Comments
Transcript
Plant Science Center - 独立行政法人 理化学研究所 植物科学研究
RIKEN Plant Science Center 2007 Annual Report RIKEN Plant Science Center http://www.psc.riken.jp/indexE.html The PSC Logo 新しい PSC の出発に際して作成したロゴマーク。緑は植物、青は水と地球を意味する。 中央に、「P」「S」「C」をもとに無限大を表した。植物の無限の能力を引き出し、地球 規模問題の解決に貢献したいとの意図を込めている。 Green signifies plants and blue refers to water and the earth. The letters "P", "S" and "C" at the center of the logo form an infinity sign. This logo reflects our wish to exploit the infinite abilities of plants and to contribute solutions to global issues. RIKEN Plant Science Center 2007 Annual Report 植物科学研究センター 2007 アニュアルレポート 【表紙説明】 貧硫黄栄養下におかれた植物は、成長に直ちに必要とされる一次代謝 系へと優先的に硫黄を分配することで、環境に適応する。このダイナ ミックな代謝変換を司る転写因子 SLIM1 を初めて明らかにした。写真 は、slim1 変異体では貧硫黄栄養下における硫酸イオントランスポーター SULTR1;2 の発現誘導が認められない様子を示す。 【On the Cover】 Plants dramatically change the metabolic flow of sulfur in response 独立行政法人 理化学研究所 横浜研究所 〒 230-0045 神奈川県横浜市鶴見区末広町 1 丁目 7 番 22 号 TEL . 045-503-9111 FAX . 045-503-9113 RIKEN YOKOHAMA INSTITUTE to shortage of external sulfur source. SLIM1 has been firstly identified as a key transcription factor that essentially contributes to metabolic regulations necessary for plant adaptation to sulfur deficiency. The cover shows the slim1 mutant which cannot induce the expression of SULTR1;2 sulfate transporter under sulfur deficient conditions. 230-0045,Japan 編集委員／ Editorial Staff 榊原 均 Hitoshi SAKAKIBARA 豊岡 公徳 Kiminori TOYOOKA PHONE : +81-45-503-9111 FAX : +81-45-503-9113 百瀬有紀子 Yukiko MOMOSE 1-7-22,Suehiro-Cho,Tsurumi-Ku,Yokohama-Shi,Kanagawa, E-mail : [email protected] http://www.yokohama.riken.jp 菊地 淳 Jun KIKUCHI 小林 宏美 Hiromi KOBAYASHI 写真撮影 /Photo 豊岡 公徳 Kiminori TOYOOKA このアニュアルレポートは読みやすさ に 考 慮 し て UD フ ォ ン ト を 使 用 し、 FSC 森 林 認 証 紙 に ノ ン VOC イ ン キ （石油系溶剤 0％）で印刷しています。 RIKEN YOKOHAMA INSTITUTE 独立行政法人 理化学研究所 横浜研究所 Plant Science Center Organization Chart Contents ●Organization Chart ／組織図 ……………………………………………………… 2 ●Message from the Director ／ごあいさつ ……………………………………… 4 ●Highlights ／主な研究成果及びイベント …………………………………………… 6 ●Press Releases ／プレスリリース ………………………………………………… 8 ●PSC Seminar ／ PSC セミナー…………………………………………………… 10 組織図 Metabolomics Research Group ［メタボローム基盤研究グループ］ 斉藤 和季／ Kazuki SAITO Director ●センタ̶長 篠崎 一雄 Kazuo SHINOZAKI (D.Sci) Special Advisor ●特別顧問 杉山 達夫（農博） Tatsuo SUGIYAMA (D.Agr.) Advisory Council ●アドバイザリー・カウンシル ●Wilhelm GRUISSEM (Chair) スイス連邦工科大学チューリッヒ校 教授 Professor Swiss Federal Institute of Technology, Zurich (ETH Zurich) ●Peter McCOURT カナダ トロント大学 教授 Professor Department of Botany University of Toronto ●田中 良和 Yoshikazu TANAKA サントリー株式会社 先進技術応用研究所 シニアスペシャリスト Senior Specialist Suntory Institute for Advanced Technology Application ●渋谷 直人 Naoto SHIBUYA 明治大学農学部生命科学科 環境応答生物学研究室 教授 Professor Dept. of Life Sciences, School of Agriculture, Meiji University Coordinator Gene Discovery Research Group ［機能開発研究グループ］ 篠崎 一雄／ Kazuo SHINOZAKI ［生長制御研究グループ］ 神谷 勇治／ Yuji KAMIYA Senior Visiting Scientists 岡田 清孝 Kiyotaka OKADA, 山谷 知行 Tomoyuki YAMAYA, 柴田 大輔 Daisuke SHIBATA, 曽我 朋義 Tomoyoshi SOGA, 福田 裕穂 Hiroo FUKUDA, 荻原 保成 Yasunari OGIHARA, 冨田 勝 Masaru TOMITA, 研究支援部門（事務担当） Research Support Section ●横浜研究推進部 Yokohama Research Promotion Div. 土井 高明 Takaaki DOI, 岩波由美子 Yumiko IWANAMI 田中 淑子 Yoshiko TANAKA, ●植物科学研究センタ̶ アシスタント PSC Assistants 小林 宏美 Hiromi KOBAYASHI, 杉山 麻衣 Mai SUGIYAMA, 正代 初代 Hatsuyo SHODAI, 桑田かおり Kaori KUWATA, 須佐 文子 Fumiko SUSA, 角田美菜子 Minako SUMITA, 土居 裕子 Yuko DOI 百瀬有紀子 Yukiko MOMOSE, 吉満 朋子 Tomoko YOSHIMITSU, 小澤久美子 Kumiko OZAWA, 橋本 葉子 Yoko HASHIMOTO, 福村有希子 Yukiko FUKUMURA, 永井 葉子 Yoko NAGAI, 26 28 30 14 32 34 36 38 15 16 17 18 ■Plant Immunity Research Team ……………………………………………… 56 ［植物免疫研究チーム］ 白須 賢／ Ken SHIRASU Plant Functional Genomics Research Group ［植物ゲノム機能研究グループ］ 松井 南／ Minami MATSUI 24 ■Biodynamics Research Team ………………………………………………… 52 ［生産制御研究チーム］ 榊原 均／ Hitoshi SAKAKIBARA ■Morphoregulation Research Team …………………………………………… 54 ［形態制御研究チーム］ 出村 拓／ Taku DEMURA Plant Immunity Research Group ［植物免疫研究グループ］ 白須 賢／ Ken SHIRASU 22 ■Metabolic Function Research Team ………………………………………… 46 ［代謝機能研究チーム］ 斉藤 和季／ Kazuki SAITO ■Metabolic Diversity Research Team ………………………………………… 48 ［多様性代謝研究チーム］ 村中 俊哉／ Toshiya MURANAKA ■Plant Nutrition and Basal Metabolism Research Team ……………… 50 ［基礎代謝研究チーム］ 高橋 秀樹／ Hideki TAKAHASHI Plant Productivity Systems Research Group ［生産機能研究グループ］ 榊原 均／ Hitoshi SAKAKIBARA 20 ■Growth Regulation Research Team ………………………………………… 40 ［生長制御研究チーム］ 神谷 勇治／ Yuji KAMIYA ■Dormancy and Adaptation Research Team ……………………………… 42 ［適応制御研究チーム］ 南原 英司／ Eiji NAMBARA ■Cellular Growth and Development Research Team …………………… 44 ［促進制御研究チーム］ 山口 信次郎／ Shinjiro YAMAGUCHI Metabolic Function Research Group 吉田 茂男（農博） Shigeo YOSHIDA (D.Agr.) ●客員主管研究員 ■Gene Discovery Research Team ……………………………………………… ［機能開発研究チーム］ 篠崎 一雄／ Kazuo SHINOZAKI ■Cell Function Research Team ………………………………………………… ［細胞機能研究チーム］ 松岡 健／ Ken MATSUOKA ■Gene Expression Research Team …………………………………………… ［機能発現研究チーム］ 和田 拓治／ Takuji WADA ■Genetic Regulatory Systems Research Team …………………………… ［制御機能研究チーム］ 酒井 達也／ Tatsuya SAKAI Growth Regulation Research Group ［代謝機能研究グループ］ 斉藤 和季／ Kazuki SAITO ●コーディネータ ■Metabolome Analysis Research Team ……………………………………… ［メタボローム解析研究チーム］ 斉藤 和季／ Kazuki SAITO ■Metabolic Systems Research Unit …………………………………………… ［代謝システム解析ユニット］ 平井 優美／ Masami YOKOTA HIRAI ■Advanced NMR Metabomics Research Unit ……………………………… ［先端 NMR メタボミクスユニット］ 菊地 淳／ Jun KIKUCHI ■Integrated Genomics Research Team ……………………………………… ［ゲノム機能統合化研究チーム］ 篠崎 一雄／ Kazuo SHINOZAKI ■Integrated Genome Informatics Research Unit ………………………… ［ゲノム情報統合化ユニット］ 櫻井 哲也／ Tetsuya SAKURAI ■Metabolome Informatics Research Unit …………………………………… ［メタボローム情報ユニット］ 有田 正規／ Masanori ARITA 13 19 ■Plant Functional Genomics Research Team ……………………………… 58 ［植物ゲノム機能研究チーム］ 松井 南／ Minami MATSUI ■Plant Genomic Network Research Team…………………………………… 60 ［植物ゲノム発現研究チーム］ 関 原明／ Motoaki SEKI ●Publications, Press Releases & Patents …………………………………… 62 グループディレクター、チームリーダー、ユニットリーダーの業績 ̶公表論文、プレスリリース、特許等 免疫応答 長 形態形成 生 謝 です。 植物科学には、植物の機能を理解し、その生産力を向上させることにより、食糧、 代 21 世紀に入って人口爆発、急速な工業化が進んでおり、2020 年には食糧、 物質生産能力とのアンバランスによる地球規模の危機が顕在化するとさ れています。これを回避するためには、植物科学をベースにした研究が重要である 指しています。 メタボリック機能探索研究では植物の様々な機能についてメタボローム解析とゲノム機能 伝子の探索を進め、作物、樹木への応用に関して、大学、関連研究機関、さらには 篠崎 一雄 産業界や海外の研究機関などと共同で研究成果を上げることを目指しています。最 Kazuo SHINOZAKI 終的に研究成果が、食糧、バイオマス生産、さらに健康向上や環境の保全に活用さ れ、我々の次の世代に続く持続的な社会の構築に貢献したいと考えています。 Promotion of Plant Science for Sustainable Life and Environment and Human Health he rapid increase in population accompanied by rapid industrialization as we enter the 21st century has caused imbalances in the supply of food and energy, leading many to predict that a global crisis of food, energy and environment will occur around 2020. Research and development based on plant science is thought to be extremely important for solving these problems. In 2000, RIKEN Plant Science Center started as one of the millennium projects in Japan. In the second phase of research at the Center starting in 2005, we are conducting projects aimed at improving plant production, both quantitatively and qualitatively. This new research program is founded on functional genomics in model plants with known 環境保全 ンフォマティクスにより統合化し、生物全体をシステム的に理解する研究を行っています。 究を推進していきます。 ゲノム機能研究を基盤に植物の量的、質的な生産力の飛躍的な向上に結びつく遺 草 メタボローム解析基盤研究は質量分析計や NMR を用いたメタボローム解析結果をバイオイ バイオマス生産、環境保全に役立つ植物遺伝子を探索し、植物の生産機能の基盤研 Director of Plant Science Center 康 能探索研究から構成されるメタボリックシステムの解明研究を行っています。 健 物の質的・量的生産力向上を目指し、メタボローム解析基盤研究とメタボリック機 薬 ジーンディスカバリー センター運営の特色 植 メタボローム解析基盤 植物の質的・量的生産力向上 物 するために新たなプロジェクトを開始しました。食糧増産、健康向上だけでなく、 により成果を社会に還元するとともに、植物科学研究の国際的な研究拠点となることを目 糧 御、形態形成、光合成や代謝、環境応答などの制御機構をシステム全体として理解 問題、環境問題の解決に貢献することも目標としています。 さらに、産業連携や国際貢献 作 メタボロームやトランスクリプトームなどのゲノム機能解析技術を基礎に、生長制 植物の環境耐性、感染抵抗性の向上や、新規物質の探索や生産による人の健康向上や食糧 ゲノム機能解析 トランスクリプトーム・メタボローム 代謝ネットワーク解析 食 は、2005 年に第 2 期に入り、シロイヌナズナ、イネなどのモデル植物を用いた ために、光合成機能、生長制御、物質生産機能に関わる基盤的な研究を推進します。また、 木 2000 年に国のミレニアム・プロジェクトとして設立された植物科学研究センター そこで植物科学研究センターでは、植物の生産力の向上に関わる生理機能を明らかにする 樹 との認識が広まってきています。 T 全する役割も果たしています。すなわち、植物は人の生活にとってなくてはならないもの メタボリック機能探索研究 エネルギーや環境などの地球規模での諸問題を解決することが期待されています。 人の健康、持続的社会、環境保全に貢献する植物科学を目指して 植物科学研究センター長 人を含む動物は植物を食糧として生存しています。また、植物は地球上の環境を保 環境対応 ごあいさつ 植 物は太陽光のエネルギーを用いた光合成により、様々な代謝産物を作り出します。 光合成 Plant Science Center Message from the Director 植物のシステム的理解 センターの目標 持続的な社会への貢献 と結びつけて解析することにより、有用遺伝子探索を行っています。 理研 PSC におけるメタボローム基盤技術構築の戦略 有 用物質の高生産や多収量などの有用形質をもつ植物の作 出の試みは、既に長年にわたり行われてきています。生 D N A 命現象は、転写産物・タンパク質・代謝産物などの複雑な分子 ゲノミクス ネットワークで構成されており、その改変は一つの遺伝子や生 体反応を制御するだけでは達成できない場合が多くあります。 そのため、有用生物資源の開発には、代謝反応をシステムとし 転写産物 生物情報科学 トランスクリプトミクス て理解することが不可欠となります。 タンパク質 そこで、我々は各種 MS 法、ならびに多次元 NMR 法の特徴 プロテオミクス 代謝産物群 を活かしながら代謝産物の化学的性質に応じた計測技術開発を GC/MS LC/MS CE/MS FT/MS 行なっています。さらに、これらの代謝産物データに加えて DNA マイクロアレイによるトランスクリプトームデータも統 合させた PRIMe データベースの構築も推進しています。 代謝産物 DB の構築 これらのデータを包括的に生物情報科学解析を行うメタボロー メタボロミクス NMR 表 現 型 フェノミクス ム解析基盤の構築を目指しています。 genomic sequences, such as Arabidopsis and rice, and particularly on metabolome and transcriptome research. On the basis of these genomic studies, we are exploring important genes and analyzing the molecular functions involved in plant productivity, and promoting research that emphasizes the understanding of genomic systems unique to plants. We also collaborate with universities, institutes, industry, and international organizations with the aim of linking オールジャパン ・ 分散型メタボロームプラットフォーム D NA 分子中に刻まれた遺伝情報はタンパク質に翻訳され、その酵素反応に より多様な代謝産物を生合成・分解します。植物の代謝産物には人の健康 やバイオマスに関わる重要な物質が多く、植物科学研究センターでは質的・量 research findings on model plants to the improved production of crops and trees. This 的生産力向上を目指し、ゲノム情報から代謝産物へ至るトータルとしての植物 research program contributes to uncovering new plant functions that can ensure a reliable のシステム的理解を推進しています。 supply of food, materials, and energy from plants, and to supporting human health and environment. We believe that our new program will contribute to this purpose in the next generation. 4 RIKEN PSC 2007 Annual Report 慶應義塾大学先端生命科学研究所（山形県鶴岡市）、かずさ DNA 研究所（千葉 県木更津市）と連携し、基盤技術や人材を交流しながら世界的イニシアティブ 慶応大先端生命研 ■メタボローム基盤技術 理研中央研 ■化合物バンク ■微生物メタボローム かずさDNA研究所 ■メタボローム基盤技術 理研PSC ■植物遺伝子リソース RIKEN PSC ■メタボローム基盤技術 を図るメタボロームプラットフォームを構築しています。 RIKEN PSC 2007 Annual Report 5 Highlights 2006 - 2007 主な研究成果及びイベント 2006/12/1 2006/4/19-21 イベント EVENT イベント EVENT アドバイザリーカウンシル（外部評価委員会） イベント イベント EVENT EVENT PSC Advisory Council (External evaluation) 2006/4/27 お知らせ News お知らせ News 植物バイオテクノロジー分野の 2005 年論文引用トップに メタボローム基盤研究グループ アドバイザリーカウンシル（外部評価委員会） The Most Cited Paper in Plant Biotechnology in 2005 2006/5/12 研究成果 イベント 研究成果 EVENT Research Progress イベント EVENT 2006/6/24 イベント EVENT お知らせ News 2006/7/13 お知らせ News イベント EVENT お知らせ News 2006/7/23 研究成果 Research Progress 研究成果 Research Progress お知らせ News 研究成果 横浜研究所 一般公開 Riken Yokohama Institute Open Day 2006 研究成果 EVENT PSC 第 2 期活動報告会 Research Progress Outreach Lecture in Okayama “Rice FOX (Full-length cDNA Over-eXpressor gene hunting system).” ゲノムにコードされている有用遺伝子機能を高速に解析で きる「フォックスハンティングシステム」を確立 Establishment of“FOX Hunting System”, comprehensive 乾燥・高温に強い植物の開発に成功 振興調整費課題「イネ完全長 cDNA を用いた 有用形質高速探索」のアウトリーチ講演会 Dual function of an Arabidopsis transcription factor DREB2A expression アニュアルレポート 2006 刊行 PSC 第 2 期活動報告会 PSC Annual Report 2006 2007/2/09 お知らせ News イベント EVENT PSC 成果報告会 PSC Progress Report 2007/2/20 「植物代謝およびメタボローム 集中セミナー」 研究成果 Research Progress Special Seminar on Plant Metabolism and Metabolome お知らせ News 植物の触覚に大切な遺伝子を発見 − ダーウィン以来の難題の解決に糸口 − PSC インターナショナルシンポジウム Arabidopsis plasma membrane protein crucial for Ca2+ influx and touch sensing in roots PSC ボーリング大会 ボーリング大会 PSC Bowling Party 2007/3/1-2 イベント イベント EVENT 研究成果 EVENT Research Progress 第一回理研植物科学研究センター植物形質転換勉強会 1st Plant Transformation Seminar お知らせ News RIKEN PSC 2007 Annual Report 研究成果 Research Progress 探索」のアウトリーチ講演会 岡山にて in water-stress-responsive and heat-stress-responsive gene Progress Report on PSC Ⅱ PSC International Symposium -Trends in Plant Hormones植物ホルモン代謝・新しいホルモン様物質の研究 微量物質分析技術の最先端（PSC 国際シンポジウム） 2007/3/14 お知らせ お知らせ News News Research Progress 6 植物科学シンポジウム「植物の総合的理解と生産性向上」 gene functional analysis system イベント Research Progress 2006/11/30 イベント EVENT お知らせ News 研究成果 振興調整費課題「イネ完全長 cDNA を用いた有用形質高速 2007/1/16 研究成果 Research Progress 2006/11/17 イベント EVENT お知らせ News イベント お知らせ お知らせ EVENT News イベント News EVENT お知らせ 研究成果 研究成果 News Research Progress お知らせ Research Progress News PSC Retreat 2006/8/1 Research Progress イベント EVENT 研究成果 Plant Science Symposium in Shinagawa, Tokyo. 2006/12/26 リトリート 横浜研究所 一般公開 品川にて 2006/12/23 (Metabolomics Research Group) Research Progress 植物科学シンポジウム「植物の総合的理解と生産性向上」 第一回理研植物科学研究センター植物形質転換勉強会 中国南京林業大学と研究協力覚書きを締結 Conclusion of MOU with Nanjing Forestry University, China 中国南京林業大学と研究協力覚書き調印式 RIKEN PSC 2007 Annual Report 7 Press Releases 2006 - 2007 プレスリリース 2007/1/18 植物の形を自由に小さくする新しい酵素を発見 −植物生長ホルモンの作用を止め、ミニ植物を作る− 2006/4/4 乾燥耐性を発揮する植物ホルモンを自在に操る 山口 信次郎チームリーダー、神谷 勇治チームリーダー 篠崎 一雄チームリーダー、梅澤 泰史研究員 Gene-Based Manipulation of a Plant Hormone Regulating Drought Tolerance PSC research teams found a novel enzyme that inactivates a growth-promoting hormone. (Dr. Kazuo SHINOZAKI and Dr. Taishi UMEZAWA) (Dr. Shinjiro YAMAGUCHI and Dr. Yuji KAMIYA) 図：CYP707A3 遺伝子破壊株 CYP707A3 遺伝子破壊株（cyp707a3-1 , cyp707a3-2 ） では内在 ABA 量が増加し、乾燥耐性の向上が認められた。 2006/7/27 モデル植物の形態変化を写真付きデータベースで公開 −全遺伝子の機能解明に向けたマイルストーン− 2007/2/8 篠崎 一雄チームリーダー、黒森 崇研究員 榊原 均チームリーダー A PHENOMEnal plant collection for an international effort to identify the function of a Joint research conducted by the Plant Productivity Systems Research Group of PSC complete plant genome and The University of Tokyo found a novel gene that activates a hormone regulating rice (Dr. Kazuo SHINOZAKI and Dr. Takashi KUROMORI) crop growth. イネの収量ホルモンを活性化する遺伝子発見 (Dr. Hitoshi SAKAKIBARA) 2006/10/24 特殊な細胞周期「エンドリデュプリケーション」を制御する遺伝子を発見 −植物細胞の大きさを決める機構を解明− 松井 南チームリーダー、吉積 毅リサーチアソシエイト 2007/2/22 植物のフラボノイドの構造を決定する酵素を発見 −植物の抗酸化成分を活用する健康機能増強に期待− Screening for genes that regulate chromosomal duplication 斉藤 和季チームリーダー、榊原 圭子研究員、峠 隆之リサーチアソシエイト (Dr. Minami MATSUI and Dr. Takeshi YOSHIZUMI) The PSC Metabolic Function Research Team and Metabolome Analysis Research Team have identified a novel gene that determines flavonoid pattern for major antioxidants in plants. 2006/11/22 植物の“硫黄代謝”を調節する転写因子を発見 −転写因子「SLIM1」が、がん予防効果がある天然硫黄成分量を調節− 高橋 秀樹チームリーダー、丸山 明子研究員 How plants work with sulfur - Finding of SLIM1, a key transcription factor which increases the efficiency of uptake and use of sulfur by plants in sulfur-deficient (Dr. Kazuki SAITO, Dr. Keiko YONEKURA - SAKAKIBARA and Dr. Takayuki TOHGE) 2007/3/19 植物の耐病・耐傷害メカニズムを操る新規 MAPK 経路を発見 −病虫害・傷害耐性などストレスに強い植物の開発に期待− environments 篠崎 一雄チームリーダー、高橋 史憲リサーチアソシエイト (Dr. Hideki TAKAHASHI and Dr. Akiko MARUYAMA - NAKASHITA) Gene Discovery Research Team of PSC identified the cellular signal transduction pathway mediated by a plant hormone, jasmonate, and JA 病虫害・傷害耐性 全身獲得抵抗性 a new protein kinase cascade MKK3-MPK6 that played a critical role 2006/12/11 「陸上最大のバイオマス」の生産を制御する遺伝子を発見 ―転写因子「SND1」が繊維細胞の二次細胞壁成分の生合成を調節− in a defense-responding mechanism through jasmonate signaling. (Dr. Kazuo SHINOZAKI and Dr. Fuminori TAKAHASHI) 植物細胞 シグナル伝達回路 MAPK? MeJA JA 受容体 JA 耐性遺伝子の発現 傷害・食害 病虫害・傷害耐性の獲得 出村 拓チームリーダー Discovering genes related to the production of the largest scale bio-mass in the land (Dr. Taku DEMURA) 8 RIKEN PSC 2007 Annual Report RIKEN PSC 2007 Annual Report 9 Metabolomics Research Group Metabolomics Research Group Plant Science Center Seminar 2006 - 2007 PSC セミナー 2006 - 2007 講演者 所 属 主催研究室 Plant Sterol metabolism: elements of molecular Hubert Schaller regulation, and physiological implications Group leader at IBMP/CNRS, Isoprenoid Department, France 多様性代謝研究チーム 2006/4/11 植物のプログラム細胞死におけるメタカスパーゼ遺伝 子ファミリーと Bax Inhibitor-1 遺伝子の役割 について Biotech Center, Rutgers, The State University of New Jersey, USA 形態制御研究チーム 2006/5/1 代謝関連遺伝子改変植物のノンターゲット型代謝プロ ファイル分析 2006/5/16 10 years anniversary of VIB: making the different in (plant) Lieve Ongena biotechnology research Science Advisor, VIB (Flanders Interuniversity Institute for Biotechnology), Belgium メタボローム基盤研究グループ 2006/5/29 アブラナ科植物における自家不和合性の自他識別分子 メカニズム 東北大学大学院生命科学研究科 教授 適応制御研究チーム 渡辺 尚英 松田 史生 渡辺 正夫 科学技術振興機構 CREST 「植物の機能と制御」研究員 メタボローム基盤研究グループ 開催日 テーマ／タイトル 講演者 所 属 主催研究室 Professor of Systems Biology Institute of Molecular Plant Sciences, University of Edinburgh, UK 植物ゲノム機能研究チーム 2006/10/11 昆虫によるゴール形成機構および植物細胞の生存・ 徳田 誠 成長制御機構解明に向けたアプローチ 産総研生物機能工学 生長制御研究チーム 2006/10/18 Genes to energy… and back! Ian Small Director, ARC Centre of Excellence in Plant Energy Biology (Based at UWA), Australia 植物科学研究センター 2006/10/18 Mobilisation of oil and starch reserves in plants Steven Smith ARC Centre of Excellence in Plant Energy Biology (Based at UWA), Australia 植物科学研究センター 2006/10/26 The root endophytic fungus Piriformospora indica forms a novel type of mutualistic symbiosis with crop plants, Frank Waller providing systemic resistance Group leader, Institute of phytopathology and Applied Zoology, Germany 植物免疫研究グループ 2006/11/13 Specificity of cytokinin signaling in senescence and vascular development Ildoo Hwang POSTECH , Korea 生産制御研究チーム 2006/11/15 Unraveling the secrets of cellulose and (1,3)-beta-Dglucan biosynthesis in plants Vincent Bulone Professor, Department of Wood Biotechnology, KTH, Sweden 形態制御研究チーム 2006/11/20 S w e Tr e e Te c h n o l o g i e s , a c o m p a n y i n f o r e s t b i o t e c h n o l o g y o r C o m m e rc i a l i z a t i o n o f f o re s t Mats Jonson biotechnology 2006/11/20 Decoding developmental mechanisms that control size in 水上 由紀子 higher plants Purdue University, USA 2006/11/22 サイエンスのためのイネ、作物としてのイネ 名古屋大学・生物機能開発利用研究センター 助教授 植物科学研究センター 2006/11/24 The Role of the FT mRNA in Photoperiodic Regulation of Ove Nilsson Plant Growth and Development Professor, Umea Plant Science Centre (UPSC), Sweden 形態制御研究チーム 2006/11/27 Recent developments in DNP-NMR Oxford Instruments Molecular Biotools Ltd., UK 先端 NMR メタボミクス研究ユニット 2006/11/28 The circadian clock and light signaling converge on bHLH transcriptional regulators to control rhythmic Kazunari Nozue hypocotyl growth Section of Plant Biology, University of California, Davis 植物ゲノム機能研究チーム 2006/12/5 フィトクロムのシグナル伝達機構 長谷 あきら 京都大学大学院理学研究科生物化学専攻 形態制御研究チーム 2006/12/5 質量顕微鏡を用いた マルチディメンジョナルメタボロミクス 瀬藤 光利 自然科学研究機構 生理学研究所 岡崎統合バイオサイエンスセンター 助教授 メタボローム基盤研究グループ Chloroplast biogenesis – targeting and maturation of the protein translocation channel in the outer envelope of Kentaro Inoue chloroplasts Assistant Professor, Department of Plant Sciences University California, Davis, USA 植物免疫研究グループ 2006/6/13 COMATOSE: more than just a fatty acid transporter? University of Leeds, UK 適応制御研究チーム 2006/6/19 Agilent's New Technologies for Proteomics and Pat Perkins Metabolomics Analysis". Senior Application Chemist, Santa Clara lab., Agilent Technologies Inc., USA 生長制御研究チーム 2006/6/21 Golgi proteins involved in plant cell wall synthesis. Group Leader, Department of Biochemistry, University of Cambridge, UK 形態制御研究チーム 2006/6/26 Pathogen portals and plant immune responses to fungal Paul Schulze-Lefert invasion Director, Max-Planck-Institut für Züchtungsforschung, Cologne, Germany 植物免疫研究グループ 2006/6/26 Host-Microbe Interactions Shaping the Evolution of Plant Brian Staskawicz Innate Immunity Professor, National Academy Member, University of California, Berkeley, USA 植物免疫研究グループ 2006/7/5 植物の microRNA 生合成経路の解析 東京大学大学院・総合文化研究科・生命環境科学系・ 植物ゲノム発現研究チーム 渡辺雄一郎研究室 2006/7/7 A PSC-GSC Joint Seminar on "Systems biology and Pawan Dhar 他 Omics" ゲノム科学総合研究センター、植物科学研究センター 植物ゲノム機能研究チーム 2006/7/7 トランスクリプトームおよびプロテオーム解析に基づ くイネ根のリン欠乏・アルミニウムストレス条件にお ける代謝応答の網羅的解析 北海道大学創成科学共同研究機構 戦略重点プロジェクト「食の安全・安定 供給」 2006/7/11 １．Balanced control of phytochrome A signaling by the COP1 E3 ligase complex Yusuke Saijo ２．Signaling crosstalk between PAMP-triggered immunity and UVB stress response Max-Planck-Institut für Züchtungsforschung, Cologne, Germany 2006/7/18 CropDesign: Innovation in Crop Productivity through Yves Hatzfeld Biotechnology Technology Management Coordinator, CropDesign N.V., メタボローム基盤研究グループ Belgium 2006/12/12 イネ自然変異の理解にむけた基盤整備とその活用 矢野 昌裕 農業生物資源研究所 QTL ゲノム育種研究センター長 植物科学研究センター 2006/7/27 自然淘汰圧の推定法の検討とその応用 Plant Biology Department, Michigan State University, USA 植物科学研究センター 2006/12/14 進化するプロテオミクス質量分析 石濱 泰 慶應義塾大学先端生命科学研究所 植物免疫研究グループ 2006/8/2 Methylerythritol pasway for isoprenoid biosynthesis in Michel Rohmer bacteria and plants: current critical aspects Professor, Université Louis Pasteur-CNRS, France 促進制御研究チーム 2006/12/18 Full length cDNA inventory project at URGV (Grape fl-cDNAs) Christian Clepet URGV, France 植物ゲノム機能研究チーム 2006/8/8 脂質メタボローム解析の手法と適用 東京大学大学院医学系研究科 教授 分子細胞生物学専攻 メタボローム寄付講座 メタボローム基盤研究グループ 2007/1/5 Poplar researches in China 諸葛 強 (Qiang Zhuge) Professor, Nanjing Forestry University, China 形態制御研究チーム 2006/8/9 The significance of multigene families in gibberellin Peter Hedden biosynthesis and signal transduction. Rothamsted Research, UK 生長制御研究チーム 2007/1/5 中国のポプラ育成について―耐塩性などに関する研究 唐 羅忠 (Luozhong Tang) 南京林業大学 , China 形態制御研究チーム 2006/8/9 Genome-wide comparative analysis of MYB-related transcription factors in Arabidopsis and rice, and a case 瞿 礼嘉（Lijia QU） study for circadian regulation 北京大学・生命科学学院 教授 College of Life Sciences, Peking University, China 植物ゲノム機能研究チーム 2007/1/18 A logic model of Arabidopsis root hair patterning Natasha Saint Savage Computational Systems Biology Group The Kroto Research Institute University of Sheffield, U.K. 