1
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Alam JM, Maruyama T, Noshiro D, Kakuta C, Kotani T, Nakatogawa H, Noda NN. Complete set of the Atg8-E1-E2-E3 conjugation machinery forms an interaction web that mediates membrane shaping. Nat Struct Mol Biol 2024; 31:170-178. [PMID: 38057553 DOI: 10.1038/s41594-023-01132-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 09/20/2023] [Indexed: 12/08/2023]
Abstract
Atg8, a ubiquitin-like protein, is conjugated with phosphatidylethanolamine (PE) via Atg7 (E1), Atg3 (E2) and Atg12-Atg5-Atg16 (E3) enzymatic cascade and mediates autophagy. However, its molecular roles in autophagosome formation are still unclear. Here we show that Saccharomyces cerevisiae Atg8-PE and E1-E2-E3 enzymes together construct a stable, mobile membrane scaffold. The complete scaffold formation induces an in-bud in prolate-shaped giant liposomes, transforming their morphology into one reminiscent of isolation membranes before sealing. In addition to their enzymatic roles in Atg8 lipidation, all three proteins contribute nonenzymatically to membrane scaffolding and shaping. Nuclear magnetic resonance analyses revealed that Atg8, E1, E2 and E3 together form an interaction web through multivalent weak interactions, where the intrinsically disordered regions in Atg3 play a central role. These data suggest that all six Atg proteins in the Atg8 conjugation machinery control membrane shaping during autophagosome formation.
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Affiliation(s)
| | | | - Daisuke Noshiro
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Chika Kakuta
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Kotani
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitoshi Nakatogawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
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2
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Noshiro D, Noda NN. Immobilization of lipid nanorods onto two-dimensional crystals of protein tamavidin 2 for high-speed atomic force microscopy. STAR Protoc 2023; 4:102633. [PMID: 38043055 PMCID: PMC10701432 DOI: 10.1016/j.xpro.2023.102633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/08/2023] [Accepted: 09/21/2023] [Indexed: 12/05/2023] Open
Abstract
High-speed atomic force microscopy is a technique that allows real-time observation of biomolecules and biological phenomena reconstituted on a substrate. Here, we present a protocol for immobilizing lipid nanorods onto two-dimensional crystals of biotin-binding protein tamavidin 2. We describe steps for the preparation of tamavidin 2 protein, lipid nanorods, and two-dimensional crystals of tamavidin 2 formed on mica. Immobilized lipid nanorods are one of the useful tools for observation of specific proteins in action. For complete details on the use and execution of this protocol, please refer to Fukuda et al. (2023).1.
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Affiliation(s)
- Daisuke Noshiro
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido 060-0815, Japan
| | - Nobuo N Noda
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido 060-0815, Japan; Institute of Microbial Chemistry (BIKAKEN), Shinagawa-ku, Tokyo 141-0021, Japan.
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3
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Fukuda T, Furukawa K, Maruyama T, Yamashita SI, Noshiro D, Song C, Ogasawara Y, Okuyama K, Alam JM, Hayatsu M, Saigusa T, Inoue K, Ikeda K, Takai A, Chen L, Lahiri V, Okada Y, Shibata S, Murata K, Klionsky DJ, Noda NN, Kanki T. The mitochondrial intermembrane space protein mitofissin drives mitochondrial fission required for mitophagy. Mol Cell 2023; 83:2045-2058.e9. [PMID: 37192628 PMCID: PMC10330776 DOI: 10.1016/j.molcel.2023.04.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/30/2023] [Accepted: 04/21/2023] [Indexed: 05/18/2023]
Abstract
Mitophagy plays an important role in mitochondrial homeostasis by selective degradation of mitochondria. During mitophagy, mitochondria should be fragmented to allow engulfment within autophagosomes, whose capacity is exceeded by the typical mitochondria mass. However, the known mitochondrial fission factors, dynamin-related proteins Dnm1 in yeasts and DNM1L/Drp1 in mammals, are dispensable for mitophagy. Here, we identify Atg44 as a mitochondrial fission factor that is essential for mitophagy in yeasts, and we therefore term Atg44 and its orthologous proteins mitofissin. In mitofissin-deficient cells, a part of the mitochondria is recognized by the mitophagy machinery as cargo but cannot be enwrapped by the autophagosome precursor, the phagophore, due to a lack of mitochondrial fission. Furthermore, we show that mitofissin directly binds to lipid membranes and brings about lipid membrane fragility to facilitate membrane fission. Taken together, we propose that mitofissin acts directly on lipid membranes to drive mitochondrial fission required for mitophagy.
