Updated on 2025/06/24

写真a

 
FUKUDA Tomoyuki
 
Organization
Academic Assembly Institute of Medicine and Dentistry IGAKU KEIRETU Associate Professor
Graduate School of Medical and Dental Sciences Biological Functions and Medical Control Nephrology Associate Professor
Title
Associate Professor
External link

Degree

  • 博士（生命科学） ( 2005.3   東京大学 )

Research Interests

  • Cell cycle

  • Meiosis

  • Cell proliferation

  • Chromosome

  • Autophagy

  • Signal transduction

  • cell division

  • Life science

  • organelle

  • cell differentiation

Research Areas

  • Life Science / Cell biology

  • Life Science / Functional biochemistry

  • Life Science / Genetics

  • Life Science / Molecular biology

Research History (researchmap)

  • Niigata University   Graduate School of Medical and Dental Sciences   Associate Professor

    2016.4

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  • Nara Institute of Science and Technology   Graduate School of Biological Sciences   Assistant Professor

    2013.3 - 2016.3

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  • Karolinska Institutet   Department of Cellular and Molecular Biology   Senior Lab Manager

    2011.4 - 2013.2

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  • Karolinska Institutet   Department of Cellular and Molecular Biology   Postdoctoral Researcher

    2008.4 - 2011.3

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  • Riken   Special Postdoctoral Researcher

    2005.4 - 2008.3

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Research History

  • Niigata University   Graduate School of Medical and Dental Sciences Biological Functions and Medical Control Nephrology   Associate Professor

    2016.4

Education

  • University of Tokyo   Graduate School of Frontier Sciences   Department of Integrated Biosciences

    2000.4 - 2005.3

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  • Kyoto University   Graduate School of Science

    1996.4 - 2000.3

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Professional Memberships

  • YEAST GENETICS SOCIETY OF JAPAN

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  • THE MOLECULAR BIOLOGY SOCIETY OF JAPAN

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Papers

  • Comprehensive analysis of non-selective and selective autophagy in yeast atg mutants and characterization of autophagic activity in the absence of the Atg8 conjugation system. International journal

    Tamara Ginevskaia, Aleksei Innokentev, Kentaro Furukawa, Tomoyuki Fukuda, Manabu Hayatsu, Shun-Ichi Yamashita, Keiichi Inoue, Shinsuke Shibata, Tomotake Kanki

    Journal of biochemistry   176 ( 3 )   217 - 227   2024.9

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

    Abstract

    Most autophagy-related genes, or ATG genes, have been identified in studies using budding yeast. Although the functions of the ATG genes are well understood, the contributions of individual genes to non-selective and various types of selective autophagy remain to be fully elucidated. In this study, we quantified the activity of non-selective autophagy, the cytoplasm-to-vacuole targeting (Cvt) pathway, mitophagy, endoplasmic reticulum (ER)-phagy, and pexophagy in all Saccharomyces cerevisiae atg mutants. Among the mutants of the core autophagy genes considered essential for autophagy, the atg13 mutant and mutants of the genes involved in the two ubiquitin-like conjugation systems retained residual autophagic functionality. In particular, mutants of the Atg8 ubiquitin-like conjugation system (the Atg8 system) exhibited substantial levels of non-selective autophagy, the Cvt pathway, and pexophagy, although mitophagy and ER-phagy were undetectable. Atg8-system mutants also displayed intravacuolar vesicles resembling autophagic bodies, albeit at significantly reduced size and frequency. Thus, our data suggest that membranous sequestration and vacuolar delivery of autophagic cargo can occur in the absence of the Atg8 system. Alongside these findings, the comprehensive analysis conducted here provides valuable datasets for future autophagy research.

    DOI： 10.1093/jb/mvae042

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  • Fission yeast Pib2 localizes to vacuolar membranes and regulates TOR complex 1 through evolutionarily conserved domains. International journal

    Yuichi Morozumi, Yumi Hayashi, Cuong Minh Chu, Fajar Sofyantoro, Yutaka Akikusa, Tomoyuki Fukuda, Kazuhiro Shiozaki

    FEBS letters   598 ( 23 )   2886 - 2896   2024.7

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    TOR complex 1 (TORC1) is a multi-protein kinase complex that coordinates cellular growth with environmental cues. Recent studies have identified Pib2 as a critical activator of TORC1 in budding yeast. Here, we show that loss of Pib2 causes severe growth defects in fission yeast cells, particularly when basal TORC1 activity is diminished by hypomorphic mutations in tor2, the gene encoding the catalytic subunit of TORC1. Consistently, TORC1 activity is significantly compromised in the tor2 hypomorphic mutants lacking Pib2. Moreover, as in budding yeast, fission yeast Pib2 localizes to vacuolar membranes via its FYVE domain, with its tail motif indispensable for TORC1 activation. These results strongly suggest that Pib2-mediated positive regulation of TORC1 is evolutionarily conserved between the two yeast species.

    DOI： 10.1002/1873-3468.14980

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  • Atg44/Mdi1/mitofissin facilitates Dnm1-mediated mitochondrial fission International journal

    Kentaro Furukawa, Manabu Hayatsu, Kentaro Okuyama, Tomoyuki Fukuda, Shun-Ichi Yamashita, Keiichi Inoue, Shinsuke Shibata, Tomotake Kanki