機能発現研究チーム 2006/8/14 シロイヌナズナ R1R2R3-Myb 遺伝子の働き 伊藤 正樹 名古屋大学大学院生命農学研究科 助教授 形態制御研究チーム 2007/1/24 植物細胞の脱分化・分裂再活性化過程の 分子遺伝学的解析 杉山 宗隆 東京大学大学院理学系研究科附属植物園 植物ゲノム発現研究チーム 2006/8/21 新規な遺伝子サイレンシング法を用いた 遺伝子機能解析 転写因子から植物機能解明へのアプローチ 高木 優 独立行政法人産業技術総合研究所 ゲノムファクトリー研究部門 遺伝子転写制御研究グループ 形態制御研究チーム 2007/2/7 BAH1(benzoic acid hypersensitive 1) may regulate an alternative SA synthesis pathway 八丈野 孝 九州大学大学院 理学研究院 生物科学部門 植物生理学研究室 植物免疫研究グループ マメ科植物と土壌微生物の共生における共通シグナル 伝達経路とその先にあるもの 林 誠 Ludwig-Maximilian-Universitat Munchen, Germany 促進制御研究チーム 2007/2/15 2006/8/29 シロイヌナズナを用いたエピジェネティクス研究 角谷 徹仁 国立遺伝学研究所 植物ゲノム発現研究チーム Application of metabolite profiling to systems biology: Richard Trethewey small molecules take center stage! Scientific Director Metanomics GmbH, Berlin, Germany メタボローム基盤研究グループ 2007/3/8 2006/9/15 転写レベルのゲノム監視機構におけるシロイヌナズナ 土生 芳樹 のサイレンシング因子 MOM1 の意義 農業生物資源研究所 遺伝子組換え技術研究ユニット 植物ゲノム発現研究チーム Parasitic Plants- From Field to Mass Spec 宇都宮大学 適応制御研究チーム 2007/3/9 2006/9/27 ペプチドミクスを活用した 哺乳類新規生理活性ペプチドの探索 国立循環器病センター研究所・薬理部 植物免疫研究グループ 2006/10/10 Building dynamic models from functional genomics data Pedro Mendes - a systems biology challenge 2007/3/14 Suppression of immunity-associated host cell death by the E3 ubiquitin ligase activity of Pseudomonas type III Gregory Martin effector AvrPtoB Professor, Department of Plant Pathology, Cornell University Boyce Schulze Downey Chair, Boyce Thompson Institute, USA 植物免疫研究グループ Paul Dupree 栗原 志夫 福田 琢哉 花田 耕介 田口 良 植物免疫研究グループ Associate Professor, Virginia Bioinformatics Institute at メタボローム基盤研究グループ Virginia Tech, USA Steven Reynolds 佐々木 一樹 形態制御研究チーム 植物ゲノム機能研究チーム RIKEN PSC 2007 Annual Report Plant Functional Genomics Research Group Plant Functional Genomics Research Group Yaakov Goldwasser 細胞機能研究チーム 芦苅 基行 CEO of SweTree Technologies, Sweden （スウェーデンの SweTree テクノロジー社） Plant Immunity Research Group Plant Immunity Research Group RIKEN PSC 2007 Annual Report Alison Baker Plant Productivity Systems Research Group Plant Productivity Systems Research Group Mathematical models inform experiments on the Andrew J. Millar Arabidopsis circadian clock.（PSC スペシャルセミナー） Metabolic Function Research Group Metabolic Function Research Group 2006/10/10 Growth Regulation Research Group Growth Regulation Research Group 2006/4/4 2006/6/8 10 テーマ／タイトル Gene Discovery Research Group Gene Discovery Research Group 開催日 11 メタボローム基盤研究グループ building a research platform founded on metabolome research. exhaustive metabolite analyses analyses of gene expression metabolism-related functions in plant physiological responses and growth processes investigate R e s e a r c h i n T h e C e n t e r [Laboratory] Research Group, Research Team, Research Unit identifying new gene functions identifying networks bioinformatics analyses systematic analyses of plants プラットフォームの構築 20 万種類近くあると推定される植物の多様な代謝産物を網羅的に解析 斉藤 和季 / Kazuki SAITO するために、メタボローム研究プラットフォームの構築を行います。 統合ゲノム科学を推進することにより、シロイヌナズナなどのモデル植物や農 作物、薬用植物などを用い網羅的な代謝産物の解析と遺伝子発現の解析を統合 的に行います。本研究により植物の生理応答、成長過程での代謝に関わる機能 を研究し、新規遺伝子の発見やネットワークの解明を進めます。さらに統合ゲ ノム科学の推進のためのバイオインフォマティクス解析を行い、植物のシステ ム的理解を目指します。 Building a Research Platform W e are responsible for building a research platform aimed at improving plant production based on integrated genome sciences founded on metabolome research. We perform comprehensive analyses of gene expression and exhaustive metabolite analyses using model plants, such as Arabidopsis, and plants in practical use, such as crops and medicinal plants. Using this information, we investigate metabolism-related functions in plant physiological responses and growth processes with the objective of identifying new and useful gene functions and networks. In addition, we focus on bioinformatics analyses in order to integrate metabolomes, transcriptomes, and proteomes with the aim of a systematic analysis of plants. ●メタボローム解析とは 生物の細胞内で生産された全ての代謝産物の 種類とその量を網羅的に調べ、ゲノム機能と 対応させてゲノムから代謝産物に至るまでの 流れを明らかにすることである。 ● Metabolomics The identification and quantification of all metabolites in a cell and correlating these to genomic functions. Kazuki Saito was born in Nagano in 1954, Japan. He graduated from the Faculty of Pharmaceutical Sciences, the University of Tokyo, Japan in 1977 and then obtained his PhD for bio-organic chemistry/biochemistry of pharmaceutical sciences from the University of Tokyo in 1982. After staying in Keio University in Japan and Ghent University in Belgium (Prof. Marc Van Montagu’s laboratory), he began molecular biology and biotechnology of plant primary and secondary metabolism in Chiba University. After being appointed as a lecturer and an associate professor, he has been appointed as a full professor since 1995 at the Graduate School of Pharmaceutical Sciences, Chiba University, Japan, until now. Since 2002, he has been a Special Guest Researcher in Kazusa DNA Research Institute in Kisarazu. Since April, 2005, he has been appointed as a group director at RIKEN Plant Science Center in Yokohama to direct Metabolomics Group and Metabolic Function Group. He has published more than 170 original papers and 70 invited reviews and book chapters. His research interests are metabolome-based functional genomics, biochemistry, molecular biology and biotechnology of primary and secondary metabolism in plants. He is also interested in music, movies, detective novels and Bon-Sai. RIKEN PSC 2007 Annual Report 13 Metabolomics Research Group Metabolomics Research Group 1977 年東京大学薬学部製薬化学科卒業。た だちに同大学院薬学系研究科に進学し（応 用微生物研究所、 （現）分子細胞生物学研究 所、配属） 、生物有機化学・生化学を専攻す る。1982 年に薬学博士号取得。1981 年慶 應義塾大学医学部助手、発がん物質の代謝活 性化と DNA 修飾を研究。1985 年千葉大学 薬学部助手、植物化学・生化学およびバイオ テクノロジー研究を開始する。1987 年 ベ ルギー、ゲント大学分子遺伝学教室、Marc Van Montagu 教授のもとに留学して、植 物分子生物学と遺伝子組み換え研究を開始す る。その後、千葉大学薬学部、講師、助教授 を経て、1995 年千葉大学薬学部・大学院薬 学研究科、遺伝子資源応用研究室、教授。現 在に至る。2002 年より、かずさ DNA 研究 所特別客員研究員を兼務。2005 年 4 月よ り理研植物科学研究センターグループディレ クターを兼務してメタボロミクス研究に本格 的に携わる。専門は、メタボロミクスを基盤 とする植物ゲノム機能科学と遺伝子資源応用 学、植物の一次・二次代謝研究とバイオテク ノロジー応用など。 Gene Discovery Research Group 機能開発研究グループ Gene Discovery Research Group environmental stresses morphogenesis cell functions gene networks involved in intra-cellular communication regulate gene exploring gene expression, gene transfer Growth Regulation Research Group 生長制御研究グループ Growth and development Plant hormones Increase in quantitative and qualitative production Growth regulation research maximum production, new varieties Cellular growth and development Growth regulation Dormancy and adaptation High sensitivity, high throughput analysis of plant hormones Development development 生産性向上に関わる遺伝子の探索 シ ロイヌナズナや作物を用いて生産性向上に関る重要な機能を持つ遺伝子 の探索を進めます。植物の環境応答、形態形成、細胞機能に関与する重 要な制御遺伝子の探索と遺伝子間の相互調節ネットワークの解析を行います。 これらの遺伝子を利用して効率の良い遺伝子発現法や遺伝子導入法の開発を進 め、植物の機能向上、生産力向上を目指します。さらに種々の環境で最大の生 産性を発揮できるような新機能を付与した作物開発のための研究技術開発を行 います。 Looking for New Genes Related to Improving Plant Production T his research group examines Arabidopsis and crops for new genes having vital functions related to improving plant production. We are also searching for genes that are related to quantitative improvements in plants and are conducting studies and technological development aimed at producing crops endowed with new functions capable of minimizing the effects of environmental stresses and achieving maximum productivity. In addition, we are exploring and analyzing genes involved in environmental responses and morphogenesis, as well as regulatory factors and signaling factors that regulate their expression. This group also analyzes gene networks involved in inter- and intra-cellular communication and communication with environmental stimuli. Using this information, we hope to develop highly efficient methods of gene expression and gene transfer aimed at improving plant functions. Based on our research findings in gene discovery we are developing basic technologies that are instrumental in developing, through gene transfer, crops capable of minimizing the effects of the environment to obtain maximum yields. 14 RIKEN PSC 2007 Annual Report New genes Novel Identification functional compounds New technology for higher quantitative and qualitative plant production 植物の生産力向上に貢献する研究 篠崎 一雄／ Kazuo SHINOZAKI Dr. Shinozaki took Ph. D. at the Institute of Molecular Biology, Faculty of Science, Nagoya University. The title of his thesis is “Discontinuous DNA replication of T7 phage”. He was appointed to be Research Associate of Department of Molecular Biology, National Institute of Genetics, and studied molecular cloning of tobacco chloroplast genes and analyzed the structure and gene expression. In 1983, he became Assistant Professor of Department of Biology, Faculty of Science, Nagoya University, and studied gene structure and expression of cyanobacteria and tobacco chloroplast. Then, he became Associate Professor, Center for Gene Research, Nagoya U n i v e r s i t y, a n d d e t e r m i n e d n u c l e o t i d e sequence of tobacco chloroplast genome in 1986. As a Visiting Scientist, he studied transgenic plant technology in Prof. NamHai Chua’s laboratory of The Rockefeller University. Dr. Shinozaki was appointed to be Chief Scientist (Director) of Plant Molecular Biology Laboratory, RIKEN Tsukuba Institute in 1989 to start molecular biology of Plant abiotic stress response using Arabidopsis. In 1999, he started Arabidopsis functional genomics (collection of full-length cDNAs and Ds insertion mutants) as Project Director of Plant Functional Genomics Group, RIKEN Genomic Sciences Center. In 2005, he was appointed to be Director of Plant Science Center, RIKEN Yokohama Institute. 植 物の生長・分化の調節に重要な低分子シグナル物質 ( 植物ホルモン ) に 関する多面的な研究を行ない、植物の量的、質的な生産力の向上に貢献 する生長制御研究を進めます。そのために、生長促進、生長抑制、適応制御に 関わる重要な遺伝子と新規機能物質をモデル植物と作物で特定化します。高感 度な植物ホルモンの分析法を開発し、メタボローム基盤研究グループと連携し て有用物質の量的、質的生産に関わる基盤技術を開発します。 Increase of Plant Production by Hormonal Regulation T 1970 年東京大学農学部農芸化学科を卒業 後、東京大学大学院農学研究科 ( 生物有機化 学 ) に進学し、1975 年農学博士号を取得し た。同年から理化学研究所農薬合成第三研 究室の研究員として、異担子菌酵母の接合管 誘導物質の構造決定を行った。1980 年より 2 年間ドイツフンボルト招聘研究員として、 ゲッチンゲン大学の植物生理学研究所でジベ レリンの生合成研究を行った。以後一貫して ジベレリンの生合成研究を進め、1991 年か ら 1999 年まで国際フロンティア研究プログ ラムのホルモン機能研究室のチームリーダー を務め、全ジベレリン生合成酵素の遺伝子ク ローニングに貢献した。2000 年 7 月より 発芽生理機構研究チームのチームリーダー、 2000 年 10 月より生長生理グループのディ レクターとして、ジベレリン、アブシジン 酸の生合成・情報伝達の研究を進めている。 Growth Regulation Research Group analysis 1977 年名古屋大学大学院理学研究科分子生 物学専攻で理学博士を取得した。学論文は 「T7 ファージの不連続複製の分子機構」 。国 立遺伝学研究所、分子遺伝部の研究員として タバコ葉緑体の遺伝子のクローニングと構造 機能解析を始めた。その後、名古屋大学、生 物学科助手、同遺伝子実験施設助教授として タバコ葉緑体やシアノバクテリアの遺伝子の 構造と発現解析を進めた。1986 年にはタバ コ葉緑体ゲノムの全塩基配列を初めて決定し た。その後、ロックフェラー大学に留学し、 トランスジェニック植物の研究技術を習得し た。1989 年には理化学研究所筑波研究所の 植物分子生物学研究室の主任研究員に就任 し、シロイヌナズナを用いて植物の環境スト レス応答、耐性獲得の分子生物学的研究を進 めた。1999 年には理化学研究所ゲノム科学 総合研究センター植物ゲノム機能情報研究グ ループのプロジェクトディレクターとしてシ ロイヌナズナの完全長 cDNA の収集、マイ クロアレイによる発現解析、トランスポゾン タグラインの整備を行い、ゲノム機能研究を 実施した。2005 年には理化学研究所横浜研 究所植物科学研究センター長に就任して植物 科学の推進に努めている。 o have enough food to sustain our population in the 21st century, we need to study the basic mechanisms of plant growth, which are closely related to the biosyntheses and signaling of plant hormones. The Growth Regulation Research Group in collaboration with the Metabolomics Group will study the relationships among plant hormones and the production of metabolites to discover new functional genes. We will try to increase the production of crops by the future 神谷 勇治／ Yuji KAMIYA Yuji Kimiya graduated from the Department of Agricultural Chemistry, the University of Tokyo in 1970, and obtained his Ph. D. in agriculture from the University of Tokyo in 1975. He joined the Pesticide Synthesis Laboratory 3 of RIKEN in 1975 and determined the chemical structure of the mating factors of basidiomycetes yeast, Rhodosporidium toruloides . From 1980, for two years he conducted research on gibberellins biosynthesis at the Institute of Plant Physiology, University of Göttingen, as a research fellow of the Alexander von Humboldt Foundation. Since that time he has continued to study gibberellins biosynthesis. He was appointed as the Head of the Laboratory for Plant Hormone Function of the RKEN Frontier Research Program from 1991 to 1998. He contributed to the cloning of all genes related to gibberellin biosynthesis. In July 2000, he joined the Plant Science Center as the Head of the Laboratory of Cellular Growth Development and in October 2000 he was promoted to the position of Group Director, Growth Physiology Group. He is currently working on gibberellins and abscisic acid biosynthesis and signaling. application of these genes. RIKEN PSC 2007 Annual Report 15 Metabolic Function Research Group 代謝機能研究グループ production of useful metabolites gene functions and network regulatory mechanisms for the production and storage of key metabolites identify identify 1977 年東京大学薬学部製薬化学科卒業。た だちに同大学院薬学系研究科に進学し（応 用微生物研究所、（現）分子細胞生物学研究 所、配属 )、生物有機化学・生化学を専攻す る。1982 年に薬学博士号取得。1981 年慶 應義塾大学医学部助手、発がん物質の代謝活 性化と DNA 修飾を研究。1985 年千葉大学 薬学部助手、植物化学・生化学およびバイ オテクノロジー研究を開始する。1987 年ベ ルギー、ゲント大学分子遺伝学教室、Marc Van Montagu 教授のもとに留学して、植 物分子生物学と遺伝子組み換え研究を開始す る。その後、千葉大学薬学部、講師、助教授 を経て、1995 年千葉大学薬学部・大学院薬 学研究科、遺伝子資源応用研究室、教授。現 在に至る。2002 年より、かずさ DNA 研究 所特別客員研究員を兼務。2005 年 4 月よ り理研植物科学研究センターグループディレ クターを兼務してメタボロミクス研究に本格 的に携わる。専門は、メタボロミクスを基盤 とする植物ゲノム機能科学と遺伝子資源応用 学、植物の一次・二次代謝研究とバイオテク ノロジー応用など。 artificially regulate the production of primary and secondary products Plant Productivity Systems Research Group 生産機能研究グループ 1988 年 3 月名古屋大学農学部農芸化学科卒 業。同年名古屋大学大学院農学研究科博士課 程前期課程に進学し、1992 年 4 月から名古 屋大学大学院農学研究科の助手として勤務し た。その間 1995 年 5 月に博士号 ( 農学博士 ) を授与された。2000 年 10 月にコミュニケー ション分子機構研究チームのチームリーダー に就任し、2005 年 4 月より生産制御研究 チーム・チームリーダー、2006 年 10 月よ り生産機能研究グループ・グループディレク ター。これまで窒素同化系遺伝子の機能発現 制御機構、サイトカイニンを介した窒素情報 伝達機構とサイトカイニン生合成機構につい て、生化学、分子生物学的視点から研究を続 けている。 geonomic function information and comparative genome studies production of biomaterials and energy production control, sink function, material transport understanding systems techniques aimed at productivity control production of foods, pharmaceuticals, functional foods 榊原 均 / Hitoshi SAKAKIBARA Metabolic Function Research Group production of crops and trees 遺伝子の機能とネットワークを解明 での解析）などのゲノム関連科学を基盤として、有用物質生産に関わる 遺伝子の機能とネットワークを解明し、重要な代謝産物の生産および蓄積の制 御機構を明らかにすることを目指しています。これらの基礎的な知見により、 合理的な手法で一次・二次代謝物生産の人為的制御が可能となり、食料、医薬、 高機能食品などへの応用展開が期待できます。 Identifying Gene Functions and Networks I n this research group, we use metabolomics and other genomics-related sciences to identify gene functions and networks involved in the production of useful metabolites, with the objective of elucidating the mechanisms that regulate the production and storage of key metabolites. Such fundamental findings will enable us to artificially regulate the production of primary and secondary products by rational ways, with application to the production of foods, pharmaceuticals, functional foods, industrial materials, and energy. 16 RIKEN PSC 2007 Annual Report Kazuki Saito was born in Nagano in 1954, Japan. He graduated from the Faculty of Pharmaceutical Sciences, the University of Tokyo, Japan in 1977 and then obtained his PhD for bio-organic chemistry/biochemistry of pharmaceutical sciences from the University of Tokyo in 1982. After staying in Keio University in Japan and Ghent University in Belgium (Prof. Marc Van Montagu’s laboratory), he began molecular biology and biotechnology of plant primary and secondary metabolism in Chiba University. After being appointed as a lecturer and an associate professor, he has been appointed as a full professor since 1995 at the Graduate School of Pharmaceutical Sciences, Chiba University, Japan, until now. Since 2002, he has been a Special Guest Researcher in Kazusa DNA Research Institute in Kisarazu. Since April, 2005, he has been appointed as a group director at RIKEN Plant Science Center in Yokohama to direct Metabolomics Group and Metabolic Function Group. He has published more than 170 original papers and 70 invited reviews and book chapters. His research interests are metabolome-based functional genomics, biochemistry, molecular biology and biotechnology of primary and secondary metabolism in plants. He is also interested in music, movies, detective novels and Bon-Sai. 植物資源の効果的な利用のために 植 物は光合成により様々な有機化合物を生合成します。植物の生産性には 光合成能の向上、生合成産物の効果的な輸送、蓄積などさまざまなプロ セスが関わっています。当研究グループでは物質生産やエネルギー生産に役立 つ植物資源の効果的な利用のための生産制御に関わる研究開発を行います。植 物の生産制御、シンク機能、効果的な物質輸送に関わるシステムの解明と生産 制御への利用技術の研究開発を進めます。モデル植物のゲノム機能情報、比較 ゲノム研究を基盤として作物、樹木への展開をしていきます。 Effectively Utilizing Plant Resources P lants synthesize a variety of organic compounds through photosynthesis and unique metabolic pathways. Numerous metabolic processes are involved in plant productivity, such as an efficient photosynthetic capacity and effective transport and storage of biosynthesized products. This research group conducts research and development on production control aimed at effectively utilizing plant resources that aid in the production of biomaterials and energy. We are conducting studies to understand the systems involved in plant productivity, sink function, and effective material transport, as well as R&D on techniques aimed at productivity control. We hope to utilize the various genomic functions of model plants and comparative studies on genomes as a foundation for the production of more and better crops and trees. RIKEN PSC 2007 Annual Report 17 Plant Productivity Systems Research Group 当 研究グループでは、メタボロミクス（網羅的な代謝産物のゲノムレベル 斉藤 和季／ Kazuki SAITO Hitoshi Sakakibara graduated from the School of Agricultural Sciences, Nagoya University in 1988. He obtained his Ph.D. in agriculture from Nagoya University in 1995. He was appointed as Research Associate (1992) and then Assistant Professor (1995) of the School of Agricultural Sciences, Nagoya University. He joined the Plant Science Center (PSC) in October 2000 as Head of the Laboratory for Communication Mechanisms. He continues his research project in the second phase of PSC as Team Leader of Biodynamics Research Team and as Group Director of Plant Productivity Systems Research Group. Since graduate school he has been conducting biochemical and molecular physiological studies on the regulation mechanism of expression of nitrogen assimilatory genes, cytokinin-mediated nitrogen signaling, and cytokinin biosynthesis. Plant Immunity Research Group 1988 年、東京大学農学部農芸化学科卒業。 1993 年、カリフォルニア大学デービス校 Ph.D( 遺伝学 ) 取得。1993 年から米国ソー ク・ノーブル研究所ポスドク。1996 年より 英国セインズベリー研究所研究員。2000 年 に同グループリーダーとなる。一貫して植物 免疫の研究に従事。2005 年 10 月より現職。 植物免疫研究グループ Plant Functional Genomics Research Group 植物ゲノム機能研究グループ Genome infomation Proteomic analysis Metabolomic analysis Genome Information Functional analysis of immunity-related proteins Identification of immunityrelated compounds Elucidation of plant immunity mechanisms Development of disease resistance crops Transcription network 白須 賢／ Ken SHIRASU Protein network Ken Shirasu attended the University of Tokyo before earning his Ph.D. in genetics at University of California, Davis in 1993. Then Shirasu obtained a Salk/Noble postdoctoral fellowship to study plant immunity at the Salk Institute. In 1996 Shirasu moved to the Sainsbury Laboratory (UK) as a researcher, where he later became a group leader in 2000. His current position at RIKEN PSC started in October 2005. Technology Innovations Integration of Information and Technology Transformation Chemical treatment 持続的な耐病性植物の作出をめざして ゲノム機能解析による植物システムの解明 植 植 物は本来病原体に対する高い防御能力を備えています。本研究グループ はこの植物の耐病性に関与する遺伝子、タンパク質、および低分子化学 物質をゲノミクス、プロテオミクス、メタボロミクス的解析手法を用いて網羅 Ecological effects (Elucidation of plan system) Economical effects (Production of functional plants) の発現からタンパク質生産、2 次代謝産物の制御までの包括的な理解が 必要です。当研究グループでは、新規なゲノム解析技法を開発し、駆使するこ とで有用な形質の探索を通じてこれらの制御ネットワークを理解し、種々の研 パターンと信号伝達ネットワークを解析し、また免疫システムの制御に関与す 究の基礎となる植物ゲノム機能の研究を推進します。 るタンパク質の修飾などによるスイッチ機能を明らかにし、農薬に頼らない持 Plant Immunity Research Group Towards Sustainable Crop Protection Strategy T he main goal of my group is to understand the molecular mechanism of Understanding Plant Systems through Functional Genomics Research T o improve plant productivity and environmental adaptability, a systematical understanding of regulatory networks is indispensable, from gene expression to protein and secondary metabolite production. Our group will perform plant immunity in plants. We plan to systematically identify and characterize genes, functional genomic research fundamental to all plant research through the proteins and small molecular compounds that are important for the defense analysis of useful traits in crops, and the development and the application of new by using genomics, proteomics and metabolomics approaches. We aim to genome technologies. patterns of defense related genes and their post transcriptional regulation, such as protein modification. Pathogen infection of plants is economically damaging to agricultural industries worldwide. Understanding the molecular basis of disease resistance mechanisms plants utilize in nature will provide new strategies to combat pathogens. 