1
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Murray M, Davidson L, Ferenbach AT, Lefeber D, van Aalten DMF. Neuroectoderm phenotypes in a human stem cell model of O-GlcNAc transferase associated with intellectual disability. Mol Genet Metab 2024; 142:108492. [PMID: 38759397 DOI: 10.1016/j.ymgme.2024.108492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
Pathogenic variants in the O-GlcNAc transferase gene (OGT) have been associated with a congenital disorder of glycosylation (OGT-CDG), presenting with intellectual disability which may be of neuroectodermal origin. To test the hypothesis that pathology is linked to defects in differentiation during early embryogenesis, we developed an OGT-CDG induced pluripotent stem cell line together with isogenic control generated by CRISPR/Cas9 gene-editing. Although the OGT-CDG variant leads to a significant decrease in OGT and O-GlcNAcase protein levels, there were no changes in differentiation potential or stemness. However, differentiation into ectoderm resulted in significant differences in O-GlcNAc homeostasis. Further differentiation to neuronal stem cells revealed differences in morphology between patient and control lines, accompanied by disruption of the O-GlcNAc pathway. This suggests a critical role for O-GlcNAcylation in early neuroectoderm architecture, with robust compensatory mechanisms in the earliest stages of stem cell differentiation.
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Affiliation(s)
- Marta Murray
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lindsay Davidson
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Andrew T Ferenbach
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, DK, Denmark
| | - Dirk Lefeber
- Department of Neurology, Department of Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, NL, the Netherlands
| | - Daan M F van Aalten
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK; Department of Molecular Biology and Genetics, Aarhus University, Aarhus, DK, Denmark.
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2
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Ma B, Khan KS, Xu T, Xeque Amada J, Guo Z, Huang Y, Yan Y, Lam H, Cheng ASL, Ng BWL. Targeted Protein O-GlcNAcylation Using Bifunctional Small Molecules. J Am Chem Soc 2024; 146:9779-9789. [PMID: 38561350 PMCID: PMC11009946 DOI: 10.1021/jacs.3c14380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
Protein O-linked β-N-acetylglucosamine modification (O-GlcNAcylation) plays a crucial role in regulating essential cellular processes. The disruption of the homeostasis of O-GlcNAcylation has been linked to various human diseases, including cancer, diabetes, and neurodegeneration. However, there are limited chemical tools for protein- and site-specific O-GlcNAc modification, rendering the precise study of the O-GlcNAcylation challenging. To address this, we have developed heterobifunctional small molecules, named O-GlcNAcylation TArgeting Chimeras (OGTACs), which enable protein-specific O-GlcNAcylation in living cells. OGTACs promote O-GlcNAcylation of proteins such as BRD4, CK2α, and EZH2 in cellulo by recruiting FKBP12F36V-fused O-GlcNAc transferase (OGT), with temporal, magnitude, and reversible control. Overall, the OGTACs represent a promising approach for inducing protein-specific O-GlcNAcylation, thus enabling functional dissection and offering new directions for O-GlcNAc-targeting therapeutic development.
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Affiliation(s)
- Bowen Ma
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
| | - Khadija Shahed Khan
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
- School
of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Tongyang Xu
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
| | - Josefina Xeque Amada
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
| | - Zhihao Guo
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
| | - Yunpeng Huang
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
| | - Yu Yan
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
| | - Henry Lam
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Sai Kung, Hong Kong
| | - Alfred Sze-Lok Cheng
- School
of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Billy Wai-Lung Ng
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, Hong Kong
- Li Ka
Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Sha Tin, Hong
Kong
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3
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Mitchell CW, Galan Bartual S, Ferenbach AT, Scavenius C, van Aalten DMF. Exploiting O-GlcNAc transferase promiscuity to dissect site-specific O-GlcNAcylation. Glycobiology 2023; 33:1172-1181. [PMID: 37856504 DOI: 10.1093/glycob/cwad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/04/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023] Open
Abstract
Protein O-GlcNAcylation is an evolutionary conserved post-translational modification catalysed by the nucleocytoplasmic O-GlcNAc transferase (OGT) and reversed by O-GlcNAcase (OGA). How site-specific O-GlcNAcylation modulates a diverse range of cellular processes is largely unknown. A limiting factor in studying this is the lack of accessible techniques capable of producing homogeneously O-GlcNAcylated proteins, in high yield, for in vitro studies. Here, we exploit the tolerance of OGT for cysteine instead of serine, combined with a co-expressed OGA to achieve site-specific, highly homogeneous mono-glycosylation. Applying this to DDX3X, TAB1, and CK2α, we demonstrate that near-homogeneous mono-S-GlcNAcylation of these proteins promotes DDX3X and CK2α solubility and enables production of mono-S-GlcNAcylated TAB1 crystals, albeit with limited diffraction. Taken together, this work provides a new approach for functional dissection of protein O-GlcNAcylation.
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Affiliation(s)
- Conor W Mitchell
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus, Denmark
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dow St., Dundee, DD1 5EH, United Kingdom
| | - Sergio Galan Bartual
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus, Denmark
| | - Andrew T Ferenbach
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus, Denmark
| | - Carsten Scavenius
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus, Denmark
| | - Daan M F van Aalten
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus, Denmark
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dow St., Dundee, DD1 5EH, United Kingdom
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4
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Lu P, Liu Y, He M, Cao T, Yang M, Qi S, Yu H, Gao H. Cryo-EM structure of human O-GlcNAcylation enzyme pair OGT-OGA complex. Nat Commun 2023; 14:6952. [PMID: 37907462 PMCID: PMC10618255 DOI: 10.1038/s41467-023-42427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 10/10/2023] [Indexed: 11/02/2023] Open
Abstract
O-GlcNAcylation is a conserved post-translational modification that attaches N-acetyl glucosamine (GlcNAc) to myriad cellular proteins. In response to nutritional and hormonal signals, O-GlcNAcylation regulates diverse cellular processes by modulating the stability, structure, and function of target proteins. Dysregulation of O-GlcNAcylation has been implicated in the pathogenesis of cancer, diabetes, and neurodegeneration. A single pair of enzymes, the O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), catalyzes the addition and removal of O-GlcNAc on over 3,000 proteins in the human proteome. However, how OGT selects its native substrates and maintains the homeostatic control of O-GlcNAcylation of so many substrates against OGA is not fully understood. Here, we present the cryo-electron microscopy (cryo-EM) structures of human OGT and the OGT-OGA complex. Our studies reveal that OGT forms a functionally important scissor-shaped dimer. Within the OGT-OGA complex structure, a long flexible OGA segment occupies the extended substrate-binding groove of OGT and positions a serine for O-GlcNAcylation, thus preventing OGT from modifying other substrates. Conversely, OGT disrupts the functional dimerization of OGA and occludes its active site, resulting in the blocking of access by other substrates. This mutual inhibition between OGT and OGA may limit the futile O-GlcNAcylation cycles and help to maintain O-GlcNAc homeostasis.
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Affiliation(s)
- Ping Lu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- New Cornerstone Science Laboratory, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Yusong Liu
- New Cornerstone Science Laboratory, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Maozhou He
- New Cornerstone Science Laboratory, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Ting Cao
- New Cornerstone Science Laboratory, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Mengquan Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- New Cornerstone Science Laboratory, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Shutao Qi
- New Cornerstone Science Laboratory, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Hongtao Yu
- New Cornerstone Science Laboratory, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
| | - Haishan Gao
- New Cornerstone Science Laboratory, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
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5
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Omelková M, Fenger CD, Murray M, Hammer TB, Pravata VM, Bartual SG, Czajewski I, Bayat A, Ferenbach AT, Stavridis MP, van Aalten DMF. An O-GlcNAc transferase pathogenic variant linked to intellectual disability affects pluripotent stem cell self-renewal. Dis Model Mech 2023; 16:dmm049132. [PMID: 37334838 DOI: 10.1242/dmm.049132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 04/19/2023] [Indexed: 06/21/2023] Open
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) is an essential enzyme that modifies proteins with O-GlcNAc. Inborn OGT genetic variants were recently shown to mediate a novel type of congenital disorder of glycosylation (OGT-CDG), which is characterised by X-linked intellectual disability (XLID) and developmental delay. Here, we report an OGTC921Y variant that co-segregates with XLID and epileptic seizures, and results in loss of catalytic activity. Colonies formed by mouse embryonic stem cells carrying OGTC921Y showed decreased levels of protein O-GlcNAcylation accompanied by decreased levels of Oct4 (encoded by Pou5f1), Sox2 and extracellular alkaline phosphatase (ALP), implying reduced self-renewal capacity. These data establish a link between OGT-CDG and embryonic stem cell self-renewal, providing a foundation for examining the developmental aetiology of this syndrome.
