1
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Yadav A, Kumar N, Kashyap S. Bi(OTf) 3-promoted direct activation of formidable per-O-acetylated ʟ-rhamnose Donor: Stereoselective access to α-ʟ-rhamnopyranosides. Carbohydr Res 2025; 554:109527. [PMID: 40424804 DOI: 10.1016/j.carres.2025.109527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2025] [Revised: 05/10/2025] [Accepted: 05/13/2025] [Indexed: 05/29/2025]
Abstract
Rare ʟ-hexoses, including deoxy ʟ-hexoses, serve as potential chemical probes for carbohydrate-based drug discovery and vaccine development. 6-Deoxy sugars, particularly ʟ-rhamnose, are essential components of bacterial surface glycans, playing a key role in pathogen-host cell recognition and various physiological functions. Herein, we present an alternative and highly efficient ʟ-rhamnosylation utilizing the milder oxo-philic Bi(OTf)3 as the promoter, enabling the assembly of biologically significant α-ʟ-rhamnopyranosides in good yields. The Bi-mediated direct anomeric activation of peracetylated ʟ-rhamnose (ʟ-Rha) is amenable to a wide range of acceptors, including sugars, amino acids, natural products, and bioactive scaffolds. The stereocontrolled glycosylation offers significant advantages, utilizing greener catalysts and atom-economical transformations, avoiding expensive ligands/additives, and tolerating the diverse functional groups.
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Affiliation(s)
- Ankit Yadav
- Carbohydrate Chemistry Research Laboratory (CCRL), Department of Chemistry, Malaviya National Institute of Technology Jaipur (MNITJ), J. L. N. Marg, Jaipur, 302017, India
| | - Nitin Kumar
- Carbohydrate Chemistry Research Laboratory (CCRL), Department of Chemistry, Malaviya National Institute of Technology Jaipur (MNITJ), J. L. N. Marg, Jaipur, 302017, India
| | - Sudhir Kashyap
- Carbohydrate Chemistry Research Laboratory (CCRL), Department of Chemistry, Malaviya National Institute of Technology Jaipur (MNITJ), J. L. N. Marg, Jaipur, 302017, India.
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2
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Saxena H, Patel R, Kelly J, Wakarchuk W. Differential substrate preferences IN ACTINOBACTERIAL protein O-MANNOSYLTRANSFERASES and alteration of protein-O-MANNOSYLATION by choice of secretion pathway. Glycobiology 2025; 35:cwae095. [PMID: 39673494 PMCID: PMC11727336 DOI: 10.1093/glycob/cwae095] [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: 07/07/2024] [Revised: 11/14/2024] [Accepted: 11/28/2024] [Indexed: 12/16/2024] Open
Abstract
Protein-O-mannosylation (POM) is a form of O-glycosylation that is ubiquitous and has been studied extensively throughout in fungi and animals. The key glycosyltransferase, protein O-mannosyltransferase (PMT), a member of family GT-39, is also found in over 3,800 bacterial genomes but has only been minimally examined from prokaryotes. In prokaryotes POM has only been investigated in terms of pathogenicity (in Mycobacterium tuberculosis) even though there are far more non-pathogenic bacteria that appear to carry out POM. To date, there is no consensus on what benefit POM imparts to the non-pathogenic bacteria that can perform it. Through the generation of a POM deficient mutant of Corynebacterium glutamicum - a widely utilized and known protein O-mannosylating actinobacteria - this work shows that even closely related actinobacterial GT-39 s (the enzymes responsible for the initiation of POM) can have different substrate specificities for targets of POM. Moreover, presented here is evidence that POM does not only occur in a SEC-dependent manner; POM also occurs with TAT and non-SEC secreted substrates in a specific and likely tightly regulated manner. Together these results highlight the need for further biochemical characterization of POM in these and other bacterial species to help elucidate the true nature of its biological functions.
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Affiliation(s)
- Hirak Saxena
- Department of Biological Sciences, University of Alberta, 116 St & 85 Ave, Edmonton, AB T6G 2R3
| | - Rucha Patel
- Department of Biological Sciences, University of Alberta, 116 St & 85 Ave, Edmonton, AB T6G 2R3
| | - John Kelly
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Dr, Ottawa, ON K1N 1J1
| | - Warren Wakarchuk
- Department of Biological Sciences, University of Alberta, 116 St & 85 Ave, Edmonton, AB T6G 2R3
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3
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Hendershot LM, Buck TM, Brodsky JL. The Essential Functions of Molecular Chaperones and Folding Enzymes in Maintaining Endoplasmic Reticulum Homeostasis. J Mol Biol 2024; 436:168418. [PMID: 38143019 PMCID: PMC12015986 DOI: 10.1016/j.jmb.2023.168418] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
It has been estimated that up to one-third of the proteins encoded by the human genome enter the endoplasmic reticulum (ER) as extended polypeptide chains where they undergo covalent modifications, fold into their native structures, and assemble into oligomeric protein complexes. The fidelity of these processes is critical to support organellar, cellular, and organismal health, and is perhaps best underscored by the growing number of disease-causing mutations that reduce the fidelity of protein biogenesis in the ER. To meet demands encountered by the diverse protein clientele that mature in the ER, this organelle is populated with a cadre of molecular chaperones that prevent protein aggregation, facilitate protein disulfide isomerization, and lower the activation energy barrier of cis-trans prolyl isomerization. Components of the lectin (glycan-binding) chaperone system also reside within the ER and play numerous roles during protein biogenesis. In addition, the ER houses multiple homologs of select chaperones that can recognize and act upon diverse peptide signatures. Moreover, redundancy helps ensure that folding-compromised substrates are unable to overwhelm essential ER-resident chaperones and enzymes. In contrast, the ER in higher eukaryotic cells possesses a single member of the Hsp70, Hsp90, and Hsp110 chaperone families, even though several homologs of these molecules reside in the cytoplasm. In this review, we discuss specific functions of the many factors that maintain ER quality control, highlight some of their interactions, and describe the vulnerabilities that arise from the absence of multiple members of some chaperone families.
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Affiliation(s)
- Linda M Hendershot
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
| | - Teresa M Buck
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
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4
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Sharma AK, Khandelwal R, Wolfrum C. Futile cycles: Emerging utility from apparent futility. Cell Metab 2024; 36:1184-1203. [PMID: 38565147 DOI: 10.1016/j.cmet.2024.03.008] [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: 01/05/2024] [Revised: 02/15/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024]
Abstract
Futile cycles are biological phenomena where two opposing biochemical reactions run simultaneously, resulting in a net energy loss without appreciable productivity. Such a state was presumed to be a biological aberration and thus deemed an energy-wasting "futile" cycle. However, multiple pieces of evidence suggest that biological utilities emerge from futile cycles. A few established functions of futile cycles are to control metabolic sensitivity, modulate energy homeostasis, and drive adaptive thermogenesis. Yet, the physiological regulation, implication, and pathological relevance of most futile cycles remain poorly studied. In this review, we highlight the abundance and versatility of futile cycles and propose a classification scheme. We further discuss the energetic implications of various futile cycles and their impact on basal metabolic rate, their bona fide and tentative pathophysiological implications, and putative drug interactions.
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Affiliation(s)
- Anand Kumar Sharma
- Laboratory of Translational Nutrition Biology, Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland.
| | - Radhika Khandelwal
- Laboratory of Translational Nutrition Biology, Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Christian Wolfrum
- Laboratory of Translational Nutrition Biology, Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland.
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5
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Strawn G, Wong RWK, Young BP, Davey M, Nislow C, Conibear E, Loewen CJR, Mayor T. Genome-wide screen identifies new set of genes for improved heterologous laccase expression in Saccharomyces cerevisiae. Microb Cell Fact 2024; 23:36. [PMID: 38287338 PMCID: PMC10823697 DOI: 10.1186/s12934-024-02298-0] [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: 07/12/2023] [Accepted: 01/04/2024] [Indexed: 01/31/2024] Open
Abstract
The yeast Saccharomyces cerevisiae is widely used as a host cell for recombinant protein production due to its fast growth, cost-effective culturing, and ability to secrete large and complex proteins. However, one major drawback is the relatively low yield of produced proteins compared to other host systems. To address this issue, we developed an overlay assay to screen the yeast knockout collection and identify mutants that enhance recombinant protein production, specifically focusing on the secretion of the Trametes trogii fungal laccase enzyme. Gene ontology analysis of these mutants revealed an enrichment of processes including vacuolar targeting, vesicle trafficking, proteolysis, and glycolipid metabolism. We confirmed that a significant portion of these mutants also showed increased activity of the secreted laccase when grown in liquid culture. Notably, we found that the combination of deletions of OCA6, a tyrosine phosphatase gene, along with PMT1 or PMT2, two genes encoding ER membrane protein-O-mannosyltransferases involved in ER quality control, and SKI3, which encode for a component of the SKI complex responsible for mRNA degradation, further increased secreted laccase activity. Conversely, we also identified over 200 gene deletions that resulted in decreased secreted laccase activity, including many genes that encode for mitochondrial proteins and components of the ER-associated degradation pathway. Intriguingly, the deletion of the ER DNAJ co-chaperone gene SCJ1 led to almost no secreted laccase activity. When we expressed SCJ1 from a low-copy plasmid, laccase secretion was restored. However, overexpression of SCJ1 had a detrimental effect, indicating that precise dosing of key chaperone proteins is crucial for optimal recombinant protein expression. This study offers potential strategies for enhancing the overall yield of recombinant proteins and provides new avenues for further research in optimizing protein production systems.