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Affiliation(s)
- Tomoyuki Fukuda
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Kentaro Furukawa
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Tatsuro Maruyama
- Institute of Microbial Chemistry (BIKAKEN), Shinagawa-ku, Tokyo 141-0021, Japan
| | - Shun-Ichi Yamashita
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Daisuke Noshiro
- Institute of Microbial Chemistry (BIKAKEN), Shinagawa-ku, Tokyo 141-0021, Japan; Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido 060-0815, Japan
| | - Chihong Song
- National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences (NINS), Okazaki, Aichi 444-8585, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), Okazaki, Aichi 444-8585, Japan
| | - Yuta Ogasawara
- Institute of Microbial Chemistry (BIKAKEN), Shinagawa-ku, Tokyo 141-0021, Japan; Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido 060-0815, Japan
| | - Kentaro Okuyama
- Division of Microscopic Anatomy, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Jahangir Md Alam
- Institute of Microbial Chemistry (BIKAKEN), Shinagawa-ku, Tokyo 141-0021, Japan
| | - Manabu Hayatsu
- Division of Microscopic Anatomy, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Tetsu Saigusa
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Keiichi Inoue
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Kazuho Ikeda
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka 565-0874, Japan
| | - Akira Takai
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka 565-0874, Japan
| | - Lin Chen
- National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences (NINS), Okazaki, Aichi 444-8585, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), Okazaki, Aichi 444-8585, Japan
| | - Vikramjit Lahiri
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yasushi Okada
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka 565-0874, Japan; Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; Universal Biology Institute (UBI) and International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo 113-0033, Japan
| | - Shinsuke Shibata
- Division of Microscopic Anatomy, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences (NINS), Okazaki, Aichi 444-8585, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), Okazaki, Aichi 444-8585, Japan
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Shinagawa-ku, Tokyo 141-0021, Japan; Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido 060-0815, Japan.
| | - Tomotake Kanki
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan.
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4
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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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5
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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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6
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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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7
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Tanigawa M, Yamamoto K, Nagatoishi S, Nagata K, Noshiro D, Noda NN, Tsumoto K, Maeda T. A glutamine sensor that directly activates TORC1. Commun Biol 2021; 4:1093. [PMID: 34535752 PMCID: PMC8448839 DOI: 10.1038/s42003-021-02625-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/31/2021] [Indexed: 01/08/2023] Open
Abstract
TOR complex 1 (TORC1) is an evolutionarily-conserved protein kinase that controls cell growth and metabolism in response to nutrients, particularly amino acids. In mammals, several amino acid sensors have been identified that converge on the multi-layered machinery regulating Rag GTPases to trigger TORC1 activation; however, these sensors are not conserved in many other organisms including yeast. Previously, we reported that glutamine activates yeast TORC1 via a Gtr (Rag ortholog)-independent mechanism involving the vacuolar protein Pib2, although the identity of the supposed glutamine sensor and the exact TORC1 activation mechanism remain unclear. In this study, we successfully reconstituted glutamine-responsive TORC1 activation in vitro using only purified Pib2 and TORC1. In addition, we found that glutamine specifically induced a change in the folding state of Pib2. These findings indicate that Pib2 is a glutamine sensor that directly activates TORC1, providing a new model for the metabolic control of cells.
