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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] [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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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] [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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