Molecular mechanisms of reprogramming that is regulated by changes in endogenous phytohormone levels

• Project/Area Number: 16K07398
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Plant molecular biology/Plant physiology
• Research Institution: Kyoto University
• Principal Investigator: Nishihama Ryuichi 京都大学, 生命科学研究科, 准教授 (70283455)
• Research Collaborator: Ishida Sakiko ; Suzuki Hidemasa ; Hainiwa Emi ; Yamaoka Shohei ; Shigenobu Shuji ; Sakakibara Hitoshi ; Kohchi Takayuki
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2018: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2017: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2016: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
• Keywords: リプログラミング / 再生 / オーキシン / サイトカイニン / 苔類ゼニゴケ / コケ植物 / ゼニゴケ / 幹細胞新生 / 脱分化 / RNA-seq / ホルモン定量 / 細胞周期再開 / 植物 / 発生・分化 / 進化 / 遺伝子 / シグナル伝達

Outline of Final Research Achievements

In the liverwort Marchantia polymorpha, thallus regeneration occurs efficiently from excised thalli on phytohormone-free media. Based on the observations that the endogenous level of auxin decreased transiently a few hours after excision and that regenerant formation was repressed in the presence of auxin, transient reduction of auxin was suggested to trigger cellular reprogramming. In addition, genes for auxin and cytokinin biosynthesis and for a transcription factor were upregulated in auxin-reduction-dependent manner. Overexpression of this transcription factor promoted regenerant formation in the presence of auxin. This study revealed a relationship between changes in endogenous phytohormone levels and reprogramming of cells, and a key factor that links these two processes.

Academic Significance and Societal Importance of the Research Achievements

植物は挿し木で増やせることや、単離した1細胞から個体を再生できることから、分化全能性があると古くから知られている。傷害が引き金となって分化全能性が発揮されることはわかっているものの、その分子的な仕組みについての詳細はあまりわかっていなかった。本研究ではコケ植物のゼニゴケを用いて、葉状体切断後に起こる植物ホルモン・オーキシンの内生レベルの一時的な低下が、分化全能性を発揮するための遺伝子発現変化（リプログラミング）を引き起こすことを示唆する結果が得られた。この成果は、この分野に新たな概念をもたらすと考えられる。

