Formation mechanism and physiological significance of proteasome speckle

• Project/Area Number: 26293018
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Biological pharmacy
• Research Institution: Tokyo Metropolitan Institute of Medical Science
• Principal Investigator: SAEKI Yasushi 公益財団法人東京都医学総合研究所, 生体分子先端研究分野, 副参事研究員 (80462779)
• Research Collaborator: YASUDA Sayaka 公益財団法人東京都医学総合研究所, 生体分子先端研究分野, 研究員 (80624353) ; KAIHO Ai 公益財団法人東京都医学総合研究所, 生体分子先端研究分野, 研究補助員
• Project Period (FY): 2014-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥16,900,000 (Direct Cost: ¥13,000,000、Indirect Cost: ¥3,900,000); Fiscal Year 2017: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2016: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2015: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2014: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
• Keywords: プロテアソーム / ユビキチン / タンパク質分解 / リボソーム / タンパク質品質管理 / 細胞 / 生体分子 / 核内構造体 / ストレス応答 / 遺伝子 / 蛋白質 / 酵素 / プロテオーム / 転写 / クロマチン構造

Outline of Final Research Achievements

The proteasome is the primary proteolytic machinery in cells and thus is a central regulator of the proteostasis network, but protein quality control (PQC) in the nucleus is largely unknown. Using EGFP knock-in cell lines of the proteasome subunit, we find that hyperosmotic stress induces rapid formation of nuclear foci of proteasomes within a few seconds. The foci are reversible structure that contains K48-linked ubiquitylated proteins, p97, and multiple proteasome-interacting proteins. The foci formation is dependent on ubiquitylation and their clearance requires active proteasomes, p97, and RAD23B, suggesting that this structure is a novel nuclear proteolytic center for adapting to nuclear stress. We identified ribosomal proteins as major ubiquitylated substrates that degraded in the foci, suggesting that the assembly process of the ribosome is vulnerable to hyperosmotic stress. Collectively, we identified the p97-RAD23B axis and the proteasome as a nuclear PQC pathway.