18 RIKEN PSC 2007 Annual Report Minami Matsui graduated from the department of Biochemistry, Saitama University in 1981 and received Ph.D. in Biophysics from Kyoto University in 1986. After receiving Ph.D. he joined Nippon Medical School and studied human oncogenes. He cloned human fra-1 and fra-2 genes and analyzed their expression during monocyte-macrophage differentiation. He also worked on characterization of human A-myb and B-myb oncogenes. At the same time he screened oncogene-related genes from Arabidopsis and cloned small GTPase gene related to ras -oncogene. He learned photomorphogenesis at Yale University in US and after returning to Japan he joined RIKEN Frontier research program as a deputy head in 1995 and worked on plant photomorphogenesis using Arabidopsis and tomato. From 1999 he joined Plant Functional Genomics Research Group in Genomic Sciences Center at RIKEN Yokohama Institute and produced and analyzed Arabidopsis Activation tagged lines, and also performed plant genome research by developing “rapid genome function identification platform”. From 2006 he joined Plant Science Center as a group director of Plant Functional Genomics Research Group and continues plant genome research. RIKEN PSC 2007 Annual Report 19 Plant Functional Genomics Research Group elucidate signaling network system for plant immunity by analyzing expression 松井 南／ Minami MATSUI 物が持つ物質生産力、環境適応力の向上を目指すためには、植物遺伝子 的に単離し、植物の免疫システムの解明をめざします。感染応答遺伝子の発現 続的な耐病性植物の作出をめざします。 1981 年に埼玉大学理学部生化学科を卒業。 1986 年京都大学大学院理学研究科生物物理 学専攻で理学博士を取得した。博士取得後、 日本医科大学にて、ヒトガン関連遺伝子 fra1 ,fra-2 の単離と単球からマクロファージへ の分化における発現、A-myb , B-myb の単 離と発現解析を進めた。同時にシロイヌナズ ナからのガン関連遺伝子探索を行い ras 関 連遺伝子の small GTPase 遺伝子単離を行っ た。その後、米国エール大学へ留学し、植物 の光形態形成を学んだ。帰国後、1995 年よ り理化学研究所フロンティア研究システム分 子機構研究チームの副チームリーダーとして シロイヌナズナ、トマトを用いた光形態形成 研究を進めた。1999 年にゲノム科学総合研 究センター、植物ゲノム機能情報研究グルー プのチームリーダーとしてシロイヌナズナの アクティベーションタグラインの作成、完全 長を用いた遺伝子探索法の開発を行い、ゲノ ム機能研究を実施した。2006 年から植物科 学研究センターの植物ゲノム機能研究グルー プのグループディレクターとしてゲノム研究 を継続している。 ●チームリーダー 斉藤 和季 ●研究員 草野 都 及川 彰 メタボローム解析研究チーム 松田 史生 ●JSPS 外国人特別研究員 研究内容 ● 質量分析計を用いたメタボロームの精密ハイスループット解析手法の開発 ● 代謝産物同定のためのデータベースの構築とメタボロームデータ解析のバ イオインフォマティクス ● シロイヌナズナ、イネなどの遺伝子組み換え体ラインなどの代謝プロファ イリング、ストレス応答、細胞分化および代謝機能分化に伴うメタボロー 斉藤 和季 / Kazuki SAITO ム解析 Content of Research ● Development of analytical techniques for mass spectrometry. ● Database construction and bioinformatics for metabolomic data analysis. ● Metabolomic analysis for plant biology through collaboration with other groups. メタボロミクス研究の基盤−質量分析による網羅的解析の確立 Fundamentals for metabolomics research - comprehensive metabolic profiling by mass spectrometry メタボロミクスである。当研究チームでは、主に高性能質量分析計を用 分析データのデータベースおよびバイオインフォマティクスツールの開発 ● シロイヌナズナや重要作物、実用植物の機能解明を目的とした、センター 内外のグループとのメタボローム解析共同研究 Result of Research Outline of Research ドリス アルビンスキー 新井田 理絵 篠田 祥子 ●客員研究員 岡咲 洋三 ●研修生 鈴木 誠 ●Team Leader Kazuki SAITO ●Research Scientists Miyako KUSANO Akira OIKAWA Fumio MATSUDA ●Research Associate Takayuki TOHGE ワークの解明 同定をセンター内外の研究チームと共同で行っている。 林 尚美 ● 遺伝子機能同定や代謝ネットワーク解析のための GC-MS および LC-MS ● メタボローム解析のための、植物代謝産物のクロマトグラフィーおよび質量 ている。また、これらの解析データからのデータマイニングと未知遺伝子機能 ●テクニカルスタッフ 小林 誠 ●JSPS Foreign Research Fellow Celine DIAZ 胞内の全代謝産物を同定および定量し、ゲノム機能と対応させることが いて網羅的な代謝産物解析の技術開発とハイスループット代謝産物解析を行っ セリーヌ ディアス ●リサーチアソシエイト 峠 隆之 研究成果 と多変量解析を用いたメタボローム解析パイプラインの構築と代謝ネット 研究概要 細 Metabolomics Research Group Metabolomics Research Group Metabolome Analysis Research Team Research Staff ●Technical Staffs Makoto KOBAYASHI Naomi HAYASHI Doris ALBINSKY Rie NIIDA Shoko SHINODA ●Visiting Scientist Yozo OKAZAKI ●Student Trainee Makoto SUZUKI ● Establishing a GC-MS and LC-MS based metabolomics pipeline for W e perform high-throughput metabolite analyses and develop technologies identification of gene function by combination of multivariate analysis and for the comprehensive analysis of metabolites with high-performance mass functional metabolic network analysis. ● Database construction for chromatography and mass spectrometry of plant spectrometers. We collaborate with other research groups in the center and outside of the center for metabolomic study. metabolites and bioinformatics for metabolomic data analysis. ● Metabolomic analysis as collaborative projects with internal and external groups for a variety of plant functions with Arabidopsis thaliana and crops. CE-TOF/MS 20 RIKEN PSC 2007 Annual Report LC-Q-TOF/MS RIKEN PSC 2007 Annual Report 21 ●ユニットリーダー 平井 優美 ●リサーチアソシエイト 澤田 有司 ●テクニカルスタッフ 代謝システム解析ユニット 鈴木 あかね 高橋 晶子 ●研修生 矢野 美弦 研究内容 ● メタボロミクスとトランスクリプトミクスの統合による網羅的遺伝子機能 予測と分子生物学・逆遺伝学などによる予測の検証 ● 有用代謝産物の生産性向上にかかわる遺伝子の同定 ● システム生物学的方法論による代謝制御機構の解明 平井 優美／ Masami YOKOTA HIRAI 代謝物と転写産物の一斉分析により植物の物質生産の仕組を解明する Elucidation of plant production by comprehensive analyses of metabolites and transcripts 研究概要 栄 養分の同化やエネルギー・物質生産のプロセスである代謝は生命現象の 根幹であり、植物細胞のなかで複雑なメカニズムによって制御されてい る。植物細胞内の代謝をシステムとして捉えその全体像を解明することを目指 し、トランスクリプトミクスおよびメタボロミクスにより得られる網羅的な遺 伝子発現・代謝産物蓄積情報をバイオインフォマティクスを駆使して解析し、 分子生物学的知見と統合する。 Outline of Research M etabolism, the process of nutrient assimilation and energy/material production, is a basis of life, and hence regulated by the complicated mechanism in the plant cell. In order to elucidate a whole plant metabolism as a system, we analyze the comprehensive data of gene expression and metabolite accumulation obtained by transcriptomics and metabolomics with the help of bioinformatics. We integrate the findings obtained by bioinformatics and by molecular biology. Metabolomics Research Group Metabolomics Research Group Metabolic Systems Research Unit Research Staff 1989 年 3 月に東京大学農学部農芸化学科 卒業。1994 年 3 月に東京大学大学院農学系 研究科にて博士号（農学）を取得した。博士 論文の研究テーマは、硫黄栄養応答性遺伝子 の発現制御機構の解析。引き続き 1994 年 4 月から 1997 年 3 月まで日本学術振興会 特別研究員として同研究に従事した。1997 年 7 月から 2001 年 3 月まで日本学術振興 会未来開拓学術研究推進事業研究員 ( 千葉 大学リサーチアソシエイト ) としてアルカロ イド生合成に関する研究に従事。2001 年 4 月から 2005 年 3 月まで科学技術振興機構 CREST 研究員として千葉大学大学院薬学研 究院にて栄養ストレス下の植物のトランスク リプトミクスおよびメタボロミクスを行っ た。2005 年 4 月から代謝システム解析ユ ニットのユニットリーダーとして、植物科学 研究センターに参加している。 Masami Yokota Hirai graduated in agricultural chemistry from The University of Tokyo in 1989, and got her Ph.D. in agriculture from The University of Tokyo in 1994. The theme of her doctoral thesis was “Studies on the regulatory mechanism of the expression of sulfur-responsive genes”. She continued the study until March 1997 as a research fellow of the Japan Society for the Promotion of Science (JSPS). From July 1997 to March 2001, she was engaged in the study on alkaroid biosynthesis as a post-doctoral fellow of JSPS Research for the Future Program (a research associate of Chiba University). From April 2001 to March 2005, she was engaged in the integrated analysis of transcriptome and metabolome of Arabidopsis under nutritional stresses as a post-doctoral fellow of CREST of Japan Science and Technology Agency in Chiba University. In April 2005, she joined the Plant Science Center as the unit leader of the Metabolic Systems Research Unit. 井出 曜子 ●訪問研究員 ロミー クラウスニッツァー ●客員研究員 西澤 治 荒木 良一 Content of Research ●Unit Leader Masami YOKOTA HIRAI ● Prediction of unknown gene function based on integration of metabolomics ●Research Associate Yuji SAWADA and transcriptomics. Confirmation of the predicted function by molecular biology and reversed genetics ● Identification of the genes useful for improvement of plant production ● Elucidation of regulatory mechanism of metabolism by systems-biological approach ●Technical Staffs Akane SUZUKI Akiko WATANABE-TAKAHASHI ●Student Trainees Mitsuru YANO Yoko IDE ●Visiting Researcher Romy KLAUSNITZER ●Visiting Scientists Osamu ISHIZAKI NISHIZAWA 研究成果 ● 硫黄栄養欠乏シロイヌナズナのトランスクリプトームデータおよびデー Ryoichi ARAKI タベース上で公開されている多数のシロイヌナズナマイクロアレイデー タを元にした遺伝子共発現解析により、抗変異原活性を持つグルコシノ レートの生合成に関与する遺伝子群の機能を包括的に予測し、メチオニン 由来グルコシノレート生合成の鍵調節因子である PMG1(Production of Methionine-derived Glucosinolate 1) 遺伝子を発見した (Hirai et al. Proc. Natl. Acad. Sci. USA,104 : 6478-6483)。 Result of Research ● Based on coexpression analysis using the transcriptome data of sulfurstarved Arabidopsis and publicly-available Arabidopsis microarray data, we predicted the genes involved in glucosinolate biosynthesis comprehensively, and identified PMG1 gene, a key regulator of methionine-derived glucosinolate biosynthesis (Hirai et al. Proc. Natl. Acad. Sci. USA, 104 : 6478-6483). シロイヌナズナの全遺伝子（転写産物）と全 化合物（代謝産物）を分析して、グルコシノ レートの生合成に関わる酵素遺伝子群が同じ 発現パターンを示すことを明らかにし、これ らを正に制御する鍵転写因子 PMG1 を発見 した。またグルコシノレート生合成に関わる 未知遺伝子の機能を包括的に予測した。 22 RIKEN PSC 2007 Annual Report RIKEN PSC 2007 Annual Report 23 先端 NMR メタボミクスユニット ● 生物組織安定同位体標識化技術の高度化 ● 溶液・固体 NMR 法の潜在能力を活かした代謝産物群計測・解析技術の高 度化 ● 植物バイオマス利用のための代謝動態、ネットワーク解析法の開発 Content of Research ● Advancement of the uniform stable isotope labeling methodology ● Technological advancement of solution / solid-state NMR measurements for studies of metabolite mixtures ● Development of the methods for metabolic dynamics and network analysis toward plant biomass utilization 菊地 淳／ Jun KIKUCHI 計測科学の進展は、生命科学のブレークスルーを拓く Novel methods for measurement of living systems are making new breakthroughs in life science. 研究概要 核 磁気共鳴（NMR）は観測核さえ選べば、可溶・不溶を問わずほぼ全て の生体分子種を計測する事ができる方法である。当研究ユニットでは NMR 法の高定量性・非侵襲性・生体内位置情報選択性・原子核環境情報選択 性・試・生体分子構造決定能、 といった潜在能力を惹き出した方法論開発を行い、 NMR 代謝物解析のイニシアティブを狙う。さらに食糧による健康向上と環境 問題緩和へと貢献させるために、植物バイオマス利用のための代謝動態・ネッ トワーク解析法の構築を推進する。 Outline of Research N uclear Magnetic Resonance(NMR) can measure diverse biomolecules including soluble and insoluble states, if adequate nucleus are observed. Our laboratory intends to initiate metabolic analysis by developing new methods using an NMR-based approach, such as high quantification, non-invasive measurements, localized spectroscopy in vivo , selectivity of nuclear environments, versatility of pre- treatments of the samples, and validity of structure analysis of diverse biomolecules including stereo-isomers. Furthermore, we will develop the methods for metabolic dynamics and network analysis toward plant biomass utilization, for better improvements of food nutrition and global environment. 24 RIKEN PSC 2007 Annual Report 1993 年 3 月に東京農工大学物質生物工学 科卒業。1998 年 3 月に東京農工大学大学 院物質生物工学研究科にて博士号 ( 工学 ) を 取得した。途中 1994 年シェフィールド大 学ならびに 1996 年ノースウエスタン大学 留学、1996-1998 年日本学術振興会特別研 究員 (DC2)、1996-1997 年国立東京工業高 等専門学校非常勤講師 ( 物理化学 )。1998 年 4 月 -10 月まで、JST・ERATO 研究員、 1998-2005 年まで理研 GSC タンパク質構 造・機能研究グループでタンパク質溶液構 造決定の方法論開発、ならびに世界最高磁 場 920MHz-NMR 装置の開発等に携わった。 2005 年 4 月から先端 NMR メタボミクス ユニットのユニットリーダーとして、植物 科学研究センターに参加している。2005 年 12 月より名古屋大学大学院生命農学研究科 客員助教授を兼任。 Jun Kikuchi graduated from the Department o f B i o t e c h n o l o g y, To k y o U n i v e r s i t y o f Agriculture and Technology, in March 1993, and obtained his Ph.D. in Engineering from the Graduate School of Technology, Tokyo University of Agriculture and Technology, in March 1998. During this period, he studied abroad at The University of Sheffield, 1994 and at Northwestern University, 1996. In addition to this, he taught physical chemistry as lecturer of Tokyo National College of Technology, 1996-1997, and he was prepost doctoral fellow of JSPS (DC2), 1996-1998. From April 1998 to October 1998, he was a research scientist of ERATO/JST and joined Protein Research Group of GSC/RIKEN from 1998-2005. During this period, he conducted solution structure determination of proteins by long-range order information and achieved development of the world highest-field (920 MHz) high-resolution NMR. In April 2005, he joined the Plant Science Center as Unit Leader of Advanced NMR Metabomics Research Unit. From December 2005, he installed Guest Associate Professor of Graduate School of Agriculture, Nagoya University. 研究成果 ● 理研や共同研究者が有する多様な変異体・交雑系統についてハイスループッ トな多検体処理を可能とするための、代謝プロファイリング法を整備した。 ● 異種核多次元 NMR 計測により得られたシグナル群から、物質同定を行な うために欠かせない標準物質のデータベースを、有機溶媒２種・水溶液の 計３種で充実化させた。さらに、これらのデータベースから効率的な物質 同定を行うオリジナル Java ソフトウエア、SpinAssign の開発・改良を行 Metabolomics Research Group Metabolomics Research Group Advanced NMR Metabomics Research Unit 研究内容 Research Staff ●ユニットリーダー 菊地 淳 ●技師 近山 英輔 ●研究員 泉川 美穂 関山 恭代 ●研修生 岡本 真美 森 哲哉 中西 裕美子 木村 悠一 古田 拓 ●Unit Leader Jun KIKUCHI ●Technical Scientist Eisuke CHIKAYAMA ●Research Scientists Miho IZUMIKAWA Yasuyo SEKIYAMA ●Student Trainees Mami OKAMOTO Tetsuya MORI Yumiko NAKANISHI Yuuichi KIMURA Taku FURUTA なった。 ● 不溶な代謝産物群やバイオマスの計測を可能とする、高分解能マジック角 回転法や固体 NMR 法の解析法を整備した。 Result of Research ● NMR-based metabolic profiling methodologies were developed for highthroughput analysis of various mutants and natural variants available from RIKEN and collaborators. ● Standard NMR database of major metabolites measured in two organic solvents and aqueous solution were prepared for accurate molecular identification in hetero-nuclear multi-dimensional NMR. Furthermore, we have developed and improved original Java-software SpinAssign for an efficient molecular identification from metabolite mixtures using the standard NMR database. ● High-resolution magic angle spinning and solid-state NMR methodologies were applied for characterization of insoluble metabolites and plant biomass. RIKEN PSC 2007 Annual Report 25 ●チームリーダー 篠崎 一雄 ●上級研究員 嶋田 幸久 ●研究員 ゲノム機能統合化研究チーム 郷田 秀樹 添野 和雄 研究内容 ● AtGenExpress プロジェクトの一環として、シロイヌナズナのホルモン関 連変異体のトランスクリプトーム・メタボロームデータの収集・解析と公開 ● EST、完全長 cDNA を利用したコムギゲノム解析 ● 統合ゲノム情報を利用した新規遺伝子、新規植物生長調節物質などの機能 解析 篠崎 一雄／ Kazuo SHINOZAKI Content of Research ● Transcriptome and metabolome analysis of Arabidopsis hormone-related mutants, as a part of AtGenExpress project ● Analysis of wheat genome and gene expression using large-scale EST and fulllength cDNAs T ● Analysis and discovery of novel genes, compounds, and regulatory mechanisms by using integrated genomics information オーミックスデータの統合から生まれる新しい世界 Integration of omics data brings in a new era 研究成果 研究概要 主 ● AtGenExpress プロジェクトのシロイヌナズナ遺伝子の発現データを階 にシロイヌナズナやコムギの EST, DNA マイクロアレイ解析を通してス 層クラスター法で解析し、その結果を簡便に検索して閲覧できるシステ トレス応答やホルモン応答に関するトランスクリプトームデータの収集 ム Cluster Cutting を 開 発 し た。 こ の シ ス テ ム を ウ ェ ブ サ イ ト PRIMe を行う。このトランスクリプトームデータをメタボロームデータやその他ゲノ （Platform for RIKEN Metabolomics）に搭載し、公開した。 ム情報と統合し、新規遺伝子や新規化合物の機能解明を行う。これらの研究を 持田 恵一 綾野 まどか ●テクニカルスタッフ 立川 巴 高橋 知登世 ●パートタイマー 大野 さち代 西塚 幸子 澤 加奈 佐々木 江理子 ●Team Leader Kazuo SHINOZAKI ●Senior Research Scientist Yukihisa SHIMADA ●Research Scientists Hideki GODA Kazuo SOENO ●Research Associates Keiichi MOCHIDA Madoka AYANO ●Technical Staffs Tomoe TACHIKAWA Chitose TAKAHASHI ●Part Timers Sachiyo OHNO Yukiko NISHIZUKA Kana SAWA Eriko SASAKI また、イネ遺伝子との比較を通してコムギ特異的遺伝子を特定した。 ● コムギ EST 解析を通して、ストレス応答性遺伝子を同定した。さらに、転 Outline of Research his team will collect transcriptome data of Arabidopsis and wheat as a part of international and domestic collaborative DNA microarray Result of Research information in response to environmental changes and hormone ● We analyzed transcriptome data from the AtGenExpress project by hierarchical responses. The integrated information will be exploited to discover novel genes, compounds, and regulatory mechanisms 写因子遺伝子の器官特異的発現やストレス応答性を明らかにした。 ● シロイヌナズナ DNA マイクロアレイを通して、新規オーキシン阻害剤候 補を同定した。 activities. The team will also integrate and analyze genomics to improve plant functions. ●リサーチアソシエイト ● コムギの EST と完全長 cDNA の解析を通して転写因子遺伝子を同定した。 通して植物の機能向上を目指す。 T Metabolomics Research Group Metabolomics Research Group Integrated Genomics Research Team Research Staff clustering and developed a web-based data viewer, Cluster Cutting, to present Wheat ESTs & full length cDNA Integrated database the result. This system is open for public access at our web site, PRIMe (Platform for RIKEN Metabolomics). ● We performed functional annotation of wheat EST and full-length cDNAs and identified genes encoding transcription factors. We also compared the data with that of rice to discover wheat-specific genes. GC-TOFMS & LC-Q-TOFMS ● We analyzed wheat EST in large scale and screened genes responsive to abiotic stresses. ● We analyzed plant growth regulators using Arabidopsis DNA microarray and found a candidate of novel auxin inhibitor. discovery of new genes and new compounds 26 RIKEN PSC 2007 Annual Report RIKEN PSC 2007 Annual Report 3 27 ●ユニットリーダー 櫻井 哲也 ●技師 秋山 顕治 ●技術支援 ゲノム情報統合化ユニット 石渡 敦 吉田 拓広 研究内容 ●Unit Leader Tetsuya SAKURAI ● 自由度の高いアクセス方法を実装した情報基盤の整備 ●Technical Scientist Kenji AKIYAMA ● 比較ゲノムに基づくデータマイニング技術の開発 ● トランスクリプトーム・メタボロームにおける解析環境の提供 櫻井 哲也／ Tetsuya SAKURAI 植物情報の比較と統合、解析支援環境の提供 研究概要 シ ロイヌナズナ、イネ、ポプラなど多生物種の生命情報へ自由にアクセス できる情報基盤の整備を推進すると共に、比較ゲノムに基づくデータマ イニング技術を開発し、トランスクリプトーム・メタボロームの解析支援環境 を提供する。 Outline of Research W e promote the implementation of the research platform that is freely accessible to various species information. Also, we develop data mining technology based on comparative genomics, and provide analysis environment of transcriptomics and metabolomics. 1996 年 3 月に横浜市立大学文理学部理科 生物学課程卒業。システムエンジニアを経 て、2000 年 8 月から植物ゲノム機能情報 研究グループの技師として、ゲノム科学総合 研究センターへ赴任。シロイヌナズナ完全 長 cDNA コレクションやシロイヌナズナタ グ挿入変異体解析プロジェクトに参加し、大 規模データ解析、データベース構築等のイン フォマティクスに従事した。2003 年 4 月よ りゲノム情報科学研究グループへ移籍し、シ ロイヌナズナ統合データベース RARGE を 構築した。2005 年 4 月からゲノム情報統 合化ユニットのユニットリーダーとして、植 物科学研究センターに参加している。 Te t s u y a S A K U R A I g r a d u a t e d f ro m t h e department of literature and science, biology course, the Yokohama City University, in March 1996. After a career as a system engineer in the computer industry, he joined Plant Functional Genomics Research Group, the Genome Science Center as a technical engineer in August 2000. He engaged analysis of Arabidopsis full-length cDNA collection and transposon tagged mutants, and conducted a study in informatics such as large scale analysis and database construction. In April 2003, he transferred to Genome Informatics Group, and constructed the Arabidopsis integrated database “RARGE”. In April 2005, he joined the Plant Science Center as a unit leader of Integrated Genome Informatics Research Unit. ●Technical Assistances Atsushi ISHIWATA Takuhiro YOSHIDA Content of Research Integration of plant information, and development of analysis support environment Metabolomics Research Group Metabolomics Research Group Integrated Genome Informatics Research Unit Research Staff ● Improvement of information infrastructure for freely accessible ● Development of data mining technology based on comparative genomics ● Provision of analysis environment for transcriptomics and metabolomics 研究成果 ● キャッサバ（Manihot esculenta ） 、ダイズ（Glycine max ）完全長 cDNA 解析 ● PRIMe Web（http://prime.psc.riken.jp/）の開発 ● イネ完全長 cDNA による有用形質高速探索プロジェクトの推進を目的とし た表現形質データ収集支援システム及びデータベースの構築 Result of Research ● EST analyses of cassava (P. nigra var. italica ) and soybean (G. max ). This work is a part of comparative genomics research. ● Development of “PRIMe web”. It’s a web-based service for metabolomics and transcriptomics as systems understanding of life science. ● Construction of a phenotype data accumulation support system and the database for rapid characterization of useful trait using rice cDNA FOX lines of Arabidopsis . Arabidopsis DBs PRIMe Web RARGE, RARTF & RAPID 28 RIKEN PSC 2007 Annual Report RIKEN PSC 2007 Annual Report 29 ●ユニットリーダー メタボローム情報ユニット ●客員主管研究員 有田 正規 ●リサーチアソシエイト 福島 敦史 森岡 涼子 金谷 重彦 研究内容 ● メタボロームデータの解析ソフトウェアの開発 ● 代謝ネットワークの解析およびシミュレーションソフトウェアの開発 Content of Research ● Development of software for metabolomic data analysis 有田 正規／ Masanori ARITA 生物学は計算機科学と融合する Biology will marry with computer science. 研究概要 メ タボロームの定量データ解析、ネットワーク解析、シミュレーションに 必要な基盤ソフトウェアの開発をおこなう。また、未知代謝産物の同定 に寄与できる各種データベースを構築する。開発したソフトウェアは他チーム において集積したメタボローム、トランスクリプトームデータに応用し、植物 のシステム的理解を実現する。 Outline of Research Metabolomics Research Group Metabolomics Research Group Metabolome Informatics Research Unit Research Staff ● Development of software for network analyses and simulations 1999 年東京大学大学院理学系研究科情報科 学専攻、博士課程満期退学、同年博士（理学） 。 同年、通商産業省工業技術院・電子技術総合 研究所、2001 年、経済産業省産業技術総合 研究所・生命情報科学研究センターを経て、 2003 年より東京大学大学院新領域創成科 学研究科情報生命科学専攻、助教授。2006 年 11 月よりメタボローム基盤グループ副グ ループディレクターを兼任。 研究成果 1999 Ph. D. from Department of Information Science, Graduate School of Science, University of Tokyo.1999 Researcher at Electrotechnical Laboratory, Agency of Industrial Science and Technology. 2001 R e s e a rc h e r a t C o m p u t a t i o n a l B i o l o g y R e s e a rc h C e n t e r, N a t i o n a l I n s t i t u t e o f Advanced Industrial Science and Technology. 