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Creation of artificial enzymes that enable targeted editing of any DNA bases

Research Project

Project/Area Number 17H04994
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field System genome science
Research InstitutionKobe University

Principal Investigator

Nishida Keiji  神戸大学, 先端バイオ工学研究センター, 教授 (10620338)

Project Period (FY) 2017-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥23,400,000 (Direct Cost: ¥18,000,000、Indirect Cost: ¥5,400,000)
Fiscal Year 2020: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2019: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2018: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2017: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Keywordsゲノム編集 / CRISPR / 塩基編集 / 合成生物学 / Target-AID / Base editing / synthetic biology / 合成生物 / バイオテクノロジー / ゲノム / 遺伝子
Outline of Final Research Achievements

As a new base-editing technology, we have succeeded in creating an artificial enzyme that can be expressed in cells without causing genomic instability using DNA glycosylase as a matrix, and can debase thymine only in targeted regions. This enabled the conversion of thymine to other bases. Furthermore, they increased the efficiency by adding factors involved in post-debase repair. In order to increase the versatility of the enzyme, they were able to find a way to make it work in combination with CRISPR variants.

Translated with www.DeepL.com/Translator (free version)

Academic Significance and Societal Importance of the Research Achievements

生物のゲノムを書き換えることができる新たなゲノム編集技術として、これまで困難であったTの一文字の書き換えに関わる酵素について、自然界では異なる文字を認識する酵素を改変することによって新たに生み出すことに成功した。これによってより自由度の高いゲノム情報の書き換えが可能になり、遺伝子治療法や、微生物・農水産物の育種技術として応用可能性が期待される。

Report

(5 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (19 results)

All 2021 2020 2019 2018 2017

All Journal Article (18 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 12 results,  Open Access: 5 results) Book (1 results)

  • [Journal Article] Efficient base editing in tomato using a highly expressed transient system2021

    • Author(s)
      Yuan Shaoze、Kawasaki Shunsuke、Abdellatif Islam M. Y.、Nishida Keiji、Kondo Akihiko、Ariizumi Tohru、Ezura Hiroshi、Miura Kenji
    • Journal Title

      Plant Cell Reports

      Volume: 40 Issue: 4 Pages: 667-676

    • DOI

      10.1007/s00299-021-02662-z

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] CRISPR-derived genome editing technologies for metabolic engineering2021

    • Author(s)
      Nishida Keiji、Kondo Akihiko
    • Journal Title

      Metabolic Engineering

      Volume: 63 Pages: 141-147

    • DOI

      10.1016/j.ymben.2020.12.002

    • Related Report
      2020 Annual Research Report
  • [Journal Article] Multiple gene substitution by Target-AID base-editing technology in tomato2020

    • Author(s)
      Hunziker Johan、Nishida Keiji、Kondo Akihiko、Kishimoto Sanae、Ariizumi Tohru、Ezura Hiroshi
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 20471-20471

    • DOI

      10.1038/s41598-020-77379-2

    • NAID

      120007028992

    • Related Report
      2020 Annual Research Report
  • [Journal Article] Fruit setting rewires central metabolism via gibberellin cascades2020

    • Author(s)
      Shinozaki Yoshihito et al.
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 117 Issue: 38 Pages: 23970-23981

    • DOI

      10.1073/pnas.2011859117

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Production of Herbicide-Sensitive Strain to Prevent Volunteer Rice Infestation Using a CRISPR-Cas9 Cytidine Deaminase Fusion2020

    • Author(s)
      Komatsu Akira、Ohtake Miki、Shimatani Zenpei、Nishida Keiji
    • Journal Title

      Frontiers in Plant Science

      Volume: 11 Pages: 00925-00925

    • DOI

      10.3389/fpls.2020.00925

    • Related Report
      2020 Annual Research Report
  • [Journal Article] Base editors for simultaneous introduction of C-to-T and A-to-G mutations2020

    • Author(s)
      Sakata Rina C.、Ishiguro Soh、Mori Hideto、Tanaka Mamoru、Tatsuno Kenji、Ueda Hiroki、Yamamoto Shogo、Seki Motoaki、Masuyama Nanami、Nishida Keiji、Nishimasu Hiroshi、Arakawa Kazuharu、Kondo Akihiko、Nureki Osamu、Tomita Masaru、Aburatani Hiroyuki、Yachie Nozomu
    • Journal Title

      Nature Biotechnology

      Volume: na Issue: 7 Pages: 865-869

    • DOI

      10.1038/s41587-020-0509-0

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Mammalian synthetic biology by CRISPRs engineering and applications2019

    • Author(s)
      Katayama Kenta、Mitsunobu Hitoshi、Nishida Keiji
    • Journal Title

      Current Opinion in Chemical Biology

      Volume: 52 Pages: 79-84

    • DOI

      10.1016/j.cbpa.2019.05.020

    • Related Report
      2019 Annual Research Report
  • [Journal Article] A method using electroporation for the protein delivery of Cre recombinase into cultured Arabidopsis cells with an intact cell wall2019

    • Author(s)
      Furuhata Yuichi、Sakai Ayako、Murakami Tomi、Morikawa Mone、Nakamura Chikashi、Yoshizumi Takeshi、Fujikura Ushio、Nishida Keiji、Kato Yoshio
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 2163-2163

    • DOI

      10.1038/s41598-018-38119-9

    • NAID

      120006559318

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Targeted Base Editing with CRISPR-Deaminase in Tomato2019

    • Author(s)
      Shimatani Zenpei、Ariizumi Tohru、Fujikura Ushio、Kondo Akihiko、Ezura Hiroshi、Nishida Keiji
    • Journal Title

      Methods Mol Biol.

