Noda Nobuo

Institute for Genetic Medicine　Disease ControlProfessor
Last Updated :2025/06/07

■Researcher basic information

Researchmap personal page

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J-Global ID

Research Keyword

  • 膜界面
  • Liquid-liquid phase separation
  • Autophagy
  • Membraneless organelle
  • Fluorescence Imaging
  • in vitro reconstitution
  • 天然変性タンパク質
  • cell biology
  • Cryo-EM
  • High-speed AFM
  • Solution NMR
  • Structural Biology
  • X線結晶構造解析

Research Field

  • Life sciences, Functional biochemistry
  • Life sciences, Structural biochemistry
  • Life sciences, Cell biology
  • Life sciences, Pharmaceuticals - health and biochemistry

Educational Organization

■Career

Career

  • Jan. 2022 - Present
    Hokkaido University, Institute for Genetic Medicine, Professor, Japan
  • Apr. 2017 - Dec. 2021
    Microbial Chemistry Research Foundation, Laboratory of Structural Biology, Institute of Microbial Chemistry, Laboratory Head
  • Apr. 2011 - Mar. 2017
    Microbial Chemistry Research Foundation, Institute of Microbial Chemistry, Chief Researcher
  • Apr. 2008 - Mar. 2011
    Hokkaido University, Graduate School of Pharmaceutical Sciences, Lecturer with tenure
  • Apr. 2007 - Mar. 2008
    Hokkaido University, Graduate School of Pharmaceutical Sciences, Research associate
  • May 2005 - Mar. 2007
    Hokkaido University, Graduate School of Pharmaceutical Sciences, Research associate
  • Apr. 2001 - Apr. 2005
    Hokkaido University, Graduate School of Pharmaceutical Sciences, posdoc

Educational Background

  • Apr. 1996 - Mar. 2001, The University of Tokyo, Graduate School of Pharmaceutical Sciences

■Research activity information

Papers

  • Mechanisms of autophagosome formation
    Yuko FUJIOKA, Nobuo N. NODA
    Proceedings of the Japan Academy, Series B, 101, 1, 32, 40, Japan Academy, 2025
    Scientific journal
  • Phase separation promotes Atg8 lipidation for autophagy progression
    Yuko Fujioka, Takuma Tsuji, Tetsuya Kotani, Hiroyuki Kumeta, Chika Kakuta, Toyoshi Fujimoto, Hitoshi Nakatogawa, Nobuo N Noda
    Cold Spring Harbor Laboratory, 30 Aug. 2024
    Upon starvation, the autophagy-initiating Atg1 complex undergoes phase separation to organize the pre-autophagosomal structure (PAS) in yeast, from which autophagosome formation is considered to proceed. However, the physiological roles of the PAS as a liquid droplet remain unclear. Here we show that core Atg proteins are recruited into early PAS droplets that are formed by phase separation of the Atg1 complex with different efficiencies in vitro. The Atg12-Atg5-Atg16 E3 ligase complex for Atg8 lipidation is the most efficiently condensed in the droplets via specific Atg12-Atg17 interaction, which is also important for the PAS targeting of the E3 complex in vivo. In vitro reconstitution experiments reveal that E3-enriched early PAS droplets promote Atg8 lipidation and incorporate Atg8-coated vesicles to the interior, thereby protecting them from Atg4-mediated delipidation. These data suggest that the PAS utilizes its liquid-like property to function as an efficient production site for lipidated Atg8 and pool membrane seeds to drive autophagosome formation.
  • The triad interaction of ULK1, ATG13, and FIP200 is required for ULK complex formation and autophagy
    Yutaro Hama, Yuko Fujioka, Hayashi Yamamoto, Noboru Mizushima, Nobuo N. Noda
    Cold Spring Harbor Laboratory, 02 Aug. 2024
    Abstract

    In mammals, autophagosome formation, a central event in autophagy, is initiated by the ULK complex comprising ULK1/2, FIP200, ATG13, and ATG101. However, the structural basis and mechanism of the ULK complex formation remain poorly understood. Here, we predicted the core interactions organizing the ULK complex using AlphaFold, which proposed that the intrinsically disordered region of ATG13 binds to the base of the two UBL domains in the FIP200 dimer using two phenylalanines and to the tandem MIT domain of ULK1, allowing for the 1:1:2 stoichiometry of the ULK1–ATG13–FIP200 complex. We confirmed the predicted interactions by point mutations and revealed the existence of direct triad interactions among ULK1, ATG13, and FIP200 in vitro and in cells, in which each interaction was additively important for autophagic flux. These results indicate that the ULK1–ATG13–FIP200 triadic interaction is crucial for autophagosome formation and provide a structural basis and insights into the regulation mechanism of autophagy initiation in mammals.
  • A role for condensin-mediator interaction in mitotic chromosomal organization.
    Osamu Iwasaki, Sanki Tashiro, Claire Chung, Tomomi Hayashi, Hideki Tanizawa, Xuebing Wang, Shinya Ohta, Yuko Fujioka, Joseph Han, Gabrielle Tabor, Mikihiro Kawagoe, Ronen Marmorstein, Nobuo N Noda, Ken-Ichi Noma
    bioRxiv : the preprint server for biology, 28 Jun. 2024, [International Magazine]
    English, Scientific journal, Eukaryotic genomes are organized by condensin into 3D chromosomal architectures suitable for chromosomal segregation during mitosis. However, molecular mechanisms underlying the condensin-mediated chromosomal organization remain largely unclear. Here, we investigate the role of newly identified interaction between the Cnd1 condensin and Pmc4 mediator subunits in fission yeast, Schizosaccharomyces pombe. We develop a condensin mutation, cnd1-K658E, that impairs the condensin-mediator interaction and find that this mutation diminishes condensinmediated chromatin domains during mitosis and causes chromosomal segregation defects. The condensin-mediator interaction is involved in recruiting condensin to highly transcribed genes and mitotically activated genes, the latter of which demarcate condensin-mediated domains. Furthermore, this study predicts that mediator-driven transcription of mitotically activated genes contributes to forming domain boundaries via phase separation. This study provides a novel insight into how genome-wide gene expression during mitosis is transformed into the functional chromosomal architecture suitable for chromosomal segregation.
  • The UFM1 system: Working principles, cellular functions, and pathophysiology.
    Masaaki Komatsu, Toshifumi Inada, Nobuo N Noda
    Molecular cell, 84, 1, 156, 169, 04 Jan. 2024, [International Magazine]
    English, Scientific journal, Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like protein covalently conjugated with intracellular proteins through UFMylation, a process similar to ubiquitylation. Growing lines of evidence regarding not only the structural basis of the components essential for UFMylation but also their biological properties shed light on crucial roles of the UFM1 system in the endoplasmic reticulum (ER), such as ER-phagy and ribosome-associated quality control at the ER, although there are some functions unrelated to the ER. Mouse genetics studies also revealed the indispensable roles of this system in hematopoiesis, liver development, neurogenesis, and chondrogenesis. Of critical importance, mutations of genes encoding core components of the UFM1 system in humans cause hereditary developmental epileptic encephalopathy and Schohat-type osteochondrodysplasia of the epiphysis. Here, we provide a multidisciplinary review of our current understanding of the mechanisms and cellular functions of the UFM1 system as well as its pathophysiological roles, and discuss issues that require resolution.
  • Complete set of the Atg8-E1-E2-E3 conjugation machinery forms an interaction web that mediates membrane shaping.
    Jahangir Md Alam, Tatsuro Maruyama, Daisuke Noshiro, Chika Kakuta, Tetsuya Kotani, Hitoshi Nakatogawa, Nobuo N Noda
    Nature structural & molecular biology, 31, 170, 178, Jan. 2024, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
    English, Scientific journal, 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.
  • Immobilization of lipid nanorods onto two-dimensional crystals of protein tamavidin 2 for high-speed atomic force microscopy.
    Daisuke Noshiro, Nobuo N Noda
    STAR protocols, 4, 4, 102633, 102633, 02 Dec. 2023, [International Magazine]
    English, Scientific journal, 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.
  • Mechanisms of mitochondrial reorganization
    Tatsuro Maruyama, Yutaro Hama, Nobuo N Noda
    The Journal of Biochemistry, Oxford University Press (OUP), 28 Nov. 2023
    Scientific journal, Abstract