2003 Associate Professor at Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo. 2006 Group sub-director of Metabolomics Research Group, PSC (adjunct position). Result of Research ● メタボロミクス研究をサポートする代謝産物やその質量分析データベー ●客員研究員 時松 敏明 ●企業派遣（アクシオへリックス社） 長田 洋明 ●Unit Leader Masanori ARITA ●Research Associates Atsushi FUKUSHIMA Ryoko MORIOKA ●Senior Visiting Scientist Shigehiko KANAYA ●Visiting Scientist Toshiaki TOKIMATSU ●Visiting Staff (AxioHelix Inc.) Hiroaki OSADA スや解析ツールを開発し、それらをウェブサイト "PRIMe（Platform for RIKEN Metabolomics）" に搭載、公開（http://prime.psc.riken.jp/） ● トランスクリプトームやメタボロームデータから特異的な細胞応答を検出 する統計学的手法を開発 ● Development of a metabolite and mass spectral database and analytical tools supporting metabolomics research. These have been installed at a web-based portal, "PRIMe (Platform for RIKEN Metabolomics) ". Its web-based service is available at http://prime.psc.riken.jp/. ● Development of a statistical method for finding particular response pathways through integrated analysis of metabolomic and transcriptomic data. W e develop platform software and database necessary for metabolomic analyses, network analyses, and simulations. The software is applied to integrated analysis of metabolomic and transcriptomic data towards systematic understanding of plants. 30 RIKEN PSC 2007 Annual Report RIKEN PSC 2007 Annual Report 31 Gene Discovery Research Team 研究内容 Research Staff ● 環境ストレス応答に関わる制御因子、シグナル伝達因子の探索と解析 ●チームリーダー 篠崎 一雄 ● 環境ストレス耐性に関与する遺伝子の機能解析と利用 ●研究員 ● 逆遺伝学および比較ゲノム解析に基づいた植物の生産性と関わる遺伝子の 藤田 美紀 梅澤 泰史 探索と利用 機能開発研究チーム 片桐 健（植物分子生物学研究室） Gene Discovery Research Group 関 原明（植物分子生物学研究室） ●リサーチアソシエイト 浦野 薫 ● Exploration and analysis of regulatory factors and signaling factors in environmental stress responses ●基礎科学特別研究員 西山 りゑ ● Functional analysis and use of genes involved in environmental stress ●テクニカルスタッフ resistance 水門 佐保 ● Exploration and use of genes involved in plant productivity using a reverse 小林 裕子 ●研修生 genetic approach 篠崎 一雄／ Kazuo SHINOZAKI 高橋 史憲（筑波大学大学院） 中村 正輝（筑波大学大学院） ●パートタイマー 研究成果 大貫 真知子 衛藤 美智江 松尾 久美子 ● 乾燥ストレスや ABA による制御機構を解明するために、転写因子およびシ グナル伝達因子に焦点を絞って研究を行った。特に、AP2、NAC、bZIP 型 ●Team Leader Kazuo SHINOZAKI 転写因子や SnRK2, MAP キナーゼファミリーについて、その機能やシグ ●Research Scientists Miki FUJITA ナル伝達機構を解析した。転写因子に関してはクレストプロジェクトで新 規転写因子の cDNA の収集と機能解析を進めた。 ABA の分解酵素遺伝子の機能解析や、メタボローム解析によるアミノ酸、 糖、二次代謝産物などの代謝関連遺伝子の解析を進めた。 研究概要 植 ● 比較ゲノム解析による有用遺伝子単離を目指して、ダイズの完全長 cDNA 物の量的な向上に関わる生理機能を持つシロイヌナズナ遺伝子、栽培環 ライブラリーを作成し、リソースの整備を行った。また、40000 個のダイ 境の影響を最小限にして最大限の生産性を発揮できるような新機能の付 ズ完全長 cDNA クローンについてシーケンス解析を進めた。 与に関連するシロイヌナズナ遺伝子の探索を行う。遺伝子破壊変異体や遺伝子 代謝制御に関わる遺伝子等を研究対象とする。さらに新規の生産性 向上関連遺伝子の探索にはトランスクリプトーム、メタボローム解 Fig.1 The outline of reseach activitie in Gene Discovery Reseach Team Stress Response in plants を解析する。 Signal Perception Signal Transduction PostTranscriptional Regulation his research team is discovering Arabidopsis genes of which functions are linked to quantitative improvements in plants and those with new functions for minimizing the effects of the Reverse & Forward Genetics approach using gene destruction and transgenic overexpression. Kinase P Transcription Factors Transcription Factors Gene Expression Transcriptome Analysis Physiological Responses Functional Proteins Stress Tolerant Plants Metabolome Analysis are also exploring new genes involved in improved productivity at the The outline of research activities in Gene Discovery Research Team is illustrated (Fig.1). Fig.2 Drought tolerance of CYP707A3 mutant Wild-type cyp707a3 mutant nced3 mutant control of gene expression. ●Student Trainees Fuminori TAKAHASHI (Univ. of Tsukuba, graduate course) Masaki NAKAMURA Fig.2 Drought tolerance of CYP707A3 mutant cyp707a3 nced3 (Univ. of Tsukuba, graduate course) Wild-type mutant ●Part Timers Machiko OHNUKI Drought stress Michie ETOH novel functions. ● To analyze plant responses to abiotic stress, we analyzed functions of focused on genes involved in ABA biosynthesis and metabolism. We used transcriptome and metabolome analysis to determine the signaling networks Fig.3 Schematic model of novel MAP kinase cascade "MKK3-MPK6" in jasmonate signaling Wounding Pathogen (local) MKK3 MKK2 ● We prepared a full-length enriched cDNA library, which is one of the most MPK6 MPK6 MPK6 important resources for post-genomic research, from soybean plants. About ACS2/6 40000 clones from the library were sequenced and analyzed. ET MKK4/ MKK5 MKK3 ATMYC2 VSP2 Wounding response genes Root growth sensitivity Cold and Salt stress response genes We also found the novel MAP kinase cascade, MKK3-MPK6, which is activated by JA in Arabidopsis and plays a key role in the JA-dependent negative regulation of ATMYC2 expression (Fig.3). Cold/Salt stress JA RIKEN PSC 2007 Annual Report Cold/Salt stress JA PDF1.2 Wounding (systemic) Wounding (systemic) MKK4/ MKK5 Pathogen response genes CYP707A3 , a major ABA 8’-hydroxylase, regulates ABA levels Fig.3 Schematic model ofrehydration, novel MAP kinase cascademutant and gene expressions after and cyp707a3 "MKK3-MPK6" in jasmonate signaling exhibited drought tolerance (Fig.2). mutant Kumiko MATSUO ERF1 Drought stress Wounding Pathogen (local) 32 ●Special Postdoctoral Researcher Rie NISHIYAMA full-length cDNAs for novel transcription factors were collected to analyze their in abiotic stress response. genome level using transcriptome and metabolome analyses, and are analyzing regulatory factors and signaling factors involved in the involved in plant’s responses to drought stress or ABA. We performed stress-inducible genes in drought stress responses. Among them, we Osmolytes Scavengers etc. Drought Tolerance Other targets of research include genes that respond to environmental changes and stimuli and genes involved in metabolic regulation. We focused our work on transcription factors or signal transduction factors transcription factors, or SnRK2 and MAP kinase families. In the CREST project, Biochemical Analysis environmental stresses to achieve maximum productivity. We are attempting to elucidate genetic functions through a reverse genetic ● To understand regulatory network in environmental stress responses, we functional analyses or biochemical analyses for NAC, bZIP and AP2 Second Messenger Outline of Research T Genetic Engineering Drought Stress 析技術を活用する。組織特異的発現、植物ホルモンや環境刺激によ る誘導などの遺伝子発現調節に関わる制御因子、シグナル伝達因子 Gene Discovery Motoaki SEKI(PMB) ●Research Associate Kaoru URANO ●Technical Staffs Saho MIZUKADO Hiroko KOBAYASHI Result of Research 導入による過剰発現トランスジェニック植物を用いて逆遺伝学的方法で遺伝子 機能を明らかにする。環境変化、刺激に応答して機能する遺伝子、 Taishi UMEZAWA Takeshi KATAGIRI(PMB) Takuya ITO(PMB) ● 乾燥ストレスや ABA 誘導性の遺伝子に関して機能解析を行った。特に 環境ストレス応答、耐性獲得のシステムを理解し、ストレス耐性の遺伝子組換作物や樹木の開発を目指す We study plant systems involved in stress responses and tolerance. Gene Discovery Research Group 伊藤 卓也（植物分子生物学研究室） Content of Research RIKEN PSC 2007 Annual Report MKK2 33 Cell Function Research Team Research Staff ●チームリーダー 松岡 健 （2006 年 10 月九州大学へ異動・2007 年 3 月まで兼任） ●研究員 イワン ガリス 細胞機能研究チーム （2007 年 2 月マックスプランク研究所へ異動・2007 年 3 月まで兼任） 研究内容 ● 植物細胞における多糖、糖タンパク質の合成装置の同定 ● 植物細胞におけるタンパク質とオルガネラの分解機構 松岡 健／ Ken MATSUOKA タンパク質の細胞内輸送機構と分解機構の解析 Elucidation of mechanisms of protein transport and degradation 研究概要 植 物の生産性の向上のために、分泌系の解析を通じて、植物細胞の増殖と 増大に関係する遺伝子産物と、液胞の機能発現と機能制御に関わる遺伝 子産物の探索を進めている。 Outline of Research W e are looking for genes related to the function of plant cell growth and expansion and of differentiation of vacuoles to improve the productivity of plants through the analysis of secretory pathway. T .doc 3 Tobacco BY-2 transcriptome Post-translational protein modification, Golgi localization signal, Visualization of autophagic degradation Endomembrane markers Fruits of PSC1 Arabidopsis Tagline & Transcriptome Cell Biological and Biochemical Analyses of Tobacco BY-2 cells and Plants Identification of novel genes involved in cell wall synthesis, post-harvest protein degradation and plant mass increase. 34 RIKEN PSC 2007 Annual Report 松岡健は 1986 年名古屋大学農学部農芸化学 科を卒業している。名古屋大学大学院農学研 究科を 1991 年に修了し（専門科目 : 生物化 学）農学博士号を授与されている。大学院在 学中には、スポラミン前駆体プロペプチドを、 植物液胞への輸送シグナルとしては世界で初 めて同定した。1991 年より名古屋大学農学 部・大学院生命農学研究科の助手として勤務 し、植物液胞へのタンパク質輸送機構と植物 タンパク質の分泌系での修飾機構の解析に従 事した。また、1996 年秋から 1998 年秋に かけてカリフォルニア大学バークレイ校に Visiting Associate Research Biochemist として滞在し、小胞体からのタンパク質輸送 に関わる COPII 輸送小胞の形成機構の研究 に従事している。2000 年 10 月より形態構 築研究チームのチームリーダーとして植物科 学研究センターに加わった。2006 年 10 月 より九州大学 大学院 農学研究院 植物資源科 学部門の教授として異動した。 Ken Matsuoka obtained his Ph.D. in agricultural science from the Graduate School of Agriculture, Nagoya University in 1991 (major: biochemistry). In graduate school, he found that the propeptide of the sporamin precursor functions as a vacuolar-targeting signal. This finding is the first identification of the vacuolar-targeting signal in plants. After obtaining a position in the same university, he continued to work on the vacuolar targeting in plant cells. From 1996 to 1998, he was at the University of California, Berkeley as a Visiting Associate Research Biochemist and pursued research on the mechanism of COPII transport vesicles, which are involved in the protein transport from the endoplasmic reticulum (ER) to the Golgi apparatus. He joined the Plant Science Center in October 2000 as the Head of the Laboratory for Structural Construction. He moved to Kyushu University in October 2007 as the professor of Plant Nutrition, Faculty of Agriculture. 小林 由樹子（2007 年 3 月退職） ●テクニカルスタッフ 成澤 知子 （2007 年 1 月メタボローム基盤研究グループへ異動） ● 植物細胞分泌系の解析 ●特定協力技術員 Content of Research ●派遣技術職員 ● Characterization of synthesis machineries in plant cell walls ● Protein and organelle degradation in plant cells ● Characterization of plant secretory pathway organelles 後藤 友美（2007 年 3 月退職） 小泉 公人（2006 年 10 月東京工業大学へ異動） 中村 香奈（2007 年 4 月免疫アレルギーセンターへ異動） ●Team Leader Ken MATSUOKA (Moved to Kyushu Univ. on October 2006) 研究成果 ● フェニルプロパノイド生合成遺伝子を制御する新規な転写因子を見出した。 ● 植物細胞に、選択的なオートファジー分解機構が存在することを、初めて 明らかにした。 ● ゴルジ体以降の分泌に関与する新規な小胞クラスターを見出した。 Result of Research ● Characterization of a novel transcription factor that regulate phenylpropanoid biosynthesis genes ● First identification of selective autophagy in plant cells ● Discovery of a novel vesicle cluster involved in post-Golgi secretion ●Research Scientists Ivan GALIS (Moved to Max-Planck-Institute on February 2007) Kiminori TOYOOKA (Working at Gene Discovery Research Group from April 2007) ●Special Research Associates Satoru ASATSUMA (Moved to Kyushu Univ. from April 2007) Yukiko KOBAYASHI (Left in March 2007) ●Technical Staff Tomoko NARISAWA (Working at Metabolomics Research Group from January 2007) ●Special Technical Staff Yumi GOTO (Left in March 2007) ●Technical Support Staffs Masato KOIZUMI (Moved to Tokyo Institute of Technology on October 2006) Kana NAKAMURA (Working at RIKEN RCAI from April 2007) Understanding mechanisms of protein transport, protein degradation and cytokinesis. RIKEN PSC 2007 Annual Report 35 Gene Discovery Research Group Gene Discovery Research Group 豊岡 公徳（2007 年 4 月機能開発研究グループへ異動） ●特定協力研究員 浅妻 悟（2007 年 4 月九州大学へ異動） Gene Expression Research Team ●チームリーダー 機能発現研究チーム ●テクニカルスタッフ Research Staff 和田 拓治 ●研究員 冨永 るみ 石田 哲也 研究内容 ● 表皮細胞分化に関与する細胞間移行転写因子群の解析 ● 表皮細胞分化関連転写因子の下流遺伝子群の解明 Content of Research Gene Discovery Research Group Gene Discovery Research Group 郷原 健 ●Team Leader Takuji WADA ●Research Scientists Rumi TOMINAGA Tetsuya ISHIDA ●Technical Staff Takeshi GOHARA ● Analysis of mobile transcriptional factors involved in epidermal cell 和田 拓治／ Takuji WADA 高等植物の細胞分化機構を理解する為の表皮細胞分化機構の研究 Research on epidermal cell of higher plant 研究概要 植 物の表皮細胞は環境（ストレス）にさらされる最前線であり、その機能 発現機構の解明を通して、植物の機能性・生産性向上を目指す。 Outline of Research R esearch on epidermal cell differentiation will enhance our understanding of plant development and its function. 1991 年、京都大学理学部卒業。1993 年、 京都大学大学院人間・環境学研究科修士課程 修了。1993 年より総合研究大学院大学生命 科学研究科博士課程 ( 基礎生物学研究所 ) に 進 学 し、1996 年 博 士 ( 理 学 ) 取 得。1996 年から生物分子工学研究所ポスドク。大学院 博士課程より一貫して京都大学理学部岡田清 孝教授の下で、シロイヌナズナで根毛形成の 研究を行う。1998 年より米国ソーク生物学 研究所ポスドク。Detlef Weigel 博士の下 で、シロイヌナズナの花の形態形成の研究を 行う。2000 年 10 月より現職。 Takuji Wada graduated from the Faculty of Science at Kyoto University in 1991. Two years later he completed his Master’s degree at the Graduate School of Human and Environmental Studies at Kyoto University. In 1996 he received his Ph.D. from the Department of Molecular Biomechanics at the Graduate University for Advanced Studies, and then became a Postdoctoral Fellow at the Biomolecular Engineering Research Institute. His doctoral research involved studying root-hair formation in Arabidopsis under the guidance of Prof. Kiyotaka Okada in the Faculty of Science at Kyoto University. While on a second Postdoctoral Fellowship in 1998 at the Salk Institute for Biological Studies in the U.S.A., he studied flower morphogenesis in Arabidopsis under Dr. Detlef Weigel. He was appointed to his present position in October 2000. differentiation ● Analysis of genes downstream of regulatory factors for epidermal cell differentiation 研究成果 ● CPC の細胞間移行パートナーを探すために、遺伝学的解析によって CPC が細胞間移行しない株を分離し、現在そのクローニングを進めている。 ● CPC 相同遺伝子である cpl3 では植物体が野生型の 1.5 倍と大きくなり、 花も早咲きとなっていた。また各細胞も大きくなっていることを顕微鏡レ ベルで確認した。 ● 根 毛 細 胞 で 発 現 す る bHLH 遺 伝 子（GL3 , EGL3, AtMYC1） の promoter::GFP 形質転換体から根毛細胞由来の GFP 蛍光プロトプラスト をセル・ソーターで選別した。 ● GL3 遺伝子発現領域で発現上昇している遺伝子は代謝、核酸・タンパク質・ アミノ酸の生産や修飾、転写関連遺伝子が見られる。これは GL3 遺伝子発 現領域に静止中心が含まれており、遺伝子発現が活発であるからと考えら れる。AtMYC1 遺伝子発現領域では輸送・タンパク質リン酸化に関わる遺 伝子が発現上昇していた。この遺伝子リストには、EXP8 のような細胞伸 長関連遺伝子も含まれていた。 Result of Research ● To look for the partner of CPC, we identified the mutant, in which CPC did not move. ● In one of CPC -homologous gene mutant, cpl3 , plant became bigger and flowered earlier than wild type. ● Using cell sorter, we analyzed the nature of root-hair cell file. Metabolic genes and protein modification genes were expressed at early stage of root-hair cell. 36 RIKEN PSC 2007 Annual Report RIKEN PSC 2007 Annual Report 37 Genetic Regulatory Systems Research Team ●チームリーダー 制御機能研究チーム ●テクニカルスタッフ Research Staff 酒井 達也 ●研究員 槌田（間山） 智子 永島 明知 研究内容 ● 環境刺激に応答した成長制御機構のシロイヌナズナ突然変異体を用いた分 子遺伝学的解析 Content of Research Gene Discovery Research Group Gene Discovery Research Group 上原 由紀子 ●Team Leader Tatsuya SAKAI ●Research Scientists Tomoko TSUCHIDA-MAYAMA Akitomo NAGASHIMA ●Technical Staff Yukiko UEHARA ● Molecular genetic analysis of growth-regulation mechanisms in response to 酒井 達也／ Tatsuya SAKAI 植物の環境適応メカニズムを解明する Plant growth adapted to the environment 研究概要 本 研究チームは、様々な環境刺激に適応した植物の成長を制御するための 遺伝子の発見及びその機能の同定を目指す。特に光・重力・接触刺激へ の適応機構を研究する。 Outline of Research T 38 he purpose of this team is to elucidate the function of genes regulating the plant growth adapted to various environment stimuli, especially light and gravity. RIKEN PSC 2007 Annual Report 1992 年 3 月に国際基督教大学教養学部理学 科卒業。1997 年 3 月に東京大学大学院理学 系研究科にて博士号 ( 理学 ) を取得した。博 士論文の研究テーマは、植物ホルモン・オー キシンによって誘導される遺伝子の転写制御 の解析。1997 年 8 月から 1998 年 2 月まで、 ポスドクとしてオーストラリア国立大学大学 院生物科学研究科に従事し、微小管配向異常 突然変異体の研究を行った。1998 年 4 月か ら 2000 年 9 月まで日本学術振興会特別研 究員として京都大学大学院理学研究科に従事 し、主に光屈性の研究を分子遺伝学的解析手 法により行った。2000 年 10 月から制御機 能研究チームのチームリーダーとして、植物 科学研究センターに参加している。 Tatsuya Sakai graduated from the Department of National Science, International Christian University, in March 1992, and obtained his Ph.D. in science from the Graduate School of Science, The University of Tokyo, in March 1997. The theme of his doctoral thesis was “Analysis of the control of gene transcription induced by a phytohormone auxin”. He conducted a study on microtubule organization mutants as a postdoctoral fellow at the Graduate School of Biological Sciences, Australian National University from August 1997 to February 1998. From April 1998 to September 2000, he studied at the Graduate School of Science, Kyoto University as a research fellow of the Japan Society for the Promotion of Science, and performed molecular genetic analysis of phototropism. In October 2000, he joined the Plant Science Center as Head of Laboratory for Genetic Regulatory Systems. environmental stimuli 研究成果 ● 光屈性機構解明を目的にシグナル伝達因子 NPH3・RPT2 の発現制御を解 析した。青色光受容体 phot1 の活性化によって NPH3 の脱リン酸化及び RPT2 の転写後発現誘導がおきることが明らかになった。 ● 光による胚軸成長制御機構解明を目的に、赤色光高感受性突然変異体 flabby の解析を行った。赤色光は光受容体フィトクロムを介して、植物ホ ルモン・オーキシンの合成・代謝および極性輸送を制御することを明らか にした。 ● 根の接触刺激に応答した成長制御機構解明を目的に、根の波状成長異常突 然変異体 wav3 の解析を行った。WAV3 遺伝子は重力屈性を抑制するユビ キチン E3 ligase タンパク質をコードしていた。 Result of Research ● NPH3 and RPT2 are signal transducers, which are involved in the phototropic response of A.thaliana seedlings. Our study indicated that the blue-light (BL) photoreceptor, phot1, is necessary for the BL-dependent dephosphorylation of NPH3 and the expressional regulation of RPT2 in seedlings under BL conditions through post-transcriptional regulation. ● Our study indicated that controls of phytohormone auxin transport and accumulation by phytochromes, and probably also by cryptochromes, may be critical steps in regulation of hypocotyl growth in response to light. ● To understand how root growth direction is altered in response to environmental stimuli, we haracterized the wav3 mutant, whose roots show a shorter-pitch wavy growth pattern on inclined agar medium. Our results indicated that WAV3 encodes an E3 ligase, which is involved in a signaling pathway that regulates root bending in response to gravity. RIKEN PSC 2007 Annual Report 39 Growth Regulation Research Team Research Staff ●チームリーダー 神谷 勇治 ●上級研究員 笠原 博幸 ●リサーチアソシエイト 生長制御研究チーム 軸丸 祐介 田中 洋子 研究内容 ● 現在よりも高感度なホルモンの一斉分析システムの構築 ● オーキシン生合成中間体候補の安定同位元素標識体の合成 ● イソプレノイド生合成研究に関わる阻害剤の検索 Content of Research ● Development of high-sensitive hormone analysis system ● Preparation of stable isotope labeled intermediates of auxin ● Chemical genetics approach for identification of isoprenoid biosynthesis 花田 篤志 関本 雅代 ●Team Leader Yuji KAMIYA ●Senior Research Scientist Hiroyuki KASAHARA ●Research Associates Yusuke JIKUMARU Growth Regulation Research Group Growth Regulation Research Group 神谷 勇治／ Yuji KAMIYA ●テクニカルスタッフ Yoko TANAKA ●Technical Staffs Atsushi HANADA Masayo SEKIMOTO inhibitors 研究成果 ● LC-MS を用いて各種植物ホルモンの高感度分析を行い、1g 以下のシロイ 高感度ホルモン分析 Most sensitive hormone analysis 研究概要 世 酸 (ABA) の蓄積するシロイヌナズナ突然変異体では、その種子 1 粒から ABA の定量に成功した。 ● オーキシンの生合成中間体と考えられるトリプタミン、インドールアルド 界で最も高感度な全植物ホルモンの一斉分析システムと選択的な同位元 キシム、インドールアルデヒド、インドールアセトニトリル等を安定同位 素標識法を構築し、ホルモン関連遺伝子のネットワークとホルモン量を 元素で標識し、取り込み実験の基質を調整した。 明らかにします。また、植物におけるオーキシンの生合成経路の解明、更に、 非メバロン酸経路関連遺伝子の過剰発現体を用いたケミカルジェネティックス を展開します。 Outline of Research T ヌナズナの茎葉部の同一試料から全てのホルモンを分析した。アブシジン ● 非メバロン酸経路に関わる７つの生合成酵素の過剰発現形質転換体を用い て化合物ライブラリーから 10 種類以上の阻害剤の候補を発見した。 Result of Research ● We have developed a very sensitive plant hormone analysis system using his team will develop the most sensitive, comprehensive and high-throughput LCMS/MS (TOF) from 1g of Arabidopsis seedlings. We could quantify plant hormone analysis system and study the regulation of secondary endogenous levels of ABA even from one seed of Arabidopsis mutants, of metabolites by hormones. Study on auxin biosynthesis in plants Identification of chemicals which inhibit the non-mevalonate pathway of plants. which ABA degradation enzymes are deficient. ● We synthesized stable isotope labeled possible auxin intermediates such as tryptamine, indolealdoxime, indolealdehyde, indoleacetonitrile and used for substrates metabolic study. ● We have identified more than 10 lead chemicals which may inhibit the nonmevalonate pathway of plants using chemical libraries. 40 RIKEN PSC 2007 Annual Report RIKEN PSC 2007 Annual Report 41 Dormancy and Adaptation Research Team Research Staff ●チームリーダー 南原 英司 ●研究員 立松 圭 ●基礎科学特別研究員 適応制御研究チーム 土屋 雄一朗 ●リサーチアソシエイト 研究内容 ● アブシジン酸の代謝と応答性に関する研究 ● 種子のトランスクリプトーム解析 Content of Research 南原 英司／ Eiji NAMBARA 生命科学が種子の知られざる潜在能力を覚醒する Frontier research unravels novel functions of seed. 研究概要 当 研究チームは、植物固有の環境適応反応を最適化するために、休眠器官 の主要な調節遺伝子を同定し、その機能解析をおこないます。 Outline of Research W e aim to identify key regulators for dormancy and adaptive responses. 42 RIKEN PSC 2007 Annual Report 1990 年に名古屋大学工学部応用化学科を卒 業。同 4 月に名古屋大学大学院農学系研究 科に進学し、1994 年に博士号（農学）を取 得。学術振興会特別研究員を経て、1995 年 4 月から北海道大学農学部助手。1998 年 5 月からトロント大学植物学科のポスドクをし て、2001 年 4 月から現職。研究テーマは大 学院在学時から一貫して、シロイヌナズナを 用いた種子休眠の遺伝学的解析。 Eiji Nambara graduated in 1990 from the Faculty of Engineering, Nagoya University. He obtained his Ph.D. in 1994 from the Faculty of Agriculture, Nagoya University. From 1994 he became a JSPS postdoctoral fellow, then in 1995 he became a Research Associate in the Faculty of Agriculture, Hokkaido University. From 1998 he joined the Department of Botany, University of Toronto before becoming a Laboratory Head at the Plant Science Center, RIKEN in 2001. ● Transcriptome analysis on Arabidopsis seed ●客員研究員 岡本 昌憲 （学術振興会特別研究員：首都大学東京） ●テクニカルスタッフ 原田 祥世 菅野 裕理 ●パートタイマー 吉川 里恵 ●Team Leader Eiji NAMBARA 研究成果 ●Research Scientist Kiyoshi TATEMATSU ● シロイヌナズナ種子における植物ホルモンの代謝調節：フィトクロムによ ●Special Postdoctoral Researcher Yuichiro TSUCHIYA るアブシジン酸代謝調節とアブシジン酸によるジベレリン代謝調節 ● シロイヌナズナ ABA 代謝酵素 CYP707A ファミリーの種子形成期と発芽 期の機能解析 ●Research Associates Ryoichi YANO Akira ENDO Result of Research ●Visiting Scientist Masanori OKAMOTO (Tokyo Metropolitan Univ.) ● Regulation of hormone metabolism in Arabidopsis seeds: Phytochrome- ●Technical Staffs Sachiyo HARADA regulation of abscisic acid metabolism and abscisic acid-regulation of gibberellin metabolism. Growth Regulation Research Group Growth Regulation Research Group ● Study on the regulation of ABA metabolism and responses 矢野 亮一 遠藤 亮 Yuri KANNO ●Part Timer Satoe YOSHIKAWA ● CYP707A1 and CYP707A2, which encode abscisic acid 8’-hydroxylases, are indispensable for proper control of seed dormancy and germination in Arabidopsis. RIKEN PSC 2007 Annual Report 43 Cellular Growth and Development Research Team Research Staff ●チームリーダー 山口 信次郎 ●研究員 真籠 洋 ワディティー ルンガルーン 促進制御研究チーム 野村 崇人 研究内容 ●基礎科学特別研究員 兼目 裕充 ●訪問研究員（JSPS 外国人特別研究員） ● ジベレリンをはじめとする植物生長促進ホルモンの生合成・代謝の制御メ ●客員研究員 カニズムの解明 ● 植物ホルモンの量の調節を基盤とした生長調節技術の開発 Content of Research 植物ホルモンによる生長制御の仕組みを明らかにする We elucidate how hormones regulate plant growth. 