1
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Mamahit YP, Maki Y, Okamoto R, Kajihara Y. Semisynthesis of homogeneous misfolded glycoprotein interleukin-8. Carbohydr Res 2023; 531:108847. [PMID: 37354703 DOI: 10.1016/j.carres.2023.108847] [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: 04/26/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/26/2023]
Abstract
To uncover how cells distinguish between misfolded and correctly-folded glycoproteins, homogeneous misfolded glycoproteins are needed as a probe for analysis of their structure and chemical characteristic nature. In this study, we have synthesized misfolded glycosyl interleukin-8 (IL-8) by combining E. coli expression and chemical synthesis to improve the synthetic efficiency. In order to prepare N-terminal peptide-thioester segment (1-33), we prepared an E. coli expressed peptide and then activated the C-terminal Cys by using an intramolecular N-to-S acyl shift reaction, followed by trans-thioesterification of the Cys-thioester with an external bis(2-sulfanylethyl)amine (SEA). The glycopeptide segment (34-49) was prepared by solid phase peptide synthesis and the C-terminal peptide (50-72) was prepared in E. coli. These peptide and glycopeptide segments were successfully coupled by sequential native chemical ligation. To obtain homogeneous misfolded glycoproteins by shuffling the disulfide bond pattern, folding conditions were optimized to maximize the yield of individual homogeneous misfolded glycoproteins.
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Affiliation(s)
- Yugoviandi P Mamahit
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yuta Maki
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan; Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Ryo Okamoto
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan; Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan; Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.
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2
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Abe J, Takeda Y, Kikuma T, Kizuka Y, Kajiura H, Kajihara Y, Ito Y. Squaryl group-modified UDP analogs as inhibitors of the endoplasmic reticulum-resident folding sensor enzyme UGGT. Chem Commun (Camb) 2023; 59:2803-2806. [PMID: 36790024 DOI: 10.1039/d2cc06634c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
UDP-Glc:glycoprotein glucosyltransferase (UGGT) has a central role to retain quality control of correctly folded N-glycoprotein in the endoplasmic reticulum (ER). A selective and potent inhibitor against UGGT could lead to elucidation of UGGT-related events, but such a molecule has not been identified so far. Examples of small molecules with UGGT inhibitory activity are scarce. Here, we report squaryl group-modified UDP analogs as a promising UGGT inhibitor. Among these, the compound possessing a 2'-amino group of the uridine moiety and hydroxyethyl-substituted squaramide exhibited the highest potency, suggesting its relevance as a molecule for further optimization.
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Affiliation(s)
- Junpei Abe
- Graduate School of Science, Osaka University, Toyonaka, 560-0043, Japan
| | - Yoichi Takeda
- College of Life Sciences, Ritsumeikan University, Kusastu, 525-8577, Japan
| | - Takashi Kikuma
- College of Life Sciences, Ritsumeikan University, Kusastu, 525-8577, Japan
| | - Yasuhiko Kizuka
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Hiroyuki Kajiura
- International Center for Biotechnology, Osaka University, Suita, 565-0871, Japan
| | - Yasuhiro Kajihara
- Graduate School of Science, Osaka University, Toyonaka, 560-0043, Japan
| | - Yukishige Ito
- Graduate School of Science, Osaka University, Toyonaka, 560-0043, Japan.,RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan
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3
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Tian J, Li Y, Ma B, Tan Z, Shang S. Automated Peptide Synthesizers and Glycoprotein Synthesis. Front Chem 2022; 10:896098. [PMID: 35601548 PMCID: PMC9117762 DOI: 10.3389/fchem.2022.896098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
The development and application of commercially available automated peptide synthesizers has played an essential role in almost all areas of peptide and protein research. Recent advances in peptide synthesis method and solid-phase chemistry provide new opportunities for optimizing synthetic efficiency of peptide synthesizers. The efforts in this direction have led to the successful preparation of peptides up to more than 150 amino acid residues in length. Such success is particularly useful for addressing the challenges associated with the chemical synthesis of glycoproteins. The purpose of this review is to provide a brief overview of the evolution of peptide synthesizer and glycoprotein synthesis. The discussions in this article include the principles underlying the representative synthesizers, the strengths and weaknesses of different synthesizers in light of their principles, and how to further improve the applicability of peptide synthesizers in glycoprotein synthesis.
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Affiliation(s)
- Jiekang Tian
- Center of Pharmaceutical Technology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yaohao Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bo Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhongping Tan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Zhongping Tan, ; Shiying Shang,
| | - Shiying Shang
- Center of Pharmaceutical Technology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- *Correspondence: Zhongping Tan, ; Shiying Shang,
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4
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Nomura K, Liu Y, Kajihara Y. Synthesis of homogeneous glycoproteins with diverse N-glycans. Adv Carbohydr Chem Biochem 2022; 81:57-93. [DOI: 10.1016/bs.accb.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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5
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Manabe Y. Chemical Biology Study on N-glycans. TRENDS GLYCOSCI GLYC 2021. [DOI: 10.4052/tigg.2109.2j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University
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6
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Manabe Y. Chemical Biology Study on N-glycans. TRENDS GLYCOSCI GLYC 2021. [DOI: 10.4052/tigg.2109.2e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University
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7
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Shirakawa A, Manabe Y, Fukase K. Recent Advances in the Chemical Biology of N-Glycans. Molecules 2021; 26:molecules26041040. [PMID: 33669465 PMCID: PMC7920464 DOI: 10.3390/molecules26041040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 12/19/2022] Open
Abstract
Asparagine-linked N-glycans on proteins have diverse structures, and their functions vary according to their structures. In recent years, it has become possible to obtain high quantities of N-glycans via isolation and chemical/enzymatic/chemoenzymatic synthesis. This has allowed for progress in the elucidation of N-glycan functions at the molecular level. Interaction analyses with lectins by glycan arrays or nuclear magnetic resonance (NMR) using various N-glycans have revealed the molecular basis for the recognition of complex structures of N-glycans. Preparation of proteins modified with homogeneous N-glycans revealed the influence of N-glycan modifications on protein functions. Furthermore, N-glycans have potential applications in drug development. This review discusses recent advances in the chemical biology of N-glycans.
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Affiliation(s)
- Asuka Shirakawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
| | - Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Correspondence: (Y.M.); (K.F.); Tel.: +81-6-6850-5391 (Y.M.); +81-6-6850-5388 (K.F.)
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Correspondence: (Y.M.); (K.F.); Tel.: +81-6-6850-5391 (Y.M.); +81-6-6850-5388 (K.F.)
