1
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Zhao XY, Xu DE, Wu ML, Liu JC, Shi ZL, Ma QH. Regulation and function of endoplasmic reticulum autophagy in neurodegenerative diseases. Neural Regen Res 2025; 20:6-20. [PMID: 38767472 PMCID: PMC11246128 DOI: 10.4103/nrr.nrr-d-23-00995] [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: 06/13/2023] [Revised: 11/09/2023] [Accepted: 12/13/2023] [Indexed: 05/22/2024] Open
Abstract
The endoplasmic reticulum, a key cellular organelle, regulates a wide variety of cellular activities. Endoplasmic reticulum autophagy, one of the quality control systems of the endoplasmic reticulum, plays a pivotal role in maintaining endoplasmic reticulum homeostasis by controlling endoplasmic reticulum turnover, remodeling, and proteostasis. In this review, we briefly describe the endoplasmic reticulum quality control system, and subsequently focus on the role of endoplasmic reticulum autophagy, emphasizing the spatial and temporal mechanisms underlying the regulation of endoplasmic reticulum autophagy according to cellular requirements. We also summarize the evidence relating to how defective or abnormal endoplasmic reticulum autophagy contributes to the pathogenesis of neurodegenerative diseases. In summary, this review highlights the mechanisms associated with the regulation of endoplasmic reticulum autophagy and how they influence the pathophysiology of degenerative nerve disorders. This review would help researchers to understand the roles and regulatory mechanisms of endoplasmic reticulum-phagy in neurodegenerative disorders.
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Affiliation(s)
- Xiu-Yun Zhao
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
| | - De-En Xu
- Department of Neurology, Jiangnan University Medical Center, Wuxi, Jiangsu Province, China
| | - Ming-Lei Wu
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
| | - Ji-Chuan Liu
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
| | - Zi-Ling Shi
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
| | - Quan-Hong Ma
- Department of Neurology and Clinical Research Center of Neurological Disease, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
- Institute of Neuroscience & Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Soochow University, Suzhou, Jiangsu Province, China
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2
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Liang Z, Ning R, Wang Z, Kong X, Yan Y, Cai Y, He Z, Liu XG, Zou Y, Zhou J. The emerging roles of UFMylation in the modulation of immune responses. Clin Transl Med 2024; 14:e70019. [PMID: 39259506 PMCID: PMC11389534 DOI: 10.1002/ctm2.70019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/21/2024] [Accepted: 09/01/2024] [Indexed: 09/13/2024] Open
Abstract
Post-translational modification is a rite of passage for cellular functional proteins and ultimately regulate almost all aspects of life. Ubiquitin-fold modifier 1 (UFM1) system represents a newly identified ubiquitin-like modification system with indispensable biological functions, and the underlying biological mechanisms remain largely undiscovered. The field has recently experienced a rapid growth of research revealing that UFMylation directly or indirectly regulates multiple immune processes. Here, we summarised important advances that how UFMylation system responds to intrinsic and extrinsic stresses under certain physiological or pathological conditions and safeguards immune homeostasis, providing novel perspectives into the regulatory framework and functions of UFMylation system, and its therapeutic applications in human diseases.
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Affiliation(s)
- Zhengyan Liang
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Rongxuan Ning
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Zhaoxiang Wang
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Xia Kong
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Yubin Yan
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Yafei Cai
- Key Laboratory for Epigenetics of Dongguan City, China-America Cancer Research Institute, Guangdong Medical University, Dongguan, China
| | - Zhiwei He
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Xin-Guang Liu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Yongkang Zou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Junzhi Zhou
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, School of Basic Medicine, Guangdong Medical University, Dongguan, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
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3
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Ennis A, Wang L, Wang X, Yu C, Saidi L, Xu Y, Yun S, Huang L, Ye Y. NEMF-mediated CAT-tailing defines distinct branches of translocation-associated quality control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.610005. [PMID: 39253483 PMCID: PMC11383284 DOI: 10.1101/2024.08.27.610005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Ribosome stalling during co-translational translocation at the endoplasmic reticulum (ER) causes translocon clogging and impairs ER protein biogenesis. Mammalian cells resolve translocon clogging vial a poorly characterized translocation-associated quality control (TAQC) process. Here, we combine genome-wide CRISPR screen with live cell imaging to dissect the molecular linchpin of TAQC. We show that substrates translated from mRNAs bearing a ribosome stalling poly(A) sequence are degraded by lysosomes and the proteasome, while substrates encoded by non-stop mRNAs are degraded by an unconventional ER-associated degradation (ERAD) mechanism involving ER-to-Golgi trafficking and KDEL-dependent substrate retrieval. The triaging diversity appears to result from the heterogeneity of NEMF-mediated CATylation, because a systematic characterization of representative CAT-tail mimetics establishes an AT-rich tail as a "degron" for ERAD, whereas an AG-rich tail can direct a secretory protein to the lysosome. Our study reveals an unexpected protein sorting function for CAT-tailing that safeguards ER protein biogenesis.