研究概要 植 物の生長に促進的に作用する微量信号物質 ( 植物ホルモン ) の生合成、 作用メカニズムを明らかにし、食糧生産性の向上等に貢献しうる生長調 節技術の開発を目指します。 Outline of Research T his team will elucidate how growth-promoting hormones are synthesized and act in plants and aim to find a clue to manipulate plant growth for improved crop productions. 44 RIKEN PSC 2007 Annual Report 1991 年東京大学農学部農芸化学科を卒業 後、同大学院農学生命科学研究科に進学し、 1996 年に博士号 ( 農学 ) を取得した。同年 から理化学研究所・国際フロンティアの研 究員として 1 年間勤務し、ジベレリン生合 成酵素遺伝子の単離を行なった。1997 年 4 月から 2000 年 6 月までアメリカ合衆国、 デューク大学でシロイヌナズナにおけるジベ レリン生合成の制御機構に関する研究を行 な っ た。2000 年 7 月 か ら 2005 年 3 月 ま で植物科学研究センター・発芽生理機構研究 チームに所属し、種子発芽の調節機構とイソ プレノイド生合成の制御に関する研究を行っ た。2005 年 4 月から促進制御研究チーム において植物生長ホルモンの研究を進めてい る。 Shinjiro Yamaguchi graduated from the D e p a r t m e n t o f A g r i c u l t u r a l C h e m i s t r y, Faculty of Agriculture, the University of Tokyo in 1991. He obtained his Ph.D. in 1996 from the University of Tokyo. He joined Frontier Research Program at RIKEN and contributed to the identification of gibberellin biosynthesis genes from plants. He worked at Duke University in the United States as a postdoctoral fellow from 1997 till 2000, and studied regulation of gibberellin biosynthesis in Arabidopsis. He worked in Laboratory for Cellular Growth and Development, Plant Science Center from July 2000 to March 2005 to study regulatory mechanisms for seed germination and plant isoprenoid biosynthesis pathways. He has been studying on plant growth hormones in Cellular Growth and Development Research Team since April 2005. function in plants ● Development of a technology to control plant growth by modifying hormone content 朝比奈 雅志 ●テクニカルスタッフ 武田 紀子 花田 篤志 ●研修生 有手 友嗣 ●パートタイマー 小野塚 暁子 藤原 薫 佐藤 洋子 ●アルバイト 李 偉強 研究成果 ●Team Leader Shinjiro YAMAGUCHI ● 植物の生長ホルモン・ジベレリンを不活性化する新しい酵素の発見 ●Research Scientists Hiroshi MAGOME Rungaroon WADITEE ● 光シグナルが植物ホルモンを介して種子発芽を調節する分子メカニズムの 解明 ● 揮発性物質による気相を介した植物個体間のコミュニケーション機構の追 究 Result of Research ● Discovery of new enzymes that inactivate gibberellins, a group of growth promoting hormones ● Elucidation of molecular mechanisms for light-regulation of seed germination via plant hormones ● Investigation into the role of volatile signaling compounds in controlling growth and development between plants Growth Regulation Research Group Growth Regulation Research Group 山口 信次郎／Shinjiro YAMAGUCHI ● Investigation into how growth-promoting hormones are synthesized and アイル バライ Takahito NOMURA ●Special Postdoctoral Researcher Hiromichi KENMOKU ●Visiting Researcher (JSPS Postdoctoral Fellow) Belay AYELE ●Visiting Scientist Masashi ASAHINA ●Technical Staffs Noriko TAKEDA Atsushi HANADA ●Student Trainee Tomotsugu ARITE ●Part Timers Akiko ONOZUKA Kaoru FUJIWARA Yoko SATO ●Temporary Part-time Worker Wei Qiang LI RIKEN PSC 2007 Annual Report 45 Metabolic Function Research Team Research Staff ●チームリーダー 斉藤 和季 ●研究員 榊原 圭子 ●テクニカルスタッフ 代謝機能研究チーム 井上 恵理 奥村 玲奈 研究内容 ● シロイヌナズナにおける一次・二次代謝産物生合成や輸送に関わる遺伝子 の網羅的同定 ● 有用植物における、フラボノイド、アルカロイド、含硫黄成分、ビタミン、 アミノ酸などの生合成や蓄積に関わる新規遺伝子の同定と有用物質生産へ の応用 斉藤 和季／ Kazuki SAITO Content of Research ●協力研究員 峠 隆之 ●Team Leader Kazuki SAITO ●Research Scientist Keiko YONEKURA-SAKAKIBARA ●Technical Staffs Eri INOUE Reina OKUMURA ●Contract Researcher Takayuki TOHGE ● Comprehensive identification of genes involved in primary and secondary metabolite biosynthesis and transport in Arabidopsis ● Identification of new genes involved in the biosynthesis and accumulation of useful metabolites in non-model plants, and their application to the production ファイトケミカルゲノミクス−有用物質生産のゲノム基本原理の解明と応用 Phytochemical genomics -elucidation and application of genomics basis for production of useful chemicals 研究概要 当 研究成果 ● シロイヌナズナのトランスクリプトーム共発現データから、フラボノール 7 −Ｏ −ラムノシルトランスフェラーゼをコードする遺伝子を同定した。 研究チームでは、植物のもつ多様な物質生産機能の基本原理をシロイヌ ● 同様の手法を用いて、新規のフラボノイド糖転移酵素遺伝子を同定した。 ナズナなどのモデル植物を用いて解明するとともに、農作物、薬用植物 ● シロイヌナズナの種子のプロアントシアニジン生産に関与するラッカーゼ などの有用植物における特異的産物の生産システムをゲノムレベルで解明す る。それらの基礎的な知見を合理的にバイオテクノジー応用する事も重要であ る。 Outline of Research 遺伝子、LAC15 遺伝子と協調して発現する遺伝子を見出した。 Result of Research ● By co-expression analysis with publicly available transcriptome datasets, we identified a gene encoding a novel flavonol 7-O -rhamnosyltransferase from W ● We applied the above strategy to identify other novel genes and found a new The application of the basic findings to biotechnological engineering is also an ● We identified a polyphenol oxidase (PPO) gene, LAC15 , involved in e investigate the basic principles behind the wide arrays of plant production functions. We analyze the systems for production of specific products in crops, medicinal plants, and other useful plants at a genome level. important issue. Metabolic Function Research Group Metabolic Function Research Group of useful substances Arabidopsis and characterized it. flavonoid glycosyltransferase gene. proanthocyanidin production for seed coat pigmentation. We focused on genes expressing in concert with LAC15 . 46 RIKEN PSC 2007 Annual Report RIKEN PSC 2007 Annual Report 47 Metabolic Diversity Research Team 研究内容 ● テルペノイドネットワーク研究 ● 有用トリテルペノイド産生植物からのジーンディスカバリー ● 国際連携による未開拓植物の分子遺伝学的研究 多様性代謝研究チーム ● Analysis of terpenoids networks ● 細胞質におけるテルペン生合成経路の鍵酵素 HMGR、および、ステロール 研究概要 植 物トリテルペン、セスキテルペンの生産制御機構を研究し、有用ジーン ディスカバリー、新規な機能性植物創製のための基盤技術確立を目指す。 Outline of Research T riterpenes and sesquiterpenes have potential application to functional foods, medicines and industrial materials. Through the study of the metabolic system of these chmicals in plant, we aim gene discovery and production of novel functional plants. 48 RIKEN PSC 2007 Annual Report Toshiya Muranaka graduated from the Department of Agricultural Chemistry, Faculty of Agriculture, Kyoto University in 1983, and finished a master’s course at the Graduate School of Agriculture, Kyoto University in 1985. In the same year, he entered Sumitomo Chemical Co., Ltd. and conducted research on the production of secondary metabolites by hairy root cultures. From 1988 to 1990, as a visiting scientist he conducted research on a protein kinase which is involved in both sugar and lipid metabolites in plants, at the Department of the Biology, Faculty of Science, Nagoya University. He obtained his Ph.D. in agriculture from Kyoto University in 1993. He also had an additional post at the Research Institute of Innovative Technology for the Earth (RITE) as a senior researcher from 1995 to 2000 and conducted research on molecular biology of microalgae. In 1997, he conducted research on posttranscriptional regulation of plastid genes in green algae at UC Berkeley as a NEDO Fellow. He left Sumitomo Chemical Co., Ltd. in March 2001 and joined the Plant Science Center in April of the same year as a Team Leader. 骨格形成の初発酵素 CAS の KO 植物を用いた実験から、配偶子形成に本経 路が重要な機能を持つことを見出した。次に本経路に係わる 11 ステップ 24 遺伝子の網羅的 KO ライン整備を行った。このうち 9 割について複数の 対立遺伝子 KO 変異体を取得し、稔性低下、胚性致死などの表現型を示す ものを見出した。 ● 有用トリテルペノイドサポニンであるグリチルリチン生合成遺伝子ディス カバリーを行っている。カンゾウ EST 解析の結果から、P450 および糖転 移酵素などを抽出し、全長 cDNA 取得、遺伝子構造と発現プロファイル解 析から候補遺伝子を絞り込んだ。別途、生合成中間体の合成、GC-MS によ る分析系確立を行い、バキュロウイルスの系による発現解析により新規遺 伝子を単離した。 ● 抗マラリア活性を有するアルテミシン生合成遺伝子ディスカバーに向けて、 アジア原産のアルテミシニン産生植物（アヌア）と南アフリカ原産のアル テミシニン非産生植物（アフラ）との比較ゲノム解析、代謝産物プロファ イル解析を行っている。その結果、非産生植物であるアフラには、アルテ ミシン生合成の初発のセスキテルペン環化酵素（ADS）遺伝子が欠損して いることを見出した。 Result of Research ● Isoprenoids such as sterols, also components of lipids, are found in gametophytes. We found that either HMG1 or HMG2 is required for male gametophyte development, and metabolites downstream of mevalonate pathway are essential for the conformation of the lipid-rich organelles in the male gametophytes. ● Glycyrrhizin, a triterpene saponin is useful for medicine and functional foods. To elucidate biosynthetic pathway of the chemical, full-length cDNA library was established and ESTs were analyzed. Combined with gene expression analysis, candidate genes for P450s and glycosyltransferases are narrowed down, and new important genes have been identified. ● Artemisia annua accumulates artemisinin, a new and highly effective antimalarial drug. By comparative study between A. annua and A. afra , an 大山 清 ●協力研究員 唐 建偉 西澤 具子 鈴木 宗典 ●客員研究員 高上馬 希重（東京大） 永田 典子（日本女子大） 登谷 友紀子（常磐植物化学） ●訪問研究員 マハディ チアラトゥニア （University of Pretoria, South Africa） ヒューベルト シャラー（CNRS, France） ●ジュニアリサーチアソシエート 小林 啓子（埼玉大） ●研修生 中川 祥子（日本女子大） ●パートタイマー Metabolic Function Research Group Metabolic Function Research Group Gene discovery for functional foods and medicines 鈴木 優志 關 光 ●テクニカルスタッフ 上出 由希子 研究成果 医食同源の遺伝子を見つけ出す ●研究員 ●リサーチアソシエイト ● Molecular genetics study on unexplored plants by international collaboration 1983 年に京都大学農学部農芸化学科を卒 業、京都大学大学院農学研究科に進学し、ト ロパンアルカロイド産生植物の組織培養研究 を行った。1985 年に修士課程を修了、同年、 住友化学工業株式会社に入社し、生命工学研 究所において毛状根培養による有用物質生産 研究を行い、1993 年に京都大学博士 ( 農学 ) を授与された。1990 年秋より 2 年間、名古 屋大学理学部生物学科において糖代謝に係わ るタバコプロテインキナーゼの構造と機能解 析研究を行った。この研究を展開させ 1999 年に植物化学調節学会奨励賞を受賞した。ま た、1995 年より 4 年半、地球環境産業技 術研究機構 (RITE) 主任研究員を兼務し、微 細藻類の分子生物・培養工学的研究に従事し た。この間 1997 年にカリフォルニア大学 バークレイ校に客員研究員として滞在し葉緑 体遺伝子の発現調節に関する研究を行った。 2001 年 3 月に住友化学を退社し、同年 4 月よりバイオケミカルリソース研究チームの チームリーダーとして植物科学研究センター に加わり、2005 年より多様性代謝研究チー ムのチームリーダーとなった。 ●チームリーダー 村中 俊哉 Content of Research ● Gene discovery from medicinal plants producing useful triterpenoids 村中 俊哉／ Toshiya MURANAKA Research Staff 橋之口 裕美 鈴木 千代子 ●Team Leader Toshiya MURANAKA ●Research Scientists Masashi SUZUKI Hikaru SEKI ●Research Associate Kiyoshi OHYAMA ●Technical Staff Yukiko KAMIDE ●Contract Researchers Jianwei TANG Tomoko NISHIZAWA Munenori SUZUKI ●Visiting Scientists Mareshige KOJOMA(Univ. of Tokyo) Noriko NAGATA(Japan Women’s Univ.) Yukiko TOYA (Tokiwa Phytochemical Co., Ltd.) ●Visiting Researchers Mahdi ZIARATNIA (University of Pretoria, South Africa) Hubert SCHALLER(CNRS, France) ●Junior Research Associate Keiko KOBAYASHI(Saitama Univ.) ●Student Trainee Shoko NAKAGAWA (Japan Women’s Univ.) ●Part Timers Hiromi HASHINOKUCHI Chiyoko SUZUKI indigenous plant in South Africa, we observed that the artemisinin biosynthetic pathway could partially exist at least in some artemisinin non-producers. RIKEN PSC 2007 Annual Report 49 Plant Nutrition and Basal Metabolism Research Team ●チームリーダー 基礎代謝研究チーム ●基礎科学特別研究員 Research Staff 高橋 秀樹 ●研究員 片岡 達彦 仲下（丸山） 明子 研究内容 ● 窒素栄養・硫黄栄養に関するゲノム機能研究： 窒素及び硫黄栄養同化の制御機構、シグナル伝達機構についてシロイヌナ ズナの栄養応答変異株を用いてトランスクリプトーム解析、メタボローム 解析などのゲノムワイドな研究を展開する。 ● 窒素栄養・硫黄栄養及び代謝産物の輸送に関わるイオン輸送複合体とその 高橋 秀樹／ Hideki TAKAHASHI Improvement of Nutrient Use Efficiency 研究概要 基 礎代謝研究チームでは、主要栄養元素である窒素及び硫黄の輸送と代謝 に着目して植物栄養ゲノミクス研究を推進する。栄養ストレス環境下に おいて窒素及び硫黄の利用効率を向上させるために必要となる鍵制御因子の機 能を解明することを目的として研究を展開する。 Outline of Research T his research team focuses on “nutrient genomics” particularly on the areas of transport and primary assimilatory metabolisms of two major mineral elements, nitrogen and sulfur. The objective of this study is to discover the keyregulatory factors essential for the improvement of nitrogen and sulfur use efficiencies under nutrient-stressed environment. 50 RIKEN PSC 2007 Annual Report H i d e k i Ta k a h a s h i g r a d u a t e d f ro m t h e Department of Industrial Chemistry, Faculty of Engineering, Kyoto University in March 1990. In the same year, he joined the biochemical research section of Idemitsu Petrochemical Co. Ltd., and conducted research on the microbial production of unsaturated fatty acids and organic acids. From April 1993 to March 1995, he studied sulfur assimilation and cysteine synthesis in plants as a research student at the Graduate School of Pharmaceutical Sciences, Chiba University, under Prof. Kazuki Saito. He left Idemitsu Petrochemical Co. Ltd., and entered the Graduate School of Pharmaceutical Sciences, Chiba University, in April 1995 to continue his study on plant sulfur metabolism. During his Ph.D. study, he started the work on sulfate transporters in Arabidopsis. He obtained his Ph.D. from the Graduate School of Pharmaceutical Sciences, Chiba University, in March 1998. He stayed at Chiba University as a postdoctoral research fellow of the Japan Society for the Promotion of Science (JSPS) until September 1999. From October 1999 to September 2000 he visited the Carnegie Institution of Washington, U.S.A. as a JSPS postdoctoral research fellow, and studied the nutrient stress response of unicellular algae under Dr. Arthur Grossman. In October 2000, he joined the Plant Science Center as Research Team Leader. Content of Research ● Functional genomics studies of nitrogen and sulfur sensing and signaling networks through genome-wide transcriptomic and metabolomic interpretations of nutrient response-less or hyper-responsive Arabidopsis mutants ● Functional analysis of ion transporter complexes and their modifiers controlling nitrogen and sulfur nutrient uptake and metabolite allocation 研究成果 ● これまで機能が未解明であった EIL 転写因子の SLIM1/EIL3 がシロイヌナ ズナの硫黄同化系及びグルコシノレート生合成系を制御することを明らか にした。 ● シロイヌナズナの根における AMT アンモニウムトランスポーター遺伝子 族の機能分担を明らかにした。 ● 硫酸イオン及び硝酸イオンの吸収を制御する転写因子のシロイヌナズナ遺 ●テクニカルスタッフ 井上 恵理 中村 有美子 笹崎 容子 高宗 万希子 ●パートタイマー 小野田 温美 小森 千恵子 鈴木 葉子 中林 和恵 野島 京子 ●Team Leader Hideki TAKAHASHI ●Research Scientists Tatsuhiko KATAOKA Akiko MARUYAMA-NAKASHITA Metabolic Function Research Group Metabolic Function Research Group 無機栄養分の利用効率の向上を目指して 1990 年 3 月京都大学工学部工業化学科卒 業。同年、出光石油化学（株）に入社し微生 物を用いた不飽和脂肪酸及び有機酸生産の研 究 に 従 事 す る。1993 年 4 月 か ら 1995 年 3 月まで千葉大学大学院薬学研究科・斉藤和 季教授の下で研修生として高等植物における 硫黄同化及びシステイン合成の研究を行う。 出光石油化学（株）を退社後、1995 年 4 月 に千葉大学大学院薬学研究科博士後期課程に 入学し硫黄同化に関する研究を継続する。シ ロイヌナズナの硫酸イオントランスポーター に関する研究はこの時期にはじめたものであ る。1998 年 3 月千葉大学大学院薬学研究科 博士後期課程修了、博士号（薬学）を取得。 1999 年 9 月まで日本学術振興会特別研究員 として同研究室で研究を継続。1999 年 10 月から 2000 年 9 月まで米国カーネギー研 究所・Dr. Arthur Grossman の下で緑藻類 における栄養環境応答の研究を行う。2000 年 10 月から現職。 機能を調節する制御因子の機能解析研究 吉本 尚子 ●リサーチアソシエイト 鈴木 昭徳 ●Special Postdoctoral Researcher Naoko YOSHIMOTO ●Research Associate Akinori SUZUKI ●Technical Staffs Eri INOUE Yumiko NAKAMURA Yoko SASAZAKI Makiko TAKAMUNE ●Part Timers Atsumi ONODA Chieko KOMORI Yoko SUZUKI Kazue NAKABAYASHI Keiko NOJIMA 伝子破壊株を RT-PCR 法により迅速に単離する手法を確立した。 Result of Research ● A previously uncharacterized EIL-family transcription factor, SLIM1/EIL3, was shown to control both sulfur assimilation and glucosinolate biosynthesis in Arabidopsis . ● Job-sharing among the AMT-type ammonium transporter family members in Arabidopsis roots was elucidated. ● An RT-PCR-based knockout profiler system was established for rapid identification of transcription factors regulating nitrate and sulfate uptake in Arabidopsis . RIKEN PSC 2007 Annual Report 51 Biodynamics Research Team Research Staff ●チームリーダー 榊原 均 ●研究員 武井 兼太郎 広瀬 直也 生産制御研究チーム 井藤賀 操 須藤 恵美 研究内容 ● 植物生産機能に有用な形質を与える遺伝子の探索と主要作物イネへの応用 研究 ● サイトカイニンなど生産機能制御に関わる因子の作用機構解明 ● 植物の多様性を利用した環境浄化技術の開発 Content of Research 榊原 均／ Hitoshi SAKAKIBARA ● Identification of key genes regulating agronomical traits improving plant productivity ● Functional analysis of key genes regulating plant productivity, especially enzymes involved in cytokinin biosynthesis and metabolism in Arabidopsis and rice ● Development of clean-up technology of heavy metal pollutants using plant resources イネの生産性向上に役立つ遺伝子を見つけ出します！ Discovery and utilization of key genes improving crop productivity 研究概要 ンク・ソースバランスの改変や同化産物の効率的な輸送・集積など、作 物の生産性向上に向けた研究を展開する。 ● サイトカイニンの新規の活性化経路を発見するとともに、それに関わる遺 伝子を同定した。 ● 微量試料からの主要ホルモンハイスループット一斉解析システムを確立し た。 ● 窒素同化の鍵酵素であるグルタミン合成酵素（GS）の立体構造を明らかに Outline of Research A im of our research team is elucidation of cytokinin action on control of organ development, sink-source balance and storage profile of assimilated products in order to improve plant productivity. するとともに、細胞質型 GS がトウモロコシの穀粒収量制御に深くかかわ る遺伝子であることを示した。 Result of Research ● We discovered a novel pathway for cytokinin activation and identified the gene. ● We established a high-throughput and high-sensitivity analyzing system of 黒羽 剛 信定 知江 ●テクニカルスタッフ 小嶋 美紀子 上田 七重 槇田 庸絵 小松 由佳梨 ●派遣職員 吉田 佳代 ●訪問研究員 木羽 隆敏 ●パートタイマー 南里 雅美 鈴木 祥子 小島 浩美 ●Team Leader Hitoshi SAKAKIBARA ●Research Scientists Kentaro TAKEI Naoya HIROSE Misao ITOUGA Emi SUDO ●Research Associates Takeshi KUROHA Tomoe KAMADA-NOBUSADA ●Technical Staffs Mikiko KOJIMA Plant Productivity Systems Research Group Plant Productivity Systems Research Group 植 物生産機能の制御に本質的に関わるサイトカイニンの研究を通じて、シ 研究成果 ●リサーチアソシエイト Nanae UEDA Nobue MAKITA Yukari KOMATSU ●Temporary Staff Kayo YOSHIDA ●Visiting Researcher Takatoshi KIBA ●Part Timers Masami NANRI Shoko SUZUKI Hiromi OJIMA major plant hormones (cytokinins, auxins, ABA, GAs). ● We determined atomic structure of maize glutamine synthetase (GS), and elucidated structural bases of reaction mechanism and physicochemical stability. 52 RIKEN PSC 2007 Annual Report RIKEN PSC 2007 Annual Report 53 Morphoregulation Research Team Research Staff ●チームリーダー 出村 拓 ●研究員 西窪 伸之 山口 雅利 形態制御研究チーム ナディア グエ ●基礎科学特別研究員 研究内容 ● 木質細胞分化特異的遺伝子の同定と機能解明 ● 木質バイオマスの生産性と品質の改変技術の確立 Content of Research ● Identification and functional analysis of genes specific to xylem cell 出村 拓／ Taku DEMURA 平成 2 年 3 月に東北大学理学部生物学科を differentiation ● Establishment of methods for improving productivity and quality of woody biomass 卒業した。同年 4 月に東北大学大学院理学 研究科生物科学専攻に進学し、平成 7 年 3 月に博士号（博士（理学））を授与された。 同年 4 月から平成 9 年 3 月まで東北大学大 学院理学研究科助手、平成 9 年 4 月から平 木質バイオマスの改変による地球環境の保護 Preservation of environment by improvement of woody biomass 研究概要 て木質バイオマスは重要である。当研究チームではシロイヌナズナとポ プラを用いて、木質バイオマスの生産性向上に向けた基盤技術の確立を目指し ている。 Outline of Research F ossil fuel will be depleted in the near future and woody biomass is expected to be used as a substitute. We will elucidate the molecular mechanisms of the production of woody biomass, using Arabidopsis and poplar. れまで大学院在学中から一貫して維管束組織 分化をモデルとして植物細胞の脱分化・分化 転換・分化に関わる遺伝子群について分子生 物学的な研究に従事してきた。 Taku Demura obtained his Ph.D. in biology from Graduate School of Science, Tohoku ● 木質細胞分化の制御因子の探索を進め、新奇の NAC ドメイン転写因子 SND1 が繊維細胞の二次細胞壁形成のマスター遺伝子として働くこと、他 の複数の転写因子が道管要素分化の制御に重要な役割を果たすことを明ら かにした。 ● 樹木研究の基盤となるポプラの形質転換と育成のシステムを横浜研究所内 に確立し、これを用いて、木質細胞分化の制御因子のポプラホモログの同 定を進めた。また、中国南京林業大学と将来のポプラ分子育種に向けた共 同研究を開始した。 University, in 1995. In graduate school, he conducted molecular biological studies on Result of Research the genes expressed preferentially during vascular development, and found that the in vitro transdifferentiation system from zinnia ● We continued identification of regulators for woody cell differentiation, which mesophyll cells into tracheary elements mimics the in vivo differentiation from meristematic cells into vessels via procambial cells. He SND1, which regulates secondary wall formation of fiber cells and the finding served as an Assistant Professor at the Tohoku University and the University of Tokyo resulted in the finding of a novel NAC-domain transcription factor, Arabidopsis of several other transcription factors playing important roles in regulation of vessel element differentiation. from April 1995 to September 2000. During this period, he continued molecular biological studies on the vascular-specific genes and started a comprehensive analysis on gene ● We established the system for transformation of poplar in the Yokohama expression during vascular development. In October 2000, he joined the Plant Science Center. with researchers in Nanjing Forestry University, China, for the molecular Institute, using which we carried out identification of poplar homologues of regulators for woody cell differentiation. In addition, we started collaboration breeding of poplar trees. ●客員研究員 久保 稔（JST-ERATO） 栗山 英夫（東京大学） 張 博（南京林業大学） 程 強（南京林業大学） ●テクニカルスタッフ 大山 幸子 荒木 光孝 井原 あゆみ ●研修生 中野 仁美 ●実習生 アーニャ バン ハーペレン ●パートタイマー 佐藤 明子 北裏 佳代 橋本 陽子 松本 朋子 高木 さつき 廣山 涼子 成川 苗子 喜多 寿恵 ●Team Leader Taku DEMURA ●Research Scientists Nobuyuki NISHIKUBO Masatoshi YAMAGUCHI Nadia GOUE Plant Productivity Systems Research Group Plant Productivity Systems Research Group 近 い将来に枯渇すると予想される化石エネルギーに代わるエネルギーとし 成 12 年 9 月まで東京大学大学院理学系研究 科助手を務め、平成 12 年 10 月に形態制御 研究チームのチームリーダーに就任した。こ 研究成果 五十嵐 久子 大谷 美沙都 ●Special Postdoctoral Researchers Hisako IGARASHI Misato OHTANI ●Visiting Scientists Minoru KUBO (JST-ERATO) Hideo KURIYAMA (Univ. of Tokyo) Bo ZHANG (Nanjing Forestry Univ.) Qiang CHENG (Nanjing Forestry Univ.) ●Technical Staffs Sachiko OYAMA Mitsutaka ARAKI Ayumi IHARA ●Student Trainee Yoshimi NAKANO ●Intern Anja van HAPEREN ●Part Timers Akiko SATO Kayo KITAURA Yoko HASHIMOTO Tomoko MATSUMOTO Satsuki TAKAGI Ryoko HIROYAMA Naeko NARIKAWA Toshie KITA 54 RIKEN PSC 2007 Annual Report RIKEN PSC 2007 Annual Report 55 Plant Immunity Research Team Research Staff ●チームリーダー 白須 賢 ●研究員 市村 和也 中神 弘史 植物免疫研究チーム 能年 義輝 吉田 聡子 研究内容 ● 耐病性シグナル複合体の研究 ● 耐病性に関与するユビキチンリガーゼの研究 ● 化学遺伝学法による耐病性原因遺伝子の特定 ● プロテオミクス法による耐病性原因タンパク質の同定 Content of Research 白須 賢 / Ken SHIRASU ● Characterization of resistance signaling complexes ● Characterization of ubiquitin ligases involved in plant immunity ● Isolation and characterization of novel mutants in plant immunity by chemical genetics ● Isolation and characterization of novel proteins involved in plant immunity by proteomics 持続的な農業に貢献する植物免疫システムの研究 研究成果 Plant immunity research for sustainable agriculture ● 耐病性の発現に必須なたんぱく質である RAR1 が SGT1、HSP90 で構成 研究概要 植 されるシャペロン様シグナル 複合体形成を促進することを発見した。 