    Autophagy   20 ( 10 )   2314 - 2322   2024.5

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Informa UK Limited  

    Mitochondria undergo fission and fusion, and their coordinated balance is crucial for maintaining mitochondrial homeostasis. In yeast, the dynamin-related protein Dnm1 is a mitochondrial fission factor acting from outside the mitochondria. We recently reported the mitochondrial intermembrane space protein Atg44/mitofissin/Mdi1/Mco8 as a novel fission factor, but the relationship between Atg44 and Dnm1 remains elusive. Here, we show that Atg44 is required to complete Dnm1-mediated mitochondrial fission under homeostatic conditions. Atg44-deficient cells often exhibit enlarged mitochondria with accumulated Dnm1 and rosary-like mitochondria with Dnm1 foci at constriction sites. These mitochondrial constriction sites retain the continuity of both the outer and inner membranes within an extremely confined space, indicating that Dnm1 is unable to complete mitochondrial fission without Atg44. Moreover, accumulated Atg44 proteins are observed at mitochondrial constriction sites. These findings suggest that Atg44 and Dnm1 cooperatively execute mitochondrial fission from inside and outside the mitochondria, respectively.Abbreviation: ATG: autophagy related; CLEM: correlative light and electron microscopy; EM: electron microscopy; ER: endoplasmic reticulum; ERMES: endoplasmic reticulum-mitochondria encounter structure; GA: glutaraldehyde; GFP: green fluorescent protein; GTP: guanosine triphosphate: IMM: inner mitochondrial membrane; IMS: intermembrane space; OMM: outer mitochondrial membrane; PB: phosphate buffer; PBS: phosphate-buffered saline; PFA: paraformaldehyde; RFP: red fluorescent protein; WT: wild type.

    DOI： 10.1080/15548627.2024.2360345

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  • Mitophagy mediated by BNIP3 and NIX protects against ferroptosis by downregulating mitochondrial reactive oxygen species. International journal

    Shun-Ichi Yamashita, Yuki Sugiura, Yuta Matsuoka, Rae Maeda, Keiichi Inoue, Kentaro Furukawa, Tomoyuki Fukuda, David C Chan, Tomotake Kanki

    Cell death and differentiation   31 ( 5 )   651 - 661   2024.5

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    Mitophagy plays an important role in the maintenance of mitochondrial homeostasis and can be categorized into two types: ubiquitin-mediated and receptor-mediated pathways. During receptor-mediated mitophagy, mitophagy receptors facilitate mitophagy by tethering the isolation membrane to mitochondria. Although at least five outer mitochondrial membrane proteins have been identified as mitophagy receptors, their individual contribution and interrelationship remain unclear. Here, we show that HeLa cells lacking BNIP3 and NIX, two of the five receptors, exhibit a complete loss of mitophagy in various conditions. Conversely, cells deficient in the other three receptors show normal mitophagy. Using BNIP3/NIX double knockout (DKO) cells as a model, we reveal that mitophagy deficiency elevates mitochondrial reactive oxygen species (mtROS), which leads to activation of the Nrf2 antioxidant pathway. Notably, BNIP3/NIX DKO cells are highly sensitive to ferroptosis when Nrf2-driven antioxidant enzymes are compromised. Moreover, the sensitivity of BNIP3/NIX DKO cells is fully rescued upon the introduction of wild-type BNIP3 and NIX, but not the mutant forms incapable of facilitating mitophagy. Consequently, our results demonstrate that BNIP3 and NIX-mediated mitophagy plays a role in regulating mtROS levels and protects cells from ferroptosis.

    DOI： 10.1038/s41418-024-01280-y

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  • Fission Yeast TORC1 Promotes Cell Proliferation through Sfp1, a Transcription Factor Involved in Ribosome Biogenesis. International journal

    Yen Teng Tai, Tomoyuki Fukuda, Yuichi Morozumi, Hayato Hirai, Arisa H Oda, Yoshiaki Kamada, Yutaka Akikusa, Tomotake Kanki, Kunihiro Ohta, Kazuhiro Shiozaki

    Molecular and cellular biology   43 ( 12 )   675 - 692   2023.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    Target of rapamycin complex 1 (TORC1) is activated in response to nutrient availability and growth factors, promoting cellular anabolism and proliferation. To explore the mechanism of TORC1-mediated proliferation control, we performed a genetic screen in fission yeast and identified Sfp1, a zinc-finger transcription factor, as a multicopy suppressor of temperature-sensitive TORC1 mutants. Our observations suggest that TORC1 phosphorylates Sfp1 and protects Sfp1 from proteasomal degradation. Transcription analysis revealed that Sfp1 positively regulates genes involved in ribosome production together with two additional transcription factors, Ifh1/Crf1 and Fhl1. Ifh1 physically interacts with Fhl1, and the nuclear localization of Ifh1 is regulated in response to nutrient levels in a manner dependent on TORC1 and Sfp1. Taken together, our data suggest that the transcriptional regulation of the genes involved in ribosome biosynthesis by Sfp1, Ifh1, and Fhl1 is one of the key pathways through which nutrient-activated TORC1 promotes cell proliferation.

    DOI： 10.1080/10985549.2023.2282349

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  • Mitofissin: a novel mitochondrial fission protein that facilitates mitophagy. International journal

    Tomoyuki Fukuda, Kentaro Furukawa, Tatsuro Maruyama, Nobuo N Noda, Tomotake Kanki

    Autophagy   19 ( 11 )   3019 - 3021   2023.11

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    Atg: autophagy related; IMM: inner mitochondrial membrane; IMS: intermembrane space; PAS: phagophore assembly site; SAR: selective autophagy receptor.

    DOI： 10.1080/15548627.2023.2237343

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  • Hva22, a REEP family protein in fission yeast, promotes reticulophagy in collaboration with a receptor protein. Reviewed International journal

    Tomoyuki Fukuda, Tetsu Saigusa, Kentaro Furukawa, Keiichi Inoue, Shun-Ichi Yamashita, Tomotake Kanki

    Autophagy   19 ( 10 )   2657 - 2667   2023.10

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    The endoplasmic reticulum (ER) undergoes selective autophagy called reticulophagy or ER-phagy. Multiple reticulon- and receptor expression enhancing protein (REEP)-like ER-shaping proteins, including budding yeast Atg40, serve as reticulophagy receptors that stabilize the phagophore on the ER by interacting with phagophore-conjugated Atg8. Additionally, they facilitate phagophore engulfment of the ER by remodeling ER morphology. We reveal that Hva22, a REEP family protein in fission yeast, promotes reticulophagy without Atg8-binding capacity. The role of Hva22 in reticulophagy can be replaced by expressing Atg40 independently of its Atg8-binding ability. Conversely, adding an Atg8-binding sequence to Hva22 enables it to substitute for Atg40 in budding yeast. Thus, the phagophore-stabilizing and ER-shaping activities, both of which Atg40 solely contains, are divided between two separate factors, receptors and Hva22, respectively, in fission yeast.Abbreviations: AIM: Atg8-family interacting motif; Atg: autophagy related; DTT: dithiothreitol; ER: endoplasmic reticulum GFP: green fluorescent protein; NAA: 1-naphthaleneacetic acid; REEP: receptor expression enhancing protein; RFP: red fluorescent protein; UPR: unfolded protein response.

