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Single molecule imaging of eukaryotic transcription.

Research Project

Project/Area Number 19H03197
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43040:Biophysics-related
Research InstitutionThe University of Tokyo

Principal Investigator

TADAKUMA HISASHI  東京大学, 定量生命科学研究所, 協力研究員 (10339707)

Co-Investigator(Kenkyū-buntansha) 安達 成彦  大学共同利用機関法人高エネルギー加速器研究機構, 物質構造科学研究所, 特任准教授 (70707489)
Project Period (FY) 2019-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2021: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2020: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2019: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Keywords1分子計測(SMD) / DNAデバイス / 遺伝子発現 / 転写 / 翻訳 / クライオ電子顕微鏡 / 核酸 / 蛋白質 / 分子モーター / ナノバイオ
Outline of Research at the Start

生命の設計図であるゲノムから、RNAを作る転写反応は、生命の基本反応の1つです。しかし、従来、関与する因子の同定は進んでいるものの、実際に機能する際の3次元的な空間配置を解析する技術に限界があり、その分子機構は良くわかっていませんでした。本研究では、ナノメートル精度で設計された人工反応場を構築し、関与因子の空間配置がどのように転写反応に影響を与えるかを明らかにします。

Outline of Final Research Achievements

Gene expression is powered by weak interaction of bio-molecules. To compensate the weak interaction, related molecules are integrated on the scaffold and form super-complex and "Nano reaction field", which allows the efficient process of specific reaction while excluding unintended factors. Here, we developed basic techniques to reconstitute these "Nano reaction field". We established DNA origami-based technologies for activity and structure analysis (e.g., Cryo-EM), which would be also the platform for future gene expression control nano-device.

Academic Significance and Societal Importance of the Research Achievements

本研究では、従来の反応拡散系を基にした反応系ではなく、反応に関与する因子をDNAナノ構造の上に集積化した反応系(ナノ反応場)を構築・解析する為の基盤技術の確立を行った。確立した技術は、生体の超分子構造の解析に応用可能であり、生命科学研究の進展に寄与すると思われる。また、我々が構築してきたプログラム可能な遺伝子発現ナノデバイス(ナノチップ)に適用する事で、細胞や人工細胞の運命制御が可能となり、医薬や有用物質生産に貢献すると期待される

Report

(4 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (42 results)

All 2022 2021 2020 2019

All Journal Article (16 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 16 results,  Open Access: 10 results) Presentation (25 results) (of which Int'l Joint Research: 3 results,  Invited: 13 results) Book (1 results)

  • [Journal Article] Structural basis of the strict specificity of a bacterial GH31 α-1,3-glucosidase for nigerooligosaccharides2022

    • Author(s)
      Marina Ikegaya, Toshio Moriya, Naruhiko Adachi, Masato Kawasaki, Enoch Y. Park, Takatsugu Miyazaki
    • Journal Title

      Journal of Biological Chemistry

      Volume: 298 Issue: 5 Pages: 101827-101827

    • DOI

      10.1016/j.jbc.2022.101827

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes2021

    • Author(s)
      Mori Takahiro、Kumano Takuto、He Haibing、Watanabe Satomi、Senda Miki、Moriya Toshio、Adachi Naruhiko、Hori Sanae、Terashita Yuzu、Kawasaki Masato、Hashimoto Yoshiteru、Awakawa Takayoshi、Senda Toshiya、Abe Ikuro、Kobayashi Michihiko
    • Journal Title

      Nature Communications

      Volume: 12 Issue: 1 Pages: 6294-6294

    • DOI

      10.1038/s41467-021-26585-1

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Non-conventional octameric structure of C-phycocyanin2021

    • Author(s)
      Minato Takuo、Teramoto Takamasa、Adachi Naruhiko、Hung Nguyen Khac、Yamada Kaho、Kawasaki Masato、Akutsu Masato、Moriya Toshio、Senda Toshiya、Ogo Seiji、Kakuta Yoshimitsu、Yoon Ki-Seok
    • Journal Title