物は本来病原体に対する高い防御能力を備えています。本研究チームは ● 感染時に誘導される、ユビキチン化の基質決定因子であるユビキチンリガー この植物の耐病性に関与する遺伝子、タンパク質、および低分子化学物 ゼの U ボックスタンパク質を同定および単離し、そのいくつかが植物免疫 質をゲノミクス、プロテオミクス、メタボロミクス的解析手法を用いて網羅的 immunity in plants. We plan to systematically identify and characterize genes, 竹林 有理佳 ●学振夏期特別研究生 デビッド グリンシールズ ●Team Leader Ken SHIRASU ●Research Scientists Kazuya ICHIMURA Hiroshi NAKAGAMI Yoshiteru NOUTOSHI Satoko YOSHIDA ●JSPS Postdoctoral Fellows Yasuhiro KADOTA Marco TRUJILLO Arsalan DAUDI ●Technical Staff Kaori TAKIZAWA ●Technical Assistant Arika TAKEBAYASHI ●JSPS Summer Student David GREENSHIELDS Result of Research Figure1 Fusing ubiquitin specific binding domains, UIM and UBA from Arabidopsis AtRPN10 and AtUBP14 to GST, we created ubiquitin affinity columns. VWA(von Willebrand factor type A domain),UIM(ubiquitin interacting motif), ZnF(Zinc Finger domain),UBA (Ubiquitin associating domain). ● A highly conserved eukaryotic protein RAR1 promotes interaction between the Plant Immunity Research Group Plant Immunity Research Group he main goal of this team is to understand the molecular mechanism of 瀧澤 香 ●研究補助員 析に成功した。 タンパク質の修飾などによるスイッチ機能を明らかにし、農薬に頼らない持続 T アルサラン ダウディ ●テクニカルスタッフ ● 植物におけるプロテオーム技術を開発し、ユビキチン化プロテオームの解 ターンと信号伝達ネットワークを解析し、また免疫システムの制御に関与する Outline of Research 門田 康弘 マルコ トゥルヒロ シグナルを制御することを示した。 に単離し、植物の免疫システムの解明をめざします。感染応答遺伝子の発現パ 的な耐病性植物の作出をめざします。 ●学振研究員 molecular chaperone, HSP90 and its co-chaperone SGT1. ● We identified several Class III U-box proteins that regulate the plant immunity signaling pathway. ● We developed a novel proteome methodology to analyze the ubiquitinated proteins and small molecular compounds that are important for the defense by using genomics, proteomics and metabolomics approaches. We aim to proteome in plants. elucidate signaling network system for plant immunity by analyzing expression patterns of defense related genes and their post transcriptional regulation, such as protein modification. Understanding the molecular basis of disease resistance mechanisms plants utilize in nature will provide new strategies to combat pathogens. Figure 2 We purified ubiquitinated proteins using the ubiqutin affinity chromatography. These proteins were digested with trypsin and analyze by MudPIT analysis. As the trypsin digest leaves two glycine molecules on the target proteins, the ubiquitinated sites can be easily identified by LC-MS/MS. Ubiquitin(Ubi), Lysine(K), Arginine(R). 56 RIKEN PSC 2007 Annual Report RIKEN PSC 2007 Annual Report 57 Plant Functional Genomics Research Team Research Staff 植物ゲノム機能研究チーム 研究内容 ● 変異体ライン解析による植物遺伝子の機能探索 ● 完全長 cDNA を利用した遺伝子機能解析法の開発 ● 転写制御研究による遺伝子ネットワーク解析 ● 植物特異的な形態形成、環境応答性の研究 Content of Research 松井 南 / Minami MATSUI ● Characterization of plant gene function through analysis of plant mutant lines ● Innovation of gene function characterization technologies using full-length cDNAs ● Analysis of gene regulatory network through research on transcriptional control ● Research on plant-specific morphogenesis and environmental responses 植物機能のゲノム的理解と応用 Understanding and application of plant genome function 研究概要 有 用な植物作出のためには、遺伝子の機能とそれらの発現制御を詳しく理 解することが必要である。私たちの研究チームでは、機能付加型の変異 研究成果 ● シロイヌナズナアクティベーションタグライン 5 万 5 千系統の作成と形質 データベースの構築 ● 完全長 cDNA を用いたフォックスハンティングシステム（植物有用形質高 速探索技術）の開発とイネ有用遺伝子への応用 ● 13,000 のシロイヌナズナ FOX ラインの作成と解析 体リソース作成と遺伝子探索技術を駆使することにより、戦略的な育種に繋が ● 17,000 系統のイネ FOX ラインの作成と解析 る基礎となるゲノム機能の研究を推進する。 ● 植物 IRES 配列を持つルシフェラーゼレポーターを用いた遺伝子発現の時間 Outline of Research F or production of the useful plants comprehensive understanding of plant’s gene functions and their regulatory network is indispensable. Our team will perform functional genomic research that connects to the basis for tactical breeding through production of gain-of-function plant mutant resources and developing gene function characterization technologies. 的、空間的な変動解析 ● 細胞分裂を伴わない細胞周期 Endoreduplication による植物形態形成に関 する研究 Result of Research ● Production of 55,000 Arabidopsis Activation tagged lines and construction of phenome database ● Innovation of an FOX hunting system, -a rapid identification system of plant’s useful traits using full-length cDNAs-, and its application to rice gene function ● Production and analysis of 13,000 Arabidopsis FOX lines ● Temporal and spatial gene expression profile analysis using IRES assisted luciferase reporter system ● Study on plant morphogenesis by analysis of endoreduplication -a cell cycle without cell division- 58 RIKEN PSC 2007 Annual Report ● Team Leader Minami MATSUI ● Senior Research Scientist Takanari ICHIKAWA ● Research Scientist Hirofumi KURODA ● Research Associates Youichi KONDOU Takeshi YOSHIZUMI Mieko HIGUCHI Shinya TAKAHASHI ● Visiting Scientists Ayako KAWAMURA Ayako KIKUZAKI Kenichi TAKANE Nobuyo NISHIZAKI Syu MUTO ● Visiting Researcher Arata YONEDA ● Technical Staffs Mika KAWASHIMA Youko HORII Keiko MATSUI Yukako HASEGAWA Tomoko KURIYAMA ● Student Trainees Chika AKAGI Hiroko HARA Hiroaki HONGO ● Part Timers Mieko AMEMIYA Hitomi ARATA Harumi ITO Hiromi UEDA Akiko UENO Kaoru UTSUMI Miyuki EBASHI Jyunko ENOKIDO Michiyo KOMURA Mieko KOMOCHI Rieko SATO Chizuru SAKOYAMA Naoko SUZUKI Yuko TSUMOTO Masako FUKUDA Sumiko MIYACHI Mayumi YOSHIMURA Kyoko YOKOMIZO RIKEN PSC 2007 Annual Report Plant Functional Genomics Research Group Plant Functional Genomics Research Group ● Production and analysis of 17,000 rice FOX lines ● チームリーダー 松井 南 ● 上級研究員 市川 尚斉 ● 研究員 黒田 浩文 ● リサーチアソシエイト 近藤 陽一 吉積 毅 樋口 美栄子 高橋 真哉 ● 客員研究員 河村 彩子 菊崎 綾子 高根 健一 西崎 修代 武藤 周 ● 訪問研究員 米田 新 ● テクニカルスタッフ 川島 美香 堀井 陽子 松井 敬子 長谷川 由果子 栗山 朋子 ● 研修生 赤木 千佳 原 博子 本郷 洋明 ● パートタイマー 雨宮 三枝子 荒田 仁美 伊藤 春美 上田 浩美 上野 章子 内海 かおる 江橋 みゆき 榎戸 順子 小村 みち代 小餅 美恵子 佐藤 梨枝子 迫山 千鶴 鈴木 尚子 津本 祐子 福田 正子 宮地 寿美子 義村 真弓 横溝 京子 59 Plant Genomic Network Research Team Research Staff ●チームリーダー 関 原明（06 年 11 月から ) 篠崎 一雄（06 年 4 月から 10 月まで） ●研究員 金 鐘明 植物ゲノム発現研究チーム 黒森 崇 明賀 史純 研究内容 ● 全ゲノムタイリングアレイ等を用いた乾燥・低温・塩ストレス条件下での 全ゲノムトランスクリプトーム解析 ● シロイヌナズナや作物、樹木などの発現遺伝子の完全長 cDNA の収集と構 造・発現解析 ● 遺伝子破壊型変異体を用いた遺伝子の機能解析 関 原明／ Motoaki SEKI 1988 年に京都大学農学部を卒業。1994 年 に広島大学大学院理学研究科にて博士号（理 学）を取得した。引き続き 1995 年 3 月ま で日本学術振興会特別研究員として同研究に 従事した。1995 年 4 月から理化学研究所、 植物分子生物学研究室で植物ゲノムの発現・ ゲノム的手法による植物の発現遺伝子や機能性 RNA の探索とその機能解明 Discovery of plant novel genes and RNAs by genomic analysis 研究概要 主 にシロイヌナズナを用いてゲノム科学的方法により、種々の植物の発現 遺伝子（完全長 cDNA）の収集や植物の生産性向上等に関与する遺伝子 機能解析および植物の環境ストレス応答の分 子生物学的解析を進めた。1999 年には理化 学研究所ゲノム科学総合研究センター植物ゲ ノム機能情報研究グループ植物変異開発研究 チームの上級研究員を兼務して、シロイヌナ ズナ完全長 cDNA を用いた植物ゲノムの発 現・機能解析および乾燥・低温・塩ストレス 条件下でのトランスクリプトーム解析を行っ た。2006 年 11 月から現職 や機能性 RNA の探索およびそれらの機能解明を目指す。 Motoaki Seki graduated from the Faculty of Agriculture, Kyoto University in 1988. Outline of Research He obtained his Ph.D. in science from Hiroshima University in 1994. He continued the study until March 1995 as a Research W e are exploring new protein-coding genes (full-length cDNAs) and functional noncoding RNAs involved in the environmental stress responses, improvement of plant productivity and plant development by genomic approaches. Fellow of the Japan Society for the Promotion of Science (JSPS). In April 1995, he joined Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute and has studied plant functional genomics and molecular responses to abiotic stresses in plants. In 1999, he also became Senior Scientist of Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences conditions. In November 2006, he was appointed to be Team Leader of Plant Genomic Network Research Team, RIKEN Plant Science Center. 60 RIKEN PSC 2007 Annual Report ● Whole-genome transcriptome analysis under drought, cold and high-salinity stress conditions using whole-genome tiling array ● Collection of full-length cDNAs from Arabidopsis, various crops and trees and its application to microarray analysis for exploration of useful genes ● Functional analysis of genes using knockout mutant lines 研究成果 ● シロイヌナズナ全ゲノムタイリングアレイを用いて、乾燥・低温・塩スト レスにより誘導される新規な遺伝子（転写単位）やセンス・アンチセンス 転写産物のペアを多数同定した。 ● 乾燥・低温・塩などのストレス処理した植物体を出発材料として small RNA の大量解析を行い、新規なストレス応答性の small RNA を幾つか同 定した。 ● 国内外の研究グループと共同して、 種々の作物や樹木の完全長 cDNA クロー ンの収集を行い、完全長 cDNA を用いた植物遺伝子の発現解析を行った。 Result of Research ● We have identified many novel drought-, cold- or high-salinity- stress-inducible genes and natural sense-antisense transcript (SAT) pairs using Arabidopsis whole-genome tiling array. ● Large-scale analyses of the small RNAs by 454 sequencing technology showed that the expression of several novel small RNAs are regulated by the stress. ● We have collected the full-length cDNAs from various plants, such as wheat, soybean, poplar, and cassava, and from Arabidopsis -related halophytes (Thellungiella halophila ) in collaboration with other research teams. 栗原 志夫 ●技師 佐藤 将一 ●テクニカルスタッフ 石田 順子 神谷 麻子 中嶋 舞子 槐 亜希子 飯泉 治子 諸澤 妙子 川嶋 真貴子 ●研修生 吉田 知（横浜市立大学大学院） 浮津 広毅（横浜市立大学大学院） 藤 泰子（東京大学大学院） 細田 千恵子（東京大学大学院） ●共同研究員 本橋 令子（静岡大学） 鳴坂 義弘（東京学芸大学） 鳴坂 真理（東京学芸大学） ●Team Leader Motoaki SEKI (since November 2006) Kazuo SHINOZAKI (since April 2006 to October) ●Research Scientists Jong-Myong KIM Takashi KUROMORI Fumiyoshi MYOUGA ●Research Associates Akihiro MATSUI Yukio KURIHARA ●Technical Scientist Masakazu SATOU ●Technical Staffs Junko ISHIDA Asako KAMIYA Maiko NAKAJIMA Akiko ENJU Haruko IIZUMI Taeko MOROSAWA Makiko KAWASHIMA ●Student Trainees Tomo YOSHIDA(Yokohama City Univ.) Hiroki UKITSU(Yokohama City Univ.) Plant Functional Genomics Research Group Plant Functional Genomics Research Group Center and has performed Arabidopsis functional genomics using full-length cDNAs and whole-genome transcriptome analyses under drought, cold and high-salinity stress Content of Research ●リサーチアソシエート 松井 章浩 Taiko KIM TO(The Univ. of Tokyo) Chieko HOSODA(The Univ. of Tokyo) ●Research Collabotators Reiko MOTOHASHI(Shizuoka Univ.) Yoshihiro NARUSAKA (Tokyo Gakugei Univ.) Mari NARUSAKA(Tokyo Gakugei Univ.) RIKEN PSC 2007 Annual Report 61 グループディレクター、チームリーダー、ユニットリーダーの業績 ̶ 公表論文、プレスリリース、特許等 Metabolome Analysis Research Team Team Leader : Kazuki SAITO ■ Publications ● Original Papers Noji, M., Cintia Goulart Kawashima, Obayashi, T., and Saito, K.(2006) In Silico assessment of gene function involved in cysteine biosynthesis in Arabidopsis: Expression analysis of multiple isoforms of serine acetyltransferase. Amino Acids, 30: 163-171. Nakajima, J., Sato, Y., Hoshino, T., Yamazaki, M., and Saito, K. (2006) Mechanistic study on the oxidation of anthocyanidin synthase by quantum mechanical calculation. J. Biol. Chem., 281: 21387-21398. Higashi, Y., Hirai, M. Y., Fujiwara, T., Naito, S., Noji, M., and Saito, K. (2006) Proteomics and transcriptomic analysis of Arabidopsis seeds: Molecular evidence for successive processing of seed proteins and its implication in stress response to sulfur nutrition. Plant J., 48: 557-571. Yano, M., Kanaya, S., Altaf-Ul-Amin, Md., Kurokawa, K., Hirai, M. Y., and Saito, K. (2006) Integrated data mining of transcriptome and metabolome based on BL-SOM. J. Comp. Aid. Chem., 7: 125-136. Maruyama-Nakashita, A., Nakamura, Y., Tohge, T., Saito, K., and Takahashi, H. (2006) Central transcriptional regulator of plant sulfur response and metabolism. Plant Cell, 18: 3235-3251. Oikawa, A., Nakamura, Y., Ogura, T., Kimura, A., Suzuki, H., Sakurai, N., Shinbo, Y., Shibata, D., Kanaya, S., and Ohta, D. (2006). Clarification of Pathway Specific Inhibition by FT-ICR/ MS-Based Metabolic Phenotyping Studies. Plant Physiol, 142: 398-413. Morikawa, T., Mizutani, M., Aoki, N., Watanabe, B., Saga, H., Saito, S., Oikawa, A., Suzuki, H., Sakurai, N., Shibata, D., Wadano A., Sakata K., and Ohta D. (2006). Cytochrome P450 CYP710A encodes the sterol C-22 desaturase in Arabidopsis and tomato. Plant Cell, 18: 1008-1022 Jonsson, P., Johansson, E.S., Wuolikainen, A., Lindberg, J., Schuppe-Koistinen, I., Kusano, M., Sjostrom, M., Trygg, J., Moritz, T., and Antti, H. (2006). Predictive metabolite profiling applying hierarchical multivariate curve resolution to GC-MS data-A potential tool for multi-parametric diagnosis. J. Proteome Res., 5: 1407-1414. 62 RIKEN PSC 2007 Annual Report Obayashi, T., Kinoshita, K., Nakai, K., Shibaoka, M., Hayashi, S., Saeki, M., Shibata, D., Saito, K., and Ohta, H. (2007) ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res., 35: D863-869. Li-Yang, J., Nakajima, J., Kimura, N., Saito, K., and Seo, S. (2007) Oleanane-type triterpene glycosides from Glychyrrhiza ularensis . Nat. Prod. Comm., 2: 243-248. Luo, J., Nishiyama, Y., Fuell, C., Taguchi, G., Elliott, K., Hill, L., Tanaka, Y., Kitayama, M., Yamazaki, M., Bailey, P., Parr, A., Michael, A. J., Saito, K., and Martin, C. (2007) Convergent evolution in the BAHD family of acyl transferases; identification and characterisation of anthocyanin acyl transferases from Arabidopsis thaliana . Plant J., in press. Hirai, M. Y., Sugiyama, K., Sawada, Y., Tohge, T., Obayashi, T., Suzuki, A., Araki, R., Sakurai, N., Suzuki, H., Aoki, K., Goda, H., Nishizawa, O. I., Shibata, D., and Saito, K. (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc. Natl. Acad. Sci., USA., 104: 6478-6483. Tohge, T., Yonekura-Sakakibara, K., Niida, R., WatanabeTakahashi, A., and Saito, K. (2007) Phytochemical genomics in Arabidopsis thaliana : A case study for functional identification of flavonoid biosynthesis genes. Pure and Applied Chemistry, 79: 811-823. Yonekura-Sakakibara, K., Tohge, T., Niida, R., and Saito, K. (2007) Identification of a flavonol 7-O -rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression and reverse genetics. J Biol. Chem., 282: 14932-14941. ● Review Papers Yonekura- Sakakibara, K., and Saito, K. (2006) Review: Genetically modified plants for the promotion of human health. Biotech Lett, 28: 1983-1991. Yamazaki, M., and Saito, K. (2006) Isolation and characterization of anthocyanin 5-O-glucosyltransefrase in Perilla frutescens var. crispa by differential display. Methods in Molecular Biology, vol. 317: Differential Display Methods and Protocols. Eds by P. Liang, J.D. Meade and A.B. Pardee, Humana Press Inc. Totowa, NJ, 255-266. Asano, T., Sudo, H., Yamazaki, M., and Saito, K. (2007) Camptothecin production in cell cultures of Ophiorrhiza species. In “Medicinal Plant Biotechnology - From Basic Research to Metabolomics Research Group Metabolomics Research Group Publications, Press Releases & Patents Industrial Applications” Vol. 2, Oliver Kayser and Wim Quax, eds: pp. 451-468, WILEY-VCH Verlag, Weinheim. ● Invited Presentations in Domestic Meetings 5 invited Japanese presentations Tohge, T., Nishiyama, Y., Hirai, M. Y., Yano, M., Nakajima, J., Awazuhara, M., Inoue, E., Takahashi, H., Goodenowe, D. B., Kitayama, M., Noji, M., Yamazaki, M., and Saito, K.(2007) Identification of Genes Involved in Anthocyanin Accumulation by Integrated Analysis of Metabolome and Transcriptome in Pap1-Overexpressing Arabidopsis Plants. In “ Concepts in Plant Metabolomics” Basil J. Nikolau, Eve Syrkin Wurtele, eds: pp. 159-168, Springer, Heidelberg Yonekura-Sakakibara, K., Nakayama, T., Yamazaki, M., and Saito, K. (2007) Modification and stabilization of anthocyanins. In Anthocyanin book, in press. ● Presentations in International Meetings Tohge, T., Yonekura-Sakakibara, K., Obayashi, T., Okazaki, Y., and Saito K. (2006) Functional genomics highway by integration of metabolomics and transcriptomics with a model plant Arabidopsis thaliana. The Second Scientific Meeting of the Metabolomics Society, Jun, Boston, USA, Jun. Kusano, M., Fukushima, A., Arita, M., Jonsson, P., Moritz, T., Kitayama, M., Kanaya, S., Watanabe, M., Noji, M., and Saito, K. (2006) The 4th international conference on plant metabolomics. 7th, April, Reading, UK, Apr. 4 review chapters in Japanese. ■ Oral Presentations ● Invited Presentations in International Meetings Saito, K. (2006) Integration of omics datasets towards metabolomics-based plant systems biology. 4th International Conference on Plant Metabolomics. Reading, Berkshire, UK, April 7-10. Saito, K. (2006) Metabolomics towards phytochemical genomics. The 53rd NIBB Conference. Dynamic Organelles in Plants. Okazaki, Japan, June 14-17. Saito, K. (2006) Integration of transcriptome and metabolome for study on plant natural product biosynthesis. ICOB-5& ISCNP-25 IUPAC International Conference on Biodiversity and Natural Products (IUPAC-2006).Kyoto, Japan, July 23-28. Tohge, T., Yonekura-Sakakibara, K., Obayashi, T., and Saito, K. (2006) High-throughput functional genomic approach by integration of transcriptome coexpression analysis with metabolomics approach. The 4th international conference on plant metabolomics. 7th, April, Reading, UK, Apr. ● Presentations in Domestic Meetings 2 Japanese presentations ■ Press Releases BTJ Journal, 2006, May issue, pp. 1-8. Plant metabolomics, Leader Interview, Kazuki Saito. NIKKAN KOGYO SHINBUN, August 3, 2006. Plant Metabolomics, production of useful products, identification of genes by metabolic profiling. Saito, K., Asano, T., Sudo, H., Sirikantaramas, S., Kitayama, M., and Yamazaki, M. (2006) Gene discovery and pathway elucidation for camptothecin biosynthesis in Ophiorrhiza pumila. 8th International Congress of Plant Molecular Biology. Adelaide, Australia, August 20-25. Journal of Biological Chemistry, Feb 22, 2007, Identification of a gene encoding an enzyme which determines flavonoid patterns in Arabidopsis. Saito, K., Hirai, M.Y., Tohge, T., Yonekura-Sakakibara K., Obayashi T., Yano M., Morioka R., and Kanaya S. (2006) Towards plant systems biology by metabolome-transcriptome integration. 8th International Congress of Plant Molecular Biology. Adelaide, Australia, August 20-25. Takayuki TOHGE: Best Young Scientists Poster 2006: Highthroughput functional genomic approach by integration of transcriptome coexpression analysis with metabolomics approach. 4th International Conference on Plant Metabolomics, Reading, UK, 2006, Apr. Hirai, M.Y., and Saito, K. (2006) Comprehensive functional elucidation of the genes involved in glucosinolate biosynthesis. 1st International meeting on glucosinolates. Jena, Germany, September 10-13. Saito, K. (2006) Metabolomics-based functional genomics highway in plants. International Workshop Plant Biotechnology for Production of Industrial Materials. Osaka, Japan, September 14. Saito, K. (2006) Metabolomics-based plant functional genomics highway. The 4th Matsuyama International Symposium on CellFree Sciences. Matsuyama, Japan, October 6, ■ Award Metabolic Systems Research Unit Unit Leader : Masami Yokota HIRAI ■ Publications ● Original Papers Hirai, M.Y., Sugiyama, K., Sawada, Y., Tohge, T., Obayashi, T., Suzuki, A., Araki, R., Sakurai, N., Suzuki, H., Aoki, K., Goda, H., Nishizawa, O.I., Shibata, D., and Saito, K. (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc. Natl. Acad. Sci. USA, 104: 6478-6483. RIKEN PSC 2007 Annual Report 63 Yano, M., Kanaya, S., Altaf-Ul-Amin, M., Kurokawa, K., Hirai, M.Y., and Saito, K. (2006) Integrated data mining of transcriptome and metabolome based on BL-SOM. Journal of Computer Aided Chemistry, 7: 125-136. detected by graph clustering (DPClus). The Seventh International Conference on Systems Biology, Yokohama, Japan, Oct. (poster) Kikuchi, J., and Akamine, K. (2006) in vivo NMR J. Spect. Soc., 55: 320-330. Morioka, R., Kanaya, S., Yano, M., Nakamura, Y., Hirai, M.Y., and Saito, K. (2006) Statistical approach for finding metabolic pathways for environmental stress responses in Arabidopsis thaliana . 4th International Conference on Plant Metabolomics, Reading, UK, Apr. (poster) Kikuchi, J., and Hirayama, T. (2006) Hetero-nuclear NMR-based metabolomics Biotech. Agri. Forest. 57: 93-101. ● Book Edition Morioka, R., Kanaya, S., Okazaki, Y., Yano, M., Hirai, M.Y., and Saito, K. (2006) Systematic approach for predicting environmental stress responses from integrated omics data. Plant Biology, Boston, USA, Aug. (poster) Hirai, M.Y., Tohge, T., and Saito, K. (2006) Systems-based analysis of plant metabolism by integration of metabolomics with transcriptomics, In “Biotechnology in Agriculture and Forestry 57 Plant Metabolomics” Kazuki Saito, Richard A. Dixon, Lothar Willmitzer eds: pp. 199-210, Springer Verlag, Heidelberg. Morioka, R., Kanaya, S., Yano, M., Hirai, M.Y., and Saito, K. (2006) Prediction of sulfur stress responses in Arabidopsis thaliana . The Seventh International Conference on Systems Biology, Yokohama, Japan, Oct . (poster) Metabolomics Research Group Metabolomics Research Group Higashi, Y., Hirai, M.Y., Fujiwara, T., Naito, S., Noji, M., and Saito, K. (2006) Proteomic and transcriptomic analysis of Arabidopsis seeds: molecular evidence for successive processing of seed proteins and its implication in the stress response to sulfur nutrition. Plant J., 48: 557-571. ■ Oral Presentations ● Invited Presentation in Domestic Meeting 1 invited Jaapanese presentation ■ Oral Presentations ● Presentations in International Meetings ● Invited Presentation in International Meeting 2 presentations Kikuchi, J., Tsuboi, Y., Shinozaki, K., and Hirayama, T. (2006) “Stable isotope labeling of plants through animals for a heteronuclear NMR-based nutrition profiling. 