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Affiliation(s)
- Michaela Omelková
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Christina Dühring Fenger
- Department of Epilepsy Genetics, Filadelfia Danish Epilepsy Centre, Dianalund 4293, Denmark
- Amplexa Genetics A/S, Odense 5000, Denmark
| | - Marta Murray
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Trine Bjørg Hammer
- Department of Epilepsy Genetics, Filadelfia Danish Epilepsy Centre, Dianalund 4293, Denmark
| | - Veronica M Pravata
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Sergio Galan Bartual
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
| | - Ignacy Czajewski
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Allan Bayat
- Department of Epilepsy Genetics, Filadelfia Danish Epilepsy Centre, Dianalund 4293, Denmark
| | - Andrew T Ferenbach
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
| | - Marios P Stavridis
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Daan M F van Aalten
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
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6
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Kumar S, Wang Y, Zhou Y, Dillard L, Li FW, Sciandra CA, Sui N, Zentella R, Zahn E, Shabanowitz J, Hunt DF, Borgnia MJ, Bartesaghi A, Sun TP, Zhou P. Structure and dynamics of the Arabidopsis O-fucosyltransferase SPINDLY. Nat Commun 2023; 14:1538. [PMID: 36941311 PMCID: PMC10027727 DOI: 10.1038/s41467-023-37279-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 03/04/2023] [Indexed: 03/22/2023] Open
Abstract
SPINDLY (SPY) in Arabidopsis thaliana is a novel nucleocytoplasmic protein O-fucosyltransferase (POFUT), which regulates diverse developmental processes. Sequence analysis indicates that SPY is distinct from ER-localized POFUTs and contains N-terminal tetratricopeptide repeats (TPRs) and a C-terminal catalytic domain resembling the O-linked-N-acetylglucosamine (GlcNAc) transferases (OGTs). However, the structural feature that determines the distinct enzymatic selectivity of SPY remains unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of SPY and its complex with GDP-fucose, revealing distinct active-site features enabling GDP-fucose instead of UDP-GlcNAc binding. SPY forms an antiparallel dimer instead of the X-shaped dimer in human OGT, and its catalytic domain interconverts among multiple conformations. Analysis of mass spectrometry, co-IP, fucosylation activity, and cryo-EM data further demonstrates that the N-terminal disordered peptide in SPY contains trans auto-fucosylation sites and inhibits the POFUT activity, whereas TPRs 1-5 dynamically regulate SPY activity by interfering with protein substrate binding.
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Affiliation(s)
- Shivesh Kumar
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Yan Wang
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC, 27705, USA
| | - Lucas Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Fay-Wei Li
- Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Carly A Sciandra
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Ning Sui
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | | | - Emily Zahn
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
- Department of Pathology, University of Virginia, Charlottesville, VA, 22903, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Alberto Bartesaghi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Computer Science, Duke University, Durham, NC, 27705, USA.
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA.
| | - Tai-Ping Sun
- Department of Biology, Duke University, Durham, NC, 27708, USA.
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.
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7
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Hu CW, Xie J, Jiang J. The Emerging Roles of Protein Interactions with O-GlcNAc Cycling Enzymes in Cancer. Cancers (Basel) 2022; 14:5135. [PMID: 36291918 PMCID: PMC9600386 DOI: 10.3390/cancers14205135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 09/11/2023] Open
Abstract
The dynamic O-GlcNAc modification of intracellular proteins is an important nutrient sensor for integrating metabolic signals into vast networks of highly coordinated cellular activities. Dysregulation of the sole enzymes responsible for O-GlcNAc cycling, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), and the associated cellular O-GlcNAc profile is a common feature across nearly every cancer type. Many studies have investigated the effects of aberrant OGT/OGA expression on global O-GlcNAcylation activity in cancer cells. However, recent studies have begun to elucidate the roles of protein-protein interactions (PPIs), potentially through regions outside of the immediate catalytic site of OGT/OGA, that regulate greater protein networks to facilitate substrate-specific modification, protein translocalization, and the assembly of larger biomolecular complexes. Perturbation of OGT/OGA PPI networks makes profound changes in the cell and may directly contribute to cancer malignancies. Herein, we highlight recent studies on the structural features of OGT and OGA, as well as the emerging roles and molecular mechanisms of their aberrant PPIs in rewiring cancer networks. By integrating complementary approaches, the research in this area will aid in the identification of key protein contacts and functional modules derived from OGT/OGA that drive oncogenesis and will illuminate new directions for anti-cancer drug development.
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Affiliation(s)
| | | | - Jiaoyang Jiang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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8
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Mitchell CW, Czajewski I, van Aalten DM. Bioinformatic prediction of putative conveyers of O-GlcNAc transferase intellectual disability. J Biol Chem 2022; 298:102276. [PMID: 35863433 PMCID: PMC9428853 DOI: 10.1016/j.jbc.2022.102276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 02/09/2023] Open
Abstract
Protein O-GlcNAcylation is a dynamic posttranslational modification that is catalyzed by the enzyme O-GlcNAc transferase (OGT) and is essential for neurodevelopment and postnatal neuronal function. Missense mutations in OGT segregate with a novel X-linked intellectual disability syndrome, the OGT congenital disorder of glycosylation (OGT-CDG). One hypothesis for the etiology of OGT-CDG is that loss of OGT activity leads to hypo-O-GlcNAcylation of as yet unidentified, specific neuronal proteins, affecting essential embryonic, and postnatal neurodevelopmental processes; however, the identity of these O-GlcNAcylated proteins is not known. Here, we used bioinformatic techniques to integrate sequence conservation, structural data, clinical data, and the available literature to identify 22 candidate proteins that convey OGT-CDG. We found using gene ontology and PANTHER database data that these candidate proteins are involved in diverse processes including Ras/MAPK signaling, translational repression, cytoskeletal dynamics, and chromatin remodeling. We also identify pathogenic missense variants at O-GlcNAcylation sites that segregate with intellectual disability. This work establishes a preliminary platform for the mechanistic dissection of the links between protein O-GlcNAcylation and neurodevelopment in OGT-CDG.
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Affiliation(s)
- Conor W. Mitchell
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark,Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ignacy Czajewski
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Daan M.F. van Aalten
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark,Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom,For correspondence: Daan M. F. van Aalten
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9
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Liu Y, Hu YJ, Fan WX, Quan X, Xu B, Li SZ. O-GlcNAcylation: The Underestimated Emerging Regulators of Skeletal Muscle Physiology. Cells 2022; 11:cells11111789. [PMID: 35681484 PMCID: PMC9180116 DOI: 10.3390/cells11111789] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
O-GlcNAcylation is a highly dynamic, reversible and atypical glycosylation that regulates the activity, biological function, stability, sublocation and interaction of target proteins. O-GlcNAcylation receives and coordinates different signal inputs as an intracellular integrator similar to the nutrient sensor and stress receptor, which target multiple substrates with spatio-temporal analysis specifically to maintain cellular homeostasis and normal physiological functions. Our review gives a brief description of O-GlcNAcylation and its only two processing enzymes and HBP flux, which will help to better understand its physiological characteristics of sensing nutrition and environmental cues. This nutritional and stress-sensitive properties of O-GlcNAcylation allow it to participate in the precise regulation of skeletal muscle metabolism. This review discusses the mechanism of O-GlcNAcylation to alleviate metabolic disorders and the controversy about the insulin resistance of skeletal muscle. The level of global O-GlcNAcylation is precisely controlled and maintained in the “optimal zone”, and its abnormal changes is a potential factor in the pathogenesis of cancer, neurodegeneration, diabetes and diabetic complications. Although the essential role of O-GlcNAcylation in skeletal muscle physiology has been widely studied and recognized, it still is underestimated and overlooked. This review highlights the latest progress and potential mechanisms of O-GlcNAcylation in the regulation of skeletal muscle contraction and structural properties.
