DHX8 regulates degradation of RNA by RNautophagy.
Sakai R, Takeda E, Kabuta C, Contu VR, Fujiwara Y, Fujikake N, Hashimoto T, Ohsumi Y, Kabuta T
Nucleic acids research, 2025年08月01日, ［査読有り］
研究論文（学術雑誌）, RNautophagy is an intracellular degradation pathway in which RNA is directly taken up by lysosomes. The cytoplasmic regions of the lysosomal membrane proteins, LAMP2C and SIDT2, can interact with consecutive guanine sequences in RNA, mediating the uptake of RNA during RNautophagy. RNautophagy has also been implicated in the clearance of expanded CAG-repeat mRNA and RNA foci associated with polyQ disease. However, the mechanisms of RNA uptake during RNautophagy remain unclear. Here, we screened for proteins that bind consecutive guanine sequences and identified RNA helicase DHX8 as a binding partner. DHX8 interacts with SIDT2 and is partially localized to the cytoplasmic side of the lysosomal membrane. We found that DHX8 regulates intracellular RNA degradation via SIDT2-dependent RNautophagy but not via macroautophagy. RNA binding, but not ATPase activity, of DHX8 is likely to be important for regulating RNA degradation. DHX8 also contributes to the clearance of pathogenic CAG repeat mRNA and RNA foci, and the levels of both soluble protein and insoluble high-molecular-weight aggregates of expanded polyQ tracts. Our findings provide insights into the mechanisms underlying the regulation of intracellular RNA degradation, autophagic pathways, and possibly the pathogenesis of repeat RNA-related disorders.

Reconsidering the selectivity of bulk autophagy: cargo hitchhiking specifies cargo for degradation
Eigo Takeda, Alexander I. May, Yoshinori Ohsumi
Autophagy, 2024年12月27日, ［査読有り］, ［招待有り］, ［筆頭著者, 責任著者］
研究論文（学術雑誌）

Regulatory Dynamics of Sch9 in Response to Cytosolic Acidification: From Spatial Reconfiguration to Cellular Adaptation to Stresses
Rui Fujii, Rai Katsukawa, Eigo Takeda, Eisuke Itakura, Akira Matsuura
iScience, 2024年12月, ［査読有り］
英語, 研究論文（学術雑誌）

Atg45 is an autophagy receptor for glycogen, a non-preferred cargo of bulk autophagy in yeast
Takahiro Isoda, Eigo Takeda, Sachiko Hosokawa, Shukun Hotta-Ren, Yoshinori Ohsumi
iScience, 2024年06月, ［査読有り］
英語, 研究論文（学術雑誌）

Receptor-mediated cargo hitchhiking on bulk autophagy
Eigo Takeda, Takahiro Isoda, Sachiko Hosokawa, Yu Oikawa, Shukun Hotta-Ren, Alexander I May, Yoshinori Ohsumi
The EMBO Journal, 2024年05月16日, ［査読有り］, ［筆頭著者, 責任著者］
研究論文（学術雑誌）

A nuclear membrane-derived structure associated with Atg8 is involved in the sequestration of selective cargo, the Cvt complex, during autophagosome formation in yeast.
Baba M, Tomonaga S, Suzuki M, Gen M, Takeda E, Akira Matsuura, Yoshiaki Kamada, Baba N
Autophagy, 2018年10月11日, ［査読有り］
研究論文（学術雑誌）, Macroautophagy (hereafter autophagy) is a conserved intracellular degradation mechanism required for cell survival. A double-membrane structure, the phagophore, is generated to sequester cytosolic cargos destined for degradation in the vacuole. The mechanism involved in the biogenesis of the phagophore is still an open question. We focused on 4 autophagy-related (Atg) proteins (Atg2, Atg9, Atg14, and Atg18), which are involved in the formation of the phagophore in order to gain a more complete understanding of the membrane dynamics that occur during formation of the autophagosome. The corresponding mutants, while defective in autophagy, nonetheless generate the membrane-bound form of Atg8, allowing us to use this protein as a marker for the nascent autophagosome precursor membrane. Using electron microscopy (EM), we discovered in these atg mutants a novel single-membrane structure (~120 to 150 nm in size). Electron tomography revealed that this structure originates from a part of the nuclear membrane, and we have named it the alphasome. Our data suggest that the alphasome is associated with Atg8, and sequesters selective cargo, the Cvt complex, during autophagy. Abbreviations: 3D: three-dimensional; AB: autophagic body; AP: autophagosome; Atg: autophagy-related; Cvt: cytoplasm-to-vacuole targeting; EM: electron microscopy; IEM: immunoelectron microscopy; L: lipid droplet; N: nucleus; NM: nuclear membrane; PAS: phagophore assembly site; PE: phosphatidylethanolamine; prApe1: precursor aminopeptidase I; rER: rough endoplasmic reticulum; TEM: transmission electron microscopy; V: vacuole; VLP: virus-like particle.

