Deciphering the dynamics of chloroplast nucleoid network

• Project/Area Number: 16K14768
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Morphology/Structure
• Research Institution: Kyoto University
• Principal Investigator: Nishimura Yoshiki 京都大学, 理学研究科, 助教 (70444099)
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000); Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2016: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: 葉緑体DNA / 核様体 / マイクロ流体デバイス / ホリデイジャンクション解離酵素 / 葉緑体核様体 / ライブイメージング / 葉緑体ゲノム / 植物 / 遺伝学 / 進化

Outline of Final Research Achievements

Chloroplast (cp) DNA and the gene expression machinery are the fundamental system for the photosynthesis and biogenesis of chloroplasts. CpDNA molecules are packaged by multiple number of proteins into a minute globular structure called cp nucleoids. Cp nucleoids are the platform for multiple processes including DNA replication, repair, transcription, and inheritance. In this research, the process of chloroplast nucleoid division was visualized by our microfluidic device-based live imaging technology. Furthermore, chloroplast-localized Holliday junction resolvase was identified as a critical factor for the division of cp nucleoids.

Academic Significance and Societal Importance of the Research Achievements

遺伝情報の正確な伝達は、細胞分裂や有性生殖における最重要問題である。染色体の構造や形態、その遺伝様式はこれまで詳細かつ徹底した解析が行われてきたのに対し、葉緑体における染色体ともいうべき核様体の維持・遺伝機構は未だ謎に包まれている。本研究では、葉緑体核様体の分裂過程を生きた細胞で初めて捉えることに成功し、さらにその過程を制御する重要因子として、葉緑体DNAを正確に切り分けるハサミであるホリデイジャンクション解離酵素の遺伝子の同定に成功した。この酵素の遺伝子は緑色植物に広く保存されており、植物全般における葉緑体核様体の遺伝機構の一端が解明された。