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Affiliation(s)
- Garrett Strawn
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Ryan W K Wong
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Barry P Young
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Christopher J R Loewen
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
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6
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Cui H, Cui X, Yang X, Cui X, Sun Y, Yuan D, Cui Q, Deng Y, Sun E, Chen YQ, Guo H, Deng Z, Wang J, Xu S, Sun X, Wei Z, Liu X. Effect of ATG8 or SAC1 deficiency on the cell proliferation and lifespan of the long-lived PMT1 deficiency yeast cells. FEMS Microbiol Lett 2024; 371:fnad121. [PMID: 38258560 DOI: 10.1093/femsle/fnad121] [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: 04/18/2023] [Revised: 10/22/2023] [Accepted: 11/20/2023] [Indexed: 01/24/2024] Open
Abstract
Autophagy is pivotal in maintaining intracellular homeostasis, which involves various biological processes, including cellular senescence and lifespan modulation. Being an important member of the protein O-mannosyltransferase (PMT) family of enzymes, Pmt1p deficiency can significantly extend the replicative lifespan (RLS) of yeast cells through an endoplasmic reticulum (ER) unfolded protein response (UPR) pathway, which is participated in protein homeostasis. Nevertheless, the mechanisms that Pmt1p regulates the lifespan of yeast cells still need to be explored. In this study, we found that the long-lived PMT1 deficiency strain (pmt1Δ) elevated the expression levels of most autophagy-related genes, the expression levels of total GFP-Atg8 fusion protein and free GFP protein compared with wild-type yeast strain (BY4742). Moreover, the long-lived pmt1Δ strain showed the greater dot-signal accumulation from GFP-Atg8 fusion protein in the vacuole lumen through a confocal microscope. However, deficiency of SAC1 or ATG8, two essential components of the autophagy process, decreased the cell proliferation ability of the long-lived pmt1Δ yeast cells, and prevented the lifespan extension. In addition, our findings demonstrated that overexpression of ATG8 had no potential effect on the RLS of the pmt1Δ yeast cells, and the maintained incubation of minimal synthetic medium lacking nitrogen (SD-N medium as starvation-induced autophagy) inhibited the cell proliferation ability of the pmt1Δ yeast cells with the culture time, and blocked the lifespan extension, especially in the SD-N medium cultured for 15 days. Our results suggest that the long-lived pmt1Δ strain enhances the basal autophagy activity, while deficiency of SAC1 or ATG8 decreases the cell proliferation ability and shortens the RLS of the long-lived pmt1Δ yeast cells. Moreover, the maintained starvation-induced autophagy impairs extension of the long-lived pmt1Δ yeast cells, and even leads to the cell death.
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Affiliation(s)
- Hongjing Cui
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
- School of Basic Medicine, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Xiaojing Cui
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
- The First Dongguan Affiliated Hospital,Guangdong Medical University, No. 42 Jiaoping Road, Tangxia Town, Dongguan 523808, China
| | - Xiaodi Yang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Xingang Cui
- Mudanjiang Medical College, No. 3 Tongxiang Street, Aimin District, Mudanjiang City 157011, Hei Longjiang Proviince, China
| | - Yaxin Sun
- Mudanjiang Medical College, No. 3 Tongxiang Street, Aimin District, Mudanjiang City 157011, Hei Longjiang Proviince, China
| | - Di Yuan
- School of the Second Clinical, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Qiong Cui
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Yanwen Deng
- School of the Second Clinical, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Enhao Sun
- School of the Second Clinical, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Ya-Qin Chen
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Hongsheng Guo
- School of Basic Medicine, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Ziliang Deng
- School of Basic Medicine, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Junfang Wang
- School of Basic Medicine, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Shun Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Xuerong Sun
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Zhao Wei
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Xinguang Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
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7
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Kumar M, Kumar N, Gurawa A, Kashyap S. Stereoselective Synthesis of
α
‐ʟ‐Rhamnopyranosides from ʟ‐Rhamnal Employing Ruthenium‐Catalysis. ChemistrySelect 2022. [DOI: 10.1002/slct.202200963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Manoj Kumar
- Carbohydrate Chemistry Research Laboratory (CCRL) Department of Chemistry Malaviya National Institute of Technology Jaipur (MNIT Jaipur) J. L. N. Marg Jaipur 302 017 INDIA
| | - Nitin Kumar
- Carbohydrate Chemistry Research Laboratory (CCRL) Department of Chemistry Malaviya National Institute of Technology Jaipur (MNIT Jaipur) J. L. N. Marg Jaipur 302 017 INDIA
| | - Aakanksha Gurawa
- Carbohydrate Chemistry Research Laboratory (CCRL) Department of Chemistry Malaviya National Institute of Technology Jaipur (MNIT Jaipur) J. L. N. Marg Jaipur 302 017 INDIA
| | - Sudhir Kashyap
- Carbohydrate Chemistry Research Laboratory (CCRL) Department of Chemistry Malaviya National Institute of Technology Jaipur (MNIT Jaipur) J. L. N. Marg Jaipur 302 017 INDIA
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8
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Hang J, Wang J, Lu M, Xue Y, Qiao J, Tao L. Protein O-mannosylation across kingdoms and related diseases: From glycobiology to glycopathology. Biomed Pharmacother 2022; 148:112685. [PMID: 35149389 DOI: 10.1016/j.biopha.2022.112685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/18/2022] Open
Abstract
The post-translational glycosylation of proteins by O-linked α-mannose is conserved from bacteria to humans. Due to advances in high-throughput mass spectrometry-based approaches, a variety of glycoproteins are identified to be O-mannosylated. Various proteins with O-mannosylation are involved in biological processes, providing essential necessity for proper growth and development. In this review, we summarize the process and regulation of O-mannosylation. The multi-step O-mannosylation procedures are quite dynamic and complex, especially when considering the structural and functional inspection of the involved enzymes. The widely studied O-mannosylated proteins in human include α-Dystroglycan (α-DG), cadherins, protocadherins, and plexin, and their aberrant O-mannosylation are associated with many diseases. In addition, O-mannosylation also contributes to diverse functions in lower eukaryotes and prokaryotes. Finally, we present the relationship between O-mannosylation and gut microbiota (GM), and elucidate that O-mannosylation in microbiome is of great importance in the dynamic balance of GM. Our study provides an overview of the processes of O-mannosylation in mammalian cells and other organisms, and also associated regulated enzymes and biological functions, which could contribute to the understanding of newly discovered O-mannosylated glycoproteins.
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Affiliation(s)
- Jing Hang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Jinpeng Wang
- Department of Orthopedics, First Hospital of China Medical University, Shenyang 110001, China
| | - Minzhen Lu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yuchuan Xue
- The First Department of Clinical Medicine, China Medical University, Shenyang 110001, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China.
| | - Lin Tao
- Department of Orthopedics, First Hospital of China Medical University, Shenyang 110001, China.
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9
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Bai L, Li H. Protein N-glycosylation and O-mannosylation are catalyzed by two evolutionarily related GT-C glycosyltransferases. Curr Opin Struct Biol 2021; 68:66-73. [PMID: 33445129 PMCID: PMC8222153 DOI: 10.1016/j.sbi.2020.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/23/2020] [Indexed: 11/30/2022]
Abstract
The structural folds of glycosyltransferases are categorized into three superfamilies: GT-A, GT-B, and GT-C. Few structures of GT-C fold existed in the Protein Data Bank prior to the recent advent of high-resolution cryo-EM, because the glycosyltransferases are large membrane proteins that are difficult to crystallize. The use of cryo-EM has resulted in the structures of several key GT-C glycosyltransferases. Here we summarize the latest structural features of and mechanistic insights into these membrane enzyme complexes.
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Affiliation(s)
- Lin Bai
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing 100083, PR China.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, United States.
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10
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Chiapparino A, Grbavac A, Jonker HR, Hackmann Y, Mortensen S, Zatorska E, Schott A, Stier G, Saxena K, Wild K, Schwalbe H, Strahl S, Sinning I. Functional implications of MIR domains in protein O-mannosylation. eLife 2020; 9:61189. [PMID: 33357379 PMCID: PMC7759382 DOI: 10.7554/elife.61189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
Protein O-mannosyltransferases (PMTs) represent a conserved family of multispanning endoplasmic reticulum membrane proteins involved in glycosylation of S/T-rich protein substrates and unfolded proteins. PMTs work as dimers and contain a luminal MIR domain with a β-trefoil fold, which is susceptive for missense mutations causing α-dystroglycanopathies in humans. Here, we analyze PMT-MIR domains by an integrated structural biology approach using X-ray crystallography and NMR spectroscopy and evaluate their role in PMT function in vivo. We determine Pmt2- and Pmt3-MIR domain structures and identify two conserved mannose-binding sites, which are consistent with general β-trefoil carbohydrate-binding sites (α, β), and also a unique PMT2-subfamily exposed FKR motif. We show that conserved residues in site α influence enzyme processivity of the Pmt1-Pmt2 heterodimer in vivo. Integration of the data into the context of a Pmt1-Pmt2 structure and comparison with homologous β-trefoil – carbohydrate complexes allows for a functional description of MIR domains in protein O-mannosylation.
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Affiliation(s)
| | - Antonija Grbavac
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Hendrik Ra Jonker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main, Germany
| | - Yvonne Hackmann
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Sofia Mortensen
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Ewa Zatorska
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Andrea Schott
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Gunter Stier
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main, Germany
| | - Sabine Strahl
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
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11
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Ninagawa S, George G, Mori K. Mechanisms of productive folding and endoplasmic reticulum-associated degradation of glycoproteins and non-glycoproteins. Biochim Biophys Acta Gen Subj 2020; 1865:129812. [PMID: 33316349 DOI: 10.1016/j.bbagen.2020.129812] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND The quality of proteins destined for the secretory pathway is ensured by two distinct mechanisms in the endoplasmic reticulum (ER): productive folding of newly synthesized proteins, which is assisted by ER-localized molecular chaperones and in most cases also by disulfide bond formation and transfer of an oligosaccharide unit; and ER-associated degradation (ERAD), in which proteins unfolded or misfolded in the ER are recognized and processed for delivery to the ER membrane complex, retrotranslocated through the complex with simultaneous ubiquitination, extracted by AAA-ATPase to the cytosol, and finally degraded by the proteasome. SCOPE OF REVIEW We describe the mechanisms of productive folding and ERAD, with particular attention to glycoproteins versus non-glycoproteins, and to yeast versus mammalian systems. MAJOR CONCLUSION Molecular mechanisms of the productive folding of glycoproteins and non-glycoproteins mediated by molecular chaperones and protein disulfide isomerases are well conserved from yeast to mammals. Additionally, mammals have gained an oligosaccharide structure-dependent folding cycle for glycoproteins. The molecular mechanisms of ERAD are also well conserved from yeast to mammals, but redundant expression of yeast orthologues in mammals has been encountered, particularly for components involved in recognition and processing of glycoproteins and components of the ER membrane complex involved in retrotranslocation and simultaneous ubiquitination of glycoproteins and non-glycoproteins. This may reflect an evolutionary consequence of increasing quantity or quality needs toward mammals. GENERAL SIGNIFICANCE The introduction of innovative genome editing technology into analysis of the mechanisms of mammalian ERAD, as exemplified here, will provide new insights into the pathogenesis of various diseases.