    The cytoplasm of eukaryotes is dynamically zoned by membrane-bound and membraneless organelles. Cytoplasmic zoning allows various biochemical reactions to take place at the right time and place. Mitochondrion is a membrane-bound organelle that provides a zone for intracellular energy production and metabolism of lipids and iron. A key feature of mitochondria is their high dynamics: mitochondria constantly undergo fusion and fission, and excess or damaged mitochondria are selectively eliminated by mitophagy. Therefore, mitochondria are appropriate model systems to understand dynamic cytoplasmic zoning by membrane organelles. In this review, we summarize the molecular mechanisms of mitochondrial fusion and fission as well as mitophagy unveiled through studies using yeast and mammalian models.
  • Mitofissin: a novel mitochondrial fission protein that facilitates mitophagy.
    Tomoyuki Fukuda, Kentaro Furukawa, Tatsuro Maruyama, Nobuo N Noda, Tomotake Kanki
    Autophagy, 19, 11, 3019, 3021, Nov. 2023, [International Magazine]
    English, Scientific journal, Atg: autophagy related; IMM: inner mitochondrial membrane; IMS: intermembrane space; PAS: phagophore assembly site; SAR: selective autophagy receptor.
  • Mechanistic insights into the roles of the UFM1 E3 ligase complex in ufmylation and ribosome-associated protein quality control
    Ryosuke Ishimura, Sota Ito, Gaoxin Mao, Satoko Komatsu-Hirota, Toshifumi Inada, Nobuo N. Noda, Masaaki Komatsu
    Science Advances, 9, 33, American Association for the Advancement of Science (AAAS), 18 Aug. 2023
    Scientific journal, 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 60 S 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.
  • The Atg1 complex, Atg9, and Vac8 recruit PI3K complex I to the pre-autophagosomal structure.
    Kanae Hitomi, Tetsuya Kotani, Nobuo N Noda, Yayoi Kimura, Hitoshi Nakatogawa
    The Journal of cell biology, 222, 8, 07 Aug. 2023, [Peer-reviewed], [International Magazine]
    English, Scientific journal, In macroautophagy, cellular components are sequestered within autophagosomes and transported to lysosomes/vacuoles for degradation. Although phosphatidylinositol 3-kinase complex I (PI3KCI) plays a pivotal role in the regulation of autophagosome biogenesis, little is known about how this complex localizes to the pre-autophagosomal structure (PAS). In Saccharomyces cerevisiae, PI3KCI is composed of PI3K Vps34 and conserved subunits Vps15, Vps30, Atg14, and Atg38. In this study, we discover that PI3KCI interacts with the vacuolar membrane anchor Vac8, the PAS scaffold Atg1 complex, and the pre-autophagosomal vesicle component Atg9 via the Atg14 C-terminal region, the Atg38 C-terminal region, and the Vps30 BARA domain, respectively. While the Atg14-Vac8 interaction is constitutive, the Atg38-Atg1 complex interaction and the Vps30-Atg9 interaction are enhanced upon macroautophagy induction depending on Atg1 kinase activity. These interactions cooperate to target PI3KCI to the PAS. These findings provide a molecular basis for PAS targeting of PI3KCI during autophagosome biogenesis.
  • Phosphorylation of phase-separated p62 bodies by ULK1 activates a redox-independent stress response.
    Ryo Ikeda, Daisuke Noshiro, Hideaki Morishita, Shuhei Takada, Shun Kageyama, Yuko Fujioka, Tomoko Funakoshi, Satoko Komatsu-Hirota, Ritsuko Arai, Elena Ryzhii, Manabu Abe, Tomoaki Koga, Hozumi Motohashi, Mitsuyoshi Nakao, Kenji Sakimura, Arata Horii, Satoshi Waguri, Yoshinobu Ichimura, Nobuo N Noda, Masaaki Komatsu
    The EMBO journal, e113349, 12 Jun. 2023, [Peer-reviewed], [Corresponding author], [International Magazine]
    English, Scientific journal, 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.
  • Integrated proteomics identifies p62-dependent selective autophagy of the supramolecular vault complex.
    Reo Kurusu, Yuki Fujimoto, Hideaki Morishita, Daisuke Noshiro, Shuhei Takada, Koji Yamano, Hideaki Tanaka, Ritsuko Arai, Shun Kageyama, Tomoko Funakoshi, Satoko Komatsu-Hirota, Hikari Taka, Saiko Kazuno, Yoshiki Miura, Masato Koike, Toshifumi Wakai, Satoshi Waguri, Nobuo N Noda, Masaaki Komatsu
    Developmental cell, 09 May 2023, [Peer-reviewed], [International Magazine]
    English, Scientific journal, 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.
  • The mitochondrial intermembrane space protein mitofissin drives mitochondrial fission required for mitophagy
    Tomoyuki Fukuda, Kentaro Furukawa, Tatsuro Maruyama, Shun-ichi Yamashita, Daisuke Noshiro, Chihong Song, Yuta Ogasawara, Kentaro Okuyama, Jahangir Md Alam, Manabu Hayatsu, Tetsu Saigusa, Keiichi Inoue, Kazuho Ikeda, Akira Takai, Lin Chen, Vikramjit Lahiri, Yasushi Okada, Shinsuke Shibata, Kazuyoshi Murata, Daniel J. Klionsky, Nobuo N. Noda, Tomotake Kanki
    Molecular Cell, 83, 12, 2045, 2058.e9, Elsevier BV, May 2023, [Peer-reviewed], [Corresponding author]
    Scientific journal
  • Autophagy and cancer: Basic mechanisms and inhibitor development
    Yutaro Hama, Yuta Ogasawara, Nobuo N. Noda
    Cancer Science, Wiley, 20 Apr. 2023, [Peer-reviewed], [Invited], [Last author, Corresponding author]
    Scientific journal
  • The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3.
    Ryosuke Ishimura, Afnan H El-Gowily, Daisuke Noshiro, Satoko Komatsu-Hirota, Yasuko Ono, Mayumi Shindo, Tomohisa Hatta, Manabu Abe, Takefumi Uemura, Hyeon-Cheol Lee-Okada, Tarek M Mohamed, Takehiko Yokomizo, Takashi Ueno, Kenji Sakimura, Tohru Natsume, Hiroyuki Sorimachi, Toshifumi Inada, Satoshi Waguri, Nobuo N Noda, Masaaki Komatsu
    Nature communications, 13, 1, 7857, 7857, 21 Dec. 2022, [Peer-reviewed], [International Magazine]
    English, Scientific journal, 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.
  • Qualitative differences in disease-associated MEK mutants reveal molecular signatures and aberrant signaling-crosstalk in cancer
    Yuji Kubota, Yuko Fujioka, Ashwini Patil, Yusuke Takagi, Daisuke Matsubara, Masatomi Iijima, Isao Momose, Ryosuke Naka, Kenta Nakai, Nobuo N. Noda, Mutsuhiro Takekawa
    Nature Communications, 13, 1, Springer Science and Business Media LLC, Dec. 2022, [Peer-reviewed]
    Scientific journal, Abstract

