1
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Ishiwata A, Narita S, Kimura K, Tanaka K, Fujita K, Fushinobu S, Ito Y. Mechanism-based inhibition of GH127/146 cysteine glycosidases by stereospecifically functionalized l-arabinofuranosides. Bioorg Med Chem 2022; 75:117054. [PMID: 36334492 DOI: 10.1016/j.bmc.2022.117054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022]
Abstract
To understand the precise mechanism of the glycoside hydrolase (GH) family 127, a cysteine β-l-arabinofuranosidase (Arafase) - HypBA1 - has been isolated from Bifidobacterium longum in the human Gut microbiota, and the design and synthesis of the mechanism-based inhibitors such as l-Araf-haloacetamides have been carried out. The α-l-Araf-azide derivative was used as the monoglycosylamine equivalent to afford the l-Araf-chloroacetamides (α/β-1-Cl) as well as bromoacetamides (α/β-1-Br) in highly stereoselective manner through Staudinger reaction followed by amide formation with/without anomerization. Against HypBA1, the probes 1, especially in the case of α/β-1-Br inhibited the hydrolysis. Conformational implications of these observations are discussed in this manuscript. Additional examinations using l-Araf-azides (α/β-5) resulted in further mechanistic observations of the GH127/146 cysteine glycosidases, including the hydrolysis of β-5 as the substrate and oxidative inhibition by α-5 using the GH127 homologue.
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Affiliation(s)
- Akihiro Ishiwata
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan.
| | - Satoru Narita
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Graduate School of Systems Engineering and Science, Shibaura Institute of Technology Saitama 337-8570, Japan
| | - Kenta Kimura
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Graduate School of Systems Engineering and Science, Shibaura Institute of Technology Saitama 337-8570, Japan
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Department of Chemical Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo 113-8647, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8647, Japan
| | - Yukishige Ito
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
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2
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Maruyama S, Sawano K, Amaki S, Suzuki T, Narita S, Kimura K, Arakawa T, Yamada C, Ito Y, Dohmae N, Fujita K, Ishiwata A, Fushinobu S. Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase. Glycobiology 2021; 32:171-180. [PMID: 34735571 DOI: 10.1093/glycob/cwab103] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 09/16/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
β-l-Arabinofuranosidase HypBA1 from Bifidobacterium longum belongs to the glycoside hydrolase family 127. At the active site of HypBA1, a cysteine residue (Cys417) coordinates with a Zn2+ atom and functions as the catalytic nucleophile for the anomer-retaining hydrolytic reaction. In this study, the role of Zn2+ ion and cysteine in catalysis as well as the substrate-bound structure were studied based on biochemical and crystallographic approaches. The enzymatic activity of HypBA1 decreased after dialysis in the presence of EDTA and guanidine hydrochloride and was then recovered by the addition of Zn2+. The Michaelis complex structure was determined using a crystal of a mutant at the acid/base catalyst residue (E322Q) soaked in a solution containing the substrate p-nitrophenyl-β-l-arabinofuranoside. To investigate the covalent thioglycosyl enzyme intermediate structure, synthetic inhibitors of l-arabinofuranosyl haloacetamide derivatives with different anomer configurations were used to target the nucleophilic cysteine. In the crystal structure of HypBA1, β-configured l-arabinofuranosylamide formed a covalent link with Cys417, whereas α-configured l-arabinofuranosylamide was linked to a noncatalytic residue Cys415. Mass spectrometric analysis indicated that Cys415 was also reactive with the probe molecule. With the β-configured inhibitor, the arabinofuranoside moiety was correctly positioned at the subsite and the active site integrity was retained to successfully mimic the covalent intermediate state.