Research Products

• [Int'l Joint Research] ブリティッシュコロンビア大学(カナダ)
• [Journal Article] Chloroplast nucleoids as a transformable network revealed by live imaging with a microfluidic device (2018)
  • Author(s): Kamimura Yoshitaka、Tanaka Hitomi、Kobayashi Yusuke、Shikanai Toshiharu、Nishimura Yoshiki
  • Journal Title: Communications Biology Volume: 1:47 Issue: 1 Pages: 1-7
  • DOI: 10.1038/s42003-018-0055-1
  • NAID: 120006469191
  • Peer Reviewed / Open Access
• [Journal Article] Isolation and characterization of Chlamydomonas autophagy-related mutants in nutrient-deficient conditions. (2018)
  • Author(s): Kajikawa, M., Yamauchi, M., Shinkawa, H., Tanaka, M., Hatano, K., Nishimura, Y., Kato, M., Fukuzawa, H.
  • Journal Title: Plant Cell Physiology Volume: 60 Issue: 1 Pages: 126-138
  • DOI: 10.1093/pcp/pcy193
  • Peer Reviewed / Open Access
• [Journal Article] Identification of Holliday junction resolvases crucial for the chloroplast nucleoid morphology and segregation (2018)
  • Author(s): Kobayashi Yusuke、Misumi Osami、Nishimura Yoshiki
  • Journal Title: PLANT MORPHOLOGY Volume: 30 Issue: 1 Pages: 73-81
  • DOI: 10.5685/plmorphol.30.73
  • NAID: 130007622405
  • ISSN: 0918-9726, 1884-4154
  • Peer Reviewed
• [Journal Article] 葉緑体DNAの分配を司るホリデイジャンクション解離酵素の発見 (2018)
  • Author(s): 西村芳樹
  • Journal Title: バイオサイエンスとインダストリー Volume: 76(5) Pages: 404-404
• [Journal Article] 葉緑体核様体の進化と構造のダイナミクス (2018)
  • Author(s): 小林優介、三角修己、西村芳樹
  • Journal Title: 化学と生物 Volume: 56(10) Pages: 651-658
• [Journal Article] ゲノム編集の時代における「緑の酵母」クラミドモナスの復権 (2018)
  • Author(s): 浜地貴志・西村芳樹
  • Journal Title: 生物工学 Volume: 96(8) Pages: 475-475
• [Journal Article] Chloroplast nucleoids as a transformable network revealed by live-imaging with a microfluidic device (2018)
  • Author(s): Yoshitaka Kamimura, Hitomi Tanaka, Yusuke Kobayashi, Toshiharu Shikanai, Yoshiki Nishimura
  • Journal Title: Communications Biology Volume: 印刷中
  • NAID: 120006469191
  • Peer Reviewed / Open Access
• [Journal Article] The sexual reproduction program of Chlamydomonas reinhardtii. (2018)
  • Author(s): Yoshiki Nishimura
  • Journal Title: MICROBIOLOGY MONOGRAPHS (Springer) Chlamydomonas Biology, Biotechnology and Biomedicine. Volume: 印刷中
  • Peer Reviewed / Open Access
• [Journal Article] Holliday junction resolvases mediate chloroplast nucleoid segregation (2017)
  • Author(s): Kobayashi Y, Misumi O, Odahara M, Ishibashi K, Hirono M, Hidaka K, Endo M, Sugiyama H, Iwasaki H, Kuroiwa T, Shikanai T, Nishimura Y.
  • Journal Title: Science Volume: 356 Issue: 6338 Pages: 631-634
  • DOI: 10.1126/science.aan0038
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Gene Regulatory Networks for the Haploid-to-Diploid Transition of Chlamydomonas reinhardtii (2017)
  • Author(s): Joo Sunjoo、Nishimura Yoshiki、Cronmiller Evan、Hong Ran Ha、Kariyawasam Thamali、Wang Ming Hsiu、Shao Nai Chun、El Akkad Saif-El-Din、Suzuki Takamasa、Higashiyama Tetsuya、Jin Eonseon、Lee Jae-Hyeok
  • Journal Title: Plant Physiology Volume: 175 Issue: 1 Pages: 314-332
  • DOI: 10.1104/pp.17.00731
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 葉緑体ゲノムの分配はHollidayジャンクション解離酵素MOC1により保障される (2017)
  • Author(s): 小林優介、三角修己、西村芳樹
  • Journal Title: First Author's Volume: - Pages: 043
  • DOI: 10.7875/first.author.2017.043
• [Journal Article] Dynamic interplay between nucleoid segregation and genome integrity in Chlamydomonas chloroplasts (2016)
