Elucidation of molecular motion and new regulation mechanisms in innate immune sensors

• Project/Area Number: 19H00976
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Review Section: Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
• Research Institution: The University of Tokyo
• Principal Investigator: Shimizu Toshiyuki 東京大学, 大学院薬学系研究科(薬学部), 教授 (30273858)
• Co-Investigator(Kenkyū-buntansha): 柴田 琢磨 東京大学, 医科学研究所, 助教 (30554505)
• Project Period (FY): 2019-04-01 – 2022-03-31
• Project Status: Completed (Fiscal Year 2021)
• Budget Amount: ¥45,890,000 (Direct Cost: ¥35,300,000、Indirect Cost: ¥10,590,000); Fiscal Year 2021: ¥13,260,000 (Direct Cost: ¥10,200,000、Indirect Cost: ¥3,060,000); Fiscal Year 2020: ¥13,260,000 (Direct Cost: ¥10,200,000、Indirect Cost: ¥3,060,000); Fiscal Year 2019: ¥19,370,000 (Direct Cost: ¥14,900,000、Indirect Cost: ¥4,470,000)
• Keywords: 自然免疫 / 構造生物学 / Toll様受容体 / クライオ電子顕微鏡 / 構造生物 / Nod様受容体 / TLR / X線結晶解析

Outline of Research at the Start

自然免疫システムは病原微生物感染に対する重要な生体防御のシステムである。自然免疫を誘導する病原体センサーは膜結合型のToll様受容体 (TLR)と細胞質局在型のNod様受容体 (NLR)に大別される。本研究では、これまで断片的な構造情報しか得られていないTLRおよび数例の報告しかないNLRに焦点を当て、構造科学的側面からシグナル伝達機構の全体像を明らかにする。さらに、これまでの構造学的解析より得られた、TLR7ファミリーの制御に核酸代謝関連分子が関与するという新規の知見を活かし、TLR7ファミリーにおける新規の活性制御機構を明らかにすると共にTLR7が関与する疾患の解明を目指す。

Outline of Final Research Achievements

Innate immunity serves as the first line of defense against invading pathogens such as bacteria and viruses, and active adaptive immunity. We focused on the innate immune proteins, and tried to reveal the ligand recognition and regulation mechanisms by structural studies.
We determined the crystal structure of rabbit NOD2 in an ADP-bound state. The structure reveals an inactive closed conformation. We found a hydrophobic pocket on the concave surface of the LRR domain, suitable for accommodating glycan or peptide moieties of MDP. Structural studies of TLR sensing a single-stranded nucleic acids (TLR7, 8, 9) revealed that these TLRs share common mechanism for activation mechanism. Roquin mediates mRNA degradation by recognizing the constitutive-decay element (CDE) followed by recruitment of the deadenylation machinery. Crystal structure of Roquin-RNA complex revealed that The CDE RNA, forming a stem-loop structure, bound to the positively charged surface of the ROQ domain.

Academic Significance and Societal Importance of the Research Achievements

NLRの構造は数例に限られており、NOD2の構造情報はNLRの活性化機構を解明するうえで重要な情報となる。すでに構造解析されているNLRの一つNLRC4と比べてもドメイン配置が大きく異なることが初めて明らかにされた。一本鎖核酸を認識するTLRが有する共通性「リガンド結合部位が2ヶ所あり別のリガンドが各部位に結合することにより協調的に活性化する」を解明したことは大きなインパクトを与えた。特にTLR7,8は低分子化合物によって活性化されることが知られており、立体構造情報はあらたな化合物開発に多大な貢献を示すと考えられる。

Research Products

• [Journal Article] Tetrasubstituted imidazoles as incognito Toll-like receptor 8 a(nta)gonists (2021)
  • Author(s): Yang Yi、Csakai Adam、Jiang Shuangshuang、Smith Christina、Tanji Hiromi、Huang Jian、Jones Torey、Sakaniwa Kentaro、Broadwell Lindsey、Shi Chengrui、Soti Subada、Ohto Umeharu、Fang Yaohui、Shen Shu、Deng Fei、Shimizu Toshiyuki、Yin Hang
  • Journal Title: Nature Communications Volume: 12 Issue: 1 Pages: 4351-4351
  • DOI: 10.1038/s41467-021-24536-4
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structural and functional understanding of the toll‐like receptors (2021)
  • Author(s): Asami Jinta、Shimizu Toshiyuki
  • Journal Title: Protein Science Volume: 30 Issue: 4 Pages: 761-772
  • DOI: 10.1002/pro.4043
  • Peer Reviewed
• [Journal Article] Cryo-EM structures of Toll-like receptors in complex with UNC93B1 (2021)
  • Author(s): Ishida Hanako、Asami Jinta、Zhang Zhikuan、Nishizawa Tomohiro、Shigematsu Hideki、Ohto Umeharu、Shimizu Toshiyuki
  • Journal Title: Nature Structural & Molecular Biology Volume: 28 Issue: 2 Pages: 173-180
  • DOI: 10.1038/s41594-020-00542-w
  • Peer Reviewed / Open Access
• [Journal Article] Structural analysis reveals TLR7 dynamics underlying antagonism (2020)
  • Author(s): Tojo Shingo、Zhang Zhikuan、Matsui Hiroyuki、Tahara Masahiro、Ikeguchi Mitsunori、Kochi Mami、Kamada Mami、Shigematsu Hideki、Tsutsumi Akihisa、Adachi Naruhiko、Shibata Takuma、Yamamoto Masaki、Kikkawa Masahide、Senda Toshiya、Isobe Yoshiaki、Ohto Umeharu、Shimizu Toshiyuki
  • Journal Title: Nature Communications Volume: 11 Issue: 1 Pages: 1-11
  • DOI: 10.1038/s41467-020-19025-z
  • Peer Reviewed / Open Access
• [Journal Article] Discovery of Novel Small Molecule Dual Inhibitors Targeting Toll-like Receptor 7 and 8 (2019)
  • Author(s): Padilla-Salinas, R., Anderson, R., Sakaniwa, K., Zhang, S., Nordeen, P., Lu, C., Shimizu, T., Yin, H.
  • Journal Title: J.Med.Chem. Volume: 62 Issue: 22 Pages: 10221-20244
  • DOI: 10.1021/acs.jmedchem.9b01201
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Structural Insights into the Regulation Mechanism of Small GTPases by GEFs. (2019)
  • Author(s): Toma-Fukai S, Shimizu T
  • Journal Title: Molecules Volume: 24 Issue: 18 Pages: 3308-3308
  • DOI: 10.3390/molecules24183308
  • Peer Reviewed / Open Access
• [Journal Article] Cytidine deaminase enables Toll-like receptor 8 activation by cytidine or its analogs. (2019)
  • Author(s): Furusho K, Shibata T, Sato R, Fukui R, Motoi Y, Zhang Y, Saitoh SI, Ichinohe T, Moriyama M, Nakamura S, Miyake, K.
  • Journal Title: International immunology. Volume: 31 Issue: 3 Pages: 167-173
  • DOI: 10.1093/intimm/dxy075
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] SLC29A3異常症における発症メカニズムの解明 (2019)
  • Author(s): 柴田 琢磨
  • Organizer: 第43回 日本小児皮膚科学会学術大会
  • Invited
• [Remarks]
  • URL: https://kouzou.f.u-tokyo.ac.jp/