Plant mitochondrial genome repair and cytoplasmic male sterility using the mitoTALEN method.

• Project/Area Number: 19KK0391
• Research Category: Fund for the Promotion of Joint International Research (Fostering Joint International Research (A))
• Allocation Type: Multi-year Fund
• Review Section: Basic Section 39010:Science in plant genetics and breeding-related
• Research Institution: The University of Tokyo
• Principal Investigator: ARIMURA Shin-ichi 東京大学, 大学院農学生命科学研究科(農学部), 教授 (00396938)
• Project Period (FY): 2020 – 2024
• Project Status: Completed (Fiscal Year 2024)
• Budget Amount: ¥15,210,000 (Direct Cost: ¥11,700,000、Indirect Cost: ¥3,510,000)
• Keywords: ミトコンドリア / ゲノム編集 / 植物ミトコンドリア / ミトコンドリアゲノム編集

Outline of Research at the Start

植物ミトコンドリアゲノムは遺伝子組換え技術が確立されていなかったが，申請者らは最近ゲノム編集技術TALENを応用して標的遺伝子破壊に世界で初めて成功(mitoTALEN法)した．このmitoTALEN法を活かして①CMSと②ミトコンドリアゲノム修復について，各トップ研究者と共同研究を行う．また基課題は，mitoTALEN技術を応用発展させた遺伝子導入とCMS移植技術開発に挑戦している．それぞれの成果を基課題にフィードバックするとともに，開発する新たな技術も共同研究の枠組みに随時組み入れることで，技術開発のみに留まらずにこれを用いた研究を飛躍的に進め，国際貢献と先端研究ネットワーク構築を目指す．

Outline of Final Research Achievements

We developed and applied a novel mitochondrial genome editing technology, "mitoTALEN," to elucidate the function of orf117Sha, a causative gene of cytoplasmic male sterility (CMS) in plants. Targeted disruption of this mitochondrial ORF successfully restored fertility, confirming its role in pollen abortion. Additionally, comprehensive analysis of the mitochondrial genome after editing revealed diverse DNA repair mechanisms unique to plant mitochondria. We also established base-editing technologies for precise nucleotide substitutions in mitochondrial and plastid genomes. These achievements not only deepen our understanding of organellar genome function and repair but also offer new tools for reversible CMS control and innovative plant breeding strategies. The outcomes have led to extensive international collaborations and contributed to the formation of a global research hub on plant organelle biology.

Academic Significance and Societal Importance of the Research Achievements

本研究は、植物ミトコンドリアゲノムの標的編集および一文字塩基編集技術を世界で初めて確立し、細胞質雄性不稔の原因遺伝子の機能解明と制御を可能にしました。また、植物ミトコンドリアDNAに特徴的なゲノムの維持修復機構の一端を明らかにしました。これにより、ミトコンドリア遺伝子の機能解析が飛躍的に進むとともに、CMSを用いたF1種子生産の効率化や、外来遺伝子を使わない形質改変技術として、持続可能な農業と社会的受容性に資する新たな分子育種法の基盤が築かれました。

