.
| | - Mitsuhiro Nishigori
- Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Takashi Sato
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Naoto Minamino
- Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Hiroyuki Kaji
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Atsushi Kuno
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.
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9
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Chen Z, Huang J, Li L. Recent advances in mass spectrometry (MS)-based glycoproteomics in complex biological samples. Trends Analyt Chem 2019; 118:880-892. [PMID: 31579312 PMCID: PMC6774629 DOI: 10.1016/j.trac.2018.10.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein glycosylation plays a key role in various biological processes and disease-related pathological progression. Mass spectrometry (MS)-based glycoproteomics is a powerful approach that provides a system-wide profiling of the glycoproteome in a high-throughput manner. There have been numerous significant technological advances in this field, including improved glycopeptide enrichment, hybrid fragmentation techniques, emerging specialized software packages, and effective quantitation strategies, as well as more dedicated workflows. With increasingly sophisticated glycoproteomics tools on hand, researchers have extensively adapted this approach to explore different biological systems both in terms of in-depth glycoproteome profiling and comparative glycoproteome analysis. Quantitative glycoproteomics enables researchers to discover novel glycosylation-based biomarkers in various diseases with potential to offer better sensitivity and specificity for disease diagnosis. In this review, we present recent methodological developments in MS-based glycoproteomics and highlight its utility and applications in answering various questions in complex biological systems.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
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10
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Nakane T, Angata K, Sato T, Kaji H, Narimatsu H. Identification of mammalian glycoproteins with type-I LacdiNAc structures synthesized by the glycosyltransferase B3GALNT2. J Biol Chem 2019; 294:7433-7444. [PMID: 30898876 DOI: 10.1074/jbc.ra118.006892] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/04/2019] [Indexed: 11/06/2022] Open
Abstract
The type-I LacdiNAc (LDN; GalNAcβ1-3GlcNAc) has rarely been observed in mammalian cells except in the O-glycan of α-dystroglycan, in contrast to type-II LDN structures (GalNAcβ1-4GlcNAc) in N- and O-glycans that are present in many mammalian glycoproteins, such as pituitary and hypothalamic hormones. Although a β1,3-N-acetylgalactosaminyltransferase 2 (B3GALNT2; type-I LDN synthase) has been cloned, the function of type-I LDN in mammalian cells is still unclear, as its carrier protein(s) has not been identified. In this study, using HeLa cells, we demonstrate that inhibition of Golgi-resident glycosyltransferase increases the abundance of B3GALNT2-synthesized type-I LDN structures, recognized by Wisteria floribunda agglutinin (WFA). Using isotope-coded glycosylation site-specific tagging (IGOT)-LC/MS analysis of Lec8 Chinese hamster cells lacking galactosylation and of cells transfected with the B3GALNT2 gene, we identified the glycoproteins that carry B3GALNT2-generated type-I LDN in their N-glycans. Our results further revealed that LDN presence on low-density lipoprotein receptor-related protein 1 and nicastrin depends on B3GALNT2, indicating the occurrence of type-I LDN in vivo in mammalian cells. Our analysis also uncovered that most of the identified glycoproteins localize to intracellular organelles, particularly to the endoplasmic reticulum. Whereas B4GALNT3 and B4GALNT4 synthesized LDN on extracellular glycoproteins, B3GALNT2 primarily transferred LDN to intracellular glycoproteins, thereby clearly delineating proteins that carry type-I or type-II LDNs. Taken together, our results indicate the presence of mammalian glycoproteins carrying type-I LDN on N-glycans and suggest that type-I and type-II LDNs have different roles in vivo.
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Affiliation(s)
- Takahiro Nakane
- From the Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8568, Japan and.,Doctoral Program in Clinical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Kiyohiko Angata
- From the Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8568, Japan and
| | - Takashi Sato
- From the Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8568, Japan and
| | - Hiroyuki Kaji
- From the Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8568, Japan and
| | - Hisashi Narimatsu
- From the Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8568, Japan and .,Doctoral Program in Clinical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki 305-8575, Japan
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11
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Narimatsu H, Kaji H, Vakhrushev SY, Clausen H, Zhang H, Noro E, Togayachi A, Nagai-Okatani C, Kuno A, Zou X, Cheng L, Tao SC, Sun Y. Current Technologies for Complex Glycoproteomics and Their Applications to Biology/Disease-Driven Glycoproteomics. J Proteome Res 2018; 17:4097-4112. [PMID: 30359034 DOI: 10.1021/acs.jproteome.8b00515] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glycoproteomics is an important recent advance in the field of glycoscience. In glycomics, glycan structures are comprehensively analyzed after glycans are released from glycoproteins. However, a major limitation of glycomics is the lack of insight into glycoprotein functions. The Biology/Disease-driven Human Proteome Project has a particular focus on biological and medical applications. Glycoproteomics technologies aimed at obtaining a comprehensive understanding of intact glycoproteins, i.e., the kind of glycan structures that are attached to particular amino acids and proteins, have been developed. This Review focuses on the recent progress of the technologies and their applications. First, the methods for large-scale identification of both N- and O-glycosylated proteins are summarized. Next, the progress of analytical methods for intact glycopeptides is outlined. MS/MS-based methods were developed for improving the sensitivity and speed of the mass spectrometer, in parallel with the software for complex spectrum assignment. In addition, a unique approach to identify intact glycopeptides using MS1-based accurate masses is introduced. Finally, as an advance of glycomics, two approaches to provide the spatial distribution of glycans in cells are described, i.e., MS imaging and lectin microarray. These methods allow rapid glycomic profiling of different types of biological samples and thus facilitate glycoproteomics.