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Affiliation(s)
- Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Ginto George
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kazutoshi Mori
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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12
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Larrimore KE, Barattin-Voynova NS, Reid DW, Ng DTW. Aneuploidy-induced proteotoxic stress can be effectively tolerated without dosage compensation, genetic mutations, or stress responses. BMC Biol 2020; 18:117. [PMID: 32900371 PMCID: PMC7487686 DOI: 10.1186/s12915-020-00852-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/18/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The protein homeostasis (proteostasis) network maintains balanced protein synthesis, folding, transport, and degradation within a cell. Failure to maintain proteostasis is associated with aging and disease, leading to concerted efforts to study how the network responds to various proteotoxic stresses. This is often accomplished using ectopic overexpression of well-characterized, model misfolded protein substrates. However, how cells tolerate large-scale, diverse burden to the proteostasis network is not understood. Aneuploidy, the state of imbalanced chromosome content, adversely affects the proteostasis network by dysregulating the expression of hundreds of proteins simultaneously. Using aneuploid haploid yeast cells as a model, we address whether cells can tolerate large-scale, diverse challenges to the proteostasis network. RESULTS Here we characterize several aneuploid Saccharomyces cerevisiae strains isolated from a collection of stable, randomly generated yeast aneuploid cells. These strains exhibit robust growth and resistance to multiple drugs which induce various forms of proteotoxic stress. Whole genome re-sequencing of the strains revealed this was not the result of genetic mutations, and transcriptome profiling combined with ribosome footprinting showed that genes are expressed and translated in accordance to chromosome copy number. In some strains, various facets of the proteostasis network are mildly upregulated without chronic activation of environmental stress response or heat shock response pathways. No severe defects were observed in the degradation of misfolded proteins, using model misfolded substrates of endoplasmic reticulum-associated degradation or cytosolic quality control pathways, and protein biosynthesis capacity was not impaired. CONCLUSIONS We show that yeast strains of some karyotypes in the genetic background studied here can tolerate the large aneuploidy-associated burden to the proteostasis machinery without genetic changes, dosage compensation, or activation of canonical stress response pathways. We suggest that proteotoxic stress, while common, is not always an obligate consequence of aneuploidy, but rather certain karyotypes and genetic backgrounds may be able to tolerate the excess protein burden placed on the protein homeostasis machinery. This may help clarify how cancer cells are paradoxically both highly aneuploid and highly proliferative at the same time.
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Affiliation(s)
- Katherine E Larrimore
- Temasek Life Sciences Laboratory, Singapore, 117604, Singapore.
- Current address: Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore.
| | | | - David W Reid
- Duke-NUS Graduate Medical School, Singapore, 169857, Singapore
- Current address: Moderna Inc., Cambridge, MA, 02139, USA
| | - Davis T W Ng
- Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
- Duke-NUS Graduate Medical School, Singapore, 169857, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
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13
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Lajoie P, Snapp EL. Size-dependent secretory protein reflux into the cytosol in association with acute endoplasmic reticulum stress. Traffic 2020; 21:419-429. [PMID: 32246734 PMCID: PMC7317852 DOI: 10.1111/tra.12729] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 01/06/2023]
Abstract
Once secretory proteins have been targeted to the endoplasmic reticulum (ER) lumen, the proteins typically remain partitioned from the cytosol. If the secretory proteins misfold, they can be unfolded and retrotranslocated into the cytosol for destruction by the proteasome by ER-Associated protein Degradation (ERAD). Here, we report that correctly folded and targeted luminal ER fluorescent protein reporters accumulate in the cytosol during acute misfolded secretory protein stress in yeast. Photoactivation fluorescence microscopy experiments reveal that luminal reporters already localized to the ER relocalize to the cytosol, even in the absence of essential ERAD machinery. We named this process "ER reflux." Reflux appears to be regulated in a size-dependent manner for reporters. Interestingly, prior heat shock stress also prevents ER stress-induced reflux. Together, our findings establish a new ER stress-regulated pathway for relocalization of small luminal secretory proteins into the cytosol, distinct from the ERAD and preemptive quality control pathways. Importantly, our results highlight the value of fully characterizing the cell biology of reporters and describe a simple modification to maintain luminal ER reporters in the ER during acute ER stress.
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Affiliation(s)
- Patrick Lajoie
- Department of Anatomy and Cell BiologyThe University of Western OntarioLondonOntarioCanada
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14
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Abstract
In consistent with other membrane-bound and secretory proteins, immune checkpoint proteins go through a set of modifications in the endoplasmic reticulum (ER) to acquire their native functional structures before they function at their destinations. There are various ER-resident chaperones and enzymes synergistically regulate and catalyze the glycosylation, folding and transporting of proteins. The whole processing is under the surveillance of ER quality control system which allows the correctly folded proteins to exit from the ER with the help of coat proteinII(COPII) coated vesicles, while retains the rest of terminally misfolded ones in the ER and then eliminates them via ER-associated degradation (ERAD) or ER-to-lysosomes-associated degradation (ERLAD). The dysfunction of the ER causes ER stress which triggers unfolded protein response (UPR) to restore ER proteostasis. Unsolvable prolonged ER stress ultimately results in cell death. This chapter reviews the process that proteins undergo in the ER, and the glycosylation, folding and degradation of immune checkpoint proteins as well as the associated potential immunotherapies to date.
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15
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Castells-Ballester J, Rinis N, Kotan I, Gal L, Bausewein D, Kats I, Zatorska E, Kramer G, Bukau B, Schuldiner M, Strahl S. Translational Regulation of Pmt1 and Pmt2 by Bfr1 Affects Unfolded Protein O-Mannosylation. Int J Mol Sci 2019; 20:ijms20246220. [PMID: 31835530 PMCID: PMC6940804 DOI: 10.3390/ijms20246220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022] Open
Abstract
O-mannosylation is implicated in protein quality control in Saccharomyces cerevisiae due to the attachment of mannose to serine and threonine residues of un- or misfolded proteins in the endoplasmic reticulum (ER). This process also designated as unfolded protein O-mannosylation (UPOM) that ends futile folding cycles and saves cellular resources is mainly mediated by protein O-mannosyltransferases Pmt1 and Pmt2. Here we describe a genetic screen for factors that influence O-mannosylation in yeast, using slow-folding green fluorescent protein (GFP) as a reporter. Our screening identifies the RNA binding protein brefeldin A resistance factor 1 (Bfr1) that has not been linked to O-mannosylation and ER protein quality control before. We find that Bfr1 affects O-mannosylation through changes in Pmt1 and Pmt2 protein abundance but has no effect on PMT1 and PMT2 transcript levels, mRNA localization to the ER membrane or protein stability. Ribosome profiling reveals that Bfr1 is a crucial factor for Pmt1 and Pmt2 translation thereby affecting unfolded protein O-mannosylation. Our results uncover a new level of regulation of protein quality control in the secretory pathway.
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Affiliation(s)
- Joan Castells-Ballester
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, D-69120 Heidelberg, Germany; (J.C.-B.); (N.R.); (D.B.); (E.Z.)
| | - Natalie Rinis
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, D-69120 Heidelberg, Germany; (J.C.-B.); (N.R.); (D.B.); (E.Z.)
| | - Ilgin Kotan
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), ZMBH-DKFZ Alliance, D-69120 Heidelberg, Germany; (I.K.); (I.K.); (G.K.); (B.B.)
| | - Lihi Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel; (L.G.); (M.S.)
| | - Daniela Bausewein
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, D-69120 Heidelberg, Germany; (J.C.-B.); (N.R.); (D.B.); (E.Z.)
- spm—Safety Projects & More GmbH, D-69493 Hirschberg a. d. Bergstraße, Germany
| | - Ilia Kats
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), ZMBH-DKFZ Alliance, D-69120 Heidelberg, Germany; (I.K.); (I.K.); (G.K.); (B.B.)
| | - Ewa Zatorska
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, D-69120 Heidelberg, Germany; (J.C.-B.); (N.R.); (D.B.); (E.Z.)
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), ZMBH-DKFZ Alliance, D-69120 Heidelberg, Germany; (I.K.); (I.K.); (G.K.); (B.B.)
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), ZMBH-DKFZ Alliance, D-69120 Heidelberg, Germany; (I.K.); (I.K.); (G.K.); (B.B.)
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel; (L.G.); (M.S.)
| | - Sabine Strahl
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, D-69120 Heidelberg, Germany; (J.C.-B.); (N.R.); (D.B.); (E.Z.)
- Correspondence: ; Tel.: +49-6221-54-6286
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16
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Saad H, Patel C, Lederkremer GZ. Letting go of O-glycans. J Biol Chem 2019; 294:15912-15913. [PMID: 31676555 DOI: 10.1074/jbc.h119.011245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The generation of free N-glycans, or unconjugated oligosaccharides derived from N-linked glycoproteins, is well understood, but whether a similar fate awaits O-linked glycoprotein carbohydrates was unknown. Hirayama et al. now reveal, by using only mannose as an energy source, the generation of free O-glycans in Saccharomyces cerevisiae, in the lumen of a secretory compartment, possibly the vacuole. These findings uncover the presence of a possible regulated degradation pathway for O-mannosylated glycoproteins.
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Affiliation(s)
- Haddas Saad
- School of Molecular Cell Biology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chaitanya Patel
- School of Molecular Cell Biology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gerardo Z Lederkremer
- School of Molecular Cell Biology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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17
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Sun Z, Brodsky JL. Protein quality control in the secretory pathway. J Cell Biol 2019; 218:3171-3187. [PMID: 31537714 PMCID: PMC6781448 DOI: 10.1083/jcb.201906047] [Citation(s) in RCA: 262] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/22/2019] [Accepted: 08/29/2019] [Indexed: 12/23/2022] Open
Abstract
Protein folding is inherently error prone, especially in the endoplasmic reticulum (ER). Even with an elaborate network of molecular chaperones and protein folding facilitators, misfolding can occur quite frequently. To maintain protein homeostasis, eukaryotes have evolved a series of protein quality-control checkpoints. When secretory pathway quality-control pathways fail, stress response pathways, such as the unfolded protein response (UPR), are induced. In addition, the ER, which is the initial hub of protein biogenesis in the secretory pathway, triages misfolded proteins by delivering substrates to the proteasome or to the lysosome/vacuole through ER-associated degradation (ERAD) or ER-phagy. Some misfolded proteins escape the ER and are instead selected for Golgi quality control. These substrates are targeted for degradation after retrieval to the ER or delivery to the lysosome/vacuole. Here, we discuss how these guardian pathways function, how their activities intersect upon induction of the UPR, and how decisions are made to dispose of misfolded proteins in the secretory pathway.