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8
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Li H, Zhang J, An C, Dong S. Probing N-Glycan Functions in Human Interleukin-17A Based on Chemically Synthesized Homogeneous Glycoforms. J Am Chem Soc 2021; 143:2846-2856. [DOI: 10.1021/jacs.0c12448] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hongxing Li
- State Key Laboratory of Natural and Biomimetic Drugs, and Department of Chemical Biology at School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jun Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, and Department of Chemical Biology at School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Chuanjing An
- State Key Laboratory of Natural and Biomimetic Drugs, and Department of Chemical Biology at School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, and Department of Chemical Biology at School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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9
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Abstract
Folding of proteins is essential so that they can exert their functions. For proteins that transit the secretory pathway, folding occurs in the endoplasmic reticulum (ER) and various chaperone systems assist in acquiring their correct folding/subunit formation. N-glycosylation is one of the most conserved posttranslational modification for proteins, and in eukaryotes it occurs in the ER. Consequently, eukaryotic cells have developed various systems that utilize N-glycans to dictate and assist protein folding, or if they consistently fail to fold properly, to destroy proteins for quality control and the maintenance of homeostasis of proteins in the ER.
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10
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Izumi M, Araki H, Tominaga M, Okamoto R, Kajihara Y. Chemical Synthesis of Ubiquitinated High-Mannose-Type N-Glycoprotein CCL1 in Different Folding States. J Org Chem 2020; 85:16024-16034. [PMID: 32985191 DOI: 10.1021/acs.joc.0c01766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Degradation of misfolded glycoproteins by the ubiquitin-proteasome system (UPS) is a very important process for protein homeostasis. To demonstrate the accessibility toward a ubiquitinated glycoprotein probe for the study of glycoprotein degradation by UPS, we synthesized ubiquitinated glycoprotein CC motif chemokine 1 (CCL1) bearing a high-mannose-type N-glycan, starting from six peptide segments. A native isopeptide linkage was constructed using δ-thiolysine (thioLys)-mediated chemical ligation. CCL1 glycopeptide with a high-mannose-type N-glycan as well as a δ-thioLys residue was synthesized chemically. The chemical ligation between δ-thioLys-containing glycopeptide and ubiquitin-α-thioester successfully yielded a ubiquitinated glycopeptide with a native isopeptide bond after desulfurization, even in the presence of a large N-glycan. In vitro folding experiments under reduced and redox conditions gave the desired two types of ubiquitinated glycosylated CCL1s, consisting of unfolded CCL1 and folded ubiquitin, and the folded form of both CCL1 as well as ubiquitin. We achieved the chemical synthesis of a complex protein molecule that contains not only the two major post-translational modifications, ubiquitination and glycosylation, but also controlled folding states of ubiquitin and CCL1. These chemical probes could have useful applications in the study of complex ubiquitin biology and glycobiology.
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Affiliation(s)
- Masayuki Izumi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.,Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, 2-5-1 Akebono-cho, Kochi, Kochi 780-8520, Japan
| | - Hiroyuki Araki
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Mamiko Tominaga
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Ryo Okamoto
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.,Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.,Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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11
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Ito Y, Kajihara Y, Takeda Y. Chemical‐Synthesis‐Based Approach to Glycoprotein Functions in the Endoplasmic Reticulum. Chemistry 2020; 26:15461-15470. [DOI: 10.1002/chem.202004158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Yukishige Ito
- Project Research Center for Fundamental Sciences Graduate School of Science Osaka University Toyonaka Osaka 5600043 Japan
- RIKEN Cluster for Pioneering Research Wako Saitama 3510198 Japan
| | - Yasuhiro Kajihara
- Project Research Center for Fundamental Sciences Graduate School of Science Osaka University Toyonaka Osaka 5600043 Japan
- Department of Chemistry Graduate School of Science Osaka University Toyonaka Osaka 5600043 Japan
| | - Yoichi Takeda
- Department of Biotechnology Ritsumeikan University Kusatsu Shiga 5258577 Japan
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12
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Abstract
The translation of biological glycosylation in humans to the clinical applications involves systematic studies using homogeneous samples of oligosaccharides and glycoconjugates, which could be accessed by chemical, enzymatic or other biological methods. However, the structural complexity and wide-range variations of glycans and their conjugates represent a major challenge in the synthesis of this class of biomolecules. To help navigate within many methods of oligosaccharide synthesis, this Perspective offers a critical assessment of the most promising synthetic strategies with an eye on the therapeutically relevant targets.
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Affiliation(s)
- Larissa Krasnova
- Department of Chemistry , The Scripps Research Institute , 10550 N. Torrey Pines Road , La Jolla , California 92037 , United States
| | - Chi-Huey Wong
- Department of Chemistry , The Scripps Research Institute , 10550 N. Torrey Pines Road , La Jolla , California 92037 , United States.,Genomics Research Center, Academia Sinica , Taipei 115 , Taiwan
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13
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Kiuchi T, Izumi M, Mukogawa Y, Shimada A, Okamoto R, Seko A, Sakono M, Takeda Y, Ito Y, Kajihara Y. Monitoring of Glycoprotein Quality Control System with a Series of Chemically Synthesized Homogeneous Native and Misfolded Glycoproteins. J Am Chem Soc 2018; 140:17499-17507. [DOI: 10.1021/jacs.8b08653] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Tatsuto Kiuchi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Masayuki Izumi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuki Mukogawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Arisa Shimada
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Ryo Okamoto
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Akira Seko
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masafumi Sakono
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoichi Takeda
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yukishige Ito
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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14
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Ito Y. Exploring Future Perspective of Glycochemistry by Japanese Researchers. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Satoh T, Kato K. Structural Aspects of ER Glycoprotein Quality-Control System Mediated by Glucose Tagging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1104:149-169. [PMID: 30484248 DOI: 10.1007/978-981-13-2158-0_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
N-linked oligosaccharides attached to proteins act as tags for glycoprotein quality control, ensuring their appropriate folding and trafficking in cells. Interactions with a variety of intracellular lectins determine glycoprotein fates. Monoglucosylated glycoforms are the hallmarks of incompletely folded glycoproteins in the protein quality-control system, in which glucosidase II and UDP-glucose/glycoprotein glucosyltransferase are, respectively, responsible for glucose trimming and attachment. In this review, we summarize a recently emerging view of the structural basis of the functional mechanisms of these key enzymes as well as substrate N-linked oligosaccharides exhibiting flexible structures, as revealed by applying a series of biophysical techniques including small-angle X-ray scattering, X-ray crystallography, high-speed atomic force microscopy , electron microscopy , and computational simulation in conjunction with NMR spectroscopy.
