Developmental and molecular mechanism of the heterophylly in North American lake cress (Rorippa aquatica; Brassicaceae)

• Project/Area Number: 24770047
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Plant molecular biology/Plant physiology
• Research Institution: Kyoto Sangyo University
• Principal Investigator: KIMURA Seisuke 京都産業大学, 総合生命科学部, 准教授 (40339122)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2014: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2013: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2012: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: 発生 / 葉 / 表現型可塑性 / 異形葉生 / 異形葉性 / トランスクリプトーム / 複葉 / 環境 / 植物 / 次世代シークエンス / 重イオンビーム

Outline of Final Research Achievements

Plants show leaf form alteration in response to changes in the surrounding environment, and this phenomenon is called heterophylly. The North American lake cress, Rorippa aquatica shows heterophlly and we have studied the mechanism underlying heterophylly using this plant. R. aquatica develops pinnately dissected leaves in submerged conditions, whereas it forms simple leaves with serrated margins in terrestrial conditions. We found that the expression patern of KNOTTED1-LIKE HOMEOBOX (KNOX1) genes changed in response to surrounding environment (e.g., temperature; below or above water) and that the level of gibberellin (GA), which is thought to be regulated by KNOX1 genes, was also changed. Moreover, transcriptome analysis revealed that regulation of GA level via KNOX1 genes is involved in regulating heterophylly.

Research Products

• [Journal Article] Transcriptional, post-transcriptional and post-translational regulation of STM gene expression in Arabidopsis determine gene function in the shoot apex (2015)
  • Author(s): Aguilar-Martínez JA, Uchida N, Townsley B, West DA, Yanez A, Lynn N, Kimura S, Sinha N
  • Journal Title: Plant Physiol. Volume: 167 Issue: 2 Pages: 424-442
  • DOI: 10.1104/pp.114.248625
  • Peer Reviewed / Open Access
• [Journal Article] Regulation of the KNOX-GA Gene Module Induces Heterophyllic Alteration in North American Lake Cress (2014)
  • Author(s): Hokuto Nakayama, Naomi Nakayama, Sumer Seiki, Mikiko Kojima, Hitoshi Sakakibara, Neelima Sinha, and Seisuke Kimura,
  • Journal Title: The Plant Cell Volume: 26 Issue: 12 Pages: 4733-4748
  • DOI: 10.1105/tpc.114.130229
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] A developmental model for branching morphogenesis of lake cress compound leaf. (2014)
  • Author(s): Akiko Nakamasu, Hokuto Nakayama, Naomi Nakayama, Nobuhiko J. Suematsu, Seisuke Kimura
  • Journal Title: PlosOne Volume: 9 Issue: 11 Pages: 111615-111615
  • DOI: 10.1371/journal.pone.0111615
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The genome of the stress tolerant wild tomato species Solanum pennellii (2014)
  • Author(s): Anthony Bolger 他42名（Seisuke Kimura 24番目）
  • Journal Title: Nature Genetics Volume: 46 Issue: 9 Pages: 1034-1028
  • DOI: 10.1038/ng.3046
  • Peer Reviewed
• [Journal Article] The role of SOG1, a plant-specific transcriptional regulator, in the DNA damage response (2014)
  • Author(s): Yoshiyama, K. O., Kimura, S., Maki, H., Britt, A. B. and Umeda, M.
  • Journal Title: Plant Signal. Behav. Volume: 9 Issue: 4 Pages: 28889-28889
  • DOI: 10.4161/psb.28889
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Molecular Phylogeny Determined Using Chloroplast DNA Inferred a New Phylogenetic Relationship of Rorippa aquatica (Eaton) EJ Palmer & Steyermark (Brassicaceae)-Lake Cress. (2014)
  • Author(s): Nakayama H, Fukushima K, Fukuda T, Yokoyama J, and Kimura S.
