Genetic and biochemical analysis of the ER quality control of membrane proteins

• Project/Area Number: 18K19306
• Research Category: Grant-in-Aid for Challenging Research (Exploratory)
• Allocation Type: Multi-year Fund
• Review Section: Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
• Research Institution: Nagoya City University
• Principal Investigator: Nakatsukasa Kunio 名古屋市立大学, 大学院理学研究科, 准教授 (90547522)
• Project Period (FY): 2018-06-29 – 2022-03-31
• Project Status: Completed (Fiscal Year 2021)
• Budget Amount: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000); Fiscal Year 2020: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2019: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2018: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
• Keywords: 小胞体 / 膜タンパク質 / ユビキチン / プロテアソーム / 分解

Outline of Final Research Achievements

Misfolded or unassembled proteins in the endoplasmic reticulum (ER) are degraded by the proteasome. This process is referred to as ER-associated degradation or ERAD. In this study, we analyzed the mechanisms of membrane protein degradation during ERAD: (1)Experimental and theoretical analysis to predict membrane protein insertion in yeast cells; (2)Physiological role of the ERAD of membrane proteins; (3)Genetic analysis of the retrotranslocation complex. (4)We also performed collaborative research to study ERAD in mammals.

Academic Significance and Societal Importance of the Research Achievements

細胞には立体構造の形成に失敗した異常タンパク質を特異的に認識して分解する品質管理の仕組みが備わっている。本研究では、小胞体の膜に存在する異常タンパク質に着目し、出芽酵母の遺伝学、生化学の手法を駆使して、分解の仕組みを詳細に解析した。本研究で得られた成果は、異常タンパク質の蓄積を防ぐ方法論の開発につながるものと期待される。