Research Products

• [Int'l Joint Research] University of Strasberg(フランス) (2024)
  • Year and Date: 2024-05-24
• [Int'l Joint Research] INRA Versille(フランス) (2023)
  • Year and Date: 2023-08-20
• [Journal Article] The mitochondrial <i>orf117Sha</i> gene desynchronizes pollen development and causes pollen abortion in Arabidopsis Sha cytoplasmic male sterility (2024)
  • Author(s): Dehaene Noemie、Boussardon Clement、Andrey Philippe、Charif Delphine、Brandt Dennis、Gilouppe Taillefer Clemence、Nietzel Thomas、Ricou Anthony、Simon Matthieu、Tran Joseph、Vezon Daniel、Camilleri Christine、Arimura Shin-ichi、Schwarzlander Markus、Budar Francoise
  • Journal Title: Journal of Experimental Botany Volume: 75 Issue: 16 Pages: 4851-4872
  • DOI: 10.1093/jxb/erae214
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] The mitochondrial<i>orf117Sha</i>gene desynchronizes pollen development and causes pollen abortion in the Arabidopsis Sha CMS (2024)
  • Author(s): Dehaene No?mie、Boussardon Cl?ment、Andrey Philippe、Charif Delphine、Brandt Dennis、Gilouppe Taillefer Cl?mence、Nietzel Thomas、Ricou Anthony、Simon Matthieu、Tran Joseph、Vezon Daniel、Camilleri Christine、Arimura Shin-ichi、Schwarzl?nder Markus、Budar Fran?oise
  • Journal Title: BioRxive Volume: なし
  • DOI: 10.1101/2024.01.17.575984
  • Open Access / Int'l Joint Research
• [Journal Article] Mitochondrial DNA editing in potato through mitoTALEN and mitoTALECD: molecular characterization and stability of editing events (2024)
  • Author(s): Nicolia Alessandro、Scotti Nunzia、D’Agostino Nunzio、Festa Giovanna、Sannino Lorenza、Aufiero Gaetano、Arimura Shin-ichi、Cardi Teodoro
  • Journal Title: Plant Methods Volume: 20 Issue: 1
  • DOI: 10.1186/s13007-023-01124-9
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Mitochondrial genome editing of <i>WA352</i> via <scp>mitoTALENs</scp> restore fertility in cytoplasmic male sterile rice (2024)
  • Author(s): Zhou Jiawei、Nie Liyun、Zhang Shuo、Mao Hailiang、Arimura Shin-ichi、Jin Shuangxia、Wu Zhiqiang
  • Journal Title: Plant Biotechnology Journal Volume: 1 Issue: 7 Pages: 1-3
  • DOI: 10.1111/pbi.14315
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Targeted A-to-G base editing in the organellar genomes of Arabidopsis with monomeric programmable deaminases (2023)
  • Author(s): Zhou Chang、Okuno Miki、Nakazato Issei、Tsutsumi Nobuhiro、Arimura Shin-ichi
  • Journal Title: Plant Physiology Volume: 194 Issue: 4 Pages: 2278-2287
  • DOI: 10.1093/plphys/kiad678
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A Method for Precisely Identifying Modifications to Plant Mitochondrial Genomes by mitoTALENs (2023)
  • Author(s): Kazama Tomohiko、Arimura Shin-ichi
  • Journal Title: Methods in Molecular Biology Volume: 2615 Pages: 365-378
  • DOI: 10.1007/978-1-0716-2922-2_25
  • ISBN: 9781071629215, 9781071629222
  • Peer Reviewed
• [Journal Article] <i>orf137</i> triggers cytoplasmic male sterility in tomato (2022)
  • Author(s): Kuwabara Kosuke、Arimura Shin-ichi、Shirasawa Kenta、Ariizumi Tohru
  • Journal Title: Plant Physiology Volume: 未定 Issue: 2 Pages: 1-4
  • DOI: 10.1093/plphys/kiac082
  • Peer Reviewed / Open Access
• [Journal Article] Targeted base editing in the mitochondrial genome of Arabidopsis thaliana (2022)
  • Author(s): Issei Nakazato, Miki Okuno, Chang Zhou, Takehiko Itoh, Nobuhiro Tsutsumi, Mizuki Takenaka, Shin-ichi Arimura
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 119 Issue: 20 Pages: 1-9
  • DOI: 10.1073/pnas.2121177119
  • Peer Reviewed / Open Access
• [Journal Article] <scp>TALEN</scp> ‐mediated depletion of the mitochondrial gene <i>orf312</i> proves that it is a Tadukan‐type cytoplasmic male sterility‐causative gene in rice (2022)