    DOI： 10.1080/15548627.2023.2214029

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  • Meet the authors: Tomoyuki Fukuda, Kentaro Furukawa, and Tomotake Kanki

    Sonhita Chakraborty, Tomoyuki Fukuda, Kentaro Furukawa, Tomotake Kanki

    Molecular Cell   83 ( 12 )   1953 - 1955   2023.6

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.molcel.2023.05.016

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  • Axonal mRNA binding of hnRNP A/B is crucial for axon targeting and maturation of olfactory sensory neurons

    Nanaho Fukuda, Tomoyuki Fukuda, Piergiorgio Percipalle, Kanako Oda, Nobuyuki Takei, Kevin Czaplinski, Kazushige Touhara, Yoshihiro Yoshihara, Toshikuni Sasaoka

    Cell Reports   42 ( 5 )   112398 - 112398   2023.5

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.celrep.2023.112398

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  • 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   2023.5

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    DOI： 10.1016/j.molcel.2023.04.022

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  • Membrane perturbation by lipidated Atg8 underlies autophagosome biogenesis. International journal

    Tatsuro Maruyama, Jahangir Md Alam, Tomoyuki Fukuda, Shun Kageyama, Hiromi Kirisako, Yuki Ishii, Ichio Shimada, Yoshinori Ohsumi, Masaaki Komatsu, Tomotake Kanki, Hitoshi Nakatogawa, Nobuo N Noda

    Nature structural & molecular biology   28 ( 7 )   583 - 593   2021.7

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    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.

    DOI： 10.1038/s41594-021-00614-5

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  • Multiplexed suppression of TOR complex 1 induces autophagy during starvation. International journal

    Tomoyuki Fukuda, Kazuhiro Shiozaki

    Autophagy   1 - 2   2021.6

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    Target of rapamycin complex 1 (TORC1) promotes cellular anabolism and suppresses macroautophagy/autophagy. In mammalian cells starved of amino acid, the GATOR1 complex, a negative regulator of TORC1, is released from its inhibitor GATOR2 and inactivates TORC1. We have recently identified the evolutionarily conserved GATOR2 components in fission yeast including Sea3, an ortholog of mammalian WDR59, but, unexpectedly, Sea3 acts as a part of GATOR1 to suppress TORC1. Moreover, fission yeast GATOR1 is not required for the amino-acid starvation-induced TORC1 attenuation, which is instead mediated by the Gcn2 pathway. Conversely, absence of a nitrogen source suppresses TORC1 in a manner dependent on GATOR1 as well as the Tsc1-Tsc2 complex, whose mammalian equivalent functions as a growth-factor sensitive TORC1 inhibitor. Thus, the evolutionarily conserved signaling modules are utilized differently between fission yeast and mammals to control TORC1 activity and autophagy.

    DOI： 10.1080/15548627.2021.1938915

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  • Mitophagy reporter mouse analysis reveals increased mitophagy activity in disuse-induced muscle atrophy. International journal

    Shun-Ichi Yamashita, Masanao Kyuuma, Keiichi Inoue, Yuki Hata, Ryu Kawada, Masaki Yamabi, Yasuyuki Fujii, Junko Sakagami, Tomoyuki Fukuda, Kentaro Furukawa, Satoshi Tsukamoto, Tomotake Kanki

    Journal of cellular physiology   2021.5

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    Muscle disuse induces atrophy through increased reactive oxygen species (ROS) released from damaged mitochondria. Mitophagy, the autophagic degradation of mitochondria, is associated with increased ROS production. However, the mitophagy activity status during disuse-induced muscle atrophy has been a subject of debate. Here, we developed a new mitophagy reporter mouse line to examine how disuse affected mitophagy activity in skeletal muscles. Mice expressing tandem mCherry-EGFP proteins on mitochondria were then used to monitor the dynamics of mitophagy activity. The reporter mice demonstrated enhanced mitophagy activity and increased ROS production in atrophic soleus muscles following a 14-day hindlimb immobilization. Results also showed an increased expression of multiple mitophagy genes, including Bnip3, Bnip3l, and Park2. Our findings thus conclude that disuse enhances mitophagy activity and ROS production in atrophic skeletal muscles and suggests that mitophagy is a potential therapeutic target for disuse-induced muscle atrophy.

    DOI： 10.1002/jcp.30404

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  • Atg43, a novel autophagy-related protein, serves as a mitophagy receptor to bridge mitochondria with phagophores in fission yeast. International journal

    Tomoyuki Fukuda, Tomotake Kanki

    Autophagy   17 ( 3 )   826 - 827   2021.3

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    Mitophagy is a selective type of autophagy in which damaged or unnecessary mitochondria are sequestered by double-membranous structures called phagophores and delivered to vacuoles/lysosomes for degradation. The molecular mechanisms underlying mitophagy have been studied extensively in budding yeast and mammalian cells. To gain more diverse insights, our recent study identified Atg43 as a mitophagy receptor in the fission yeast Schizosaccharomyces pombe. Atg43 is localized on the mitochondrial outer membrane through the Mim1-Mim2 complex and binds to Atg8, a ubiquitin-like protein conjugated to phagophore membranes. Artificial tethering of Atg8 to mitochondria can bypass the requirement of Atg43 for mitophagy, suggesting that the main role of Atg43 in mitophagy is to stabilize phagophore expansion on mitochondria by interacting with Atg8. Atg43 shares no sequence similarity with mitophagy receptors in other organisms and has a mitophagy-independent function, raising the possibility that Atg43 has acquired the mitophagic function by convergent evolution.