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Affiliation(s)
- Shun Maruyama
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kota Sawano
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satoko Amaki
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takehiro Suzuki
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Satoru Narita
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma, Saitama 337-8570, Japan
| | - Kenta Kimura
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma, Saitama 337-8570, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chihaya Yamada
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yukishige Ito
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Science, Osaka University, 1-1 Machikaneyamacho, Toyonaka, Osaka 560-0043, Japan
| | - Naoshi Dohmae
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Akihiro Ishiwata
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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3
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Novel high-quantum-yield polydiacetylene conjugated AIE micelles for amplified fluorescence signaling and photodynamic therapy. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2021.113461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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4
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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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5
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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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6
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Saravanan V, Rajakumar P. Synthesis, characterization, optical and electrochemical properties and antibacterial activity of novel BODIPY glycoconjugated dendrimers. NEW J CHEM 2018. [DOI: 10.1039/c7nj04412g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new class of novel BODIPY glycoconjugated dendrimers with optical, electrochemical and antibacterial properties is reported.
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Affiliation(s)
| | - Perumal Rajakumar
- Department of Organic Chemistry
- University of Madras
- Chennai 600 025
- India
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7
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Tomlin F, Gerling-Driessen UIM, Liu YC, Flynn RA, Vangala JR, Lentz CS, Clauder-Muenster S, Jakob P, Mueller WF, Ordoñez-Rueda D, Paulsen M, Matsui N, Foley D, Rafalko A, Suzuki T, Bogyo M, Steinmetz LM, Radhakrishnan SK, Bertozzi CR. Inhibition of NGLY1 Inactivates the Transcription Factor Nrf1 and Potentiates Proteasome Inhibitor Cytotoxicity. ACS CENTRAL SCIENCE 2017; 3:1143-1155. [PMID: 29202016 PMCID: PMC5704294 DOI: 10.1021/acscentsci.7b00224] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Indexed: 05/06/2023]
Abstract
Proteasome inhibitors are used to treat blood cancers such as multiple myeloma (MM) and mantle cell lymphoma. The efficacy of these drugs is frequently undermined by acquired resistance. One mechanism of proteasome inhibitor resistance may involve the transcription factor Nuclear Factor, Erythroid 2 Like 1 (NFE2L1, also referred to as Nrf1), which responds to proteasome insufficiency or pharmacological inhibition by upregulating proteasome subunit gene expression. This "bounce-back" response is achieved through a unique mechanism. Nrf1 is constitutively translocated into the ER lumen, N-glycosylated, and then targeted for proteasomal degradation via the ER-associated degradation (ERAD) pathway. Proteasome inhibition leads to accumulation of cytosolic Nrf1, which is then processed to form the active transcription factor. Here we show that the cytosolic enzyme N-glycanase 1 (NGLY1, the human PNGase) is essential for Nrf1 activation in response to proteasome inhibition. Chemical or genetic disruption of NGLY1 activity results in the accumulation of misprocessed Nrf1 that is largely excluded from the nucleus. Under these conditions, Nrf1 is inactive in regulating proteasome subunit gene expression in response to proteasome inhibition. Through a small molecule screen, we identified a cell-active NGLY1 inhibitor that disrupts the processing and function of Nrf1. The compound potentiates the cytotoxicity of carfilzomib, a clinically used proteasome inhibitor, against MM and T cell-derived acute lymphoblastic leukemia (T-ALL) cell lines. Thus, NGLY1 inhibition prevents Nrf1 activation and represents a new therapeutic approach for cancers that depend on proteasome homeostasis.