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Affiliation(s)
- Zhihao Sun
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
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18
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Cell organelles and yeast longevity: an intertwined regulation. Curr Genet 2019; 66:15-41. [PMID: 31535186 DOI: 10.1007/s00294-019-01035-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022]
Abstract
Organelles are dynamic structures of a eukaryotic cell that compartmentalize various essential functions and regulate optimum functioning. On the other hand, ageing is an inevitable phenomenon that leads to irreversible cellular damage and affects optimum functioning of cells. Recent research shows compelling evidence that connects organelle dysfunction to ageing-related diseases/disorders. Studies in several model systems including yeast have led to seminal contributions to the field of ageing in uncovering novel pathways, proteins and their functions, identification of pro- and anti-ageing factors and so on. In this review, we present a comprehensive overview of findings that highlight the role of organelles in ageing and ageing-associated functions/pathways in yeast.
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19
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Hirayama H, Matsuda T, Tsuchiya Y, Oka R, Seino J, Huang C, Nakajima K, Noda Y, Shichino Y, Iwasaki S, Suzuki T. Free glycans derived from O-mannosylated glycoproteins suggest the presence of an O-glycoprotein degradation pathway in yeast. J Biol Chem 2019; 294:15900-15911. [PMID: 31311856 DOI: 10.1074/jbc.ra119.009491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/04/2019] [Indexed: 11/06/2022] Open
Abstract
In eukaryotic cells, unconjugated oligosaccharides that are structurally related to N-glycans (i.e. free N-glycans) are generated either from misfolded N-glycoproteins destined for the endoplasmic reticulum-associated degradation or from lipid-linked oligosaccharides, donor substrates for N-glycosylation of proteins. The mechanism responsible for the generation of free N-glycans is now well-understood, but the issue of whether other types of free glycans are present remains unclear. Here, we report on the accumulation of free, O-mannosylated glycans in budding yeast that were cultured in medium containing mannose as the carbon source. A structural analysis of these glycans revealed that their structures are identical to those of O-mannosyl glycans that are attached to glycoproteins. Deletion of the cyc8 gene, which encodes for a general transcription repressor, resulted in the accumulation of excessive amounts of free O-glycans, concomitant with a severe growth defect, a reduction in the level of an O-mannosylated protein, and compromised cell wall integrity. Our findings provide evidence in support of a regulated pathway for the degradation of O-glycoproteins in yeast and offer critical insights into the catabolic mechanisms that control the fate of O-glycosylated proteins.
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Affiliation(s)
- Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Tsugiyo Matsuda
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yae Tsuchiya
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Ritsuko Oka
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Junichi Seino
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Chengcheng Huang
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Kazuki Nakajima
- Department of Academic Research Support Promotion Facility, Center for Research Promotion and Support, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Yoichi Noda
- Collaborative Research Institute for Innovative Microbiology, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
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20
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Bai L, Kovach A, You Q, Kenny A, Li H. Structure of the eukaryotic protein O-mannosyltransferase Pmt1-Pmt2 complex. Nat Struct Mol Biol 2019; 26:704-711. [PMID: 31285605 PMCID: PMC6684406 DOI: 10.1038/s41594-019-0262-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/29/2019] [Indexed: 12/24/2022]
Abstract
In eukaryotes, a nascent peptide entering the endoplasmic reticulum (ER) is scanned by two Sec61-translocon-associated large membrane machines for protein N-glycosylation and protein O-mannosylation, respectively. While the structure of the eight-protein oligosaccharyltransferase complex has been determined recently, the structures of mannosyltransferases of the PMT family, which are an integral part of ER protein homeostasis, are still unknown. Here we report cryo-EM structures of the S. cerevisiae Pmt1–Pmt2 complex bound to a donor and an acceptor peptide at 3.2-Å resolution, showing that each subunit contains 11 transmembrane helices and a lumenal β-trefoil fold termed the MIR domain. The structures reveal the substrate recognition model and confirm an inverting mannosyl-transferring reaction mechanism by the enzyme complex. Furthermore, we found that the transmembrane domains of Pmt1 and Pmt2 share a structural fold with the catalytic subunits of oligosaccharyltransferases, confirming a previously proposed evolutionary relationship between protein O-mannosylation and protein N-glycosylation.
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Affiliation(s)
- Lin Bai
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Amanda Kovach
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Qinglong You
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Alanna Kenny
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Huilin Li
- Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA.
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21
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Scheckhuber CQ. Studying the mechanisms and targets of glycation and advanced glycation end-products in simple eukaryotic model systems. Int J Biol Macromol 2019; 127:85-94. [DOI: 10.1016/j.ijbiomac.2019.01.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 12/20/2022]
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22
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Lischik CQ, Adelmann L, Wittbrodt J. Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation. PLoS One 2019; 14:e0212956. [PMID: 30845151 PMCID: PMC6405165 DOI: 10.1371/journal.pone.0212956] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
Fish are ideally suited for in vivo-imaging due to their transparency at early stages combined with a large genetic toolbox. Key challenges to further advance imaging are fluorophore selection, immobilization of the specimen and approaches to eliminate pigmentation. We addressed all three and identified the fluorophores and anaesthesia of choice by high throughput time-lapse imaging. Our results indicate that eGFP and mCherry are the best conservative choices for in vivo-fluorescence experiments, when availability of well-established antibodies and nanobodies matters. Still, mVenusNB and mGFPmut2 delivered highest absolute fluorescence intensities in vivo. Immobilization is of key importance during extended in vivo imaging. Here, traditional approaches are outperformed by mRNA injection of α-Bungarotoxin which allows a complete and reversible, transient immobilization. In combination with fully transparent juvenile and adult fish established by the targeted inactivation of both, oca2 and pnp4a via CRISPR/Cas9-mediated gene editing in medaka we could dramatically improve the state-of-the art imaging conditions in post-embryonic fish, now enabling light-sheet microscopy of the growing retina, brain, gills and inner organs in the absence of side effects caused by anaesthetic drugs or pigmentation.
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Affiliation(s)
- Colin Q Lischik
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany.,Heidelberg Biosciences International Graduate School, Heidelberg University, Heidelberg, Germany
| | - Leonie Adelmann
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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23
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Sasako T, Ohsugi M, Kubota N, Itoh S, Okazaki Y, Terai A, Kubota T, Yamashita S, Nakatsukasa K, Kamura T, Iwayama K, Tokuyama K, Kiyonari H, Furuta Y, Shibahara J, Fukayama M, Enooku K, Okushin K, Tsutsumi T, Tateishi R, Tobe K, Asahara H, Koike K, Kadowaki T, Ueki K. Hepatic Sdf2l1 controls feeding-induced ER stress and regulates metabolism. Nat Commun 2019; 10:947. [PMID: 30814508 PMCID: PMC6393527 DOI: 10.1038/s41467-019-08591-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 01/15/2019] [Indexed: 01/11/2023] Open
Abstract
Dynamic metabolic changes occur in the liver during the transition between fasting and feeding. Here we show that transient ER stress responses in the liver following feeding terminated by Sdf2l1 are essential for normal glucose and lipid homeostasis. Sdf2l1 regulates ERAD through interaction with a trafficking protein, TMED10. Suppression of Sdf2l1 expression in the liver results in insulin resistance and increases triglyceride content with sustained ER stress. In obese and diabetic mice, Sdf2l1 is downregulated due to decreased levels of nuclear XBP-1s, whereas restoration of Sdf2l1 expression ameliorates glucose intolerance and fatty liver with decreased ER stress. In diabetic patients, insufficient induction of Sdf2l1 correlates with progression of insulin resistance and steatohepatitis. Therefore, failure to build an ER stress response in the liver may be a causal factor in obesity-related diabetes and nonalcoholic steatohepatitis, for which Sdf2l1 could serve as a therapeutic target and sensitive biomarker.
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Affiliation(s)
- Takayoshi Sasako
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan.,Translational Systems Biology and Medicine Initiative (TSBMI), The University of Tokyo, Tokyo, 113-8655, Japan.,Department of Molecular Diabetic Medicine, Diabetes Research Center, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.,Division for Health Service Promotion, The University of Tokyo, Tokyo, 113-0033, Japan.,Department of Molecular Sciences on Diabetes, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Mitsuru Ohsugi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Naoto Kubota
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan.,Translational Systems Biology and Medicine Initiative (TSBMI), The University of Tokyo, Tokyo, 113-8655, Japan.,Department of Clinical Nutrition Therapy, The University of Tokyo Hospital, The University of Tokyo, Tokyo, 113-865, Japan
| | - Shinsuke Itoh
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan.,Kowa Company Limited, Nagoya, 460-0003, Japan
| | - Yukiko Okazaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan.,Department of Molecular Diabetic Medicine, Diabetes Research Center, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Ai Terai
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan.,Department of Molecular Diabetic Medicine, Diabetes Research Center, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Tetsuya Kubota
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan.,Clinical Nutrition Program, National Institute of Health and Nutrition, Tokyo, 162-8636, Japan.,Division of Cardiovascular Medicine, Toho University Ohashi Medical Center, Tokyo, 143-8541, Japan
| | - Satoshi Yamashita
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
| | - Kunio Nakatsukasa
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, 464-8601, Japan.,Graduate School of Natural Sciences, Nagoya City University, Nagoya, 464-8601, Japan
| | - Takumi Kamura
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, 464-8601, Japan
| | - Kaito Iwayama
- Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Kumpei Tokuyama
- Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Hiroshi Kiyonari
- Animal Resource Development Unit, RIKEN Center for Life Science Technologies, Kobe, 650-0047, Japan.,Genetic Engineering Team, RIKEN Center for Life Science Technologies, Kobe, 650-0047, Japan
| | - Yasuhide Furuta
- Animal Resource Development Unit, RIKEN Center for Life Science Technologies, Kobe, 650-0047, Japan.,Genetic Engineering Team, RIKEN Center for Life Science Technologies, Kobe, 650-0047, Japan
| | - Junji Shibahara
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Kenichiro Enooku
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Kazuya Okushin
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Takeya Tsutsumi
- Department of Infectious Disease, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Ryosuke Tateishi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Kazuyuki Tobe
- The First Department of Internal Medicine, Graduate School of Medicine and Pharmaceutical Sciences of Research, The University of Toyama, Toyama, 930-8555, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan. .,Translational Systems Biology and Medicine Initiative (TSBMI), The University of Tokyo, Tokyo, 113-8655, Japan. .,Department of Prevention of Diabetes and Lifestyle-Related Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan. .,Department of Metabolism and Nutrition, Mizonokuchi Hospital, Faculty of Medicine, Teikyo University, Tokyo, 213-8507, Japan.