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Affiliation(s)
| | | | | | | | - Bin Xu
- Correspondence: (B.X.); (S.-Z.L.)
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10
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Abstract
Post-translational modification with O-linked β-N-acetylglucosamine (O-GlcNAc), a process referred to as O-GlcNAcylation, occurs on a vast variety of proteins. Mounting evidence in the past several decades has clearly demonstrated that O-GlcNAcylation is a unique and ubiquitous modification. Reminiscent of a code, protein O-GlcNAcylation functions as a crucial regulator of nearly all cellular processes studied. The primary aim of this review is to summarize the developments in our understanding of myriad protein substrates modified by O-GlcNAcylation from a systems perspective. Specifically, we provide a comprehensive survey of O-GlcNAcylation in multiple species studied, including eukaryotes (e.g., protists, fungi, plants, Caenorhabditis elegans, Drosophila melanogaster, murine, and human), prokaryotes, and some viruses. We evaluate features (e.g., structural properties and sequence motifs) of O-GlcNAc modification on proteins across species. Given that O-GlcNAcylation functions in a species-, tissue-/cell-, protein-, and site-specific manner, we discuss the functional roles of O-GlcNAcylation on human proteins. We focus particularly on several classes of relatively well-characterized human proteins (including transcription factors, protein kinases, protein phosphatases, and E3 ubiquitin-ligases), with representative O-GlcNAc site-specific functions presented. We hope the systems view of the great endeavor in the past 35 years will help demystify the O-GlcNAc code and lead to more fascinating studies in the years to come.
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Affiliation(s)
- Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, United States
| | - Chunyan Hou
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, United States
| | - Ci Wu
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, United States
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11
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Meek RW, Blaza JN, Busmann JA, Alteen MG, Vocadlo DJ, Davies GJ. Cryo-EM structure provides insights into the dimer arrangement of the O-linked β-N-acetylglucosamine transferase OGT. Nat Commun 2021; 12:6508. [PMID: 34764280 PMCID: PMC8586251 DOI: 10.1038/s41467-021-26796-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/20/2021] [Indexed: 01/17/2023] Open
Abstract
The O-linked β-N-acetylglucosamine modification is a core signalling mechanism, with erroneous patterns leading to cancer and neurodegeneration. Although thousands of proteins are subject to this modification, only a single essential glycosyltransferase catalyses its installation, the O-GlcNAc transferase, OGT. Previous studies have provided truncated structures of OGT through X-ray crystallography, but the full-length protein has never been observed. Here, we report a 5.3 Å cryo-EM model of OGT. We show OGT is a dimer, providing a structural basis for how some X-linked intellectual disability mutations at the interface may contribute to disease. We observe that the catalytic section of OGT abuts a 13.5 tetratricopeptide repeat unit region and find the relative positioning of these sections deviate from the previously proposed, X-ray crystallography-based model. We also note that OGT exhibits considerable heterogeneity in tetratricopeptide repeat units N-terminal to the dimer interface with repercussions for how OGT binds protein ligands and partners.
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Affiliation(s)
- Richard W Meek
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - James N Blaza
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK.
| | - Jil A Busmann
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Matthew G Alteen
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - David J Vocadlo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK.
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12
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Ma J, Hou C, Li Y, Chen S, Wu C. OGT Protein Interaction Network (OGT-PIN): A Curated Database of Experimentally Identified Interaction Proteins of OGT. Int J Mol Sci 2021; 22:ijms22179620. [PMID: 34502531 PMCID: PMC8431785 DOI: 10.3390/ijms22179620] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 01/01/2023] Open
Abstract
Interactions between proteins are essential to any cellular process and constitute the basis for molecular networks that determine the functional state of a cell. With the technical advances in recent years, an astonishingly high number of protein–protein interactions has been revealed. However, the interactome of O-linked N-acetylglucosamine transferase (OGT), the sole enzyme adding the O-linked β-N-acetylglucosamine (O-GlcNAc) onto its target proteins, has been largely undefined. To that end, we collated OGT interaction proteins experimentally identified in the past several decades. Rigorous curation of datasets from public repositories and O-GlcNAc-focused publications led to the identification of up to 929 high-stringency OGT interactors from multiple species studied (including Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Arabidopsis thaliana, and others). Among them, 784 human proteins were found to be interactors of human OGT. Moreover, these proteins spanned a very diverse range of functional classes (e.g., DNA repair, RNA metabolism, translational regulation, and cell cycle), with significant enrichment in regulating transcription and (co)translation. Our dataset demonstrates that OGT is likely a hub protein in cells. A webserver OGT-Protein Interaction Network (OGT-PIN) has also been created, which is freely accessible.
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Affiliation(s)
- Junfeng Ma
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA; (Y.L.); (C.W.)
- Correspondence: ; Tel.: +1-202-6873802
| | - Chunyan Hou
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China;
| | - Yaoxiang Li
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA; (Y.L.); (C.W.)
| | - Shufu Chen
- School of Engineering, Pennsylvania State University Behrend, Erie, PA 16563, USA;
| | - Ci Wu
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA; (Y.L.); (C.W.)
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13
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Izert MA, Szybowska PE, Górna MW, Merski M. The Effect of Mutations in the TPR and Ankyrin Families of Alpha Solenoid Repeat Proteins. FRONTIERS IN BIOINFORMATICS 2021; 1:696368. [PMID: 36303725 PMCID: PMC9581033 DOI: 10.3389/fbinf.2021.696368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/22/2021] [Indexed: 11/20/2022] Open
Abstract
Protein repeats are short, highly similar peptide motifs that occur several times within a single protein, for example the TPR and Ankyrin repeats. Understanding the role of mutation in these proteins is complicated by the competing facts that 1) the repeats are much more restricted to a set sequence than non-repeat proteins, so mutations should be harmful much more often because there are more residues that are heavily restricted due to the need of the sequence to repeat and 2) the symmetry of the repeats in allows the distribution of functional contributions over a number of residues so that sometimes no specific site is singularly responsible for function (unlike enzymatic active site catalytic residues). To address this issue, we review the effects of mutations in a number of natural repeat proteins from the tetratricopeptide and Ankyrin repeat families. We find that mutations are context dependent. Some mutations are indeed highly disruptive to the function of the protein repeats while mutations in identical positions in other repeats in the same protein have little to no effect on structure or function.
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Affiliation(s)
| | | | | | - Matthew Merski
- *Correspondence: Maria Wiktoria Górna, ; Matthew Merski,
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14
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Balana AT, Moon SP, Pratt MR. O-GlcNAcylated peptides and proteins for structural and functional studies. Curr Opin Struct Biol 2021; 68:84-93. [PMID: 33434850 PMCID: PMC8222092 DOI: 10.1016/j.sbi.2020.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/08/2020] [Accepted: 12/12/2020] [Indexed: 12/19/2022]
Abstract
O-GlcNAcylation is an enzymatic post-translational modification occurring in hundreds of protein substrates. This modification occurs through the addition of the monosaccharide N-acetylglucosamine to serine and threonine residues on intracellular proteins in the cytosol, nucleus, and mitochondria. As a highly dynamic form of modification, changes in O-GlcNAc levels coincide with alterations in metabolic state, the presence of stressors, and cellular health. At the protein level, the consequences of the sugar modification can vary, thus necessitating biochemical investigations on protein-specific and site-specific effects. To this end, enzymatic and chemical methods to 'encode' the modification have been developed and the utilization of these synthetic glycopeptides and glycoproteins has since been instrumental in the discovery of the mechanisms by which O-GlcNAcylation can affect a diverse array of biological processes.