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Affiliation(s)
- Frederick
M. Tomlin
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | | | - Yi-Chang Liu
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Ryan A. Flynn
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Janakiram R. Vangala
- Department
of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Christian S. Lentz
- Department
of Pathology, Stanford University School
of Medicine, 300 Pasteur
Drive, Stanford, California 94305, United States
| | - Sandra Clauder-Muenster
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Petra Jakob
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - William F. Mueller
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Diana Ordoñez-Rueda
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Malte Paulsen
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Naoko Matsui
- Glycomine,
Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Deirdre Foley
- Glycomine,
Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Agnes Rafalko
- Glycomine,
Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Tadashi Suzuki
- Glycometabolome
Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Matthew Bogyo
- Department
of Pathology, Stanford University School
of Medicine, 300 Pasteur
Drive, Stanford, California 94305, United States
- Department
of Microbiology and Immunology, Stanford
University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Lars M. Steinmetz
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
- Department
of Genetics, School of Medicine, Stanford
University, Stanford, California 94305, United States
| | - Senthil K. Radhakrishnan
- Department
of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Carolyn R. Bertozzi
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
- E-mail:
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8
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Liu Y, Fredrickson JK, Sadler NC, Nandhikonda P, Smith RD, Wright AT. Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:156. [PMID: 26413155 PMCID: PMC4582708 DOI: 10.1186/s13068-015-0343-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/16/2015] [Indexed: 06/02/2023]
Abstract
The development of renewable biofuels is a global priority, but success will require novel technologies that greatly improve our understanding of microbial systems biology. An approach with great promise in enabling functional characterization of microbes is activity-based protein profiling (ABPP), which employs chemical probes to directly measure enzyme function in discrete enzyme classes in vivo and/or in vitro, thereby facilitating the rapid discovery of new biocatalysts and enabling much improved biofuel production platforms. We review general design strategies in ABPP, and highlight recent advances that are or could be pivotal to biofuels processes including applications of ABPP to cellulosic bioethanol, biodiesel, and phototrophic production of hydrocarbons. We also examine the key challenges and opportunities of ABPP in renewable biofuels research. The integration of ABPP with molecular and systems biology approaches will shed new insight on the catalytic and regulatory mechanisms of functional enzymes and their synergistic effects in the field of biofuels production.
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Affiliation(s)
- Yun Liu
- />Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, 100029 Beijing, China
| | - James K. Fredrickson
- />Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, MSIN J4-02, Box 999, Richland, WA 99352 USA
| | - Natalie C. Sadler
- />Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, MSIN J4-02, Box 999, Richland, WA 99352 USA
| | - Premchendar Nandhikonda
- />Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, MSIN J4-02, Box 999, Richland, WA 99352 USA
| | - Richard D. Smith
- />Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, MSIN J4-02, Box 999, Richland, WA 99352 USA
| | - Aaron T. Wright
- />Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, MSIN J4-02, Box 999, Richland, WA 99352 USA
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9
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Singh S, Aggarwal A, Bhupathiraju NVSDK, Arianna G, Tiwari K, Drain CM. Glycosylated Porphyrins, Phthalocyanines, and Other Porphyrinoids for Diagnostics and Therapeutics. Chem Rev 2015; 115:10261-306. [PMID: 26317756 PMCID: PMC6011754 DOI: 10.1021/acs.chemrev.5b00244] [Citation(s) in RCA: 358] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sunaina Singh
- Department of Natural Sciences, LaGuardia Community College of the City University of New York, Long Island City, New York 11101, United States
| | - Amit Aggarwal
- Department of Natural Sciences, LaGuardia Community College of the City University of New York, Long Island City, New York 11101, United States
| | - N. V. S. Dinesh K. Bhupathiraju
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, United States
| | - Gianluca Arianna
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, United States
| | - Kirran Tiwari
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, United States
| | - Charles Michael Drain
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, United States
- The Rockefeller University, New York, New York 10065, United States
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10
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Miller GJ, Broberg KR, Rudd C, Helliwell MR, Jayson GC, Gardiner JM. A latent reactive handle for functionalising heparin-like and LMWH deca- and dodecasaccharides. Org Biomol Chem 2015; 13:11208-19. [PMID: 26381107 PMCID: PMC4672752 DOI: 10.1039/c5ob01706h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Disaccharide units containing a latent aldehyde surrogate at O4 provide late-stage access to terminal aldehyde LMWH and HS deca and dodecasaccharides.
d-Glucosamine derivatives bearing latent O4 functionality provide modified H/HS-type disaccharide donors for a final stage capping approach enabling introduction of conjugation-suitable, non-reducing terminal functionality to biologically important glycosaminoglycan oligosaccharides. Application to the synthesis of the first O4-terminus modified synthetic LMWH decasaccharide and an HS-like dodecasaccharide is reported.
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Affiliation(s)
- Gavin J Miller
- Manchester Institute of Biotechnology and School of Chemistry, 131 Princess Street, University of Manchester M1 7DN, UK.
