Mechanisms for auxin-mediated formation of pluripotent stem cells

• Project Area: Principles of pluripotent stem cells underlying plant vitality
• Project/Area Number: 18H04836
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Research Institution: Kyoto University
• Principal Investigator: 西浜 竜一 京都大学, 生命科学研究科, 准教授 (70283455)
• Project Period (FY): 2018-04-01 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000); Fiscal Year 2019: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2018: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
• Keywords: オーキシン / 頂端細胞 / 多能性幹細胞 / ゼニゴケ / 幹細胞新生 / Marchantia polymorpha / 全能性 / 多能性

Outline of Annual Research Achievements

苔類ゼニゴケにおいてオーキシン信号伝達を阻害すると、無秩序な細胞分裂を繰り返す。そこでオーキシンの作用により多能性幹細胞が規定されるとの仮説をたて、その分子機構を明らかにすることを目的として研究を行った。
ゼニゴケ唯一のオーキシン受容体MpTIR1を欠損させて生じた細胞塊のRNA-seq解析を行い、この細胞塊は幹細胞性の集団であることを明らかにした。また、オーキシン低感受性変異体として単離した、MpAMP1およびそれと関連した機能をもつMpCYP78の変異体も分化能の著しく低下した細胞塊となり、さらにオーキシン応答性遺伝子発現を促進させる遺伝的操作により葉状体形成能が再獲得されたことから、MpAMP1、MpCYP78両酵素はオーキシン応答を促進する物質を生成する可能性が示唆された。さらに、転写活性化型MpARF1と転写抑制型MpARF2は、ともに幹細胞領域において発現が低いこと、これらは幹細胞形成において拮抗的に機能することを明らかにした。以上の結果から、多能性幹細胞は異なるオーキシン応答性をもつ領域を区分けすることで形成され、低いオーキシン応答性をもつ領域が多能性幹細胞として機能することが示唆された。
MpARF1とMpARF2の誘導過剰発現株を用いてRNA-seq解析を行い、拮抗的制御を受ける遺伝子を同定した。また再生機構の研究から、幹細胞領域で特異的に発現する転写因子を同定した。詳細なオーキシンによる幹細胞形成機構を明らかにする上で重要な因子を同定することができた。また高速に核を単離する手法の確立に成功し、MpARFや修飾ヒストンなどのゲノム分布の解析やATAC-seqを行う基盤が整った。
発生学的な知見として、細胞系譜内で器官が形成される他のコケ植物とは異なり、葉状性のゼニゴケでは位置情報が器官形成を制御することを解明した（Suzuki et al. 2020）。