    Point-mutations of MEK1, a central component of ERK signaling, are present in cancer and RASopathies, but their precise biological effects remain obscure. Here, we report a mutant MEK1 structure that uncovers the mechanisms underlying abnormal activities of cancer- and RASopathy-associated MEK1 mutants. These two classes of MEK1 mutations differentially impact on spatiotemporal dynamics of ERK signaling, cellular transcriptional programs, gene expression profiles, and consequent biological outcomes. By making use of such distinct characteristics of the MEK1 mutants, we identified cancer- and RASopathy-signature genes that may serve as diagnostic markers or therapeutic targets for these diseases. In particular, two AKT-inhibitor molecules, PHLDA1 and 2, are simultaneously upregulated by oncogenic ERK signaling, and mediate cancer-specific ERK-AKT crosstalk. The combined expression of PHLDA1/2 is critical to confer resistance to ERK pathway-targeted therapeutics on cancer cells. Finally, we propose a therapeutic strategy to overcome this drug resistance. Our data provide vital insights into the etiology, diagnosis, and therapeutic strategy of cancers and RASopathies.
  • Development of new tools to study membrane-anchored mammalian Atg8 proteins
    Sang-Won Park, Pureum Jeon, Akinori Yamasaki, Hye Eun Lee, Haneul Choi, Ji Young Mun, Yong-Woo Jun, Ju-Hui Park, Seung-Hwan Lee, Soo-Kyeong Lee, You-Kyung Lee, Hyun Kyu Song, Michael Lazarou, Dong-Hyong Cho, Masaaki Komatsu, Nobuo N. Noda, Deok-Jin Jang, Jin-A Lee
    Autophagy, 1, 20, Informa UK Limited, 17 Oct. 2022, [Peer-reviewed], [Corresponding author]
    Scientific journal
  • Targeting the ATG5-ATG16L1 Protein–Protein Interaction with a Hydrocarbon-Stapled Peptide Derived from ATG16L1 for Autophagy Inhibition
    Jin Cui, Yuta Ogasawara, Ikuko Kurata, Kazuaki Matoba, Yuko Fujioka, Nobuo N. Noda, Masakatsu Shibasaki, Takumi Watanabe
    Journal of the American Chemical Society, 144, 38, 17671, 17679, American Chemical Society (ACS), 15 Sep. 2022, [Peer-reviewed], [Corresponding author]
    Scientific journal
  • Lipid Transport from Endoplasmic Reticulum to Autophagic Membranes
    Takuo Osawa, Kazuaki Matoba, Nobuo N. Noda
    Cold Spring Harbor Perspectives in Biology, a041254, a041254, Cold Spring Harbor Laboratory, 08 Aug. 2022, [Peer-reviewed], [Invited], [Last author, Corresponding author]
    Scientific journal
  • Cytoskeleton grows p62 condensates for autophagy
    Nobuo N. Noda
    Cell Research, 32, 7, 607, 608, Springer Science and Business Media LLC, 19 May 2022, [Invited], [Lead author, Last author, Corresponding author]
    Scientific journal
  • Phosphorylation by casein kinase 2 enhances the interaction between ER‐phagy receptor TEX264 and ATG8 proteins
    Haruka Chino, Akinori Yamasaki, Koji L Ode, Hiroki R Ueda, Nobuo N Noda, Noboru Mizushima
    EMBO reports, 23, 6, EMBO, 13 Apr. 2022, [Peer-reviewed], [Corresponding author]
    Scientific journal
  • Phosphorylation by casein kinase 2 ensures ER-phagy receptor TEX264 binding to ATG8 proteins
    Haruka Chino, Akinori Yamasaki, Koji L Ode, Hiroki R Ueda, Nobuo N Noda, Noboru Mizushima
    Cold Spring Harbor Laboratory, 11 Feb. 2022
    Scientific journal
  • Update and nomenclature proposal for mammalian lysophospholipid acyltransferases, which create membrane phospholipid diversity.
    William J Valentine, Keisuke Yanagida, Hiroki Kawana, Nozomu Kono, Nobuo N Noda, Junken Aoki, Hideo Shindou
    The Journal of biological chemistry, 298, 1, 101470, 101470, Jan. 2022, [Peer-reviewed], [International Magazine]
    English, Scientific journal, The diversity of glycerophospholipid species in cellular membranes is immense and affects various biological functions. Glycerol-3-phosphate acyltransferases (GPATs) and lysophospholipid acyltransferases (LPLATs), in concert with phospholipase A1/2s enzymes, contribute to this diversity via selective esterification of fatty acyl chains at the sn-1 or sn-2 positions of membrane phospholipids. These enzymes are conserved across all kingdoms, and in mammals four GPATs of the 1-acylglycerol-3-phosphate O-acyltransferase (AGPAT) family and at least 14 LPLATs, either of the AGPAT or the membrane-bound O-acyltransferase (MBOAT) families, have been identified. Here we provide an overview of the biochemical and biological activities of these mammalian enzymes, including their predicted structures, involvements in human diseases, and essential physiological roles as revealed by gene-deficient mice. Recently, the nomenclature used to refer to these enzymes has generated some confusion due to the use of multiple names to refer to the same enzyme and instances of the same name being used to refer to completely different enzymes. Thus, this review proposes a more uniform LPLAT enzyme nomenclature, as well as providing an update of recent advances made in the study of LPLATs, continuing from our JBC mini review in 2009.
  • Phase-separated protein droplets of amyotrophic lateral sclerosis-associated p62/SQSTM1 mutants show reduced inner fluidity
    Mohammad Omar Faruk, Yoshinobu Ichimura, Shun Kageyama, Satoko Komatsu-Hirota, Afnan H. El-Gowily, Yu-shin Sou, Masato Koike, Nobuo N. Noda, Masaaki Komatsu
    Journal of Biological Chemistry, 297, 6, 101405, 101405, Elsevier {BV}, Dec. 2021, [International Magazine]
    English, Scientific journal, 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.
  • A glutamine sensor that directly activates TORC1
    Mirai Tanigawa, Katsuyoshi Yamamoto, Satoru Nagatoishi, Koji Nagata, Daisuke Noshiro, Nobuo N. Noda, Kouhei Tsumoto, Tatsuya Maeda
    Communications Biology, 4, 1, 1093, 1093, Springer Science and Business Media LLC, Dec. 2021, [Last author, Corresponding author], [International Magazine]
    English, Scientific journal, AbstractTOR 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.
  • Atg12-Interacting Motif Is Crucial for E2–E3 Interaction in Plant Atg8 System
    Kazuaki Matoba, Nobuo N. Noda
    Biological and Pharmaceutical Bulletin, 44, 9, 1337, 1343, Pharmaceutical Society of Japan, 01 Sep. 2021, [Peer-reviewed], [Last author, Corresponding author]
    Scientific journal
  • Delineating the lipidated Atg8 structure for unveiling its hidden activity in autophagy
    Tatsuro Maruyama, Nobuo N. Noda
    Autophagy, 1, 2, Informa UK Limited, 12 Aug. 2021, [Last author, Corresponding author]
    Scientific journal
  • Atg2 and Atg9: Intermembrane and interleaflet lipid transporters driving autophagy
    Nobuo N. Noda
    Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, 1866, 8, 158956, 158956, Elsevier BV, Aug. 2021, [Peer-reviewed], [Invited], [Lead author, Last author, Corresponding author]
    Scientific journal
  • Membrane perturbation by lipidated Atg8 underlies autophagosome biogenesis.
    Maruyama, T, Alam, J. M, Fukuda, T, Kageyama, S, Kirisako, H, Ishii, Y, Shimada, I, Ohsumi, Y, Komatsu, M, Kanki, T, Nakatogawa, H, Noda, N. N
    Nature Structural & Molecular Biology, 28, 7, 583, 593, 08 Jul. 2021, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
    English, Scientific journal, Autophagosome biogenesis is an essential feature of autophagy. Lipidation of Atg8 plays a critical role in this process. Previous in vitro studies identified membrane tethering and hemi-fusion/fusion activities of Atg8, yet definitive roles in autophagosome biogenesis remained controversial. Here, we studied the effect of Atg8 lipidation on membrane structure. Lipidation of Saccharomyces cerevisiae Atg8 on nonspherical giant vesicles induced dramatic vesicle deformation into a sphere with an out-bud. Solution NMR spectroscopy of Atg8 lipidated on nanodiscs identified two aromatic membrane-facing residues that mediate membrane-area expansion and fragmentation of giant vesicles in vitro. These residues also contribute to the in vivo maintenance of fragmented vacuolar morphology under stress in fission yeast, a moonlighting function of Atg8. Furthermore, these aromatic residues are crucial for the formation of a sufficient number of autophagosomes and regulate autophagosome size. Together, these data demonstrate that Atg8 can cause membrane perturbations that underlie efficient autophagosome biogenesis.
  • Structural catalog of core Atg proteins opens new era of autophagy research
    Kazuaki Matoba, Nobuo N Noda
    The Journal of Biochemistry, 169, 5, 517, 525, Oxford University Press (OUP), 03 Jul. 2021, [Peer-reviewed], [Invited], [Last author, Corresponding author], [International Magazine]
    English, Scientific journal, Abstract
    Autophagy, which is an evolutionarily conserved intracellular degradation system, involves de novo generation of autophagosomes that sequester and deliver diverse cytoplasmic materials to the lysosome for degradation. Autophagosome formation is mediated by approximately 20 core autophagy-related (Atg) proteins, which collaborate to mediate complicated membrane dynamics during autophagy. To elucidate the molecular functions of these Atg proteins in autophagosome formation, many researchers have tried to determine the structures of Atg proteins by using various structural biological methods. Although not sufficient, the basic structural catalog of all core Atg proteins was established. In this review article, we summarize structural biological studies of core Atg proteins, with an emphasis on recently unveiled structures, and describe the mechanistic breakthroughs in autophagy research that have derived from new structural information.
  • 【相分離 メカニズムと疾患"膜のないオルガネラ"はいかに機能するか?神経変性疾患・ウイルス感染とどう関わるか?】(第3章)相分離と生体機能・疾患 相分離で見直すオートファジー
    藤岡 優子, 野田 展生
    実験医学, 39, 10, 1628, 1633, (株)羊土社, Jun. 2021
    Japanese
  • マルチモードオートファジー カーゴの流動性が選択的オートファジーでの分解を左右する　　　　　　　　　　　　　　　
    山崎 章徳, Alam Jahangir MD., 能代 大輔, 平田 恵理, 藤岡 優子, May Alexander I., 鈴木 邦律, 大隅 良典, 野田 展生
    日本細胞生物学会大会講演要旨集, 73回, S10, 2, (一社)日本細胞生物学会, Jun. 2021
    Japanese
  • Mutagenesis and homology modeling reveal a predicted pocket of lysophosphatidylcholine acyltransferase 2 to catch Acyl‐CoA
    Fumie Hamano, Kazuaki Matoba, Tomomi Hashidate‐Yoshida, Tomoyuki Suzuki, Kiyotake Miura, Daisuke Hishikawa, Takeshi Harayama, Koichi Yuki, Yoshihiro Kita, Nobuo N. Noda, Takao Shimizu, Hideo Shindou
    The FASEB Journal, 35, 6, e21501, Wiley, Jun. 2021, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Platelet-activating factor (PAF) is a potent proinflammatory phospholipid mediator that elicits various cellular functions and promotes several pathological events, including anaphylaxis and neuropathic pain. PAF is biosynthesized by two types of lyso-PAF acetyltransferases: lysophosphatidylcholine acyltransferase 1 (LPCAT1) and LPCAT2, which are constitutive and inducible forms of lyso-PAF acetyltransferase, respectively. Because LPCAT2 mainly produces PAF under inflammatory stimuli, understanding the structure of LPCAT2 is important for developing specific drugs against PAF-related inflammatory diseases. Although the structure of LPCAT2 has not been determined, the crystal structure was reported for Thermotoga maritima PlsC, an enzyme in the same gene family as LPCAT2. Here, we identified residues in mouse LPCAT2 essential for its enzymatic activity and a potential acyl-coenzyme A (CoA)-binding pocket, based on homology modeling of mouse LPCAT2 with PlsC. We also found that Ala115 of mouse LPCAT2 was important for acyl-CoA selectivity. In conclusion, these results predict the three-dimensional (3D) structure of mouse LPCAT2. Our findings have implications for the future development of new drugs against PAF-related diseases.
  • Biomolecular condensates in autophagy regulation
    Yuko Fujioka, Nobuo N. Noda
    Current Opinion in Cell Biology, 69, 23, 29, Elsevier BV, Apr. 2021, [Peer-reviewed], [Invited], [Last author, Corresponding author], [International Magazine]
    English, Scientific journal, Autophagy is an intracellular degradation system that contributes to cellular homeostasis. Autophagosome formation is a landmark event in autophagy, which sequesters and delivers cytoplasmic components to the lysosome for degradation. Based on selectivity, autophagy can be classified into bulk and selective autophagy, which are mechanistically distinct from each other, especially in the requirement of cargos for autophagosome formation. Recent studies revealed that liquid-like biomolecular condensates, which are formed through liquid-liquid phase separation, regulate the autophagosome formation of both bulk and selective autophagy. Here, we focus on recent findings on the involvement of biomolecular condensates in autophagy regulation and discuss their significance.