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11
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Fluorescently labelled glycans and their applications. Glycoconj J 2015; 32:559-74. [DOI: 10.1007/s10719-015-9611-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/13/2015] [Accepted: 07/15/2015] [Indexed: 01/20/2023]
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12
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Hirayama H, Hosomi A, Suzuki T. Physiological and molecular functions of the cytosolic peptide:N-glycanase. Semin Cell Dev Biol 2015; 41:110-20. [DOI: 10.1016/j.semcdb.2014.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 01/04/2023]
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13
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Suzuki T. The cytoplasmic peptide:N-glycanase (Ngly1)--basic science encounters a human genetic disorder. J Biochem 2014; 157:23-34. [DOI: 10.1093/jb/mvu068] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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14
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Convenient Access to Carbohydrate-BODIPY Hybrids by Two Complementary Methods Involving One-Pot Assembly of “Clickable” BODIPY Dyes. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402767] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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15
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Stubbs KA. Activity-based proteomics probes for carbohydrate-processing enzymes: current trends and future outlook. Carbohydr Res 2014; 390:9-19. [DOI: 10.1016/j.carres.2014.02.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/21/2014] [Accepted: 02/22/2014] [Indexed: 11/27/2022]
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16
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Park S, Jang I, Zuber C, Lee Y, Cho JW, Matsuo I, Ito Y, Roth J. ERADication of EDEM1 occurs by selective autophagy and requires deglycosylation by cytoplasmic peptide N-glycanase. Histochem Cell Biol 2014; 142:153-69. [PMID: 24664425 DOI: 10.1007/s00418-014-1204-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2014] [Indexed: 11/30/2022]
Abstract
ER degradation-enhancing α-mannosidase-like 1 protein (EDEM1) is involved in the routing of misfolded glycoproteins for degradation in the cytoplasm. Previously, we reported that EDEM1 leaves the endoplasmic reticulum via non-COPII vesicles (Zuber et al. in Proc Natl Acad Sci USA 104:4407-4412, 2007) and becomes degraded by basal autophagy (Le Fourn et al. in Cell Mol Life Sci 66:1434-1445, 2009). However, it is unknown which type of autophagy is involved. Likewise, how EDEM1 is targeted to autophagosomes remains elusive. We now show that EDEM1 is degraded by selective autophagy. It colocalizes with the selective autophagy cargo receptors p62/SQSTM1, neighbor of BRCA1 gene 1 (NBR1) and autophagy-linked FYVE (Alfy) protein, and becomes engulfed by autophagic isolation membranes. The interaction with p62/SQSTM1 and NBR1 is required for routing of EDEM1 to autophagosomes since it can be blocked by short inhibitory RNA knockdown of the cargo receptors. Furthermore, p62/SQSTM1 interacts only with deglycosylated EDEM1 that is also ubiquitinated. The deglycosylation of EDEM1 occurs by the cytosolic peptide N-glycanase and is a prerequisite for interaction and aggregate formation with p62/SQSTM1 as demonstrated by the effect of peptide N-glycanase inhibitors on the formation of protein aggregates. Conversely, aggregation of p62/SQSTM1 and EDEM1 occurs independent of cytoplasmic histone deacetylase. These data provide novel insight into the mechanism of autophagic degradation of the ER-associated protein degradation (ERAD) component EDEM1 and disclose hitherto unknown parallels with the clearance of cytoplasmic aggregates of misfolded proteins by selective autophagy.