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Affiliation(s)
- Amanda Ennis
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lihui Wang
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Current affiliation: Innovent USA, 319 N Bernardo Avenue, Mountain View, CA, 94043
| | - Xiaorong Wang
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92687, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92687, USA
| | - Layla Saidi
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yue Xu
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijung Yun
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Current affiliation: Yottabiomed, LLC. 8908 Ewing Dr., Bethesda, MD 20817
| | - Lan Huang
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92687, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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4
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Kaminskaya AN, Evpak AS, Belogurov AA, Kudriaeva AA. Tracking of Ubiquitin Signaling through 3.5 Billion Years of Combinatorial Conjugation. Int J Mol Sci 2024; 25:8671. [PMID: 39201358 PMCID: PMC11354881 DOI: 10.3390/ijms25168671] [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: 06/11/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 09/02/2024] Open
Abstract
Ubiquitination is an evolutionary, ancient system of post-translational modification of proteins that occurs through a cascade involving ubiquitin activation, transfer, and conjugation. The maturation of this system has followed two main pathways. The first is the conservation of a universal structural fold of ubiquitin and ubiquitin-like proteins, which are present in both Archaea and Bacteria, as well as in multicellular Eukaryotes. The second is the rise of the complexity of the superfamily of ligases, which conjugate ubiquitin-like proteins to substrates, in terms of an increase in the number of enzyme variants, greater variation in structural organization, and the diversification of their catalytic domains. Here, we examine the diversity of the ubiquitination system among different organisms, assessing the variety and conservation of the key domains of the ubiquitination enzymes and ubiquitin itself. Our data show that E2 ubiquitin-conjugating enzymes of metazoan phyla are highly conservative, whereas the homology of E3 ubiquitin ligases with human orthologues gradually decreases depending on "molecular clock" timing and evolutionary distance. Surprisingly, Chordata and Echinodermata, which diverged over 0.5 billion years ago during the Cambrian explosion, share almost the same homology with humans in the amino acid sequences of E3 ligases but not in their adaptor proteins. These observations may suggest that, firstly, the E2 superfamily already existed in its current form in the last common metazoan ancestor and was generally not affected by purifying selection in metazoans. Secondly, it may indicate convergent evolution of the ubiquitination system and highlight E3 adaptor proteins as the "upper deck" of the ubiquitination system, which plays a crucial role in chordate evolution.
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Affiliation(s)
- Alena N. Kaminskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.N.K.); (A.S.E.)
| | - Alena S. Evpak
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.N.K.); (A.S.E.)
| | - Alexey A. Belogurov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.N.K.); (A.S.E.)
- Department of Biological Chemistry, Russian University of Medicine, Ministry of Health of Russian Federation, 127473 Moscow, Russia
| | - Anna A. Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.N.K.); (A.S.E.)
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5
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Khan D, Vinayak AA, Sitron CS, Brandman O. Mechanochemical forces regulate the composition and function of CAT tails. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606406. [PMID: 39131335 PMCID: PMC11312545 DOI: 10.1101/2024.08.02.606406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The ribosome-associated quality control (RQC) pathway resolves stalled ribosomes. As part of RQC, stalled nascent polypeptide chains (NCs) are appended with CArboxy-Terminal amino acids (CAT tails) in an mRNA-free, non-canonical elongation process. CAT tail composition includes Ala, Thr, and potentially other residues. The relationship between CAT tail composition and function has remained unknown. Using biochemical approaches in yeast, we discovered that mechanochemical forces on the NC regulate CAT tailing. We propose CAT tailing initially operates in an "extrusion mode" that increases NC lysine accessibility for on-ribosome ubiquitination. Thr in CAT tails enhances NC extrusion by preventing formation of polyalanine, which can form α-helices. After NC ubiquitylation, pulling forces on the NC switch CAT tailing to an Ala-only "release mode" which facilitates nascent chain release from large ribosomal subunits and NC degradation. Failure to switch from extrusion to release mode leads to accumulation of NCs on large ribosomal subunits and proteotoxic aggregation of Thr-rich CAT tails.