| | - Kohjiro Ueki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan. .,Translational Systems Biology and Medicine Initiative (TSBMI), The University of Tokyo, Tokyo, 113-8655, Japan. .,Department of Molecular Diabetic Medicine, Diabetes Research Center, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
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24
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Yeast molecular chaperone gene SSB2 is involved in the endoplasmic reticulum stress response. Antonie van Leeuwenhoek 2018; 112:589-598. [DOI: 10.1007/s10482-018-1189-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/19/2018] [Indexed: 12/18/2022]
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25
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Castells-Ballester J, Zatorska E, Meurer M, Neubert P, Metschies A, Knop M, Strahl S. Monitoring Protein Dynamics in Protein O-Mannosyltransferase Mutants In Vivo by Tandem Fluorescent Protein Timers. Molecules 2018; 23:E2622. [PMID: 30322079 PMCID: PMC6222916 DOI: 10.3390/molecules23102622] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 12/27/2022] Open
Abstract
For proteins entering the secretory pathway, a major factor contributing to maturation and homeostasis is glycosylation. One relevant type of protein glycosylation is O-mannosylation, which is essential and evolutionarily-conserved in fungi, animals, and humans. Our recent proteome-wide study in the eukaryotic model organism Saccharomyces cerevisiae revealed that more than 26% of all proteins entering the secretory pathway receive O-mannosyl glycans. In a first attempt to understand the impact of O-mannosylation on these proteins, we took advantage of a tandem fluorescent timer (tFT) reporter to monitor different aspects of protein dynamics. We analyzed tFT-reporter fusions of 137 unique O-mannosylated proteins, mainly of the secretory pathway and the plasma membrane, in mutants lacking the major protein O-mannosyltransferases Pmt1, Pmt2, or Pmt4. In these three pmtΔ mutants, a total of 39 individual proteins were clearly affected, and Pmt-specific substrate proteins could be identified. We observed that O-mannosylation may cause both enhanced and diminished protein abundance and/or stability when compromised, and verified our findings on the examples of Axl2-tFT and Kre6-tFT fusion proteins. The identified target proteins are a valuable resource towards unraveling the multiple functions of O-mannosylation at the molecular level.
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Affiliation(s)
| | - Ewa Zatorska
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Matthias Meurer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany.
| | - Patrick Neubert
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Anke Metschies
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany.
- Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
| | - Sabine Strahl
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
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26
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Mehrtash AB, Hochstrasser M. Ubiquitin-dependent protein degradation at the endoplasmic reticulum and nuclear envelope. Semin Cell Dev Biol 2018; 93:111-124. [PMID: 30278225 DOI: 10.1016/j.semcdb.2018.09.013] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 01/01/2023]
Abstract
Numerous nascent proteins undergo folding and maturation within the luminal and membrane compartments of the endoplasmic reticulum (ER). Despite the presence of various factors in the ER that promote protein folding, many proteins fail to properly fold and assemble and are subsequently degraded. Regulatory proteins in the ER also undergo degradation in a way that is responsive to stimuli or the changing needs of the cell. As in most cellular compartments, the ubiquitin-proteasome system (UPS) is responsible for the majority of the degradation at the ER-in a process termed ER-associated degradation (ERAD). Autophagic processes utilizing ubiquitin-like protein-conjugating systems also play roles in protein degradation at the ER. The ER is continuous with the nuclear envelope (NE), which consists of the outer nuclear membrane (ONM) and inner nuclear membrane (INM). While ERAD is known also to occur at the NE, only some of the ERAD ubiquitin-ligation pathways function at the INM. Protein degradation machineries in the ER/NE target a wide variety of substrates in multiple cellular compartments, including the cytoplasm, nucleoplasm, ER lumen, ER membrane, and the NE. Here, we review the protein degradation machineries of the ER and NE and the underlying mechanisms dictating recognition and processing of substrates by these machineries.
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Affiliation(s)
- Adrian B Mehrtash
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, 06520, CT, USA.
| | - Mark Hochstrasser
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA; Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, 06520, CT, USA.
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27
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Marzol E, Borassi C, Bringas M, Sede A, Rodríguez Garcia DR, Capece L, Estevez JM. Filling the Gaps to Solve the Extensin Puzzle. MOLECULAR PLANT 2018; 11:645-658. [PMID: 29530817 DOI: 10.1016/j.molp.2018.03.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/28/2018] [Accepted: 03/04/2018] [Indexed: 05/20/2023]
Abstract
Extensins (EXTs) are highly repetitive plant O-glycoproteins that require several post-translational modifications (PTMs) to become functional in plant cell walls. First, they are hydroxylated on contiguous proline residues; then they are O-glycosylated on hydroxyproline and serine. After secretion into the apoplast, O-glycosylated EXTs form a tridimensional network organized by inter- and intra-Tyr linkages. Recent studies have made significant progress in the identification of the enzymatic machinery required to process EXTs, which includes prolyl 4-hydroxylases, glycosyltransferases, papain-type cysteine endopeptidases, and peroxidases. EXTs are abundant in plant tissues and are particularly important in rapidly expanding root hairs and pollen tubes, which grow in a polar manner. Small changes in EXT PTMs affect fast-growing cells, although the molecular mechanisms underlying this regulation are unknown. In this review, we highlight recent advances in our understanding of EXT modifications throughout the secretory pathway, EXT assembly in cell walls, and possible sensing mechanisms involving the Catharanthus roseus cell surface sensor receptor-like kinases located at the interface between the apoplast and the cytoplasmic side of the plasma membrane.
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Affiliation(s)
- Eliana Marzol
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina
| | - Cecilia Borassi
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina
| | - Mauro Bringas
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (INQUIMAE-CONICET), Buenos Aires, CP C1428EGA, Argentina
| | - Ana Sede
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina; Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Dr. Héctor Torres (INGEBI-CONICET), Vuelta de Obligado 2490, Buenos Aires, C1428ADN, Argentina
| | - Diana Rosa Rodríguez Garcia
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (INQUIMAE-CONICET), Buenos Aires, CP C1428EGA, Argentina
| | - Jose M Estevez
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina.
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28
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Abstract
The endoplasmic reticulum (ER) is the site of maturation for roughly one-third of all cellular proteins. ER-resident molecular chaperones and folding catalysts promote folding and assembly in a diverse set of newly synthesized proteins. Because these processes are error-prone, all eukaryotic cells have a quality-control system in place that constantly monitors the proteins and decides their fate. Proteins with potentially harmful nonnative conformations are subjected to assisted folding or degraded. Persistent folding-defective proteins are distinguished from folding intermediates and targeted for degradation by a specific process involving clearance from the ER. Although the basic principles of these processes appear conserved from yeast to animals and plants, there are distinct differences in the ER-associated degradation of misfolded glycoproteins. The general importance of ER quality-control events is underscored by their involvement in the biogenesis of diverse cell surface receptors and their crucial maintenance of protein homeostasis under diverse stress conditions.
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Affiliation(s)
- Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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29
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Preston GM, Guerriero CJ, Metzger MB, Michaelis S, Brodsky JL. Substrate Insolubility Dictates Hsp104-Dependent Endoplasmic-Reticulum-Associated Degradation. Mol Cell 2018; 70:242-253.e6. [PMID: 29677492 PMCID: PMC5912696 DOI: 10.1016/j.molcel.2018.03.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/15/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
Abstract
Misfolded proteins in the endoplasmic reticulum (ER) are destroyed by ER-associated degradation (ERAD). Although the retrotranslocation of misfolded proteins from the ER has been reconstituted, how a polypeptide is initially selected for ERAD remains poorly defined. To address this question while controlling for the diverse nature of ERAD substrates, we constructed a series of truncations in a single ER-tethered domain. We observed that the truncated proteins exhibited variable degradation rates and discovered a positive correlation between ERAD substrate instability and detergent insolubility, which demonstrates that aggregation-prone species can be selected for ERAD. Further, Hsp104 facilitated degradation of an insoluble species, consistent with the chaperone's disaggregase activity. We also show that retrotranslocation of the ubiquitinated substrate from the ER was inhibited in the absence of Hsp104. Therefore, chaperone-mediated selection frees the ER membrane of potentially toxic, aggregation-prone species.
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Affiliation(s)
- G Michael Preston
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | | - Meredith B Metzger
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Susan Michaelis
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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30
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Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T. Using deep learning to model the hierarchical structure and function of a cell. Nat Methods 2018; 15:290-298. [PMID: 29505029 PMCID: PMC5882547 DOI: 10.1038/nmeth.4627] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/07/2018] [Indexed: 01/20/2023]
Abstract
Although artificial neural networks simulate a variety of human functions, their internal structures are hard to interpret. In the life sciences, extensive knowledge of cell biology provides an opportunity to design visible neural networks (VNNs) which couple the model’s inner workings to those of real systems. Here we develop DCell, a VNN embedded in the hierarchical structure of 2526 subsystems comprising a eukaryotic cell (http://d-cell.ucsd.edu/). Trained on several million genotypes, DCell simulates cellular growth nearly as accurately as laboratory observations. During simulation, genotypes induce patterns of subsystem activities, enabling in-silico investigations of the molecular mechanisms underlying genotype-phenotype associations. These mechanisms can be validated and many are unexpected; some are governed by Boolean logic. Cumulatively, 80% of the importance for growth prediction is captured by 484 subsystems (21%), reflecting the emergence of a complex phenotype. DCell provides a foundation for decoding the genetics of disease, drug resistance, and synthetic life.