      Communications Biology

      Volume: 4 Issue: 1 Pages: 1238-1238

    • DOI

      10.1038/s42003-021-02767-x

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cryo-EM structure of the nucleosome core particle containing <i>Giardia lamblia</i> histones2021

    • Author(s)
      Sato Shoko、Takizawa Yoshimasa、Hoshikawa Fumika、Dacher Mariko、Tanaka Hiroki、Tachiwana Hiroaki、Kujirai Tomoya、Iikura Yukari、Ho Cheng-Han、Adachi Naruhiko、Patwal Indu、Flaus Andrew、Kurumizaka Hitoshi
    • Journal Title

      Nucleic Acids Research

      Volume: 49 Issue: 15 Pages: 8934-8946

    • DOI

      10.1093/nar/gkab644

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis2021

    • Author(s)
      Teramoto Takamasa、Koyasu Takeshi、Adachi Naruhiko、Kawasaki Masato、Moriya Toshio、Numata Tomoyuki、Senda Toshiya、Kakuta Yoshimitsu
    • Journal Title

      Journal of Biological Chemistry

      Volume: 297 Issue: 3 Pages: 101028-101028

    • DOI

      10.1016/j.jbc.2021.101028

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 2.85 and 2.99?? resolution structures of 110?kDa nitrite reductase determined by 200?kV cryogenic electron microscopy2021

    • Author(s)
      Adachi Naruhiko、Yamaguchi Takahide、Moriya Toshio、Kawasaki Masato、Koiwai Kotaro、Shinoda Akira、Yamada Yusuke、Yumoto Fumiaki、Kohzuma Takamitsu、Senda Toshiya
    • Journal Title

      Journal of Structural Biology

      Volume: 213 Issue: 3 Pages: 107768-107768

    • DOI

      10.1016/j.jsb.2021.107768

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Single-molecule analysis of processive double-stranded RNA cleavage by Drosophila Dicer-22021

    • Author(s)
      Naganuma Masahiro、Tadakuma Hisashi、Tomari Yukihide
    • Journal Title

      Nature Communications

      Volume: 12 Issue: 1 Pages: 4268-4268

    • DOI

      10.1038/s41467-021-24555-1

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] DNA polymerase D temporarily connects primase to the CMG-like helicase before interacting with proliferating cell nuclear antigen2021

    • Author(s)
      Oki Keisuke、Yamagami Takeshi、Nagata Mariko、Mayanagi Kouta、Shirai Tsuyoshi、Adachi Naruhiko、Numata Tomoyuki、Ishino Sonoko、Ishino Yoshizumi
    • Journal Title

      Nucleic Acids Research

      Volume: 49 Issue: 8 Pages: 4599-4612

    • DOI

      10.1093/nar/gkab243

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural and functional analyses of the tridomain‐nonribosomal peptide synthetase FmoA3 for 4‐methyloxazoline ring formation2021

    • Author(s)
      Katsuyama Yohei、Sone Kaoru、Harada Ayaka、Kawai Seiji、Urano Naoki、Adachi Naruhiko、Moriya Toshio、Kawasaki Masato、Shin-ya Kazuo、Senda Toshiya、Ohnishi Yasuo
    • Journal Title

      Angewandte Chemie International Edition

      Volume: 未定 Issue: 26 Pages: 14554-14562

    • DOI

      10.1002/anie.202102760

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of the full-length LysR-type transcription regulator2021

    • Author(s)
      Giannopoulou EA, Senda M, Koentjoro MP, Adachi N, Ogawa N, Senda T.
    • Journal Title

      FEBS J.