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Affiliation(s)
- Mirai Tanigawa
- Departments of Biology, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Katsuyoshi Yamamoto
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Kouhei Tsumoto
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Tatsuya Maeda
- Departments of Biology, Hamamatsu University School of Medicine, Shizuoka, Japan. .,Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
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8
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Kodera N, Noshiro D, Dora SK, Mori T, Habchi J, Blocquel D, Gruet A, Dosnon M, Salladini E, Bignon C, Fujioka Y, Oda T, Noda NN, Sato M, Lotti M, Mizuguchi M, Longhi S, Ando T. Structural and dynamics analysis of intrinsically disordered proteins by high-speed atomic force microscopy. Nat Nanotechnol 2021; 16:181-189. [PMID: 33230318 DOI: 10.1038/s41565-020-00798-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
Intrinsically disordered proteins (IDPs) are ubiquitous proteins that are disordered entirely or partly and play important roles in diverse biological phenomena. Their structure dynamically samples a multitude of conformational states, thus rendering their structural analysis very difficult. Here we explore the potential of high-speed atomic force microscopy (HS-AFM) for characterizing the structure and dynamics of IDPs. Successive HS-AFM images of an IDP molecule can not only identify constantly folded and constantly disordered regions in the molecule, but can also document disorder-to-order transitions. Moreover, the number of amino acids contained in these disordered regions can be roughly estimated, enabling a semiquantitative, realistic description of the dynamic structure of IDPs.
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Affiliation(s)
- Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Daisuke Noshiro
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Sujit K Dora
- Department of Physics, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Tetsuya Mori
- Department of Physics, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Johnny Habchi
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - David Blocquel
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Antoine Gruet
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Marion Dosnon
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Edoardo Salladini
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Christophe Bignon
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | | | - Takashi Oda
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | | | - Mamoru Sato
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Marina Lotti
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Milano, Italy
| | | | - Sonia Longhi
- Aix-Marseille University and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France.
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan.
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9
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Kageyama S, Gudmundsson SR, Sou YS, Ichimura Y, Tamura N, Kazuno S, Ueno T, Miura Y, Noshiro D, Abe M, Mizushima T, Miura N, Okuda S, Motohashi H, Lee JA, Sakimura K, Ohe T, Noda NN, Waguri S, Eskelinen EL, Komatsu M. p62/SQSTM1-droplet serves as a platform for autophagosome formation and anti-oxidative stress response. Nat Commun 2021; 12:16. [PMID: 33397898 PMCID: PMC7782522 DOI: 10.1038/s41467-020-20185-1] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022] Open
Abstract
Autophagy contributes to the selective degradation of liquid droplets, including the P-Granule, Ape1-complex and p62/SQSTM1-body, although the molecular mechanisms and physiological relevance of selective degradation remain unclear. In this report, we describe the properties of endogenous p62-bodies, the effect of autophagosome biogenesis on these bodies, and the in vivo significance of their turnover. p62-bodies are low-liquidity gels containing ubiquitin and core autophagy-related proteins. Multiple autophagosomes form on the p62-gels, and the interaction of autophagosome-localizing Atg8-proteins with p62 directs autophagosome formation toward the p62-gel. Keap1 also reversibly translocates to the p62-gels in a p62-binding dependent fashion to activate the transcription factor Nrf2. Mice deficient for Atg8-interaction-dependent selective autophagy show that impaired turnover of p62-gels leads to Nrf2 hyperactivation in vivo. These results indicate that p62-gels are not simple substrates for autophagy but serve as platforms for both autophagosome formation and anti-oxidative stress.
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Affiliation(s)
- Shun Kageyama
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Sigurdur Runar Gudmundsson
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, 00014, Finland
| | - Yu-Shin Sou
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yoshinobu Ichimura
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Naoki Tamura
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukushima, 960-1295, Japan
| | - Saiko Kazuno
- Laboratory of Proteomics and Biomolecular Science, Research Support Center, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Takashi Ueno
- Laboratory of Proteomics and Biomolecular Science, Research Support Center, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yoshiki Miura
- Laboratory of Proteomics and Biomolecular Science, Research Support Center, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Daisuke Noshiro
- Institute of Microbial Chemistry (BIKAKEN), Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, 951-8510, Japan
| | - Tsunehiro Mizushima
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1, Kouto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Nobuaki Miura
- Bioinformatics Laboratory, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, 951-8510, Japan
| | - Shujiro Okuda
- Bioinformatics Laboratory, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, 951-8510, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Jin-A Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, 34430, Korea
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, 951-8510, Japan
| | - Tomoyuki Ohe
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Keio University, Minato-ku, 105-8512, Tokyo, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukushima, 960-1295, Japan
| | - Eeva-Liisa Eskelinen
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, 00014, Finland.