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Affiliation(s)
- Jianzhu Ma
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Michael Ku Yu
- Department of Medicine, University of California San Diego, La Jolla, California, USA.,Program in Bioinformatics, University of California San Diego, La Jolla, California, USA
| | - Samson Fong
- Department of Medicine, University of California San Diego, La Jolla, California, USA.,Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Keiichiro Ono
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Eric Sage
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Barry Demchak
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, California, USA.,Program in Bioinformatics, University of California San Diego, La Jolla, California, USA.,Department of Bioengineering, University of California San Diego, La Jolla, California, USA
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31
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Natan E, Endoh T, Haim-Vilmovsky L, Flock T, Chalancon G, Hopper JTS, Kintses B, Horvath P, Daruka L, Fekete G, Pál C, Papp B, Oszi E, Magyar Z, Marsh JA, Elcock AH, Babu MM, Robinson CV, Sugimoto N, Teichmann SA. Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins. Nat Struct Mol Biol 2018; 25:279-288. [PMID: 29434345 PMCID: PMC5995306 DOI: 10.1038/s41594-018-0029-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 01/10/2018] [Indexed: 01/11/2023]
Abstract
Cotranslational protein folding can facilitate rapid formation of functional structures. However, it can also cause premature assembly of protein complexes, if two interacting nascent chains are in close proximity. By analyzing known protein structures, we show that homomeric protein contacts are enriched toward the C termini of polypeptide chains across diverse proteomes. We hypothesize that this is the result of evolutionary constraints for folding to occur before assembly. Using high-throughput imaging of protein homomers in Escherichia coli and engineered protein constructs with N- and C-terminal oligomerization domains, we show that, indeed, proteins with C-terminal homomeric interface residues consistently assemble more efficiently than those with N-terminal interface residues. Using in vivo, in vitro and in silico experiments, we identify features that govern successful assembly of homomers, which have implications for protein design and expression optimization.
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Affiliation(s)
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
| | - Liora Haim-Vilmovsky
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Tilman Flock
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Bálint Kintses
- Synthetic and System Biology Unit, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Peter Horvath
- Synthetic and System Biology Unit, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Lejla Daruka
- Synthetic and System Biology Unit, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Gergely Fekete
- Synthetic and System Biology Unit, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Csaba Pál
- Synthetic and System Biology Unit, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Balázs Papp
- Synthetic and System Biology Unit, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Erika Oszi
- Institute of Plant Biology, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa, Iowa City, IA, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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32
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Berner N, Reutter KR, Wolf DH. Protein Quality Control of the Endoplasmic Reticulum and Ubiquitin-Proteasome-Triggered Degradation of Aberrant Proteins: Yeast Pioneers the Path. Annu Rev Biochem 2018; 87:751-782. [PMID: 29394096 DOI: 10.1146/annurev-biochem-062917-012749] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells must constantly monitor the integrity of their macromolecular constituents. Proteins are the most versatile class of macromolecules but are sensitive to structural alterations. Misfolded or otherwise aberrant protein structures lead to dysfunction and finally aggregation. Their presence is linked to aging and a plethora of severe human diseases. Thus, misfolded proteins have to be rapidly eliminated. Secretory proteins constitute more than one-third of the eukaryotic proteome. They are imported into the endoplasmic reticulum (ER), where they are folded and modified. A highly elaborated machinery controls their folding, recognizes aberrant folding states, and retrotranslocates permanently misfolded proteins from the ER back to the cytosol. In the cytosol, they are degraded by the highly selective ubiquitin-proteasome system. This process of protein quality control followed by proteasomal elimination of the misfolded protein is termed ER-associated degradation (ERAD), and it depends on an intricate interplay between the ER and the cytosol.
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Affiliation(s)
- Nicole Berner
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany; , ,
| | - Karl-Richard Reutter
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany; , ,
| | - Dieter H Wolf
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany; , ,
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33
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Conformational folding and disulfide bonding drive distinct stages of protein structure formation. Sci Rep 2018; 8:1494. [PMID: 29367639 PMCID: PMC5784126 DOI: 10.1038/s41598-018-20014-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/11/2018] [Indexed: 12/30/2022] Open
Abstract
The causal relationship between conformational folding and disulfide bonding in protein oxidative folding remains incompletely defined. Here we show a stage-dependent interplay between the two events in oxidative folding of C-reactive protein (CRP) in live cells. CRP is composed of five identical subunits, which first fold spontaneously to a near-native core with a correctly positioned C-terminal helix. This process drives the formation of the intra-subunit disulfide bond between Cys36 and Cys97. The second stage of subunit folding, however, is a non-spontaneous process with extensive restructuring driven instead by the intra-subunit disulfide bond and guided by calcium binding-mediated anchoring. With the folded subunits, pentamer assembly ensues. Our results argue that folding spontaneity is the major determinant that dictates which event acts as the driver. The stepwise folding pathway of CRP further suggests that one major route might be selected out of the many in theory for efficient folding in the cellular environment.
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34
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Slp1-Emp65: A Guardian Factor that Protects Folding Polypeptides from Promiscuous Degradation. Cell 2017; 171:346-357.e12. [DOI: 10.1016/j.cell.2017.08.036] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/06/2017] [Accepted: 08/21/2017] [Indexed: 02/05/2023]
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35
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Engle SM, Crowder JJ, Watts SG, Indovina CJ, Coffey SZ, Rubenstein EM. Acetylation of N-terminus and two internal amino acids is dispensable for degradation of a protein that aberrantly engages the endoplasmic reticulum translocon. PeerJ 2017; 5:e3728. [PMID: 28848693 PMCID: PMC5571791 DOI: 10.7717/peerj.3728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/02/2017] [Indexed: 12/26/2022] Open
Abstract
Conserved homologues of the Hrd1 ubiquitin ligase target for degradation proteins that persistently or aberrantly engage the endoplasmic reticulum translocon, including mammalian apolipoprotein B (apoB; the major protein component of low-density lipoproteins) and the artificial yeast protein Deg1-Sec62. A complete understanding of the molecular mechanism by which translocon-associated proteins are recognized and degraded may inform the development of therapeutic strategies for cholesterol-related pathologies. Both apoB and Deg1-Sec62 are extensively post-translationally modified. Mass spectrometry of a variant of Deg1-Sec62 revealed that the protein is acetylated at the N-terminal methionine and two internal lysine residues. N-terminal and internal acetylation regulates the degradation of a variety of unstable proteins. However, preventing N-terminal and internal acetylation had no detectable consequence for Hrd1-mediated proteolysis of Deg1-Sec62. Our data highlight the importance of empirically validating the role of post-translational modifications and sequence motifs on protein degradation, even when such elements have previously been demonstrated sufficient to destine other proteins for destruction.
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Affiliation(s)
- Sarah M Engle
- Department of Biology, Ball State University, Muncie, IN, United States of America.,Immunology-Translational Science, Eli Lilly and Company, Indianapolis, IN, United States of America
| | - Justin J Crowder
- Department of Biology, Ball State University, Muncie, IN, United States of America.,Center for Medical Education, Indiana University School of Medicine, Muncie, IN, United States of America
| | - Sheldon G Watts
- Department of Biology, Ball State University, Muncie, IN, United States of America.,Marian University College of Osteopathic Medicine, Indianapolis, IN, United States of America
| | | | - Samuel Z Coffey
- Department of Biology, Ball State University, Muncie, IN, United States of America.,Medpace Reference Laboratories, Cincinnati, OH, United States of America
| | - Eric M Rubenstein
- Department of Biology, Ball State University, Muncie, IN, United States of America
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36
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Chaffey PK, Guan X, Wang X, Ruan Y, Li Y, Miller SG, Tran AH, Koelsch TN, Pass LF, Tan Z. Quantitative Effects of O-Linked Glycans on Protein Folding. Biochemistry 2017; 56:4539-4548. [DOI: 10.1021/acs.biochem.7b00483] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Patrick K. Chaffey
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Xiaoyang Guan
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Xinfeng Wang
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Yuan Ruan
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Yaohao Li
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Suzannah G. Miller
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Amy H. Tran
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Theo N. Koelsch
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Lomax F. Pass
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Zhongping Tan
- Department of Chemistry and
Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
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37
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Zatorska E, Gal L, Schmitt J, Bausewein D, Schuldiner M, Strahl S. Cellular Consequences of Diminished Protein O-Mannosyltransferase Activity in Baker's Yeast. Int J Mol Sci 2017; 18:ijms18061226. [PMID: 28598353 PMCID: PMC5486049 DOI: 10.3390/ijms18061226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 01/08/2023] Open
Abstract
O-Mannosylation is a type of protein glycosylation initiated in the endoplasmic reticulum (ER) by the protein O-mannosyltransferase (PMT) family. Despite the vital role of O-mannosylation, its molecular functions and regulation are not fully characterized. To further explore the cellular impact of protein O-mannosylation, we performed a genome-wide screen to identify Saccharomyces cerevisiae mutants with increased sensitivity towards the PMT-specific inhibitor compound R3A-5a. We identified the cell wall and the ER as the cell compartments affected most upon PMT inhibition. Especially mutants with defects in N-glycosylation, biosynthesis of glycosylphosphatidylinositol-anchored proteins and cell wall β-1,6-glucan showed impaired growth when O-mannosylation became limiting. Signaling pathways that counteract cell wall defects and unbalanced ER homeostasis, namely the cell wall integrity pathway and the unfolded protein response, were highly crucial for the cell growth. Moreover, among the most affected mutants, we identified Ost3, one of two homologous subunits of the oligosaccharyltransferase complexes involved in N-glycosylation, suggesting a functional link between the two pathways. Indeed, we identified Pmt2 as a substrate for Ost3 suggesting that the reduced function of Pmt2 in the absence of N-glycosylation promoted sensitivity to the drug. Interestingly, even though S. cerevisiae Pmt1 and Pmt2 proteins are highly similar on the sequence, as well as the structural level and act as a complex, we identified only Pmt2, but not Pmt1, as an Ost3-specific substrate protein.