      Volume: - Issue: 15 Pages: 4560-4575

    • DOI

      10.1111/febs.15764

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cryo-EM Structure of K+-Bound hERG Channel Complexed with the Blocker Astemizole2021

    • Author(s)
      Asai Tatsuki、Adachi Naruhiko、Moriya Toshio、Oki Hideyuki、Maru Takamitsu、Kawasaki Masato、Suzuki Kano、Chen Sisi、Ishii Ryohei、Yonemori Kazuko、Igaki Shigeru、Yasuda Satoshi、Ogasawara Satoshi、Senda Toshiya、Murata Takeshi
    • Journal Title

      Structure

      Volume: 29 Issue: 3 Pages: 203-212.e4

    • DOI

      10.1016/j.str.2020.12.007

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Viral RNA recognition by LGP2 and MDA5, and activation of signaling through step-by-step conformational changes2020

    • Author(s)
      Duic Ivana、Tadakuma Hisashi、Harada Yoshie、Yamaue Ryo、Deguchi Katashi、Suzuki Yuki、Yoshimura Shige H、Kato Hiroki、Takeyasu Kunio、Fujita Takashi
    • Journal Title

      Nucleic Acids Research

      Volume: 48 Issue: 20 Pages: 11664-11674

    • DOI

      10.1093/nar/gkaa935

    • NAID

      120006936359

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structural analysis reveals TLR7 dynamics underlying antagonism2020

    • 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

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Crystallographic and cryogenic electron microscopic structures and2020

    • Author(s)
      Sato Y, Yabuki T, Adachi N, Moriya T, Arakawa T, Kawasaki M, Yamada C,
    • Journal Title

      J Struct Biol X

      Volume: 4 Pages: 100030-100030

    • DOI

      10.1016/j.yjsbx.2020.100030

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Overview of the “biophysics in nano-space” session at the 57th annual meeting of the2020

    • Author(s)
      Tadakuma Hisashi and Kitagawa Daiju
    • Journal Title

      Biophysical Reviews

      Volume: 12 Issue: 2 Pages: 1-3

    • DOI

      10.1007/s12551-020-00646-z

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] HCV IRES captures an actively translating 80S ribosome2019

    • Author(s)
      Yokoyama Takeshi、Machida Kodai、Iwasaki Wakana、Shigeta Tomoaki、Nishimoto Madoka、Takahashi Mari、Sakamoto Ayako、Yonemochi Mayumi、Harada Yoshie、Shigematsu Hideki、Shirouzu Mikako、Tadakuma Hisashi、Imataka Hiroaki、Ito Takuhiro
    • Journal Title

      Molecular Cell

      Volume: 印刷中 Issue: 6 Pages: 1205-1214

    • DOI

      10.1016/j.molcel.2019.04.022

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Brief introduction of cryo-EM network and KEK cryo-EM facilit2021

    • Author(s)
      安達成彦
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] yOperation and recent activities of the cryo-EM facility in KEK2021

    • Author(s)
      安達成彦
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Construction of Tough DNA Origami2021

    • Author(s)
      Yuxiang Liu, Ruixuan Wang, Qi Chen, Kodai Fukumoto, Bingxun Wang, Yuko Murayama, Shun-ichi Sekine, Hisashi Tadakuma
    • Organizer
      第22回日本RNA学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 第3回クライオ電顕ネットワークユーザーグループミーティング:クライオ電顕・単粒子解析におけるtips2020

    • Author(s)
      安達成彦
    • Organizer
      第43回分子生物学会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] DNAオリガミを用いたキネシン-1の空間配置が輸送複合体の協調運動に与える影響の解析2020

    • Author(s)
      福本 紘大, 宮薗 侑也, 多田隈 尚史, 原田 慶恵
    • Organizer
      第43回分子生物学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] キネシン分子の空間配置が輸送複合体の運動に与える影響の評価2020

    • Author(s)
      福本 紘大, 宮薗 侑也, 多田隈 尚史, 原田 慶恵
    • Organizer
      第58回日本生物物理学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Structure analysis of transcription related complexes2020

    • Author(s)
      Naruhiko Adachi
    • Organizer
      Cold Spring Harbor Laboratory meeting
    • Related Report
      2020 Annual Research Report
  • [Presentation] クライオ電子顕微鏡:単粒子解析の原理と実際2020

    • Author(s)
      安達成彦
    • Organizer
      遺伝研カジュアルセミナー
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Oscillatory movement of a dynein-microtubule complex crosslinked with DNA-origami2019