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Affiliation(s)
- Danish Khan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ananya A Vinayak
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cole S Sitron
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Onn Brandman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
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6
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Xu X, Huang W, Bryant CN, Dong Z, Li H, Wu G. The ufmylation cascade controls COPII recruitment, anterograde transport, and sorting of nascent GPCRs at ER. SCIENCE ADVANCES 2024; 10:eadm9216. [PMID: 38905340 PMCID: PMC11192079 DOI: 10.1126/sciadv.adm9216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
Ufmylation is implicated in multiple cellular processes, but little is known about its functions and regulation in protein trafficking. Here, we demonstrate that the genetic depletion of core components of the ufmylation cascade, including ubiquitin-fold modifier 1 (UFM1), UFM1 activation enzyme 5, UFM1-specific ligase 1 (UFL1), UFM1-specific protease 2, and UFM1-binding protein 1 (UFBP1) each markedly inhibits the endoplasmic reticulum (ER)-Golgi transport, surface delivery, and recruitment to COPII vesicles of a subset of G protein-coupled receptors (GPCRs) and UFBP1's function partially relies on UFM1 conjugation. We also show that UFBP1 and UFL1 interact with GPCRs and UFBP1 localizes at COPII vesicles coated with specific Sec24 isoforms. Furthermore, the UFBP1/UFL1-binding domain identified in the receptors effectively converts non-GPCR protein transport into the ufmylation-dependent pathway. Collectively, these data reveal important functions for the ufmylation system in GPCR recruitment to COPII vesicles, biosynthetic transport, and sorting at ER via UFBP1 ufmylation and interaction directly.
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Affiliation(s)
- Xin Xu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Wei Huang
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Christian N. Bryant
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Zheng Dong
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Honglin Li
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Guangyu Wu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA
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7
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He C, Xing X, Chen HY, Gao M, Shi J, Xiang B, Xiao X, Sun Y, Yu H, Xu G, Yao Y, Xie Z, Xing Y, Budiarto BR, Chen SY, Gao Y, Lee YR, Zhang J. UFL1 ablation in T cells suppresses PD-1 UFMylation to enhance anti-tumor immunity. Mol Cell 2024; 84:1120-1138.e8. [PMID: 38377992 DOI: 10.1016/j.molcel.2024.01.024] [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: 05/30/2023] [Revised: 11/10/2023] [Accepted: 01/26/2024] [Indexed: 02/22/2024]
Abstract
UFMylation is an emerging ubiquitin-like post-translational modification that regulates various biological processes. Dysregulation of the UFMylation pathway leads to human diseases, including cancers. However, the physiological role of UFMylation in T cells remains unclear. Here, we report that mice with conditional knockout (cKO) Ufl1, a UFMylation E3 ligase, in T cells exhibit effective tumor control. Single-cell RNA sequencing analysis shows that tumor-infiltrating cytotoxic CD8+ T cells are increased in Ufl1 cKO mice. Mechanistically, UFL1 promotes PD-1 UFMylation to antagonize PD-1 ubiquitination and degradation. Furthermore, AMPK phosphorylates UFL1 at Thr536, disrupting PD-1 UFMylation to trigger its degradation. Of note, UFL1 ablation in T cells reduces PD-1 UFMylation, subsequently destabilizing PD-1 and enhancing CD8+ T cell activation. Thus, Ufl1 cKO mice bearing tumors have a better response to anti-CTLA-4 immunotherapy. Collectively, our findings uncover a crucial role of UFMylation in T cells and highlight UFL1 as a potential target for cancer treatment.
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Affiliation(s)
- Chuan He
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xixin Xing
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Hsin-Yi Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan
| | - Minling Gao
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Jie Shi
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Bolin Xiang
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiangling Xiao
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yishuang Sun
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Haisheng Yu
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Gaoshan Xu
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yingmeng Yao
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Zuosong Xie
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yujie Xing
- Department of Urology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Bugi Ratno Budiarto
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan; Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Shih-Yu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan
| | - Yang Gao
- Department of Urology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Yu-Ru Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan.
| | - Jinfang Zhang
- Department of Radiation and Medical Oncology, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China.