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Affiliation(s)
- Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan. .,Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
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16
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Satoh T, Song C, Zhu T, Toshimori T, Murata K, Hayashi Y, Kamikubo H, Uchihashi T, Kato K. Visualisation of a flexible modular structure of the ER folding-sensor enzyme UGGT. Sci Rep 2017; 7:12142. [PMID: 28939828 PMCID: PMC5610325 DOI: 10.1038/s41598-017-12283-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/06/2017] [Indexed: 01/11/2023] Open
Abstract
In the endoplasmic reticulum (ER), a protein quality control system facilitates the efficient folding of newly synthesised proteins. In this system, a series of N-linked glycan intermediates displayed on the protein surface serve as quality tags. The ER folding-sensor enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) acts as a gatekeeper in the ER quality control system by specifically catalysing monoglucosylation onto incompletely folded glycoproteins, thereby enabling them to interact with lectin-chaperone complexes. Here we characterise the dynamic structure of this enzyme. Our crystallographic data demonstrate that the sensor region is composed of four thioredoxin-like domains followed by a β-rich domain, which are arranged into a C-shaped structure with a large central cavity, while the C-terminal catalytic domain undergoes a ligand-dependent conformational alteration. Furthermore, small-angle X-ray scattering, cryo-electron microscopy and high-speed atomic force microscopy have demonstrated that UGGT has a flexible modular structure in which the smaller catalytic domain is tethered to the larger folding-sensor region with variable spatial arrangements. These findings provide structural insights into the working mechanism whereby UGGT operates as a folding-sensor against a variety of glycoprotein substrates through its flexible modular structure possessing extended hydrophobic surfaces for the recognition of unfolded substrates.
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Affiliation(s)
- Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.
- JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.
| | - Chihong Song
- National Institute for Physiological Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Tong Zhu
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
- Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- School of Physical Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Takayasu Toshimori
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Yugo Hayashi
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.
- Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
- School of Physical Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
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17
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Yang A, Cho K, Park HS. Chemical biology approaches for studying posttranslational modifications. RNA Biol 2017; 15:427-440. [PMID: 28901832 DOI: 10.1080/15476286.2017.1360468] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Posttranslational modification (PTM) is a key mechanism for regulating diverse protein functions, and thus critically affects many essential biological processes. Critical for systematic study of the effects of PTMs is the ability to obtain recombinant proteins with defined and homogenous modifications. To this end, various synthetic and chemical biology approaches, including genetic code expansion and protein chemical modification methods, have been developed. These methods have proven effective for generating site-specific authentic modifications or structural mimics, and have demonstrated their value for in vitro and in vivo functional studies of diverse PTMs. This review will discuss recent advances in chemical biology strategies and their application to various PTM studies.
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Affiliation(s)
- Aerin Yang
- a Department of Chemistry , Korea Advanced Institute of Science and Technology , 291 Daehak-ro, Yuseong-gu , Daejeon , Republic of Korea
| | - Kyukwang Cho
- a Department of Chemistry , Korea Advanced Institute of Science and Technology , 291 Daehak-ro, Yuseong-gu , Daejeon , Republic of Korea
| | - Hee-Sung Park
- a Department of Chemistry , Korea Advanced Institute of Science and Technology , 291 Daehak-ro, Yuseong-gu , Daejeon , Republic of Korea
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18
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Izumi M, Kuruma R, Okamoto R, Seko A, Ito Y, Kajihara Y. Substrate Recognition of Glycoprotein Folding Sensor UGGT Analyzed by Site-Specifically 15N-Labeled Glycopeptide and Small Glycopeptide Library Prepared by Parallel Native Chemical Ligation. J Am Chem Soc 2017; 139:11421-11426. [DOI: 10.1021/jacs.7b03277] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Masayuki Izumi
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Rie Kuruma
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Ryo Okamoto
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Akira Seko
- ERATO
Ito glycotrilogy project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yukishige Ito
- ERATO
Ito glycotrilogy project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Synthetic
Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasuhiro Kajihara
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- ERATO
Ito glycotrilogy project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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19
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Calles-Garcia D, Yang M, Soya N, Melero R, Ménade M, Ito Y, Vargas J, Lukacs GL, Kollman JM, Kozlov G, Gehring K. Single-particle electron microscopy structure of UDP-glucose:glycoprotein glucosyltransferase suggests a selectivity mechanism for misfolded proteins. J Biol Chem 2017; 292:11499-11507. [PMID: 28490633 DOI: 10.1074/jbc.m117.789495] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/07/2017] [Indexed: 11/06/2022] Open
Abstract
The enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) mediates quality control of glycoproteins in the endoplasmic reticulum by attaching glucose to N-linked glycan of misfolded proteins. As a sensor, UGGT ensures that misfolded proteins are recognized by the lectin chaperones and do not leave the secretory pathway. The structure of UGGT and the mechanism of its selectivity for misfolded proteins have been unknown for 25 years. Here, we used negative-stain electron microscopy and small-angle X-ray scattering to determine the structure of UGGT from Drosophila melanogaster at 18-Å resolution. Three-dimensional reconstructions revealed a cage-like structure with a large central cavity. Particle classification revealed flexibility that precluded determination of a high-resolution structure. Introduction of biotinylation sites into a fungal UGGT expressed in Escherichia coli allowed identification of the catalytic and first thioredoxin-like domains. We also used hydrogen-deuterium exchange mass spectrometry to map the binding site of an accessory protein, Sep15, to the first thioredoxin-like domain. The UGGT structural features identified suggest that the central cavity contains the catalytic site and is lined with hydrophobic surfaces. This enhances the binding of misfolded substrates with exposed hydrophobic residues and excludes folded proteins with hydrophilic surfaces. In conclusion, we have determined the UGGT structure, which enabled us to develop a plausible functional model of the mechanism for UGGT's selectivity for misfolded glycoproteins.
