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Small-molecule induced –1 ribosomal frameshifting and its application to the control of protein transport and localization

Research Project

Project/Area Number 18K05355
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 37030:Chemical biology-related
Research InstitutionOsaka University

Principal Investigator

Murata Asako  大阪大学, 産業科学研究所, 准教授 (50557121)

Project Period (FY) 2018-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2020: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2019: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2018: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Keywordsリボソーマルフレームシフト / RNA二次構造 / 翻訳制御 / 合成小分子 / 小分子 / RNA2次構造 / -1リボソームフレームシフト / タンパク質輸送・局在
Outline of Final Research Achievements

In this study, we aimed to develop a tool to control the synthesis of fusion protein via small molecule-induced programmed -1 ribosomal frameshifting (-1PRF). -1PRF is a mechanism that redirects the translation of an mRNA into an alternative reading frame, resulting in synthesis of two protein products from a single transcript. -1PRF is triggered by two elements: a slippery sequence and a pseudoknot in the mRNA. We engineered the pseudoknot to respond to our small molecule NCTn and applied the NCTn-responsive pseudoknot to trigger -1PRF for NCTn-dependent synthesis of a fusion protein. For demonstration, we applied the NCTn-dependent -1PRF to premature translation termination of the target protein, which altered transmembrane signaling and induced a change in subcellular localization of the protein. We also explored pseudoknot RNA sequences optimal for a small molecule-dependent -1PRF.

Academic Significance and Societal Importance of the Research Achievements

-1リボソーマルフレームシフトは(-1PRF),読み枠の異なる2つのタンパク質が,融合タンパク質として単一のmRNAから翻訳される仕組みである。本研究では,-1PRFを融合タンパク質の合成を翻訳段階で調節することが可能な分子スイッチととらえ,小分子依存的な誘導が可能なツールとして新たに開発することとした。本ツールの開発により,標的タンパク質の細胞内局在を変化させることに成功した。既存の遺伝子工学手法では実現できない翻訳段階でのタンパク質の細胞内局在シグナルの調節というアプローチを提供することができる。

Report

(5 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (33 results)

All 2022 2021 2020 2019 2018 Other

All Int'l Joint Research (4 results) Journal Article (14 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 14 results,  Open Access: 5 results) Presentation (15 results) (of which Int'l Joint Research: 10 results,  Invited: 1 results)

  • [Int'l Joint Research] National Chung Hsing University, Taiwan(その他の国・地域)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] National Chung Hsing University, Taiwan(その他の国・地域)

    • Related Report
      2020 Research-status Report
  • [Int'l Joint Research] National Chung-Hsing University(その他の国・地域)

    • Related Report
      2019 Research-status Report
  • [Int'l Joint Research] Department of Physical Biochemistry/Max Planck Institute/for Biophysical Chemistry(ドイツ)

    • Related Report
      2018 Research-status Report
  • [Journal Article] Premature translation termination mediated non-ER stress induced ATF6 activation by a ligand-dependent ribosomal frameshifting circuit2022

    • Author(s)
      Hsu Hsiu-Ting、Murata Asako、Dohno Chikara; Nakatan Kazuhiko、Chang Kung Yao
    • Journal Title

      Nucleic Acids Research

      Volume: -

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] HT-SELEX-based identification of binding pre-miRNA hairpin-motif for small molecules2022

    • Author(s)
      Mukherjee Sanjukta、Murata Asako、Ishida Ryoga、Sugai Ayako、Dohno Chikara、Hamada Michiaki、Krishna Sudhir、Nakatani Kazuhiko
    • Journal Title

      Molecular Therapy - Nucleic Acids

      Volume: 27 Pages: 165-174

    • DOI

      10.1016/j.omtn.2021.11.021

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 2-Amino-1,8-naphthyridine Dimer (ANP77), a High-Affinity Binder to the Internal Loops of C/CC and T/CC Sites in Double-Stranded DNA2021

    • Author(s)
      Das Bimolendu、Nagano Konami、Kawai Gota、Murata Asako、Nakatani Kazuhiko
    • Journal Title

      The Journal of Organic Chemistry

      Volume: 87 Issue: 1 Pages: 340-350

    • DOI

      10.1021/acs.joc.1c02383

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A small-molecule fluorescence probe ANP77 for sensing RNA internal loop of C, U and A/CC motifs and their binding molecules2021

    • Author(s)
      Das Bimolendu、Murata Asako、Nakatani Kazuhiko
    • Journal Title

      Nucleic Acids Research

      Volume: 49 Issue: 15 Pages: 8462-8470

    • DOI

      10.1093/nar/gkab650

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Speeding drug discovery targeting RNAs: An iterative “RNA selection-compounds screening cycle“ for exploring RNA-small molecule pairs2021

