Functional analysis of Type IX secretion system using nano scale biomolecule imaging approach

• Project/Area Number: 17K17085
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Morphological basic dentistry
• Research Institution: Okinawa Institute of Science and Technology Graduate University
• Principal Investigator: Satoshi Shibata 沖縄科学技術大学院大学, 生体分子電子顕微鏡解析ユニット, 研究員 (30725057)
• Project Period (FY): 2017-04-01 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2018: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2017: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: 分泌装置 / 電子顕微鏡 / 病原性細菌 / 滑走細菌 / T9SS / 歯周病 / 細菌滑走運動 / 透過型電子顕微鏡 / 浸透圧ショック法 / 超解像顕微鏡 / GldJ局在 / IX型分泌機構 / バクテロイデーテス / 滑走運動 / 歯周病細菌 / 口腔細菌

Outline of Final Research Achievements

The type IX secretion system (T9SS) is unique to phylum Bacteroidetes bacteria and involved in the secretion of pathogenic proteins and gliding motility. To understand these mechanisms of T9SS, we tried to identify the structure of T9SS complex.
In this study, we visualized the ring-like pore structure of T9SS located in the outer membrane in the oral pathogen Porphyromonas gingivalis. In addition, we established a novel rapid freezing method using silica beads. Furthermore, we clarified the existence of helical gliding machinery located inside the outer membrane of the soil bacterium Flavobacterium johnsoniae using various imaging techniques including cryo-electron microscopy. Based on the gliding machinery results a new gliding mechanism was proposed.

Academic Significance and Societal Importance of the Research Achievements

生命機能のメカニズムを解明する上で、各々の機能を担う生体超分子の立体構造の情報は欠かせない。T9SSはバクテロデーテス細菌にとって必須であり、病原性にも重要な役割を担う。研究成果はT9SSの構造、機能の理解という細菌学に新たな知見を与えるだけでなく、T9SSを標的とした分泌阻害、滑走運動阻害剤など感染防除法開発への足がかりになることが期待できる。また、新しい急速凍結法の提案は生体分子イメージング技術の発展にも寄与する。

Research Products

• [Journal Article] Tree of motility : A proposed history of motility systems in the tree of life (2020)
  • Author(s): M Miyata, R C Robinson, T QP Uyeda, Y Fukumori, S Fukushima, S Haruta, M Homma, K Inaba, M Ito, C Kaito, K Kato, TKenri, Y Kinosita, S Kojima, T Minamino, H Mori, S Nakamura, D Nakane, K Nakayama, M Nishiyama, S Shibata, K Shimabukuro, M Tamakoshi, A Taoka, Y Tashiro, ITulum, HiWada, K Wakabayashi
  • Journal Title: Genes to Cells Volume: 25 Issue: 1 Pages: 6-21
  • DOI: 10.1111/gtc.12737
  • NAID: 130007881664
  • URL: https://ocu-omu.repo.nii.ac.jp/records/2019864
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structure of polymerized type V pilin reveals assembly mechanism involving protease-mediated strand exchange (2020)
  • Author(s): Satoshi Shibata, Mikio Shoji, Kodai Okada, Hideyuki Matsunami, Melissa Matthews, Katsumi Imada, Koji Nakayama and Matthias Wolf
  • Journal Title: Nature Microbiology Volume: － Issue: 6 Pages: 830-837
  • DOI: 10.1038/s41564-020-0705-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Application of spherical substrate to observe bacterial motility machineries by Quick-Freeze-Replica Electron Microscopy (2019)
  • Author(s): Katayama Eisaku、Tahara Yuhei O.、Bertin Clothilde、Shibata Satoshi
  • Journal Title: Scientific Reports Volume: 9 Issue: 1 Pages: 14765-14765
  • DOI: 10.1038/s41598-019-51283-w
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Torque transmission mechanism of the curved bacterial flagellar hook revealed by cryo-EM. (2019)
  • Author(s): Shibata S, Matsunami H, Aizawa SI, Wolf M
  • Journal Title: Nature structural & molecular biology Volume: 26 Issue: 10 Pages: 941-945
  • DOI: 10.1038/s41594-019-0301-3
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] High‐resolution archaellum structure reveals a conserved metal‐binding site (2019)
  • Author(s): Meshcheryakov Vladimir A、Shibata Satoshi、Schreiber Makoto Tokoro、Villar‐Briones Alejandro、Jarrell Kenneth F、Aizawa Shin‐Ichi、Wolf Matthias
  • Journal Title: EMBO reports Volume: 20 Issue: 5
  • DOI: 10.15252/embr.201846340
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] バクテロイデーテス細菌の滑走運動 (2018)
  • Author(s): 柴田敏史、中山浩次
  • Journal Title: 生物工学会誌 Volume: 96 Pages: 204-207
  • Open Access
• [Presentation] Cryo-EM Structure of polymerized Type V pilus of P. gingivalis reveals assembly mechanism (2019)
  • Author(s): 柴田敏史, 庄子幹郎, 松波 秀行, Melissa Matthews, 今田 勝己, 中山 浩次, Matthias Wolf
  • Organizer: 第93回日本細菌学会総会
  • Invited
• [Presentation] Polarity and growth direction of an archaellum filament (2019)
  • Author(s): Satoshi Shibata, Shin-Ichi Aizawa and Matthias Wolf
  • Organizer: 第24回べん毛交流会
• [Presentation] Structure of FimA, a major component protein of fimbriae of Porphyromonas gingivitis (2018)
  • Author(s): 岡田 広大, 中山 浩次, 庄子 幹郎, 柴田 敏史, 今田 勝巳
  • Organizer: 日本生物物理学会第56回年会
• [Presentation] Structural analysis of Type V pilus by Cryo-electron microscopy (2018)
  • Author(s): 柴田 敏史, 庄子 幹郎, 岡田 広大, 今田 勝巳, 中山 浩次, Wolf Matthias
  • Organizer: 日本生物物理学会第56回年会
• [Presentation] A Multi-Rail structure in the cell envelope for the Bacteroidete gliding machinery (2017)
  • Author(s): Shibata S., Tahara O. Y., Katayama E., Kawamoto A., Kato T., Zhu Y., Namba K., Miyata M., Nakane D., McBride J. M., Nakayama K.
  • Organizer: Internatonal symposium Harmonized supermolecular motility machinery and its diversity
  • Int'l Joint Research
• [Presentation] Metal ion binding of the Methanococcus archaellin required for filament integrity (2017)
  • Author(s): 柴田敏史、Matthias Wolf
  • Organizer: 第23回べん毛交流会
• [Presentation] Structural analysis of Type V pilus by Cryo-electron microscopy (2017)
  • Author(s): Shibata S., Shoji M., Nakayama K., Wolf M.
  • Organizer: 第91回日本細菌学会総会