- Institute of Biomedicine, University of Turku, Turku, FI-20014, Finland.
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan.
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10
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Matoba K, Kotani T, Tsutsumi A, Tsuji T, Mori T, Noshiro D, Sugita Y, Nomura N, Iwata S, Ohsumi Y, Fujimoto T, Nakatogawa H, Kikkawa M, Noda NN. Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion. Nat Struct Mol Biol 2020; 27:1185-1193. [PMID: 33106658 DOI: 10.1038/s41594-020-00518-w] [Citation(s) in RCA: 215] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]
Abstract
The molecular function of Atg9, the sole transmembrane protein in the autophagosome-forming machinery, remains unknown. Atg9 colocalizes with Atg2 at the expanding edge of the isolation membrane (IM), where Atg2 receives phospholipids from the endoplasmic reticulum (ER). Here we report that yeast and human Atg9 are lipid scramblases that translocate phospholipids between outer and inner leaflets of liposomes in vitro. Cryo-EM of fission yeast Atg9 reveals a homotrimer, with two connected pores forming a path between the two membrane leaflets: one pore, located at a protomer, opens laterally to the cytoplasmic leaflet; the other, at the trimer center, traverses the membrane vertically. Mutation of residues lining the pores impaired IM expansion and autophagy activity in yeast and abolished Atg9's ability to transport phospholipids between liposome leaflets. These results suggest that phospholipids delivered by Atg2 are translocated from the cytoplasmic to the luminal leaflet by Atg9, thereby driving autophagosomal membrane expansion.
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Affiliation(s)
- Kazuaki Matoba
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Tetsuya Kotani
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takuma Tsuji
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | | | | | - Yuji Sugita
- RIKEN Cluster for Pioneering Research, Wako, Japan
- RIKEN Center for Computational Science, Kobe, Japan
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Toyoshi Fujimoto
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.
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11
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Matoba K, Kotani T, Tsutsumi A, Tsuji T, Mori T, Noshiro D, Sugita Y, Nomura N, Iwata S, Ohsumi Y, Fujimoto T, Nakatogawa H, Kikkawa M, Noda NN. Author Correction: Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion. Nat Struct Mol Biol 2020; 27:1209. [PMID: 33184515 DOI: 10.1038/s41594-020-00538-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Kazuaki Matoba
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Tetsuya Kotani
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takuma Tsuji
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | | | | | - Yuji Sugita
- RIKEN Cluster for Pioneering Research, Wako, Japan.,RIKEN Center for Computational Science, Kobe, Japan.,RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,RIKEN SPring-8 Center, Hyogo, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Toyoshi Fujimoto
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.
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12
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Kawasaki Y, Ariyama H, Motomura H, Fujinami D, Noshiro D, Ando T, Kohda D. Two-State Exchange Dynamics in Membrane-Embedded Oligosaccharyltransferase Observed in Real-Time by High-Speed AFM. J Mol Biol 2020; 432:5951-5965. [PMID: 33010307 DOI: 10.1016/j.jmb.2020.09.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 01/23/2023]
Abstract
Oligosaccharyltransferase (OST) is a membrane-bound enzyme that catalyzes the transfer of oligosaccharide chains from lipid-linked oligosaccharides (LLO) to asparagine residues in polypeptide chains. Using high-speed atomic force microscopy (AFM), we investigated the dynamic properties of OST molecules embedded in biomembranes. An archaeal single-subunit OST protein was immobilized on a mica support via biotin-avidin interactions and reconstituted in a lipid bilayer. The distance between the top of the protein molecule and the upper surface of the lipid bilayer was monitored in real-time. The height of the extramembranous part exhibited a two-step variation with a difference of 1.8 nm. The high and low states are designated as state 1 and state 2, respectively. The transition processes between the two states fit well to single exponential functions, suggesting that the observed dynamic exchange is an intrinsic property of the archaeal OST protein. The two sets of cross peaks in the NMR spectra of the protein supported the conformational changes between the two states in detergent-solubilized conditions. Considering the height values measured in the AFM measurements, state 1 is closer to the crystal structure, and state 2 has a more compact form. Subsequent AFM experiments indicated that the binding of the sugar donor LLO decreased the structural fluctuation and shifted the equilibrium almost completely to state 1. This dynamic behavior is likely necessary for efficient catalytic turnover. Presumably, state 2 facilitates the immediate release of the bulky glycosylated polypeptide product, thus allowing OST to quickly prepare for the next catalytic cycle.