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Affiliation(s)
- Sujin Park
- WCU Program, Department of Integrated OMICS for Biomedical Science, Yonsei University Graduate School, Seoul, 120-749, Korea
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17
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Swarts BM, Guo Z. Chemical synthesis of glycosylphosphatidylinositol anchors. Adv Carbohydr Chem Biochem 2012; 67:137-219. [PMID: 22794184 DOI: 10.1016/b978-0-12-396527-1.00004-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Synthesis of a sugar-functionalized iridium complex and its application as a fluorescent lectin sensor. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.05.075] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Masuda M, Miyazawa S, Ito Y, Matsuo I. Synthesis of a Versatile Probe for Analysis of Cytoplasmic Peptide-N-Glycanase. J CHIN CHEM SOC-TAIP 2012. [DOI: 10.1002/jccs.201100631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Wang C, Xie F, Suthiwangcharoen N, Sun J, Wang Q. Tuning the optical properties of BODIPY dye through Cu(I) catalyzed azide-alkyne cycloaddition (CuAAC) reaction. Sci China Chem 2011. [DOI: 10.1007/s11426-011-4452-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Witte MD, van der Marel GA, Aerts JMFG, Overkleeft HS. Irreversible inhibitors and activity-based probes as research tools in chemical glycobiology. Org Biomol Chem 2011; 9:5908-26. [DOI: 10.1039/c1ob05531c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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22
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Swarts BM, Guo Z. Chemical synthesis and functionalization of clickable glycosylphosphatidylinositol anchors. Chem Sci 2011; 2:2342-2352. [PMID: 22163072 PMCID: PMC3233219 DOI: 10.1039/c1sc00440a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Glycosylphosphatidylinositol (GPI) anchorage is a common posttranslational modification of eukaryotic proteins. Chemical synthesis of structurally defined GPIs and GPI derivatives is a necessary step toward understanding the properties and functions of these molecules in biological systems. In this work, the synthesis of several functionalized GPI anchors was accomplished using the para-methoxybenzyl (PMB) group for permanent hydroxyl protection, which allowed the incorporation of functionalities that are incompatible with permanent protecting groups traditionally used in carbohydrate synthesis. A flexible convergent-divergent assembly strategy enabled efficient access to a diverse set of target structures, including "clickable" Alkynyl-GPIs 1 and 2 and Azido-GPI 3. For global deprotection, a one-pot reaction was employed to afford the target GPIs in excellent yields (85-97%). Fully deprotected clickable GPIs 2 and 3 were readily conjugated to imaging and affinity probes via Cu(I)-catalyzed and Cu-free strain-promoted [3+2] cycloaddition, respectively, resulting in GPI-Fluor 4 and GPI-Biotin 5.
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Affiliation(s)
- Benjamin M. Swarts
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA. Fax: 1-313-577-8822; Tel: 1-313-577-2557
| | - Zhongwu Guo
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA. Fax: 1-313-577-8822; Tel: 1-313-577-2557
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Hua-Wei Liu, Zhang KY, Law WHT, Lo KKW. Cyclometalated Iridium(III) Bipyridine Complexes Functionalized with an N-Methylamino-oxy Group as Novel Phosphorescent Labeling Reagents for Reducing Sugars. Organometallics 2010. [DOI: 10.1021/om100597g] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hua-Wei Liu
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
| | - Kenneth Yin Zhang
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
| | - Wendell Ho-Tin Law
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
| | - Kenneth Kam-Wing Lo
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
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25
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Maerz S, Funakoshi Y, Negishi Y, Suzuki T, Seiler S. The Neurospora peptide:N-glycanase ortholog PNG1 is essential for cell polarity despite its lack of enzymatic activity. J Biol Chem 2009; 285:2326-32. [PMID: 19940117 DOI: 10.1074/jbc.m109.045302] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Secretory proteins are subjected to a stringent endoplasmic reticulum-based quality control system that distinguishes aberrant from correctly folded proteins. The cytoplasmic peptide:N-glycanase cleaves oligosaccharides from misfolded glycoproteins and prepares them for degradation by the 26 S proteasome. In contrast to abundant in vitro data on its enzymatic function, the in vivo relevance of peptide:N-glycanase activity remains unclear. Here we show that the PNG1 ortholog from the filamentous ascomycete Neurospora crassa is an essential protein, and its deletion results in strong polarity defects. PNG1 and its predicted binding partner RAD23 have distinct functions in N. crassa and are involved in cell wall integrity and DNA repair, respectively. Moreover, wild type PNG1 has substitutions in essential catalytic amino acids, and its deglycosylation activity is lost. These substitutions are conserved in many PNG1 orthologs of the fungal kingdom, implying a so far unrecognized enzyme-independent function of PNG1 that may only become apparent in highly polar cells such as fungal hyphae.