    • Author(s)
      Shimaa A. Abdellatef, Hisashi Tadakuma, Yuichi Kondo, Kangmin Yan, Rofia Boudria, Kodai Fukumoto, Takashi Fujiwara, Hideo Higuchi, and Keiko Hirose
    • Organizer
      64th Annual Meeting of Biophysical Society
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Dicer-2による二本鎖RNAプロセッシングの一分子解析2019

    • Author(s)
      永沼 政広, 多田隈 尚史, 泊 幸秀
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] KEKにおけるクライオ電顕施設の紹介2019

    • Author(s)
      千田俊哉・安達成彦・川崎政人・守屋俊夫・山田悠介・篠田晃・小祝孝太
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] KEKクライオ電顕の現状2019

    • Author(s)
      千田俊哉・安達成彦・川崎政人・守屋俊夫・山田悠介・篠田晃・小祝孝太
    • Organizer
      生理研研究会「クライオ電子顕微鏡によるタンパク質の高分解能単粒子構造解析」
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Reconstitution of kinesin-based transport complex using DNA origami2019

    • Author(s)
      Kodai Fukumoto, Yuya Miyazono, Hisashi Tadakuma, Yoshie Harada
    • Organizer
      CBI学会2019年大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] How nano-space affects biological phenomena2019

    • Author(s)
      多田隈尚史
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Oscillatory movement of the dynein-microtubule complex crosslinked with DNA-origami2019

    • Author(s)
      Abdellatef Shimaa A., 多田隈 尚史, 近藤 雄一, 厳 康敏, 樋口 秀男, 広瀬 恵子
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Evaluating coordination between kinesin motors using DNA origami-based transport complex.2019

    • Author(s)
      福本 紘大, 宮薗 侑也, 多田隈 尚史, 原田 慶恵
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 集積型遺伝子チップを用いた、転写の理解と制御2019

    • Author(s)
      多田隈尚史
    • Organizer
      第92回日本生化学会大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Structure analysis of transcription related complexes and2019

    • Author(s)
      Naruhiko Adachi, Masato Kawasaki, Toshio Moriya, Fumiaki Yumoto,
    • Organizer
      Cold Spring Harbor Laboratory meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 単粒子解析の原理と実際:KEKにおける共同利用型クライオ電子顕微鏡の2019

    • Author(s)
      安達成彦
    • Organizer
      日本プロテオーム学会2019年大会・第70回日本電気泳動学会総会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Structure analysis of transcription related complexes and2019

    • Author(s)
      Naruhiko Adachi, Masato Kawasaki, Toshio Moriya, Fumiaki Yumoto,
    • Organizer
      The 2019 American Crystallographic Association Annual Meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Dicer-2による二本鎖RNAプロセッシングの一分子解析2019

    • Author(s)
      永沼 政広, 多田隈 尚史, 泊 幸秀
    • Organizer
      第21回日本RNA学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] クライオ電子顕微鏡で生体分子の形を明らかにする2019

    • Author(s)
      安達成彦
    • Organizer
      KEK公開講座「生物学におけるクライオ電子顕微鏡」
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Protein integrated nano-chip for transcription analysis and regulation2019

    • Author(s)
      多田隈尚史
    • Organizer
      第19回 日本蛋白質科学会年会 / 第71回 日本細胞生物学会大会 合同年次大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Structure analysis of transcription related complexes and2019

    • Author(s)
      安達成彦
    • Organizer
      第19回 日本蛋白質科学会年会 / 第71回 日本細胞生物学会大会 合同年次大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] クライオ電子顕微鏡:気になっていること・困っていること@KEK2019

    • Author(s)
      安達成彦
    • Organizer
      日本顕微鏡学会・第75回学術講演会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Book] 実験医学増刊 Vol.38 No.5 イメージング時代の構造生命科学2020

    • Author(s)
      安達成彦、千田俊哉
    • Total Pages
      5
    • Publisher
      羊土社
    • ISBN
      9784758103855
    • Related Report
      2019 Annual Research Report

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Published: 2019-04-18   Modified: 2023-01-30  

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