Structural basis for innate immune pathogen sensors

• Project/Area Number: 26711002
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Partial Multi-year Fund
• Research Field: Structural biochemistry
• Research Institution: The University of Tokyo
• Principal Investigator: Ohto Umeharu 東京大学, 薬学研究科(研究院), 准教授 (90451856)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥24,700,000 (Direct Cost: ¥19,000,000、Indirect Cost: ¥5,700,000); Fiscal Year 2016: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000); Fiscal Year 2015: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000); Fiscal Year 2014: ¥12,870,000 (Direct Cost: ¥9,900,000、Indirect Cost: ¥2,970,000)
• Keywords: 構造生物学 / 結晶構造解析 / 自然免疫 / Ｘ線結晶構造解析 / Toll様受容体 / Nod様受容体

Outline of Final Research Achievements

We conducted structural studies on the innate immune receptors, TLR7, TLR8, TLR9, and NOD2. We determined the crystal structures of TLR7 and TLR8 in complex with ssRNA, and also determined the crystal structure of TLR9 in complex with CpG DNA, which revealed the activation mechanism of these nucleic acid recognizing TLRs. Moreover, we determined the crystal structure of an ADP-bound inactivated form of NOD2.

Research Products

• [Int'l Joint Research] ミネソタ大/コロラド大(米国)
• [Int'l Joint Research] ミネソタ大学/カンザス大学(米国)
• [Journal Article] The crystal structure of mouse LC3B in complex with the FYCO1 LIR reveals the importance of the flanking region of the LIR motif. (2017)
  • Author(s): Sakurai S, Tomita T, Shimizu T, Ohto U
  • Journal Title: Acta Crystallographica Section F Volume: 73 Issue: 3 Pages: 130-137
  • DOI: 10.1107/s2053230x17001911
  • Peer Reviewed
• [Journal Article] Emerging roles of the processing of nucleic acids and Toll-like receptors in innate immune responses to nucleic acids (2017)
  • Author(s): Miyake K, Shibata T, Ohto U, Shimizu T
  • Journal Title: J Leukoc Biol Volume: 101 Issue: 1 Pages: 135-142
  • DOI: 10.1189/jlb.4mr0316-108r
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Structural Analysis Reveals that Toll-like Receptor 7 Is a Dual Receptor for Guanosine and Single-Stranded RNA (2016)
  • Author(s): Zhang Z, Ohto U, Shibata T, Krayukhina E, Taoka M, Yamauchi Y, Tanji H, Isobe T, Uchiyama S, Miyake K, Shimizu T
  • Journal Title: Immunity Volume: 45 Issue: 4 Pages: 737-748
  • DOI: 10.1016/j.immuni.2016.09.011
  • Peer Reviewed
• [Journal Article] Structure of IZUMO1-JUNO reveals sperm-oocyte recognition during mammalian fertilization. (2016)
  • Author(s): Ohto U, Ishida H, Krayukhina E, Uchiyama S, Inoue N, Shimizu T.
  • Journal Title: Nature Volume: 534 Issue: 7608 Pages: 566-569
  • DOI: 10.1038/nature18596
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Crystal structure of NOD2 and its implications in human disease. (2016)
  • Author(s): Maekawa S, Ohto U, Shibata T, Miyake K, Shimizu T
  • Journal Title: Nat Commun Volume: 7 Issue: 1 Pages: 11813-11813
  • DOI: 10.1038/ncomms11813
  • Peer Reviewed / Open Access
• [Journal Article] Identification of a Human Toll-Like Receptor (TLR) 8-Specific Agonist and a Functional Pan-TLR Inhibitor in 2-Aminoimidazoles. (2016)
  • Author(s): Beesu, M., Caruso, G., Salyer, A. C., Shukla, N. M., Khetani, K. K., Smith, L. J., Fox, L. M., Tanji, H., Ohto, U., Shimizu, T., & David, S. A.
  • Journal Title: J. Med. Chem. Volume: 59 Issue: 7 Pages: 3311-3330
  • DOI: 10.1021/acs.jmedchem.6b00023
