Reassembly of active RNA editosomes in plant organelles

• Project/Area Number: 18H02462
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Review Section: Basic Section 44030:Plant molecular biology and physiology-related
• Research Institution: Kyoto University
• Principal Investigator: Takenaka Mizuki 京都大学, 理学研究科, 准教授 (10796163)
• Project Period (FY): 2018-04-01 – 2022-03-31
• Project Status: Completed (Fiscal Year 2021)
• Budget Amount: ¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000); Fiscal Year 2021: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000); Fiscal Year 2020: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000); Fiscal Year 2019: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000); Fiscal Year 2018: ¥8,190,000 (Direct Cost: ¥6,300,000、Indirect Cost: ¥1,890,000)
• Keywords: RNA編集 / PPRタンパク質 / シチジンデアミナーゼ / ミトコンドリア / RNA結合タンパク質 / 葉緑体 / DYWドメイン / 転写後調節 / MORFタンパク質 / RNA 編集 / 植物ミトコンドリア / PPR / タンパク質複合体

Outline of Final Research Achievements

Land plants have C-to-U RNA editing in chloroplasts and mitochondria. Many types of RNA editing factors have been identified last decades, their detailed molecular function is still unclear. In this research project, we successfully reproduced RNA editing reaction in E.coli as well as in vitro. Furthermore, we determined 3D structure of RNA editing enzyme, which has been enigmatic for long time, and revealed its molecular mechanism for catalysis.

Academic Significance and Societal Importance of the Research Achievements

学術的意義：現象としては30年以上前から知られていた植物オルガネラのRNA編集を一つのタンパク質で試験管内で再現したこと、また長年謎であったRNA編集酵素の構造を解明したことは学術的に大きな意義があり、この分野における大きなブレークスルーとなった。
社会的意義：植物オルガネラに独特なRNA編集に関わる分子機構、特に酵素を特定したことで植物生産性を上げ、持続可能な農業の発展に寄与することが期待される。またこのシステムを用いることで遺伝病、ガンなど遺伝子変異によって引き起こされる病気治療の新たな手法の開発も期待される。