Research Products

• [Journal Article] K63 ubiquitylation triggers proteasomal degradation by seeding branched ubiquitin chains. (2018)
  • Author(s): Ohtake, F., Tsuchiya, H., Saeki, Y., and Tanaka, K
  • Journal Title: PNAS Volume: 115 Issue: 7 Pages: 1401-1408
  • DOI: 10.1073/pnas.1716673115
  • Peer Reviewed
• [Journal Article] Ub-ProT reveals global length and composition of protein ubiquitylation in cells (2018)
  • Author(s): Tsuchiya, H., Burana, D., Ohtake, F., Arai, N., Kaiho, A., Komada, M., Tanaka,K., and Saeki, Y.
  • Journal Title: Nature Commun Volume: 9 Issue: 1 Pages: 524-524
  • DOI: 10.1038/s41467-018-02869-x
  • Peer Reviewed / Open Access
• [Journal Article] In vivo ubiquitin linkage-type analysis reveals that the Cdc48-Rad23/Dsk2 axis contributes to K48-linked chain specificity of the proteasome. (2017)
  • Author(s): Tsuchiya, H., Ohtake, F., Arai, N., Kaiho, A., Yasuda, S., Tanaka, K., and Saeki, Y.
  • Journal Title: Mol. Cell Volume: 66 Issue: 4 Pages: 488-502
  • DOI: 10.1016/j.molcel.2017.04.024
  • Peer Reviewed
• [Journal Article] Ubiquitination of stalled ribosome triggers ribosome-associated quality control (2017)
  • Author(s): Matsuo Y, Ikeuchi K, Saeki Y, Iwasaki S, Schmidt C, Udagawa T, Sato F, Tsuchiya H, Becker T, Tanaka K, Ingolia NT, Beckmann R, Inada T
  • Journal Title: Nature Communications Volume: 8 Issue: 1 Pages: 159-159
  • DOI: 10.1038/s41467-017-00188-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structural basis for specific cleavage of Lys6-linked polyubiquitin chains by USP30 (2017)
  • Author(s): Sato Yusuke、Okatsu Kei、Saeki Yasushi、Yamano Koji、Matsuda Noriyuki、Kaiho Ai、Yamagata Atsushi、Goto-Ito Sakurako、Ishikawa Minoru、Hashimoto Yuichi、Tanaka Keiji、Fukai Shuya
  • Journal Title: Nature Structural & Molecular Biology Volume: 24 Issue: 11 Pages: 911-919
  • DOI: 10.1038/nsmb.3469
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Structure of the Dnmt1 reader module complexed with a unique two-mono-ubiquitin mark on histone H3 reveals the basis for DNA methylation maintenance. (2017)
  • Author(s): Ishiyama S, Nishiyama A, Saeki Y, Moritsugu K Morimoto D, Yamaguchi L, Arai N, Matsumura R, Kawakami T, Mishima Y, Hojo H, Shimamura S, Ishikawa F, Tajima S, Tanaka K, Ariyoshi M, Shirakawa M, Ikeguchi M, Kidera A, Suetake I, Arita K, Nakanishi M
  • Journal Title: Mol Cell Volume: 68 Issue: 2 Pages: 350-360
  • DOI: 10.1016/j.molcel.2017.09.037
  • Peer Reviewed / Open Access
• [Journal Article] Ubiquitin recognition by the proteasome. (2017)
  • Author(s): Saeki, Y.
  • Journal Title: J. Biochem. Volume: 161 Pages: 113-124
  • DOI: 10.1093/jb/mvw091
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] In Vivo Ubiquitin Linkage-type Analysis Reveals that the Cdc48-Rad23/Dsk2 Axis Contributes to K48-linked Chain Specificity of the Proteasome. (2017)
  • Author(s): Tsuchiya, H., Ohtake, F., Arai, N., Kaiho, A., Yasuda, S., Tanaka, K., and Saeki, Y.
  • Journal Title: Mol Cell Volume: 印刷中
  • Acknowledgement Compliant
• [Journal Article] 分子標的薬「プロテアソーム阻害剤」 (2016)
  • Author(s): 佐伯 泰
  • Journal Title: 腎臓内科・泌尿器科 Volume: 4 Pages: 30-38
• [Journal Article] Structure, dynamics and functions of the proteasome (2015)
  • Author(s): 佐伯泰
  • Journal Title: 生化学 Volume: 87 Issue: 6 Pages: 705-722
  • DOI: 10.14952/SEIKAGAKU.2015.870705
  • NAID: 40020687379
  • ISSN: 0037-1017
  • Year and Date: 2015-12-25
  • Peer Reviewed / Open Access
• [Journal Article] Pba3-Pba4 heterodimer acts as a molecular matchmaker in proteasome α-ring formation (2014)
  • Author(s): Takagi, K., Saeki, Y., Yashiroda, H., Yagi, H., Kaiho, A., Murata, S., Yamane, T., Tanaka, K., Mizushima, T. and Kato, K.
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 450 Issue: 2 Pages: 1110-1114
  • DOI: 10.1016/j.bbrc.2014.06.119
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] p97およびRAD23によるプロテアソーム分解制御 (2017)
  • Author(s): 佐伯 泰
  • Organizer: ConBio2017
  • Invited
• [Presentation] Cdc48/p97-Rad23軸がプロテアソーム分解の主要経路である (2016)
  • Author(s): 佐伯 泰
  • Organizer: 第39回日本分子生物学会
  • Place of Presentation: パシフィコ横浜（神奈川県横浜市）
  • Invited
• [Presentation] Elucidating the proteasome dynamics and cellular ubiquitin code (2014)
  • Author(s): Yasushi Saeki
  • Organizer: The 5th International Symposium on Life Science in Toyama
  • Place of Presentation: 富山大学（富山）
  • Year and Date: 2014-12-11
  • Invited
• [Presentation] プロテアソームの分子集合と動態に関する研究 (2014)
  • Author(s): 佐伯 泰
  • Organizer: 日本生化学会 平成26年度奨励賞受賞講演
  • Place of Presentation: 国立京都国際会館（京都）
  • Year and Date: 2014-10-15
  • Invited
• [Presentation] タンパク質分解装置プロテアソームの細胞内動態 (2014)
  • Author(s): 佐伯 泰
  • Organizer: 第21回酵母合同シンポジウム
  • Place of Presentation: 東京大学（東京）
  • Year and Date: 2014-09-03 – 2014-09-04
  • Invited
• [Presentation] プロテアソームの細胞内動態 (2014)
  • Author(s): 佐伯 泰
  • Organizer: 第19回日本病態プロテアーゼ学会学術集会シンポジウム
  • Place of Presentation: 千里ライフサイエンスセンター（大阪）
  • Year and Date: 2014-08-08 – 2014-08-09
  • Invited
• [Book] 実験医学 (2017)
  • Author(s): 佐伯 泰、土屋光、大竹史明、田中啓二
  • Total Pages: 8
  • Publisher: 羊土社
  • ISBN: 9784758125000
• [Book] 生物物理「プロテアソームの細胞内動態と機能」 (2015)
  • Author(s): 佐伯 泰
  • Total Pages: 4
  • Publisher: 日本生物物理学会
• [Book] 実験医学・増刊号「構造生命科学で何がわかるのか何ができるのか」 (2014)
  • Author(s): 佐伯 泰，水島恒裕
  • Total Pages: 6
  • Publisher: 羊土社
• [Book] 細胞工学HOT PRESS「プロテアソームの細胞内ダイナミクス」 (2014)
  • Author(s): 佐伯 泰，白 燦基
  • Total Pages: 3
  • Publisher: 秀潤社
• [Remarks] 公益財団法人東京都医学総合研究所蛋白質代謝研究室ホームページ
  • URL: http://www.igakuken.or.jp/pro-meta/
• [Remarks] ユビキチン鎖の長さを決定する方法を世界で初めて開発
  • URL: http://www.igakuken.or.jp/topics/2018/0206.html
• [Remarks] ユビキチン化基質がプロテアソームに運ばれる仕組み
  • URL: http://www.igakuken.or.jp/topics/2017/0519.html
• [Remarks] ライフサイエンス 新着論文レビュー
  • URL: http://first.lifesciencedb.jp/archives/16636
• [Remarks] 蛋白質代謝研究室ホームページ
  • URL: http://www.igakuken.or.jp/pro-meta/
• [Remarks] 研究室ホームページ
  • URL: http://www.igakuken.or.jp/pro-meta/
• [Remarks] タンパク質分解酵素複合体「プロテアソーム」の動態を解明
  • URL: http://www.igakuken.or.jp/topics/2014/0306.html
• [Remarks] 東京都医学研など、「プロテアソーム」が完成後に核内に運ばれることを解明
  • URL: http://news.mynavi.jp/news/2014/03/10/032/