Research Products

• [Journal Article] Dot6/Tod6 degradation fine-tunes the repression of ribosome biogenesis under nutrient-limited conditions (2022)
  • Author(s): Kusama Kino、Suzuki Yuta、Kurita Ena、Kawarasaki Tomoyuki、Obara Keisuke、Okumura Fumihiko、Kamura Takumi、Nakatsukasa Kunio
  • Journal Title: iScience Volume: 25 Issue: 3 Pages: 103986-103986
  • DOI: 10.1016/j.isci.2022.103986
  • Peer Reviewed / Open Access
• [Journal Article] Proteolysis of adaptor protein Mmr1 during budding is necessary for mitochondrial homeostasis in Saccharomyces cerevisiae (2022)
  • Author(s): Obara Keisuke、Yoshikawa Taku、Yamaguchi Ryu、Kuwata Keiko、Nakatsukasa Kunio、Nishimura Kohei、Kamura Takumi
  • Journal Title: Nature Communications Volume: 13 Issue: 1 Pages: 1-15
  • DOI: 10.1038/s41467-022-29704-8
  • Peer Reviewed / Open Access
• [Journal Article] A positive genetic selection for transmembrane domain mutations in HRD1 underscores the importance of Hrd1 complex integrity during ERAD (2022)
  • Author(s): Nakatsukasa Kunio、Wigge Sylvia、Takano Yuki、Kawarasaki Tomoyuki、Kamura Takumi、Brodsky Jeffrey L.
  • Journal Title: Current Genetics Volume: 68 Issue: 2 Pages: 227-242
  • DOI: 10.1007/s00294-022-01227-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] ZSWIM8 is a myogenic protein that partly prevents C2C12 differentiation (2021)
  • Author(s): Okumura Fumihiko、Oki Nodoka、Fujiki Yuha、Ikuta Rio、Osaki Kana、Hamada Shun、Nakatsukasa Kunio、Hisamoto Naoki、Hara Taichi、Kamura Takumi
  • Journal Title: Scientific Reports Volume: 11 Issue: 1 Pages: 20880-20880
  • DOI: 10.1038/s41598-021-00306-6
  • Peer Reviewed / Open Access
• [Journal Article] Potential Physiological Relevance of ERAD to the Biosynthesis of GPI-Anchored Proteins in Yeast (2021)
  • Author(s): Nakatsukasa K.
  • Journal Title: Int. J. Mol. Sci. Volume: 22(3) Issue: 3 Pages: 1061-1061
  • DOI: 10.3390/ijms22031061
  • Peer Reviewed / Open Access
• [Journal Article] Cul5-type Ubiquitin Ligase KLHDC1 Contributes to the Elimination of Truncated SELENOS Produced by Failed UGA/Sec Decoding (2020)
  • Author(s): Okumura Fumihiko、Fujiki Yuha、Oki Nodoka、Osaki Kana、Nishikimi Akihiko、Fukui Yoshinori、Nakatsukasa Kunio、Kamura Takumi
  • Journal Title: iScience Volume: 23 Issue: 3 Pages: 100970-100970
  • DOI: 10.1016/j.isci.2020.100970
  • Peer Reviewed / Open Access
• [Journal Article] Harmonizing Experimental Data with Modeling to Predict Membrane Protein Insertion in Yeast (2019)
  • Author(s): Guerriero C.J., Gomez Y.K., Daskivich G.J., Reutter K.R., Augustine A.A., Weiberth K.F., Nakatsukasa K., Grabe M., and *Brodsky J.L.
  • Journal Title: Biophysical Journal Volume: 117 Issue: 4 Pages: 668-678
  • DOI: 10.1016/j.bpj.2019.07.013
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Msp1 Clears Mistargeted Proteins by Facilitating Their Transfer from Mitochondria to the ER (2019)
  • Author(s): Matsumoto S., Nakatsukasa K., Kakuta C., Tamura Y., Esaki M., and *Endo T.
  • Journal Title: Molecular Cell Volume: 76 Issue: 1 Pages: 191-205
  • DOI: 10.1016/j.molcel.2019.07.006
  • Peer Reviewed
• [Journal Article] Hepatic Sdf2l1 controls feeding-induced ER stress and regulates metabolism (2019)
  • Author(s): Sasako T., Ohsugi M., Kubota N., Itoh S., Okazaki Y, Terai A., Kubota T., Yamashita S., Nakatsukasa K., Kamura T., Iwayama K., Tokuyama K., Kiyonari H., Furuta Y., Shibahara J., Fukayama M., Enooku K., Okushin K., Tsutsumi T., Tateishi R., Tobe K., Asahara H., Koike K., *Kadowaki T. & *Ueki K.
  • Journal Title: Nature Communications Volume: 10 Issue: 1 Pages: 1-16
  • DOI: 10.1038/s41467-019-08591-6
  • Peer Reviewed / Open Access
• [Journal Article] The HECT-type ubiquitin ligase Tom1 contributes to the turnover of Spo12, a component of the FEAR network, in G2/M phase. (2018)
  • Author(s): *Nakatsukasa K., Sone M., Alemayehu D.H., Okumura F., and *Kamura T.
  • Journal Title: FEBS Letters Volume: 592 Issue: 10 Pages: 1716-1724
  • DOI: 10.1002/1873-3468.13066
  • Peer Reviewed
• [Presentation] Quality control of enzymatically active mitochondrial precursor protects cells against ectopic metabolite stress (2021)
  • Author(s): 中務邦雄
  • Organizer: 第73回日本細胞生物学会大会
• [Presentation] A possible novel mechanism for the regulation of ribosome biogenesis under starvation conditions (2020)
  • Author(s): 草間幾乃, 中務邦雄
  • Organizer: 第72回日本細胞生物学会大会
• [Presentation] Maintenance of metabolic homeostasis by the proteasomal degradation of cytosolically mislocalized citrate synthase. (2020)
  • Author(s): 川原﨑智之, 中務邦雄
  • Organizer: 第72回日本細胞生物学会大会
• [Presentation] 細胞質に誤局在したクエン酸合成酵素の分解による代謝恒常性の維持 (2020)
  • Author(s): 中務邦雄
  • Organizer: 第72回日本細胞生物学会大会
• [Presentation] 栄養ストレス条件下におけるリボソーム生合成の調節機構 (2019)
  • Author(s): 中務邦雄
  • Organizer: 第42回日本分子生物学会年会
  • Invited
• [Presentation] 可溶性の代謝酵素の分解におけるAAA ATPase Cdc48/p97の役割 (2018)
  • Author(s): 川原﨑 智之2、森山 昭彦2、〇中務 邦雄1
  • Organizer: 第41回日本分子生物学会年会
• [Presentation] ２つのAAA-ATPアーゼによるミトコンドリア外膜に誤局在したテイルアンカータンパク質の分解機構 (2018)
  • Author(s): 〇松本 俊介1、角田 千香1、中務 邦雄2、田村 康3、江崎 雅俊4、遠藤 斗志也1
  • Organizer: 第41回日本分子生物学会年会
• [Presentation] 出芽酵母E3リガーゼ複合体SCFMet30によるAry34の分解制御 (2018)
  • Author(s): 〇山口 竜1、小原 圭介1、奥村 文彦1、嘉村 巧1、中務 邦雄2
  • Organizer: 第41回日本分子生物学会年会
• [Presentation] ユビキチンリガーゼSPSB4はEphB2を介した細胞間反発運動を抑制する (2018)
  • Author(s): 〇奥村 文彦1、奥村（城尾） 晶子1、小原 圭介1、錦見 昭彦3、福井 宣規2、中務 邦雄4、嘉村 巧1
  • Organizer: 第41回日本分子生物学会年会
• [Presentation] 小胞体および小胞体から形成される膜系を舞台とした膜タンパク質の分解経路 (2018)
  • Author(s): 〇中務 邦雄
  • Organizer: 第91回日本生化学会大会
• [Presentation] Regulation of metabolic pathways by the ubiquitin-proteasome system (2018)
  • Author(s): Kunio Nakatsukasa
  • Organizer: International Symposium - Proteins: From the Cradle to the Grave
  • Int'l Joint Research
• [Remarks]
  • URL: https://www.nsc.nagoya-cu.ac.jp/~nakatsukasa/lab.html