  • Journal Title: American Journal of Plant Sciences Volume: 5 Issue: 01 Pages: 48-54
  • DOI: 10.4236/ajps.2014.51008
  • Peer Reviewed
• [Journal Article] DNA damage response in plants : Conserved and variable response compared to animals (2013)
  • Author(s): Yoshiyama Okamoto K, Sakaguchi K, Kimura S
  • Journal Title: Biology Volume: 2 Issue: 4 Pages: 1338-1356
  • DOI: 10.3390/biology2041338
  • Peer Reviewed
• [Journal Article] ATM-mediated phosphorylation of SOG1 is essential for the DNA damage response in Arabidopsis. (2013)
  • Author(s): Yoshiyama Okamoto K, Kobayashi J, Ogita N, Ueda M, Kimura S, Maki H, Umeda M
  • Journal Title: EMBO Reports Volume: 14 Issue: 9 Pages: 817-822
  • DOI: 10.1038/embor.2013.112
  • Peer Reviewed
• [Journal Article] Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato (2013)
  • Author(s): Koenig D, Jimenez-Gomez J, Kimura S, Fulop D, Chitwood D, Headland L, Kumar R, Covington M, Devisetty U, Tat AV, Tohge T, Bolger A, Schneeberger K, Ossowski S, Lanz C, Xiong G, Taylor-Teeples M, Brady SM, Pauly M, Weigel D, Usadel B, Fernie A, Peng J, Sinha N Maloof J
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 110 Issue: 28
  • DOI: 10.1073/pnas.1309606110
  • Peer Reviewed
• [Journal Article] Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716 (2013)
  • Author(s): Molly Sharlach, Douglas Dahlbeck, Lily Liu, Joshua Chiu, Jose Jimez, Seisuke Kimura, Daniel Koenig, et al
  • Journal Title: Theoretical and Applied Genetics Volume: 126 Issue: 3 Pages: 601-609
  • DOI: 10.1007/s00122-012-2004-6
  • Peer Reviewed
• [Journal Article] 複葉の発生と進化 (2013)
  • Author(s): 木村 成介
  • Journal Title: 生物の科学 遺伝 Volume: 67 Pages: 50-56
• [Journal Article] A high-throughput method for Illumina RNA-seq library preparation (2012)
  • Author(s): Ravi Kumar, Yasunori Ichihasi, Seisuke Kimura, Daniel H. Chitwood, Lauren R. Headland, Jie Peng, Julin N. Maloof, Neelima R. Sinha
  • Journal Title: Frontiers in Plant Genetics and Genomics Volume: 3 Pages: 1-10
  • DOI: 10.3389/fpls.2012.00202
• [Journal Article] Interspecific RNAi of STM disrupts Cuscuta pentagona plant parasitism (2012)
  • Author(s): Amos Alakonya*, Ravi Kumar*, Daniel Koenig*, Seisuke Kimura*, Brad Townsley*, Steven Runo, Helena M Garces, Julie Kang, Andrea Yanez, Rakafet David-Schwartz, Jesse Machuka, and Neelima Sinha
  • Journal Title: The Plant Cell Volume: 24 Pages: 3153-3166
• [Journal Article] Mechanical regulation of auxin-mediated growth (2012)
  • Author(s): Naomi Nakayama, Richard Smith, Therese Mandel, Sarah Robinson, Seisuke Kimura, Arezki Boudaoud, Cris Kuhlemeier
  • Journal Title: Current Biology Volume: 22 Issue: 16 Pages: 1468-1476
  • DOI: 10.1016/j.cub.2012.06.050
• [Journal Article] Toward elucidation the mechanisms that regulate heterophylly (2012)
  • Author(s): Hokuto Nakayama, Naomi Nakayama, Akiko Nakamasu, Neelima Sinha and Seisuke Kimura
  • Journal Title: Plant Morphology Volume: 24 Pages: 57-63
  • NAID: 130004726671
• [Presentation] Developmental and molecular studies on the mechanism of vegetative propagation in Rorippa aquatica (2015)
  • Author(s): Rumi Amano, Hokuto Nakayama, Shizuka Gunji, Ali Ferjani, Seisuke Kimura