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Affiliation(s)
- Ewa Zatorska
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Lihi Gal
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
| | - Jaro Schmitt
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Daniela Bausewein
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
| | - Sabine Strahl
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
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Corfield A. Eukaryotic protein glycosylation: a primer for histochemists and cell biologists. Histochem Cell Biol 2017; 147:119-147. [PMID: 28012131 PMCID: PMC5306191 DOI: 10.1007/s00418-016-1526-4] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2016] [Indexed: 12/21/2022]
Abstract
Proteins undergo co- and posttranslational modifications, and their glycosylation is the most frequent and structurally variegated type. Histochemically, the detection of glycan presence has first been performed by stains. The availability of carbohydrate-specific tools (lectins, monoclonal antibodies) has revolutionized glycophenotyping, allowing monitoring of distinct structures. The different types of protein glycosylation in Eukaryotes are described. Following this educational survey, examples where known biological function is related to the glycan structures carried by proteins are given. In particular, mucins and their glycosylation patterns are considered as instructive proof-of-principle case. The tissue and cellular location of glycoprotein biosynthesis and metabolism is reviewed, with attention to new findings in goblet cells. Finally, protein glycosylation in disease is documented, with selected examples, where aberrant glycan expression impacts on normal function to let disease pathology become manifest. The histological applications adopted in these studies are emphasized throughout the text.
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Affiliation(s)
- Anthony Corfield
- Mucin Research Group, School of Clinical Sciences, Bristol Royal Infirmary, University of Bristol, Bristol, BS2 8HW, UK.
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Kintaka R, Makanae K, Moriya H. Cellular growth defects triggered by an overload of protein localization processes. Sci Rep 2016; 6:31774. [PMID: 27538565 PMCID: PMC4990933 DOI: 10.1038/srep31774] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/27/2016] [Indexed: 12/21/2022] Open
Abstract
High-level expression of a protein localized to an intracellular compartment is expected to cause cellular defects because it overloads localization processes. However, overloads of localization processes have never been studied systematically. Here, we show that the expression levels of green fluorescent proteins (GFPs) with localization signals were limited to the same degree as a toxic misfolded GFP in budding yeast cells, and that their high-level expression caused cellular defects associated with localization processes. We further show that limitation of the exportin Crm1 determined the expression limit of GFP with a nuclear export signal. Although misfolding of GFP with a vesicle-mediated transport signal triggered endoplasmic reticulum stress, it was not the primary determinant of its expression limit. The precursor of GFP with a mitochondrial targeting signal caused a cellular defect. Finally, we estimated the residual capacities of localization processes. High-level expression of a localized protein thus causes cellular defects by overloading the capacities of localization processes.
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Affiliation(s)
- Reiko Kintaka
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Koji Makanae
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
| | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
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40
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Protein O-mannosylation in the early secretory pathway. Curr Opin Cell Biol 2016; 41:100-8. [DOI: 10.1016/j.ceb.2016.04.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/19/2016] [Accepted: 04/25/2016] [Indexed: 12/30/2022]
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41
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Li X, Krafczyk R, Macošek J, Li YL, Zou Y, Simon B, Pan X, Wu QY, Yan F, Li S, Hennig J, Jung K, Lassak J, Hu HG. Resolving the α-glycosidic linkage of arginine-rhamnosylated translation elongation factor P triggers generation of the first Arg Rha specific antibody. Chem Sci 2016; 7:6995-7001. [PMID: 28451135 PMCID: PMC5363779 DOI: 10.1039/c6sc02889f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 07/20/2016] [Indexed: 12/23/2022] Open
Abstract
A previously discovered posttranslational modification strategy - arginine rhamnosylation - is essential for elongation factor P (EF-P) dependent rescue of polyproline stalled ribosomes in clinically relevant species such as Pseudomonas aeruginosa and Neisseria meningitidis. However, almost nothing is known about this new type of N-linked glycosylation. In the present study we used NMR spectroscopy to show for the first time that the α anomer of rhamnose is attached to Arg32 of EF-P, demonstrating that the corresponding glycosyltransferase EarP inverts the sugar of its cognate substrate dTDP-β-l-rhamnose. Based on this finding we describe the synthesis of an α-rhamnosylated arginine containing peptide antigen in order to raise the first anti-rhamnosyl arginine specific antibody (anti-ArgRha). Using ELISA and Western Blot analyses we demonstrated both its high affinity and specificity without any cross-reactivity to other N-glycosylated proteins. Having the anti-ArgRha at hand we were able to visualize endogenously produced rhamnosylated EF-P. Thus, we expect the antibody to be not only important to monitor EF-P rhamnosylation in diverse bacteria but also to identify further rhamnosyl arginine containing proteins. As EF-P rhamnosylation is essential for pathogenicity, our antibody might also be a powerful tool in drug discovery.
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Affiliation(s)
- Xiang Li
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
| | - Ralph Krafczyk
- Department of Biology I, Microbiology , Ludwig Maximilians-Universität München , Munich , Germany.,Center for Integrated Protein Science Munich , Ludwig-Maximilians-Universität München , Munich , Germany .
| | - Jakub Macošek
- Structural and Computational Biology Unit , EMBL Heidelberg , Heidelberg 69117 , Germany
| | - Yu-Lei Li
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China . .,School of Pharmacy , Wei Fang Medical University , Shandong 261053 , China
| | - Yan Zou
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
| | - Bernd Simon
- Structural and Computational Biology Unit , EMBL Heidelberg , Heidelberg 69117 , Germany
| | - Xing Pan
- Institute of Infection and Immunity , Taihe Hospital , Hubei University of Medicine , Shiyan , Hubei 442000 , China
| | - Qiu-Ye Wu
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
| | - Fang Yan
- School of Pharmacy , Wei Fang Medical University , Shandong 261053 , China
| | - Shan Li
- Institute of Infection and Immunity , Taihe Hospital , Hubei University of Medicine , Shiyan , Hubei 442000 , China
| | - Janosch Hennig
- Structural and Computational Biology Unit , EMBL Heidelberg , Heidelberg 69117 , Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology , Ludwig Maximilians-Universität München , Munich , Germany.,Center for Integrated Protein Science Munich , Ludwig-Maximilians-Universität München , Munich , Germany .
| | - Jürgen Lassak
- Department of Biology I, Microbiology , Ludwig Maximilians-Universität München , Munich , Germany.,Center for Integrated Protein Science Munich , Ludwig-Maximilians-Universität München , Munich , Germany .
| | - Hong-Gang Hu
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
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Abstract
Protein glycosylation is an essential co- and post-translational modification of secretory and membrane proteins in all eukaryotes. The initial steps of N-glycosylation and N-glycan processing are highly conserved between plants, mammals and yeast. In contrast, late N-glycan maturation steps in the Golgi differ significantly in plants giving rise to complex N-glycans with β1,2-linked xylose, core α1,3-linked fucose and Lewis A-type structures. While the essential role of N-glycan modifications on distinct mammalian glycoproteins is already well documented, we have only begun to decipher the biological function of this ubiquitous protein modification in different plant species. In this review, I focus on the biosynthesis and function of different protein N-linked glycans in plants. Special emphasis is given on glycan-mediated quality control processes in the ER and on the biological role of characteristic complex N-glycan structures.
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Affiliation(s)
- Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
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43
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Ninagawa S, Mori K. Trypsin Sensitivity Assay to Study the Folding Status of Proteins. Bio Protoc 2016. [DOI: 10.21769/bioprotoc.1953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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44
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Shao S, Hegde RS. Target Selection during Protein Quality Control. Trends Biochem Sci 2015; 41:124-137. [PMID: 26628391 DOI: 10.1016/j.tibs.2015.10.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/18/2015] [Accepted: 10/20/2015] [Indexed: 11/25/2022]
Abstract
Protein quality control (QC) pathways survey the cellular proteome to selectively recognize and degrade faulty proteins whose accumulation can lead to various diseases. Recognition of the occasional aberrant protein among an abundant sea of similar normal counterparts poses a considerable challenge to the cell. Solving this problem requires protein QC machinery to assay multiple molecular criteria within a spatial and temporal context. Although each QC pathway has unique criteria and mechanisms for distinguishing right from wrong, they appear to share several general concepts. We discuss principles of high-fidelity target recognition, the decisive event of all protein QC pathways, to guide future work in this area.
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Affiliation(s)
- Sichen Shao
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
| | - Ramanujan S Hegde
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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45
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Ninagawa S, Okada T, Sumitomo Y, Horimoto S, Sugimoto T, Ishikawa T, Takeda S, Yamamoto T, Suzuki T, Kamiya Y, Kato K, Mori K. Forcible destruction of severely misfolded mammalian glycoproteins by the non-glycoprotein ERAD pathway. J Cell Biol 2015; 211:775-84. [PMID: 26572623 PMCID: PMC4657166 DOI: 10.1083/jcb.201504109] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/07/2015] [Indexed: 11/27/2022] Open
Abstract
Higher eukaryotes, but not yeast, are able to extract severely misfolded glycoproteins from the endoplasmic reticulum–associated degradation (ERAD) pathway for glycoproteins and target them to the ERAD pathway for non-glycoproteins to maintain the homeostasis of the ER. Glycoproteins and non-glycoproteins possessing unfolded/misfolded parts in their luminal regions are cleared from the endoplasmic reticulum (ER) by ER-associated degradation (ERAD)-L with distinct mechanisms. Two-step mannose trimming from Man9GlcNAc2 is crucial in the ERAD-L of glycoproteins. We recently showed that this process is initiated by EDEM2 and completed by EDEM3/EDEM1. Here, we constructed chicken and human cells simultaneously deficient in EDEM1/2/3 and analyzed the fates of four ERAD-L substrates containing three potential N-glycosylation sites. We found that native but unstable or somewhat unfolded glycoproteins, such as ATF6α, ATF6α(C), CD3-δ–ΔTM, and EMC1, were stabilized in EDEM1/2/3 triple knockout cells. In marked contrast, degradation of severely misfolded glycoproteins, such as null Hong Kong (NHK) and deletion or insertion mutants of ATF6α(C), CD3-δ–ΔTM, and EMC1, was delayed only at early chase periods, but they were eventually degraded as in wild-type cells. Thus, higher eukaryotes are able to extract severely misfolded glycoproteins from glycoprotein ERAD and target them to the non-glycoprotein ERAD pathway to maintain the homeostasis of the ER.