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8
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Inada T, Beckmann R. Mechanisms of Translation-coupled Quality Control. J Mol Biol 2024; 436:168496. [PMID: 38365086 DOI: 10.1016/j.jmb.2024.168496] [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: 12/05/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
Stalling of ribosomes engaged in protein synthesis can lead to significant defects in the function of newly synthesized proteins and thereby impair protein homeostasis. Consequently, partially synthesized polypeptides resulting from translation stalling are recognized and eliminated by several quality control mechanisms. First, if translation elongation reactions are halted prematurely, a quality control mechanism called ribosome-associated quality control (RQC) initiates the ubiquitination of the nascent polypeptide chain and subsequent proteasomal degradation. Additionally, when ribosomes with defective codon recognition or peptide-bond formation stall during translation, a quality control mechanism known as non-functional ribosomal RNA decay (NRD) leads to the degradation of malfunctioning ribosomes. In both of these quality control mechanisms, E3 ubiquitin ligases selectively recognize ribosomes in distinct translation-stalling states and ubiquitinate specific ribosomal proteins. Significant efforts have been devoted to characterize E3 ubiquitin ligase sensing of ribosome 'collision' or 'stalling' and subsequent ribosome is rescued. This article provides an overview of our current understanding of the molecular mechanisms and physiological functions of ribosome dynamics control and quality control of abnormal translation.
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Affiliation(s)
- Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku, Tokyo 108-8639, Japan.
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany.
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9
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Wang L, Xu Y, Fukushige T, Saidi L, Wang X, Yu C, Lee JG, Krause M, Huang L, Ye Y. Mono-UFMylation promotes misfolding-associated secretion of α-synuclein. SCIENCE ADVANCES 2024; 10:eadk2542. [PMID: 38489364 PMCID: PMC10942102 DOI: 10.1126/sciadv.adk2542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
Stressed cells secret misfolded proteins lacking signaling sequence via an unconventional protein secretion (UcPS) pathway, but how misfolded proteins are targeted selectively in UcPS is unclear. Here, we report that misfolded UcPS clients are subject to modification by a ubiquitin-like protein named ubiquitin-fold modifier 1 (UFM1). Using α-synuclein (α-Syn) as a UcPS model, we show that mutating the UFMylation sites in α-Syn or genetic inhibition of the UFMylation system mitigates α-Syn secretion, whereas overexpression of UFBP1, a component of the endoplasmic reticulum-associated UFMylation ligase complex, augments α-Syn secretion in mammalian cells and in model organisms. UFM1 itself is cosecreted with α-Syn, and the serum UFM1 level correlates with that of α-Syn. Because UFM1 can be directly recognized by ubiquitin specific peptidase 19 (USP19), a previously established UcPS stimulator known to associate with several chaperoning activities, UFMylation might facilitate substrate engagement by USP19, allowing stringent and regulated selection of misfolded proteins for secretion and proteotoxic stress alleviation.
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Affiliation(s)
- Lihui Wang
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yue Xu
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tetsunari Fukushige
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Layla Saidi
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaorong Wang
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
| | - Jin-Gu Lee
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Krause
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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10
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Makhlouf L, Peter JJ, Magnussen HM, Thakur R, Millrine D, Minshull TC, Harrison G, Varghese J, Lamoliatte F, Foglizzo M, Macartney T, Calabrese AN, Zeqiraj E, Kulathu Y. The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons. Nature 2024; 627:437-444. [PMID: 38383789 PMCID: PMC10937380 DOI: 10.1038/s41586-024-07093-w] [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: 04/03/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024]
Abstract
Stalled ribosomes at the endoplasmic reticulum (ER) are covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit protein RPL26 (also known as uL24)1,2. This modification, which is known as UFMylation, is orchestrated by the UFM1 ribosome E3 ligase (UREL) complex, comprising UFL1, UFBP1 and CDK5RAP3 (ref. 3). However, the catalytic mechanism of UREL and the functional consequences of UFMylation are unclear. Here we present cryo-electron microscopy structures of UREL bound to 60S ribosomes, revealing the basis of its substrate specificity. UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other. A UFL1 loop inserts into and remodels the peptidyl transferase centre. These features of UREL suggest a crucial function for UFMylation in the release and recycling of stalled or terminated ribosomes from the ER membrane. In the absence of functional UREL, 60S-SEC61 translocon complexes accumulate at the ER membrane, demonstrating that UFMylation is necessary for releasing SEC61 from 60S subunits. Notably, this release is facilitated by a functional switch of UREL from a 'writer' to a 'reader' module that recognizes its product-UFMylated 60S ribosomes. Collectively, we identify a fundamental role for UREL in dissociating 60S subunits from the SEC61 translocon and the basis for UFMylation in regulating protein homeostasis at the ER.