  • Organizer: 第56回日本植物生理学会年会
  • Place of Presentation: 東京農業大学（東京都）
  • Year and Date: 2015-03-16 – 2015-03-20
• [Presentation] 変動する環境（温度など）と発生（主に葉）への衝撃 -アブラナ科植物Rorippa aquaticaの場合- (2014)
  • Author(s): 中山北斗
  • Organizer: 第7回Evo-devo青年の会「変動する環境と発生への衝撃」
  • Place of Presentation: 遺伝学研究所（静岡県）
  • Year and Date: 2014-10-11
  • Invited
• [Presentation] 非均一な成長場におけるチューリングパターンの挙動とそれを元に形成される分岐構造について (2014)
  • Author(s): 中益朗子、末松J信彦、木村成介
  • Organizer: 第11回生物数学の理論とその応用
  • Place of Presentation: 京都大学（京都府）
  • Year and Date: 2014-09-16 – 2014-09-19
• [Presentation] RNA-seqによるトランスクリプトーム解析を用いたRorippa aquaticaにおける異形葉性の分子基盤の解明 (2014)
  • Author(s): 中山北斗，市橋泰範、坂本智昭、倉田哲也、木村成介
  • Organizer: 日本植物学会第78回大会
  • Place of Presentation: 明治大学生田キャンパス（神奈川県）
  • Year and Date: 2014-09-12 – 2014-09-14
• [Presentation] 複葉に見られる分岐構造の非対称性形成に関する理論的なアプローチ (2014)
  • Author(s): 中益朗子、末松信彦、木村成介
  • Organizer: 日本植物学会第78回大会
  • Place of Presentation: 明治大学生田キャンパス（神奈川県）
  • Year and Date: 2014-09-12 – 2014-09-14
• [Presentation] 葉断面から再生するRorippa aquaticaの栄養繁殖機構の解析 (2014)
  • Author(s): 天野瑠美、中山北斗、Ali Ferjani、木村成介
  • Organizer: 日本植物学会第78回大会
  • Place of Presentation: 明治大学生田キャンパス（神奈川県）
  • Year and Date: 2014-09-12 – 2014-09-14
• [Presentation] 環境に応じて葉形を変化させる植物Rorippa aquaticaを用いた葉形制御機構の解明 (2014)
  • Author(s): 中山北斗、中山尚美、小島美紀子、榊原均、Neelima Sinha, 木村成介
  • Organizer: 植物形態学会第26回大会
  • Place of Presentation: 明治大学生田キャンパス（神奈川県）
  • Year and Date: 2014-09-11
• [Presentation] Developmental and molecular mechanism of the heterophylly in North American lake cress (Rorippa aquatica; Brassicaceae) (2014)
  • Author(s): Hokuto Nakayama, Naomi Nakayama, Mikiko Kojima, Hitoshi Sakakibara, Neelima Sinha, Seisuke Kimura
  • Organizer: The 25th International Conference on Arabidopsis Research (ICAR 2014)
  • Place of Presentation: The University of British Columbia, Vancouver, Canada
  • Year and Date: 2014-07-28 – 2014-08-01
• [Presentation] Behavior of Tuning Pattern on Non-uniform Growing Filed, and Asymmetric Branched Patterns Generated by The Anisotropic Growth (2014)
  • Author(s): Akiko Nakamasu, Nobuhiko J. Suematsu, Seisuke Kimura
  • Organizer: he Joint Annual Meeting of the Japanese Society for Mathematical Biology and the Society for Mathematical Biology (JSMB SMB 2014)
  • Place of Presentation: Osaka International Convention Center (Osaka, Japan)
  • Year and Date: 2014-07-28 – 2014-08-01
• [Presentation] Theoretical Approach for the Mechanisms Underlying the Heterophylly of Lake Cress (Rorippa aquatica) (2014)
  • Author(s): kiko Nakamasu, Hokuto Nakayama, Nobuhiko J. Suematsu, Seisuke Kimura
  • Organizer: 47th Annual Meeting of the Japanese Society of Developmental Biologists
  • Place of Presentation: WINC AICH (Nagoya, Japan)
  • Year and Date: 2014-05-27 – 2014-05-30
• [Presentation] 生育環境により葉の形態を変化させる植物ニューベキア（Rorippa aquatica）を用いた表現型可塑性の研究 (2014)
  • Author(s): 木村成介
  • Organizer: 東京理科大学応用生物科学専攻セミナー
  • Place of Presentation: 東京理科大学野田キャンパス（千葉県）
  • Year and Date: 2014-05-19
  • Invited
• [Presentation] Detection of leaf morphological trait loci in Mizuna and Mibuna by QTL analysis (2014)