  • Author(s): Takatsuka Ayumu、Kazama Tomohiko、Arimura Shin‐ichi、Toriyama Kinya
  • Journal Title: The Plant Journal Volume: 未定 Issue: 4 Pages: 1-11
  • DOI: 10.1111/tpj.15715
  • Peer Reviewed / Open Access
• [Journal Article] Plant genome engineering from lab to field-a Keystone Symposia report (2021)
  • Author(s): Cable J, Ronald PC, Voytas D, Zhang F, Levy AA, Takatsuka A, Arimura S, Jacobsen SE, Toki S, Toda E, Gao C, Zhu J, Boch J, Van Eck J, Mahfouz M, Andersson M, Fridman E, Weiss T, Wang K, Qi Y, Jores T, Adams T, Bagchi R
  • Journal Title: Annals of the New York Academy of Sciences Volume: 1506 Issue: 1 Pages: 35-54
  • DOI: 10.1111/nyas.14675
  • Open Access / Int'l Joint Research
• [Journal Article] Targeted base editing in the plastid genome of Arabidopsis thaliana (2021)
  • Author(s): Nakazato Issei、Okuno Miki、Yamamoto Hiroshi、Tamura Yoshiko、Itoh Takehiko、Shikanai Toshiharu、Takanashi Hideki、Tsutsumi Nobuhiro、Arimura Shin-ichi
  • Journal Title: Nature Plants Volume: 7 Issue: 7 Pages: 906-913
  • DOI: 10.1038/s41477-021-00954-6
  • Peer Reviewed / Open Access
• [Journal Article] Effects of mitoTALENs-Directed Double-Strand Breaks on Plant Mitochondrial Genomes (2021)
  • Author(s): Arimura Shin-ichi
  • Journal Title: Genes Volume: 12 Issue: 2 Pages: 153-153
  • DOI: 10.3390/genes12020153
  • Peer Reviewed / Open Access
• [Journal Article] Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing (2021)
  • Author(s): Bansho Masutani, Shin-ichi Arimura, Shinichi Morishita
  • Journal Title: PLOS Computational Biology Volume: 17 Issue: 1 Pages: e1008597-e1008597
  • DOI: 10.1371/journal.pcbi.1008597
  • Peer Reviewed / Open Access
• [Journal Article] FMT, a protein that affects mitochondrial distribution, interacts with translation-related proteins in Arabidopsis thaliana (2021)
  • Author(s): Ayabe Hiroki、Kawai Narumi、Shibamura Mitsuhiro、Fukao Yoichiro、Fujimoto Masaru、Tsutsumi Nobuhiro、Arimura Shin-ichi
  • Journal Title: Plant Cell Reports Volume: 40 Issue: 2 Pages: 327-337
  • DOI: 10.1007/s00299-020-02634-9
  • Peer Reviewed
• [Journal Article] Recent advances and perspectives in plant mitochondrial biology for plant breeding (2020)
  • Author(s): Kubo Tomohiko、Arakawa Takumi、Kitazaki Kazuyoshi、Kazama Tomohiko、Takenaka Mizuki、Sakamoto Wataru、Ishihara Naotada、Nakamura Takahiro、Niikura Satoshi、Arimura Shin-ichi、Handa Hirokazu、Koizuka Nobuya
  • Journal Title: Breeding Research Volume: 22 Issue: 1 Pages: 87-94
  • DOI: 10.1270/jsbbr.22.W05
  • NAID: 130007869258
  • ISSN: 1344-7629, 1348-1290
  • Year and Date: 2020-06-01
  • Peer Reviewed / Open Access
• [Journal Article] Targeted gene disruption of ATP synthases 6‐1 and 6‐2 in the mitochondrial genome of Arabidopsis thaliana by mitoTALENs (2020)
  • Author(s): Arimura Shin‐ichi、Ayabe Hiroki、Sugaya Hajime、Okuno Miki、Tamura Yoshiko、Tsuruta Yu、Watari Yuta、Yanase Shungo、Yamauchi Takaki、Itoh Takehiko、Toyoda Atsushi、Takanashi Hideki、Tsutsumi Nobuhiro
  • Journal Title: The Plant Journal Volume: 104 Issue: 6 Pages: 1459-1471
  • DOI: 10.1111/tpj.15041
  • Peer Reviewed / Open Access
• [Presentation] 植物ミトコンドリアのゲノム編集 (2021)
  • Author(s): 有村慎一
  • Organizer: 植物生理学会
  • Invited
• [Presentation] mitoTALEN法による標的遺伝子破壊から垣間見えた植物ミトコンドリアゲノムの修復尾維持機構と特徴 (2020)
  • Author(s): 有村慎一
  • Organizer: 分子生物学会
  • Invited
• [Patent(Industrial Property Rights)] 植物ゲノムの編集方法 (2021)
  • Inventor(s): 有村慎一、
  • Industrial Property Rights Holder: 有村慎一、
  • Industrial Property Rights Type: 特許
  • Filing Date: 2021
  • Overseas