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Affiliation(s)
- Yuki Kawasaki
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hirotaka Ariyama
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Hajime Motomura
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daisuke Fujinami
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daisuke Noshiro
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan.
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13
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Fujioka Y, Alam JM, Noshiro D, Mouri K, Ando T, Okada Y, May AI, Knorr RL, Suzuki K, Ohsumi Y, Noda NN. Phase separation organizes the site of autophagosome formation. Nature 2020; 578:301-305. [PMID: 32025038 DOI: 10.1038/s41586-020-1977-6] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 12/02/2019] [Indexed: 11/09/2022]
Abstract
Many biomolecules undergo liquid-liquid phase separation to form liquid-like condensates that mediate diverse cellular functions1,2. Autophagy is able to degrade such condensates using autophagosomes-double-membrane structures that are synthesized de novo at the pre-autophagosomal structure (PAS) in yeast3-5. Whereas Atg proteins that associate with the PAS have been characterized, the physicochemical and functional properties of the PAS remain unclear owing to its small size and fragility. Here we show that the PAS is in fact a liquid-like condensate of Atg proteins. The autophagy-initiating Atg1 complex undergoes phase separation to form liquid droplets in vitro, and point mutations or phosphorylation that inhibit phase separation impair PAS formation in vivo. In vitro experiments show that Atg1-complex droplets can be tethered to membranes via specific protein-protein interactions, explaining the vacuolar membrane localization of the PAS in vivo. We propose that phase separation has a critical, active role in autophagy, whereby it organizes the autophagy machinery at the PAS.
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Affiliation(s)
- Yuko Fujioka
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | | | - Daisuke Noshiro
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.,Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Kazunari Mouri
- Center for Biosystems Dynamics Research (BDR), RIKEN, Osaka, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Yasushi Okada
- Center for Biosystems Dynamics Research (BDR), RIKEN, Osaka, Japan.,Department of Physics, Universal Biology Institute (UBI) and International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
| | - Alexander I May
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Roland L Knorr
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.,Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.,Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Kuninori Suzuki
- Life Science Data Research Center, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.
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14
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Yamasaki A, Alam JM, Noshiro D, Hirata E, Fujioka Y, Suzuki K, Ohsumi Y, Noda NN. Liquidity Is a Critical Determinant for Selective Autophagy of Protein Condensates. Mol Cell 2020; 77:1163-1175.e9. [PMID: 31995729 DOI: 10.1016/j.molcel.2019.12.026] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [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: 07/18/2019] [Revised: 11/22/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022]
Abstract
Clearance of biomolecular condensates by selective autophagy is thought to play a crucial role in cellular homeostasis. However, the mechanism underlying selective autophagy of condensates and whether liquidity determines a condensate's susceptibility to degradation by autophagy remain unknown. Here, we show that the selective autophagic cargo aminopeptidase I (Ape1) undergoes phase separation to form semi-liquid droplets. The Ape1-specific receptor protein Atg19 localizes to the surface of Ape1 droplets both in vitro and in vivo, with the "floatability" of Atg19 preventing its penetration into droplets. In vitro reconstitution experiments reveal that Atg19 and lipidated Atg8 are necessary and sufficient for selective sequestration of Ape1 droplets by membranes. This sequestration is impaired by mutational solidification of Ape1 droplets or diminished ability of Atg19 to float. Taken together, we propose that cargo liquidity and the presence of sufficient amounts of autophagic receptor on cargo are crucial for selective autophagy of biomolecular condensates.
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Affiliation(s)
- Akinori Yamasaki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan; Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Jahangir Md Alam
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Daisuke Noshiro
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Eri Hirata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Yuko Fujioka
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Kuninori Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan; Life Science Data Research Center, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan; Collaborative Research Institute for Innovative Microbiology, University of Tokyo, Tokyo 113-8657, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan.