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Affiliation(s)
- Daniel Calles-Garcia
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada
| | - Meng Yang
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada
| | - Naoto Soya
- Department of Physiology, McGill University, Montreal, Quebec H3G1Y6, Canada
| | - Roberto Melero
- Biocomputing Unit, Centro Nacional de Biotectnologíay, 28049 Madrid, Spain
| | - Marie Ménade
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada
| | - Yukishige Ito
- Synthetic Cellular Chemistry Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Javier Vargas
- Biocomputing Unit, Centro Nacional de Biotectnologíay, 28049 Madrid, Spain.,Bioengineering Lab, Escuela Politécnica Superior, Universidad San Pablo CEU, 28668 Madrid, Spain, and
| | - Gergely L Lukacs
- Department of Physiology, McGill University, Montreal, Quebec H3G1Y6, Canada
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350
| | - Guennadi Kozlov
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada
| | - Kalle Gehring
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada,
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20
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Minh Hien N, Izumi M, Sato H, Okamoto R, Kajihara Y. Chemical Synthesis of Glycoproteins with the Specific Installation of Gradient-Enriched 15
N-Labeled Amino Acids for Getting Insights into Glycoprotein Behavior. Chemistry 2017; 23:6579-6585. [DOI: 10.1002/chem.201606049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Nguyen Minh Hien
- Deprtment of Chemistry; Osaka University; 1-1, Machikaneyama Toyonaka 560-0043 Japan
- Current address: Department of Chemistry; Da Nang University of Education; the University of Da Nang; Vietnam
| | - Masayuki Izumi
- Deprtment of Chemistry; Osaka University; 1-1, Machikaneyama Toyonaka 560-0043 Japan
| | - Hajime Sato
- Bruker BioSpin K.K.; 3-9, Moriya-cho Kanagawa-ku, Yokohama, Kanagawa
| | - Ryo Okamoto
- Deprtment of Chemistry; Osaka University; 1-1, Machikaneyama Toyonaka 560-0043 Japan
| | - Yasuhiro Kajihara
- Deprtment of Chemistry; Osaka University; 1-1, Machikaneyama Toyonaka 560-0043 Japan
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21
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Song Q, Wu Z, Fan Y, Song W, Zhang P, Wang L, Wang F, Xu Y, Wang PG, Cheng J. Production of homogeneous glycoprotein with multisite modifications by an engineered N-glycosyltransferase mutant. J Biol Chem 2017; 292:8856-8863. [PMID: 28381551 DOI: 10.1074/jbc.m117.777383] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/04/2017] [Indexed: 12/26/2022] Open
Abstract
Naturally occurring N-glycoproteins exhibit glycoform heterogeneity with respect to N-glycan sequon occupancy (macroheterogeneity) and glycan structure (microheterogeneity). However, access to well-defined glycoproteins is always important for both basic research and therapeutic purposes. As a result, there has been a substantial effort to identify and understand the catalytic properties of N-glycosyltransferases, enzymes that install the first glycan on the protein chain. In this study we found that ApNGT, a newly discovered cytoplasmic N-glycosyltransferase from Actinobacillus pleuropneumoniae, has strict selectivity toward the residues around the Asn of N-glycosylation sequon by screening a small library of synthetic peptides. The inherent stringency was subsequently demonstrated to be closely associated with a critical residue (Gln-469) of ApNGT which we propose hinders the access of bulky residues surrounding the occupied Asn into the active site. Site-saturated mutagenesis revealed that the introduction of small hydrophobic residues at the site cannot only weaken the stringency of ApNGT but can also contribute to enormous improvement of glycosylation efficiency against both short peptides and proteins. We then employed the most efficient mutant (Q469A) other than the wild-type ApNGT to produce a homogeneous glycoprotein carrying multiple (up to 10) N-glycans, demonstrating that this construct is a promising biocatalyst for potentially addressing the issue of macroheterogeneity in glycoprotein preparation.
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Affiliation(s)
- Qitao Song
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Zhigang Wu
- the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Yueyuan Fan
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Woran Song
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Peiru Zhang
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Li Wang
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Faxing Wang
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Yangyang Xu
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Peng G Wang
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
| | - Jiansong Cheng
- From the State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China and
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22
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Hachisu M, Ito Y. Chemical Approaches to Elucidate Enzymatic Profiles of UDP-Glucose: Glycoprotein Glucosyltransferase. Chem Pharm Bull (Tokyo) 2017; 64:687-90. [PMID: 27373624 DOI: 10.1248/cpb.c16-00209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the endoplasmic reticulum (ER), uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferase 1 (UGGT1) recognizes misfolded glycoproteins and transfers a glucose residue to the specific non-reducing end of high-mannose-type glycans. However, precise molecular mechanism by which UGGT1 senses the folding has not been understood clearly. To address this issue, various model substrates for UGGT1 have been prepared using biological approaches. Recently, we introduced chemical approaches using synthetic glycan probes that were designed for studying N-glycan processing in the ER and Golgi apparatus. Our approach can outfit the homogeneous and functionalized glycan probes. In this review, recent results on functional analysis of UGGT1 are summarized.
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Affiliation(s)
- Masakazu Hachisu
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST)
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23
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Corsini S, Tortora M, Nistri A. Nicotinic receptor activation contrasts pathophysiological bursting and neurodegeneration evoked by glutamate uptake block on rat hypoglossal motoneurons. J Physiol 2016; 594:6777-6798. [PMID: 27374167 PMCID: PMC5108918 DOI: 10.1113/jp272591] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/21/2016] [Indexed: 12/11/2022] Open
Abstract
KEY POINTS Impaired uptake of glutamate builds up the extracellular level of this excitatory transmitter to trigger rhythmic neuronal bursting and delayed cell death in the brainstem motor nucleus hypoglossus. This process is the expression of the excitotoxicity that underlies motoneuron degeneration in diseases such as amyotrophic lateral sclerosis affecting bulbar motoneurons. In a model of motoneuron excitotoxicity produced by pharmacological block of glutamate uptake in vitro, rhythmic bursting is suppressed by activation of neuronal nicotinic receptors with their conventional agonist nicotine. Emergence of bursting is facilitated by nicotinic receptor antagonists. Following excitotoxicity, nicotinic receptor activity decreases mitochondrial energy dysfunction, endoplasmic reticulum stress and production of toxic radicals. Globally, these phenomena synergize to provide motoneuron protection. Nicotinic receptors may represent a novel target to contrast pathological overactivity of brainstem motoneurons and therefore to prevent their metabolic distress and death. ABSTRACT Excitotoxicity is thought to be one of the early processes in the onset of amyotrophic lateral sclerosis (ALS) because high levels of glutamate have been detected in the cerebrospinal fluid of such patients due to dysfunctional uptake of this transmitter that gradually damages brainstem and spinal motoneurons. To explore potential mechanisms to arrest ALS onset, we used an established in vitro model of rat brainstem slice preparation in which excitotoxicity is induced by the glutamate uptake blocker dl-threo-β-benzyloxyaspartate (TBOA). Because certain brain neurons may be neuroprotected via activation of nicotinic acetylcholine receptors (nAChRs) by nicotine, we investigated if nicotine could arrest excitotoxic damage to highly ALS-vulnerable hypoglossal motoneurons (HMs). On 50% of patch-clamped HMs, TBOA induced intense network bursts that were inhibited by 1-10 μm nicotine, whereas nAChR antagonists facilitated burst emergence in non-burster cells. Furthermore, nicotine inhibited excitatory transmission and enhanced synaptic inhibition. Strong neuroprotection by nicotine prevented the HM loss observed after 4 h of TBOA exposure. This neuroprotective action was due to suppression of downstream effectors of neurotoxicity such as increased intracellular levels of reactive oxygen species, impaired energy metabolism and upregulated genes involved in endoplasmic reticulum (ER) stress. In addition, HMs surviving TBOA toxicity often expressed UDP-glucose glycoprotein glucosyltransferase, a key element in repair of misfolded proteins: this phenomenon was absent after nicotine application, indicative of ER stress prevention. Our results suggest nAChRs to be potential targets for inhibiting excitotoxic damage of motoneurons at an early stage of the neurodegenerative process.