  • Author(s): Yaichi Kawakatsu, Kaori Kaminoyama, Kaori Igarashi, Hokuto Nakayama, Nakao Kubo, Kentaro Yano, Seisuke Kimura
  • Organizer: 第55回日本植物生理学会年会
  • Place of Presentation: 富山大学五福キャンパス
• [Presentation] Transcriptome analysis using RNA-seq of Rorippa aquatica, an emerging model of heterophylly (2014)
  • Author(s): Hokuto Nakayama, Tomoaki Sakamoto, Yasunori Ichihashi, Testuya Kurata, Seisuke Kimura
  • Organizer: 第55回日本植物生理学会年会
  • Place of Presentation: 富山大学五福キャンパス
• [Presentation] 植物ゲノムの恒常性維持に働くDNA損傷応答因子のマスターレギュレーターSOG1の制御メカニズム (2014)
  • Author(s): 愿山（岡本）郁、小林純也、木村成介
  • Organizer: 第55回日本植物生理学会年会
  • Place of Presentation: 富山大学五福キャンパス
• [Presentation] Theoretical Approach to Elucidate the Mechanisms Underlying the Heterophylly of Lake Cress (2014)
  • Author(s): Akiko Nakamasu, Hokuto Nakayama, Nobuhiko J. Suematsu, Seisuke Kimura
  • Organizer: CDB Symposium 2014, Regeneration of Organs: Programming and Self-Organization
  • Place of Presentation: RIKEN Center for Developmental Biology
• [Presentation] Comparative analysis on the RNA editing sites between common wheat and Aegilops geniculate mitochondrial genome by RNA-seq data (2013)
  • Author(s): Gyawali Yadav Prasad, Seisuke Kimura, Satosi Kitagawa, Koji Murai, Toru Terachi
  • Organizer: 日本育種学会第124回講演会
  • Place of Presentation: 鹿児島大学
• [Presentation] 植物のDNA損傷チェックポイント因子SOG1は動物ガン抑制遺伝子p53のカウンターパートか？ (2013)
  • Author(s): 愿山郁、真木寿治、梅田正明、木村成介
  • Organizer: 日本遺伝学会第85回大会
  • Place of Presentation: 慶応義塾大学日吉キャンパス
• [Presentation] 異形葉性を示す植物ニューベキア（Neobeckia aquatica）を用いた葉形変化制御機構の解析 (2013)
  • Author(s): 中山北斗、小嶋美紀子、榊原均、木村成介
  • Organizer: 日本植物学会第77回大会
  • Place of Presentation: 北海道大学
• [Presentation] 京野菜のミズナとミブナに観察される葉形の多様性の発生学的・遺伝学的背景の解明 (2013)
  • Author(s): 川勝弥一、上ノ山華織、五十嵐香里、中山北斗、久保中央、矢野健太郎、木村成介
  • Organizer: 日本植物学会第77回大会
  • Place of Presentation: 北海道大学
• [Presentation] ニューベキアの葉の発生過程における表現型可塑性のモデリング (2013)
  • Author(s): 中益朗子、木村成介、末松J信彦
  • Organizer: 日本植物学会第77回大会シンポジウム「形態形成研究の新たなるステップ：遺伝子ネットワークから多細胞動態へ -」
  • Place of Presentation: 北海道大学
• [Presentation] 環境に応じて葉の形態を変える植物ニューベキアを用いたトランスクリプトーム解析 (2013)
  • Author(s): 中山北斗，坂本智昭、倉田哲也、木村成介
  • Organizer: NGS現場の会第3回研究会
  • Place of Presentation: 神戸国際会議場
• [Presentation] ーキシン極性輸送に基づくパターンの成長場における数値解析 (2013)
  • Author(s): 中益朗子、木村成介、末松J信彦
  • Organizer: 第46回日本発生生物学会
  • Place of Presentation: くにびきメッセ
• [Presentation] 生育条件により葉の形態を変化させるアブラナ科植物ニューベキアを用いた表現型可塑性の研究 (2013)
  • Author(s): 木村成介
  • Organizer: 第54回日本植物生理学会年会シンポジウム「シロイヌナズナ野生株と近縁種～研究最前線と未来」
  • Place of Presentation: 岡山大学津島キャンパス
  • Invited
• [Presentation] 環境に応答して葉形を変化させる植物ニューベキア（Neobeckia aquatica）を用いた植物ホルモンの網羅的定量解析 (2013)
  • Author(s): 中山北斗、小嶋美紀子、榊原均、木村成介
  • Organizer: 第54回日本植物生理学会年会シンポジウム
  • Place of Presentation: 岡山大学津島キャンパス
• [Presentation] 木村成介、真木寿治、梅田正明、愿山（岡本）郁 (2013)
  • Author(s): 植物が独自に獲得したDNA損傷応答のマスターレギュレーターSOG1の制御メカニズム
  • Organizer: 第54回日本植物生理学会年会シンポジウム
  • Place of Presentation: 岡山大学津島キャンパス
• [Presentation] 植物の複葉の分岐パターンに見られる非対称性のモデリング (2012)
  • Author(s): 中益明子、木村成介
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: 福岡国際会議場
• [Presentation] Modeling and analysis of branching patterns in compound leaves (2012)
  • Author(s): Akiko Nakamasu, Nobuhiko J Suematsu, Seisuke Kimura
