Elucidation of the whole structure of type V pilus of a periodontal pathogen by using cryo-EM

• Project/Area Number: 19K10083
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 57020:Oral pathobiological science-related
• Research Institution: Tottori University (2021-2022); Okinawa Institute of Science and Technology Graduate University (2019-2020)
• Principal Investigator: SHIBATA Satoshi 鳥取大学, 医学部, 講師 (30725057)
• Co-Investigator(Kenkyū-buntansha): 庄子 幹郎 長崎大学, 医歯薬学総合研究科(歯学系), 准教授 (10336175) ; 松波 秀行 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, スタッフサイエンティスト (80444511) ; Wolf Matthias 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, 教授 (90630947)
• Project Period (FY): 2019-04-01 – 2023-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2022: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2021: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2020: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2019: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
• Keywords: V 型線毛 / 歯周病 / Bacteroidota 門 / クライオ電子顕微鏡 / 細菌叢 / バイオフィルム / V型線毛 / Bacteroidota門 / アドヘジン / cryo-EM / 付着 / 5型線毛 / Type V pili / P. gingivalis / 線毛

Outline of Research at the Start

慢性歯周炎において最も重要な病原性細菌であるPorphyromonas gingivalis の病原性には菌体表面に形成されるV 型線毛が重要である。本研究はこの線毛の天然状態の構造をクライオ電子顕微鏡解析によって近原子分解能で明らかにし、形成機構や構造と機能の関連性を解明することを目的とする。創薬研究においてターゲットタンパク質複合体の立体構造に基づく薬剤探索は主流であり、研究成果は将来、線毛の重合・定着阻害剤などの開発に繋がり、慢性歯周炎および関連疾患の予防・治療に貢献できると考えられる。

Outline of Final Research Achievements

Adhesive pili are essential for colonization, biofilm formation, virulence, and pathogenesis of many environmental and pathogenic bacteria. Type V pili are unique to bacteria belonging to the phylum Bacteroidota (formerly Bacteroidetes), a major member of the human microbiota. We have determined the structures of the polymerized and monomeric states of type V pili from a periodontal pathogen Porphyromonas gingivalis by cryo-EM and crystallography. We propose a sequential polar assembly mechanism for type V pili at the cell surface, involving protease-mediated strand-exchange.

Academic Significance and Societal Importance of the Research Achievements

V 型線毛は歯周病及びそれを発端とした全身疾患を引き起こす P. gingivalis の感染に重要な役割を果たす。明らかになったV 型線毛の構造と構築機構は創薬研究の鋳型として活用ができる。これにより歯周病および関連疾患の予防・治療に用いる事ができる線毛重合や付着阻害薬の開発が期待される。また、V 型線毛は新規に分類された線毛であり、細菌線毛の多様性を理解するという細菌学の発展にも貢献できる。