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Affiliation(s)
- Aaron T Balana
- Departments of Chemistry, University of Southern California, Los Angeles, CA, 90089, United States
| | - Stuart P Moon
- Departments of Chemistry, University of Southern California, Los Angeles, CA, 90089, United States
| | - Matthew R Pratt
- Departments of Chemistry, University of Southern California, Los Angeles, CA, 90089, United States; Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States.
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15
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Joiner CM, Hammel FA, Janetzko J, Walker S. Protein Substrates Engage the Lumen of O-GlcNAc Transferase's Tetratricopeptide Repeat Domain in Different Ways. Biochemistry 2021; 60:847-853. [PMID: 33709700 DOI: 10.1021/acs.biochem.0c00981] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glycosylation of nuclear and cytoplasmic proteins is an essential post-translational modification in mammals. O-GlcNAc transferase (OGT), the sole enzyme responsible for this modification, glycosylates more than 1000 unique nuclear and cytoplasmic substrates. How OGT selects its substrates is a fundamental question that must be answered to understand OGT's unusual biology. OGT contains a long tetratricopeptide repeat (TPR) domain that has been implicated in substrate selection, but there is almost no information about how changes to this domain affect glycosylation of individual substrates. By profiling O-GlcNAc in cell extracts and probing glycosylation of purified substrates, we show here that ladders of asparagines and aspartates that extend the full length of OGT's TPR lumen control substrate glycosylation. Different substrates are sensitive to changes in different regions of OGT's TPR lumen. We also found that substrates with glycosylation sites close to the C-terminus bypass lumenal binding. Our findings demonstrate that substrates can engage OGT in a variety of different ways for glycosylation.
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Affiliation(s)
- Cassandra M Joiner
- Department of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Forrest A Hammel
- Department of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States.,Program in Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - John Janetzko
- Department of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
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16
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Shi J, Sharif S, Balsollier C, Ruijtenbeek R, Pieters RJ, Jongkees SAK. C-Terminal Tag Location Hampers in Vitro Profiling of OGT Peptide Substrates by mRNA Display. Chembiochem 2021; 22:666-671. [PMID: 33022805 PMCID: PMC7894566 DOI: 10.1002/cbic.202000624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/06/2020] [Indexed: 12/17/2022]
Abstract
O-GlcNAc transferase (OGT) is the only enzyme that catalyzes the post-translational modification of proteins at Ser/Thr with a single β-N-acetylglucosamine (O-GlcNAcylation). Its activity has been associated with chronic diseases such as cancer, diabetes and neurodegenerative disease. Although numerous OGT substrates have been identified, its accepted substrate scope can still be refined. We report here an attempt to better define the peptide-recognition requirements of the OGT active site by using mRNA display, taking advantage of its extremely high throughput to assess the substrate potential of a library of all possible nonamer peptides. An antibody-based selection process is described here that is able to enrich an OGT substrate peptide from such a library, but with poor absolute recovery. Following four rounds of selection for O-GlcNAcylated peptides, sequencing revealed 14 peptides containing Ser/Thr, but these were shown by luminescence-coupled assays and peptide microarray not to be OGT substrates. By contrast, subsequent testing of an N-terminal tag approach showed exemplary recovery. Our approach demonstrates the power of genetically encoded libraries for selection of peptide substrates, even from a very low initial starting abundance and under suboptimal conditions, and emphasizes the need to consider the binding biases of antibodies and both C- and N-terminal tags in profiling peptide substrates by high-throughput display.
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Affiliation(s)
- Jie Shi
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUniversiteitsweg 99Utrecht3584 CGThe Netherlands
- Key Laboratory of Carbohydrate Chemistry & Biotechnology Ministry of Education, School of BiotechnologyJiangnan University214122WuxiP. R. China
| | - Suhela Sharif
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUniversiteitsweg 99Utrecht3584 CGThe Netherlands
| | - Cyril Balsollier
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUniversiteitsweg 99Utrecht3584 CGThe Netherlands
| | - Rob Ruijtenbeek
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUniversiteitsweg 99Utrecht3584 CGThe Netherlands
- PamGene International BV's-Hertogenbosch5211 HHThe Netherlands
| | - Roland J. Pieters
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUniversiteitsweg 99Utrecht3584 CGThe Netherlands
| | - Seino A. K. Jongkees
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUniversiteitsweg 99Utrecht3584 CGThe Netherlands
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17
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Kositzke A, Fan D, Wang A, Li H, Worth M, Jiang J. Elucidating the protein substrate recognition of O-GlcNAc transferase (OGT) toward O-GlcNAcase (OGA) using a GlcNAc electrophilic probe. Int J Biol Macromol 2021; 169:51-59. [PMID: 33333092 PMCID: PMC7856287 DOI: 10.1016/j.ijbiomac.2020.12.078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022]
Abstract
The essential human O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) is the sole enzyme responsible for modifying thousands of intracellular proteins with the monosaccharide O-GlcNAc. This unique modification plays crucial roles in human health and disease, but the substrate recognition of OGT remains poorly understood. Intriguingly, the only human enzyme reported to remove this modification, O-GlcNAcase (OGA), is O-GlcNAc modified. Here, we exploited a GlcNAc electrophilic probe (GEP1A) to rapidly screen OGT mutants in a fluorescence assay that can discriminate between altered OGT-sugar and -protein substrate binding to help elucidate the binding mode of OGT toward OGA protein substrate. Since OGT tetratricopeptide repeat (TPR) domain plays a key role in OGT-OGA binding, we screened 30 OGT TPR mutants, which revealed 15 "ladder like" asparagine or aspartate residues spanning TPRs 3-7 and 10-13.5 that affect OGA O-GlcNAcylation. By applying a truncated OGA construct, we found that OGA's N-terminal region or pseudo histone acetyltransferase domain is not required for its O-GlcNAcylation, suggesting OGT functionally interacts with OGA through its catalytic and/or stalk domains. This work represents the first effort to systemically investigate each OGT TPR and our findings will facilitate the development of new strategies to investigate the role of substrate-specific O-GlcNAcylation.
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Affiliation(s)
- Adam Kositzke
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Dacheng Fan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ao Wang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Hao Li
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Matthew Worth
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jiaoyang Jiang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
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18
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Ma J, Wu C, Hart GW. Analytical and Biochemical Perspectives of Protein O-GlcNAcylation. Chem Rev 2021; 121:1513-1581. [DOI: 10.1021/acs.chemrev.0c00884] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington D.C. 20057, United States
| | - Ci Wu
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington D.C. 20057, United States
| | - Gerald W. Hart
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
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19
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Abstract
O-GlcNAcylation is an abundant and dynamic protein posttranslational modification (PTM), with crucial roles in metazoans. Studies of this modification are hampered by the lack of convenient methods for detecting native O-GlcNAcylation. Here, we describe a novel gel-based approach, Separation of O-GlcNAcylated Proteins by Polyacrylamide Gel Electrophoresis (SOPAGE), which enables detection of O-GlcNAc levels and dynamics.
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Affiliation(s)
- Chuan Fu
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, UK.