    DOI： 10.1080/15548627.2021.1874662

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  • Tripartite suppression of fission yeast TORC1 signaling by the GATOR1-Sea3 complex, the TSC complex, and Gcn2 kinase. International journal

    Tomoyuki Fukuda, Fajar Sofyantoro, Yen Teng Tai, Kim Hou Chia, Takato Matsuda, Takaaki Murase, Yuichi Morozumi, Hisashi Tatebe, Tomotake Kanki, Kazuhiro Shiozaki

    eLife   10   2021.2

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    Mammalian target of rapamycin complex 1 (TORC1) is controlled by the GATOR complex composed of the GATOR1 subcomplex and its inhibitor, the GATOR2 subcomplex, sensitive to amino acid starvation. Previously, we identified fission yeast GATOR1 that prevents deregulated activation of TORC1 (Chia et al., 2017). Here, we report identification and characterization of GATOR2 in fission yeast. Unexpectedly, the GATOR2 subunit Sea3, an ortholog of mammalian WDR59, is physically and functionally proximal to GATOR1, rather than GATOR2, attenuating TORC1 activity. The fission yeast GATOR complex is dispensable for TORC1 regulation in response to amino acid starvation, which instead activates the Gcn2 pathway to inhibit TORC1 and induce autophagy. On the other hand, nitrogen starvation suppresses TORC1 through the combined actions of the GATOR1-Sea3 complex, the Gcn2 pathway, and the TSC complex, another conserved TORC1 inhibitor. Thus, multiple, parallel signaling pathways implement negative regulation of TORC1 to ensure proper cellular starvation responses.

    DOI： 10.7554/eLife.60969

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  • Association and dissociation between the mitochondrial Far complex and Atg32 regulate mitophagy. International journal

    Aleksei Innokentev, Kentaro Furukawa, Tomoyuki Fukuda, Tetsu Saigusa, Keiichi Inoue, Shun-Ichi Yamashita, Tomotake Kanki

    eLife   9   2020.12

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    Mitophagy plays an important role in mitochondrial homeostasis. In yeast, the phosphorylation of the mitophagy receptor Atg32 by casein kinase 2 is essential for mitophagy. This phosphorylation is counteracted by the yeast equivalent of the STRIPAK complex consisting of the PP2A-like protein phosphatase Ppg1 and Far3-7-8-9-10-11 (Far complex), but the underlying mechanism remains elusive. Here we show that two subpopulations of the Far complex reside in the mitochondria and endoplasmic reticulum, respectively, and play distinct roles; the former inhibits mitophagy via Atg32 dephosphorylation, and the latter regulates TORC2 signaling. Ppg1 and Far11 form a subcomplex, and Ppg1 activity is required for the assembling integrity of Ppg1-Far11-Far8. The Far complex preferentially interacts with phosphorylated Atg32, and this interaction is weakened by mitophagy induction. Furthermore, the artificial tethering of Far8 to Atg32 prevents mitophagy. Taken together, the Ppg1-mediated Far complex formation and its dissociation from Atg32 are crucial for mitophagy regulation.

    DOI： 10.7554/eLife.63694

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  • Atg43 tethers isolation membranes to mitochondria to promote starvation-induced mitophagy in fission yeast. Reviewed International journal

    Tomoyuki Fukuda, Yuki Ebi, Tetsu Saigusa, Kentaro Furukawa, Shun-Ichi Yamashita, Keiichi Inoue, Daiki Kobayashi, Yutaka Yoshida, Tomotake Kanki

    eLife   9   2020.11

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    Degradation of mitochondria through mitophagy contributes to the maintenance of mitochondrial function. In this study, we identified that Atg43, a mitochondrial outer membrane protein, serves as a mitophagy receptor in the model organism Schizosaccharomyces pombe to promote the selective degradation of mitochondria. Atg43 contains an Atg8-family-interacting motif essential for mitophagy. Forced recruitment of Atg8 to mitochondria restores mitophagy in Atg43-deficient cells, suggesting that Atg43 tethers expanding isolation membranes to mitochondria. We found that the mitochondrial import factors, including the Mim1-Mim2 complex and Tom70, are crucial for mitophagy. Artificial mitochondrial loading of Atg43 bypasses the requirement of the import factors, suggesting that they contribute to mitophagy through Atg43. Atg43 not only maintains growth ability during starvation but also facilitates vegetative growth through its mitophagy-independent function. Thus, Atg43 is a useful model to study the mechanism and physiological roles, as well as the origin and evolution, of mitophagy in eukaryotes.

    DOI： 10.7554/eLife.61245

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  • Gemcitabine induces Parkin-independent mitophagy through mitochondrial-resident E3 ligase MUL1-mediated stabilization of PINK1. Reviewed International journal

    Ryoko Igarashi, Shun-Ichi Yamashita, Tomohiro Yamashita, Keiichi Inoue, Tomoyuki Fukuda, Takeo Fukuchi, Tomotake Kanki

    Scientific reports   10 ( 1 )   1465 - 1465   2020.1

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    Mitophagy plays an important role in the maintenance of mitochondrial homeostasis. PTEN-induced kinase (PINK1), a key regulator of mitophagy, is degraded constitutively under steady-state conditions. During mitophagy, it becomes stabilized in the outer mitochondrial membrane, particularly under mitochondrial stress conditions, such as in treatment with uncouplers, generation of excessive mitochondrial reactive oxygen species, and formation of protein aggregates in mitochondria. Stabilized PINK1 recruits and activates E3 ligases, such as Parkin and mitochondrial ubiquitin ligase (MUL1), to ubiquitinate mitochondrial proteins and induce ubiquitin-mediated mitophagy. Here, we found that the anticancer drug gemcitabine induces the stabilization of PINK1 and subsequent mitophagy, even in the absence of Parkin. We also found that gemcitabine-induced stabilization of PINK1 was not accompanied by mitochondrial depolarization. Interestingly, the stabilization of PINK1 was mediated by MUL1. These results suggest that gemcitabine induces mitophagy through MUL1-mediated stabilization of PINK1 on the mitochondrial membrane independently of mitochondrial depolarization.