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Affiliation(s)
- Sabine Maerz
- DFG Research Center of Molecular Physiology of the Brain (CMPB), D-37073 Goettingen, Germany
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26
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Abstract
Sarcoglycanopathies are a group of autosomal recessive muscle-wasting disorders caused by genetic defects in one of four cell membrane glycoproteins, alpha-, beta-, gamma- or delta-sarcoglycan. These four sarcoglycans form a subcomplex that is closely linked to the major dystrophin-associated protein complex, which is essential for membrane integrity during muscle contraction and provides a scaffold for important signalling molecules. Proper assembly, trafficking and targeting of the sarcoglycan complex is of vital importance, and mutations that severely perturb tetramer formation and localisation result in sarcoglycanopathy. Gene defects in one sarcoglycan cause the absence or reduced concentration of the other subunits. Most genetic defects generate mutated proteins that are degraded through the cell's quality control system; however, in many cases, conformational modifications do not affect the function of the protein, yet it is recognised as misfolded and prematurely degraded. Recent evidence shows that misfolded sarcoglycans could be rescued to the cell membrane by assisting their maturation along the ER secretory pathway. This review summarises the etiopathogenesis of sarcoglycanopathies and highlights the quality control machinery as a potential pharmacological target for therapy of these genetic disorders.
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Affiliation(s)
- Dorianna Sandonà
- Department of Biomedical Sciences, University of Padova, 35121
Padova, Italy
| | - Romeo Betto
- C.N.R. Institute of Neuroscience, Neuromuscular Biology and
Physiopathology, 35121 Padova, Italy
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Witte MD, Horst D, Wiertz EJHJ, van der Marel GA, Overkleeft HS. Synthesis and biological evaluation of a chitobiose-based peptide N-glycanase inhibitor library. J Org Chem 2009; 74:605-16. [PMID: 19072094 DOI: 10.1021/jo801906s] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptide N-glycanase (PNGase), the enzyme responsible for the deglycosylation of N-linked glycoproteins, has an active site related to that of cysteine proteases. Chitiobiose was equipped with electrophilic traps often used in cysteine protease inhibitors, and the resulting compounds were evaluated as PNGase inhibitors. We found that the electrophilic trap of the inhibitor has a great influence on the potency of the compounds with the chloromethyl ketone inhibitor being the first potent C-glycoside-based PNGase inhibitor.
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Affiliation(s)
- Martin D Witte
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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28
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Miyazaki A, Matsuo I, Hagihara S, Kakegawa A, Suzuki T, Ito Y. Systematic synthesis and inhibitory activity of haloacetamidyl oligosaccharide derivatives toward cytoplasmic peptide:N-glycanase. Glycoconj J 2008; 26:133-40. [PMID: 18695987 DOI: 10.1007/s10719-008-9171-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2007] [Revised: 06/25/2008] [Accepted: 07/08/2008] [Indexed: 11/29/2022]
Abstract
A series of glycosyl haloacetamides were synthesized as potential inhibitors of cytoplasmic peptide:N-glycanase (PNGase), an enzyme that removes N-glycans from misfolded glycoproteins. Chloro-, bromo-, and iodoacetamidyl chitobiose and chitotetraose derivatives exhibited a significant inhibitory activity. No inhibitory activity was observed with of fluoroacetamididyl derivatives. Moreover, N-acetylglucosamine derivatives, beta-chloropropionamidyl chitobiose, and chloroacetamidyl cellooligosaccharide derivatives did not show any activity. These results underscore the importance of the N-acetyl groups of chitobiose for PNGase recognition. In addition, reactivity and position of the leaving group at the reducing end are also important factors.
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Affiliation(s)
- Ayako Miyazaki
- The Institute of Physical and Chemical Research, Wako, Saitama, Japan
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29
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Chantret I, Moore SEH. Free oligosaccharide regulation during mammalian protein N-glycosylation. Glycobiology 2007; 18:210-24. [DOI: 10.1093/glycob/cwn003] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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30
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Suzuki T. Cytoplasmic peptide:N-glycanase and catabolic pathway for free N-glycans in the cytosol. Semin Cell Dev Biol 2007; 18:762-9. [DOI: 10.1016/j.semcdb.2007.09.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 08/07/2007] [Accepted: 09/05/2007] [Indexed: 10/22/2022]
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