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20
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Gorelik A, van Aalten DMF. Tools for functional dissection of site-specific O-GlcNAcylation. RSC Chem Biol 2020; 1:98-109. [PMID: 34458751 PMCID: PMC8386111 DOI: 10.1039/d0cb00052c] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022] Open
Abstract
Protein O-GlcNAcylation is an abundant post-translational modification of intracellular proteins with the monosaccharide N-acetylglucosamine covalently tethered to serines and threonines. Modification of proteins with O-GlcNAc is required for metazoan embryo development and maintains cellular homeostasis through effects on transcription, signalling and stress response. While disruption of O-GlcNAc homeostasis can have detrimental impact on cell physiology and cause various diseases, little is known about the functions of individual O-GlcNAc sites. Most of the sites are modified sub-stoichiometrically which is a major challenge to the dissection of O-GlcNAc function. Here, we discuss the application, advantages and limitations of the currently available tools and technologies utilised to dissect the function of O-GlcNAc on individual proteins and sites in vitro and in vivo. Additionally, we provide a perspective on future developments required to decipher the protein- and site-specific roles of this essential sugar modification.
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Affiliation(s)
- Andrii Gorelik
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee Dundee UK
| | - Daan M F van Aalten
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee Dundee UK
- Institute for Molecular Precision Medicine, Xiangya Hospital, Central South University Changsha China
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21
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Chang YH, Weng CL, Lin KI. O-GlcNAcylation and its role in the immune system. J Biomed Sci 2020; 27:57. [PMID: 32349769 PMCID: PMC7189445 DOI: 10.1186/s12929-020-00648-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/27/2020] [Indexed: 12/13/2022] Open
Abstract
O-linked-N-acetylglucosaminylation (O-GlcNAcylation) is a type of glycosylation that occurs when a monosaccharide, O-GlcNAc, is added onto serine or threonine residues of nuclear or cytoplasmic proteins by O-GlcNAc transferase (OGT) and which can be reversibly removed by O-GlcNAcase (OGA). O-GlcNAcylation couples the processes of nutrient sensing, metabolism, signal transduction and transcription, and plays important roles in development, normal physiology and physiopathology. Cumulative studies have indicated that O-GlcNAcylation affects the functions of protein substrates in a number of ways, including protein cellular localization, protein stability and protein/protein interaction. Particularly, O-GlcNAcylation has been shown to have intricate crosstalk with phosphorylation as they both modify serine or threonine residues. Aberrant O-GlcNAcylation on various protein substrates has been implicated in many diseases, including neurodegenerative diseases, diabetes and cancers. However, the role of protein O-GlcNAcylation in immune cell lineages has been less explored. This review summarizes the current understanding of the fundamental biochemistry of O-GlcNAcylation, and discusses the molecular mechanisms by which O-GlcNAcylation regulates the development, maturation and functions of immune cells. In brief, O-GlcNAcylation promotes the development, proliferation, and activation of T and B cells. O-GlcNAcylation regulates inflammatory and antiviral responses of macrophages. O-GlcNAcylation promotes the function of activated neutrophils, but inhibits the activity of nature killer cells.
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Affiliation(s)
- Yi-Hsuan Chang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Chia-Lin Weng
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang Dist., Taipei, 115, Taiwan.,Graduate Institute of Immunology, College of Medicine, National Taiwan University, Taipei, 110, Taiwan
| | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang Dist., Taipei, 115, Taiwan. .,Graduate Institute of Immunology, College of Medicine, National Taiwan University, Taipei, 110, Taiwan.
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22
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Llabrés S, Tsenkov MI, MacGowan SA, Barton GJ, Zachariae U. Disease related single point mutations alter the global dynamics of a tetratricopeptide (TPR) α-solenoid domain. J Struct Biol 2020; 209:107405. [PMID: 31628985 PMCID: PMC6961204 DOI: 10.1016/j.jsb.2019.107405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 10/04/2019] [Accepted: 10/15/2019] [Indexed: 01/18/2023]
Abstract
Tetratricopeptide repeat (TPR) proteins belong to the class of α-solenoid proteins, in which repetitive units of α-helical hairpin motifs stack to form superhelical, often highly flexible structures. TPR domains occur in a wide variety of proteins, and perform key functional roles including protein folding, protein trafficking, cell cycle control and post-translational modification. Here, we look at the TPR domain of the enzyme O-linked GlcNAc-transferase (OGT), which catalyses O-GlcNAcylation of a broad range of substrate proteins. A number of single-point mutations in the TPR domain of human OGT have been associated with the disease Intellectual Disability (ID). By extended steered and equilibrium atomistic simulations, we show that the OGT-TPR domain acts as an elastic nanospring, and that each of the ID-related local mutations substantially affect the global dynamics of the TPR domain. Since the nanospring character of the OGT-TPR domain is key to its function in binding and releasing OGT substrates, these changes of its biomechanics likely lead to defective substrate interaction. We find that neutral mutations in the human population, selected by analysis of the gnomAD database, do not incur these changes. Our findings may not only help to explain the ID phenotype of the mutants, but also aid the design of TPR proteins with tailored biomechanical properties.
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Affiliation(s)
- Salomé Llabrés
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Maxim I Tsenkov
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Stuart A MacGowan
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Geoffrey J Barton
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK; Physics, School of Science and Engineering, University of Dundee, Dundee, UK.
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23
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Pravata VM, Gundogdu M, Bartual SG, Ferenbach AT, Stavridis M, Õunap K, Pajusalu S, Žordania R, Wojcik MH, van Aalten DMF. A missense mutation in the catalytic domain of O-GlcNAc transferase links perturbations in protein O-GlcNAcylation to X-linked intellectual disability. FEBS Lett 2019; 594:717-727. [PMID: 31627256 PMCID: PMC7042088 DOI: 10.1002/1873-3468.13640] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 06/25/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023]
Abstract
X‐linked intellectual disabilities (XLID) are common developmental disorders. The enzyme O‐GlcNAc transferase encoded by OGT, a recently discovered XLID gene, attaches O‐GlcNAc to nuclear and cytoplasmic proteins. As few missense mutations have been described, it is unclear what the aetiology of the patient phenotypes is. Here, we report the discovery of a missense mutation in the catalytic domain of OGT in an XLID patient. X‐ray crystallography reveals that this variant leads to structural rearrangements in the catalytic domain. The mutation reduces in vitro OGT activity on substrate peptides/protein. Mouse embryonic stem cells carrying the mutation reveal reduced O‐GlcNAcase (OGA) and global O‐GlcNAc levels. These data suggest a direct link between changes in the O‐GlcNAcome and intellectual disability observed in patients carrying OGT mutations.
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Affiliation(s)
- Veronica M Pravata
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, UK
| | - Mehmet Gundogdu
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, UK
| | - Sergio G Bartual
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, UK
| | - Andrew T Ferenbach
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, UK
| | - Marios Stavridis
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, UK
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Estonia
| | - Riina Žordania
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Estonia
| | - Monica H Wojcik
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daan M F van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, UK
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24
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Gorelik A, Bartual SG, Borodkin VS, Varghese J, Ferenbach AT, van Aalten DMF. Genetic recoding to dissect the roles of site-specific protein O-GlcNAcylation. Nat Struct Mol Biol 2019; 26:1071-1077. [PMID: 31695185 PMCID: PMC6858883 DOI: 10.1038/s41594-019-0325-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022]
Abstract
Modification of specific Ser and Thr residues of nucleocytoplasmic proteins with O-GlcNAc, catalyzed by O-GlcNAc transferase (OGT), is an abundant posttranslational event essential for proper animal development and is dysregulated in various diseases. Due to the rapid concurrent removal by the single O-GlcNAcase (OGA), precise functional dissection of site-specific O-GlcNAc modification in vivo is currently not possible without affecting the entire O-GlcNAc proteome. Exploiting the fortuitous promiscuity of OGT, we show that S-GlcNAc is a hydrolytically stable and accurate structural mimic of O-GlcNAc that can be encoded in mammalian systems with CRISPR-Cas9 in an otherwise unperturbed O-GlcNAcome. Using this approach, we target an elusive Ser 405 O-GlcNAc site on OGA, showing that this site-specific modification affects OGA stability.