Research Products

• [Int'l Joint Research] Wageningen University(オランダ)
• [Int'l Joint Research] University of Bristol(英国)
• [Int'l Joint Research] Universidad Veracruzana, INBIOTECA(メキシコ)
• [Journal Article] Control of proliferation in the haploid meristem by CLE peptide signaling in Marchantia polymorpha. (2019)
  • Author(s): Hirakawa Y, Uchida N, Yamaguchi YL, Tabata R, Ishida S, Ishizaki K, Nishihama R, Kohchi T, Sawa S, Bowman JL
  • Journal Title: PLoS Genet. Volume: 7 Issue: 3 Pages: e1007997-e1007997
  • DOI: 10.1371/journal.pgen.1007997
  • NAID: 120006621164
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Physiological function of photoreceptor UVR8 in UV-B tolerance in the liverwort Marchantia polymorpha (2019)
  • Author(s): Kondou Youichi、Miyagi Yuta、Morito Takeshi、Fujihira Kenta、Miyauchi Wataru、Moriyama Asami、Terasawa Takuya、Ishida Sakiko、Iwabuchi Kosei、Kubo Hiroyoshi、Nishihama Ryuichi、Ishizaki Kimitsune、Kohchi Takayuki
  • Journal Title: Planta Volume: 249 Issue: 5 Pages: 1349-1364
  • DOI: 10.1007/s00425-019-03090-w
  • Peer Reviewed / Open Access
• [Journal Article] Reproductive Induction is a Far-Red High Irradiance Response that is Mediated by Phytochrome and PHYTOCHROME INTERACTING FACTOR in Marchantia polymorpha (2019)
  • Author(s): Inoue K, Nishihama R, Araki T, Kohchi T
  • Journal Title: Plant and Cell Physiology Volume: pcz029 Issue: 5 Pages: 1136-1145
  • DOI: 10.1093/pcp/pcz029
  • Peer Reviewed
• [Journal Article] Observation of Phototropic Responses in the Liverwort Marchantia polymorpha (2019)
  • Author(s): Komatsu A, Nishihama R, Kohchi T
  • Journal Title: Methods in Molecular Biology Volume: 1924 Pages: 53-61
  • DOI: 10.1007/978-1-4939-9015-3_6
  • ISBN: 9781493990146, 9781493990153
  • Peer Reviewed
• [Journal Article] A cis-acting bidirectional transcription switch controls sexual dimorphism in the liverwort. (2019)
  • Author(s): Hisanaga T, Okahashi K, Yamaoka S, Kajiwara T, Nishihama R, Shimamura M, Yamato KT, Bowman JL, Kohchi T, Nakajima K.
  • Journal Title: EMBO J. Volume: 38 Issue: 6
  • DOI: 10.15252/embj.2018100240
  • NAID: 120006547401
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A Single JAZ Repressor Controls the Jasmonate Pathway in Marchantia polymorpha (2019)
  • Author(s): Monte I, Franco-Zorrilla JM, Garcia-Casado G, Zamarreno AM, Garcia-Mina JM, Nishihama R, Kohchi T, Solano R
  • Journal Title: Molecular Plant Volume: 12 Issue: 2 Pages: 185-198
  • DOI: 10.1016/j.molp.2018.12.017
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants (2018)
  • Author(s): Higo, A., Kawashima, T., Borg, M., Zhao, M., Lopez-Vidriero, I., Sakayama, H., et al. (他18名)
  • Journal Title: Nature Communications Volume: 9 Issue: 1 Pages: 5283-5283
  • DOI: 10.1038/s41467-018-07728-3
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] An Evolutionarily Conserved Abscisic Acid Signaling Pathway Regulates Dormancy in the Liverwort Marchantia polymorpha (2018)
  • Author(s): Eklund D. Magnus、Kanei Masakazu、Flores-Sandoval Eduardo、Ishizaki Kimitsune、Nishihama Ryuichi、Kohchi Takayuki、Lagercrantz Ulf、Bhalerao Rishikesh P.、Sakata Yoichi、Bowman John L.
  • Journal Title: Current Biology Volume: 28 Issue: 22 Pages: 3691-3699
  • DOI: 10.1016/j.cub.2018.10.018
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Efficient CRISPR/Cas9-based genome editing and its application to conditional genetic analysis in Marchantia polymorpha (2018)
  • Author(s): Sugano Shigeo S.、Nishihama Ryuichi、Shirakawa Makoto、Takagi Junpei、Matsuda Yoriko、Ishida Sakiko、Shimada Tomoo、Hara-Nishimura Ikuko、Osakabe Keishi、Kohchi Takayuki
  • Journal Title: PLOS ONE Volume: 13 Issue: 10 Pages: 0205117-0205117
  • DOI: 10.1371/journal.pone.0205117