A substrate localization model for the selective regulation of TORC1 downstream pathways.
Takeda E, Akira Matsuura
Communicative & integrative biology, 2018年06月18日, ［査読有り］, ［筆頭著者］
研究論文（学術雑誌）, Target of rapamycin complex 1 (TORC1) is a protein kinase complex conserved in eukaryotes that coordinates diverse cellular processes critical for cell growth to environmental conditions. Previous studies have shown that TORC1 is localized mainly in the lysosome/vacuoles, and its localization is important for signaling to downstream pathways. We recently demonstrated that signaling to Sch9, an S6K-related substrate of TORC1 in budding yeast, was selectively suppressed upon oxidative stress, which was mediated by the delocalization of phosphatidylinositol 3, 5-bisphosphate (PI[3,5]P₂) from vacuolar membranes following stress. We propose that TORC1 downstream pathways can be regulated separately via the modulation of organelle localization of a specific target protein.

Vacuole-mediated selective regulation of TORC1-Sch9 signaling following oxidative stress.
Takeda E, Jin N, Eisuke Itakura, Kira S, Kamada Y, Weisman LS, Takeshi Noda, Akira Matsuura
Molecular biology of the cell, 2017年12月13日, ［査読有り］, ［筆頭著者］
研究論文（学術雑誌）, Target of rapamycin complex 1 (TORC1) is a central cellular signaling coordinator that allows eukaryotic cells to adapt to the environment. In the budding yeast, Saccharomyces cerevisiae, TORC1 senses nitrogen and various stressors and modulates proteosynthesis, nitrogen uptake and metabolism, stress responses, and autophagy. There is some indication that TORC1 may regulate these downstream pathways individually. However, the potential mechanisms for such differential regulation are unknown. Here we show that the serine/threonine protein kinase Sch9 branch of TORC1 signaling depends specifically on the integrity of the vacuolar membrane, and this dependency originates in changes in Sch9 localization reflected by phosphatidylinositol 3,5-bisphosphate. Moreover, oxidative stress induces the delocalization of Sch9 from vacuoles, contributing to the persistent inhibition of the Sch9 branch after stress. Thus, our results establish that regulation of the vacuolar localization of Sch9 serves as a selective switch for the Sch9 branch in divergent TORC1 signaling. We propose that the Sch9 branch integrates the intrinsic activity of TORC1 kinase and vacuolar status, which is monitored by the phospholipids of the vacuolar membrane, into the regulation of macromolecular synthesis.

Dynamic relocation of the TORC1-Gtr1/2-Ego1/2/3 complex is regulated by Gtr1 and Gtr2.
Kira S, Kumano Y, Ukai H, Takeda E, Akira Matsuura, Takeshi Noda
Molecular biology of the cell, 2015年11月25日, ［査読有り］
研究論文（学術雑誌）, TORC1 regulates cellular growth, metabolism, and autophagy by integrating various signals, including nutrient availability, through the small GTPases RagA/B/C/D in mammals and Gtr1/2 in budding yeast. Rag/Gtr is anchored to the lysosomal/vacuolar membrane by the scaffold protein complex Ragulator/Ego. Here we show that Ego consists of Ego1 and Ego3, and novel subunit Ego2. The ∆ego2 mutant exhibited only partial defects both in Gtr1-dependent TORC1 activation and Gtr1 localization on the vacuole. Ego1/2/3, Gtr1/2, and Tor1/Tco89 were colocalized on the vacuole and associated puncta. When Gtr1 was in its GTP-bound form and TORC1 was active, these proteins were preferentially localized on the vacuolar membrane, whereas when Gtr1 was in its GDP-bound form, they were mostly localized on the puncta. The localization of TORC1 to puncta was further facilitated by direct binding to Gtr2, which is involved in suppression of TORC1 activity. Thus regulation of TORC1 activity through Gtr1/Gtr2 is tightly coupled to the dynamic relocation of these proteins.

Receptor-mediated cargo hitchhiking on bulk autophagy　　　　　　　　　　　　　　　
Eigo Takeda
5th Sino-Japan Symposium on Autophagy, 2024年06月20日, 英語, 口頭発表（招待・特別）
2024年06月17日 - 2024年06月21日, ［招待講演］