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Affiliation(s)
- Andrii Gorelik
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Sergio Galan Bartual
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Vladimir S Borodkin
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Joby Varghese
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Andrew T Ferenbach
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Daan M F van Aalten
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.
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25
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King DT, Males A, Davies GJ, Vocadlo DJ. Molecular mechanisms regulating O-linked N-acetylglucosamine (O-GlcNAc)-processing enzymes. Curr Opin Chem Biol 2019; 53:131-144. [PMID: 31654859 DOI: 10.1016/j.cbpa.2019.09.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/04/2019] [Accepted: 09/09/2019] [Indexed: 12/28/2022]
Abstract
The post-translational modification of proteins by O-linked N-acetylglucosamine (O-GlcNAc) dynamically programmes cellular physiology to maintain homoeostasis and tailor biochemical pathways to meet context-dependent cellular needs. Despite diverse roles of played by O-GlcNAc, only two enzymes act antagonistically to govern its cycling; O-GlcNAc transferase installs the monosaccharide on target proteins, and O-GlcNAc hydrolase removes it. The recent literature has exposed a network of mechanisms regulating these two enzymes to choreograph global, and target-specific, O-GlcNAc cycling in response to cellular stress and nutrient availability. Herein, we amalgamate these emerging mechanisms from a structural and molecular perspective to explore how the cell exerts fine control to regulate O-GlcNAcylation of diverse proteins in a selective fashion.
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Affiliation(s)
- Dustin T King
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Alexandra Males
- Department of Chemistry, University of York, York, YO10 5DD, England
| | - Gideon J Davies
- Department of Chemistry, University of York, York, YO10 5DD, England
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.
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26
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Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S. Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection. J Am Chem Soc 2019; 141:12974-12978. [PMID: 31373491 DOI: 10.1021/jacs.9b06061] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
O-GlcNAc is an abundant post-translational modification found on nuclear and cytoplasmic proteins in all metazoans. This modification regulates a wide variety of cellular processes, and elevated O-GlcNAc levels have been implicated in cancer progression. A single essential enzyme, O-GlcNAc transferase (OGT), is responsible for all nucleocytoplasmic O-GlcNAcylation. Understanding how this enzyme chooses its substrates is critical for understanding, and potentially manipulating, its functions. Here we use protein microarray technology and proteome-wide glycosylation profiling to show that conserved aspartate residues in the tetratricopeptide repeat (TPR) lumen of OGT drive substrate selection. Changing these residues to alanines alters substrate selectivity and unexpectedly increases rates of protein glycosylation. Our findings support a model where sites of glycosylation for many OGT substrates are determined by TPR domain contacts to substrate side chains five to fifteen residues C-terminal to the glycosite. In addition to guiding design of inhibitors that target OGT's TPR domain, this information will inform efforts to engineer substrates to explore biological functions.
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Affiliation(s)
- Cassandra M Joiner
- Department of Microbiology , Harvard Medical School , 4 Blackfan Circle , Boston , Massachusetts 02115 , United States
| | - Zebulon G Levine
- Department of Microbiology , Harvard Medical School , 4 Blackfan Circle , Boston , Massachusetts 02115 , United States
| | - Chanat Aonbangkhen
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Suzanne Walker
- Department of Microbiology , Harvard Medical School , 4 Blackfan Circle , Boston , Massachusetts 02115 , United States
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27
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Li Y, Xie M, Men L, Du J. O-GlcNAcylation in immunity and inflammation: An intricate system (Review). Int J Mol Med 2019; 44:363-374. [PMID: 31198979 PMCID: PMC6605495 DOI: 10.3892/ijmm.2019.4238] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/06/2019] [Indexed: 12/20/2022] Open
Abstract
Chronic, low‑grade inflammation associated with obesity and diabetes result from the infiltration of adipose and vascular tissue by immune cells and contributes to cardiovascular complications. Despite an incomplete understanding of the mechanistic underpinnings of immune cell differentiation and inflammation, O‑GlcNAcylation, the addition of O‑linked N‑acetylglucosamine (O‑GlcNAc) to cytoplasmic, nuclear and mitochondrial proteins by the two cycling enzymes, the O‑linked N‑acetylglucosamine transferase (OGT) and the O‑GlcNAcase (OGA), may contribute to fine‑tune immunity and inflammation in both physiological and pathological conditions. Early studies have indicated that O‑GlcNAcylation of proteins play a pro‑inflammatory role in diabetes and insulin resistance, whereas subsequent studies have demonstrated that this post‑translational modification could also be protective against acute injuries. These studies suggest that diverse types of insults result in dynamic changes to O‑GlcNAcylation patterns, which fluctuate with cellular metabolism to promote or inhibit inflammation. In this review, the current understanding of O‑GlcNAcylation and its adaptive modulation in immune and inflammatory responses is summarized.
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Affiliation(s)
- Yu Li
- Department of Endocrinology
| | - Mingzheng Xie
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, P.R. China
| | | | - Jianling Du
- Department of Endocrinology
- Correspondence to: Dr Jianling Du, Department of Endocrinology, The First Affiliated Hospital of Dalian Medical University, 193 Lianhe Road, Dalian, Liaoning 116011, P.R. China, E-mail:
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28
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Zou Z, Xie X, Li W, Song X, Tan Y, Wu H, Xiao J, Feng H. Black carp TAB1 up-regulates TAK1/IRF7/IFN signaling during the antiviral innate immune activation. FISH & SHELLFISH IMMUNOLOGY 2019; 89:736-744. [PMID: 31002927 DOI: 10.1016/j.fsi.2019.04.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/04/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
TAK1-binding protein 1 (TAB1) forms the protein complex with TAK1 and enhances its kinase activity in human and mammals. To elucidate the role of TAB1 in the innate immunity of teleost sfih, the TAB1 homologue of black carp (Mylopharyngodon piceus) (bcTAB1) has been cloned and characterized in this paper. bcTAB1 is composed of 498 amino acids and contains a typical PP2Cc domain like its mammalian counterpart. The transcription of bcTAB1 gene in vivo and ex vivo varied in response to different stimuli; and the immunofluorescence staining showed that bcTAB1 was distributed in both cytoplasm and nucleus of host cell. The reporter assay showed that neither bcTAB1-expression alone nor co-expression of bcTAB1 and bcTAK1 could activate the transcription of IFN in EPC cells. Accordingly, EPC cells expressing bcTAB1 or co-expressing bcTAB1 and bcTAK1 showed no improved antiviral activity against grass carp reovirus (GCRV) and spring viremia of carp virus (SVCV). However, EPC cells co-expressing bcTAB1, bcTAK1 and bcIRF7 showed fiercely increased IFN-inducing ability in reporter assay and obviously improved antiviral activity in plaque assay compared with EPC cells co-expressing bcTAK1 and bcIRF7. The subsequent co-immunoprecipitation assay identified that bcTAB1 associated with bcTAK1 but not interacted with bcIRF7. Based on our previous finding that bcTAK1 up-regulates bcIRF7-mediated IFN signaling during host innate immune activation, the data generated in this study support the conclusion that bcTAB1 interacts with bcTAK1 and boosts bcTAK1-activated bcIRF7/IFN signaling during host antiviral innate immune response against GCRV and SVCV.
