2024

• Kurikawa Y, Koyama-Honda I, Tamura N, Koike S, Mizushima N. Organelle landscape analysis using a multiparametric particle-based method. PLoS biology. Sep;22(9):e3002777. (2024)
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• Shinoda S, Sakai Y, Matsui T, Uematsu M, Koyama-Honda I, Sakamaki JI, Yamamoto H, Mizushima N. Syntaxin 17 recruitment to mature autophagosomes is temporally regulated by PI4P accumulation. eLife Jun;12. (2024)
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• Yamashita SI, Sugiura Y, Matsuoka Y, Maeda R, Inoue K, Furukawa K, Fukuda T, Chan DC, Kanki T. Mitophagy mediated by BNIP3 and NIX protects against ferroptosis by downregulating mitochondrial reactive oxygen species. Cell death and differentiation. May;31(5):651-661. (2024)
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• Furukawa K, Hayatsu M, Okuyama K, Fukuda T, Yamashita SI, Inoue K, Shibata S, Kanki T. Atg44/Mdi1/mitofissin facilitates Dnm1-mediated mitochondrial fission. Autophagy. Jun;1-9. (2024)
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• Shinozaki D, Takayama E, Kawakami N, Yoshimoto K. Autophagy maintains endosperm quality during seed storage to preserve germination ability in Arabidopsis. Proc. Natl. Acad. Sci. USA. Apr;121(14):e2321612121. (2024)
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• Sasaki T, Kushida Y, Norizuki T, Kosako H, Sato K, Sato M. ALLO-1- and IKKE-1-dependent positive feedback mechanism promotes the initiation of paternal mitochondrial autophagy. Nat Commun. Feb;15(1):1460. (2024)
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• Fujiwara Y, Oroku K, Zhou Y, Takahashi M, Katayama T, Wada K, Tsutsumi N, Sato T, Kabuta T. Expression of RNautophagy/DNautophagy-related genes is regulated under control of an innate immune receptor. RNA biology. Jan;21(1):1-9. (2024)
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• Kawasaki I, Sugiura K, Sasaki T, Matsuda N, Sato M, Sato K. MARC-3, a membrane-associated ubiquitin ligase, is required for fast polyspermy block in Caenorhabditis elegans. Nat Commun. Jan;15(1):91. (2024)
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• Eguchi T, Sakurai M, Wang Y, Saito C, Yoshii G, Wileman T, Mizushima N, Kuwahara T, Iwatsubo T. The V-ATPase-ATG16L1 axis recruits LRRK2 to facilitate the lysosomal stress response. J Cell Biol. Mar;223(3):. (2024)
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• Sakai Y, Takahashi S, Koyama-Honda I, Saito C, Mizushima N. Experimental determination and mathematical modeling of standard shapes of forming autophagosomes. Nat Commun. Jan;15(1):792. (2024)
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2023

• Komatsu M, Inada T, Noda NN. The UFM1 system: Working principles, cellular functions, and pathophysiology. Mol. Cell. Dec;. (2023)
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• Ogura M, Kaminishi T, Shima T, Torigata M, Bekku N, Tabata K, Minami S, Nishino K, Nezu A, Hamasaki M, Kosako H, Yoshimori T, Nakamura S. Microautophagy regulated by STK38 and GABARAPs is essential to repair lysosomes and prevent aging. EMBO reports. Dec;24(12):e57300. (2023)
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• Alam JM, Maruyama T, Noshiro D, Kakuta C, Kotani T, Nakatogawa H, Noda NN. Complete set of the Atg8-E1-E2-E3 conjugation machinery forms an interaction web that mediates membrane shaping. Nat Struct Mol Biol. Dec;. (2023)