    DOI： 10.1038/s41598-020-58315-w

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  • The PP2A-like Protein Phosphatase Ppg1 and the Far Complex Cooperatively Counteract CK2-Mediated Phosphorylation of Atg32 to Inhibit Mitophagy Reviewed

    Kentaro Furukawa, Tomoyuki Fukuda, Shun-ichi Yamashita, Tetsu Saigusa, Yusuke Kurihara, Yutaka Yoshida, Hiromi Kirisako, Hitoshi Nakatogawa, Tomotake Kanki

    Cell Reports   23 ( 12 )   3579 - 3590   2018.6

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier B.V.  

    DOI： 10.1016/j.celrep.2018.05.064

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  • H2AFX and MDC1 promote maintenance of genomic integrity in male germ cells Reviewed

    Erika Testa, Daniela Nardozi, Cristina Antinozzi, Monica Faieta, Stefano Di Cecca, Cinzia Caggiano, Tomoyuki Fukuda, Elena Bonanno, Lou Zhenkun, Andros Maldonado, Ignasi Roig, Monica Di Giacomo, Marco Barchi

    Journal of Cell Science   131 ( 6 )   2018.3

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    Language：English   Publisher：Company of Biologists Ltd  

    DOI： 10.1242/jcs.214411

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  • Mechanisms and Physiological Roles of Mitophagy in Yeast. Reviewed

    Fukuda T, Kanki T

    Molecules and cells   41 ( 1 )   35 - 44   2018.1

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  • The Rag GTPase-Ragulator complex attenuates TOR complex 1 signaling in fission yeast. Reviewed

    Fukuda T, Shiozaki K

    Autophagy   14 ( 6 )   1105 - 1106   2018

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  • Ragulator and GATOR1 complexes promote fission yeast growth by attenuating TOR complex 1 through rag GTPases Reviewed

    Kim Hou Chia, Tomoyuki Fukuda, Fajar Sofyantoro, Takato Matsuda, Takamitsu Amai, Kazuhiro Shiozaki

    eLife   6   2017.12

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：eLife Sciences Publications Ltd  

    DOI： 10.7554/eLife.30880

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  • The central element of the synaptonemal complex in mice is organized as a bilayered junction structure Reviewed

    Abrahan Hernandez-Hernandez, Sergej Masich, Tomoyuki Fukuda, Anna Kouznetsova, Sara Sandin, Bertil Daneholt, Christer Hoog

    JOURNAL OF CELL SCIENCE   129 ( 11 )   2239 - 2249   2016.6

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    DOI： 10.1242/jcs.182477

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  • Sororin loads to the synaptonemal complex central region independently of meiotic cohesin complexes Reviewed

    Rocio Gomez, Natalia Felipe-Medina, Miguel Ruiz-Torres, Ines Berenguer, Alberto Viera, Sara Perez, Jose Luis Barbero, Elena Llano, Tomoyuki Fukuda, Manfred Alsheimer, Alberto M. Pendas, Ana Losada, Jose A. Suja

    EMBO REPORTS   17 ( 5 )   695 - 707   2016.5

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    DOI： 10.15252/embr.201541060

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  • STAG3-mediated stabilization of REC8 cohesin complexes promotes chromosome synapsis during meiosis Reviewed

    Tomoyuki Fukuda, Nanaho Fukuda, Ana Agostinho, Abrahan Hernandez-Hernandez, Anna Kouznetsova, Christer Hoog

    EMBO JOURNAL   33 ( 11 )   1243 - 1255   2014.6

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    DOI： 10.1002/embj.201387329

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  • The Transacting Factor CBF-A/Hnrnpab Binds to the A2RE/RTS Element of Protamine 2 mRNA and Contributes to Its Translational Regulation during Mouse Spermatogenesis

    Nanaho Fukuda, Tomoyuki Fukuda, John Sinnamon, Abrahan Hernandez-Hernandez, Manizheh Izadi, Chandrasekhar S. Raju, Kevin Czaplinski, Piergiorgio Percipalle

    PLoS Genetics   9 ( 10 )   e1003858 - e1003858   2013.10

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    DOI： 10.1371/journal.pgen.1003858

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  • Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling Reviewed

    Yuval Tabach, Tamar Golan, Abrahan Hernandez-Hernandez, Arielle R. Messer, Tomoyuki Fukuda, Anna Kouznetsova, Jian-Guo Liu, Ingrid Lilienthal, Carmit Levy, Gary Ruvkun

    MOLECULAR SYSTEMS BIOLOGY   9   692   2013.10

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    DOI： 10.1038/msb.2013.50

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  • Dynamic localization of SMC5/6 complex proteins during mammalian meiosis and mitosis suggests functions in distinct chromosome processes Reviewed

    Rocio Gomez, Philip W. Jordan, Alberto Viera, Manfred Alsheimer, Tomoyuki Fukuda, Rolf Jessberger, Elena Llano, Alberto M. Pendas, Mary Ann Handel, Jose A. Suja

    JOURNAL OF CELL SCIENCE   126 ( 18 )   4239 - 4252   2013.9

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    DOI： 10.1242/jcs.130195

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  • ATR acts stage specifically to regulate multiple aspects of mammalian meiotic silencing. Reviewed

    Royo H, Prosser H, Ruzankina Y, Mahadevaiah SK, Cloutier JM, Baumann M, Fukuda T, Höög C, Tóth A, de Rooij DG, Bradley A, Brown EJ, Turner JM

    Genes & development   27 ( 13 )   1484 - 1494   2013.7

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  • Phosphorylation of Chromosome Core Components May Serve as Axis Marks for the Status of Chromosomal Events during Mammalian Meiosis Reviewed