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Affiliation(s)
- Ziqi Zou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xinchi Xie
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Wanzhen Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xuejiao Song
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yaqi Tan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Hui Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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29
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Shi J, Ruijtenbeek R, Pieters RJ. Demystifying O-GlcNAcylation: hints from peptide substrates. Glycobiology 2019; 28:814-824. [PMID: 29635275 DOI: 10.1093/glycob/cwy031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
O-GlcNAcylation, analogous to phosphorylation, is an essential post-translational modification of proteins at Ser/Thr residues with a single β-N-acetylglucosamine moiety. This dynamic protein modification regulates many fundamental cellular processes and its deregulation has been linked to chronic diseases such as cancer, diabetes and neurodegenerative disorders. Reversible attachment and removal of O-GlcNAc is governed only by O-GlcNAc transferase and O-GlcNAcase, respectively. Peptide substrates, derived from natural O-GlcNAcylation targets, function in the catalytic cores of these two enzymes by maintaining interactions between enzyme and substrate, which makes them ideal models for the study of O-GlcNAcylation and deglycosylation. These peptides provide valuable tools for a deeper understanding of O-GlcNAc processing enzymes. By taking advantage of peptide chemistry, recent progress in the study of activity and regulatory mechanisms of these two enzymes has advanced our understanding of their fundamental specificities as well as their potential as therapeutic targets. Hence, this review summarizes the recent achievements on this modification studied at the peptide level, focusing on enzyme activity, enzyme specificity, direct function, site-specific antibodies and peptide substrate-inspired inhibitors.
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Affiliation(s)
- Jie Shi
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands
| | - Rob Ruijtenbeek
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands.,PamGene International BV, HH's-Hertogenbosch, The Netherlands
| | - Roland J Pieters
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands
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30
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Structural characterization of the O-GlcNAc cycling enzymes: insights into substrate recognition and catalytic mechanisms. Curr Opin Struct Biol 2019; 56:97-106. [PMID: 30708324 DOI: 10.1016/j.sbi.2018.12.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 12/05/2018] [Indexed: 12/19/2022]
Abstract
Dysregulation of nuclear and cytoplasmic O-linked β-N-acetylglucosamine (O-GlcNAc) cycling is implicated in a range of diseases including diabetes and cancer. This modification maintains cellular homeostasis by regulating several biological processes, such as cell signaling. This highly regulated cycle is governed by two sole essential enzymes, O-GlcNAc transferase and O-GlcNAcase that add O-GlcNAc and remove it from over a thousand substrates, respectively. Until recently, due to lack of structural information, the mechanism of substrate recognition has eluted researchers. Here, we review recent successes in structural characterization of these enzymes and how this information has illuminated key features essential for catalysis and substrate recognition. Additionally, we highlight recent studies which have used this information to expand our understanding of substrate specificity by each enzyme.
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31
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Xu S, Chong K. Remembering winter through vernalisation. NATURE PLANTS 2018; 4:997-1009. [PMID: 30478363 DOI: 10.1038/s41477-018-0301-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 10/12/2018] [Indexed: 05/10/2023]
Abstract
Vernalisation is the programmed physiological process in which prolonged cold-exposure provides competency to flower in plants; widely found in winter and biennial species, such as Arabidopsis, fruit trees, vegetables and wheat. This phenomenon is regulated by diverse genetic networks, and memory of vernalisation in a life cycle mainly depends on epigenetic mechanisms. However, less is known about how to count winter-dosage for flowering in plants. Here, we compare the vernalisation genetic framework between the dicots Arabidopsis, temperate grasses, wheat, barley and Brachypodium. We discuss vernalisation mechanisms involving crosstalk between phosphorylation and O-GlcNAcylation modification of key proteins, and epigenetic modifications of the key gene VRN1 in wheat. We also highlight the potential evolutionary origins of vernalisation in various species. Current progress toward understanding the regulation of vernalisation requirements provides insight that will inform the design of molecular breeding strategies for winter crops.
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Affiliation(s)
- Shujuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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32
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Zachara NE. Critical observations that shaped our understanding of the function(s) of intracellular glycosylation (O-GlcNAc). FEBS Lett 2018; 592:3950-3975. [PMID: 30414174 DOI: 10.1002/1873-3468.13286] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/30/2022]
Abstract
Almost 100 years after the first descriptions of proteins conjugated to carbohydrates (mucins), several studies suggested that glycoproteins were not restricted to the serum, extracellular matrix, cell surface, or endomembrane system. In the 1980s, key data emerged demonstrating that intracellular proteins were modified by monosaccharides of O-linked β-N-acetylglucosamine (O-GlcNAc). Subsequently, this modification was identified on thousands of proteins that regulate cellular processes as diverse as protein aggregation, localization, post-translational modifications, activity, and interactions. In this Review, we will highlight critical discoveries that shaped our understanding of the molecular events underpinning the impact of O-GlcNAc on protein function, the role that O-GlcNAc plays in maintaining cellular homeostasis, and our understanding of the mechanisms that regulate O-GlcNAc-cycling.
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Affiliation(s)
- Natasha E Zachara
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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33
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Hu CW, Worth M, Li H, Jiang J. Chemical and Biochemical Strategies To Explore the Substrate Recognition of O-GlcNAc-Cycling Enzymes. Chembiochem 2018; 20:312-318. [PMID: 30199580 DOI: 10.1002/cbic.201800481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Indexed: 12/11/2022]
Abstract
The O-linked N-acetylglucosamine (O-GlcNAc) modification is an essential component in cell regulation. A single pair of human enzymes conducts this modification dynamically on a broad variety of proteins: O-GlcNAc transferase (OGT) adds the GlcNAc residue and O-GlcNAcase (OGA) hydrolyzes it. This modification is dysregulated in many diseases, but its exact effect on particular substrates remains unclear. In addition, no apparent sequence motif has been found in the modified proteins, and the factors controlling the substrate specificity of OGT and OGA are largely unknown. In this minireview, we will discuss recent developments in chemical and biochemical methods toward addressing the challenge of OGT and OGA substrate recognition. We hope that the new concepts and knowledge from these studies will promote research in this area to advance understanding of O-GlcNAc regulation in health and disease.
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Affiliation(s)
- Chia-Wei Hu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Matthew Worth
- Department of Chemistry, University of Wisconsin-Madison, 101 University Avenue, Madison, WI, 53706, USA
| | - Hao Li
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Jiaoyang Jiang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
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34
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Tan HY, Eskandari R, Shen D, Zhu Y, Liu TW, Willems LI, Alteen MG, Madden Z, Vocadlo DJ. Direct One-Step Fluorescent Labeling of O-GlcNAc-Modified Proteins in Live Cells Using Metabolic Intermediates. J Am Chem Soc 2018; 140:15300-15308. [PMID: 30296064 DOI: 10.1021/jacs.8b08260] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The modification of proteins with O-linked N-acetylglucosamine ( O-GlcNAc) by the enzyme O-GlcNAc transferase (OGT) has emerged as an important regulator of cellular physiology. Metabolic labeling strategies to monitor O-GlcNAcylation in cells have proven of great value for uncovering the molecular roles of O-GlcNAc. These strategies rely on two-step labeling procedures, which limits the scope of experiments that can be performed. Here, we report on the creation of fluorescent uridine 5'-diphospho- N-acetylglucosamine (UDP-GlcNAc) analogues in which the N-acyl group of glucosamine is modified with a suitable linker and fluorophore. Using human OGT, we show these donor sugar substrates permit direct monitoring of OGT activity on protein substrates in vitro. We show that feeding cells with a corresponding fluorescent metabolic precursor for the last step of the hexosamine biosynthetic pathway (HBP) leads to its metabolic assimilation and labeling of O-GlcNAcylated proteins within live cells. This one-step metabolic feeding strategy permits labeling of O-GlcNAcylated proteins with a fluorescent glucosamine-nitrobenzoxadiazole (GlcN-NBD) conjugate that accumulates in a time- and dose-dependent manner. Because no genetic engineering of cells is required, we anticipate this strategy should be generally amenable to studying the roles of O-GlcNAc in cellular physiology as well as to gain an improved understanding of the regulation of OGT within cells. The further expansion of this one-step in-cell labeling strategy should enable performing a range of experiments including two-color pulse chase experiments and monitoring OGT activity on specific protein substrates in live cells.