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• Kagohashi Y, Sasaki M, May AI, Kawamata T, Ohsumi Y. The mechanism of Atg15-mediated membrane disruption in autophagy. J Cell Biol. Dec;222(12):. (2023)
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• Shioda T, Takahashi I, Ikenaka K, Fujita N, Kanki T, Oka T, Mochizuki H, Antebi A, Yoshimori T, Nakamura S. Neuronal MML-1/MXL-2 regulates systemic aging via glutamate transporter and cell nonautonomous autophagic and peroxidase activity. Proc. Natl. Acad. Sci. USA. Sep;120(39):e2221553120. (2023)
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• Kotani T, Sakai Y, Kirisako H, Kakuta C, Kakuta S, Ohsumi Y, Nakatogawa. A mechanism that ensures non-selective cytoplasm degradation by autophagy. Nat Commun. Sep;14(1):5815. (2023)
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• Ishimura R, Ito S, Mao G, Komatsu-Hirota S, Inada T, Noda NN, Komatsu M. Mechanistic insights into the roles of the UFM1 E3 ligase complex in ufmylation and ribosome-associated protein quality control. Sci. Adv. Aug;9(33):eadh3635. (2023)
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• Ikeda R, Noshiro D, Morishita H, Takada S, Kageyama S, Fujioka Y, Funakoshi T, Komatsu-Hirota S, Arai R, Ryzhii E, Abe M, Koga T, Motohashi H, Nakao M, Sakimura K, Horii A, Waguri S, Ichimura Y, Noda NN, Komatsu M. Phosphorylation of phase-separated p62 bodies by ULK1 activates a redox-independent stress response. EMBO j. Jun;e113349. (2023)
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• Fukuda T, Furukawa K, Maruyama T, Yamashita SI, Noshiro D, Song C, Ogasawara Y, Okuyama K, Alam JM, Hayatsu M, Saigusa T, Inoue K, Ikeda K, Takai A, Chen L, Lahiri V, Okada Y, Shibata S, Murata K, Klionsky DJ, Noda NN, Kanki T. The mitochondrial intermembrane space protein mitofissin drives mitochondrial fission required for mitophagy. Mol. Cell. May;. (2023)
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• Kurusu R, Fujimoto Y, Morishita H, Noshiro D, Takada S, Yamano K, Tanaka H, Arai R, Kageyama S, Funakoshi T, Komatsu-Hirota S, Taka H, Kazuno S, Miura Y, Koike M, Wakai T, Waguri S, Noda NN, Komatsu M. Integrated proteomics identifies p62-dependent selective autophagy of the supramolecular vault complex. Dev. Cell. May;. (2023)
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• Ishii S, Chino H, Ode KL, Kurikawa Y, Ueda HR, Matsuura A, Mizushima N, Itakura E. CCPG1 recognizes endoplasmic reticulum luminal proteins for selective ER-phagy. Mol. Biol. Cell. Apr;34(4):ar29. (2023)
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• Contu VR, Sakai R, Fujiwara Y, Kabuta C, Wada K, Kabuta T. Nucleic acid uptake occurs independent of lysosomal acidification but dependent on ATP consumption during RNautophagy/DNautophagy. BBRC. Feb;644105-111. (2023)
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• Onishi M, Kubota M, Duan L, Tian Y, Okamoto K. The GET pathway serves to activate Atg32-mediated mitophagy by ER targeting of the Ppg1-Far complex. Life science alliance. Apr;6(4):. (2023)
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2022

• Ishimura R, El-Gowily AH, Noshiro D, Komatsu-Hirota S, Ono Y, Shindo M, Hatta T, Abe M, Uemura T, Lee-Okada HC, Mohamed TM, Yokomizo T, Ueno T, Sakimura K, Natsume T, Sorimachi H, Inada T, Waguri S, Noda NN, Komatsu M. The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3. Nat Commun. Dec;13(1):7857. (2022)