  • Peer Reviewed / Open Access
• [Journal Article] Novel gateway binary vectors for rapid tripartite DNA assembly and promoter analysis with various reporters and tags in the liverwort Marchantia polymorpha. (2018)
  • Author(s): Mano, S., Nishihama, R., Ishida, S., Hikino, K., Kondo, M., Nishimura, M., Yamato, T.K., Kohchi, K., and Nakagawa, T.
  • Journal Title: PLOS ONE Volume: 3 Issue: 10 Pages: e0204964-e0204964
  • DOI: 10.1371/journal.pone.0204964
  • NAID: 120006534596
  • Peer Reviewed / Open Access
• [Journal Article] ANGUSTIFOLIA contributes to the regulation of three-dimensional morphogenesis in the liverwort Marchantia polymorpha (2018)
  • Author(s): Furuya T, Hattori K, Kimori Y, Ishida S, Nishihama R, Kohchi T, Tsukaya H
  • Journal Title: Development Volume: 145 Issue: 18
  • DOI: 10.1242/dev.161398
  • Peer Reviewed
• [Journal Article] Loss of CG Methylation in Marchantia polymorpha Causes Disorganization of Cell Division and Reveals Unique DNA Methylation Regulatory Mechanisms of Non-CG Methylation. (2018)
  • Author(s): Ikeda Y, Nishihama R, Yamaoka S, Arteaga-Vazquez MA, Aguilar-Cruz A, Grimanelli D, Pogorelcnik R, Martienssen RA, Yamato KT, Kohchi T, Hirayama T, Mathieu O.
  • Journal Title: Plant Cell Physiol. Volume: 12 Pages: 2421-2431
  • DOI: 10.1093/pcp/pcy161
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Identification and Biochemical Characterization of the Serine Biosynthetic Enzyme 3-Phosphoglycerate Dehydrogenase in Marchantia polymorpha (2018)
  • Author(s): Akashi H, Okamura E, Nishihama R, Kohchi T, Hirai MY
  • Journal Title: Frontiers in Plant Science Volume: 9 Pages: 956-956
  • DOI: 10.3389/fpls.2018.00956
  • NAID: 120006554787
  • Peer Reviewed / Open Access
• [Journal Article] CRISPR/Cas9-Based Genome Editing of Transcription Factor Genes in Marchantia polymorpha (2018)
  • Author(s): Sugano Shigeo S.、Nishihama Ryuichi
  • Journal Title: Methods in Molecular Biology Volume: 1830 Pages: 109-126
  • DOI: 10.1007/978-1-4939-8657-6_7
  • ISBN: 9781493986569, 9781493986576
  • Peer Reviewed
• [Journal Article] Ligand-receptor co-evolution shaped the jasmonate pathway in land plants (2018)
  • Author(s): Monte Isabel、Ishida Sakiko、Zamarreno Angel M.、Hamberg Mats、Franco-Zorrilla Jose M.、Garcia-Casado Gloria、Gouhier-Darimont Caroline、Reymond Philippe、Takahashi Kosaku、Garcia-Mina Jose M.、Nishihama Ryuichi、Kohchi Takayuki、Solano Roberto
  • Journal Title: Nature Chemical Biology Volume: 14 Issue: 5 Pages: 480-488
  • DOI: 10.1038/s41589-018-0033-4
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] The liverwort Marchantia polymorpha: an emerging model organism (2018)
  • Author(s): 西浜竜一，河内孝之
  • Journal Title: Leading Author's Volume: 7 Pages: e008
  • DOI: 10.7875/leading.author.7.e008
  • Peer Reviewed / Open Access
• [Journal Article] Generative Cell Specification Requires Transcription Factors Evolutionarily Conserved in Land Plants (2018)
  • Author(s): Yamaoka, S., Nishihama, R., Yoshitake, Y., Ishida, S., Inoue, K., Saito, M., Okahashi, K., Bao, H., Nishida, H., Yamaguchi, K., Shigenobu, S., Ishizaki, K., Yamato, K.T., and Kohchi, T.
  • Journal Title: Current Biology Volume: 28 Issue: 3 Pages: 479-486
  • DOI: 10.1016/j.cub.2017.12.053
  • Peer Reviewed / Open Access
• [Journal Article] Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. (2017)
  • Author(s): Bowman J, Kouchi T,..(106名）..Yokoyama R, ..(4名)
  • Journal Title: Cell Volume: 171 Issue: 2 Pages: 287-304
  • DOI: 10.1016/j.cell.2017.09.030
  • NAID: 120006353839
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Evolution of nuclear auxin signaling: lessons from genetic studies with basal land plants (2017)