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Affiliation(s)
- Silvia Corsini
- Department of NeuroscienceInternational School for Advanced Studies (SISSA)TriesteItaly
| | - Maria Tortora
- Department of NeuroscienceInternational School for Advanced Studies (SISSA)TriesteItaly
| | - Andrea Nistri
- Department of NeuroscienceInternational School for Advanced Studies (SISSA)TriesteItaly
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24
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Chuh KN, Batt AR, Pratt MR. Chemical Methods for Encoding and Decoding of Posttranslational Modifications. Cell Chem Biol 2016; 23:86-107. [PMID: 26933738 DOI: 10.1016/j.chembiol.2015.11.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/25/2015] [Accepted: 11/25/2015] [Indexed: 12/13/2022]
Abstract
A large array of posttranslational modifications can dramatically change the properties of proteins and influence different aspects of their biological function such as enzymatic activity, binding interactions, and proteostasis. Despite the significant knowledge that has been gained about the function of posttranslational modifications using traditional biological techniques, the analysis of the site-specific effects of a particular modification, the identification of the full complement of modified proteins in the proteome, and the detection of new types of modifications remains challenging. Over the years, chemical methods have contributed significantly in both of these areas of research. This review highlights several posttranslational modifications where chemistry-based approaches have made significant contributions to our ability to both prepare homogeneously modified proteins and identify and characterize particular modifications in complex biological settings. As the number and chemical diversity of documented posttranslational modifications continues to rise, we believe that chemical strategies will be essential to advance the field in years to come.
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Affiliation(s)
- Kelly N Chuh
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Anna R Batt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
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25
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Takeda Y, Seko A, Fujikawa K, Izumi M, Kajihara Y, Ito Y. Effects of domain composition on catalytic activity of human UDP-glucose:glycoprotein glucosyltransferases. Glycobiology 2016; 26:999-1006. [DOI: 10.1093/glycob/cww069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 06/21/2016] [Indexed: 12/11/2022] Open
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26
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Izumi M, Komaki S, Okamoto R, Seko A, Takeda Y, Ito Y, Kajihara Y. Synthesis of misfolded glycoprotein dimers through native chemical ligation of a dimeric peptide thioester. Org Biomol Chem 2016; 14:6088-94. [PMID: 27248046 DOI: 10.1039/c6ob00928j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glycoprotein quality control processes are very important for an efficient production of glycoproteins and for avoiding the accumulation of unwanted toxic species in cells. These complex processes consist of multiple enzymes and chaperones such as UGGT, calnexin/calreticulin, and glucosidase II. We designed and synthesized monomeric and dimeric misfolded glycoprotein probes. Synthetic homogeneous monomeric glycoproteins proved to be useful substrates for kinetic analyses of the folding sensor enzyme UGGT. For a concise synthesis of a bismaleimide-linked dimer, we examined double native chemical ligation (dNCL) of a dimeric peptide-α-thioester. The dNCL to two equivalents of glycopeptides gave a homodimer. The dNCL to a 1 : 1 mixture of a glycopeptide and a non-glycosylated peptide gave all the three possible ligation products consisting of two homodimers and a heterodimer. Both the homodimer bearing two Man9GlcNAc2 (M9) oligosaccharides and the heterodimer bearing one M9 oligosaccharide were found to be good substrates of UGGT.
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Affiliation(s)
- Masayuki Izumi
- Department of Chemistry, Graduate School of Science, Osaka Univeristy, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
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27
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Kajihara Y. Studies on the Precise Chemical Synthesis of Human Glycoproteins. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20150275] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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28
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Izumi M, Oka Y, Okamoto R, Seko A, Takeda Y, Ito Y, Kajihara Y. Synthesis of Glc1
Man9
-Glycoprotein Probes by a Misfolding/Enzymatic Glucosylation/Misfolding Sequence. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511491] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Masayuki Izumi
- Department of Chemistry; Graduate School of Science; Osaka University; 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Yukiho Oka
- Department of Chemistry; Graduate School of Science; Osaka University; 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Ryo Okamoto
- Department of Chemistry; Graduate School of Science; Osaka University; 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Akira Seko
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST); 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Yoichi Takeda
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST); 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Yukishige Ito
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST); 2-1 Hirosawa, Wako Saitama 351-0198 Japan
- Synthetic Cellular Chemistry Laboratory; RIKEN; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Yasuhiro Kajihara
- Department of Chemistry; Graduate School of Science; Osaka University; 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST); 2-1 Hirosawa, Wako Saitama 351-0198 Japan
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29
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Izumi M, Oka Y, Okamoto R, Seko A, Takeda Y, Ito Y, Kajihara Y. Synthesis of Glc1Man9-Glycoprotein Probes by a Misfolding/Enzymatic Glucosylation/Misfolding Sequence. Angew Chem Int Ed Engl 2016; 55:3968-71. [PMID: 26890995 DOI: 10.1002/anie.201511491] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Indexed: 12/12/2022]
Abstract
Glycoproteins in non-native conformations are often toxic to cells and may cause diseases, thus the quality control (QC) system eliminates these unwanted species. Lectin chaperone calreticulin and glucosidase II, both of which recognize the Glc1 Man9 oligosaccharide on glycoproteins, are important components of the glycoprotein QC system. Reported herein is the preparation of Glc1 Man9 -glycoproteins in both native and non-native conformations by using the following sequence: misfolding of chemically synthesized Man9 -glycoprotein, enzymatic glucosylation, and another misfolding step. By using synthetic glycoprotein probes, calreticulin was found to bind preferentially to a hydrophobic non-native glycoprotein whereas glucosidase II activity was not affected by glycoprotein conformation. The results demonstrate the ability of chemical synthesis to deliver homogeneous glycoproteins in several non-native conformations for probing the glycoprotein QC system.