  • Author(s): Odahara M, Kobayashi Y (equal contribution), Shikanai T, and Nishimura Y.
  • Journal Title: Plant Physiology Volume: 172 Issue: 4 Pages: 2337-2346
  • DOI: 10.1104/pp.16.01533
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] C-Terminal Region of Sulfite Reductase Is Important to Localize to Chloroplast Nucleoids in Land Plants. (2016)
  • Author(s): Kobayashi, Y., Otani, T., Ishibashi, K., Shikanai, T., *Nishimura, Y.
  • Journal Title: Genome Biol. Evol. Volume: 22 Issue: 5 Pages: 1459-1466
  • DOI: 10.1093/gbe/evw093
  • NAID: 120006822490
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Sequence of the Gonium pectorale Mating Locus Reveals a Complex and Dynamic History of Changes in Volvocine Algal Mating Haplotypes. (2016)
  • Author(s): Hamaji T, Mogi Y, Ferris PJ, Mori T, Miyagishima S, Kabeya Y, Nishimura Y, Toyoda A, Noguchi H, Fujiyama A, Olson BJ, Marriage TN, Nishii I, Umen JG, Nozaki H.
  • Journal Title: G3 Volume: 未定 Issue: 5 Pages: 1179-1189
  • DOI: 10.1534/g3.115.026229
  • NAID: 120005997691
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Presentation] 葉緑体核様体のかたちを司るDNAリガーゼの同定 (2019)
  • Author(s): 西村芳樹、小林優介、浜地貴志、鹿内利治
  • Organizer: 第60回日本植物生理学会年会
• [Presentation] 核様体局在のHMGBタンパク質がDNA結合ドメインを２つもつ利点 (2019)
  • Author(s): 田草川真理, 小林優介, 深尾陽一朗, 日高久美, 遠藤政幸, 杉山弘, 宮川勇, 鹿内利治, 三角修己, 西村芳樹
  • Organizer: 第60回日本植物生理学会年会
• [Presentation] Chloroplast chromosomes on the move - Exploring the dynamics of chloroplast nucleoids - (2018)
  • Author(s): Yoshiki Nishimura
  • Organizer: 理研/ERATO/CSRSセミナー
  • Invited
• [Presentation] 葉緑体核様体ネットワークの動態制御機構 (2018)
  • Author(s): 西村 芳樹，浜地 貴志，小林 優介，鹿内 利治
  • Organizer: 日本植物学会第８２回大会
• [Presentation] Dynamic network structure of chloroplast nucleoids. (2018)
  • Author(s): Yoshiki Nishimura, Yusuke Kobayashi, Yoshitaka Kamimura, Osami Misumi, Toshiharu Shikanai
  • Organizer: 1st Asia-Oceania International Congress on Photosynthesis.
  • Int'l Joint Research / Invited
• [Presentation] 葉緑体核様体のダイナミクスと進化 (2018)
  • Author(s): 西村芳樹
  • Organizer: SIC研究部セミナー
  • Invited
• [Presentation] Dynamic transformable network of chloroplast nucleoids (2018)
  • Author(s): Yoshiki Nishimura, Yusuke Kobayashi, Yoshitaka Kamimura, Osami Misumi, Toshiharu Shikanai
  • Organizer: International symposium on photosynthesis and chloroplast biogenesis.
  • Int'l Joint Research
• [Presentation] Dynamic Network Structure of Chloroplast Nucleoids. (2018)
  • Author(s): Yoshiki Nishimura, Yusuke Kobayashi, Yoshitaka Kamimura, Osami Misumi, Toshiharu Shikanai, Mari Takusagawa, Yusuke Kobayashi, Yoichiro Fukao, Isamu Miyakawa, Toshiharu Shikanai.
  • Organizer: 18th International Conference on the Cell and Molecular Biology of Chlamydomonas
  • Int'l Joint Research
• [Presentation] ボルボックス系列異型配偶ユードリナにおける配偶子誘導要因の解析 (2018)
  • Author(s): 豊岡 博子，浜地 貴志，西村 芳樹，宮城島 進也，箕浦 高子，野崎 久義
  • Organizer: 日本植物学会第８２回大会
• [Presentation] 母性遺伝メカニズムの解明に向けたクラミドモナス有性生殖のゲノム編集アプローチ (2018)
  • Author(s): 浜地 貴志，山岡 尚平，鹿内 利治，西村 芳樹
  • Organizer: 日本植物学会第８２回大会
• [Presentation] 雌雄異株種・同株種ボルボックスの性染色体領域・相同領域における比較ゲノム解析 (2018)
  • Author(s): 山本 荷葉子，浜地 貴志，豊岡 博子，新垣 陽子，野口 英樹，豊田 敦，水口 洋平，野崎 久義
  • Organizer: 日本植物学会第８２回大会
• [Presentation] Biological analysis of plastid nucleoid-associated HMG-box protein in Chlamydomonas reinhardtii. (2018)
  • Author(s): Mari Takusagawa, Yusuke Kobayashi, Yoichiro Fukao, Isamu Miyakawa, Toshiharu Shikanai, Osami Misumi, and Yoshiki Nishimura.