Research Products

• [Int'l Joint Research] University of Greifswald/University Ulm/Helmholtz-Zentrum Berlin(ドイツ)
• [Int'l Joint Research] The Hebrew University of Jerusalem(イスラエル)
• [Int'l Joint Research] Univerity Ulm/University of Bonn/Helmholtz-Zentrum Berlin(ドイツ)
• [Int'l Joint Research] The Hebrew University of Jerusalem(イスラエル)
• [Int'l Joint Research] Helmholtz-Zentrum/Ulm University/Bonn University(ドイツ)
• [Int'l Joint Research] CONICET - University of Mar del Plata(アルゼンチン)
• [Int'l Joint Research] University of Nebraska-Lincoln(米国)
• [Int'l Joint Research] The Hebrew University of Jerusalem(イスラエル)
• [Int'l Joint Research] Institute of Plant Science Paris-Saclay(フランス)
• [Int'l Joint Research] Helmholtz-Zentrum/Ulm University/Bonn University(ドイツ)
• [Int'l Joint Research] CONICET - University of Mar del Plata(アルゼンチン)
• [Int'l Joint Research] Institute of Plant Science Paris-Saclay(フランス)
• [Int'l Joint Research] University of Nebraska-Lincoln(米国)
• [Int'l Joint Research] The Hebrew University of Jerusalem(イスラエル)
• [Int'l Joint Research]
• [Journal Article] Quantification of Mitochondrial RNA Editing Efficiency Using Data (2021)
  • Author(s): Takenaka Mizuki
  • Journal Title: Methods in Molecular Biology Volume: 2363 Pages: 263-278
  • DOI: 10.1007/978-1-0716-1653-6_18
  • ISBN: 9781071616529, 9781071616536
  • Peer Reviewed
• [Journal Article] DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis (2021)
  • Author(s): Takenaka Mizuki、Takenaka Sachi、Barthel Tatjana、Frink Brody、Haag Sascha、Verbitskiy Daniil、Oldenkott Bastian、Schallenberg-Ru?dinger Mareike、Feiler Christian G.、Weiss Manfred S.、Palm Gottfried J.、Weber Gert
  • Journal Title: Nature Catalysis Volume: 4 Issue: 6 Pages: 510-522
  • DOI: 10.1038/s41929-021-00633-x
  • NAID: 120007089252
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A single nucleotide substitution in the coding region of Ogura male sterile gene, orf138, determines effectiveness of a fertility restorer gene, Rfo, in radish. (2021)
  • Author(s): Hiroshi Yamagishi, Megumi Jikuya, Kanako Okushiro, Ayako Hashimoto, Asumi Fukunaga, Mizuki Takenaka and Toru Terachi
  • Journal Title: Mol. Genet. Genomics Volume: - Issue: 3 Pages: 705-717
  • DOI: 10.1007/s00438-021-01777-y
  • Peer Reviewed / Open Access
• [Journal Article] The Pentatricopeptide Repeat Protein PGR3 Is Required for the Translation of petL and ndhG by Binding Their 5′ UTRs (2021)
  • Author(s): Higashi Haruka、Kato Yoshinobu、Fujita Tomoya、Iwasaki Shintaro、Nakamura Masayuki、Nishimura Yoshiki、Takenaka Mizuki、Shikanai Toshiharu
  • Journal Title: Plant and Cell Physiology Volume: - Issue: 7 Pages: 1-10
  • DOI: 10.1093/pcp/pcaa180
  • Peer Reviewed
• [Journal Article] One C-to-U RNA Editing Site and Two Independently Evolved Editing Factors: Testing Reciprocal Complementation with DYW-Type PPR Proteins from the Moss Physcomitrium (Physcomitrella) patens and the Flowering Plants Macadamia integrifolia and Arabidopsis (2020)
  • Author(s): Oldenkott Bastian、Burger Matthias、Hein Anke-Christiane、J?rg Anja、Senkler Jennifer、Braun Hans-Peter、Knoop Volker、Takenaka Mizuki、Schallenberg-R?dinger Mareike
  • Journal Title: The Plant Cell Volume: 32 Issue: 9 Pages: 2997-3018
  • DOI: 10.1105/tpc.20.00311
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] MEF46 and MEF47 are novel specificity factors for RNA editing sites in mitochondrial nad transcripts (2020)
  • Author(s): Brehme Nadja、Glass Franziska、J?rg Anja、Takenaka Mizuki
  • Journal Title: Mitochondrion Volume: 53 Pages: 121-127
  • DOI: 10.1016/j.mito.2020.05.002
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Mitochondrial Pentatricopeptide Repeat Protein, EMB2794, Plays a Pivotal Role in NADH Dehydrogenase Subunit nad2 mRNA Maturation in Arabidopsis thaliana (2020)
  • Author(s): Marchetti Fernanda、Cainzos Maximiliano、Shevtsov Sof?a、C?rdoba Juan Pablo、Sultan Laure Dora、Brennicke Axel、Takenaka Mizuki、Pagnussat Gabriela、Ostersetzer-Biran Oren、Zabaleta Eduardo
  • Journal Title: Plant and Cell Physiology Volume: 61 Issue: 6 Pages: 1080-1094
  • DOI: 10.1093/pcp/pcaa028
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] The Analysis of the Editing Defects in the dyw2 Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins (2020)
  • Author(s): Malbert Bastien、Burger Matthias、Lopez-Obando Mauricio、Baudry Kevin、Launay-Avon Alexandra、Haertel Barbara、Verbitskiy Daniil、Joerg Anja、Berthome Richard、Lurin Claire、Takenaka Mizuki、Delannoy Etienne
  • Journal Title: Plants Volume: 9 Issue: 2 Pages: 280-280
  • DOI: 10.3390/plants9020280