    • Author(s)
      Furuzono Tomoko、Murata Asako、Okuda Satoshi、Mizutani Kenji、Adachi Tsuyoshi、Nakatani Kazuhiko
    • Journal Title

      Bioorganic & Medicinal Chemistry

      Volume: 36 Pages: 116070-116070

    • DOI

      10.1016/j.bmc.2021.116070

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Small Molecule-Induced Dimerization of Hairpin RNA Interfered with the Dicer Cleavage Reaction2021

    • Author(s)
      Murata Asako、Mori Yuki、Di Yue、Sugai Ayako、Das Bimolendu、Takashima Yusuke、Nakatani Kazuhiko
    • Journal Title

      Biochemistry

      Volume: 60 Issue: 4 Pages: 245-249

    • DOI

      10.1021/acs.biochem.0c00920

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] The dimeric form of 1, 3 - diaminoisoquinoline derivative rescued the mis - splicing of Atp2a1 and Clcn1 genes in myotonic dystrophy type 1 mouse model2020

    • Author(s)
      Matsumoto, J. ; Nakamori, M. ; Okamoto, T. ; Murata, A. ; Dohno, C. ; Nakatani, K.
    • Journal Title

      Chem. Eur. J.

      Volume: 26 Issue: 63 Pages: 14305-14309

    • DOI

      10.1002/chem.202001572

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A slipped-CAG DNA-binding small molecule induces trinucleotide-repeat contractions in vivo2020

    • Author(s)
      Nakamori Masayuki, Panigrahi Gagan B., Lanni Stella, et. al.
    • Journal Title

      Nature Genetics

      Volume: 52 Issue: 2 Pages: 146-159

    • DOI

      10.1038/s41588-019-0575-8

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Inhibition of pre-miRNA-136 processing by Dicer with small molecule BzDANP suggested the formation of ternary complex of pre-miR-136?BzDANP?Dicer2019

    • Author(s)
      Otabe Takahiro、Nagano Konami、Kawai Gota、Murata Asako、Nakatani Kazuhiko
    • Journal Title

      Bioorganic & Medicinal Chemistry

      Volume: 27 Issue: 10 Pages: 2140-2148

    • DOI

      10.1016/j.bmc.2019.03.031

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Modulating RNA secondary and tertiary structures by mismatch binding ligands2019

    • Author(s)
      Murata Asako、Nakamori Masayuki、Nakatani Kazuhiko
    • Journal Title

      Methods

      Volume: 167 Pages: 78-91

    • DOI

      10.1016/j.ymeth.2019.05.006

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] RT‐Hpro‐PCR: A MicroRNA Detection System Using a Primer with a DNA Tag2019

    • Author(s)
      Takei Fumie、Akiyama Misaki、Murata Asako、Sugai Ayako、Nakatani Kazuhiko、Yamashita Ichiro
    • Journal Title

      ChemBioChem

      Volume: 21 Issue: 4 Pages: 477-480

    • DOI

      10.1002/cbic.201900382

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structural insights into synthetic ligands targeting A?A pairs in disease-related CAG RNA repeats2019

    • Author(s)
      Mukherjee Sanjukta、Blaszczyk Leszek、Rypniewski Wojciech、Falschlunger Christoph、Micura Ronald、Murata Asako、Dohno Chikara、Nakatani Kazuhiko、Kiliszek Agnieszka
    • Journal Title

      Nucleic Acids Research

      Volume: 47 Issue: 20 Pages: 10906-10913

    • DOI

      10.1093/nar/gkz832

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Small synthetic molecule-stabilized RNA pseudoknot as an activator for -1 ribosomal frameshifting2018

    • Author(s)
      Matsumoto Saki、Caliskan Neva、Rodnina Marina V、Murata Asako、Nakatani Kazuhiko
    • Journal Title

      Nucleic Acids Research

      Volume: 46 Issue: 16 Pages: 8079-8089

    • DOI

      10.1093/nar/gky689

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A Dimeric 2,9‐Diamino‐1,10‐phenanthroline Derivative Improves Alternative Splicing in Myotonic Dystrophy Type 1 Cell and Mouse Models2018

    • Author(s)
      Li Jinxing、Nakamori Masayuki、Matsumoto Jun、Murata Asako、Dohno Chikara、Kiliszek Agnieszka、Taylor Katarzyna、Sobczak Krzysztof、Nakatani Kazuhiko
    • Journal Title

      Chemistry - A European Journal

      Volume: 24 Issue: 68 Pages: 18115-18122

    • DOI

      10.1002/chem.201804368

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Regulation of circular RNA biogenesis via nucleic acid binding small molecule in cells2021