    Tomoyuki Fukuda, Florencia Pratto, John C. Schimenti, James M. A. Turner, R. Daniel Camerini-Otero, Christer Hoog

    PLOS GENETICS   8 ( 2 )   e1002485   2012.2

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    DOI： 10.1371/journal.pgen.1002485

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  • The Mouse Cohesin-Associated Protein PDS5B Is Expressed in Testicular Cells and Is Associated with the Meiotic Chromosome Axes Reviewed

    Tomoyuki Fukuda, Christer Hoog

    GENES   1 ( 3 )   484 - 494   2010.12

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    DOI： 10.3390/genes1030484

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  • A novel mammalian HORMA domain-containing protein, HORMAD1, preferentially associates with unsynapsed meiotic chromosomes Reviewed

    Tomoyuki Fukuda, Katrin Daniel, Lukasz Wojtasz, Attila Toth, Christer Hoog

    EXPERIMENTAL CELL RESEARCH   316 ( 2 )   158 - 171   2010.1

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    DOI： 10.1016/j.yexcr.2009.08.007

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  • Rec8 Guides Canonical Spo11 Distribution along Yeast Meiotic Chromosomes Reviewed

    Kazuto Kugou, Tomoyuki Fukuda, Shintaro Yamada, Masaru Ito, Hiroyuki Sasanuma, Saori Mori, Yuki Katou, Takehiko Itoh, Kouji Matsumoto, Takehiko Shibata, Katsuhiko Shirahige, Kunihiro Ohta

    MOLECULAR BIOLOGY OF THE CELL   20 ( 13 )   3064 - 3076   2009.7

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    DOI： 10.1091/mbc.E08-12-1223

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  • Analysis of chromatin structure at meiotic DSB sites in yeasts Reviewed

    Kouji Hirota, Tomoyuki Fukuda, Takatomi Yamada, Kunihiro Ohta

    Methods in Molecular Biology   557   253 - 266   2009

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    DOI： 10.1007/978-1-59745-527-5_16

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  • Targeted induction of meiotic double-strand breaks reveals chromosomal domain-dependent regulation of Spo11 and interactions among potential sites of meiotic recombination Reviewed

    Tomoyuki Fukuda, Kazuto Kugou, Hiroyuki Sasanuma, Takehiko Shibata, Kunihiro Ohta

    NUCLEIC ACIDS RESEARCH   36 ( 3 )   984 - 997   2008.2

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    DOI： 10.1093/nar/gkm1082

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  • Cdc7-dependent phosphorylation of Mer2 facilitates initiation of yeast meiotic recombination Reviewed

    Hiroyuki Sasanuma, Kouji Hirota, Tomoyuki Fukuda, Naoko Kakusho, Kazuto Kugou, Yasuo Kawasaki, Takehiko Shibata, Hisao Masai, Kunihiro Ohta

    GENES & DEVELOPMENT   22 ( 3 )   398 - 410   2008.2

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    DOI： 10.1101/gad.1626608

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  • Conditional genomic rearrangement by designed meiotic recombination using VDE (PI-SceI) in yeast Reviewed

    Tomoyuki Fukuda, Yoshikazu Ohya, Kunihiro Ohta

    MOLECULAR GENETICS AND GENOMICS   278 ( 4 )   467 - 478   2007.10

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    DOI： 10.1007/s00438-007-0264-7

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  • Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114 Reviewed

    Hiroyuki Sasanuma, Hajime Murakami, Tomoyuki Fukuda, Takehiko Shibata, Alain Nicolas, Kunihiro Ohta

    NUCLEIC ACIDS RESEARCH   35 ( 4 )   1119 - 1133   2007.2

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    DOI： 10.1093/nar/gkl1162

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  • Investigation of the mechanism of meiotic DNA cleavage by VMA1-derived endonuclease uncovers a meiotic alteration in chromatin structure around the target site Reviewed

    T Fukuda, K Ohta, Y Ohya

    EUKARYOTIC CELL   5 ( 6 )   981 - 990   2006.6

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    DOI： 10.1128/EC.00052-06

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  • Recruitment of RecA homologs Dmc1p and Rad51p to the double-strand break repair site initiated by meiosis-specific endonuclease VDE (PI-SceI). Reviewed International journal

    Tomoyuki Fukuda, Yoshikazu Ohya

    Molecular genetics and genomics : MGG   275 ( 2 )   204 - 14   2006.2

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    DOI： 10.1007/s00438-005-0078-4

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  • High-dimensional and large-scale phenotyping of yeast mutants Reviewed

    Y Ohya, J Sese, M Yukawa, F Sano, Y Nakatani, TL Saito, A Saka, T Fukuda, S Ishihara, S Oka, G Suzuki, M Watanabe, A Hirata, M Ohtani, H Sawai, N Fraysse, JP Latge, JM Francois, M Aebi, S Tanaka, S Muramatsu, H Araki, K Sonoike, S Nogami, S Morishita

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   102 ( 52 )   19015 - 19020   2005.12

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    DOI： 10.1073/pnas.0509436102

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  • Molecular mechanism of VDE-initiated intein homing in yeast nuclear genome Reviewed

    Tomoyuki Fukuda, Yuri Nagai, Yoshikazu Ohya

    Advances in Biophysics   38   215 - 232   2004

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    DOI： 10.1016/S0065-227X(04)80181-3

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  • VDE-initiated intein homing in Saccharomyces cerevisiae proceeds in a meiotic recombination-like manner Reviewed

    T Fukuda, S Nogami, Y Ohya

    GENES TO CELLS   8 ( 7 )   587 - 602   2003.7

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  • Homing at an extragenic locus mediated by VDE (PI-Scel) in Saccharomyces cerevisiae Reviewed

    S Nogami, T Fukuda, Y Nagai, S Yabe, M Sugiura, R Mizutani, Y Satow, Y Anraku, Y Ohya

    YEAST   19 ( 9 )   773 - 782   2002.6

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    DOI： 10.1002/yea.872

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  • Viability of Escherichia coli cells under long-term cultivation in a rich nutrient medium Reviewed