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35
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Martin SES, Tan ZW, Itkonen HM, Duveau DY, Paulo JA, Janetzko J, Boutz PL, Törk L, Moss FA, Thomas CJ, Gygi SP, Lazarus MB, Walker S. Structure-Based Evolution of Low Nanomolar O-GlcNAc Transferase Inhibitors. J Am Chem Soc 2018; 140:13542-13545. [PMID: 30285435 DOI: 10.1021/jacs.8b07328] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Reversible glycosylation of nuclear and cytoplasmic proteins is an important regulatory mechanism across metazoans. One enzyme, O-linked N-acetylglucosamine transferase (OGT), is responsible for all nucleocytoplasmic glycosylation and there is a well-known need for potent, cell-permeable inhibitors to interrogate OGT function. Here we report the structure-based evolution of OGT inhibitors culminating in compounds with low nanomolar inhibitory potency and on-target cellular activity. In addition to disclosing useful OGT inhibitors, the structures we report provide insight into how to inhibit glycosyltransferases, a family of enzymes that has been notoriously refractory to inhibitor development.
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Affiliation(s)
- Sara E S Martin
- Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Zhi-Wei Tan
- Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Harri M Itkonen
- Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Damien Y Duveau
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - John Janetzko
- Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States.,Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Paul L Boutz
- The David H. Koch Institute for Integrative Cancer Research , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Lisa Törk
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Frederick A Moss
- Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Michael B Lazarus
- Department of Pharmacological Sciences , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Suzanne Walker
- Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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36
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Kapuria V, Röhrig UF, Waridel P, Lammers F, Borodkin VS, van Aalten DMF, Zoete V, Herr W. The conserved threonine-rich region of the HCF-1 PRO repeat activates promiscuous OGT:UDP-GlcNAc glycosylation and proteolysis activities. J Biol Chem 2018; 293:17754-17768. [PMID: 30224358 PMCID: PMC6240873 DOI: 10.1074/jbc.ra118.004185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/05/2018] [Indexed: 12/28/2022] Open
Abstract
O-Linked GlcNAc transferase (OGT) possesses dual glycosyltransferase–protease activities. OGT thereby stably glycosylates serines and threonines of numerous proteins and, via a transient glutamate glycosylation, cleaves a single known substrate—the so-called HCF-1PRO repeat of the transcriptional co-regulator host-cell factor 1 (HCF-1). Here, we probed the relationship between these distinct glycosylation and proteolytic activities. For proteolysis, the HCF-1PRO repeat possesses an important extended threonine-rich region that is tightly bound by the OGT tetratricopeptide-repeat (TPR) region. We report that linkage of this HCF-1PRO-repeat, threonine-rich region to heterologous substrate sequences also potentiates robust serine glycosylation with the otherwise poor Rp-αS-UDP-GlcNAc diastereomer phosphorothioate and UDP-5S-GlcNAc OGT co-substrates. Furthermore, it potentiated proteolysis of a non-HCF-1PRO-repeat cleavage sequence, provided it contained an appropriately positioned glutamate residue. Using serine- or glutamate-containing HCF-1PRO-repeat sequences, we show that proposed OGT-based or UDP-GlcNAc–based serine-acceptor residue activation mechanisms can be circumvented independently, but not when disrupted together. In contrast, disruption of both proposed activation mechanisms even in combination did not inhibit OGT-mediated proteolysis. These results reveal a multiplicity of OGT glycosylation strategies, some leading to proteolysis, which could be targets of alternative molecular regulatory strategies.
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Affiliation(s)
- Vaibhav Kapuria
- From the Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Ute F Röhrig
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Patrice Waridel
- Protein Analysis Facility, Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Fabienne Lammers
- From the Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vladimir S Borodkin
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Daan M F van Aalten
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Vincent Zoete
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Department of Fundamental Oncology, Ludwig Lausanne Branch, Faculty of Biology and Medicine, University of Lausanne, 1066 Epalinges, Switzerland
| | - Winship Herr
- From the Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
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37
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Laarse SAM, Leney AC, Heck AJR. Crosstalk between phosphorylation and O‐Glc
NA
cylation: friend or foe. FEBS J 2018; 285:3152-3167. [DOI: 10.1111/febs.14491] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/27/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Saar A. M. Laarse
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
| | - Aneika C. Leney
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
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38
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Abstract
Residue interaction networks (RINs) have been shown to be relevant representations of the tertiary or quaternary structures of proteins, in particular thanks to network centrality analyses. We recently developed the RINspector 1.0.0 Cytoscape app, which couples centrality analyses with backbone flexibility predictions. This combined approach permits the identification of crucial residues for the folding or function of the protein that can constitute good targets for mutagenesis experiments. Here we present an application programming interface (API) for RINspector 1.1.0 that enables interplay between Cytoscape, RINspector and external languages, such as R or Python. This API provides easy access to batch centrality calculations and flexibility predictions, and allows for the easy comparison of results between different structures. These comparisons can lead to the identification of specific and conserved central residues, and show the impact of mutations to these and other residues on the flexibility of the proteins. We give two use cases to demonstrate the interest of these functionalities and provide the corresponding scripts: the first concerns NMR conformers, the second focuses on mutations in a structure.
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Affiliation(s)
| | - Théo Mauri
- CNRS UMR 8576 UGSF, University of Lille, Lille, F-59000, France
| | - Marc F Lensink
- CNRS UMR 8576 UGSF, University of Lille, Lille, F-59000, France
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39
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The O-GlcNAc Transferase Intellectual Disability Mutation L254F Distorts the TPR Helix. Cell Chem Biol 2018; 25:513-518.e4. [PMID: 29606577 PMCID: PMC5967971 DOI: 10.1016/j.chembiol.2018.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/30/2018] [Accepted: 02/28/2018] [Indexed: 01/18/2023]
Abstract
O-linked β-N-acetyl-D-glucosamine (O-GlcNAc) transferase (OGT) regulates protein O-GlcNAcylation, an essential post-translational modification that is abundant in the brain. Recently, OGT mutations have been associated with intellectual disability, although it is not understood how they affect OGT structure and function. Using a multi-disciplinary approach we show that the L254F OGT mutation leads to conformational changes of the tetratricopeptide repeats and reduced activity, revealing the molecular mechanisms contributing to pathogenesis. The intellectual disability L254F mutation in OGT affects activity The L254F mutation leads to shifts up to 12 Å in the OGT structure Thermal denaturing studies reveal reduction in TPR stability caused by L254F Simulations suggest the presence of alternate TPRL254F conformations
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Levine ZG, Fan C, Melicher MS, Orman M, Benjamin T, Walker S. O-GlcNAc Transferase Recognizes Protein Substrates Using an Asparagine Ladder in the Tetratricopeptide Repeat (TPR) Superhelix. J Am Chem Soc 2018; 140:3510-3513. [PMID: 29485866 PMCID: PMC5937710 DOI: 10.1021/jacs.7b13546] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The essential mammalian enzyme O-GlcNAc Transferase (OGT) is uniquely responsible for transferring N-acetylglucosamine to over a thousand nuclear and cytoplasmic proteins, yet there is no known consensus sequence and it remains unclear how OGT recognizes its substrates. To address this question, we developed a protein microarray assay that chemoenzymatically labels de novo sites of glycosylation with biotin, allowing us to simultaneously assess OGT activity across >6000 human proteins. With this assay we examined the contribution to substrate selection of a conserved asparagine ladder within the lumen of OGT's superhelical tetratricopeptide repeat (TPR) domain. When five asparagines were mutated, OGT retained significant activity against short peptides, but showed limited limited glycosylation of protein substrates on the microarray. O-GlcNAcylation of protein substrates in cell extracts was also greatly attenuated. We conclude that OGT recognizes the majority of its substrates by binding them to the asparagine ladder in the TPR lumen proximal to the catalytic domain.
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Affiliation(s)
- Zebulon G. Levine
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Chenguang Fan
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Michael S. Melicher
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Marina Orman
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Tania Benjamin
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
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