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15
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Noshiro D, Ando T. Substrate protein dependence of GroEL-GroES interaction cycle revealed by high-speed atomic force microscopy imaging. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0180. [PMID: 29735734 DOI: 10.1098/rstb.2017.0180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2018] [Indexed: 11/12/2022] Open
Abstract
A double-ring-shaped tetradecameric GroEL complex assists proper protein folding in cooperation with the cochaperonin GroES. The dynamic GroEL-GroES interaction reflects the allosteric intra- and inter-ring communications and the chaperonin reaction. Therefore, revealing this dynamic interaction is essential to understanding the allosteric communications and the operation mechanism of GroEL. Nevertheless, how this interaction proceeds in the chaperonin cycle has long been controversial. Here, we directly image the dynamic GroEL-GroES interaction under conditions with and without foldable substrate protein using high-speed atomic force microscopy. Then, the imaging results obtained under these conditions and our previous results in the presence of unfoldable substrate are compared. The molecular movies reveal that the entire reaction pathway is highly complicated but basically identical irrespective of the substrate condition. A prominent (but moderate) difference is in the population distribution of intermediate species: symmetric GroEL : GroES2 and asymmetric GroEL : GroES1 complexes, and GroES-unbound GroEL. This difference is mainly attributed to the longer lifetime of GroEL : GroES1 complexes in the presence of foldable substrate. Moreover, the inter-ring communication, which is the basis for the alternating action of the two rings, occurs at two distinct (GroES association and dissociation) steps in the main reaction pathway, irrespective of the substrate condition.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Daisuke Noshiro
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.,CREST, Japan Science and Technology Agency, Tokyo 102-0076, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan .,CREST, Japan Science and Technology Agency, Tokyo 102-0076, Japan
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16
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Sone E, Noshiro D, Ikebuchi Y, Nakagawa M, Khan M, Tamura Y, Ikeda M, Oki M, Murali R, Fujimori T, Yoda T, Honma M, Suzuki H, Ando T, Aoki K. The induction of RANKL molecule clustering could stimulate early osteoblast differentiation. Biochem Biophys Res Commun 2018; 509:435-440. [PMID: 30594398 DOI: 10.1016/j.bbrc.2018.12.093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 11/30/2018] [Accepted: 12/13/2018] [Indexed: 11/26/2022]
Abstract
We recently found that the membrane-bound receptor activator of NF-κB ligand (RANKL) on osteoblasts works as a receptor to stimulate osteoblast differentiation, however, the reason why the RANKL-binding molecules stimulate osteoblast differentiation has not been well clarified. Since the induction of cell-surface receptor clustering is known to lead to cell activation, we hypothesized that the induction of membrane-RANKL clustering on osteoblasts might stimulate osteoblast differentiation. Immunoblotting showed that the amount of RANKL on the membrane was increased by the RANKL-binding peptide OP3-4, but not by osteoprotegerin (OPG), the other RANKL-binding molecule, in Gfp-Rankl-transfected ST2 cells. Observation under a high-speed atomic force microscope (HS-AFM) revealed that RANKL molecules have the ability to form clusters. The induction of membrane-RANKL-OPG-Fc complex clustering by the addition of IgM in Gfp-Rankl-transfected ST2 cells could enhance the expression of early markers of osteoblast differentiation to the same extent as OP3-4, while OPG-Fc alone could not. These results suggest that the clustering-formation of membrane-RANKL on osteoblasts could stimulate early osteoblast differentiation.