    T Fukuda, K Nakahigashi, H Inokuchi

    GENES & GENETIC SYSTEMS   76 ( 5 )   271 - 278   2001.10

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Books

  • 酵母のすべて (系統, 細胞から分子まで)

    福田智行, 太田邦史（ Role： Contributor ,  組換え、修復、突然変異）

    シュプリンガー・ジャパン  2007.9 

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Industrial property rights

Awards

  • 酵母コンソーシアムフェロー

    2023.11   大隅基礎科学創成財団  

    福田智行

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  • 会長賞

    2019.9   酵母遺伝学フォーラム  

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  • キャッチコピー「無限の可能性、ここが最先端」採用

    2013.11   奈良先端科学技術大学院大学  

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  • Poster Winner

    2009.10   Solbacka 2009 (14th Karolinska Institutet CMB/Ludwig Conference)  

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  • 日本学術振興会海外特別研究員

    2009.4  

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  • 海外留学助成ポストドクトラルフェローシップ

    2008.4   上原記念生命科学財団  

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  • 博士論文特別賞

    2005.3   東京大学大学院新領域創成科学研究科先端生命科学専攻  

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  • 日本学術振興会特別研究員（DC1）

    2002.4  

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  • IB賞（最優秀修士論文）

    2002.3   東京大学大学院新領域創成科学研究科先端生命科学専攻  

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Research Projects

  • TORC1シグナル伝達経路の活性調節と代謝制御によるTSCの機能補償

    2025.2 - 2026.3

    Awarding organization：公益信託康本徳守記念結節性硬化症関連神経難病研究基金

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    Authorship：Principal investigator 

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  • 脂質膜リモデリング因子によるオルガネラの動態と機能の制御

    2023.11 - 2025.10

    System name：第7期（2023年度）基礎科学（酵母）研究助成

    Awarding organization：公益財団法人大隅基礎科学創成財団

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  • オルガネラを選択的オートファジーで分解する機構と生理的意義

    Grant number：23K05679

    2023.4 - 2026.3

    System name：科学研究費助成事業

    Research category：基盤研究(C)

    Awarding organization：日本学術振興会

    福田 智行

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    Grant amount：\4680000 （ Direct Cost: \3600000 、 Indirect Cost：\1080000 ）

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  • ミトコンドリア分裂の分子機序と生理機能の解明

    2023.4 - 2025.3

    System name：2023年度一般研究助成

    Awarding organization：公益財団法人発酵研究所

    福田智行

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  • レセプター依存的マイトファジーの誘導制御と生理機能の解明

    Grant number：22H02615

    2022.4 - 2025.3

    System name：科学研究費助成事業

    Research category：基盤研究(B)

    Awarding organization：日本学術振興会

    神吉 智丈, 井上 敬一, 山下 俊一, 福田 智行

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    Grant amount：\17420000 （ Direct Cost: \13400000 、 Indirect Cost：\4020000 ）

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  • マイトファジーによるミトコンドリア分解の機構と生理機能の解明

    2021.11 - 2024.5

    System name：2021年度医学系研究継続助成（基礎）

    Awarding organization：公益財団法人武田科学振興財団

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  • 選択的オートファジーによるオルガネラ分解の機構と意義の解明

    Grant number：20K06552

    2020.4 - 2023.3

    System name：科学研究費助成事業 基盤研究(C)

    Research category：基盤研究(C)

    Awarding organization：日本学術振興会

    福田 智行

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    Grant amount：\4290000 （ Direct Cost: \3300000 、 Indirect Cost：\990000 ）

    オルガネラはそれぞれ特化した機能を果たすため、その質や量は厳密に制御される。その制御の１つとして、オルガネラは選択的なオートファジーにより分解される。選択的オートファジーでは、オルガネラの一部が隔離膜で包まれ、液胞へ輸送され、分解される。本研究はこうしたオルガネラ分解の機構や制御を明らかにすることを目的とする。
    本年度は、分裂酵母の遺伝学的スクリーニングで得られた因子の中から、ミトコンドリアの選択的分解（マイトファジー）の際にレセプターとしてはたらき、隔離膜をミトコンドリアに安定化させるAtg43について詳細な解析を行った。泳動パターンからAtg43がリン酸化される可能性を見いだし、ホスファターゼ処理により、実際にリン酸化されていることを示した。Atg43のリン酸化は栄養増殖時にもみられるが、栄養飢餓によりさらに増強されていた。リン酸化箇所を同定するため、複数の組み合わせでセリン・スレオニン残基に変異を導入したAtg43を発現させた株を作製し、Atg43の泳動度を評価した。その結果、栄養増殖時に起きるリン酸化と、飢餓時に起きるリン酸化は異なる箇所で起きていることが示唆された。また、栄養増殖時のリン酸化は特定のセリン残基で生じるのに対し、飢餓時のリン酸化は複数のセリン残基でリダンダントに生じる可能性が示された。次に、リン酸化が生じることが予想されたセリン残基に変異を導入したAtg43を発現する株におけるマイトファジー活性を評価したところ、リン酸化の減少に比例してマイトファジーが低下していた。以上から、Atg43は栄養状況に依存してリン酸化による制御を受けること、このリン酸化はマイトファジーを促進すること、が明らかになった。リン酸化に関わるキナーゼや、リン酸化がAtg43の分子特性に与える影響を解析するための準備を進めた。

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  • マイトファジーによるミトコンドリア分解の機構と生理機能の解明

    2018.11 - 2020.3

    System name：2018年度医学系研究助成（基礎）

    Awarding organization：公益財団法人武田科学振興財団

    福田 智行

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    Authorship：Principal investigator  Grant type：Competitive

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  • TOR複合体が刺激に応答して細胞増殖を制御する仕組みの解明

    2017.4 - 2020.3

    System name：基盤研究(C)

    Awarding organization：日本学術振興会

    福田 智行

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    Authorship：Principal investigator  Grant type：Competitive