  • Author(s): Kato, H., Nishihama, R., Weijers, D., and Kohchi, T.
  • Journal Title: Journal of Experimental Botany Volume: 69 Issue: 2 Pages: 291-301
  • DOI: 10.1093/jxb/erx267
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] The Roles of the Sole Activator-Type Auxin Response Factor in Pattern Formation of Marchantia polymorpha (2017)
  • Author(s): Kato, H., Kouno, M., Takeda, M., Suzuki, H., Ishizaki, K., Nishihama, R., and Kohchi, T.
  • Journal Title: Plant and Cell Physiology Volume: 58 Issue: 10 Pages: 1642-1651
  • DOI: 10.1093/pcp/pcx095
  • Peer Reviewed
• [Journal Article] Evolutionary origin of phytochrome responses and signaling in land plants (2017)
  • Author(s): Inoue, K., Nishihama, R., and Kohchi, T.
  • Journal Title: Plant Cell Environ. Volume: 印刷中 Issue: 11 Pages: 2502-2508
  • DOI: 10.1111/pce.12908
  • Peer Reviewed
• [Journal Article] Phytochrome signaling is mediated by PHYTOCHROME INTERACTING FACTOR in the liverwort Marchantia polymorpha (2016)
  • Author(s): Inoue, K., Nishihama, R., Kataoka, H., Hosaka, M., Manabe, R., Nomoto, M., Tada, Y., Ishizaki, K., and Kohchi, T.
  • Journal Title: Plant Cell Volume: 28 Issue: 6 Pages: 1406-1421
  • DOI: 10.1105/tpc.15.01063
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] Auxin regulation of meristem formation and maintenance in Marchantia polymorpha (2019)
  • Author(s): Nishihama R
  • Organizer: Mini Symposium on Marchantia
  • Int'l Joint Research / Invited
• [Presentation] Connections between apical cell function and auxin response in the liverwort Marchantia polymorpha (2018)
  • Author(s): Nishihama R, Kohchi T
  • Organizer: JPR International Symposium "Apical stem cell(s): evolutionary basis for 3D body plans in land plants"
  • Int'l Joint Research / Invited
• [Presentation] Cellular reprogramming as a response to the loss of apical dominance in the liverwort Marchantia polymorpha (2018)
  • Author(s): Ishida S, Kojima M, Takebayashi Y, Sakakibara H, Yamaguchi K, Shigenobu S, Yamaoka S, Kohchi T, Nishihama R
  • Organizer: EMBO Workshop New shores in land plant evolution
  • Int'l Joint Research
• [Presentation] Tissue regeneration is associated with temporal changes in the levels of auxin and gene expression in Marchantia polymorpha (2017)
  • Author(s): Sakiko Ishida, Shohei Yamaoka, Mikiko Kojima, Yumiko Takebayashi, Hitoshi Sakakibara, Katsushi Yamaguchi, Shuji Shigenobu, Takayuki Kohchi and Ryuichi Nishihama
  • Organizer: The 65th NIBB Conference Renaissance of Marchantia polymorpha ‐the genome and beyond‐
  • Int'l Joint Research
• [Presentation] Primary target for the photoregulation of cell cycle progression is cyclin D gene expression in the liverwort Marchantia polymorpha (2017)
  • Author(s): Keita Kinose, Ryo Manabe, Eri Nakamura, Takayuki Kohchi, Ryuichi Nishihama
  • Organizer: Taiwan-Japan Plant Biology 2017
  • Int'l Joint Research
• [Presentation] 核オーキシンシグナリングによるゼニゴケ幹細胞機能調節 (2017)
  • Author(s): 鈴木秀政，加藤大貴，片山みなみ，灰庭瑛実，山岡尚平，西浜竜一，河内孝之
  • Organizer: 日本植物学会第81回大会
• [Presentation] 植物再生における極性と細胞周期制御 (2016)
  • Author(s): 西浜竜一
  • Organizer: 基生研研究会「細胞分化を誘導する細胞周期制御システム」
  • Place of Presentation: 基礎生物学研究所（愛知・岡崎）
  • Year and Date: 2016-11-21
  • Invited
• [Presentation] Phytohormonal regulation of tissue dedifferentiation and cell-cycle re-entry during regeneration in the liverwort Marchantia polymorpha (2016)
  • Author(s): Sakiko Ishida, Shohei Yamaoka, Ryuichi Nishihama, Takayuki Kohchi
  • Organizer: Auxin 2016
  • Place of Presentation: Haitang Bay, Sanya (People's Republic of China)
  • Year and Date: 2016-10-21
  • Int'l Joint Research
• [Book] 京大発！ フロンティア生命科学 (2018)
  • Author(s): 京都大学大学院生命科学研究科
  • Total Pages: 336
  • Publisher: 講談社
  • ISBN: 9784065038017