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Affiliation(s)
- Masayuki Izumi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yukiho Oka
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Ryo Okamoto
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Akira Seko
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoichi Takeda
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yukishige Ito
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan. .,ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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30
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Hachisu M, Seko A, Daikoku S, Takeda Y, Sakono M, Ito Y. Hydrophobic Tagged Dihydrofolate Reductase for Creating Misfolded Glycoprotein Mimetics. Chembiochem 2016; 17:300-3. [PMID: 26670196 DOI: 10.1002/cbic.201500595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Indexed: 12/18/2022]
Abstract
In the endoplasmic reticulum (ER), nascent glycoproteins that have not acquired the native conformation are either repaired or sorted for degradation by specific quality-control systems composed by various proteins. Among them, UDP-glucose:glycoprotein glucosyltransferase (UGGT) serves as a folding sensor in the ER. However, the molecular mechanism of its recognition remains obscure. This study used pseudo-misfolded glycoproteins, comprising a modified dihydrofolate reductase with artificial pyrene-cysteine moiety on the protein surface (pDHFR) and Man9 GlcNAc2 -methotrexate (M9-MTX). All five M9-MTX/pDHFR complexes, with a pyrene group at different positions, were found to be good substrates of UGGT, irrespective of the site of pyrene modification. These results suggest UGGT's mode of substrate recognition is fuzzy, thus allowing various glycoproteins to be accommodated in the folding cycle.
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Affiliation(s)
- Masakazu Hachisu
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Akira Seko
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shusaku Daikoku
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoichi Takeda
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Department of Biotechnology, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan.
| | - Masafumi Sakono
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Department of Applied Chemistry, University of Toyama, 3190 Gofuku, Toyama, Toyama, 930-855, Japan
| | - Yukishige Ito
- ERATO Ito Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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31
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32
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Murakami M, Kiuchi T, Nishihara M, Tezuka K, Okamoto R, Izumi M, Kajihara Y. Chemical synthesis of erythropoietin glycoforms for insights into the relationship between glycosylation pattern and bioactivity. SCIENCE ADVANCES 2016; 2:e1500678. [PMID: 26824070 PMCID: PMC4730857 DOI: 10.1126/sciadv.1500678] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 11/06/2015] [Indexed: 05/28/2023]
Abstract
The role of sialyloligosaccharides on the surface of secreted glycoproteins is still unclear because of the difficulty in the preparation of sialylglycoproteins in a homogeneous form. We selected erythropoietin (EPO) as a target molecule and designed an efficient synthetic strategy for the chemical synthesis of a homogeneous form of five EPO glycoforms varying in glycosylation position and the number of human-type biantennary sialyloligosaccharides. A segment coupling strategy performed by native chemical ligation using six peptide segments including glycopeptides yielded homogeneous EPO glycopeptides, and folding experiments of these glycopeptides afforded the correctly folded EPO glycoforms. In an in vivo erythropoiesis assay in mice, all of the EPO glycoforms displayed biological activity, in particular the EPO bearing three sialyloligosaccharides, which exhibited the highest activity. Furthermore, we observed that the hydrophilicity and biological activity of the EPO glycoforms varied depending on the glycosylation pattern. This knowledge will pave the way for the development of homogeneous biologics by chemical synthesis.
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Affiliation(s)
- Masumi Murakami
- Department of Chemistry, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 5460-0043, Japan
| | - Tatsuto Kiuchi
- Department of Chemistry, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 5460-0043, Japan
| | - Mika Nishihara
- Glytech Inc., 134, Chudoji, Minamimachi KRP#1-109, Shimogyo-ku, Kyoto 600-8813, Japan
| | - Katsunari Tezuka
- Glytech Inc., 134, Chudoji, Minamimachi KRP#1-109, Shimogyo-ku, Kyoto 600-8813, Japan
| | - Ryo Okamoto
- Department of Chemistry, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 5460-0043, Japan
| | - Masayuki Izumi
- Department of Chemistry, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 5460-0043, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 5460-0043, Japan
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33
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Zhu T, Yamaguchi T, Satoh T, Kato K. A Hybrid Strategy for the Preparation of 13C-labeled High-mannose-type Oligosaccharides with Terminal Glucosylation for NMR Study. CHEM LETT 2015. [DOI: 10.1246/cl.150898] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tong Zhu
- School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies)
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Takumi Yamaguchi
- School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies)
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- JST, PRESTO
| | - Koichi Kato
- School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies)
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- Medical and Biological Laboratories Co., Ltd
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34
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Ohara K, Takeda Y, Daikoku S, Hachisu M, Seko A, Ito Y. Profiling Aglycon-Recognizing Sites of UDP-glucose:glycoprotein Glucosyltransferase by Means of Squarate-Mediated Labeling. Biochemistry 2015. [PMID: 26196150 DOI: 10.1021/acs.biochem.5b00785] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Because of its ability to selectively glucosylate misfolded glycoproteins, UDP-glucose:glycoprotein glucosyltransferase (UGGT) functions as a folding sensor in the glycoprotein quality control system in the endoplasmic reticulum (ER). The unique property of UGGT derives from its ability to transfer a glucose residue to N-glycan moieties of incompletely folded glycoproteins. We have previously discovered nonproteinic synthetic substrates of this enzyme, allowing us to conduct its high-sensitivity assay in a quantitative manner. In this study, we aimed to conduct site-selective affinity labeling of UGGT using a functionalized oligosaccharide probe to identify domain(s) responsible for recognition of the aglycon moiety of substrates. To this end, a probe 1 was designed to selectively label nucleophilic amino acid residues in the proximity of the canonical aglycon-recognizing site of human UGGT1 (HUGT1) via squaramide formation. As expected, probe 1 was able to label HUGT1 in the presence of UDP. Analysis by nano-LC-ESI/MS(n) identified a unique lysine residue (K1424) that was modified by 1. Kyte-Doolittle analysis as well as homology modeling revealed a cluster of hydrophobic amino acids that may be functional in the folding sensing mechanism of HUGT1.