  • p62/SQSTM1-droplet serves as a platform for autophagosome formation and anti-oxidative stress response.
    Kageyama, S, Gudmundsson, S, Sou, Y.-S, Ichimura, Y, Tamura, N, Kazuno, S, Ueno, T, Miura, Y, Noshiro, D, Abe, M, Mizushima, T, Miura, N, Okuda, S, Motohashi, H, Lee, J.-A, Sakimura, K, Ohe, T, Noda, N. N, Waguri, S, Eskelinen, E.-L, Komatsu, M
    Nature Communications, 12, 1, 16, Springer Science and Business Media LLC, 04 Jan. 2021, [Peer-reviewed]
    Scientific journal, 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.
  • Secret of Atg9: lipid scramblase activity drives de novo autophagosome biogenesis.
    Kazuaki Matoba, Nobuo N Noda
    Cell death and differentiation, 27, 12, 3386, 3388, Dec. 2020, [International Magazine]
    English, Scientific journal
  • Author Correction: Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion.
    Kazuaki Matoba, Tetsuya Kotani, Akihisa Tsutsumi, Takuma Tsuji, Takaharu Mori, Daisuke Noshiro, Yuji Sugita, Norimichi Nomura, So Iwata, Yoshinori Ohsumi, Toyoshi Fujimoto, Hitoshi Nakatogawa, Masahide Kikkawa, Nobuo N Noda
    Nature structural & molecular biology, 27, 12, 1209, 1209, Dec. 2020, [International Magazine]
    English, An amendment to this paper has been published and can be accessed via a link at the top of the paper.
  • Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes
    Keisuke Mochida, Akinori Yamasaki, Kazuaki Matoba, Hiromi Kirisako, Nobuo N. Noda, Hitoshi Nakatogawa
    Nature Communications, 11, 1, 3306, 3306, Springer Science and Business Media LLC, Dec. 2020, [Peer-reviewed], [Corresponding author], [International Magazine]
    English, Scientific journal, The endoplasmic reticulum (ER) is selectively degraded by autophagy (ER-phagy) through proteins called ER-phagy receptors. In Saccharomyces cerevisiae, Atg40 acts as an ER-phagy receptor to sequester ER fragments into autophagosomes by binding Atg8 on forming autophagosomal membranes. During ER-phagy, parts of the ER are morphologically rearranged, fragmented, and loaded into autophagosomes, but the mechanism remains poorly understood. Here we find that Atg40 molecules assemble in the ER membrane concurrently with autophagosome formation via multivalent interaction with Atg8. Atg8-mediated super-assembly of Atg40 generates highly-curved ER regions, depending on its reticulon-like domain, and supports packing of these regions into autophagosomes. Moreover, tight binding of Atg40 to Atg8 is achieved by a short helix C-terminal to the Atg8-family interacting motif, and this feature is also observed for mammalian ER-phagy receptors. Thus, this study significantly advances our understanding of the mechanisms of ER-phagy and also provides insights into organelle fragmentation in selective autophagy of other organelles.
  • Structural and dynamics analysis of intrinsically disordered proteins by high-speed atomic force microscopy.
    Kodera, N, Noshiro, D, Dora, S. K, Mori, T, Habchi, J, Blocquel, D, Gruet, A, Dosnon, M, Salladini, E, Bignon, C, Fujioka, Y, Oda, T, Noda, N. N, Sato, M, Lotti, M, Mizuguchi, M, Longhi, S, Ando, T
    Nature Nanotechnology, 16, 2, 181, 189, Springer Science and Business Media LLC, 23 Nov. 2020, [Peer-reviewed]
    Scientific journal, 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.
  • Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion.
    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, N. N
    Nature Structural & Molecular Biology, 27, 12, 1185, 1193, Springer Science and Business Media LLC, 26 Oct. 2020, [Peer-reviewed], [Last author, Corresponding author]
    Scientific journal, 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.
  • Liquid–liquid phase separation in autophagy
    Nobuo N. Noda, Zheng Wang, Hong Zhang
    Journal of Cell Biology, 219, 8, Rockefeller University Press, 03 Aug. 2020, [Peer-reviewed], [Invited], [Lead author, Corresponding author]
    Scientific journal, Liquid–liquid phase separation (LLPS) compartmentalizes and concentrates biomacromolecules into distinct condensates. Liquid-like condensates can transition into gel and solid states, which are essential for fulfilling their different functions. LLPS plays important roles in multiple steps of autophagy, mediating the assembly of autophagosome formation sites, acting as an unconventional modulator of TORC1-mediated autophagy regulation, and triaging protein cargos for degradation. Gel-like, but not solid, protein condensates can trigger formation of surrounding autophagosomal membranes. Stress and pathological conditions cause aberrant phase separation and transition of condensates, which can evade surveillance by the autophagy machinery. Understanding the mechanisms underlying phase separation and transition will provide potential therapeutic targets for protein aggregation diseases.
  • 【イメージング時代の構造生命科学 細胞の動態、膜のないオルガネラ、分子の構造変化をトランススケールに観る】(第2章)構造生命科学からトランススケール・イメージングによる細胞動態学へ トランススケールな解析が待たれる生命科学の未解決課題 柔らかい構造の可視化 LLPSと膜動態を例に
    能代 大輔, 野田 展生
    実験医学, 38, 5, 750, 755, (株)羊土社, Mar. 2020
    Japanese
  • Liquidity Is a Critical Determinant for Selective Autophagy of Protein Condensates
    Akinori Yamasaki, Jahangir Md. Alam, Daisuke Noshiro, Eri Hirata, Yuko Fujioka, Kuninori Suzuki, Yoshinori Ohsumi, Nobuo N. Noda
    Molecular Cell, 77, 6, 1163, 1175.e9, Elsevier BV, Mar. 2020, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
    English, Scientific journal, 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.
  • Phase separation organizes the site of autophagosome formation
    Yuko Fujioka, Jahangir Md. Alam, Daisuke Noshiro, Kazunari Mouri, Toshio Ando, Yasushi Okada, Alexander I. May, Roland L. Knorr, Kuninori Suzuki, Yoshinori Ohsumi, Nobuo N. Noda
    Nature, 578, 7794, 301, 305, Springer Science and Business Media LLC, Feb. 2020, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
    English, Scientific journal, 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.
  • Human ATG2B possesses a lipid transfer activity which is accelerated by negatively charged lipids and WIPI4
    Takuo Osawa, Yuki Ishii, Nobuo N. Noda
    Genes to Cells, 25, 1, 65, 70, Wiley, Jan. 2020, [Last author, Corresponding author]
    Scientific journal
  • Atg2: A novel phospholipid transfer protein that mediates de novo autophagosome biogenesis
    Takuo Osawa, Nobuo N. Noda
    Protein Science, 28, 6, 1005, 1012, Wiley, Jun. 2019, [Peer-reviewed], [Invited], [Last author, Corresponding author]
    Scientific journal
  • Evolution from covalent conjugation to non-covalent interaction in the ubiquitin-like ATG12 system
    Yu Pang, Hayashi Yamamoto, Hirokazu Sakamoto, Masahide Oku, Joe Kimanthi Mutungi, Mayurbhai Himatbhai Sahani, Yoshitaka Kurikawa, Kiyoshi Kita, Nobuo N. Noda, Yasuyoshi Sakai, Honglin Jia, Noboru Mizushima
    Nature Structural & Molecular Biology, 26, 4, 289, 296, Apr. 2019, [Peer-reviewed]
    English, Scientific journal
  • Atg2 mediates direct lipid transfer between membranes for autophagosome formation
    Takuo Osawa, Tetsuya Kotani, Tatsuya Kawaoka, Eri Hirata, Kuninori Suzuki, Hitoshi Nakatogawa, Yoshinori Ohsumi, Nobuo N. Noda
    Nature Structural & Molecular Biology, 26, 4, 281, 288, Springer Science and Business Media LLC, Apr. 2019, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
    English, Scientific journal, A key event in autophagy is autophagosome formation, whereby the newly synthesized isolation membrane (IM) expands to form a complete autophagosome using endomembrane-derived lipids. Atg2 physically links the edge of the expanding IM with the endoplasmic reticulum (ER), a role that is essential for autophagosome formation. However, the molecular function of Atg2 during ER-IM contact remains unclear, as does the mechanism of lipid delivery to the IM. Here we show that the conserved amino-terminal region of Schizosaccharomyces pombe Atg2 includes a lipid-transfer-protein-like hydrophobic cavity that accommodates phospholipid acyl chains. Atg2 bridges highly curved liposomes, thereby facilitating efficient phospholipid transfer in vitro, a function that is inhibited by mutations that impair autophagosome formation in vivo. These results suggest that Atg2 acts as a lipid-transfer protein that supplies phospholipids for autophagosome formation.
  • A C4N4 Diaminopyrimidine Fluorophore
    Hidetoshi Noda, Yasuko Asada, Tatsuro Maruyama, Naoki Takizawa, Nobuo N. Noda, Masakatsu Shibasaki, Naoya Kumagai
    Chemistry – A European Journal, 25, 17, 4299, 4304, Mar. 2019, [Peer-reviewed]
    English, Scientific journal
  • Structural Studies of Selective Autophagy in Yeast.
    Yamasaki A, Watanabe Y, Noda NN
    Methods in molecular biology (Clifton, N.J.), 1880, 77, 90, 2019, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
    English, Scientific journal, Budding yeast has been utilized as a model system for studying basic mechanisms of autophagy. The cytoplasm-to-vacuole targeting (Cvt) pathway, which delivers some vacuolar enzymes into the vacuole selectively and constitutively, is one of the most characterized examples of selective autophagy in budding yeast. Here we summarize the methods of X-ray crystallography, NMR, and other biophysical analyses to study the structural basis of the Cvt pathway.
  • Membrane-binding domains in autophagy
    Takuo Osawa, Jahangir, Md. Alam, Nobuo N. Noda
    Chemistry and Physics of Lipids, 218, 1, Elsevier {BV}, Jan. 2019, [Peer-reviewed], [Last author, Corresponding author]
  • Lipidation-independent vacuolar functions of Atg8 rely on its noncanonical interaction with a vacuole membrane protein
    Xiao-Man Liu, Akinori Yamasaki, Xiao-Min Du, Valerie C Coffman, Yoshinori Ohsumi, Hitoshi Nakatogawa, Jian-Qiu Wu, Nobuo N Noda, Li-Lin Du
    eLife, 7, eLife Sciences Publications, Ltd, 19 Nov. 2018, [Peer-reviewed], [Corresponding author]
    Scientific journal, The ubiquitin-like protein Atg8, in its lipidated form, plays central roles in autophagy. Yet, remarkably, Atg8 also carries out lipidation-independent functions in non-autophagic processes. How Atg8 performs its moonlighting roles is unclear. Here we report that in the fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae, the lipidation-independent roles of Atg8 in maintaining normal morphology and functions of the vacuole require its interaction with a vacuole membrane protein Hfl1 (homolog of human TMEM184 proteins). Crystal structures revealed that the Atg8-Hfl1 interaction is not mediated by the typical Atg8-family-interacting motif (AIM) that forms an intermolecular β-sheet with Atg8. Instead, the Atg8-binding regions in Hfl1 proteins adopt a helical conformation, thus representing a new type of AIMs (termed helical AIMs here). These results deepen our understanding of both the functional versatility of Atg8 and the mechanistic diversity of Atg8 binding.
  • Atg7 Activates an Autophagy-Essential Ubiquitin-like Protein Atg8 through Multi-Step Recognition.
    Masaya Yamaguchi, Kenji Satoo, Hironori Suzuki, Yuko Fujioka, Yoshinori Ohsumi, Fuyuhiko Inagaki, Nobuo N Noda
    Journal of molecular biology, 430, 3, 249, 257, 02 Feb. 2018, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
    English, Scientific journal, Atg8 is a unique ubiquitin-like protein that is covalently conjugated with a phosphatidylethanolamine through reactions similar to ubiquitination and plays essential roles in autophagy. Atg7 is the E1 enzyme for Atg8, and it activates the C-terminal Gly116 of Atg8 using ATP. Here, we report the crystal structure of Atg8 bound to the C-terminal domain of Atg7 in an unprecedented mode. Atg8 neither contacts with the central β-sheet nor binds to the catalytic site of Atg7, both of which were observed in previously reported Atg7-Atg8 structures. Instead, Atg8 binds to the C-terminal α-helix and crossover loop, thereby changing the autoinhibited conformation of the crossover loop observed in the free Atg7 structure into a short helix and a disordered loop. Mutational analyses suggested that this interaction mode is important for the activation reaction. We propose that Atg7 recognizes Atg8 through multiple steps, which would be necessary to induce a conformational change in Atg7 that is optimal for the activation reaction.
  • Endosomal rab cycles regulate parkin-mediated mitophagy
    Koji Yamano, Chunxin Wang, Shireen A. Sarraf, Christian Münch, Reika Kikuchi, Nobuo N. Noda, Yohei Hizukuri, Masato T. Kanemaki, Wade Harper, Keiji Tanaka, Noriyuki Matsuda, Richard J. Youle
    eLife, 7, eLife Sciences Publications Ltd, 23 Jan. 2018, [Peer-reviewed]
    English, Scientific journal