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Autoinhibition and relief mechanism by the proteolytic processing of Toll-like receptor 8. (2016)
  • Author(s): Tanji, H., Ohto, U., Motoi, Y., Shibata, T., Miyake, K., & Shimizu, T.
  • Journal Title: Proc. Natl. Acad. Sci. U S A Volume: 113 Issue: 11 Pages: 3012-3017
  • DOI: 10.1073/pnas.1516000113
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Eritoran inhibits S100A8-mediated TLR4/MD-2 activation and tumor growth by changing the immune microenvironment. (2016)
  • Author(s): Deguchi A, Tomita T, Ohto U, Takemura K, Kitao A, Akashi-Takamura, S, Miyake K, and Maru Y.
  • Journal Title: Oncogene Volume: 35 Issue: 11 Pages: 1445-1456
  • DOI: 10.1038/onc.2015.211
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Structure-based Design of Human TLR8-specific Agonists with Augmented Potency and Adjuvanticity. (2015)
  • Author(s): Beesu, M., Caruso, G., Salyer, A., Khetani, K., Sil, D., Weerasinghe, M., Tanji, H., Ohto, U., Shimizu, T., & David, S. A.
  • Journal Title: J. Med. Chem. Volume: 58 Issue: 19 Pages: 7833-7849
  • DOI: 10.1021/acs.jmedchem.5b01087
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] The Imidazoquinoline Toll-Like Receptor-7/8 Agonist Hybrid-2 Potently Induces Cytokine Production by Human Newborn and Adult Leukocytes. (2015)
  • Author(s): Ganapathi, L., Van Haren, S., Dowling, D. J., Bergelson, I., Shukla, N. M., Malladi, S. S., Balakrishna, R., Tanji, H., Ohto, U., Shimizu, T., David, S. A., & Levy, O.
  • Journal Title: PLoS One Volume: 10 Issue: 8 Pages: 0134640-0134640
  • DOI: 10.1371/journal.pone.0134640
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Structure of human Roquin-2 and its complex with constitutive-decay element RNA. (2015)
  • Author(s): Sakurai, S., Ohto, U., & Shimizu, T.
  • Journal Title: Acta Crystallogr. Sect. F Volume: 71 Issue: 8 Pages: 1048-1054
  • DOI: 10.1107/s2053230x15011887
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Toll-like receptor 8 senses degradation products of single-stranded RNA. (2015)
  • Author(s): Tanji H, Ohto U, Shibata T, Taoka M, Yamauchi Y, Isobe T, Miyake K,
  • Journal Title: Nat Struct Mol Biol. Volume: 22 Issue: 2 Pages: 109-115
  • DOI: 10.1038/nsmb.2943
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Determinants of activity at human Toll-like receptors 7 and 8: quantitative structure-activity (2014)
  • Author(s): Yoo E, Salunke DB, Sil D, Guo X, Salyer AC, Hermanson AR, Kumar M,
  • Journal Title: J Med Chem. Volume: 57 Issue: 19 Pages: 7955-7970
  • DOI: 10.1021/jm500744f
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Structural basis of pharmacological chaperoning for human β-galactosidase (2014)
  • Author(s): Suzuki H, et al.
  • Journal Title: J. Biol. Chem. Volume: 289 Issue: 21 Pages: 14560-14568
  • DOI: 10.1074/jbc.m113.529529
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] Structures of nucleic acids sensing Toll-like receptors (2016)
  • Author(s): Umeharu Ohto and Toshiyuki Shimizu
  • Organizer: The 45th annual meeting of the Japanese Society for Immunology (JSI)
  • Place of Presentation: 沖縄コンベンションセンター（沖縄、宜野湾）
  • Year and Date: 2016-12-05
  • Invited
• [Presentation] Structural studies of innate immune RNA receptor human TLR8 (2016)
  • Author(s): Hiromi Tanji, Umeharu Ohto, Toshiyuki Shimizu
  • Organizer: 14th Conference of the Asian Crystallographic Association