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  • TOR複合体シグナル伝達経路による細胞増殖と代謝の制御機構解明

    2014.11 - 2015.10

    System name：平成26年度調査研究助成金

    Awarding organization：公益財団法人鈴木謙三記念医科学応用研究財団

    福田 智行

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  • TOR kinase complexes that sense and integrate major nutritional signals

    Grant number：26291024

    2014.4 - 2018.3

    System name：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)

    Research category：Grant-in-Aid for Scientific Research (B)

    Awarding organization：Japan Society for the Promotion of Science

    Shiozaki Kazuhiro, TATEBE Hisashi, FUKUDA Tomoyuki, KOJIMA Chojiro

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    Grant amount：\16510000 （ Direct Cost: \12700000 、 Indirect Cost：\3810000 ）

    TOR protein kinase forms two distinct complexes, called TOR complex 1 (TORC1) and TOR complex 2 (TORC2), both of which are implicated in cancerous cell proliferation and metabolic syndrome. By using fission yeast as a genetically amenable model system, we have demonstrated that a Rab-family GTPase activates TORC2 in response to extracellular glucose. Within TORC2, we have found that the Sin1 subunit is responsible for binding the TORC2 substrates. The TORC2 substrates interact with the Sin1 CRIM domain, whose NMR structure has a ubiquitin-like fold with a characteristic acidic loop. Lastly, we have shown that the Rag-family GTPase heterodimer Gtr1-Gtr2 at vacuolar membranes plays an important role in suppressing TORC1 activity. This negative regulation of TORC1 requires the GATOR1 complex that functions as GTPase-Activating Protein (GAP) for the Gtr1 GTPase.

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  • TOR複合体の活性制御機構の解明

    2014.4 - 2016.3

    System name：若手研究(B)

    Awarding organization：日本学術振興会

    福田 智行

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    Authorship：Principal investigator  Grant type：Competitive

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  • 哺乳類シナプトネマ複合体の分子ネットワークの解明

    2013.4 - 2014.3

    System name：研究活動スタート支援

    Awarding organization：日本学術振興会

    福田 智行

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    Authorship：Principal investigator  Grant type：Competitive

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  • 可動性遺伝因子による部位特異的染色体切断を利用した組換えの研究

    2006.4 - 2008.3

    System name：若手研究(スタートアップ)

    Awarding organization：日本学術振興会

    福田 智行

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    Authorship：Principal investigator  Grant type：Competitive

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  • 利己的遺伝子VDEによる染色体DNA切断を用いた減数分裂期組換えに関する研究

    2005.4 - 2006.3

    System name：平成17年度研究奨励ファンド

    Awarding organization：理化学研究所

    福田 智行

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    Authorship：Principal investigator  Grant type：Competitive

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  • Interplay among recombination, replication, segregation, and chromatin structure.

    Grant number：17080011

    2005 - 2009

    System name：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Priority Areas

    Research category：Grant-in-Aid for Scientific Research on Priority Areas

    Awarding organization：Japan Society for the Promotion of Science

    OHTA Kunihiro, HIROTA Kouji, FUKUDA Tomoyuki, BRANZEI Dana, YAMADA Takatomi

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    Grant amount：\64700000 （ Direct Cost: \64700000 ）

    Meiotic recombination plays crucial roles in establishment of genetic diversity and gametes formation. The regulation of meiotic recombination involves various DNA-related processes. This project uncovered that meiotic recombination initiator Spo11 is activated by phosphorylation of a Spo11-accesspry protein Mer2 by Cdc7-Dbf4 kinase, which is a master regulator of DNA replication cycle. We also discovered that Spo11 distribution is regulated by meiotic chromatid cohesion protein Rec8 and replication. In addition, we found several factors involved in chromatin modification required for the activation of meiotic recombination hotspots. Finally, we discovered a new class of long mRNA-type non-coding RNA involved in chromatin control for the stress-induced gene activation in fission yeast.

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  • 出芽酵母の可動性DNA領域VDEがゲノム中で伝播する分子機構に関する研究

    Grant number：02J08383

    2002 - 2004

    System name：科学研究費助成事業 特別研究員奨励費

    Research category：特別研究員奨励費

    Awarding organization：日本学術振興会

    福田 智行

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    Grant amount：\3000000 （ Direct Cost: \3000000 ）

    出芽酵母の可動性DNA領域VDEは、コードする部位特異的エンドヌクレアーゼVDEが減数分裂期特異的に染色体の二重鎖切断を誘導し、宿主がこの切断を修復することでゲノム中を動く。これらの反応機構をより詳細に解析するために、1)VDEによって切断されたDNAとDNA修復系タンパク質との結合解析、2)VDEによる切断の減数分裂期特異性を産み出す機構の解析を行った。
    1)VDEによる二重鎖切断末端にはRecAホモログであるDmc1pとRad51pが互いに独立に結合することをクロマチン免疫沈降法により明らかにした。また、RAD52、RAD55、RAD57遺伝子破壊株においてはいずれもRad51pの結合に欠損が見られた。一方、SAE3遺伝子破壊株ではDmc1pの結合が欠損していた。以上の結果からRad51pはRad52p、Rad55p、Rad57pの働きにより、Dmc1pはSae3pの働きによりそれぞれ独立に二重鎖切断部位にリクルートされ、修復反応をおこなうことが示唆された。
    2)昨年度の解析によりVDEの認識配列付近のクロマチン構造は減数分裂期に変化していることを示したが、今年度は、種々の変異株を用いた解析により、このクロマチン構造の変化は減数分裂の進行に依存していることを明らかにした。また、VDEは減数分裂誘導前にも発現しており、エンドヌクレアーゼ活性も保持していることを確認した。一方、抗VDE抗体を用いたクロマチン免疫沈降法により、VDEは減数分裂期に初めて認識配列に結合し得ることを示した。従ってVDEの減数分裂期特異的な切断はaccessibilityにより制御されており、減数分裂期に見られたクロマチン構造の変化はこのaccessibilityの上昇を反映している可能性が示唆された。

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