Research Products

• [Int'l Joint Research] ETH Zurich(スイス)
• [Int'l Joint Research] Academia Sinica(その他の国・地域)
• [Int'l Joint Research] University of Wisconsin-Milwaukee(米国)
• [Int'l Joint Research] Technical University of Denmark(デンマーク)
• [Int'l Joint Research] Xi’an Jiaotong-Liverpool University(中国)
• [Journal Article] Temporal dynamics of charge buildup in cryo-electron microscopy (2023)
  • Author(s): Schreiber Makoto Tokoro、Maigne Alan、Beleggia Marco、Shibata Satoshi、Wolf Matthias
  • Journal Title: Journal of Structural Biology: X Volume: 7 Pages: 100081-100081
  • DOI: 10.1016/j.yjsbx.2022.100081
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Filamentous structures in the cell envelope are associated with bacteroidetes gliding machinery (2023)
  • Author(s): Shibata Satoshi, Tahara Yuhei O., Katayama Eisaku, Kawamoto Akihiro, Kato Takayuki, Zhu Yongtao, Nakane Daisuke, Namba Keiichi, Miyata Makoto, McBride Mark J., Nakayama Koji
  • Journal Title: Communications Biology Volume: 6 Issue: 1 Pages: 94-94
  • DOI: 10.1038/s42003-023-04472-3
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Live Cell Imaging of Gliding Motility of Flavobacterium johnsoniae Under High-Resolution Microscopy (2023)
  • Author(s): Nakane Daisuke, Shibata Satoshi
  • Journal Title: Methods in Molecular Biology, Bacterial and Archaeal Motility Volume: 2646 Pages: 277-286
  • DOI: 10.1007/978-1-0716-3060-0_22
  • ISBN: 9781071630594, 9781071630600
  • Peer Reviewed / Open Access
• [Journal Article] Isolation and Visualization of Gliding Motility Machinery in Bacteroidota (2023)
  • Author(s): Shibata Satoshi, Nakane Daisuke
  • Journal Title: Methods in Molecular Biology, Bacterial and Archaeal Motility Volume: 2646 Pages: 267-276
  • DOI: 10.1007/978-1-0716-3060-0_21
  • ISBN: 9781071630594, 9781071630600
  • Peer Reviewed / Open Access
• [Journal Article] Type V Pilus is Assembled by a Protease-mediated Strand-exchange Mechanism (2022)
  • Author(s): SHIBATA Satoshi
  • Journal Title: Seibutsu Butsuri Volume: 62 Issue: 1 Pages: 32-35
  • DOI: 10.2142/biophys.62.32
  • ISSN: 0582-4052, 1347-4219
  • Peer Reviewed / Open Access
• [Journal Article] SARS-CoV-2 IgG seroprevalence in the Okinawa Main Island and remote islands in Okinawa, Japan, 2020-2021 (2022)
  • Author(s): Mizumoto Kenji et al.,
  • Journal Title: MedRxiv Volume: -
  • DOI: 10.1101/2022.03.02.22271759
  • Open Access
• [Journal Article] A Multi-Rail Structure in the Cell Envelope for the Bacteroidetes Gliding Machinery (2022)
  • Author(s): Shibata Satoshi、Tahara Yuhei O.、Katayama Eisaku、Kawamoto Akihiro、Kato Takayuki、Zhu Yongtao、Nakane Daisuke、Namba Keiichi、Miyata Makoto、McBride Mark J.、Nakayama Koji
  • Journal Title: Research Square Volume: -
  • DOI: 10.21203/rs.3.rs-1802191/v1
  • Open Access / Int'l Joint Research
• [Journal Article] Investigation of Bacteria from Spoiled Bottled Salad Dressing Leading to Gas Explosion (2022)
  • Author(s): Obata Fumiko、Murota Hiromi、Shibata Satoshi、Ozuru Ryo、Fujii Jun
  • Journal Title: Yonago Acta Medica Volume: 65 Issue: 3 Pages: 207-214
  • DOI: 10.33160/yam.2022.08.005
  • ISSN: 0513-5710, 1346-8049
  • Peer Reviewed / Open Access
• [Journal Article] 細菌の新奇Ⅴ型線毛でみられる原子レベルでの「ほぞ継ぎ」技法 (2021)
  • Author(s): 柴田敏史
  • Journal Title: 実験医学 Volume: 38(14) Pages: 2380-2383
• [Journal Article] Biogenesis of Type V pili. (2020)
  • Author(s): Shoji M, Shibata S, Sueyoshi T, Naito M, Nakayama K.
  • Journal Title: Microbiology and Immunology Volume: 64(10) Issue: 10 Pages: 643-656
  • DOI: 10.1111/1348-0421.12838
  • NAID: 120006988474
  • 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] Transport and Polymerization of Porphyromonas gingivalis Type V Pili (2020)
  • Author(s): Shoji M, Shibata S, Naito M, Nakayama K.
  • Journal Title: Methods in Molecular Microbiology Volume: 2210 Pages: 61-73
  • DOI: 10.1007/978-1-0716-0939-2_7
  • ISBN: 9781071609385, 9781071609392
  • Peer Reviewed / Open Access / Int'l Joint Research
• [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: 120006881482
  • 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
• [Presentation] Study of protein secretion mechanisms in Porphyromonas gingivalis (2023)
  • Author(s): 庄子幹郎, 佐々木祐子, 末吉峻幸, 柴田敏史, 松尾長大, 雪竹英治, Matthias Wolf, 内藤 真理子
  • Organizer: 第96回日本細菌学会総会
• [Presentation] Cryo-EM structure of the Mfa minor type V pilus from the oral pathogen Porphyromonas gingivalis (2023)
  • Author(s): 柴田敏史, 庄子幹郎, 松波秀行, Matthias Wolf, 藤井潤
  • Organizer: 第96回日本細菌学会総会
• [Presentation] 歯周病菌Mfa53線毛の構造 (2023)
  • Author(s): 小島嶺, 庄子幹郎, 柴田敏史, 竹川宜宏, 今田勝巳
  • Organizer: 第26回べん毛研究交流会
• [Presentation] 細菌表面のフィラメント状超分子複合体の構造解析 (2022)
  • Author(s): 柴田敏史
  • Organizer: 第 16 回細菌学若手コロッセウム
• [Presentation] The assembly mechanism and structures of Type V pili (2021)
  • Author(s): 柴田 敏史, 庄子 幹郎, Matthias Wolf, 藤井 潤
  • Organizer: 第95回日本細菌学会総会
  • Invited
• [Presentation] バクテロイデア綱細菌のV型線毛の構築機構 (2021)
  • Author(s): 柴田敏史
  • Organizer: 第15回細菌学若手コロッセウム
  • Invited
• [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
• [Book] クライオ電子顕微鏡ハンドブック (2023)
  • Author(s): 柴田敏史 (分担)、難波 啓一、加藤 貴之、牧野 文信(編集)、
  • Total Pages: 460
  • Publisher: エヌ・ティー・エス
  • ISBN: 9784860438043
• [Remarks] researchmap
  • URL: https://researchmap.jp/helical
• [Remarks] 鳥取大学医学部医学科細菌学分野HP
  • URL: https://www.med.tottori-u.ac.jp/introduction/medicine/about/3318/3326/23768.html
• [Remarks] 鳥取大学研究者詳細
  • URL: http://researchers.adm.tottori-u.ac.jp/html/100002310_ja.html
• [Remarks] 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 HP
  • URL: https://groups.oist.jp/mcemu