  • Autophagy-regulating protease Atg4: Structure, function, regulation and inhibition
    Tatsuro Maruyama, Nobuo N. Noda
    Journal of Antibiotics, 71, 1, 72, 78, Nature Publishing Group, 01 Jan. 2018, [Peer-reviewed], [Invited], [Last author, Corresponding author]
    English
  • Biophysical characterization of Atg11, a scaffold protein essential for selective autophagy in yeast
    Hironori Suzuki, Nobuo N. Noda
    FEBS Open Bio, 8, 1, 110, 116, Wiley Blackwell, 01 Jan. 2018, [Peer-reviewed], [Last author, Corresponding author]
    English, Scientific journal
  • Structural biology of the core autophagy machinery
    Hironori Suzuki, Takuo Osawa, Yuko Fujioka, Nobuo N. Noda
    CURRENT OPINION IN STRUCTURAL BIOLOGY, 43, 10, 17, Apr. 2017, [Peer-reviewed], [Invited], [Last author, Corresponding author]
    English, Scientific journal
  • Structural Biology of the Cvt Pathway
    Akinori Yamasaki, Nobuo N. Noda
    JOURNAL OF MOLECULAR BIOLOGY, 429, 4, 531, 542, Feb. 2017, [Peer-reviewed], [Invited], [Last author, Corresponding author]
    English
  • The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes
    Hayashi Yamamoto, Yuko Fujioka, Sho W. Suzuki, Daisuke Noshiro, Hironori Suzuki, Chika Kondo-Kakuta, Yayoi Kimura, Hisashi Hirano, Toshio Ando, Nobuo N. Noda, Yoshinori Ohsumi
    Developmental Cell, 38, 1, 86, 99, Jul. 2016, [Peer-reviewed], [Corresponding author]
    English, Scientific journal
  • Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates
    Akinori Yamasaki, Yasunori Watanabe, Wakana Adachi, Kuninori Suzuki, Kazuaki Matoba, Hiromi Kirisako, Hiroyuki Kumeta, Hitoshi Nakatogawa, Yoshinori Ohsumi, Fuyuhiko Inagaki, Nobuo N. Noda
    CELL REPORTS, 16, 1, 19, 27, Jun. 2016, [Peer-reviewed], [Last author, Corresponding author]
    English, Scientific journal
  • Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions
    Mariko Yokogawa, Takashi Tsushima, Nobuo N. Noda, Hiroyuki Kumeta, Yoshiaki Enokizono, Kazuo Yamashita, Daron M. Standley, Osamu Takeuchi, Shizuo Akira, Fuyuhiko Inagaki
    SCIENTIFIC REPORTS, 6, 22324, Mar. 2016, [Peer-reviewed]
    English, Scientific journal
  • Small differences make a big impact: Structural insights into the differential function of the 2 Atg8 homologs in C-elegans
    Fan Wu, Peng Wang, Yuxian Shen, Nobuo N. Noda, Hong Zhang
    AUTOPHAGY, 12, 3, 606, 607, 2016, [Peer-reviewed]
    English
  • Atg101: Not Just an Accessory Subunit in the Autophagy-initiation Complex
    Nobuo N. Noda, Noboru Mizushima
    CELL STRUCTURE AND FUNCTION, 41, 1, 13, 20, 2016, [Peer-reviewed], [Invited], [Lead author, Corresponding author]
    English
  • Structural Basis of the Differential Function of the Two C. elegans Atg8 Homologs, LGG-1 and LGG-2, in Autophagy
    Fan Wu, Yasunori Watanabe, Xiang-Yang Guo, Xin Qi, Peng Wang, Hong-Yu Zhao, Zheng Wang, Yuko Fujioka, Hui Zhang, Jin-Qi Ren, Tian-Cheng Fang, Yu-Xian Shen, Wei Feng, Jun-Jie Hu, Nobuo N. Noda, Hong Zhang
    Molecular Cell, 60, 6, 914, 929, Dec. 2015, [Peer-reviewed], [Corresponding author], [International Magazine]
    English, Scientific journal
  • The Thermotolerant Yeast Kluyveromyces marxianus Is a Useful Organism for Structural and Biochemical Studies of Autophagy
    Hayashi Yamamoto, Takayuki Shima, Masaya Yamaguchi, Yuh Mochizuki, Hisashi Hoshida, Soichiro Kakuta, Chika Kondo-Kakuta, Nobuo N. Noda, Fuyuhiko Inagaki, Takehiko Itoh, Rinji Akada, Yoshinori Ohsumi
    JOURNAL OF BIOLOGICAL CHEMISTRY, 290, 49, 29506, U476, Dec. 2015, [Peer-reviewed]
    English, Scientific journal
  • Open and closed HORMAs regulate autophagy initiation
    Hironori Suzuki, Takeshi Kaizuka, Noboru Mizushima, Nobuo N. Noda
    AUTOPHAGY, 11, 11, 2123, 2124, Nov. 2015, [Peer-reviewed], [Invited], [Last author, Corresponding author]
    English
  • Atg1 family kinases in autophagy initiation
    Nobuo N. Noda, Yuko Fujioka
    CELLULAR AND MOLECULAR LIFE SCIENCES, 72, 16, 3083, 3096, Aug. 2015, [Peer-reviewed], [Invited], [Lead author, Corresponding author]
    English
  • Structure of the Atg101-Atg13 complex reveals essential roles of Atg101 in autophagy initiation
    Hironori Suzuki, Takeshi Kaizuka, Noboru Mizushima, Nobuo N. Noda
    Nature Structural & Molecular Biology, 22, 7, 572, +, Jul. 2015, [Peer-reviewed], [Last author, Corresponding author]
    English, Scientific journal
  • Mechanisms of Autophagy
    Nobuo N. Noda, Fuyuhiko Inagaki
    ANNUAL REVIEW OF BIOPHYSICS, VOL 44, 44, 101, 122, 2015, [Peer-reviewed], [Invited], [Lead author, Corresponding author]
    English, In book
  • Structural basis of starvation-induced assembly of the autophagy initiation complex
    Yuko Fujioka, Sho W. Suzuki, Hayashi Yamamoto, Chika Kondo-Kakuta, Yayoi Kimura, Hisashi Hirano, Rinji Akada, Fuyuhiko Inagaki, Yoshinori Ohsumi, Nobuo N. Noda
    Nature Structural & Molecular Biology, 21, 6, 513, 521, Jun. 2014, [Peer-reviewed], [Last author, Corresponding author]
    English, Scientific journal
  • Proteomic Profiling of Autophagosome Cargo in Saccharomyces cerevisiae
    Kuninori Suzuki, Shingo Nakamura, Mayumi Morimoto, Kiyonaga Fujii, Nobuo N. Noda, Fuyuhiko Inagaki, Yoshinori Ohsumi
    PLOS ONE, 9, 3, e91651, Mar. 2014, [Peer-reviewed]
    English, Scientific journal
  • Architecture of the Atg12-Atg5-Atg16 Complex and its Molecular Role in Autophagy
    Nobuo N. Noda, Fuyuhiko Inagaki
    Autophagy: Cancer, Other Pathologies, Inflammation, Immunity, Infection, and Aging, 3, 57, 65, Elsevier Inc., 31 Jan. 2014, [Peer-reviewed]
    English, In book
  • Selective Autophagy: Role of Interaction between the Atg8 Family Interacting Motif and Atg8 Family Proteins
    Nobuo N. Noda, Fuyuhiko Inagaki
    Autophagy: Cancer, Other Pathologies, Inflammation, Immunity, Infection, and Aging, 39, 48, Elsevier Inc., Oct. 2013, [Peer-reviewed]
    English, In book
  • Two-colored fluorescence correlation spectroscopy screening for LC3-P62 interaction inhibitors
    Keiko Tsuganezawa, Yoshiyasu Shinohara, Naoko Ogawa, Shun Tsuboi, Norihisa Okada, Masumi Mori, Shigeyuki Yokoyama, Nobuo N. Noda, Fuyuhiko Inagaki, Yoshinori Ohsumi, Akiko Tanaka
    Journal of Biomolecular Screening, 18, 9, 1103, 1109, Oct. 2013, [Peer-reviewed]
    English, Scientific journal
  • Atg18 phosphoregulation controls organellar dynamics by modulating its phosphoinositide-binding activity
    Naoki Tamura, Masahide Oku, Moemi Ito, Nobuo N. Noda, Fuyuhiko Inagaki, Yasuyoshi Sakai
    JOURNAL OF CELL BIOLOGY, 202, 4, 685, 698, Aug. 2013, [Peer-reviewed]
    English, Scientific journal
  • Atg12-Atg5 conjugate enhances E2 activity of Atg3 by rearranging its catalytic site
    MacHiko Sakoh-Nakatogawa, Kazuaki Matoba, Eri Asai, Hiromi Kirisako, Junko Ishii, Nobuo N Noda, Fuyuhiko Inagaki, Hitoshi Nakatogawa, Yoshinori Ohsumi
    Nature Structural and Molecular Biology, 20, 4, 433, 439, May 2013, [Peer-reviewed]
    English, Scientific journal
  • Structure of the Atg12-Atg5 conjugate reveals a platform for stimulating Atg8-PE conjugation.
    Nobuo N Noda, Yuko Fujioka, Takao Hanada, Yoshinori Ohsumi, Fuyuhiko Inagaki
    EMBO reports, 14, 2, 206, 11, Feb. 2013, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Atg12 is conjugated to Atg5 through enzymatic reactions similar to ubiquitination. The Atg12-Atg5 conjugate functions as an E3-like enzyme to promote lipidation of Atg8, whereas lipidated Atg8 has essential roles in both autophagosome formation and selective cargo recognition during autophagy. However, the molecular role of Atg12 modification in these processes has remained elusive. Here, we report the crystal structure of the Atg12-Atg5 conjugate. In addition to the isopeptide linkage, Atg12 forms hydrophobic and hydrophilic interactions with Atg5, thereby fixing its position on Atg5. Structural comparison with unmodified Atg5 and mutational analyses showed that Atg12 modification neither induces a conformational change in Atg5 nor creates a functionally important architecture. Rather, Atg12 functions as a binding module for Atg3, the E2 enzyme for Atg8, thus endowing Atg5 with the ability to interact with Atg3 to facilitate Atg8 lipidation.
  • Crystallographic and NMR Evidence for Flexibility in Oligosaccharyltransferases and Its Catalytic Significance
    James Nyirenda, Shunsuke Matsumoto, Takashi Saitoh, Nobuo Maita, Nobuo N. Noda, Fuyuhiko Inagaki, Daisuke Kohda
    STRUCTURE, 21, 1, 32, 41, Jan. 2013, [Peer-reviewed]
    English, Scientific journal
  • Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7
    Masaya Yamaguchi, Kazuaki Matoba, Ryoko Sawada, Yuko Fujioka, Hitoshi Nakatogawa, Hayashi Yamamoto, Yoshihiro Kobashigawa, Hisashi Hoshida, Rinji Akada, Yoshinori Ohsumi, Nobuo N. Noda, Fuyuhiko Inagaki
    Nature Structural & Molecular Biology, 19, 12, 1250, +, Dec. 2012, [Peer-reviewed], [Corresponding author]
    English, Scientific journal
  • Structure-based Analyses Reveal Distinct Binding Sites for Atg2 and Phosphoinositides in Atg18
    Yasunori Watanabe, Takafumi Kobayashi, Hayashi Yamamoto, Hisashi Hoshida, Rinji Akada, Fuyuhiko Inagaki, Yoshinori Ohsumi, Nobuo N. Noda
    JOURNAL OF BIOLOGICAL CHEMISTRY, 287, 38, 31681, 31690, Sep. 2012, [Peer-reviewed]
    English, Scientific journal
  • Differential Function of the Two Atg4 Homologues in the Aggrephagy Pathway in Caenorhabditis elegans
    Fan Wu, Yuping Li, Fuxin Wang, Nobuo N. Noda, Hong Zhang
    JOURNAL OF BIOLOGICAL CHEMISTRY, 287, 35, 29457, 29467, Aug. 2012, [Peer-reviewed]
    English, Scientific journal
  • The Autophagy-related Protein Kinase Atg1 Interacts with the Ubiquitin-like Protein Atg8 via the Atg8 Family Interacting Motif to Facilitate Autophagosome Formation
    Hitoshi Nakatogawa, Shiran Ohbayashi, Machiko Sakoh-Nakatogawa, Soichiro Kakuta, Sho W. Suzuki, Hiromi Kirisako, Chika Kondo-Kakuta, Nobuo N. Noda, Hayashi Yamamoto, Yoshinori Ohsumi
    JOURNAL OF BIOLOGICAL CHEMISTRY, 287, 34, 28503, 28507, Aug. 2012, [Peer-reviewed]
    English, Scientific journal
  • Structural Insights into Atg10-Mediated Formation of the Autophagy-Essential Atg12-Atg5 Conjugate
    Masaya Yamaguchi, Nobuo N. Noda, Hayashi Yamamoto, Takayuki Shima, Hiroyuki Kumeta, Yoshihiro Kobashigawa, Rinji Akada, Yoshinori Ohsumi, Fuyuhiko Inagaki
    STRUCTURE, 20, 7, 1244, 1254, Jul. 2012, [Peer-reviewed]
    English, Scientific journal
  • Tertiary Structure-Function Analysis Reveals the Pathogenic Signaling Potentiation Mechanism of Helicobacter pylori Oncogenic Effector CagA
    Takeru Hayashi, Miki Senda, Hiroko Morohashi, Hideaki Higashi, Masafumi Horio, Yui Kashiba, Lisa Nagase, Daisuke Sasaya, Tomohiro Shimizu, Nagarajan Venugopalan, Hiroyuki Kumeta, Nobuo N. Noda, Fuyuhiko Inagaki, Toshiya Senda, Masanori Hatakeyama
    CELL HOST & MICROBE, 12, 1, 20, 33, Jul. 2012, [Peer-reviewed]
    English, Scientific journal
  • Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase from Archaeoglobus fulgidus at 1.75 angstrom Resolution
    Shunsuke Matsumoto, Mayumi Igura, James Nyirenda, Masaki Matsumoto, Satoru Yuzawa, Nobuo Noda, Fuyuhiko Inagaki, Daisuke Kohda
    BIOCHEMISTRY, 51, 20, 4157, 4166, May 2012, [Peer-reviewed]
    English, Scientific journal
  • Structure of the Novel C-terminal Domain of Vacuolar Protein Sorting 30/Autophagy-related Protein 6 and Its Specific Role in Autophagy
    Nobuo N. Noda, Takafumi Kobayashi, Wakana Adachi, Yuko Fujioka, Yoshinori Ohsumi, Fuyuhiko Inagaki
    JOURNAL OF BIOLOGICAL CHEMISTRY, 287, 20, 16256, 16266, May 2012, [Peer-reviewed]
    English, Scientific journal
  • Autophagy-related Protein 32 Acts as Autophagic Degron and Directly Initiates Mitophagy
    Noriko Kondo-Okamoto, Nobuo N. Noda, Sho W. Suzuki, Hitoshi Nakatogawa, Ikuko Takahashi, Miou Matsunami, Ayako Hashimoto, Fuyuhiko Inagaki, Yoshinori Ohsumi, Koji Okamoto
    JOURNAL OF BIOLOGICAL CHEMISTRY, 287, 13, 10631, 10638, Mar. 2012, [Peer-reviewed]
    English, Scientific journal
  • Autoinhibition and phosphorylation-induced activation mechanisms of human cancer and autoimmune disease-related E3 protein Cbl-b
    Yoshihiro Kobashigawa, Akira Tomitaka, Hiroyuki Kumeta, Nobuo N. Noda, Masaya Yamaguchi, Fuyuhiko Inagaki
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108, 51, 20579, 20584, Dec. 2011, [Peer-reviewed]
    English, Scientific journal
  • Structural Basis of Atg8 Activation by a Homodimeric E1, Atg7
    Nobuo N. Noda, Kenji Satoo, Yuko Fujioka, Hiroyuki Kumeta, Kenji Ogura, Hitoshi Nakatogawa, Yoshinori Ohsumi, Fuyuhiko Inagaki
    Molecular Cell, 44, 3, 462, 475, Nov. 2011, [Peer-reviewed], [Lead author, Corresponding author]
    English, Scientific journal