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Affiliation(s)
- Linda Makhlouf
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joshua J Peter
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Helge M Magnussen
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Rohan Thakur
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - David Millrine
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Translational Immunology, Cancer Biomarker Centre, Manchester CRUK Institute, Manchester, UK
| | - Thomas C Minshull
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Grace Harrison
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Joby Varghese
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Martina Foglizzo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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11
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DaRosa PA, Penchev I, Gumbin SC, Scavone F, Wąchalska M, Paulo JA, Ordureau A, Peter JJ, Kulathu Y, Harper JW, Becker T, Beckmann R, Kopito RR. UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. Nature 2024; 627:445-452. [PMID: 38383785 DOI: 10.1038/s41586-024-07073-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024]
Abstract
Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour1. UFM1 is a UBL that predominantly modifies a single lysine residue on a single ribosomal protein, uL24 (also called RPL26), on ribosomes at the cytoplasmic surface of the endoplasmic reticulum (ER)2,3. UFM1 conjugation (UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER3,4. Neither the molecular mechanism by which the UFMylation machinery achieves such precise target selection nor how this ribosomal modification promotes 60S rescue is known. Here we show that ribosome UFMylation in vivo occurs on free 60S and we present sequential cryo-electron microscopy snapshots of the heterotrimeric UFM1 E3 ligase (E3(UFM1)) engaging its substrate uL24. E3(UFM1) binds the L1 stalk, empty transfer RNA-binding sites and the peptidyl transferase centre through carboxy-terminal domains of UFL1, which results in uL24 modification more than 150 Å away. After catalysing UFM1 transfer, E3(UFM1) remains stably bound to its product, UFMylated 60S, forming a C-shaped clamp that extends all the way around the 60S from the transfer RNA-binding sites to the polypeptide tunnel exit. Our structural and biochemical analyses suggest a role for E3(UFM1) in post-termination release and recycling of the large ribosomal subunit from the ER membrane.
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Affiliation(s)
- Paul A DaRosa
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Ivan Penchev
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany
| | | | | | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joshua J Peter
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas Becker
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany
| | - Roland Beckmann
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany.
| | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, CA, USA.
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12
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Komatsu M, Inada T, Noda NN. The UFM1 system: Working principles, cellular functions, and pathophysiology. Mol Cell 2024; 84:156-169. [PMID: 38141606 DOI: 10.1016/j.molcel.2023.11.034] [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: 08/14/2023] [Revised: 10/21/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like protein covalently conjugated with intracellular proteins through UFMylation, a process similar to ubiquitylation. Growing lines of evidence regarding not only the structural basis of the components essential for UFMylation but also their biological properties shed light on crucial roles of the UFM1 system in the endoplasmic reticulum (ER), such as ER-phagy and ribosome-associated quality control at the ER, although there are some functions unrelated to the ER. Mouse genetics studies also revealed the indispensable roles of this system in hematopoiesis, liver development, neurogenesis, and chondrogenesis. Of critical importance, mutations of genes encoding core components of the UFM1 system in humans cause hereditary developmental epileptic encephalopathy and Schohat-type osteochondrodysplasia of the epiphysis. Here, we provide a multidisciplinary review of our current understanding of the mechanisms and cellular functions of the UFM1 system as well as its pathophysiological roles, and discuss issues that require resolution.
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Affiliation(s)
- Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan.
| | - Toshifumi Inada
- Division of RNA and gene regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku, Tokyo 108-8639, Japan.
| | - Nobuo N Noda
- Institute for Genetic Medicine, Hokkaido University, Kita-Ku, Sapporo 060-0815, Japan; Institute of Microbial Chemistry (Bikaken), Shinagawa-ku, Tokyo 141-0021, Japan.
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13
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Zhou X, Mahdizadeh SJ, Le Gallo M, Eriksson LA, Chevet E, Lafont E. UFMylation: a ubiquitin-like modification. Trends Biochem Sci 2024; 49:52-67. [PMID: 37945409 DOI: 10.1016/j.tibs.2023.10.004] [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: 04/29/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
Post-translational modifications (PTMs) add a major degree of complexity to the proteome and are essential controllers of protein homeostasis. Amongst the hundreds of PTMs identified, ubiquitin and ubiquitin-like (UBL) modifications are recognized as key regulators of cellular processes through their ability to affect protein-protein interactions, protein stability, and thus the functions of their protein targets. Here, we focus on the most recently identified UBL, ubiquitin-fold modifier 1 (UFM1), and the machinery responsible for its transfer to substrates (UFMylation) or its removal (deUFMylation). We first highlight the biochemical peculiarities of these processes, then we develop on how UFMylation and its machinery control various intertwined cellular processes and we highlight some of the outstanding research questions in this emerging field.
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Affiliation(s)
- Xingchen Zhou
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Sayyed J Mahdizadeh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Matthieu Le Gallo
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Eric Chevet
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.
| | - Elodie Lafont
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.