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Affiliation(s)
- Eri Sone
- Department of Oral Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan; Department of Basic Oral Health Engineering, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Daisuke Noshiro
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Yuki Ikebuchi
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Mami Nakagawa
- Division of Embryology, National Institute for Basic Biology, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Masud Khan
- Department of Basic Oral Health Engineering, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Yukihiko Tamura
- Department of Bio-Matrix (Pharmacology), Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Masaomi Ikeda
- Department of Oral Prosthetic Engineering, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Meiko Oki
- Department of Basic Oral Health Engineering, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Ramachandran Murali
- Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Toshihiko Fujimori
- Division of Embryology, National Institute for Basic Biology, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Tetsuya Yoda
- Department of Oral Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Masashi Honma
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Kazuhiro Aoki
- Department of Basic Oral Health Engineering, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
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17
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Yamamoto H, Fujioka Y, Suzuki SW, Noshiro D, Suzuki H, Kondo-Kakuta C, Kimura Y, Hirano H, Ando T, Noda NN, Ohsumi Y. The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes. Dev Cell 2017; 38:86-99. [PMID: 27404361 DOI: 10.1016/j.devcel.2016.06.015] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 05/11/2016] [Accepted: 06/12/2016] [Indexed: 12/21/2022]
Abstract
Autophagosome formation in yeast entails starvation-induced assembly of the pre-autophagosomal structure (PAS), in which multiple Atg1 complexes (composed of Atg1, Atg13, and the Atg17-Atg29-Atg31 subcomplex) are initially engaged. However, the molecular mechanisms underlying the multimeric assembly of these complexes remain unclear. Using structural and biological techniques, we herein demonstrate that Atg13 has a large intrinsically disordered region (IDR) and interacts with two distinct Atg17 molecules using two binding regions in the IDR. We further reveal that these two binding regions are essential not only for Atg1 complex assembly in vitro, but also for PAS organization in vivo. These findings underscore the structural and functional significance of the IDR of Atg13 in autophagy initiation: Atg13 provides intercomplex linkages between Atg17-Atg29-Atg31 complexes, thereby leading to supramolecular self-assembly of Atg1 complexes, in turn accelerating the initial events of autophagy, including autophosphorylation of Atg1, recruitment of Atg9 vesicles, and phosphorylation of Atg9 by Atg1.
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Affiliation(s)
- Hayashi Yamamoto
- Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yuko Fujioka
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Sho W Suzuki
- Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Daisuke Noshiro
- Department of Physics, College of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Hironori Suzuki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan
| | - Chika Kondo-Kakuta
- Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | - Hisashi Hirano
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | - Toshio Ando
- Department of Physics, College of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan.
| | - Yoshinori Ohsumi
- Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan.
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18
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Oku A, Imanishi M, Noshiro D, Murayama T, Takeuchi T, Nakase I, Futaki S. Calmodulin EF-hand peptides as Ca 2+ -switchable recognition tags. Biopolymers 2016; 108. [PMID: 27554421 DOI: 10.1002/bip.22937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 04/08/2016] [Revised: 08/05/2016] [Accepted: 08/21/2016] [Indexed: 11/08/2022]
Abstract
Calmodulin is a representative calcium-binding protein comprised of four Ca2+ -binding motifs with a helix-loop-helix structure (EF-hands). In this study, we clarified the potential of peptide segments derived from the third and fourth EF-hands (EF3 and EF4) to act as recognition tags. Through an analysis of the mode of disulfide formation among cysteines inserted at the N- or C-terminus of these peptide segments, EF3 and EF4 peptides were suggested to form a heterodimer with a topology similar to that in the wild-type protein. Heterodimer formation was shown to be a function of the Ca2+ concentration, suggesting that these structures may be used as Ca2+ -switchable recognition tags. An example of an "EF-tag" system involving the membrane fusion of liposomes decorated with EF3 and EF4 peptides is presented. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2016.