  • Autophagy-related Protein 8 (Atg8) Family Interacting Motif in Atg3 Mediates the Atg3-Atg8 Interaction and Is Crucial for the Cytoplasm-to-Vacuole Targeting Pathway
    Masaya Yamaguchi, Nobuo N. Noda, Hitoshi Nakatogawa, Hiroyuki Kumeta, Yoshinori Ohsumi, Fuyuhiko Inagaki
    JOURNAL OF BIOLOGICAL CHEMISTRY, 285, 38, 29599, 29607, Sep. 2010, [Peer-reviewed]
    English, Scientific journal
  • Selective Transport of alpha-Mannosidase by Autophagic Pathways STRUCTURAL BASIS FOR CARGO RECOGNITION BY Atg19 AND Atg34
    Yasunori Watanabe, Nobuo N. Noda, Hiroyuki Kumeta, Kuninori Suzuki, Yoshinori Ohsumi, Fuyuhiko Inagaki
    JOURNAL OF BIOLOGICAL CHEMISTRY, 285, 39, 30026, 30033, Sep. 2010, [Peer-reviewed]
    English, Scientific journal
  • Ser386 phosphorylation of transcription factor IRF-3 induces dimerization and association with CBP/p300 without overall conformational change
    Kiyohiro Takahasi, Masataka Horiuchi, Kiyonaga Fujii, Shingo Nakamura, Nobuo N. Noda, Mitsutoshi Yoneyama, Takashi Fujita, Fuyuhiko Inagaki
    GENES TO CELLS, 15, 8, 901, 910, Aug. 2010, [Peer-reviewed]
    English, Scientific journal
  • The NMR structure of the autophagy-related protein Atg8
    Hiroyuki Kumeta, Masahiro Watanabe, Hitoshi Nakatogawa, Masaya Yamaguchi, Kenji Ogura, Wakana Adachi, Yuko Fujioka, Nobuo N. Noda, Yoshinori Ohsumi, Fuyuhiko Inagaki
    JOURNAL OF BIOMOLECULAR NMR, 47, 3, 237, 241, Jul. 2010, [Peer-reviewed]
    English, Scientific journal
  • Atg8-family interacting motif crucial for selective autophagy
    Nobuo N. Noda, Yoshinori Ohsumi, Fuyuhiko Inagaki
    FEBS LETTERS, 584, 7, 1379, 1385, Apr. 2010, [Peer-reviewed]
    English
  • Dimeric Coiled-coil Structure of Saccharomyces cerevisiae Atg16 and Its Functional Significance in Autophagy
    Yuko Fujioka, Nobuo N. Noda, Hitoshi Nakatogawa, Yoshinori Ohsumi, Fuyuhiko Inagaki
    JOURNAL OF BIOLOGICAL CHEMISTRY, 285, 2, 1508, 1515, Jan. 2010, [Peer-reviewed]
    English, Scientific journal
  • Characterization of the Atg17-Atg29-Atg31 complex specifically required for starvation-induced autophagy in Saccharomyces cerevisiae
    Yukiko Kabeya, Nobuo N. Noda, Yuko Fujioka, Kuninori Suzuki, Fuyuhiko Inagaki, Yoshinori Ohsumi
    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 389, 4, 612, 615, Nov. 2009, [Peer-reviewed]
    English, Scientific journal
  • Crystallization of Saccharomyces cerevisiae alpha-mannosidase, a cargo protein of the Cvt pathway
    Yasunori Watanabe, Nobuo N. Noda, Kazuya Honbou, Kuninori Suzuki, Yasuyoshi Sakai, Yoshinori Ohsumi, Fuyuhiko Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 65, Pt 6, 571, 573, Jun. 2009, [Peer-reviewed]
    English, Scientific journal
  • Structural Basis for the Antiproliferative Activity of the Tob-hCaf1 Complex
    Masataka Horiuchi, Kosei Takeuchi, Nobuo Noda, Nobuyuki Muroya, Toru Suzuki, Takahisa Nakamura, Junko Kawamura-Tsuzuku, Kiyohiro Takahasi, Tadashi Yamamoto, Fuyuhiko Inagaki
    JOURNAL OF BIOLOGICAL CHEMISTRY, 284, 19, 13244, 13255, May 2009, [Peer-reviewed]
    English, Scientific journal
  • The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy
    Kenji Satoo, Nobuo N. Noda, Hiroyuki Kumeta, Yuko Fujioka, Noboru Mizushima, Yoshinori Ohsumi, Fuyuhiko Inagaki
    EMBO JOURNAL, 28, 9, 1341, 1350, May 2009, [Peer-reviewed]
    English, Scientific journal
  • ATG Systems from the Protein Structural Point of View
    Nobuo N. Noda, Yoshinori Ohsumi, Fuyuhiko Inagaki
    CHEMICAL REVIEWS, 109, 4, 1587, 1598, Apr. 2009, [Peer-reviewed]
    English
  • Structural basis of target recognition by Atg8/LC3 during selective autophagy
    Nobuo N. Noda, Hiroyuki Kumeta, Hitoshi Nakatogawa, Kenji Satoo, Wakana Adachi, Junko Ishii, Yuko Fujioka, Yoshinori Ohsumi, Fuyuhiko Inagaki
    GENES TO CELLS, 13, 12, 1211, 1218, Dec. 2008, [Peer-reviewed]
    English, Scientific journal
  • Crystallization of the coiled-coil domain of Atg16 essential for autophagy
    Yuko Fujioka, Nobuo N. Noda, Minako Matsushita, Yoshinori Ohsumi, Fuyuhiko Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 64, 1046, 1048, Nov. 2008, [Peer-reviewed]
    English, Scientific journal
  • Crystallization of the Atg12-Atg5 conjugate bound to Atg16 by the free-interface diffusion method
    Nobuo N. Noda, Yuko Fujioka, Yoshinori Ohsumi, Fuyuhiko Inagaki
    JOURNAL OF SYNCHROTRON RADIATION, 15, Pt 3, 266, 268, May 2008, [Peer-reviewed]
    English, Scientific journal
  • In vitro reconstitution of plant ATG8 and ATG12 conjugation systems essential for autophagy
    Yuko Fujioka, Nobuo N. Noda, Kiyonaga Fujii, Kohki Yoshimoto, Yoshinori Ohsumi, Fuyuhiko Inagaki
    JOURNAL OF BIOLOGICAL CHEMISTRY, 283, 4, 1921, 1928, Jan. 2008, [Peer-reviewed]
    English, Scientific journal
  • Crystallization and preliminary crystallographic analysis of the Tob-hCaf1 complex
    Kinya Nishida, Masataka Horiuchi, Nobuo N. Noda, Kiyohiro Takahasi, Norimasa Iwasaki, Akio Minami, Fuyuhiko Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 63, 1061, 1063, Dec. 2007, [Peer-reviewed]
    English, Scientific journal
  • The Atg12-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy
    Takao Hanada, Nobuo N. Noda, Yoshinori Satomi, Yoshinobu Ichimura, Yuko Fujioka, Toshifumi Takao, Fuyuhiko Inagaki, Yoshinori Ohsumi
    JOURNAL OF BIOLOGICAL CHEMISTRY, 282, 52, 37298, 37302, Dec. 2007, [Peer-reviewed]
    English, Scientific journal
  • Crystallization and preliminary X-ray analysis of Atg10
    Masaya Yamaguti, Nobuo N. Suzuki, Yuko Fujioka, Yoshinori Ohsumi, Fuyuhiko Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 63, 443, 445, May 2007, [Peer-reviewed]
    English, Scientific journal
  • Crystallization of Saccharomyces cerevisiae aminopeptidase 1, the major cargo protein of the Cvt pathway
    Wakana Adachi, Nobuo N. Suzuki, Yuko Fujioka, Kuninori Suzuki, Yoshinori Ohsumi, Fuyuhiko Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 63, 3, 200, 203, Mar. 2007
    English, Scientific journal
  • Structure of Atg5 center dot Atg16, a complex essential for autophagy
    Minako Matsushita, Nobuo N. Suzuki, Keisuke Obara, Yuko Fujioka, Yoshinori Ohsumi, Fuyuhiko Inagaki
    JOURNAL OF BIOLOGICAL CHEMISTRY, 282, 9, 6763, 6772, Mar. 2007, [Peer-reviewed]
    English, Scientific journal
  • The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation
    Yuya Yamada, Nobuo N. Suzuki, Takao Hanada, Yoshinobu Ichimura, Hiroyuki Kumeta, Yuko Fujioka, Yoshinori Ohsumi, Fuyuhiko Inagaki
    JOURNAL OF BIOLOGICAL CHEMISTRY, 282, 11, 8036, 8043, Mar. 2007, [Peer-reviewed]
    English, Scientific journal
  • Crystallization and preliminary crystallographic analysis of human Atg4B-LC3 complex
    Kenji Satoo, Nobuo N. Suzuki, Yuko Fujioka, Noboru Mizushima, Yoshinori Ohsumi, Fuyuhiko Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 63, 99, 102, Feb. 2007, [Peer-reviewed]
    English, Scientific journal
  • Full-length p40(phox) structure suggests a basis for regulation mechanism of its membrane binding
    Kazuya Honbou, Reiko Minakami, Satoru Yuzawa, Ryu Takeya, Nobuo N. Suzuki, Sachiko Kamakura, Hideki Sumimoto, Fuyuhiko Inagaki
    EMBO JOURNAL, 26, 4, 1176, 1186, Feb. 2007, [Peer-reviewed]
    English, Scientific journal
  • Expression, purification and crystallization of the Atg5-Atg16 complex essential for autophagy
    Minako Matsushita, Nobuo N. Suzuki, Yuko Fujioka, Yoshinori Ohsumi, Fuyuhiko Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 62, 1021, 1023, Oct. 2006, [Peer-reviewed]
    English, Scientific journal
  • Crystallization and preliminary X-ray analysis of Atg3
    Yuya Yamada, Nobuo N. Suzuki, Yuko Fujioka, Yoshinobu Ichimura, Yoshinori Ohsumi, Fuyuhiko Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 62, 1016, 1017, Oct. 2006, [Peer-reviewed]
    English, Scientific journal
  • Crystallization and preliminary crystallographic analysis of p40(phox), a regulatory subunit of NADPH oxidase
    Kazuya Honbou, Satoru Yuzawa, Nobuo N. Suzuki, Yuko Fujioka, Hideki Sumimoto, Fuyuhiko Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, 62, 1018, 1020, Oct. 2006, [Peer-reviewed]
    English, Scientific journal
  • Crystal structure of the human Atg4B-LC3 complex
    Kenji Sato, Nobuo N. Suzuki, Kenji Sugawara, Yuko Fujioka, Noboru Mizushima, Yoshinori Ohsumi, Fuyuhiko Inagaki
    AUTOPHAGY, 2, 4, 354, 354, Oct. 2006, [Peer-reviewed]
    English
  • Structural basis for the specificity and catalysis of human Atg4B responsible for mammalian autophagy
    K Sugawara, NN Suzuki, Y Fujioka, N Mizushima, Y Ohsumi, F Inagaki
    JOURNAL OF BIOLOGICAL CHEMISTRY, 280, 48, 40058, 40065, Dec. 2005, [Peer-reviewed]
    English, Scientific journal
  • Tor2 directly phosphorylates the AGC kinase Ypk2 to regulate actin polarization
    Y Kamada, Y Fujioka, NN Suzuki, F Inagaki, S Wullschleger, R Loewith, MN Hall, Y Ohsumi
    MOLECULAR AND CELLULAR BIOLOGY, 25, 16, 7239, 7248, Aug. 2005, [Peer-reviewed]
    English, Scientific journal
  • The crystal structure of plant ATG12 and its biological implication in autophagy
    NN Suzuki, K Yoshimoto, Y Fujioka, Y Ohsumi, F Inagaki
    AUTOPHAGY, 1, 2, 119, 126, Jul. 2005, [Peer-reviewed]
    English, Scientific journal
  • Structure of a cell polarity regulator, a complex between atypical PKC and Par6 PB1 domains
    Y Hirano, S Yoshinaga, R Takeya, NN Suzuki, M Horiuchi, M Kohjima, H Sumimoto, F Inagaki
    JOURNAL OF BIOLOGICAL CHEMISTRY, 280, 10, 9653, 9661, Mar. 2005, [Peer-reviewed]
    English, Scientific journal
  • Solution structure of the tandem src homology 3 domains of p47(phox) in an autoinhibited form
    S Yuzawa, K Ogura, M Horiuchi, NN Suzuki, Y Fujioka, M Kataoka, H Sumimoto, F Inagaki
    JOURNAL OF BIOLOGICAL CHEMISTRY, 279, 28, 29752, 29760, Jul. 2004, [Peer-reviewed]
    English, Scientific journal
  • The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8
    K Sugawara, NN Suzuki, Y Fujioka, N Mizushima, Y Ohsumi, F Inagaki
    GENES TO CELLS, 9, 7, 611, 618, Jul. 2004, [Peer-reviewed]
    English, Scientific journal
  • Binding of FAD to cytochrome b(558) is facilitated during activation of the phagocyte NADPH oxidase, leading to superoxide production
    S Hashida, S Yuzawa, NN Suzuki, Y Fujioka, T Takikawa, H Sumimoto, F Inagaki, H Fujii
    JOURNAL OF BIOLOGICAL CHEMISTRY, 279, 25, 26378, 26386, Jun. 2004, [Peer-reviewed]
    English, Scientific journal
  • A molecular mechanism for autoinhibition of the tandem SH3 domains of p47(phox), the regulatory subunit of the phagocyte NADPH oxidase
    S Yuzawa, NN Suzuki, Y Fujioka, K Ogura, H Sumimoto, F Inagaki
    GENES TO CELLS, 9, 5, 443, 456, May 2004, [Peer-reviewed]
    English, Scientific journal
  • Structural basis for the specificity, catalysis, and regulation of human uridine-cytidine kinase
    NN Suzuki, K Koizumi, M Fukushima, A Matsuda, F Inagaki
    STRUCTURE, 12, 5, 751, 764, May 2004, [Peer-reviewed]
    English, Scientific journal
  • X-ray crystal structure of IRF-3 and its functional implications
    K Takahasi, NN Suzuki, M Horiuchi, M Mori, W Suhara, Y Okabe, Y Fukuhara, H Terasawa, S Akira, T Fujita, F Inagaki
    NATURE STRUCTURAL BIOLOGY, 10, 11, 922, 927, Nov. 2003, [Peer-reviewed]
    English, Scientific journal
  • Crystallization and preliminary X-ray analysis of human uridine-cytidine kinase 2
    NN Suzuki, K Koizumi, M Fukushima, A Matsuda, F Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 59, 1477, 1478, Aug. 2003, [Peer-reviewed]
    English, Scientific journal
  • Crystallization and preliminary X-ray analysis of LC3-I
    K Sugawara, NN Suzuki, Y Fujioka, N Mizushima, Y Ohsumi, F Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 59, 1464, 1465, Aug. 2003, [Peer-reviewed]
    English, Scientific journal
  • Crystallization and preliminary crystallographic analysis of the autoinhibited form of the tandem SH3 domain of p47(phox)
    S Yuzawa, NN Suzuki, Y Fujioka, K Ogura, H Sumimoto, F Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 59, 1479, 1480, Aug. 2003, [Peer-reviewed]
    English, Scientific journal
  • Crystallization and preliminary crystallographic analysis of DJ-1, a protein associated with male fertility and parkinsonism
    K Honbou, NN Suzuki, M Horiuchi, T Taira, T Niki, H Ariga, F Inagaki
    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 59, 1502, 1503, Aug. 2003, [Peer-reviewed]
    English, Scientific journal
  • The crystal structure of DJ-1, a protein related to male fertility and bParkinson's disease
    K Honbou, NN Suzuki, M Horiuchi, T Niki, T Taira, H Ariga, F Inagaki
    JOURNAL OF BIOLOGICAL CHEMISTRY, 278, 33, 31380, 31384, Aug. 2003, [Peer-reviewed]
    English, Scientific journal