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14
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Pan X, Alvarez AN, Ma M, Lu S, Crawford MW, Briere LC, Kanca O, Yamamoto S, Sweetser DA, Wilson JL, Napier RJ, Pruneda JN, Bellen HJ. Allelic strengths of encephalopathy-associated UBA5 variants correlate between in vivo and in vitro assays. eLife 2023; 12:RP89891. [PMID: 38079206 PMCID: PMC10712953 DOI: 10.7554/elife.89891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
Protein UFMylation downstream of the E1 enzyme UBA5 plays essential roles in development and endoplasmic reticulum stress. Variants in the UBA5 gene are associated with developmental and epileptic encephalopathy 44 (DEE44), an autosomal recessive disorder characterized by early-onset encephalopathy, movement abnormalities, global developmental delay, intellectual disability, and seizures. DEE44 is caused by at least 12 different missense variants described as loss of function (LoF), but the relationships between genotypes and molecular or clinical phenotypes remain to be established. We developed a humanized UBA5 fly model and biochemical activity assays in order to describe in vivo and in vitro genotype-phenotype relationships across the UBA5 allelic series. In vivo, we observed a broad spectrum of phenotypes in viability, developmental timing, lifespan, locomotor activity, and bang sensitivity. A range of functional effects was also observed in vitro across comprehensive biochemical assays for protein stability, ATP binding, UFM1 activation, and UFM1 transthiolation. Importantly, there is a strong correlation between in vivo and in vitro phenotypes, establishing a classification of LoF variants into mild, intermediate, and severe allelic strengths. By systemically evaluating UBA5 variants across in vivo and in vitro platforms, this study provides a foundation for more basic and translational UBA5 research, as well as a basis for evaluating current and future individuals afflicted with this rare disease.
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Affiliation(s)
- Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Albert N Alvarez
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Michael W Crawford
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - David A Sweetser
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for ChildrenBostonUnited States
| | - Jenny L Wilson
- Division of Pediatric Neurology, Department of Pediatrics, Oregon Health & Science UniversityPortlandUnited States
| | - Ruth J Napier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
- VA Portland Health Care SystemPortlandUnited States
- Division of Arthritis & Rheumatic Diseases, Oregon Health & Science UniversityPortlandUnited States
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
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15
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Meydan S, Guydosh NR. Is there a localized role for translational quality control? RNA (NEW YORK, N.Y.) 2023; 29:1623-1643. [PMID: 37582617 PMCID: PMC10578494 DOI: 10.1261/rna.079683.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
It is known that mRNAs and the machinery that translates them are not uniformly distributed throughout the cytoplasm. As a result, the expression of some genes is localized to particular parts of the cell and this makes it possible to carry out important activities, such as growth and signaling, in three-dimensional space. However, the functions of localized gene expression are not fully understood, and the underlying mechanisms that enable localized expression have not been determined in many cases. One consideration that could help in addressing these challenges is the role of quality control (QC) mechanisms that monitor translating ribosomes. On a global level, QC pathways are critical for detecting aberrant translation events, such as a ribosome that stalls while translating, and responding by activating stress pathways and resolving problematic ribosomes and mRNAs at the molecular level. However, it is unclear how these pathways, even when uniformly active throughout the cell, affect local translation. Importantly, some QC pathways have themselves been reported to be enriched in the proximity of particular organelles, but the extent of such localized activity remains largely unknown. Here, we describe the major QC pathways and review studies that have begun to explore their roles in localized translation. Given the limited data in this area, we also pose broad questions about the possibilities and limitations for how QC pathways could facilitate localized gene expression in the cell with the goal of offering ideas for future experimentation.
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Affiliation(s)
- Sezen Meydan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
- National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nicholas R Guydosh
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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16
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Luo H, Jiao QB, Shen CB, Gong WY, Yuan JH, Liu YY, Chen Z, Liu J, Xu XL, Cong YS, Zhang XW. UFMylation of HRD1 regulates endoplasmic reticulum homeostasis. FASEB J 2023; 37:e23221. [PMID: 37795761 DOI: 10.1096/fj.202300004rrrr] [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: 01/02/2023] [Revised: 08/28/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023]
Abstract
Ubiquitin fold modifier 1 is a small ubiquitin-like protein modifier that is essential for embryonic development of metazoans. Although UFMylation has been connected to endoplasmic reticulum homeostasis, the underlying mechanisms and the relevant cellular targets are largely unknown. Here, we show that HRD1, a ubiquitin ligase of ER-associated protein degradation (ERAD), is a novel substrate of UFM1 conjugation. HRD1 interacts with UFMylation components UFL1 and DDRGK1 and is UFMylated at Lys610 residue. In UFL1-depleted cells, the stability of HRD1 is increased and its ubiquitination modification is reduced. In the event of ER stress, the UFMylation and ubiquitination modification of HRD1 is gradually inhibited over time. Alteration of HRD1 Lys610 residue to arginine impairs its ability to degrade unfolded or misfolded proteins to disturb protein processing in ER. These results suggest that UFMylation of HRD1 facilitates ERAD function to maintain ER homeostasis.