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Plant organellar RNA editing: what 30?years of research has revealed (2020)
  • Author(s): Small Ian D.、Schallenberg‐Ruedinger Mareike、Takenaka Mizuki、Mireau Hakim、Ostersetzer‐Biran Oren
  • Journal Title: The Plant Journal Volume: 101 Issue: 5 Pages: 1040-1056
  • DOI: 10.1111/tpj.14578
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] RNA editing mutants as surrogates for mitochondrial SNP mutants (2019)
  • Author(s): Takenaka Mizuki、Joerg Anja、Burger Matthias、Haag Sascha
  • Journal Title: Plant Physiology and Biochemistry Volume: 135 Pages: 310-321
  • DOI: 10.1016/j.plaphy.2018.12.014
  • Peer Reviewed / Int'l Joint Research
• [Presentation] 構造解析から見えてきた植物オルガネラのRNA編集反応の分子機構 (2022)
  • Author(s): 竹中 瑞樹
  • Organizer: 第24回植物オルガネラワークショップ
  • Invited
• [Presentation] 植物オルガネラのC-to-U RNA編集酵素の構造が示すユニークな活性制御機構 (2022)
  • Author(s): 竹中 瑞樹
  • Organizer: 63rd 日本植物生理学会
  • Invited
• [Presentation] DYWドメインのシチジンデアミナーゼ活性は標的シチジンとその周辺配列に依存する (2021)
  • Author(s): 前田彩子、竹中佐知、竹中瑞樹
  • Organizer: 62nd 日本植物生理学会
• [Presentation] The DYW deaminase domains of plant C-to-U RNA editing factors contribute target site selection (2021)
  • Author(s): Mizuki Takenaka, Sachi Takenaka, Tatjana Barthel, Brody Frink, Sascha Haag, Daniil Verbitskiy, Bastian Oldenkott, Mareike Schallenberg-Ruedinger, Christian G. Feiler Manfred S. Weiss, Gottfried J. Palm, Gert Weber
  • Organizer: 第22回 日本RNA学会
• [Presentation] DTWドメインのシチジンデアミナーゼ活性は標的シチジンとその周辺配列に依存する (2021)
  • Author(s): 前田 彩子、竹中 佐知、竹中 瑞樹
  • Organizer: 第62回 日本植物生理学会年会
• [Presentation] On the C-terminal DYW domain of PPR type RNA editing factors in plant organelles (2020)
  • Author(s): Mizuki Takenaka, Brody Frink, Ayako Maeda, Sachi Takenaka, Matthias Burger, Gert Weber
  • Organizer: 第61回日本植物生理学会
• [Presentation] RNA編集因子のDYWドメインはRNA配列の認識に関与するのか (2020)
  • Author(s): 前田彩子、竹中佐知、竹中瑞樹
  • Organizer: 第61回日本植物生理学会
• [Presentation] Multiple RNA editing factors form active protein complexes in plant organelles (2019)
  • Author(s): Mizuki Takenaka, Matthias Burger, Sascha Haag, Anja Zehrmann, Gert Weber
  • Organizer: 第21回日本RNA学会年会
• [Presentation] Molecular machinery of C to U RNA editing in plant mitochondria and chloroplasts (2019)
  • Author(s): Mizuki Takenaka
  • Organizer: 第92回日本生化学会
  • Invited
• [Presentation] 植物オルガネラRNA editing複合体のフロンティア (2019)
  • Author(s): 竹中瑞樹
  • Organizer: 第136回日本植物育種学会
  • Invited
• [Presentation] C-to-U RNA editing in chloroplasts and plant mitochondria requires PPR proteins and several co-factors (2019)
  • Author(s): Mizuki Takenaka, Matthias Burger, Sascha Haag, Anja Zehrmann, Brody Frink, Ayako Maeda, Sachi Takenaka, Gert Weber
  • Organizer: 1st Japan-US Binational Seminer
  • Int'l Joint Research / Invited
• [Presentation] 植物オルガネラのRNA編集を担う酵素とその複合体 (2019)
  • Author(s): 竹中瑞樹
  • Organizer: 植物RNA研究ネットワークシンポジウム
• [Presentation] Dimerization is required for function of MORF proteins in the RNA editing complex in plant organelles. (2019)
  • Author(s): Mizuki Takenaka
  • Organizer: Gordon Research Conference: RNA editing, Lucca, Italy
  • Int'l Joint Research
• [Presentation] Reassembly of complex plant RNA editosomes in mitochondria of Marchantia polymorpha. (2019)
  • Author(s): Mizuki Takenaka
  • Organizer: 11th International congress of plant mitochondria, Ein Gedi, Israel
  • Int'l Joint Research
• [Presentation] RNA editing factors in chloroplasts (2018)
  • Author(s): Mizuki Takenaka
  • Organizer: International Symposium on Photosynthesis and Chloroplast Biogenesis, Kurashiki
• [Presentation] Function of MORF proteins in RNA editosomes of plant organelles. (2018)
  • Author(s): Mizuki Takenaka
  • Organizer: The 1st Asia-Oceania International Congress on Photosynthesis, Beijing, China
  • Int'l Joint Research / Invited
• [Book] Requirement of Various Protein Combinations for Each C-to-U RNA Editosome in Plant Organelles. RNA Metabolism in Mitochondria. Nucleic Acids and Molecular Biology, vol 34 (2018)
  • Author(s): Mizuki Takenaka, Anja Joerg, Matthias Burger, Sascha Haag
  • Publisher: Springer
• [Book] The Yeast Three-Hybrid System for Protein Interactions (2018)
  • Author(s): Franziska Glass, Mizuki Takenaa
  • Publisher: Humana Press, New York, NY
• [Remarks] RNA上の遺伝情報を書き換える酵素であるDYWドメインの構造を解明
  • URL: https://www.kyoto-u.ac.jp/ja/research-news/2021-06-23-0
• [Remarks] Mizuki Takenaka's lab
  • URL: https://sites.google.com/site/mizukitakenakassite/home
• [Remarks] 京都大学理学研究科 竹中 瑞樹
  • URL: http://www.sci.kyoto-u.ac.jp/ja/research/researcher/mizukitakenaka-bi.html
• [Remarks] 京都大学理学研究科 植物分子遺伝学
  • URL: https://sites.google.com/view/shikanailab/