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• Suzuki C, Yamaguchi J, Sanada T, Oliva Trejo JA, Kakuta S, Shibata M, Tanida I, Uchiyama Y. Lack of Cathepsin D in the central nervous system results in microglia and astrocyte activation and the accumulation of proteinopathy-related proteins. Sci. Rep. Jul;12(1):11662. (2022)
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• Fujiwara Y, Kabuta C, Sano T, Murayama S, Saito Y, Kabuta T. Pathology-associated change in levels and localization of SIDT2 in postmortem brains of Parkinson's disease and dementia with Lewy bodies patients. Neurochem. Int. Jan;152105243. (2022)
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• Sasazawa Y, Souma S, Furuya N, Miura Y, Kazuno S, Kakuta S, Suzuki A, Hashimoto R, Hirawake-Mogi H, Date Y, Imoto M, Ueno T, Kataura T, Korolchuk VI, Tsunemi T, Hattori N, Saiki S. Oxidative stress-induced phosphorylation of JIP4 regulates lysosomal positioning in coordination with TRPML1 and ALG2. EMBO J. Nov;41(22):e111476. (2022)
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• Sanada T, Yamaguchi J, Furuta Y, Kakuta S, Tanida I, Uchiyama Y. In-resin CLEM of Epon-embedded cells using proximity labeling. Sci. Rep. 07;12(1):11130. (2022)
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• Kawamata T, Makino S, Kagohashi Y, Sasaki M, Ohsumi Y. A method for the isolation and characterization of autophagic bodies from yeast provides a key tool to investigate cargos of autophagy. J. Biol. Chem. Oct;102641. (2022)
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• Suzuki K, Hirata E. Liquid droplet formation and cytoplasm to vacuole targeting of aminopeptidase I are temperature sensitive in Saccharomyces cerevisiae. FEBS letters. Oct;. (2022)
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• Cui J, Ogasawara Y, Kurata I, Matoba K, Fujioka Y, Noda NN, Shibasaki M, Watanabe T. Targeting the ATG5-ATG16L1 Protein-Protein Interaction with a Hydrocarbon-Stapled Peptide Derived from ATG16L1 for Autophagy Inhibition. J. Am. Chem. Soc. Sep;. (2022)
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• Goh T, Sakamoto K, Wang P, Kozono S, Ueno K, Miyashima S, Toyokura K, Fukaki H, Kang BH, Nakajima K. Autophagy promotes organelle clearance and organized cell separation of living root cap cells in Arabidopsis thaliana. Development. Jun 15;149(11):dev200593. (2022)
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• Chino H, Yamasaki A, Ode KL, Ueda HR, Noda NN, Mizushima N. Phosphorylation by casein kinase 2 enhances the interaction between ER-phagy receptor TEX264 and ATG8 proteins. EMBO reports. Apr;e54801. (2022)
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• Yoshitake Y, Shinozaki D, Yoshimoto K. Autophagy triggered by iron mediated ER stress is an important stress response to the early phase of Pi starvation in plants. Plant J. 110(5):1370-1381. (2022)
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• Murakawa T, Nakamura T, Kawaguchi K, Murayama F, Zhao N, Stasevich TJ, Kimura H, Fujita N. A Drosophila toolkit for HA-tagged proteins unveils a block in autophagy flux in the last instar larval fat body. Development. Mar 15;149(6). (2022)
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• Yamamuro T, Nakamura S, Yanagawa K, Tokumura A, Kawabata T, Fukuhara A, Teranishi H, Hamasaki M, Shimomura I, Yoshimori T. Loss of RUBCN/rubicon in adipocytes mediates the upregulation of autophagy to promote the fasting response. Autophagy. Mar;1-11. (2022)