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Affiliation(s)
- Hisashi Narimatsu
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Hiroyuki Kaji
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics , University of Copenhagen , Blegdamsvej 3 , Copenhagen 2200 , Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics , University of Copenhagen , Blegdamsvej 3 , Copenhagen 2200 , Denmark
| | - Hui Zhang
- Center for Biomarker Discovery and Translation , Johns Hopkins University , 400 North Broadway , Baltimore , Maryland 21205 , United States
| | - Erika Noro
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Akira Togayachi
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Chiaki Nagai-Okatani
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Atsushi Kuno
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Xia Zou
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan.,Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Li Cheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Yangyang Sun
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
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12
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Togayachi A, Tomioka A, Fujita M, Sukegawa M, Noro E, Takakura D, Miyazaki M, Shikanai T, Narimatsu H, Kaji H. Identification of Poly-N-Acetyllactosamine-Carrying Glycoproteins from HL-60 Human Promyelocytic Leukemia Cells Using a Site-Specific Glycome Analysis Method, Glyco-RIDGE. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1138-1152. [PMID: 29675740 PMCID: PMC6004004 DOI: 10.1007/s13361-018-1938-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 05/15/2023]
Abstract
To elucidate the relationship between the protein function and the diversity and heterogeneity of glycans conjugated to the protein, glycosylation sites, glycan variation, and glycan proportions at each site of the glycoprotein must be analyzed. Glycopeptide-based structural analysis technology using mass spectrometry has been developed; however, complicated analyses of complex spectra obtained by multistage fragmentation are necessary, and sensitivity and throughput of the analyses are low. Therefore, we developed a liquid chromatography/mass spectrometry (MS)-based glycopeptide analysis method to reveal the site-specific glycome (Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile, Glyco-RIDGE). This method used accurate masses and retention times of glycopeptides, without requiring MS2, and could be applied to complex mixtures. To increase the number of identified peptide, fractionation of sample glycopeptides for reduction of sample complexity is required. Therefore, in this study, glycopeptides were fractionated into four fractions by hydrophilic interaction chromatography, and each fraction was analyzed using the Glyco-RIDGE method. As a result, many glycopeptides having long glycans were enriched in the highest hydrophilic fraction. Based on the monosaccharide composition, these glycans were thought to be poly-N-acetyllactosamine (polylactosamine [pLN]), and 31 pLN-carrier proteins were identified in HL-60 cells. Gene ontology enrichment analysis revealed that pLN carriers included many molecules related to signal transduction, receptors, and cell adhesion. Thus, these findings provided important insights into the analysis of the glycoproteome using our novel Glyco-RIDGE method. Graphical Abstract ᅟ.
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Affiliation(s)
- Akira Togayachi
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Azusa Tomioka
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Mika Fujita
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Masako Sukegawa
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Erika Noro
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Daisuke Takakura
- Project for utilizing glycans in the development of innovative drug discovery technologies, Japan Bioindustry Association (JBA), Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Michiyo Miyazaki
- Project for utilizing glycans in the development of innovative drug discovery technologies, Japan Bioindustry Association (JBA), Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Toshihide Shikanai
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Hisashi Narimatsu
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan.
| | - Hiroyuki Kaji
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan.
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13
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Narimatsu H, Sato T. Wisteria floribunda agglutinin positive glycobiomarkers: a unique lectin as a serum biomarker probe in various diseases. Expert Rev Proteomics 2017; 15:183-190. [DOI: 10.1080/14789450.2018.1419066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Hisashi Narimatsu
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Takashi Sato
- Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
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14
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Zhang S, Cao X, Gao Q, Liu Y. Protein glycosylation in viral hepatitis-related HCC: Characterization of heterogeneity, biological roles, and clinical implications. Cancer Lett 2017; 406:64-70. [DOI: 10.1016/j.canlet.2017.07.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/26/2017] [Accepted: 07/30/2017] [Indexed: 12/12/2022]
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15
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Identification of PNGase-dependent ERAD substrates in Saccharomyces cerevisiae. Biochem J 2016; 473:3001-12. [DOI: 10.1042/bcj20160453] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 07/18/2016] [Indexed: 12/24/2022]
Abstract
Endoplasmic reticulum (ER)-associated degradation (ERAD) is a proteolytic pathway for handling misfolded or improperly assembled proteins that are synthesized in the ER. Cytoplasmic peptide:N-glycanase (PNGase) is a deglycosylating enzyme that cleaves N-glycans that are attached to ERAD substrates. While the critical roles of N-glycans in monitoring the folding status of carrier proteins in the ER lumen are relatively well understood, the physiological role of PNGase-mediated deglycosylation in the cytosol remained poorly understood. We report herein the identification of endogenous substrates for the cytoplasmic PNGase in Saccharomyces cerevisiae. Using an isotope-coded glycosylation site-specific tagging (IGOT) method-based LC/MS analysis, 11 glycoproteins were specifically detected in the cytosol of PNGase-deletion cells (png1Δ). Among these molecules, at least five glycoproteins were clearly identified as ERAD substrates in vivo. Moreover, four out of the five proteins were found to be either deglycosylated by PNGase in vivo or the overall degradation was delayed in a png1Δ mutant. Our results clearly indicate that the IGOT method promises to be a powerful tool for the identification of endogenous substrates for the cytoplasmic PNGase.