  • Organizer: International symposium on photosynthesis and chloroplast biogenesis.
  • Int'l Joint Research
• [Presentation] Organelle nucleoid-associated HMG-box proteins may have been evolved independently through tandem domain duplications. (2018)
  • Author(s): Mari Takusagawa, Yusuke Kobayashi, Yoichiro Fukao, Isamu Miyakawa, Toshiharu Shikanai, Osami Misumi, and Yoshiki Nishimura
  • Organizer: 第14回植物縦横無尽の会
• [Presentation] Organelle nucleoid-associated HMG-box proteins may have been evolved independently through tandem domain duplications. (2018)
  • Author(s): Mari Takusagawa, Yusuke Kobayashi, Yoichiro Fukao, Isamu Miyakawa, Toshiharu Shikanai, Osami Misumi, and Yoshiki Nishimura.
  • Organizer: Gordon Research Conference, Mitochondria and Chloroplasts.
  • Int'l Joint Research
• [Presentation] マイクロ流体デバイスが捉えた葉緑体核様体の柔軟なネットワーク (2018)
  • Author(s): 上村嘉誉、田中瞳、小林優介、鹿内利治、西村芳樹
  • Organizer: 第５９回日本植物生理学会年会
• [Presentation] Identification of a Holliday junction resolvase in chloroplasts (2017)
  • Author(s): Kobayashi, Y., Misumi, O., Odahara, M., Hirono, M., Hidaka, K., Endo, M., Sugiyama, H., Kuroiwa, T., Shikanai, T., Nishimura, Y.
  • Organizer: 第５８回日本植物生理学会年会
  • Place of Presentation: 鹿児島大学、鹿児島
  • Year and Date: 2017-03-16
• [Presentation] Dynamics of chloroplast nucleoid divisions captured by microfluidic device (2017)
  • Author(s): Kamimura, Y., Kobayashi, Y., Shikanai, T., Nishimura, Y.
  • Organizer: 第５８回日本植物生理学会年会
  • Place of Presentation: 鹿児島大学、鹿児島
  • Year and Date: 2017-03-16
• [Presentation] Mechanism for the Cell-type Specific Expression of the Chloroplast ndh Genes in Zea Mays. (2017)
  • Author(s): Yano, H., Ishibashi, K., Nishimura, Y., Shikanai, T.
  • Organizer: 第５８回日本植物生理学会年会
  • Place of Presentation: 鹿児島大学、鹿児島
  • Year and Date: 2017-03-16
• [Presentation] Visualization of chloroplast-targeted autophagy in Chlamydomonas reinhardtii (2017)
  • Author(s): Li, N., Nishimura, Y., Ramundo, S., Hidema, J., Izumi, M.
  • Organizer: 第５８回日本植物生理学会年会
  • Place of Presentation: 鹿児島大学、鹿児島
  • Year and Date: 2017-03-16
• [Presentation] 葉緑体核様体の形や遺伝はホリデイジャンクション解離酵素によって制御される (2017)
  • Author(s): usuke Kobayashi, Osami Misumi, Masaki Odahara, Kota Ishibashi, Masafumi Hirono, Kumi Hidaka, Masayuki Endo, Hiroshi Sugiyama, Hiroshi Iwasaki, Tsuneyoshi Kuroiwa, Toshiharu Shikanai, Yoshiki Nishimura
  • Organizer: 日本植物学会第８１回大会
• [Presentation] Dynamics of chloroplast nucleoid divisions captured by microfluidic device (2017)
  • Author(s): 上村嘉誉, 小林優介, 鹿内利治, 西村芳樹
  • Organizer: 第５８回日本植物生理学会年会
• [Presentation] オルガネラ核様体のダイナミズム (2017)
  • Author(s): 西村芳樹
  • Organizer: 京都産業大学 バイオフォーラム
  • Invited
• [Presentation] 亜硫酸還元酵素のC 末端領域は葉緑体核様体局在に重要である (2016)
  • Author(s): 小林優介, 鹿内利治, 西村芳樹
  • Organizer: 日本植物学会第８０回大会
  • Place of Presentation: 沖縄コンベンションセンター、沖縄
  • Year and Date: 2016-09-16
• [Presentation] Restructuring of chloroplast nucleoids factor during the green plant evolution. (2016)
  • Author(s): Nishimura, Y.
  • Organizer: The 13th International Colloquium of Endocytobiology and Symbiosis
  • Place of Presentation: 京都府立大学、京都
  • Year and Date: 2016-09-10
  • Int'l Joint Research
• [Remarks] 京都大学大学院 理学研究科 植物分子遺伝学研究室
  • URL: http://www.bot.kyoto-u.ac.jp/j/5_iden.html
• [Remarks] 京都大学理学研究科植物教室 植物分子遺伝学
  • URL: http://www.bot.kyoto-u.ac.jp/annual/5_iden.html