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• Mochida K, Otani T, Katsumata Y, Kirisako H, Kakuta C, Kotani T, Nakatogawa H. Atg39 links and deforms the outer and inner nuclear membranes in selective autophagy of the nucleus. J Cell Biol. Feb 7;221(2):e202103178 (2022)
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2021

• Sakai SS, Hasegawa A, Ishimura R, Tamura N, Kageyama S, Komatsu-Hirota S, Abe M, Ling Y, Okuda S, Funayama M, Kikkawa M, Miura Y, Sakimura K, Narita I, Waguri S, Shimizu R, Komatsu M. Loss of and impairs the maintenance of the hematopoietic stem cell pool size. Mol Cell Biol. Nov 8;MCB0002421 (2021)
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• Faruk MO, Ichimura Y, Kageyama S, Komatsu-Hirota S, El-Gowily AH, Sou YS, Koike M, Noda NN, Komatsu M. Phase-separated protein droplets of amyotrophic lateral sclerosis-associated p62/SQSTM1 mutants show reduced inner fluidity. J Biol Chem. Nov 11;101405. (2021)
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• Tanigawa M, Yamamoto K, Nagatoishi S, Nagata K, Noshiro D, Noda NN, Tsumoto K, Maeda. A glutamine sensor that directly activates TORC1. Commun. Biol. 09;4(1):1093. (2021)
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• Shi SL, Fukuda H, Chujo T, Kouwaki T, Oshiumi H, Tomizawa K, Wei FY. Export of RNA-derived modified nucleosides by equilibrative nucleoside transporters defines the magnitude of autophagy response and Zika virus replication. RNA Biol. Aug;1-18. (2021)
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• Nagai A, Mori K, Shiomi Y, Yoshihisa T. OTTER, a new method quantifying absolute amounts of tRNAs. RNA (New York, N.Y.) Mar 5;27(5):628-640 (2021)
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• Shinozaki D, Yoshimoto K. Autophagy balances the zinc-iron seesaw caused by Zn-stress. Trends Plant Sci. Sep;26(9):882-884. (2021)
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• Yamamuro T, Nakamura S, Yamano Y, Endo T, Yanagawa K, Tokumura A, Matsumura T, Kobayashi K, Mori H, Enokidani Y, Yoshida G, Imoto H, Kawabata T, Hamasaki M, Kuma A, Kuribayashi S, Takezawa K, Okada Y, Ozawa M, Fukuhara S, Shinohara T, Ikawa M, Yoshimori T. Rubicon prevents autophagic degradation of GATA4 to promote Sertoli cell function. PLoS genetics. Aug;17(8):e1009688. (2021)
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• Maruyama T, Alam JM, Fukuda T, Kageyama S, Kirisako H, Ishii Y, Shimada I, Ohsumi Y, Komatsu M, Kanki T, Nakatogawa H, Noda NN. Membrane perturbation by lipidated Atg8 underlies autophagosome biogenesis. Nat Struct Mol Biol. Jul 8. (2021)
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• Tanida I, Haruta T, Suga M, Takei S, Takebe A, Furuta Y, Yamaguchi J, Trejo JAO, Kakuta S, Uchiyama Y. Membranous Structures Directly Come in Contact With p62/SQSTM1 Bodies. J Histochem Cytochem. 69(6):407-414. (2021)
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• Tanida I, Furuta Y, Yamaguchi J, Kakuta S, Trejo JAO, Uchiyama Y. Two-color in-resin CLEM of Epon-embedded cells using osmium resistant green and red fluorescent proteins. Sci Rep. 10(1):21871. (2021)
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• Tanida I, Kakuta S, Trejo JAO, Uchiyama Y. Visualization of cytoplasmic organelles via in-resin CLEM using an osmium-resistant far-red protein. Sci Rep. 10(1):11314. (2021)
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• Trejo JAO, Tanida I, Suzuki C, Kakuta S, Tada N, Uchiyama Y. Characterization of starvation-induced autophagy in cerebellar Purkinje cells of pHluorin-mKate2-human LC3B transgenic mice. Sci Rep. 10(1):9643. (2021)