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Affiliation(s)
- Keiichiro Ohara
- †Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoichi Takeda
- †Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shusaku Daikoku
- †Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masakazu Hachisu
- †Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akira Seko
- †Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yukishige Ito
- †Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,‡RIKEN, Synthetic Cellular Chemistry Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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35
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Caramelo JJ, Parodi AJ. A sweet code for glycoprotein folding. FEBS Lett 2015; 589:3379-87. [PMID: 26226420 DOI: 10.1016/j.febslet.2015.07.021] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/15/2015] [Accepted: 07/15/2015] [Indexed: 12/11/2022]
Abstract
Glycoprotein synthesis is initiated in the endoplasmic reticulum (ER) lumen upon transfer of a glycan (Glc3Man9GlcNAc2) from a lipid derivative to Asn residues (N-glycosylation). N-Glycan-dependent quality control of glycoprotein folding in the ER prevents exit to Golgi of folding intermediates, irreparably misfolded glycoproteins and incompletely assembled multimeric complexes. It also enhances folding efficiency by preventing aggregation and facilitating formation of proper disulfide bonds. The control mechanism essentially involves four components, resident lectin-chaperones (calnexin and calreticulin) that recognize monoglucosylated polymannose protein-linked glycans, lectin-associated oxidoreductase acting on monoglucosylated glycoproteins (ERp57), a glucosyltransferase that creates monoglucosylated epitopes in protein-linked glycans (UGGT) and a glucosidase (GII) that removes the glucose units added by UGGT. This last enzyme is the only mechanism component sensing glycoprotein conformations as it creates monoglucosylated glycans exclusively in not properly folded glycoproteins or in not completely assembled multimeric glycoprotein complexes. Glycoproteins that fail to properly fold are eventually driven to proteasomal degradation in the cytosol following the ER-associated degradation pathway, in which the extent of N-glycan demannosylation by ER mannosidases play a relevant role in the identification of irreparably misfolded glycoproteins.
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Affiliation(s)
- Julio J Caramelo
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avda. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina.
| | - Armando J Parodi
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avda. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina.
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36
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Wang N, Seko A, Takeda Y, Kikuma T, Ito Y. Cooperative role of calnexin and TigA in Aspergillus oryzae glycoprotein folding. Glycobiology 2015; 25:1090-9. [PMID: 26085184 DOI: 10.1093/glycob/cwv043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/14/2015] [Indexed: 12/15/2022] Open
Abstract
Calnexin (CNX), known as a lectin chaperone located in the endoplasmic reticulum (ER), specifically recognizes G1M9GN2-proteins and facilitates their proper folding with the assistance of ERp57 in mammalian cells. However, it has been left unidentified how CNX works in Aspergillus oryzae, which is a filamentous fungus widely exploited in biotechnology. In this study, we found that a protein disulfide isomerase homolog TigA can bind with A. oryzae CNX (AoCNX), which was revealed to specifically recognize monoglucosylated glycans, similarly to CNX derived from other species, and accelerate the folding of G1M9GN2-ribonuclease (RNase) in vitro. For refolding experiments, a homogeneous monoglucosylated high-mannose-type glycoprotein G1M9GN2-RNase was chemoenzymatically synthesized from G1M9GN-oxazoline and GN-RNase. Denatured G1M9GN2-RNase was refolded with highest efficiency in the presence of both soluble form of AoCNX and TigA. TigA contains two thioredoxin domains with CGHC motif, mutation analysis of which revealed that the one in N-terminal regions is involved in binding to AoCNX, while the other in catalyzing protein refolding. The results suggested that in glycoprotein folding process of A. oryzae, TigA plays a similar role as ERp57 in mammalian cells, as a partner protein of AoCNX.
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Affiliation(s)
- Ning Wang
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akira Seko
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoichi Takeda
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takashi Kikuma
- Department of Biotechnology, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yukishige Ito
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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37
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Preparation of asparagine-linked monoglucosylated high-mannose-type oligosaccharide from egg yolk. Carbohydr Res 2015; 411:37-41. [DOI: 10.1016/j.carres.2015.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 11/18/2022]
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38
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Functional analysis of endoplasmic reticulum glucosyltransferase (UGGT): Synthetic chemistry's initiative in glycobiology. Semin Cell Dev Biol 2015; 41:90-8. [DOI: 10.1016/j.semcdb.2014.11.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/28/2014] [Accepted: 11/28/2014] [Indexed: 01/03/2023]
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39
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Izumi M, Dedola S, Ito Y, Kajihara Y. Chemical Synthesis of Homogeneous Glycoproteins for the Study of Glycoprotein Quality Control System. Isr J Chem 2015. [DOI: 10.1002/ijch.201400154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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40
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Wang LX, Amin MN. Chemical and chemoenzymatic synthesis of glycoproteins for deciphering functions. ACTA ACUST UNITED AC 2015; 21:51-66. [PMID: 24439206 DOI: 10.1016/j.chembiol.2014.01.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 12/31/2013] [Accepted: 01/02/2014] [Indexed: 12/11/2022]
Abstract
Glycoproteins are an important class of biomolecules involved in a number of biological recognition processes. However, natural and recombinant glycoproteins are usually produced as mixtures of glycoforms that differ in the structures of the pendent glycans, which are difficult to separate in pure glycoforms. As a result, synthetic homogeneous glycopeptides and glycoproteins have become indispensable probes for detailed structural and functional studies. A number of elegant chemical and biological strategies have been developed for synthetic construction of tailor-made, full-size glycoproteins to address specific biological problems. In this review, we highlight recent advances in chemical and chemoenzymatic synthesis of homogeneous glycoproteins. Selected examples are given to demonstrate the applications of tailor-made, glycan-defined glycoproteins for deciphering glycosylation functions.
