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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. Sci Adv 2023; 9:eadh3635. [PMID: 37595036 PMCID: PMC10438457 DOI: 10.1126/sciadv.adh3635] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Ikeda R, Noshiro D, Morishita H, Takada S, Kageyama S, Fujioka Y, Funakoshi T, Komatsu-Hirota S, Arai R, Ryzhii E, Abe M, Koga T, Motohashi H, Nakao M, Sakimura K, Horii A, Waguri S, Ichimura Y, Noda NN, Komatsu M. Phosphorylation of phase-separated p62 bodies by ULK1 activates a redox-independent stress response. EMBO J 2023:e113349. [PMID: 37306101 DOI: 10.15252/embj.2022113349] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
NRF2 is a transcription factor responsible for antioxidant stress responses that is usually regulated in a redox-dependent manner. p62 bodies formed by liquid-liquid phase separation contain Ser349-phosphorylated p62, which participates in the redox-independent activation of NRF2. However, the regulatory mechanism and physiological significance of p62 phosphorylation remain unclear. Here, we identify ULK1 as a kinase responsible for the phosphorylation of p62. ULK1 colocalizes with p62 bodies, directly interacting with p62. ULK1-dependent phosphorylation of p62 allows KEAP1 to be retained within p62 bodies, thus activating NRF2. p62S351E/+ mice are phosphomimetic knock-in mice in which Ser351, corresponding to human Ser349, is replaced by Glu. These mice, but not their phosphodefective p62S351A/S351A counterparts, exhibit NRF2 hyperactivation and growth retardation. This retardation is caused by malnutrition and dehydration due to obstruction of the esophagus and forestomach secondary to hyperkeratosis, a phenotype also observed in systemic Keap1-knockout mice. Our results expand our understanding of the physiological importance of the redox-independent NRF2 activation pathway and provide new insights into the role of phase separation in this process.
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Affiliation(s)
- Ryo Ikeda
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Otolaryngology Head and Neck Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Daisuke Noshiro
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Hideaki Morishita
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shuhei Takada
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shun Kageyama
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuko Fujioka
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Tomoko Funakoshi
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Satoko Komatsu-Hirota
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Ritsuko Arai
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Elena Ryzhii
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Tomoaki Koga
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Arata Horii
- Department of Otolaryngology Head and Neck Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yoshinobu Ichimura
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobuo N Noda
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Kurusu R, Fujimoto Y, Morishita H, Noshiro D, Takada S, Yamano K, Tanaka H, Arai R, Kageyama S, Funakoshi T, Komatsu-Hirota S, Taka H, Kazuno S, Miura Y, Koike M, Wakai T, Waguri S, Noda NN, Komatsu M. Integrated proteomics identifies p62-dependent selective autophagy of the supramolecular vault complex. Dev Cell 2023:S1534-5807(23)00191-0. [PMID: 37192622 DOI: 10.1016/j.devcel.2023.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/13/2023] [Accepted: 04/25/2023] [Indexed: 05/18/2023]
Abstract
In addition to membranous organelles, autophagy selectively degrades biomolecular condensates, in particular p62/SQSTM1 bodies, to prevent diseases including cancer. Evidence is growing regarding the mechanisms by which autophagy degrades p62 bodies, but little is known about their constituents. Here, we established a fluorescence-activated-particle-sorting-based purification method for p62 bodies using human cell lines and determined their constituents by mass spectrometry. Combined with mass spectrometry of selective-autophagy-defective mouse tissues, we identified vault, a large supramolecular complex, as a cargo within p62 bodies. Mechanistically, major vault protein directly interacts with NBR1, a p62-interacting protein, to recruit vault into p62 bodies for efficient degradation. This process, named vault-phagy, regulates homeostatic vault levels in vivo, and its impairment may be associated with non-alcoholic-steatohepatitis-derived hepatocellular carcinoma. Our study provides an approach to identifying phase-separation-mediated selective autophagy cargoes, expanding our understanding of the role of phase separation in proteostasis.
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Affiliation(s)
- Reo Kurusu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Yuki Fujimoto
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Hideaki Morishita
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan.
| | - Daisuke Noshiro
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Shuhei Takada
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Koji Yamano
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hideaki Tanaka
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ritsuko Arai
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukushima 960-1295, Japan
| | - Shun Kageyama
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Tomoko Funakoshi
- 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
| | - Hikari Taka
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Saiko Kazuno
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Yoshiki Miura
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Masato Koike
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata City, Niigata 951-8510, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukushima 960-1295, Japan
| | - Nobuo N Noda
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan.