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Affiliation(s)
- Hui Luo
- School of Clinical Medicine, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
| | - Qi-Bin Jiao
- School of Clinical Medicine, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
| | - Chuan-Bin Shen
- School of Clinical Medicine, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
| | - Wen-Yan Gong
- School of Clinical Medicine, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
| | - Jing-Hua Yuan
- School of Clinical Medicine, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
| | - Ying-Ying Liu
- School of Clinical Medicine, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
| | - Zhen Chen
- School of Clinical Medicine, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
| | - Jiang Liu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiao-Ling Xu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yu-Sheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xing-Wei Zhang
- School of Clinical Medicine, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
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17
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Samba-Louaka A, Labruyère E, Matondo M, Locard-Paulet M, Olivo-Marin JC, Guillen N. Encystation and Stress Responses under the Control of Ubiquitin-like Proteins in Pathogenic Amoebae. Microorganisms 2023; 11:2670. [PMID: 38004682 PMCID: PMC10673212 DOI: 10.3390/microorganisms11112670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Amoebae found in aquatic and terrestrial environments encompass various pathogenic species, including the parasite Entamoeba histolytica and the free-living Acanthamoeba castellanii. Both microorganisms pose significant threats to public health, capable of inducing life-threatening effects on humans. These amoebae exist in two cellular forms: trophozoites and cysts. The trophozoite stage is the form used for growth and reproduction while the cyst stage is the resistant and disseminating form. Cysts occur after cellular metabolism slowdown due to nutritional deprivation or the appearance of environmental conditions unfavourable to the amoebae's growth and division. The initiation of encystation is accompanied by the activation of stress responses, and scarce data indicate that encystation shares factors and mechanisms identified in stress responses occurring in trophozoites exposed to toxic compounds derived from human immune defence. Although some "omics" analyses have explored how amoebae respond to diverse stresses, these studies remain limited and rarely report post-translational modifications that would provide knowledge on the molecular mechanisms underlying amoebae-specific stress responses. In this review, we discuss ubiquitin-like proteins associated with encystation and cell survival during oxidative damage. We aim to shed light on the signalling pathways involved in amoebic defence mechanisms, with a focus on their potential clinical implications against pathogenic amoebae, addressing the pressing need for effective therapies.
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Affiliation(s)
- Ascel Samba-Louaka
- Université de Poitiers, Centre National de la Recherche Scientifique UMR7267, Laboratoire Ecologie et Biologie des Interactions, TSA51106, 86073 Poitiers, France
| | - Elisabeth Labruyère
- Institut Pasteur, Biological Image Analysis Unit, Centre National de la Recherche Scientifique UMR3691, Université Paris Cité, 75015 Paris, France; (E.L.); (J.-C.O.-M.)
| | - Mariette Matondo
- Institut Pasteur, Proteomics Core Facility, Mass Spectrometry for Biology Unit, Centre National de la Recherche Scientifique UAR 2024, Université Paris Cité, 75015 Paris, France;
| | - Marie Locard-Paulet
- Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique UMR 5089, Université Toulouse III-Paul Sabatier, 31077 Toulouse, France;
- Infrastructure Nationale de Proteomique ProFI—FR2048, 2048 Toulouse, France
| | - Jean-Christophe Olivo-Marin
- Institut Pasteur, Biological Image Analysis Unit, Centre National de la Recherche Scientifique UMR3691, Université Paris Cité, 75015 Paris, France; (E.L.); (J.-C.O.-M.)
| | - Nancy Guillen
- Institut Pasteur, Biological Image Analysis Unit, Centre National de la Recherche Scientifique UMR3691, Université Paris Cité, 75015 Paris, France; (E.L.); (J.-C.O.-M.)