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Affiliation(s)
- Lai-Xi Wang
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Mohammed N Amin
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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41
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Glycopeptide probes for understanding peptide specificity of the folding sensor enzyme UGGT. Bioorg Med Chem Lett 2014; 24:5563-5567. [DOI: 10.1016/j.bmcl.2014.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/01/2014] [Accepted: 11/04/2014] [Indexed: 12/22/2022]
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42
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Program Overview * Conference Program * Conference Posters * Conference Abstracts. Glycobiology 2014. [DOI: 10.1093/glycob/cwu087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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43
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Okamoto R, Izumi M, Kajihara Y. Decoration of proteins with sugar chains: recent advances in glycoprotein synthesis. Curr Opin Chem Biol 2014; 22:92-9. [DOI: 10.1016/j.cbpa.2014.09.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/20/2014] [Accepted: 09/22/2014] [Indexed: 12/19/2022]
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44
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Zheng JS, Chen X, Tang S, Chang HN, Wang FL, Zuo C. A New Method for Synthesis of Peptide Thioesters via Irreversible N-to-S Acyl Transfer. Org Lett 2014; 16:4908-11. [DOI: 10.1021/ol5024213] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ji-Shen Zheng
- High
Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
- Department
of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xin Chen
- Tsinghua-Peking
Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shan Tang
- Tsinghua-Peking
Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Department
of Chemistry, Tsinghua University, Beijing 100084, China
| | - Hao-Nan Chang
- Department
of Chemistry, Tsinghua University, Beijing 100084, China
| | - Feng-Liang Wang
- Department
of Chemistry, Tsinghua University, Beijing 100084, China
| | - Chao Zuo
- Department
of Chemistry, Tsinghua University, Beijing 100084, China
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45
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Brunschweiger A. Report from the Third Annual Symposium of the RIKEN-Max Planck Joint Research Center for Systems Chemical Biology. ACS Chem Biol 2014; 9:1649-52. [PMID: 25123304 DOI: 10.1021/cb500579u] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The third Annual Symposium of the RIKEN-Max Planck Joint Research Center for Systems Chemical Biology was held at Ringberg castle, May 21-24, 2014. At this meeting 45 scientists from Japan and Germany presented the latest results from their research spanning a broad range of topics in chemical biology and glycobiology.
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Affiliation(s)
- Andreas Brunschweiger
- Fakultät
Chemie - Chemische
Biologie, Technische Universität Dortmund, Otto-Hahn-Str.
6, 44227 Dortmund, Germany
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46
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Kamiya Y, Satoh T, Kato K. Recent advances in glycoprotein production for structural biology: toward tailored design of glycoforms. Curr Opin Struct Biol 2014; 26:44-53. [PMID: 24841384 DOI: 10.1016/j.sbi.2014.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 03/20/2014] [Accepted: 03/25/2014] [Indexed: 01/01/2023]
Abstract
Because of the complexity, heterogeneity, and flexibility of the glycans, the structural analysis of glycoproteins has been eschewed until recently, with a few prominent exceptions. This aversion may have branded structural biologists as glycophobics. However, recent technological advancements in glycoprotein expression systems, employing genetically engineered production vehicles derived from mammalian, insect, yeast, and even bacterial cells, have yielded encouraging breakthroughs. The major advance is the active control of glycoform expression of target glycoproteins based on the genetic manipulation of glycan biogenetic pathways, which was previously overlooked, abolished, or considered unmanageable. Moreover, synthetic and/or chemoenzymatic approaches now enable the preparation of glycoproteins with uniform glycoforms designed in a tailored fashion.
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Affiliation(s)
- Yukiko Kamiya
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; The Glycoscience Institute, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan; GLYENCE Co., Ltd., 2-22-8 Chikusa, Chikusa-ku, Nagoya 464-0858, Japan.
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47
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Aikawa JI, Takeda Y, Matsuo I, Ito Y. Trimming of glucosylated N-glycans by human ER α1,2-mannosidase I. ACTA ACUST UNITED AC 2014; 155:375-84. [DOI: 10.1093/jb/mvu008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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48
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Dedola S, Izumi M, Makimura Y, Seko A, Kanamori A, Sakono M, Ito Y, Kajihara Y. Folding of Synthetic Homogeneous Glycoproteins in the Presence of a Glycoprotein Folding Sensor Enzyme. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309665] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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49
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Dedola S, Izumi M, Makimura Y, Seko A, Kanamori A, Sakono M, Ito Y, Kajihara Y. Folding of synthetic homogeneous glycoproteins in the presence of a glycoprotein folding sensor enzyme. Angew Chem Int Ed Engl 2014; 53:2883-7. [PMID: 24500819 DOI: 10.1002/anie.201309665] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 12/20/2013] [Indexed: 11/09/2022]
Abstract
UDP-glucose:glycoprotein glucosyltransferase (UGGT) plays a key role in recognizing folded and misfolded glycoproteins in the glycoprotein quality control system of the endoplasmic reticulum. UGGT detects misfolded glycoproteins and re-glucosylates them as a tag for misfolded glycoproteins. A flexible model to reproduce in vitro folding of a glycoprotein in the presence of UGGT in a mixture containing correctly folded, folding intermediates, and misfolded glycoproteins is described. The data demonstrates that UGGT can re-glucosylate all intermediates in the in vitro folding experiments, thus indicating that UGGT inspects not only final folded products, but also the glycoprotein folding intermediates.
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Affiliation(s)
- Simone Dedola
- Department of Chemistry, Graduate School of Science, Institution Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043 (Japan); Institution Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama, 351-0198 (Japan)
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50
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Limtipsuntorn U, Haga Y, Kondo H, Hirono I, Satoh S. Microarray analysis of hepatic gene expression in juvenile Japanese flounder Paralichthys olivaceus fed diets supplemented with fish or vegetable oils. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:88-102. [PMID: 24052493 DOI: 10.1007/s10126-013-9535-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 07/15/2013] [Indexed: 05/25/2023]
Abstract
Gene expression profiling was performed in Japanese flounder Paralichthys olivaceus fed diets supplemented with fish oil (FO), linseed oil (LO), or olive oil (OO) for 6 weeks. The LO and OO groups showed significantly retarded growth, lower feed intake, lower protein efficiency ratio, and lower hepatosomatic index (P < 0.05). Liver fatty acid composition reflected the dietary fatty acid composition. Microarray analysis revealed that dietary n - 3 highly unsaturated fatty acid (HUFA) deficiency affected 169 transcripts. In the LO group, 57 genes were up-regulated and 38 genes were down-regulated, whereas in the OO group nine genes were up-regulated and 87 genes were down-regulated. Analysis of the functional annotations suggested that dietary n - 3 HUFA affected genes involved in signal transduction (23.2 %), cellular processes (21.1 %), metabolism (including glucose, lipid, and nucleobase; 15.5 %), transport (11.3 %), regulation of transcription (10.5 %), and immune response (4.2 %). Several genes encoding serine/threonine kinases such as protein kinase C and calmodulin-dependent kinase and nuclear hormone receptors such as vitamin D receptor, retinoic acid receptor, and receptors for cytokines (bone morphogenic protein and transforming growth factor β) were affected. Among 169 transcripts, 22 genes were affected in both LO and OO groups. The present study identified several genes involved in n - 3 HUFA deficiency-sensitive pathways, which will be useful for selective breeding of flounder strains able to adapt to n - 3 HUFA deficiency.
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Affiliation(s)
- Ubonrat Limtipsuntorn
- Department of Marine Bioscience, Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan, Minato 4-5-7, Tokyo, 108-8477, Japan
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