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16
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Haji-Ghassemi O, Gilbert M, Spence J, Schur MJ, Parker MJ, Jenkins ML, Burke JE, van Faassen H, Young NM, Evans SV. Molecular Basis for Recognition of the Cancer Glycobiomarker, LacdiNAc (GalNAc[β1→4]GlcNAc), by Wisteria floribunda Agglutinin. J Biol Chem 2016; 291:24085-24095. [PMID: 27601469 DOI: 10.1074/jbc.m116.750463] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Indexed: 01/10/2023] Open
Abstract
Aberrant glycosylation and the overexpression of specific carbohydrate epitopes is a hallmark of many cancers, and tumor-associated oligosaccharides are actively investigated as targets for immunotherapy and diagnostics. Wisteria floribunda agglutinin (WFA) is a legume lectin that recognizes terminal N-acetylgalactosaminides with high affinity. WFA preferentially binds the disaccharide LacdiNAc (β-d-GalNAc-[1→4]-d-GlcNAc), which is associated with tumor malignancy in leukemia, prostate, pancreatic, ovarian, and liver cancers and has shown promise in cancer glycobiomarker detection. The mechanism of specificity for WFA recognition of LacdiNAc is not fully understood. To address this problem, we have determined affinities and structure of WFA in complex with GalNAc and LacdiNAc. Affinities toward Gal, GalNAc, and LacdiNAc were measured via surface plasmon resonance, yielding KD values of 4.67 × 10-4 m, 9.24 × 10-5 m, and 5.45 × 10-6 m, respectively. Structures of WFA in complex with LacdiNAc and GalNAc have been determined to 1.80-2.32 Å resolution. These high resolution structures revealed a hydrophobic groove complementary to the GalNAc and, to a minor extent, to the back-face of the GlcNAc sugar ring. Remarkably, the contribution of this small hydrophobic surface significantly increases the observed affinity for LacdiNAc over GalNAc. Tandem MS sequencing confirmed the presence of two isolectin forms in commercially available WFA differing only in the identities of two amino acids. Finally, the WFA carbohydrate binding site is similar to a homologous lectin isolated from Vatairea macrocarpa in complex with GalNAc, which, unlike WFA, binds not only αGalNAc but also terminal Ser/Thr O-linked αGalNAc (Tn antigen).
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Affiliation(s)
- Omid Haji-Ghassemi
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - Michel Gilbert
- Human Health Therapeutics, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Jenifer Spence
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - Melissa J Schur
- Human Health Therapeutics, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Matthew J Parker
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - Meredith L Jenkins
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - John E Burke
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - Henk van Faassen
- Human Health Therapeutics, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - N Martin Young
- Human Health Therapeutics, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Stephen V Evans
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
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Thaysen-Andersen M, Packer NH, Schulz BL. Maturing Glycoproteomics Technologies Provide Unique Structural Insights into the N-glycoproteome and Its Regulation in Health and Disease. Mol Cell Proteomics 2016; 15:1773-90. [PMID: 26929216 PMCID: PMC5083109 DOI: 10.1074/mcp.o115.057638] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/09/2016] [Indexed: 12/21/2022] Open
Abstract
The glycoproteome remains severely understudied because of significant analytical challenges associated with glycoproteomics, the system-wide analysis of intact glycopeptides. This review introduces important structural aspects of protein N-glycosylation and summarizes the latest technological developments and applications in LC-MS/MS-based qualitative and quantitative N-glycoproteomics. These maturing technologies provide unique structural insights into the N-glycoproteome and its synthesis and regulation by complementing existing methods in glycoscience. Modern glycoproteomics is now sufficiently mature to initiate efforts to capture the molecular complexity displayed by the N-glycoproteome, opening exciting opportunities to increase our understanding of the functional roles of protein N-glycosylation in human health and disease.
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Affiliation(s)
- Morten Thaysen-Andersen
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia;
| | - Nicolle H Packer
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Benjamin L Schulz
- §School of Chemistry & Molecular Biosciences, St Lucia, The University of Queensland, Brisbane, QLD, Australia
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