- Institut Pasteur, Centre National de la Recherche Scientifique ERL9195, 75015 Paris, France
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18
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Pan X, Alvarez AN, Ma M, Lu S, Crawford MW, Briere LC, Kanca O, Yamamoto S, Sweetser DA, Wilson JL, Napier RJ, Pruneda JN, Bellen HJ. Allelic strengths of encephalopathy-associated UBA5 variants correlate between in vivo and in vitro assays. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.17.23292782. [PMID: 37502976 PMCID: PMC10371176 DOI: 10.1101/2023.07.17.23292782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Protein UFMylation downstream of the E1 enzyme UBA5 plays essential roles in development and ER stress. Variants in the UBA5 gene are associated with developmental and epileptic encephalopathy 44 (DEE44), an autosomal recessive disorder characterized by early-onset encephalopathy, movement abnormalities, global developmental delay, intellectual disability, and seizures. DEE44 is caused by at least twelve different missense variants described as loss of function (LoF), but the relationships between genotypes and molecular or clinical phenotypes remains to be established. We developed a humanized UBA5 fly model and biochemical activity assays in order to describe in vivo and in vitro genotype-phenotype relationships across the UBA5 allelic series. In vivo, we observed a broad spectrum of phenotypes in viability, developmental timing, lifespan, locomotor activity, and bang sensitivity. A range of functional effects was also observed in vitro across comprehensive biochemical assays for protein stability, ATP binding, UFM1 activation, and UFM1 transthiolation. Importantly, there is a strong correlation between in vivo and in vitro phenotypes, establishing a classification of LoF variants into mild, intermediate, and severe allelic strengths. By systemically evaluating UBA5 variants across in vivo and in vitro platforms, this study provides a foundation for more basic and translational UBA5 research, as well as a basis for evaluating current and future individuals afflicted with this rare disease.
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Affiliation(s)
- Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Albert N. Alvarez
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Michael W. Crawford
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lauren C. Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A. Sweetser
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Jenny L. Wilson
- Division of Pediatric Neurology, Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ruth J. Napier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
- VA Portland Health Care System, Portland, OR 97239, USA
- Division of Arthritis & Rheumatic Diseases, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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19
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Ishimura R, Ito S, Mao G, Komatsu-Hirota S, Inada T, Noda NN, Komatsu M. Mechanistic insights into the roles of the UFM1 E3 ligase complex in ufmylation and ribosome-associated protein quality control. SCIENCE ADVANCES 2023; 9:eadh3635. [PMID: 37595036 PMCID: PMC10438457 DOI: 10.1126/sciadv.adh3635] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like protein covalently conjugated with intracellular proteins through ufmylation, similar to ubiquitylation. Ufmylation is involved in processes such as endoplasmic reticulum (ER)-associated protein degradation, ribosome-associated protein quality control (RQC) at the ER (ER-RQC), and ER-phagy. However, it remains unclear how ufmylation regulates such distinct ER-related functions. Here, we provide insights into the mechanism of the UFM1 E3 complex in not only ufmylation but also ER-RQC. The E3 complex consisting of UFL1 and UFBP1 interacted with UFC1, UFM1 E2, and, subsequently, CDK5RAP3, an adaptor for ufmylation of ribosomal subunit RPL26. Upon disome formation, the E3 complex associated with ufmylated RPL26 on the 60S subunit through the UFM1-interacting region of UFBP1. Loss of E3 components or disruption of the interaction between UFBP1 and ufmylated RPL26 attenuated ER-RQC. These results provide insights into not only the molecular basis of the ufmylation but also its role in proteostasis.
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Affiliation(s)
- Ryosuke Ishimura
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Sota Ito
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
| | - Gaoxin Mao
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Satoko Komatsu-Hirota
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Kita-Ku, Sapporo 060-0815, Japan
- Institute of Microbial Chemistry (Bikaken), Shinagawa-ku, Tokyo 141-0021, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
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Gullberg RC, Frydman J. Novel Mode of nanoLuciferase Packaging in SARS-CoV-2 Virions and VLPs Provides Versatile Reporters for Virus Production. Viruses 2023; 15:1335. [PMID: 37376634 DOI: 10.3390/v15061335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
SARS-CoV-2 is a positive-strand RNA virus in the Coronaviridae family that is responsible for morbidity and mortality worldwide. To better understand the molecular pathways leading to SARS-CoV-2 virus assembly, we examined a virus-like particle (VLP) system co-expressing all structural proteins together with an mRNA reporter encoding nanoLuciferase (herein nLuc). Surprisingly, the 19 kDa nLuc protein itself was encapsidated into VLPs, providing a better reporter than nLuc mRNA itself. Strikingly, infecting nLuc-expressing cells with the SARS-CoV-2, NL63 or OC43 coronaviruses yielded virions containing packaged nLuc that served to report viral production. In contrast, infection with the flaviviruses, dengue or Zika, did not lead to nLuc packaging and secretion. A panel of reporter protein variants revealed that the packaging is size-limited and requires cytoplasmic expression, indicating that the large virion of coronaviruses can encaspidate a small cytoplasmic reporter protein. Our findings open the way for powerful new approaches to measure coronavirus particle production, egress and viral entry mechanisms.
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Affiliation(s)
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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