  • Organizer: 2012 International Conference on Modeling, Analysis and Simulation
  • Place of Presentation: Meiji University, Tokyo
• [Presentation] 環境に応じて葉の形態を変える植物ニューベキア（Neobeckia aquatica）を用いた異形葉性制御メカニズムの解析 (2012)
  • Author(s): 中山北斗、木村成介
  • Organizer: 日本植物学会第76回大会
  • Place of Presentation: 兵庫県立大学姫路書写キャンパス
• [Presentation] 外部環境変化に対するニューベキアの葉の表現型可塑性の解析とモデリング (2012)
  • Author(s): 中益明子、末松J信彦、木村成介
  • Organizer: 日本植物学会第76回大会
  • Place of Presentation: 兵庫県立大学姫路書写キャンパス
• [Presentation] Mechanical regulation of auxin-mediated growth (2012)
  • Author(s): Naomi Nakayama, Richard Smith, Therese Mandel, Sarah Robinson, Seisuke Kimura, Arezki Boudaoud, Cris Kuhlemeier,
  • Organizer: 7th Plant Biomechanics International Conference
  • Place of Presentation: Clermont-Ferrand, France
• [Presentation] Reproduction of fractal structures of Neobeckia leaves by using the Turing mechanism (2012)
  • Author(s): Akiko Nakamasu, Nobuhiko J Suematsu, Seisuke Kimura
  • Organizer: Gordon Research Conference, Oscillations & Dynamic Instabilities in Chemical Systems
  • Place of Presentation: Colby College, Waterville, ME, USA
• [Presentation] The relation of a periodic pattern formation to iterative protrusion structures in Neobeckia leaves (2012)
  • Author(s): Akiko Nakamasu, Nobuhiko J Suematsu, Seisuke Kimura
  • Organizer: Joint Meeting of the 45th Annual Meeting of the Japanese Society of Developmental Biologist & the 64th Annual Meeting of the Japan Society for Cell Biology
  • Place of Presentation: Kobe, Japan
• [Presentation] Modeling and analysis for iterative protrusion on Neobeckia leaf (2012)
  • Author(s): Akiko Nakamasu, Nobuhiko J Suematsu, Seisuke Kimura
  • Organizer: CBS symposium 2012, Quantitative Developmental Biology
  • Place of Presentation: Kobe, Japan
• [Presentation] 生育環境により葉の形態を変化させる植物ニューベキア（Rorippa aquatica）を用いた表現型可塑性の研究
  • Author(s): 中山北斗、中益朗子、天野瑠美、木村成介
  • Organizer: 第一回生態進化発生コロキウム
  • Place of Presentation: 東京大学駒場キャンパス
• [Presentation] Developmental and molecular mechanisms of the heterophylly of lake cress
  • Author(s): Hokuto Nakayama, Seisuke Kimura
  • Organizer: The 31st Plant Biotechnology Symposium Program, International Plant Meeting in Kyoto; Messages from young scientist -
  • Place of Presentation: 京都産業大学
  • Invited
• [Presentation] 植物ゲノムの恒常性維持に働く転写因子SOG1の役割
  • Author(s): 愿山（岡本）郁、小林純也、真木寿治、梅田正明、木村成介
  • Organizer: 第36回日本分子生物学会年会ワークショップ「染色体DNA複製とゲノムintegrity維持研究の今」
  • Place of Presentation: 神戸国際会議場
• [Presentation] 葉の形態に表現型可塑性を示すニューベキア（Neobeckia aquatica）が多様な葉形を生み出すメカニズムについての理論的な取り組み
  • Author(s): 中益朗子、中山北斗、末松信彦、木村成介
  • Organizer: 第36回日本分子生物学会年会
  • Place of Presentation: 神戸国際会議場
• [Presentation] 分岐形成の時空間パターンの解析から推測される複葉の成長プロファイルについて
  • Author(s): 中益朗子、木村成介、末松J信彦
  • Organizer: 第20回日本時間生物学会学術大会サテライトシンポジウム「生物リズム現象の数理フロンティア」
  • Place of Presentation: 近畿大学東大阪キャンパス
• [Presentation] 京野菜であるミズナ・ミブナに見られる葉形の多様性について
  • Author(s): 川勝弥一、上ノ山華織、五十嵐香里、中山北斗、久保中央、矢野健太郎、木村成介
  • Organizer: 日本植物形態学会第25回総会
  • Place of Presentation: 北海道大学
• [Remarks] 植物生態進化発生学研究室
  • URL: http://www.cc.kyoto-su.ac.jp/~seisuke/index-j.html/HOME.html
• [Remarks] 植物分子発生生物学研究室（木村研究室）
  • URL: http://www.cc.kyoto-su.ac.jp/~seisuke/index-j.html/HOME.html