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• Makino S, Kawamata T, Iwasaki S, Ohsumi Y. Selectivity of mRNA degradation by autophagy in yeast. Nat Commun. 12(1):2316. (2021)
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• Ogawa A, Nagiri C, Shihoya W, Inoue A, Kawakami K, Hiratsuka S, Aoki J, Ito Y, Suzuki T, Suzuki T, Inoue T, Nureki O, Tanihara H, Tomizawa K, Wei F-Y. N 6-methyladenosine (m 6 A) is an endogenous A3 adenosine receptor ligand. Mol Cell. 81(4):659-674.e7. (2021)
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• Ohsawa S, Inoue K, Isoda T, Oku M, Yurimoto H, Sakai Y. The methanol sensor Wsc1 and MAPK Mpk1 suppress degradation of methanol-induced peroxisomes in methylotrophic yeast. J Cell Sci. 134(9):jcs254714. (2021)
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• Hirata E, Shirai K, Kawaoka T, Sato K, Kodama F, Suzuki K. Atg15 in Saccharomyces cerevisiae consists of two functionally distinct domains. Mol Biol Cell. 32(8):645-663. (2021)
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• Kira S, Noguchi M, Araki Y, Oikawa Y, Yoshimori T, Miyahara A, Noda T. Vacuolar protein Tag1 and Atg1-Atg13 regulate autophagy termination during persistent starvation in S. cerevisiae. J Cell Sci. 134(4):jcs253682. (2021)
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• Kageyama S, Gudmundsson SR, Sou YS, Ichimura Y, Tamura N, Kazuno S, Ueno T, Miura Y, Noshiro D, Abe M, Mizushima T, Miura N, Okuda S, Motohashi H, Lee J-A , Sakimura K, Ohe T, Noda NN, Waguri S, Eskelinen E-L, Komatsu M. p62/SQSTM1-droplet serves as a platform for autophagosome formation and anti-oxidative stress response. Nat Commun. 4;12(1):16. (2021)
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• Orii M, Tsuji T, Ogasawara Y, Fujimoto T. Transmembrane phospholipid translocation mediated by Atg9 is involved in autophagosome formation. J Cell Biol. 220(3):e202009194. (2021)
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2020

• Innokentev A, Furukawa K, Fukuda T, Saigusa T, Inoue K, Yamashita S-I, Kanki T. Association and dissociation between the mitochondrial Far complex and Atg32 regulate mitophagy. Elife. 39:e63694. (2020)
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• Murakawa T, Kiger AA, Sakamaki Y, Fukuda M, Fujita N. An autophagy-dependent tubular lysosomal network synchronizes degradative activity required for muscle remodeling. J Cell Sci. 133 (21): jcs248336. (2020)
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• Fukuda T, Ebi Y, Saigusa T, Furukawa K, Yamashita S, Inoue K, Kobayashi D, Yoshida Y, Kanki T. Atg43 tethers isolation membranes to mitochondria to promote starvation-induced mitophagy in fission yeast. Elife. 9:e61245 (2020)
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• Matoba K, Kotani T, Tsutsumi A, Tsuji T, Mori T, Noshiro D, Sugita Y, Nomura N, Iwata S, Ohsumi Y, Fujimoto T, Nakatogawa H, Kikkawa M, Noda NN. Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion. Nat Struct Mol Biol. 27, 1185–1193 (2020)
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• Nakamura S, Shigeyama S, Minami S, Shima T, Akayama S, Matsuda T, Esposito A, Napolitano G, Kuma A, Namba-Hamano T, Nakamura J, Yamamoto K, Sasai M, Tokumura A, Miyamoto M, Oe Y, Fujita T, Terawaki S, Takahashi A, Hamasaki M, Yamamoto M, Okada Y, Komatsu M, Nagai T, Takabatake Y, Haoxing Xu, Isaka Y, Andrea Ballabio, Yoshimori T. LC3 lipidation is essential for TFEB activation during the lysosomal damage response to kidney injury. Nat Cell Biol. 22(10):1252-1263. (2020)