Other Activities and Achievements

Lectures, oral presentations, etc.

  • Protein phase separation in autophagy regulation.　　　　　　　　　　　　　　　
    Nobuo N. Noda
    World Life Science Conference 2024, 20 Oct. 2024, English, Invited oral presentation
    [Invited]
  • In vitro reconstitution of autophagosome formation.　　　　　　　　　　　　　　　
    Nobuo N. Noda
    Gordon Research Conference: Autophagy in Stress, Development and Disease, Molecular Mechanisms and Physiology, 13 Mar. 2024, English, Invited oral presentation
    [Invited]
  • Molecular mechanisms of autophagy.　　　　　　　　　　　　　　　
    Nobuo N. Noda
    BCSIR Congress-2023, 08 Mar. 2024, English, Keynote oral presentation
    [Invited]
  • Autophagosomal membrane shaping by autophagy-related proteins.　　　　　　　　　　　　　　　
    Nobuo N. Noda
    5th EMBO COB Workshop on Membrane Shaping and Remodeling by Proteins, 11 Nov. 2023, English, Invited oral presentation
    [Invited]
  • オートファゴソーム新生の分子機構　　　　　　　　　　　　　　　
    野田展生
    令和4 年度「感染・免疫・がん・炎症」全国共同研究拠点シンポジウム, 29 Mar. 2023, Japanese
    [Invited]
  • オートファゴソーム膜の伸展・成形機構　　　　　　　　　　　　　　　
    野田展生
    タンパク質研究シンポジウム～タンパク質研究はいま新たなステージに入ろうとしている！～, 12 Dec. 2022, Japanese
    [Invited]
  • Molecular mechanisms underlying autophagosome biogenesis　　　　　　　　　　　　　　　
    Nobuo N. Noda
    The 17th International Symposium of the Institute Network for Biomedical Sciences, 13 Oct. 2022, English, Invited oral presentation
    [Invited]
  • Mechanisms of autophagy initiation by liquid-liquid phase separation　　　　　　　　　　　　　　　
    Nobuo N. Noda
    3rd Frankfurt Conference on Quality Control in Life Processes, 06 Oct. 2022, English, Invited oral presentation
    [Invited]
  • 液－液相分離によるオートファジー制御機構の解明　　　　　　　　　　　　　　　
    野田展生
    第１回生理学研究所—遺伝子病制御研究所連携シンポジウム, 12 Aug. 2022, Japanese
    [Invited]
  • Membrane dynamics regulated by autophagy-related proteins　　　　　　　　　　　　　　　
    Nobuo N. Noda
    FASEB The Protein Folding in the Cell Conference, 13 Jul. 2022, English
    [Invited]
  • 液－液相分離によるオートファジー制御　　　　　　　　　　　　　　　
    野田展生
    第59回 日本生化学会北海道支部例会, 09 Jul. 2022, Japanese
    [Invited]
  • 蛍光イメージングを駆使したオートファジー膜動態と液－液相分離研究　　　　　　　　　　　　　　　
    野田展生
    第74回 日本細胞生物学会大会, 29 Jun. 2022, Japanese
    [Invited]
  • Regulation of autophagic membrane dynamics by Atg8 lipidation system　　　　　　　　　　　　　　　
    Tatsuro Maruyama, Alam Md. Jahangir, Nobuo N. Noda
    Ubiquitin & Friends Symposium 2022, 29 Apr. 2022, English
    [Invited]

Affiliated academic society

  • THE PHARMACEUTICAL SOCIETY OF JAPAN　　　　　　　　　　　　　　　
  • THE MOLECULAR BIOLOGY SOCIETY OF JAPAN　　　　　　　　　　　　　　　
  • THE JAPANESE BIOCHEMICAL SOCIETY　　　　　　　　　　　　　　　
  • 日本癌学会　　　　　　　　　　　　　　　