      Volume: 1917 Pages: 297-307

    • DOI

      10.1007/978-1-4939-8991-1_22

    • ISBN
      9781493989904, 9781493989911
    • Related Report
      2018 Annual Research Report
  • [Journal Article] Herbicide tolerance-assisted multiplex targeted nucleotide substitution in rice2018

    • Author(s)
      Shimatani Zenpei、Fujikura Ushio、Ishii Hisaki、Terada Rie、Nishida Keiji、Kondo Akihiko
    • Journal Title

      Data in Brief

      Volume: 20 Pages: 1325-1331

    • DOI

      10.1016/j.dib.2018.08.124

    • NAID

      120006543325

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] In vivo targeted single-nucleotide editing in zebrafish.2018

    • Author(s)
      Tanaka, S., Yoshioka, S., Nishida, K., Hosokawa, H., Kakizuka, A., and Maegawa, S.
    • Journal Title

      Sci. Rep.

      Volume: 8 Issue: 1 Pages: 11423-11423

    • DOI

      10.1038/s41598-018-29794-9

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Targeted nucleotide editing technologies for microbial metabolic engineering2018

    • Author(s)
      Arazoe, T., Kondo, A., Nishida, K.
    • Journal Title

      Biotechnology Journal

      Volume: 13 Issue: 9 Pages: 170596-170596

    • DOI

      10.1002/biot.201700596

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Inheritance of co-edited genes by CRISPR-based targeted nucleotide substitutions in rice2018

    • Author(s)
      Shimatani Zenpei、Fujikura Ushio、Ishii Hisaki、Matsui Yusuke、Suzuki Minoru、Ueke Yuki、Taoka Ken-ichiro、Terada Rie、Nishida Keiji、Kondo Akihiko
    • Journal Title

      Plant Physiology and Biochemistry

      Volume: 131 Pages: 78-83

    • DOI

      10.1016/j.plaphy.2018.04.028

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genetic and physiological basis for antibody production by Kluyveromyces marxianus2018

    • Author(s)
      Nambu-Nishida Yumiko、Nishida Keiji、Hasunuma Tomohisa、Kondo Akihiko
    • Journal Title

      AMB Express

      Volume: 8 Issue: 1 Pages: 56-56

    • DOI

      10.1186/s13568-018-0588-1

    • NAID

      120006462314

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Deaminase-mediated multiplex genome editing in Escherichia coli2018

    • Author(s)
      Banno S, Nishida K, Arazoe T, Mitsunobu H and Kondo A.
    • Journal Title

      Nature Microbiology

      Volume: 3 Issue: 4 Pages: 423-429

    • DOI

      10.1038/s41564-017-0102-6

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Development of a comprehensive set of tools for genome engineering in a cold- and thermo-tolerant Kluyveromyces marxianus yeast strain2017

    • Author(s)
      Nambu-Nishida Yumiko、Nishida Keiji、Hasunuma Tomohisa、Kondo Akihiko
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 8993-8993

    • DOI

      10.1038/s41598-017-08356-5

    • NAID

      120006346142

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Glycosyltransferase MDR1 assembles a dividing ring for mitochondrial proliferation comprising polyglucan nanofilaments2017

    • Author(s)
      Yoshida Yamato, Kuroiwa Haruko, Shimada Takashi, Yoshida Masaki, Ohnuma Mio, Fujiwara Takayuki, Imoto Yuuta, Yagisawa Fumi, Nishida Keiji, Hirooka Shunsuke, Misumi Osami, Mogi Yuko, Akakabe Yoshihiko, Matsushita Kazunobu, Kuroiwa Tsuneyoshi
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 114 Issue: 50 Pages: 13284-13289

    • DOI

      10.1073/pnas.1715008114

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Beyond Native Cas9: Manipulating Genomic Information and Function2017

    • Author(s)
      Mitsunobu Hitoshi、Teramoto Jun、Nishida Keiji、Kondo Akihiko
    • Journal Title

      Trends in Biotechnology

      Volume: 35 Issue: 10 Pages: 983-996

    • DOI

      10.1016/j.tibtech.2017.06.004

    • Related Report
      2017 Annual Research Report
  • [Book] 完全版 ゲノム編集実験スタンダード2019

    • Author(s)
      中井明日也,Ang Li,西田敬二
    • Total Pages
      386
    • Publisher
      羊土社
    • ISBN
      9784758122443
    • Related Report
      2019 Annual Research Report

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Published: 2017-04-28   Modified: 2022-12-28  

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