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• Yamamuro T, Kawabata T, Fukuhara A, Saita S, Nakamura S, Takeshita H, Fujiwara M, Enokidani Y, Yoshida G, Tabata K, Hamasaki M, Kuma A, Yamamoto K, Shimomura I, Yoshimori T. Age-dependent loss of adipose Rubicon promotes metabolic disorders via excess autophagy. Nat Commun. 11(1):4150. (2020)
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• Yamano K, Kikuchi R, Kojima W, Hayashida R, Koyano F, Kawawaki J, Shoda T, Demizu Y, Naito M, Tanaka K, Matsuda N. Critical role of mitochondrial ubiquitination and the OPTN-ATG9A axis in mitophagy. J Cell Biol. 7;219(9):e201912144. (2020)
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• Mochida K, Yamasaki A, Matoba K, Kirisako H, Noda NN, Nakatogawa H. Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes. Nat Commun. 3;11(1):3306. (2020)
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• Nakatogawa H. Mechanisms governing autophagosome biogenesis. Nat Rev Mol Cell Biol. 21(8):439-458. (2020)
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• Tomioka Y, Kotani T, Kirisako H, Oikawa Y, Kimura Y, Hirano H, Ohsumi Y, Nakatogawa H. TORC1 inactivation stimulates autophagy of nucleoporin and nuclear porecomplexes. J Cell Biol. 219(7):e201910063. (2020)
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• Yamamoto YH, Kasai A, Omori H, Takino T, Sugihara M, Umemoto T, Hamasaki M, Hatta T, Natsume T, Morimoto RI , Arai R, Waguri S, Sato M, Sato K, Bar-Nun S, Yoshimori T, Noda T, Nagata K. ERdj8 governs the size of autophagosomes during the formation process. J Cell Biol. 3;219(8):e201903127 (2020)
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• Fujioka Y, Alam JM, Noshiro D, Mouri K, Ando T, Okada Y,4, May AI, Knorr RL, Suzuki K, Ohsumi Y, Noda NN. Phase separation organizes the site of autophagosome formation. Nature. 578(7794):301-305 (2020)
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• Yamasaki A, Alam JM, Noshiro 2, Hirata E, Fujioka Y, Suzuki K, Ohsumi Y, Noda NN. Liquidity Is a Critical Determinant for Selective Autophagy of Protein Condensates. Mol Cell. S1097-2765(19)30956-6 (2020)
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• Hase K Contu VR, Kabuta C, Sakai R, Takahashi M, Kataoka N, Hakuno F, Takahashi SI, Fujiwara Y, Wada K, Kabuta T. Cytosolic domain of SIDT2 carries an arginine-rich motif that binds to RNA/DNA and is important for the direct transport of nucleic acids into lysosomes. Autophagy. Jan 16;1-15 (2020)
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• Sánchez-Martín P, Sou YS, Kageyama S, Koike M, Waguri S, Komatsu M. NBR1-mediated p62-liquid droplets enhance the Keap1-Nrf2 system. EMBO Rep. 21:e48902 (2020)
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2019

• Takahashi SS, Sou YS, Saito T, Kuma A, Yabe T, Sugiura Y, Lee HC, Suematsu M, Yokomizo T, Koike M, Terai S, Mizushima N, Waguri S, Komatsu M. Loss of autophagy impairs physiological steatosis by accumulation of NCoR1.Life Sci Alliance. 10.26508/lsa.201900513 (2019)
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• Saito T, Kuma A, Sugiura Y, Ichimura Y, Obata M, Kitamura H, Okuda S, Lee HC, Ikeda K, Kanegae Y, Saito I, Auwerx J, Motohashi H, Suematsu M, Soga T, Yokomizo T, Waguri S, Mizushima N, Komatsu M. Autophagy regulates lipid metabolism through selective turnover of NCoR1. Nat Commun. 10(1):1567 (2019)
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