Research Themes

  • Autophagy expanded: decoding membrane interface biology
    Grants-in-Aid for Scientific Research
    01 Apr. 2025 - 31 Mar. 2030
    野田 展生
    Japan Society for the Promotion of Science, Grant-in-Aid for Transformative Research Areas (A), 25A303
  • オートファジーから拡がる膜界面生物学
    科学研究費助成事業
    01 Apr. 2025 - 31 Mar. 2030
    野田 展生
    日本学術振興会, 学術変革領域研究(A), 北海道大学, 25H01320
  • 膜界面の分子協奏から迫るオートファジーの作動原理
    科学研究費助成事業
    01 Apr. 2025 - 31 Mar. 2030
    野田 展生
    日本学術振興会, 学術変革領域研究(A), 北海道大学, 25H01321
  • Interdisciplinary research on autophagy: From working principles to pathophysiology
    Grants-in-Aid for Scientific Research
    17 Nov. 2023 - 31 Mar. 2030
    小松 雅明, 笹澤 有紀子, 野田 展生, 中戸川 仁, 綿田 裕孝, 安藤 美樹, 服部 信孝, 洲崎 悦生, 日置 寛之
    Japan Society for the Promotion of Science, Fund for the Promotion of Joint International Research (International Leading Research ), Juntendo University, 23K20044
  • A study on stress responses by co-creation of liquid-liquid phase separation and autophagy
    Grants-in-Aid for Scientific Research
    Apr. 2024 - Mar. 2029
    小松 雅明, 野田 展生, 和栗 聡, 森下 英晃, 三浦 芳樹
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (S), Juntendo University, 24H00060
  • 多次元相分離が駆動するマイトファジーの分子機構
    科学研究費助成事業
    01 Apr. 2025 - 31 Mar. 2028
    野田 展生
    日本学術振興会, 基盤研究(A), 北海道大学, 25H00966
  • オートファジーを標的とする膵がんの新規治療法の開発
    科学研究費助成事業
    01 Apr. 2023 - 31 Mar. 2026
    大塩 貴子, 園下 将大, 野田 展生
    日本学術振興会, 基盤研究(C), 北海道大学, 23K06667
  • 液－液相分離による「ねむり」制御の分子基盤の解明
    科学研究費助成事業
    01 Apr. 2022 - 31 Mar. 2025
    野田 展生, 戸田 浩史
    日本学術振興会, 基盤研究(A), 北海道大学, 22H00411
  • Studies on the regulatory mechanism of aggresome formatiion and clearance
    Grants-in-Aid for Scientific Research
    01 Apr. 2021 - 31 Mar. 2024
    井本 正哉, 斉木 臣二, 野田 展生
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Juntendo University, 21H02072
  • オートファジーシステムの構造学的解明
    科学研究費助成事業
    28 Jun. 2019 - 31 Mar. 2024
    野田 展生, 福田 善之
    脂質化Atg8は隔離膜に強く結合し、効率的なオートファゴソーム形成において重要な役割を担う。昨年度NMR法を用いることで同定した、膜との相互作用に関わるAtg8内の２つのフェニルアラニンについて変異体解析を行った結果、これらはin vitroにおいて巨大リポソーム膜の変形に重要な役割を担うこと、膜変形は脂質二重層の２つの層の間で面積差が生じることで引き起こされることを見出した。そしてこれらの残基は酵母および哺乳類における効率的なオートファジーに重要であることを明らかにし、Atg8が持つ膜摂動活性がオートファゴソーム形成に重要な役割を担うという新しいモデルを提唱した（Maruyama et al., Nat Struct Mol Biol 2021）。
    これまでの研究で我々はAtg2が脂質輸送活性を持つこと、N末端領域に脂質を結合する疎水性ポケットを持つことを明らかにしてきたが、最近公開されたAtg2全長のAlphaFold2予測構造に基づき変異体解析を行なった結果、分子全体にわたって存在する疎水性ポアがAtg2の脂質輸送活性および酵母におけるオートファゴソーム形成に重要であることを明らかにした。
    オートファゴソーム形成機構を理解するためには、実際にオートファジーが進行している細胞における膜形態を詳細に明らかにすることが重要である。ラパマイシン処理したAtg8-ｍNeonGreen発現酵母株を急速凍結したものを試料として、cryo-CLEMによる観察対象の局在の可視化、cryo-FIBで細胞のラメラ（薄片）作製を行った。cryo-TEMでラメラを観察したところ、一般的に知られている形状の隔離膜だけでなく、多層の膜構造を有する隔離膜と思われる構造が観察された。
    日本学術振興会, 新学術領域研究(研究領域提案型), 19H05707
  • Elucidation of the function of the pre-autophagosomal structure through in vitro reconstitution
    Grants-in-Aid for Scientific Research
    01 Apr. 2018 - 31 Mar. 2021
    Noda Nobuo
    Despite the importance in autophagy, the entity of the PAS has been a long-standing mystery. We showed that the PAS behaves as a liquid droplet with high fluidity in budding yeast. In vitro experiments using purified proteins revealed that the Atg1 complex can undergo liquid-liquid phase separation to form a liquid droplet. Mutations inhibiting phase separation of the Atg1 complex impaired PAS formation in vivo, suggesting that the entity of the PAS is a liquid droplet formed by phase separation of the Atg1 complex. Further in vitro analyses revealed that phospho-regulation of Atg13 by TORC1 and Ptc2 regulate the phase separation of the Atg1 complex, thereby regulating the PAS formation. Finally, using synthetic liposomes and protein droplets, we reconstituted the PAS attached to the vacuole in vitro. These data suggest that the PAS is a liquid droplet formed on the vacuole, which will function as a place for autophagosome formation by concentrating various Atg proteins and membranes.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), Microbial Chemistry Research Foundation, 18H03989
  • Chemical Biology for Parkinson's disease
    Grants-in-Aid for Scientific Research
    01 Apr. 2018 - 31 Mar. 2021
    Imoto Masaya
    We have conducted mechanism studies of three Parkinson’s disease (PD) drug-seeds, which were obtained by the screening for metabolome analysis of PD and for clearance of protein aggregation seen in the brain of PD patients. We found that they function by targeting inhibition of Keap1-Nrf2 binding, activation of PLC -mediated TFEB transcription activity, and stimulation of liquid-liquid phase separation of target protein, respectively, thereby showing neuro-protection in PD-model neuronal cells.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), 18H02099
  • International Activities Support for Autophagy Research
    Grants-in-Aid for Scientific Research
    06 Nov. 2015 - 31 Mar. 2018
    Mizushima Noboru
    This Grant-in-Aid for Scientific Research on Innovative Areas was established to promote multidisciplinary research on autophagy by coordinating in vitro reconstitution biology, structural biology, cell biology, genetics of model organisms, and human pathophysiology. This "International Activities Supporting Group" set up Researcher Exchange Program Committee and Collaboration Promoting Committee. Aiming to promote bilateral joint research or international collaboration, our focus was on placing Japanese researchers overseas and on inviting or employing foreign researchers
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), The University of Tokyo, 15K21749
  • Structural basis of Atg proteins responsible for autophagy
    Grants-in-Aid for Scientific Research
    28 Jun. 2013 - 31 Mar. 2018
    NODA Nobuo
    We have determined the crystal structures of the autophagy-initiating Atg1 complex and Atg101, the worm homologs of Atg8 that mediate autophagosome formation and cargo recognition, as well as the selective cargo Ape1 and its adaptor Atg19. By functional analyses based on the structural information, we have revealed the molecular mechanisms of autophagy initiation upon starvation, different functions mediated by Atg8 homologs, and selective recognition of protein aggregates during selective autophagy.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Microbial Chemistry Research Foundation, 25111004
  • Multidisciplinary research on autophagy: from molecular mechanisms to disease states
    Grants-in-Aid for Scientific Research
    28 Jun. 2013 - 31 Mar. 2018
    Mizushima Noboru, IWAI Kazuhiro, UCHIYAMA Yasuo, OHSUMI Yoshinori, OHNO Hiroshi, KOMINAMI Eiki, TANAKA Keiji, SATO Shigeto, SUGAWARA Hideaki
    This Grant-in-Aid for Scientific Research on Innovative Areas was established to promote multidisciplinary research on autophagy by coordinating in vitro reconstitution biology, structural biology, cell biology, genetics of model organisms, and human pathophysiology. This "Administrative Group" multilaterally supported and coordinated our studies in this Innovative Area; supporting our annual meetings and international symposium. On our website, we opened the Autophagy Forum, which is a discussion forum for our research outcomes. Autophagy protocols have also become available on the website.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), The University of Tokyo, 25111001
  • 天然変性タンパク質Ａｔｇ１３によるオートファジー始動の制御機構
    科学研究費助成事業
    01 Apr. 2012 - 31 Mar. 2014
    野田 展生
    天然変性タンパク質Atg13は、飢餓時速やかに脱リン酸化され、Atg1およびAtg17と結合することでAtg1複合体を形成し、オートファジーの始動を引き起こす。しかしAtg13がその天然変性領域を用いてどのように他のAtg因子と相互作用するのか、リン酸化によるそれら相互作用の制御はどのように行われているのか等、分子機構の詳細ほほとんどわかっていなかった。
    昨年度、Atg1-Atg13複合体の構造決定に成功したが、本年度はAtg13-Atg17複合体の結晶構造解析を行った。その結果、Atg13は天然変性領域内の短い領域二ヶ所を用いて、Atg17のN末端付近とC末端付近の互いに遠く離れた２つの酸性ポケットに結合することが明らかとなった。In vitro、in vivo両面での機能解析の結果、Atg13の２つのAtg17結合領域内に含まれるセリン残基のリン酸化により、Atg17との結合が直接負に制御されることを示した。リン酸化によりAtg13に導入される負電荷が、Atg17の酸性ポケットの負電荷と反発することで結合が減弱されると考えられる。さらにLC-MS/MSおよびリン酸化抗体を用いた解析により、これら結合を負に制御するリン酸化セリンが飢餓により脱リン酸化されることを明らかにした。すなわち飢餓によりAtg13の天然変性領域内の特定のセリン残基が脱リン酸化されると、Atg1およびAtg17両方への高い親和性を獲得し、その結果Atg1複合体の形成およびオートファジーの始動が起きることが明らかとなった。
    日本学術振興会, 新学術領域研究(研究領域提案型), 公益財団法人微生物化学研究会, 24113725
  • Prediction and screening of selective autophagy cargo in Saccharomyces cerevisiae
    Grants-in-Aid for Scientific Research
    01 Apr. 2012 - 31 Mar. 2014
    SUZUKI Kuninori, NODA Nobuo
    Macroautophagy (autophagy) is a bulk protein-degradation system ubiquitously conserved in eukaryotic cells. During autophagy, cytoplasmic components are enclosed in a membrane compartment, called an autophagosome. In this study, we developed a method for monitoring intact autophagosomes ex vivo by detecting the fluorescence of GFP-fused aminopeptidase I, the best-characterized selective cargo of autophagosomes in Saccharomyces cerevisiae. A combination of LC-MS/MS with subsequent statistical analyses revealed a list of autophagosome cargo proteins. The methods we describe will be useful for analyzing the mechanisms and physiological significance of Atg11-independent selective autophagy.
    Japan Society for the Promotion of Science, Grant-in-Aid for Challenging Exploratory Research, The University of Tokyo, 24657083
  • Structural basis of the autophagy-specific E1 enzyme Atg7
    Grants-in-Aid for Scientific Research
    01 Apr. 2011 - 31 Mar. 2014
    NODA Nobuo
    The crystal structure of Atg7, the E1 enzyme specific to autophagy, has been determined alone and in complex with various Atg factors. Using the structural information, mutational analyses were performed, which revealed that Atg7 recognizes ubiquitin-like proteins and E2 enzymes using unique structures that were not observed in other E1 enzymes and that Atg7 catalyzes the conjugation reaction between ubiquitin-like proteins and E2 enzymes using a novel mechanism that has never been observed in other E1 enzymes. Since the reactions catalyzed by Atg7 are essential only to autophagy, the obtained knowledge will contribute to the development of novel compounds that specifically regulate autophagy.
    Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (A), Microbial Chemistry Research Foundation, 23687012
  • Structural analysis of the intracellular proteolytic system
    Grants-in-Aid for Scientific Research
    2006 - 2010
    TOCHIO Hidehito, KURIMOTO Eiji, NODA Nobuo, YAMAGUCHI Yoshiki
    Structural studies of proteins and protein complexes related to the ubiquitin-proteasome system and autophagy were conducted using X-ray crystallography, NMR and small-angle neutron scattering techniques. The details of the ubiquitin interaction mode of ubiquitin receptors,the working mechanism of E2 (UbcH5b) and the activation mechanism of SCF E3 by NEDD8 were revealed. We also determined the structures of deconjugating enzyme Atg4B bound to LC3, E1-like enzyme Atg7, Atg12-Atg5 conjugate, and Atg8-Atg19 and LC3-p62 complexes, clarifying the molecular mechanisms of reversible Atg8 lipidation and autophagic receptor recognition byAtg8/LC3.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Priority Areas, Kyoto University, 18076003
  • Structural Biology of Innate Immunity
    Grants-in-Aid for Scientific Research
    2005 - 2009
    INAGAKI Fuyuhiko, NODA Nobuo, OGURA Kenji, HORIUCHI Masataka
    (1)We elucidated the molecular mechanism for tethering p^<47> and p^<40> to cyt b558 or membrane on the structural basis.
    (2)We found that IRF-3 is phosphorylated by IKKi at Ser386 and form a homodimer to bind CBP/p300in vitro and produces type Iinterferons.
    (3)RIG-I like receptor family proteins (RLR) play essential roles to recognize double stranded RNA (dsRNA) in cytosol. We found that the C terminal domain of RLR recognizes viral specific dsRNA. Wedetermined the structure of C-terminal domain of RLR and discussed the specific interaction with viral specific dsRNA.
    (4)dsRNA and LPS bind to TLR3 and TLR4, respectively to activate downstream signaling to producetype 1 interferons. Here, we determined the structure of TIR domains of TRIF and TRAM andelucidated their oligomerization process which is essential for down stream signaling.
    (5)We elucidated the recognition mechanism of β1-3 glucan by βGRP from Bombyx Mori.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (S), Hokkaido University, 17109002