Research Progress Status

令和元年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和元年度が最終年度であるため、記入しない。

Research Products

• [Int'l Joint Research] University of Bristol(英国)
• [Int'l Joint Research] Max Planck Institute(ドイツ)
• [Int'l Joint Research] Wageningen University(オランダ)
• [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] Positional cues regulate dorsal organ formation in the liverwort Marchantia polymorpha (2020)
  • Author(s): Suzuki H, Harrison CJ, Shimamura M, Kohchi T, Nishihama R
  • Journal Title: J Plant Res. Volume: 133 Issue: 3 Pages: 311-321
  • DOI: 10.1007/s10265-020-01180-5
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Kinase in the liverwort Marchantia polymorpha; A photosynthesis-dependent kinase for carbon metabolism (2020)
  • Author(s): Koide E, Suetsugu N, Iwano M, Gotoh E, Nomura Y, Stolze SC, Nakagami H, Kohchi T, Nishihama R
  • Journal Title: Plant Cell & Physiology Volume: 61 Issue: 3 Pages: 631-643
  • DOI: 10.1093/pcp/pcz232
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Regulation of the Poly(A) Status of Mitochondrial mRNA by Poly(A)-Specific Ribonuclease Is Conserved among Land Plants (2019)
  • Author(s): Kanazawa Mai、Ikeda Yoko、Nishihama Ryuichi、Yamaoka Shohei、Lee Nam-Hee、Yamato Katsuyuki T、Kohchi Takayuki、Hirayama Takashi
  • Journal Title: Plant and Cell Physiology Volume: 61 Issue: 3 Pages: 470-480
  • DOI: 10.1093/pcp/pcz212
  • NAID: 120006900804
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Isolation of Natural Fungal Pathogens from Marchantia polymorpha Reveals Antagonism between Salicylic Acid and Jasmonate during Liverwort?Fungus Interactions (2019)
  • Author(s): Matsui Hidenori、Iwakawa Hidekazu、Hyon Gang-Su、Yotsui Izumi、Katou Shinpei、Monte Isabel、Nishihama Ryuichi、Franzen Rainer、Solano Roberto、Nakagami Hirofumi
  • Journal Title: Plant and Cell Physiology Volume: 61 Issue: 2 Pages: 265-275
  • DOI: 10.1093/pcp/pcz187
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] GEMMA CUP-ASSOCIATED MYB1, an ortholog of axillary meristem regulators, is essential in vegetative reproduction in Marchantia polymorpha. (2019)
  • Author(s): Yasui Y, Tsukamoto S, Sugaya T, Nishihama R, Wang Q, Kato H, Yamato KT, Fukaki H, Mimura T, Kubo H, Theres K, Kohchi T, Ishizaki K.
  • Journal Title: Curr Biol. Volume: 29 Issue: 23 Pages: 3987-3995
  • DOI: 10.1016/j.cub.2019.10.004
  • NAID: 120006773950
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] A conserved regulatory mechanism mediates the convergent evolution of plant shoot lateral organs. (2019)
  • Author(s): Naramoto S, Jones VAS, Nicola, N, Sato M,Toyooka K, Shimamura M, Ishida S, Nishitani K,Ishizaki K, Nishihama R, Kohchi T, Dolan L, Kyozuka J.
  • Journal Title: PLoS Biology Volume: 17 Issue: 12 Pages: 12-12
  • DOI: 10.1371/journal.pbio.3000560
  • NAID: 120006813343
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Cytokinin signaling coordinates development of diverse organs in Marchantia polymorpha (2019)
  • Author(s): Aki Shiori S.、Nishihama Ryuichi、Kohchi Takayuki、Umeda Masaaki
  • Journal Title: Plant Signaling & Behavior Volume: 14 Issue: 11 Pages: 1668232-1668232
  • DOI: 10.1080/15592324.2019.1668232
  • NAID: 120006731887
  • Peer Reviewed
• [Journal Article] Phytochrome and light signaling in Marchantia (2019)
  • Author(s): Inoue K, Nishihama R, Kohchi T
  • Journal Title: Methods Mol. Biol. Volume: 2026 Pages: 215-223
  • DOI: 10.1007/978-1-4939-9612-4_18
  • ISBN: 9781493996117, 9781493996124
  • Peer Reviewed
• [Journal Article] Cytokinin signaling is essential for organ formation in Marchantia polymorpha (2019)
  • Author(s): Aki Shiori S、Mikami Tatsuya、Naramoto Satoshi、Nishihama Ryuichi、Ishizaki Kimitsune、Kojima Mikiko、Takebayashi Yumiko、Sakakibara Hitoshi、Kyozuka Junko、Kohchi Takayuki、Umeda Masaaki
  • Journal Title: Plant and Cell Physiology Volume: 60 Issue: 8 Pages: 1842-1854
  • DOI: 10.1093/pcp/pcz100
  • NAID: 120006711216
  • Peer Reviewed
• [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
• [Presentation] ゼニゴケにおける幹細胞性と低オーキシン応答性の関係 (2020)
  • Author(s): 西浜竜一、河内孝之
  • Organizer: 第61回日本植物生理学会年会シンポジウム「幹細胞に対するオーキシン作用の二面性」
  • Invited
• [Presentation] Division Patterns and Apical Cell Lineages in Developing Gemma Revealed by Clonal Analysis in the Liverwort Marchantia polymorpha (2020)
  • Author(s): Suzuki H, Harrison CJ, Shimamura M, Kohchi T, Nishihama R
  • Organizer: 第61回日本植物生理学会年会
• [Presentation] ゼニゴケAMP1およびCYP78酵素のオーキシン応答とメリステム形成における機能 (2020)
  • Author(s): 副島裕乃，鈴木秀政，池田敬登，桐田啓如，武田真由子，西浜竜一，河内孝之
  • Organizer: 第61回日本植物生理学会年会
• [Presentation] ゼニゴケの無性芽発生における分裂パターンと幹細胞系譜の解明に向けたクローナル解析 (2019)
  • Author(s): 鈴木秀政、Harrison CJ、嶋村正樹、河内孝之、西浜竜一
  • Organizer: 2019年度（第8回）近畿植物学会講演会
• [Presentation] Roles of Auxin in Cellular Reprogramming and Meristem Formation in Marchantia polymorpha (2019)
  • Author(s): Ishida S, Suzuki H, Hainiwa E, Kohchi T, Nishihama R
  • Organizer: Marchantia Workshop 2019
  • Int'l Joint Research / Invited
• [Presentation] Clonal Analysis to Revealing Division Patterns and Stem Cell Lineages in Developing Gemma of Marchantia polymorpha (2019)
  • Author(s): Suzuki H, Harrison CJ, Shimamura M, Kohchi R, Nishihama R
  • Organizer: Marchantia Workshop 2019
  • Int'l Joint Research
• [Presentation] ゼニゴケ唯一のTIR1/AFB ホモログMpTIR1 は生存に必須でないが正常な器官形成に必須である (2019)
  • Author(s): 鈴木秀政, 加藤大貴, 西浜竜一, 河内孝之
  • Organizer: 日本植物学会第83回大会
• [Presentation] Clonal analysis approach to revealing the mechanisms of stem cell formation in Marchantia polymorpha (2019)
  • Author(s): Suzuki H, Harrison CJ, Shimamura M, Kohchi R, Nishihama R
  • Organizer: 国際シンポジウム「Principles of pluripotent stem cells underlying plant vitality」
  • Int'l Joint Research / Invited
• [Presentation] The sole conserved auxin receptor MpTIR1 is dispensable for cell survival but critical for organized 3D body plan (2019)
  • Author(s): Suzuki H, Kato H, Nishihama R, Kohchi T
  • Organizer: 国際シンポジウム「Principles of pluripotent stem cells underlying plant vitality」
  • Int'l Joint Research
• [Presentation] A Raf-like kinase that is involved in the signaling of photosynthesis in the liverwort Marchantia polymorpha (2019)
  • Author(s): Koide E, Shintaku A, Terai M, Nomura Y, Yotsui I, Suetsugu N, Nakagami H, Kohchi T, Nishihama R
  • Organizer: 2019 18th International Joint Mini-symposium on Molecular and Cell Biology @NTU
  • Int'l Joint Research / Invited
• [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
• [Remarks] 遺伝子特性学分野 発表論文 Publications
  • URL: http://www.plantmb.lif.kyoto-u.ac.jp/publications/
• [Funded Workshop] JPR International Symposium "Apical stem cell(s): evolutionary basis for 3D body plans in land plants" (2018)