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Affiliation(s)
- Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan
| | - Tetsuya Okada
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yoshiki Sumitomo
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Satoshi Horimoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takehiro Sugimoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tokiro Ishikawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Tadashi Suzuki
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, Wako, Saitama 351-0198, Japan
| | - Yukiko Kamiya
- Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan
| | - Koichi Kato
- Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8787, Japan Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Kazutoshi Mori
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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46
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Xu C, Ng DTW. Glycosylation-directed quality control of protein folding. Nat Rev Mol Cell Biol 2015; 16:742-52. [PMID: 26465718 DOI: 10.1038/nrm4073] [Citation(s) in RCA: 300] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Membrane-bound and soluble proteins of the secretory pathway are commonly glycosylated in the endoplasmic reticulum. These adducts have many biological functions, including, notably, their contribution to the maturation of glycoproteins. N-linked glycans are of oligomeric structure, forming configurations that provide blueprints to precisely instruct the folding of protein substrates and the quality control systems that scrutinize it. O-linked mannoses are simpler in structure and were recently found to have distinct functions in protein quality control that do not require the complex structure of N-linked glycans. Together, recent studies reveal the breadth and sophistication of the roles of these glycan-directed modifications in protein biogenesis.
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Affiliation(s)
- Chengchao Xu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Davis T W Ng
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Duke University-National University of Singapore Graduate Medical School, 8 College Road, Singapore 169857
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47
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Abstract
N-Glycosylation has long been linked to protein folding and quality control in the endoplasmic reticulum (ER). Recent work has shown that O-linked glycosylation and the corresponding glycosyltransferases also participate in this important function. Notably, Protein O-fucosyltransferase 1 (Ofut1/Pofut1), a soluble, ER localized enzyme that fucosylates Epidermal Growth Factor-like (EGF) repeats, functions as a chaperone involved in the proper localization of the Notch receptor in certain contexts. Pofut2, a related enzyme that modifies Thrombospondin type I repeats (TSRs), has also been hypothesized to play a role in the folding and quality control of TSR-containing proteins. Both enzymes only modify fully folded substrates suggesting that they are able to distinguish between folded and unfolded structures. Pofuts have known physiological relevance and are conserved across metazoans. Though consensus sequences for O-fucosylation have been established and structures of both Pofuts have been studied, the mechanism of how they participate in protein folding is not known. This article discusses past and recent advances made in novel roles for these protein O-glycosyltransferases.
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Affiliation(s)
- Deepika Vasudevan
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794-5215, USA
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48
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Cui HJ, Liu XG, McCormick M, Wasko BM, Zhao W, He X, Yuan Y, Fang BX, Sun XR, Kennedy BK, Suh Y, Zhou ZJ, Kaeberlein M, Feng WL. PMT1 deficiency enhances basal UPR activity and extends replicative lifespan of Saccharomyces cerevisiae. AGE (DORDRECHT, NETHERLANDS) 2015; 37:9788. [PMID: 25936926 PMCID: PMC4417673 DOI: 10.1007/s11357-015-9788-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
Pmt1p is an important member of the protein O-mannosyltransferase (PMT) family of enzymes, which participates in the endoplasmic reticulum (ER) unfolded protein response (UPR), an important pathway for alleviating ER stress. ER stress and the UPR have been implicated in aging and age-related diseases in several organisms; however, a possible role for PMT1 in determining lifespan has not been previously described. In this study, we report that deletion of PMT1 increases replicative lifespan (RLS) in the budding yeast Saccharomyces cerevisiae, while overexpression of PMT1 (PMT1-OX) reduces RLS. Relative to wild-type and PMT1-OX strains, the pmt1Δ strain had enhanced HAC1 mRNA splicing and elevated expression levels of UPR target genes. Furthermore, the increased RLS of the pmt1Δ strain could be completely abolished by deletion of either IRE1 or HAC1, two upstream modulators of the UPR. The double deletion strains pmt1Δhac1Δ and pmt1Δire1Δ also displayed generally reduced transcription of UPR target genes. Collectively, our results suggest that PMT1 deficiency enhances basal activity of the ER UPR and extends the RLS of yeast mother cells through a mechanism that requires both IRE1 and HAC1.
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Affiliation(s)
- Hong-Jing Cui
- />Department of Clinical Hematology, Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, Chongqing Medical University, No. 1, Yixueyuan Road, Chongqing, 400016 People’s Republic of China
| | - Xin-Guang Liu
- />Institute of Aging Research, Guangdong Medical College, Dongguan, 523808 People’s Republic of China
- />Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, 523808 People’s Republic of China
| | - Mark McCormick
- />Buck Institute for Research on Aging, Novato, CA 98945 USA
| | - Brian M. Wasko
- />Department of Pathology, University of Washington, Seattle, WA 98159 USA
| | - Wei Zhao
- />Institute of Aging Research, Guangdong Medical College, Dongguan, 523808 People’s Republic of China
- />Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, 523808 People’s Republic of China
| | - Xin He
- />Institute of Aging Research, Guangdong Medical College, Dongguan, 523808 People’s Republic of China
- />Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, 523808 People’s Republic of China
| | - Yuan Yuan
- />Institute of Aging Research, Guangdong Medical College, Dongguan, 523808 People’s Republic of China
- />Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, 523808 People’s Republic of China
| | - Bing-Xiong Fang
- />Institute of Aging Research, Guangdong Medical College, Dongguan, 523808 People’s Republic of China
- />Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, 523808 People’s Republic of China
| | - Xue-Rong Sun
- />Institute of Aging Research, Guangdong Medical College, Dongguan, 523808 People’s Republic of China
- />Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, 523808 People’s Republic of China
| | - Brian K. Kennedy
- />Institute of Aging Research, Guangdong Medical College, Dongguan, 523808 People’s Republic of China
- />Buck Institute for Research on Aging, Novato, CA 98945 USA
| | - Yousin Suh
- />Institute of Aging Research, Guangdong Medical College, Dongguan, 523808 People’s Republic of China
- />Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Zhong-Jun Zhou
- />Institute of Aging Research, Guangdong Medical College, Dongguan, 523808 People’s Republic of China
- />Department of Biochemistry, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong, Hong Kong
| | - Matt Kaeberlein
- />Institute of Aging Research, Guangdong Medical College, Dongguan, 523808 People’s Republic of China
- />Department of Pathology, University of Washington, Seattle, WA 98159 USA
| | - Wen-Li Feng
- />Department of Clinical Hematology, Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, Chongqing Medical University, No. 1, Yixueyuan Road, Chongqing, 400016 People’s Republic of China
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49
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Xu C, Ng DT. O-mannosylation: The other glycan player of ER quality control. Semin Cell Dev Biol 2015; 41:129-34. [DOI: 10.1016/j.semcdb.2015.01.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 01/30/2015] [Indexed: 01/07/2023]
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50
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Dubé AK, Bélanger M, Gagnon-Arsenault I, Bourbonnais Y. N-terminal entrance loop of yeast Yps1 and O-glycosylation of substrates are determinant factors controlling the shedding activity of this GPI-anchored endopeptidase. BMC Microbiol 2015; 15:50. [PMID: 25886139 PMCID: PMC4353680 DOI: 10.1186/s12866-015-0380-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/10/2015] [Indexed: 11/19/2022] Open
Abstract
Background S. cerevisiae Yps1 is the prototypical aspartic endopeptidase of the fungal yapsin family. This glycosylphosphatidylinositol (GPI) anchored enzyme was recently shown to be involved in the shedding of the GPI proteins Utr2, Gas1 and itself. It was also proposed to be part of a novel quality control mechanism that eliminates excess and/or misfolded GPI proteins. What regulates its shedding activity at the cell surface is however poorly understood. Yps1 is initially synthesized as a zymogen requiring proteolytic activation to remove a pro-peptide and further processing within a large insertion loop (N-entrance loop) generates a two-subunit endopeptidase. To investigate the role of this loop on its shedding activity, which typically takes place within Ser/Thr-rich domains, it was replaced with the short peptide found at the analogous position in Yps3. We also tested whether O-glycosylation might protect against proteolytic processing by Yps1. Results We show here that replacement of the N-entrance loop (N-ent loop) of Yps1 generates a single chain endopeptidase that undergoes partial (pH 6.0) or complete (pH 3.0) pro-peptide removal. At both pH, the shedding activity of the chimeric endopeptidase (Yps1-DL) toward Gas1 and itself is strongly and drastically increased, respectively. A direct correlation between endoproteolytic cleavage of this loop in native Yps1 and its shedding is observed. The Yps1-dependent shedding of two model GPI proteins (Gas1 and Yps1) is also stimulated by the absence of the O-mannosyltransferases, Pmt4 and Pmt2 respectively, involved in O-glycosylation of their Ser/Thr-rich domains. Under these conditions, some Yps1-independent shedding is also observed. Conclusions Partial pro-peptide removal is essential to produce a functional Yps1 endopeptidase. The Yps1 N-ent loop plays a major role in regulating the shedding activity of the endopeptidase, most likely by limiting access to the active site, and its cleavage in native Yps1 is associated with its shedding. O-glycosylation protects against Yps1-dependent and -independent shedding of GPI proteins. It is postulated that hypoglycosylation of cell surface proteins, which may occur for misfolded proteins that escaped the ER-associated degradation, might target their elimination through shedding by Yps1 and possibly other yapsin members.
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Affiliation(s)
- Alexandre K Dubé
- Département de biochimie, microbiologie et bio-informatique, Institut de biologie intégrative et des systèmes and Regroupement PROTEO, Université Laval, Québec, QC, Canada.
| | - Marc Bélanger
- Département de biochimie, microbiologie et bio-informatique, Institut de biologie intégrative et des systèmes and Regroupement PROTEO, Université Laval, Québec, QC, Canada.
| | - Isabelle Gagnon-Arsenault
- Département de biochimie, microbiologie et bio-informatique, Institut de biologie intégrative et des systèmes and Regroupement PROTEO, Université Laval, Québec, QC, Canada.
| | - Yves Bourbonnais
- Département de biochimie, microbiologie et bio-informatique, Institut de biologie intégrative et des systèmes and Regroupement PROTEO, Université Laval, Québec, QC, Canada.
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