    • Author(s)
      Lu Ni, Takeshi Yamada, Asako Murata, Kazuhiko Nakatani
    • Organizer
      The 48th International Symposium on Nucleic Acids Chemistry (ISNAC2021)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Effect of Guanine-guanine Mismatch Binding Ligand on Repair Enzymes' reactions in vitro2021

    • Author(s)
      Anisa Ul'Husna, Asako Murata, Kazuhiko Nakatani
    • Organizer
      The 48th International Symposium on Nucleic Acids Chemistry (ISNAC2021)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Cell-based screening of chemical libraries for small molecules that target SARS-CoV-2 frameshifting signal2021

    • Author(s)
      Risa Anami, Asako Murata, Kazuhiko Nakatani
    • Organizer
      The 48th International Symposium on Nucleic Acids Chemistry (ISNAC2021)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Identification of small molecules that can bind to the SARS-CoV-2 frameshifting signal by SPR-based screening of chemical libraries2021

    • Author(s)
      Hiyori Fujii, Asako Murata, Kazuhiko Nakatani
    • Organizer
      The 48th International Symposium on Nucleic Acids Chemistry (ISNAC2021)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Regulation of circular RNA biogenesis using nucleic acid binding small molecule in cellular environment2021

    • Author(s)
      Lu Ni, Takeshi Yamada, Asako Murata, Kazuhiko Nakatani
    • Organizer
      The International Chemical Congress of Pcific Basin Societies 2021 (Pacifichem 2021)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Dicer切断産物のハイスループットシーケンシングによる RNA-小分子結合モチーフの同定2021

    • Author(s)
      高島 裕介、村田 亜沙子、中谷 和彦
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Regulation of circular RNA biogenesis via RNA binding small molecule2021

    • Author(s)
      Lu Ni, Takeshi Yamada, Asako Murata, Kazuhiko Nakatani
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Synthesis and the properties of naphthyridine-azaquinolone dimer (NAD) tatgeting CAG-repeat RNA2021

    • Author(s)
      Qingwen Chen, Takeshi Yamada, Asako Murata, Kazuhiko Nakatani
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Research-status Report
  • [Presentation] SARS-CoV-2フレームシフトシグナルを標的とする低分子化合物の表面プラズモン共鳴(SPR)アッセイによるスクリーニング2021

    • Author(s)
      藤井 陽和、村田 亜沙子、中谷 和彦
    • Organizer
      日本化学会第101春季年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Comprehensive Analysis of Dicer Substrates by High-Throughput Sequencing Identified New Target RNA Motifs for Small Molecules2020

    • Author(s)
      Asako Murata, Yusuke Takashima, Kei Iida, Ayako Sugai, Masatoshi Hagiwara, Kazuhiko Nakatani
    • Organizer
      The 43rd Annual Meeting of the Molecular Biology Society of Japan (MBSJ2020)
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] Controlling -1 ribosomal frameshifting by small molecules in cells2020

    • Author(s)
      Asako Murata, Saki Matsumoto, Neva Caliskan, Marina V. Rodnina, Kazuhiko Nakatani
    • Organizer
      The 23rd SANKEN INTERNATIONAL SYMPOSIUM
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Exploration of RNA sequences in pre-miRNA affecting the efficiency of Dicer cleavage reactions by the small molecules binding2019

    • Author(s)
      Yusuke Takashima, Asako Murata, Kazuhiko Nakatani
    • Organizer
      The 24th Annual Meeting of the RNA Society (RNA 2019)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats2019

    • Author(s)
      Sanjukta Mukherjee, Leszek Blaszczyk, Wojciech Rypniewski, Christoph Falschlunger, Ronald Micura, Asako Murata, Chikara Dohno, Kazuhiko Nakatani, Agnieszka Kiliszek
    • Organizer
      The 24th Annual Meeting of the RNA Society (RNA 2019)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Kinetic analysis of the inhibitory effect of BzDANP on Dicer cleavage of pre-miR-1362019

    • Author(s)
      Asako Murata, Takahiro Otabe, Konami Nagano, Gota Kawai, Ayako Sugai, Kazuhiko Nakatani
    • Organizer
      The Commemorative International Symposium of the Japan Society of Nucleic Acids Chemistry (CISNAC 2019)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Synthetic small molecule-stabilized RNA pseudoknot as an activator for -1 ribosomal frameshifting2018

    • Author(s)
      Asako Murata, Saki Matsumoto, Neva Caliskan, Marina V. Rodnina, Kazuhiko Nakatani
    • Organizer
      International Symposium on Nucleic Acids Chemistry (ISNAC) 2018
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research

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Published: 2018-04-23   Modified: 2023-01-30  

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