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Affiliation(s)
- Akihiko Oku
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Daisuke Noshiro
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Tomo Murayama
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Toshihide Takeuchi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Ikuhiko Nakase
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan.,Nanoscience and Nanotechnology Research Center, Research Organization for the 21st Century, Osaka Prefecture University, Naka-ku, Sakai, Osaka, 599-8570, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
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19
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Abstract
Ion channels allow the influx and efflux of specific ions through a plasma membrane. Many ion channels can sense, for example, the membrane potential (the voltage gaps between the inside and the outside of the membrane), specific ligands such as neurotransmitters, and mechanical tension within the membrane. They modulate cell function in response to these stimuli. Researchers have focused on developing peptide- and non-peptide-based model systems to elucidate ion-channel protein functions and to create artificial sensing systems. In this Account, we employed a typical peptide that forms ion channels,alamethicin, as a model to evaluate our methodologies for controlling the assembly states of channel-forming molecules in membranes. As alamethicin self-assembles in membranes, it prompts channel formation, but number of peptide molecules in these channels is not constant. Using planar-lipid bilayer methods, we monitored the association states of alamethicin in real time. Many ligand-gated, natural-ion channel proteins have large extramembrane domains. As these proteins interact with specific ligands, those conformational alterations in the extramembrane domains are transmitted to the transmembrane, pore-forming domains to open and close the channels. We hypothesized that if we conjugated suitable extramembrane segments to alamethicin, ligand binding to the extramembrane segments could alter the structure of the extramembrane domains and influence the association states or association numbers of alamethicin in the membranes. We could then assess those changes by using single-channel current recording. We found that we could modulate channel assembly and eventual ion flux with attached leucine-zipper extramembrane peptide segments. Using conformationally switchable leucine-zipper extramembrane segments that respond to Fe(3+), we fabricated an artificial Fe(3+)-sensitive ion channel; a decrease in the helical content of the extramembrane segment led to an increase in the channel current. When we added a calmodulin C-terminus segment, we formed a channel that was sensitive to Ca(2+). This result demonstrated that we could prepare artificial channels that were sensitive to specific ligands by adding appropriate extramembrane segments from natural protein motifs that respond to external stimuli. In conclusion, our research points to the possibility of creating tailored sensor or signal transduction systems through the conjugation of a conformationally switchable extramembrane peptide/protein segment to a suitable transmembrane peptide segment.
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Affiliation(s)
- Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Daisuke Noshiro
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tatsuto Kiwada
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Koji Asami
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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20
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Noshiro D, Sonomura K, Yu HH, Imanishi M, Asami K, Futaki S. Construction of a Ca(2+)-gated artificial channel by fusing alamethicin with a calmodulin-derived extramembrane segment. Bioconjug Chem 2013; 24:188-95. [PMID: 23272973 DOI: 10.1021/bc300468x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Using native chemical ligation, we constructed a Ca(2+)-gated fusion channel protein consisting of alamethicin and the C-terminal domain of calmodulin. At pH 5.4 and in the absence of Ca(2+), this fusion protein yielded a burst-like channel current with no discrete channel conductance levels. However, Ca(2+) significantly lengthened the specific channel open state and increased the mean channel current, while Mg(2+) produced no significant changes in the channel current. On the basis of 8-anilinonaphthalene-1-sulfonic acid (ANS) fluorescent measurement, Ca(2+)-stimulated gating may be related to an increased surface hydrophobicity of the extramembrane segment of the fusion protein.
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Affiliation(s)
- Daisuke Noshiro
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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21
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Noshiro D, Asami K, Futaki S. Control of leakage activities of alamethicin analogs by metals: Side chain-dependent adverse gating response to Zn2+. Bioorg Med Chem 2012; 20:6870-6. [DOI: 10.1016/j.bmc.2012.09.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 09/16/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
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22
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Noshiro D, Asami K, Futaki S. Metal-assisted channel stabilization: disposition of a single histidine on the N-terminus of alamethicin yields channels with extraordinarily long lifetimes. Biophys J 2010; 98:1801-8. [PMID: 20441743 DOI: 10.1016/j.bpj.2010.01.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 11/08/2009] [Accepted: 01/04/2010] [Indexed: 10/19/2022] Open
Abstract
Alamethicin, a member of the peptaibol family of antibiotics, is a typical channel-forming peptide with a helical structure. The self-assembly of the peptide in the membranes yields voltage-dependent channels. In this study, three alamethicin analogs possessing a charged residue (His, Lys, or Glu) on their N-termini were designed with the expectation of stabilizing the transmembrane structure. A slight elongation of channel lifetime was observed for the Lys and Glu analogs. On the other hand, extensive stabilization of certain channel open states was observed for the His analog. This stabilization was predominantly observed in the presence of metal ions such as Zn(2+), suggesting that metal coordination with His facilitates the formation of a supramolecular assembly in the membranes. Channel stability was greatly diminished by acetylation of the N-terminal amino group, indicating that the N-terminal amino group also plays an important role in metal coordination.
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Affiliation(s)
- Daisuke Noshiro
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
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23
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Imanishi M, Nakaya T, Morisaki T, Noshiro D, Futaki S, Sugiura Y. Metal-Stimulated Regulation of Transcription by an Artificial Zinc-Finger Protein. Chembiochem 2010; 11:1653-5. [DOI: 10.1002/cbic.201000334] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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