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4
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Ishimura R, El-Gowily AH, Noshiro D, Komatsu-Hirota S, Ono Y, Shindo M, Hatta T, Abe M, Uemura T, Lee-Okada HC, Mohamed TM, Yokomizo T, Ueno T, Sakimura K, Natsume T, Sorimachi H, Inada T, Waguri S, Noda NN, Komatsu M. The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3. Nat Commun 2022; 13:7857. [PMID: 36543799 PMCID: PMC9772183 DOI: 10.1038/s41467-022-35501-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Protein modification by ubiquitin-like proteins (UBLs) amplifies limited genome information and regulates diverse cellular processes, including translation, autophagy and antiviral pathways. Ubiquitin-fold modifier 1 (UFM1) is a UBL covalently conjugated with intracellular proteins through ufmylation, a reaction analogous to ubiquitylation. Ufmylation is involved in processes such as endoplasmic reticulum (ER)-associated protein degradation, ribosome-associated protein quality control at the ER and ER-phagy. However, it remains unclear how ufmylation regulates such distinct ER-related functions. Here we identify a UFM1 substrate, NADH-cytochrome b5 reductase 3 (CYB5R3), that localizes on the ER membrane. Ufmylation of CYB5R3 depends on the E3 components UFL1 and UFBP1 on the ER, and converts CYB5R3 into its inactive form. Ufmylated CYB5R3 is recognized by UFBP1 through the UFM1-interacting motif, which plays an important role in the further uyfmylation of CYB5R3. Ufmylated CYB5R3 is degraded in lysosomes, which depends on the autophagy-related protein Atg7- and the autophagy-adaptor protein CDK5RAP3. Mutations of CYB5R3 and genes involved in the UFM1 system cause hereditary developmental disorders, and ufmylation-defective Cyb5r3 knock-in mice exhibit microcephaly. Our results indicate that CYB5R3 ufmylation induces ER-phagy, which is indispensable for brain development.
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Affiliation(s)
- Ryosuke Ishimura
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Afnan H El-Gowily
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Daisuke Noshiro
- Division of Biological Molecular Mechanisms, Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Satoko Komatsu-Hirota
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yasuko Ono
- Calpain Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Mayumi Shindo
- Advanced Technical Support Department, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Tomohisa Hatta
- National Institutes of Advanced Industrial Science and Technology, Biological Information Research Center (JBIRC), Kohtoh-ku, Tokyo, 135-0064, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Chuo-ku, Niigata, 951-8585, Japan
| | - Takefumi Uemura
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukshima, 960-1295, Japan
| | - Hyeon-Cheol Lee-Okada
- Department of Biochemistry, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Tarek M Mohamed
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Takehiko Yokomizo
- Department of Biochemistry, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Takashi Ueno
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Chuo-ku, Niigata, 951-8585, Japan
| | - Tohru Natsume
- National Institutes of Advanced Industrial Science and Technology, Biological Information Research Center (JBIRC), Kohtoh-ku, Tokyo, 135-0064, Japan
| | - Hiroyuki Sorimachi
- Calpain Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Toshifumi Inada
- Division of RNA and gene regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku, 108-8639, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukshima, 960-1295, Japan
| | - Nobuo N Noda
- Division of Biological Molecular Mechanisms, Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan.
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5
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Faruk MO, Ichimura Y, Kageyama S, Komatsu-Hirota S, El-Gowily AH, Sou YS, Koike M, Noda NN, Komatsu M. Phase-separated protein droplets of amyotrophic lateral sclerosis-associated p62/SQSTM1 mutants show reduced inner fluidity. J Biol Chem 2021; 297:101405. [PMID: 34774801 PMCID: PMC8649403 DOI: 10.1016/j.jbc.2021.101405] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
Several amyotrophic lateral sclerosis (ALS)-related proteins such as FUS, TDP-43, and hnRNPA1 demonstrate liquid–liquid phase separation, and their disease-related mutations correlate with a transition of their liquid droplet form into aggregates. Missense mutations in SQSTM1/p62, which have been identified throughout the gene, are associated with ALS, frontotemporal degeneration (FTD), and Paget’s disease of bone. SQSTM1/p62 protein forms liquid droplets through interaction with ubiquitinated proteins, and these droplets serve as a platform for autophagosome formation and the antioxidative stress response via the LC3-interacting region (LIR) and KEAP1-interacting region (KIR) of p62, respectively. However, it remains unclear whether ALS/FTD-related p62 mutations in the LIR and KIR disrupt liquid droplet formation leading to defects in autophagy, the stress response, or both. To evaluate the effects of ALS/FTD-related p62 mutations in the LIR and KIR on a major oxidative stress system, the Keap1-Nrf2 pathway, as well as on autophagic turnover, we developed systems to monitor each of these with high sensitivity. These methods such as intracellular protein–protein interaction assay, doxycycline-inducible gene expression system, and gene expression into primary cultured cells with recombinant adenovirus revealed that some mutants, but not all, caused reduced NRF2 activation and delayed autophagic cargo turnover. In contrast, while all p62 mutants demonstrated sufficient ability to form liquid droplets, all of these droplets also exhibited reduced inner fluidity. These results indicate that like other ALS-related mutant proteins, p62 missense mutations result in a primary defect in ALS/FTD via a qualitative change in p62 liquid droplet fluidity.
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Affiliation(s)
- Mohammad Omar Faruk
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan; Department of Cell Physiology, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Yoshinobu Ichimura
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan.
| | - Shun Kageyama
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Satoko Komatsu-Hirota
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Afnan H El-Gowily
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan; Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Yu-Shin Sou
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Masato Koike
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Nobuo N Noda
- Laboratory of Structural Biology, Institute of Microbial Chemistry (BIKAKEN), Shinagawa-ku, Tokyo, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan.
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