  • Place of Presentation: Hanoi, Vietnam
  • Year and Date: 2016-12-04
  • Int'l Joint Research
• [Presentation] 自然免疫受容体 TLR7 の構造学的研究 (2016)
  • Author(s): 張志寛、大戸梅治、清水敏之
  • Organizer: 第16回日本蛋白質科学会年会
  • Place of Presentation: 福岡国際会議場（福岡、博多）
  • Year and Date: 2016-06-07
• [Presentation] 核酸認識Toll様受容体によるリガンド認識とシグナル伝達の構造基盤 (2015)
  • Author(s): 大戸梅治、清水敏之
  • Organizer: BMB2015 第38回日本分子生物学会年会 第88回日本生化学会大会 合同大会
  • Place of Presentation: 神戸ポートアイランド（神戸）
  • Year and Date: 2015-12-01
  • Invited
• [Presentation] mRNA分解に関与するタンパク質Roquin-2とRNA複合体のX線結晶構造解析 (2015)
  • Author(s): 櫻井駿也、大戸梅治、清水敏之
  • Organizer: 平成27年度日本結晶学会
  • Place of Presentation: 大阪府立大学（大阪）
  • Year and Date: 2015-10-17
• [Presentation] Structural studies of single-stranded RNA receptor TLR8 (2015)
  • Author(s): Hiromi Tanji, Umeharu Ohto, Takuma Shibaga, Kensuke Miyake, Toshiyuki Shimizu
  • Organizer: Toll meeting 2015
  • Place of Presentation: Marbella, Spain
  • Year and Date: 2015-09-30
  • Int'l Joint Research
• [Presentation] Crystallographic analyses of Toll-like receptor 9 recognizing CpG DNA (2015)
  • Author(s): U. Ohto, T. Shibata, H. Tanji, H. Ishida, E. Krayukhina, S. Uchiyama, K. Miyake, and T. Shimizu
  • Organizer: Toll meeting 2015
  • Place of Presentation: Marbella, Spain
  • Year and Date: 2015-09-30
  • Int'l Joint Research
• [Presentation] Ligand recognition and signal transduction by Toll-like receptor (2015)
  • Author(s): Umeharu Ohto
  • Organizer: 第53回日本生物物理学会
  • Place of Presentation: 金沢大学（金沢）
  • Year and Date: 2015-09-13
• [Presentation] 自然免疫受容体NOD2の構造学的研究 (2015)
  • Author(s): 前川早貴子、大戸梅治、清水敏之
  • Organizer: 第15回日本蛋白質科学会年会
  • Place of Presentation: あわぎんホール（徳島）
  • Year and Date: 2015-06-24
• [Presentation] 自然免疫系一本鎖RNA受容体TLR8の構造基盤 (2015)
  • Author(s): 丹治裕美、大戸梅治、柴田琢磨、田岡万悟、山内芳雄、礒邉俊明、三宅健介、清水敏之
  • Organizer: 第15回日本蛋白質科学会年会
  • Place of Presentation: あわぎんホール（徳島）
  • Year and Date: 2015-06-24
• [Presentation] Toll様受容体8(TLR8)と一本鎖RNA複合体の結晶構造 (2015)
  • Author(s): 丹治裕美、大戸梅治、柴田琢磨、田岡万悟、山内芳雄、礒邊俊明、三宅健介、清水敏之
  • Organizer: 日本薬学会第135年会
  • Place of Presentation: 神戸
  • Year and Date: 2015-03-25 – 2015-03-28
• [Presentation] 自然免疫受容体NOD2の結晶構造解析 (2015)
  • Author(s): 前川早貴子、大戸梅治、清水敏之
  • Organizer: 日本薬学会第135年会
  • Place of Presentation: 神戸
  • Year and Date: 2015-03-25 – 2015-03-28
• [Presentation] Structural study of Toll-like receptor 8 recognizing viral single stranded RNA (2014)
  • Author(s): Umeharu Ohto
  • Organizer: The International Symposium ‘Molecular basis of host cell competency in virus infection’ 2014
  • Place of Presentation: Yokohama
  • Year and Date: 2014-11-08 – 2014-11-09
  • Invited
• [Presentation] 自然免疫系Toll様受容体の構造生物学研究 (2014)
  • Author(s): 大戸梅治、清水敏之
  • Organizer: 第87回日本生化学会年会
  • Place of Presentation: 京都
  • Year and Date: 2014-10-15 – 2014-10-18
• [Presentation] Structural studies of nucleic acid sensing Toll-like receptor (2014)
  • Author(s): U. Ohto, H. Tanji, T. Shibata, K. Miyake, and T. Shimizu
  • Organizer: 23rd Congress and General Assembly of The International Union of Crystallography (IUCr 2014)
  • Place of Presentation: Montreal, Canada
  • Year and Date: 2014-08-05 – 2014-08-12
• [Presentation] TLR8と一本鎖RNAとの複合体の結晶構造 (2014)
  • Author(s): 丹治裕美、大戸梅治、柴田琢磨、三宅健介、清水敏之
  • Organizer: 第14回日本蛋白質科学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2014-06-25 – 2014-06-27
• [Remarks] 研究室ホームページ
  • URL: http://www.f.u-tokyo.ac.jp/~kouzou/index.html