1st International Conference on Nutrigenomics and Gut Health, Auckland, NewZealand. ● Presentations in Domestic Meetings ● Invited Presentations in Domestic Meetings Madoka AYANO: Best Paper Award 2006, Journal of Plant Research. 10 Japanese presentations ■ Award 5 invited Japanese presentations ■ Oral Presentations ● Presentations in Domestic Meetings ● Invited Presentations in International Meetings 11 Japanese presentations Hirai, M.Y., and Saito, K. (2006) Metabolomics-based functional genomics for understanding of plant secondary metabolism. The First International Symposium on Development and Application of Functional Biomaterials from Natural Resources. Kyung Hee University, Suwon, Korea, 16 Nov. Hirai, M.Y., and Saito, K. (2006) Comprehensive functional elucidation of the genes involved in glucosinolate biosynthesis. The First International Conference on Glucosinolates. Jena, Germany, 10-14 Sep. ● Invited Presentations in Domestic Meetings 2 invited Japanese presentations ● Presentations in International Meetings Hirai, M.Y., Klein, M., Fujikawa, Y., Yano M., Goodenowe, D.B., Yamazaki, Y., Kanaya, S., Suzuki, H., Sakurai, N., Shibata, D., Tokuhisa, J., Reichelt, M., Gershenzon, J., Papenbrock, J., and Saito, K. (2006) Functional genomics by integrated analysis of metabolome and transcriptome. 4th International Conference on Plant Metabolomics, Reading, UK, Apr. (poster) Sawada, Y., Saito, K., and Hirai, M.Y. (2006) Identification of the side-chain-elongation enzyme in the glucosinolate biosynthesis. The First International Conference on Glucosinolates. Jena, Germany, 10-14 Sep.(poster) Fukushima, A., Kusano, M., Akiyama, K., Obayashi, T., Tohge, T., Hirai, M.Y., Kanaya, S., Arita, M., Shinbo, Y., Shinozaki, K., Sakurai, T., and Saito, K. (2006) PRIMe: Platform for RIKEN Metabolomics. 4th International Conference on Plant Metabolomics, Reading, UK, Apr. (poster) Fukushima, A., Altaf-Ul-Amin, M., Kurokawa, K., Kanaya, S., Hirai, M.Y., and Saito, K. (2006) Highly correlated groups of multiple genes and/or metabolites in Arabidopsis thaliana 64 RIKEN PSC 2007 Annual Report Advanced NMR Metabomics Research Unit Unit Leader : Jun KIKUCHI ■ Publications ● Original Papers Tian, C.J. Chikayama, E., Tsuboi, Y., Kuromori, T., Shinozaki, K., Kikuchi, J., and Hirayama, T. Top-down phenomics of Arabidopsis thaliana –One and two-dimensional NMR metabolic profiling and transcriptome analysis of albino mutants. J. Biol. Chem., in press. Sekiyama, Y., and Kikuchi, J. Toward dynamic metabolic network measurement by multi-dimensional NMR-based fluxomics. Phytochemistry, in press. Sasaki, R., Sasaki, H., Fukuzawa, S., Kikuchi, J., Hirota, H., and Tachibana, K. Thermal analyses of phospholipid mixtures by differential scanning calorimetry and effect of doping with a bolaform amphiphile Bull. Chem. Soc. Jpn., in press. Elmi, M. M., Aminiasaab, M., Hondo, T., Kikuchi, J., Kuroda, Y., Naderi-Manesh, H., and Sarbolouki, M. M. (2006) Structural and functional characterization of a mutant of Pseudocerastes persicus natriutic peptide Prot. Pept. Lett. 13: 295-300. Izumikawa, M., Cheng, Q., and Moore, B. S. (2006) Priming type II polyketide synthases via a type II nonribosomal peptide synthetase mechanism. J. Am. Chem. Soc. 128: 1428-1429. ● Review Papers Kikuchi, J., and Hirayama, T. (2007) Practical aspects of stable isotope labeling of higher plants for a hetero-nuclear multidimensional NMR-based metabolomics. Method Mol. Biol. 358: 273-286. ● Presentations in International Meetings Integrated Genome Informatics Research Unit Unit Leader : Tetsuya SAKURAI 18 English presentations ■ Publications ● Presentations in Domestic Meetings ● Original Papers 25 Japanese presentations Itoh, T., Tanaka, T., Barrero, RA., Yamasaki, C., Fujii, Y., Hilton, PB., Antonio, BA., Aono, H., Apweiler, R., Bruskiewich, R., Bureau, T., Burr, F., Costa de Oliveira, A., Fuks, G., Habara, T., Haberer, G., Han, B., Harada, E., Hiraki, AT., Hirochika, H., Hoen, D., Hokari, H., Hosokawa, S., Hsing, YI., Ikawa, H., Ikeo, K., Imanishi, T., Ito, Y., Jaiswal, P., Kanno, M., Kawahara, Y., Kawamura, T., Kawashima, H., Khurana, JP., Kikuchi, S., Komatsu, S., Koyanagi, KO., Kubooka, H., Lieberherr, D., Lin, YC., Lonsdale, D., Matsumoto, T., Matsuya, A., McCombie, WR., Messing, J., Miyao, A., Mulder, N., Nagamura, Y., Nam, J., Namiki, N., Numa, H., Nurimoto, S., O'Donovan, C., Ohyanagi, H., Okido, T., Oota, S., Osato, N., Palmer, LE., Quetier, F., Raghuvanshi, S., Saichi, N., Sakai, H., Sakai, Y., Sakata, K., Sakurai, T., Sato, F., Sato, Y., Schoof, H., Seki, M., Shibata, M., Shimizu, Y., Shinozaki, K., Shinso, Y., Singh, NK., Smith-White, B., Takeda, J., Tanino, M., Tatusova, T., Thongjuea, S., Todokoro, F., Tsugane, M., Tyagi, AK., Vanavichit, A., Wang, A., Wing, RA., Yamaguchi, K., Yamamoto, M., Yamamoto, N., Yu, Y., Zhang, H., Zhao, Q., Higo, K., Burr, B., Gojobori, T., and Sasaki, T. (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana . Genome Res, 17: 175-183. Integrated Genomics Research Team Team Leader : Kazuo SHINOZAKI ■ Publications ● Original Papers Ayano, M., Imaichi, R., and Kato, K. (2005) Developmental morphology of the Asian one-leaf plant, Monophyllaea glabra (Gesneriaceae), with emphasis on inflorescence morphology. Journal of Plant Research, 118: 99-109. Tsuji, H., Aya, K., Ueguchi-Tanaka, M., Shimada, Y., Nakazono, N., Watanabe, R., Nishizawa, N., Gomi, K., Shimada, A., Kitano, H., Ashikari, M., and Matsuoka, M. (2006) GAMYB controls different sets of genes and is differentially regulated by microRNA in aleurone cells and anthers. Plant Journal, 47:427-444. Mochida, K., Kawaura, K., Shimosaka, E., Shin-I, T., Kohara, Y., Yamazaki, Y., and Ogihara, Y. (2006) Tissue expression map of comprehensive expressed sequence tags and its application to in silico screening of stress response genes in common wheat. Mol Genet Genomics. Sep;276(3):304-12. Epub 2006 Jul 11. Torada, A., Koike, M., Mochida, K., and Ogihara, Y. (2006) SSR-based linkage map with new markers using an intraspecific population of common wheat. Theor Appl Genet. Apr;112(6):1042-51. Epub 2006 Feb 1. Yamamoto, YY., Ichida, H., Matsui, M., Obokata, J., Sakurai, T., Satou, M., Seki, M., Shinozaki, K., and Abe, T. (2007) Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics, 8: 67. Hasegawa, Y., Seki, M., Mochizuki, Y., Heida, N., Hirosawa, K., Okamoato, N., Sakurai, T., Satou, M., Akiyama, K., Iida, K., Lee, K., Kanaya, S., Demura, T., Shinozaki, K., Konagaya, A., and Toyoda, T. (2006) A flexible representation of omic knowledge for thorough analysis of microarray data. Plant Methods, 2: 5. Kuromori, T., Wada, T., Kamiya, A., Yuguchi, M., Yokouchi, T., RIKEN PSC 2007 Annual Report 65 Metabolomics Research Group Okada, K., Asai, K., and Arita, M. (2007) Flow model of the protein-protein interaction network for finding credible interactions. In Proceedings of 5th Asia Pacific Bioinformatics Conference (APBC2007), Jan. 15-17 Hong Kong. Qin F., Kakimoto M., Sakuma Y., Maruyama K., Osakabe Y., Tran L-S., Shinzoaki K., and Yamaguchi-Shinozaki K. (2007) Regulation and functional analysis of ZmDREB2A in response to droutht and heat stresses in Zea mays L., Plant J., 50: 54-69. ■ Oral Presentations ● Review Papers ● Invited Presentation in Domestic Meeting Arita, M., Fujiwara, Y., and Nakanishi, Y. (2006) Map Editor for the Atomic Reconstruction of Metabolism (ARM) Chapter II.3 In Plant Metabolomics (Eds. K Saito, RA Dixon, L Willmitzer) Biotechnology in Agriculture and Forestry Vol.57, Springer Verlag, 129-140. Ichikawa, T., Nakazawa, M., Kawashima, M., Iizumi, H., Kuroda, H., Kondou, Y., Tsuhara, Y., Suzuki, K., Ishikawa, A., Seki, M., Fujita, M., Motohashi, R., Nagata, N., Takagi, T., Shinozaki, K., and Matsui, M. (2006) The FOX hunting system: an alternative gain-of-function gene hunting technique. Plant J., 45: 974-986. 1 invited Japanese presentation ● Presentations in International Meetings Myouga, F., Akiyama, K., Sakurai, T., Motohashi, R., and Shinozaki, K. (2006) Gene discovery for chloroplast proteins involved in drought tolerance in Arabidopsis using the RARGE detabase, 8th International Congress of Plant Molecular Biology, Adelaide, Australia, Aug. Umezawa, T., Todaka, D., Totoki, Y., Sakurai, T., Seki, M., Toyoda, A., Maruyama, K., Nakashima, K., Mizukado, S., Kasuga, M., Ahmed, S., Sado, H., Harada, H., Tsubokura, Y., Satoh, S., Anai, T., Ishimoto, M., Funatsuki, H., Teraishi, M., Shinano, T., Akaishi, R., Sakaki, Y., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Construction of a soybean full-length cDNA library and oligonucleotide microarray, The Kazusa Conference on Legume Genetics and Genomics in Asia, Kisarazu, Nov. Fukushima, A., Kusano, M., Akiyama, K., Obayashi, T., Tohge, T., Hirai, M., Kanaya, S., Arita, M., Shinbo, Y., Shinozaki, K., Sakurai, T., and Saito, K. (2006) PRIMe: Platform for RIKEN Metabolomics, 4th International Conference on Plant Metabolomics, (Rothamsted Research), Reading, UK, Apr. Mochida, K., Kawaura, K., Sakurai, T., Shinozaki, K., and Ogihara, Y. (2007) Comprehensive analysis of wheat ESTs and comparative study between wheat and rice, Plant and Animal Genomes XV Conference, San Diego, USA, Jan. ● Presentations in Domestic Meetings 7 Japanese presentations Metabolome Informatics Research Unit Unit Leader : Masanori ARITA ■ Publications ● Original Papers Nagasaki, H., Arita, M., Nishizawa, T., Suwa, M., and Gotoh, O. (2006). Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns. Bioinformatics 22(10): 1211-1216. Tuji, H., Altaf-Ul-Amin, Md., Arita, M., Nishio, H., Shinbo, Y., Kurokawa, K., and Kanaya, S. (2006) Comparison of protein complexes predicted from PPI networks by DPClus and newman clustering algorithms. IPSJ Trans. Bioinformatics 47 (SIG17): 31-41 66 RIKEN PSC 2007 Annual Report Shinbo, Y., Nakamura, Y., Altaf-Ul-Amin, M., Asahi, H., Kurokawa, K., Arita, M., Saito, K., Ohta, D., Shibata, D., and Kanaya, S. (2006) KNApSAcK: A Comprehensive Species-Metabolite Relationship Database. Chapter II.6 In Plant Metabolomics (Eds. K Saito, RA Dixon, L Willmitzer) Biotechnology in Agriculture and Forestry Vol.57, Springer Verlag, 165-184. 時松 敏明 , 有田 正規（2006） 「代謝マップビューワで見るフ ラボノイド」 細胞工学 , 25（12）: 1388-1393. 小林 徹也 , 有田 正規 , 森下 喜弘 , 合原 一幸（2006） 「細胞内 現象のシステム的理解―今理論に何が求められているのか？」 システム / 制御 / 情報、50（8） 、システム制御情報学会誌 杉峰伸明、大塚一路、有田正規、合原一幸（2006） 「ネットワー ク的思考で生命現象をよみとく」 （特集「意識・脳・身体の接 続へ」 ）科学、76（3） 、岩波書店 Gene Discovery Research Team Team Leader : Kazuo SHINOZAKI ■ Publications ● Original Papers Nakagawa, Y., Katagiri, T., Shinozaki, K., Qi, Z., Tatsumi, H., Furuichi, T., Kishigami, A., Sokabe, M., Kojima, I., Sato, S., Kato, T., Tabata, S., Iida, K., Terashima, A., Nakano, M., Ikeda, M., Yamanaka, T., and Iida, H. (2007) Arabidopsis plasma membrane protein crucial for Ca2+ influx and touch sensing in roots, Proc. Natl. Acad. Sci. USA., 104: 3639-3644. Takahashi, F., Yoshida, R., Ichimura, K., Mizoguchi, T., Seo, S., Yonezawa, M., Maruyama, K., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2007) Dissecting the jasmonate signaling pathway by a novel MAP kinase cascade, MKK3-MPK6, in Arabidopsis, Plant Cell, 19:808-818. Mitsuda, N., Iwase, A., Yamamoto, H., Yoshida, M., Seki, M., Shinozaki, K., and Ohme-Takagi, M. (2007) NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis , Plant Cell, 19: 270-280. Matsuda, T., Kigawa, T., Koshiba, S., Inoue, M., Aoki, M., Yamasaki, K., Seki, M., Shinozaki, K., and Yokoyama, S. (2006) Cell-free synthesis of zinc-binding proteins. J Struct Funct Genomics, 7: 93-100. Ichimura, K., Casais, C., Peck, SC., Shinozaki, K., and Shirasu, K. (2006) MEKK1 is required for MPK4 activation and regulates tissue specific and temperature dependent cell death in Arabidopsis, J. Bio. Chem., 281: 36969-36976. Tran, P. L-S., Nakashima, K., Sakuma, Y., Fujita, Y., Osakabe, Y., Qin, F., Simpson, SD., Maruyama, K., Fujita, Y., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2007) Co-expression of the stressinducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances exporession of the ERD1 gene in Arabidopsis, Plant J., 49: 46-63. Sakuma, Y., Maruyama, K., Qin, F., Osakabe, Y., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006) Dual functiona of an Arabidopsis transcription factor DREB2A in water-stressresponsive and heat-stress-responsive gene expression, Proc. Natl. Acad. Sci. USA., 103: 18822-18827. Myouga, F., Motohashi, R., Kuromori, T., Nagata, N., and Shinozaki, K. (2006) An Arabidopsis chloroplast-targeted Hsp101 homolog, APG6, has an essential role in choloroplast development as well as heat stress response, Plant J., 48: 249-260. Oono, Y., Seki, M., Satou, M., Iida, K., Akiyama, K., Sakurai, T., Fujita, M., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays, Funct. Integr. Genomics, 6: 212-234 Gross, J., Cho, W-K., Lezhneva, L., Falk, J., Krupinska, K., Shinzoaki, K., Seki, M., Herrmann, R.G., and Meurer, J. (2006) A plant locus essential for phylloquinone (Vitamin K1) Biosynthesis orininated from a fusion of foure eubacterial genes, J. Biol. Chem., 281: 17189-17196. Machida, M., Takechi, K., Sato, H., Chung, S.J., Kuroiwa, H., Takio, S., Seki, M., Shinozaki, K., Fujita, T., Hasebe, M., and Takano, H. (2006) Gene for the peptidoglycan synthesis pathway are essential for chloroplast division in moss, Proc. Natl. Acad. Sci. USA., 103: 6753-6758. Nishiuchi, T., Masuda, D., Nakashita, H., Ichimura, K., Shinozaki, K., Yoshida, S., Kimura, M., Yamaguchi, I., and Yamaguchi, K. (2006) Fusarium phytotoxin trichothecenes have an elicitorlike activity in Arabidopsis thaliana , but the activity differed significantly among their molecular species., Mol Plant Microve Interact., 19: 512-520. Kitahata, N., Han, S-Y., Noji, N., Saito, T., Kobayashi, M., Nakano, T., Kuchitsu, K., Shinozaki, K., Yoshida, S., Matsumoto, S., Tsujimoto, M., and Asami, T. (2006) A 9-cis -epoxycarotenoid dioxygenase inhibitor for use in the elucidation of abscisic acid action mechanisms, Bioorganic & Medicinal Chem., 15: 5555-5561. Kuromori, T., Wada, T., Kamiya, A., Yuguchi, M., Yokouchi, T., Imura, Y., Takabe, H., Sakurai, T., Akiyama, K., Hirayama, T., Okada, K., and Shinzoaki, K. (2006) A trial of phenome analysis using 4000 Ds -insertional mutants in gene-coding regions of Arabidopsis , Plant J., 47: 640-651. Noutoshi, Y., Kuromori, T., Wada, T., Hirayama, T., Kamiya, A., Imura, Y., Yasuda, M., Nakashita, H., Shirasu, K., and Shinzoaki, K. (2006) Loss of NECROTIC SPOTTED LESIONS 1 associates with cell death and defense responses in Arabidopsis thaliana , Plant Mol. Biol., 62: 29-42. Sakuma, Y., Maruyama, K., Osakabe, Y., Qin, F., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006) Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell, 18:1292-1309. Hasegawa, Y., Seki, M., Mochizuki, Y., Heida, N., Hirosawa, K., Okamoto, N., Sakurai, T., Satou, M., Akiyama, K., Iida, K., Lee, K., Kanaya, S., Demura, T., Shinozaki, K., Konagaya, A., and Toyoda, T. (2006) A flexible representation of omic knowledge for thorough analysis of microarray data, Plant methods: 2,5. Yamasaki, K., Kigawa, T., Inoue, M., Yamasaki, T., Yabuki, T., Aoki, M., Seki, E., Matsuda, T., Tomo, Y., Terada, T., Shirouzu, M., Tanaka, A., Seki, M., Shinozaki, K., and Yokoyama, S. (2006) An Arabidopsis SBP-domain fragment with a disrupted C-terminal zinc-binding site retains its tertiary structure, FEBS Lett., 580: 2109-2116. Yoshida, R., Umezawa, T., Mizoguchi, T., Takahashi, S., Takahashi, F., and Shinozaki, K. (2006) The regulatory domain of SRK2E/OST1/SnRK2.6 interacts with ABI1 and integrates ABA and osmotic stress signals controlling stomatal closure in Arabidopsis , J. Bio. Chem., 281: 5310-5318. Furihata, T., Maruyama, K., Fujita, Y., Umezawa, T., Yoshida, R., Shinozaki,K., and Yamaguchi-Shinozaki, K. (2006) ABAdependent multisite phosphorylation regulates the activity of a transcription activation AREB1, Proc. Natl. Acad. Sci. USA., 103: 1988-1993. Umezawa, T., Okamoto, M., Kushiro, T., Nambara, E., Oono, Y., Seki, M., Kobayashi, M., Koshiba, T., Kamiya, Y., and Shinozaki, K. (2006) CYP707A3, a major ABA 8’-hydroxylase involved in dehydration and rehydration response in Arabidopsis thaliana , Plant J., 46: 171-182 ● Review Papers Shinozaki, K., and Yamaguchi-Shinozaki, K. (2007) Gene networks involved in drought stress response and tolerance. J. Exp Bot. 58: 221-227. RIKEN PSC 2007 Annual Report 67 Gene Discovery Research Group Gene Discovery Research Group Imura, Y., Takabe, H., Sakurai, T., Akiyama, K., Hirayama, T., Okada, K., and Shinozaki, K. (2006) A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis. Plant J, 47: 640-651 Yamaguchi-Shinozaki, K., Sakuma, Y., Ito Y., and Shinozaki, K. (2006) The DRE/DREB Regulon of gene expression in Arabidopsis and rice in response to erought and cold stress, Drought Adaptation in Cereals, Edted by Jean-Marcel Ribaut, Food Products Press: 583-597. Fujita, M., Fujita, Y., Noutoshi, Y., Takahashi, F., Narusaka, Y., Yamaguchi-Shinzoaki, K., and Shinozaki, K. (2006) Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks, Curr. Opin. Plant Biol., 9: 436-442. Seki, M., Umezawa, T., Kim, J.M., Matsui, A., To, T., and Shinozaki, K. (2006) Transcriptome analysis of plant drought and salt stress response, Advances in Molecular Breeding toward Drought and Salt Tolerant Crops, Edited by Drs. M.A. Jenks, P.M. Hasegawa and S.M. Jain., Springer Publishing., in press. Seki,M., Kamiya, A., Carninci, P., Hayashizaki, Y., and Shinozaki, K. (2006) Generation of full-length cDNA libraries from plant materials. In "Methods in Molecular Biology-ESTs (Edited by Dr. John Parkinson)". Humana Press Inc., NJ., in press. Taji T., Takahashi S., and Shinozaki K. (2006) Inositols and their metabolites in abiotic and biotic stress responses, Subcellular Biochemistry Vol 39 on Biology of Inositols and Phosphoinositides, Edetid by Arun Lahiri Majumder and B.B. Biswas: 239-264. Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006) Global analysis of gene networks to solve complex abiotic stress responses, Cold Hardiness in Plants; Molecular Genetics, Cell Biology and Physiology, Proceeding of 7th Internationa Plant Cold Hardiness Seminar in Sapporo Japan, Edited by T.H.H. Chen, M. Uemura and S. Fujikawa, CABI Publishing: 1-10. Umezawa, T., Fujita, M., Fujita, Y., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Enginieering drought tolerance in plants: 68 RIKEN PSC 2007 Annual Report discovering and tailoring genes to unlock the future, Curr.Opin. Biotech., 17: 113-122. Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006) Functional genomics for gene discovery in abiotic stress response and tolerance. Proceedings of Rice Functional Genomics 5 at IRRI, in press. Shinozaki, K., and Yamaguchi-Shinzoaki, K. (2006) Signaling and transcription networks in drought stress response, Keystone Symposia on Plant Responses to Abiotic Stress, Colorado, USA, April 8-13. ● Invited Presentations in Domestic Meetings 2 invited Japanese presentations Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses, Annual Review of Plant Biology, 57: 781-803. ■ Oral Presentations ● Invited Presentations in International Meetings Umezawa, T., Todaka, D., Totoki, Y., Sakurai, T., Seki, M., Toyoda, A., Maruyama, K., Nakashima, K., Mizukado, S., Kasuga, M., Ahmed, S, Sado, H., Harada, K., Tsubokura, Y., Sato, S., Anai, T., Ishimoto, M., Funatsuki, H., Teraishi, M., Shinano, T., Akashi, R., Sakaki, Y., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Construction of a soybean full-length cDNA library and oligonucleotide microarray, The KAZUSA Conference on legume Genetics and Genomics in Asia, Kisarazu, Japan, Nov. 27-28. Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Regulatory networks of gene expression in environmental stress response, GARNet 2006, Bristol, UK, Sep 11-12. Shinozaki, K. (2006) Functional genomics in RIKEN Plant Science Center for the improvement of plant productivity, PKU-CCASTRIKEN Joint Symposium-Life Science Panel, Beijing, China, Nov. 10. Seki, M., Ishida, J., Morosawa, T., Matsui, A., Kim, J.M., Nakajima, M., Enju, A., To, T., Iida, K., Go, M., Mochizuki, Y., Hasegawa, Y., Kaminuma, E., Toyoda, T., and Shinozaki, K. (2006) Arabidopsis shole-genome expression profiling under abiotic stress conditions, 8th International Congress of Plant Molecular Biology, Adelaide, Australia, Aug. 20-25. Shinzoaki, K., and Yamaguchi-Shinozaki, K. (2006) Regulatory networks in drought stress response and tolerance, 8th International Congress of Plant Molecular Biology, Adelaide, Australia, Aug. 20-25. Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006) Regulatory gene networks in drought stress responses and tolerance, Tropical Crop Biotechnology conference 2006, Cair ns Queensland, Australia, Aug. 16-19. Shinzoaki, K., and Yamaguchi-Shinozaki, K. (2006) Molecular responses and tolerance to drought stress in higher plants, The First International Conference on the Theory and Plactices in Biological Water Saving, Beijing, China, May 21-25. Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006) Gene networks involved in drought stress responses and tolerance, Bio Vision Alexandira, Alexandria, Egypt, 2006, Apri.26-29. ● Presentations in International Meetings Seki, M., Matsui, A., Kim, J-M., Ishida, J., Nakajima, M., Morosawa, T., Kawashima, M., Satou, M., Kim, T., Kurihara, Y., Kaminuma, E., Endo, T., Mochizuki, Y., Kobayashi, N., Toyoda, T., and Shinozaki, K. (2007) Arabidopsis whole-genome transcriptome analysis under drought, cold, high-salinity, and ABA treatment conditions using tiling array and 454 sequencing technology, 24th Symposium in Plant Biology on Gene Silincing: The Biology of Small RNAs and the Epigenome, Riverside, USA, Jan. 18-20. Todaka, D., Nakashima, K., Ito, Y., Ohme-Takagi, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2007) Functional Analysis of the OsPIF1 Gene Down-regulated by Drought Stress in Rice. ICGEB Meeting: Biotic and Abiotic Stress Responses in Plants, New Delhi, India, Dec 11-13. Maruyama, K., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2007) Comprehensive analysis of transcriptiome and metabolome under low-temperature and drought conditions, Gordon Research Conferences on Temperature Stress in Plants, Ventura, CA, USA, Jan 21-26. Kidokoro, S., Maruyama, K., Nakashima, K., Sakuma, Y., Imura, Y., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2007) Transcriptional regulation of the DREB1C gene in response to low temperature, Gordon Research Conferences on Temperature Stress in Plants, Ventura, CA, USA, Jan 21-26. Ito, Y., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2007) Comprehensive analysis of 10 DREB/CBF family genes in rice, Gordon Research Conferences on Temperature Stress in Plants, Ventura, CA, USA, Jan 21-26. Osakabe, Y., Mizuno, S., Shinozaki, K., and YamaguchiShinozaki, K. (2007) Functional analysis of a leucine-rich repeat receptor like kinase, RPK1, involved in ABA signal transduction of Arabidopsis , Gordon Research Conferences on Temperature Stress in Plants, Ventura, CA, USA, Jan 21-26. Qin, F., Sakuma, Y., Tran, L-S P., Osakabe, Y., Shinozaki, K., and Yamaguchi-Shinzoaki, K. (2007) The function and regulation of an Arabidopsis transcription factor DREB2A in plant water deficit and high temperature stresses, Gordon Research Conferences on Temperature Stress in Plants, Ventura, CA, USA, Jan 21-26. Nakashima, K., Tran, L-S Phan., Dong, NV., Fujita, M., Maruyama, K., Todaka, D., Ito, Y., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006) Functional analysis of NAC-type transcription factor OsNACC6 involved in abiotic stress-responsive gene expression in rice, 4th Internationa Rice Functional Genomics Symposium, Montpellier, France, Oct. 9-11. Fujita, Y., Fujita, M., Satoh, R., Maruyama, K., Sayama, H., Seki, M., Hiratsu, K., Ohme-Takagi, M., Shinzoaki, K., and YamaguchiShinozaki, K. (2006) AREB1 mediates novel ABRE-dependent ABA-signaling that enhances drought stress tolerance in Arabidopsis thaliana , 2006 Gordon Research Conference on Salt & Water Stress in Plants, Oxford, UK, Sep. 3-8. Tran, L-S., Urao, T., Qin, F., Osakabe, Y., Kakimoto T., Shinzoaki, K., and Yamaguchi-Shinozaki, K. (2006) Functional analyses of AtHK1, AHK2, AHK3 and AHK4.CRE1 in response to abiotic stress, 2006 Gordon Research Conference on Salt & Water Stress in Plants, Oxford, UK, Sep. 3-8. Urano, K., Maruyama, K., Takeda, M., Suzuki, H., Saito, K., Shibata, D., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Analysis of ABA-dependent metabolic networks in drought stress response, 2006 Gordon Research Conference on Salt & Water Stress in Plants, Oxford UK, Sep. 3-8. Ichikawa, H., Nakamura, H., Hakata, M., Kajikawa, M., Ando, S., Amano, S., Toki, N., Higashi, N., Fujita, M., Enju, A., Seki, M., Nakazawa, M., Ichikawa, T., Matsui, M., Shinozaki, K., Miyao, A., Toki, T., and Hirochika, H. (2006) FOX hunting system: a genomewide functional analysis of rice genes using transgenic plants, 8th International Congress of Plant Molecular Biology WorkShop, Adelaide, Australia, Aug. 20-25. Hakata, M., Nakamura, H., Asano, T., Kajikawa, M., Amano, K., Toki, N., Higashi, N., Fujita, M., Enju, A., Seki, M., Nakazawa, M., Ichikawa, T., Shinozaki, K., Matsui, M., Komatsu, S., Miyao, A., Toki, S., Hirochika, H., and Ichikawa, H. (2006) Genomewide functional analysis of rice genes using fox hunting system 2. Analysis and identificaiton of introduced cDNAs in the foxrice lines, 8th International Congress of Plant Molecular Biology, Adelaide, Australia, Aug. 20-25. Nakamura, H., Hakata, M., Kajikawa, M., Ando, S., Amano, K., Toki, N., Higashi, N., Fujita, M., Enju, A., Seki, M., Nakazawa, M., Ichikawa, T., Matsui, M., Shinzoaki, K., Miyao, A., Toki, T., Hirochika, H., and Ichikawa, H. (2006) Genome-wide functional analysis of rice genes using foc hunting system 1. Overview and current status, 8th International Congress of Plant Molecular Biology, Adelaide, Australia, Aug. 20-25. Kim, J.M., Kuromori, T., To, T., Hirayama, T., Seki, M., and Shinozaki, K. (2006) Functional analysis of AtORC1a in a phase progression, 8th International Congress of Plant Molecular Biology, Adelaide, Australia, Aug. 20-25. Yasuda, M., Ishikawa, A., Asami, T., Kamiya, Y., Shinozaki, K., Kudo, T., Yoshida, S., and Nakashita, H. (2006) Antagonistic interaction between environmental stress response and systemic acquired resistance in Arabidopsis , 8th International Congress of Plant Molecular Biology, Adelaide, Australia, Aug. 20-25. Myouga, F., Akiyama, K., Sakurai, T., Motohashi, R., and Shinozaki, K. (2006) Gene discovery for chloroplast proteins involved in drought tolerance in Arabidopsis using the RARGE database, 8th International Congress of Plant Molecular Biology, RIKEN PSC 2007 Annual Report 69 Gene Discovery Research Group Gene Discovery Research Group Itoh, T., Tanaka, T., Barrero, R.A., Yamasaki, C., Fujii, Y., Hilton, P.B., Antonio, B.A., Aono, H., Apweiler, R., Bruskiewich, R., Bureau, T., Burr, F., Fuks, G., Habara, T., Haberer, G., Han, B., Harada, E., Hiraki, A.T., Hirochika, H., Hoen, D., Hokari, H., Hosokawa, S., Hsing, Y.I., Ikawa, H., Ikeo, K., Imanishi, T., Ito, Y., Jaiswal, P., Kanno, M., Kawahara, Y., Kawamura, T., Kawashima, H., Khurana, J.P., Kikuchi, S., Komatsu, S., Koyanagi, K.O., Kubooka, H., Lieberherr, D., Lin, Y.C., Lonsdale, D., Matsumoto, T., Matsuya, A., McCombie, W.R., Messing, J., Miyao, A., Mulder, N., Nagamura, Y., Nam, J., Namiki, N., Numa, H., Nurimoto, S., O'Donovan, C., Ohyanagi, H., Okido, T., de Oliveira, A.C., Oota, S., Osato, N., Palmer, L.E., Quetier, F., Raghuvanshi,S.,Saichi ,N.,Sakai, H., Sakai, Y., Sakata, K., Sakurai, T., Sato, F., Sato, Y., Schoof, H., Seki, M., Shibata, M., Shimizu, Y., Shinozaki, K., Shinso, Y., Singh, N.K., Smith-White, B., Takeda, J., Tanino, M., Tatusova, T., Thongjuea, S., Todokoro, F., Tsugane, M., Tyagi, A.K., Vanavichit, A., Wang, A., Wing, R.A., Yamaguchi, K., Yamamoto, M., Yamamoto, N., Yu, Y., Zhang, H., Zhao, Q., Higo, K., Burr, B., Gojobori, T., and Sasaki, T. (2006) Curated Genome Annotation of Oryza sativa ssp. Japonica and Comparative Genome Analysis with Arabidopsis thaliana . Genome Res., in press. Adelaide, Australia, Aug. 20-25. Yoshida, T., Nishimura, N., Kitahata, N., Kuromori, T.,Kuroda, H., Matsui, M., Asami, T., Shinozaki, K., and Hirayama, T. (2006) ABA-hypersensitive germination3 encodes a protein phosphatase 2C (AtPP2CA) that strongly regulates abscisic acid signaling during germination among Arabidopsis protein phosphatase 2Cs, Plant Biology 2006, Boston, USA, Aug. 5-9. Hirayama, T., Tian, C., Tsuboi, Y., Chikayama, E., Sekiyama, Y., Kuromori, T., Shinozaki, K., and Kikuchi, J. (2006) Adcances in getero-nuclear NMR-based metabolomics approach in plant systems, Plant Biology 2006, Boston, USA, Aug. 5-9. Nishimura, N., Yoshida, T., Kitahata, N., Asami, T., Shinozaki, K., and Hirayama, T. (2006) Characterization of novel ABA hypersensitive mutant, ahg1 ,Plant Biology 2006, Boston USA, Aug. 5-9. Motohashi, R., Okada, E., Kuroda, H., Nagata, N., Matsui, M., and Shinozaki, K. (2006) Functional analysis or ribosome binding factor (RBFA) homologue using Ac/Ds transposon system in Arabidopsis thaliana . Plant Biology 2006, Boston, USA, Aug. 5-9. Katagiri, T., and Shinozaki, K. (2006) Functional analysis of phosphatidic acid during germination, 17th International Conference on Arabidopsis Research, Wisconsin-Madison, USA, June 28- July 2. Ichimura, K., Casais, C., Peck, S., Shinozaki, K., and Shirasu, K. (2006) MEKK1 negatively regulates tissue specific and temperature dependent cell death in Arabidopsis, 17th International Conference on Arabidopsis Research, WisconsinMadison, USA, June 28- July 2. Ichikawa, T., Nakazawa, M., Kondou, Y., Ishikawa, A., Kawashima, M., Iizumi, H., Seki, M., Fujita, M., Muto, S., Shinozaki, K., and Matsui, M. (2006) Evaluation of Arabidopsis FOX line: T2 phenotype and phenotype recapitulation by transformation, 17th International Conference on Arabidopsis Research, Wisconsin-Madison, USA, June 28- July 2. Tian, C., Tsuboi, Y., Chikayama, E., Sekiyama, Y., Kuromori, T., Shinozaki, K., Hirayama, T., and Kikuchi, J. (2006) An efficient strategy for the metabolic characterization of Arabidopsis mutants with visible and silent phenotypes by fast 1D-NMRscreening followed multi-dimensional NMR analysis, Metabolomics 2006 on the Second Scientific Meeting of the Metabolomics Society, Boston, USA, June 24-29. Hirayama, T., Tsuboi, Y., Shinozaki, K., and Kikuchi, J. (2006) Toward an NMR-based nutrigenomics assisted by stable isotope labeling of plants through animals, Metabolomics 2006 on the Second Scientific Meeting of the Metabolomics Society, Boston, USA, June 24-29. 70 RIKEN PSC 2007 Annual Report Hirayama, T., Tian, C., Tsuboi, Y., Chikayama, E., Sekiyama, Y., Kuromori, T., Shinozaki, K., and Kikuchi, J. (2006) Advances in getero-nuclear NMR-based metabolomics approach in plant systems, 20th IUBMB Internationa Congress of Biochemistry and Molecular Biology and 11th FAOBMB Congress, Kyoto, Japan, June 18-23. Seki, M., Ishida, J., Morosawa, T., Matusi, A., Kim, J.M., Nakajima, M., Enju, A., To, T., Iida, K., Go, M., Mochizuki, Y., Hasegawa, Y., Toyoda, T., and Shinzoaki, K. (2006) Arabidopsis whole-genome transcriptome analysis under abiotic stress conditions, The 16th Penn Atate Symposium in Plant Physiologyon RNA Biology: Novel Insights from Plant Systems, Penn State, USA, May 18-20. ● Presentations in Domestic Meetings 13 Japanese presentations ■ Patents Patent No : NA Country : USA Title of invention : A method for increasing stress-resistance to a plant Applicants : RIKEN, Ajinomoto Ltd. Name of Inventors : Taji, T., Shinozaki, K., and Ohsumi, C. Application date : 2001. 3.19 Issued date : 2006.7.18 Application Serial Number : 09/810186 Patent No : 6753461 Country : USA Title of invention : A method for increasing stress-resistance to a plant Applicants : RIKEN, Ajinomoto Ltd. Name of Inventors : Taji, T., Shinozaki, K., and Ohsumi, C. Application date : 2001. 1.12 Issued date : 2006.5.23 Application Serial Number : 09/758269 Patent No : 7049487 Country : USA Title of invention : Transgenic plants carrying Neoxanthin cleavage enzyme gene Applicants : RIKEN Name of Inventors : Iuchi, S., Kobayashi, M., and Shinozaki, K. Application date : 2006. 11.27 (Divisional) Issued date : NA Application Serial Number : 2006-318668 Patent No : NA Country : Japan Title of invention : Environmental stress responsive promoter Applicants : RIKEN Name of Inventors : Seki, M., and Shinozaki, K. ■ Press Releases Application date : 2006. 11.27 (Divisional) Issued date : NA Application Serial Number : 2006-318803 Patent No : NA Country : Japan Title of invention : Genes encoding transcription functions responsive to environmental stress Applicants : RIKEN Name of Inventors : Seki, M., and Shinozaki, K. ■ Award Application date : 2006. 10.20 Issued date: NA Application Serial Number : 2006-318803 Patent No : NA Country : Japan Title of invention : Environmental stress-responsive promoters and the methods to drive the tissue-specific gene expression using the promoters Applicants : RIKEN Name of Inventors : Seki, M., Kim, J.M., Shinozaki, K., Fujita, M., Enju, A., Kobayashi, H., and Nakajima, M. ■ Publications Application date : 2006. 9.5 Issued date : NA Application Serial Number : 11/470154 Succession in the development of environmental stress tolerant plant for both of dehydration and high temperature, Jan 11, 2007 Discovery of the novel MAP kinase cascade "MKK3-MPK6" that regulates the pathogen and wounding resistance in plants, Mar 19, 2007 Kazuo SHINOZAKI: 2006 MEXT minister awards for the promotion of science and technology Toyooka, K., Liu, F., Ishii, M., Saito, S., Kirikae, T., Asano, Y., and Shinomiya, H. (2006) Generation and characterization of monoclonal antibodies that specifically recognize p65/L-plastin isoform but not T-plastin isoform. Biosci. Biotechnol, Biochem., 70:1402-1407. Shinya, T., Menard, R., Kozone, I., Matsuoka, H., Shibuya, N., Kauffmann, S., Matsuoka, K., and Saito, M. (2006) Novel beta-1,3-, 1,6-oligoglucan elicitor from Alternaria alternata 102 for defense responses in tobacco. FEBS J., 273: 2421-2431. He, Y., Sugiura, R., Ma, Y., Kita, A., Deng, L., Takegawa, K., Matsuoka, K., Shuntoh, H., and Kuno, T. (2006) Genetic and functional interaction between Ryh1 and Ypt3: two Rab GTPases that function in S. pombe secretory pathway. Genes to Cells, 11: 207-221. Kasukabe, N., Watanabe-Sugimoto, M., Matsuoka, K., Okuma, E., Obi, I., Nakamura, Y., Shimoishi, Y., Murata, Y., and Kakutani, K. (2006) Expression and Ca2+ dependency of plasma membrane K+ channels of Tobacco suspension cells adapted to salt stress. Plant Cell Physiol., 47: 1674-1677. Shinya, T., Hanai, K., Suzuki, K., Matsuoka, K., Matsuoka, H., and Saito, M. (2007) Characterization of NtChitIV, a class IV chitinase induced by b -1,3-, 1,6-glucan elicitor from Alternaria alternata 102: Antagonistic effect of salicylic acid and methyl jasmonate on the induction of NtChitIV. Bioche. Biophys. Res. Commun., 353: 311-317. Matsuki, Y., Ohmura-Hoshino, M., Goto, E., Aoki, M., MitoYoshida,M., Uematsu, M., Hasegawa, T., Koseki, H., Ohara, O., Nakayama, M., Toyooka, K., Matsuoka, K., Hotta, H., Yamamoto, A., and Ishido, S. (2007) Novel regulation of MHC class II function in B cells. EMBO J., 26: 846-854. Nakagawa, T., Kurose, T., Hino, T., Tanaka, K., Kawamukai, M., Niwa, Y., Toyooka, K., Matsuoka, K., Jinbo, T., and Kimura, T. (2007) Development of the series of gateway binary vectors, pGWB, realize efficient construction of fusion genes for plant transformation. J. Biosci. Bioeng., in press. Taishi UMEZAWA: HFSP Short Term Fellowship Cell Function Research Team Team Leader : Ken MATSUOKA ● Book Edition Nagata,T., Matsuoka, K., and Inze, D. Ed. (2006) Biotechnology in Agriculture and Forestry 58: Tobacco BY-2 Cells: From Cellular Dynamics to Omics. ● Original Papers ● Book Chapters Toyooka, K., Moriyasu, Y., Goto, Y., Takeuchi, M., Fukuda, H., and Matsuoka, K. (2006) Protein aggregates are transported to vacuoles by macroautophagic mechanism in nutrient-starved plant cells. Autophagy, 2: 96-106. Toyooka, K., and Matsuoka, K. (2006) Autophagy and nonclassical vacuolar targeting in tobacco BY-2 cells. Biotechnology in Agriculture and Forestry 58: Tobacco BY-2 Cells: From Cellular Dynamics to Omics: 167-180. Galis, I., Simek, P., Narisawa, T., Sasaki, M., Horiguchi, T., Fukuda, H., and Matsuoka, K. (2006) A novel R2R3 MYB transcription factor NtMYBJS1 is a methyl jasmonate-dependent regulator of phenylpropanoid-conjugate biosynthesis in tobacco. Plant J., 46: 573-592. Matsuoka ,K., and Galis, I. (2006) EST and microarray analysis of tobacco BY-2 cells. Biotechnology in Agriculture and Forestry 58, Tobacco BY-2 cells: From Cellular Dynamics to Omics: 293-311. Matsuoka, H., Yamada, Y., Matsuoka, K., and Saito, M. (2006) High throughput microinjection technology for the single-cell RIKEN PSC 2007 Annual Report 71 Gene Discovery Research Group Gene Discovery Research Group Hayashi, S., Kuromoti, T., Shinozaki, K., and Hirayama, T. (2006) Analysis of an Arabidopsis root hair defective mutant shv3, Plant Biology 2006, Boston, USA, Aug. 5-9. Tsuboi, Y., Hirayama, T., Shinozaki, K., and Kikuchi, J. (2006) Toward an NMR-based nutrigenomics assisted by stable isotope labeling of plants through animals, 20th IUBMB Internationa Congress of Biochemistry and Molecular Biology and 11th FAOBMB Congress, Kyoto, Japan, June 18-23. analysis of BY-2 in vivo. Biotechnology in Agriculture and Forestry 58, Tobacco BY-2 cells: From Cellular Dynamics to Omics: 339-346. Aniento, F., Matsuoka, K., and Robinson, DG. (2006) ER-toGolgi transport: the COPII-Pathwayc in the plant endoplasmic reticulum. Plant Cell Monographs, 4: 99-124. ■ Oral Presentations ● Invited Presentation in International Meeting ● Invited Presentation in Domestic Meeting 1 invited Japanese presentation ● Presentations in International Meetings Toyooka, K., Galis, I., Goto, Y., and Matsuoka, K. (2006) Movement of Secretory Carrier Membrane Protein (SCAMP) during cell plate formation. 8th International Congress of Plant Molecular Biology, Australia. Inai, K., Sato, Y., Goto, Y., Toyooka, K., Matsuoka, K., and Hashimoto, T. (2006) Tobacco tonoplast transporters facilitate root-to-leaf transport of nicotine. 8th International Congress of Plant Molecular Biology, Australia. Matsuoka, K., Goto, Y., Takata, S., and Toyooka, K. (2006) Characterization of basic motif in the cytosolic region of Golgi type II membrane proteins allows the identification of probable plant-specific Golgi protein families. 8th International Congress of Plant Molecular Biology, Australia. Toyooka, K., Goto, Y., Galis, I., and Matsuoka, K. (2006) SCAMP (Secretory Carrier Mebrane Protein) is localized on phragmoplast in plant cell. 20th IUBMB International Congress of Biochemistry and Molecular Biology and 11th FAOBMB Congress, Japan. Galis, I., Toyooka, K., and Matsuoka, K. (2006) Monitoring of stress signals that induce autophagic pathway in plant cells. 20th IUBMB International Congress of Biochemistry and Molecular Biology and 11th FAOBMB Congress, Japan. Galis, I., Toyooka, K., and Matsuoka, K. (2006) Regulation of autophagy in tobacco cells by stress treatments. 15th Congress of the Federation of European Societies of Plant Biology (FESPB 2006), France. Galis, I., Toyooka, K., Goto, Y., and Matsuoka, K. (2006) Induction of autophagy by inhibitors of respiration in tobacco cells. 4th International Symposium on Autophagy, Japan. 72 RIKEN PSC 2007 Annual Report ● Presentations in Domestic Meetings Genetic Regulatory Systems Research Team Team Leader : Tatsuya SAKAI ■ Publications ● Original Paper Blakeslee, J. J., Bandyopadhyay, A., Lee, O. R., Mravec, J., Titapiwatanakun, B., Sauer, M., Makam, N.S., Cheng, Y., Bouchard, R., Adamec, J., Geisler, M., Nagashima, A., Sakai, T., Martinoia, E., Frim, J., Peer, W. A., and Murhy A. S. (2007). Interactions among PIN-FORMED and P-Glycoprotein auxin transporters in Arabidopsis. Plant Cell, 19:131-147. 3 Japanese presentations ■ Oral Presentations ■ Patent ● Invited Presentations in International Meetings 1 patent application Sakai, T. (2007) Light regulation of auxin transport and accumulation in Arabidopsis. RIKEN Plant Science Center International Symposium. Yokohama, Japan. Gene Expression Research Team Team Leader : Takuji WADA ■ Publications ● Original Papers Noutoshi, Y., Kuromori T., Wada, T., Hirayama, T., Kamiya, A., Imura, Y., Yasuda, M., Nakashita, H., Shirasu, K., and Shinozaki, K. (2006) Loss of NECROTIC SPOTTED LESION1 associates with cell death and defense responses in Arabidopthis taliana. Plant Mol. Biol., 62: 29-42. Stacey, N.J., Kuromori, T., Azumi, Y., Roberts, G., Breuer, C., Wada, T., Maxwell, A., Roberts, K., and Sugimoto-Shirasu, K. (2006) Arabidopsis SPO11-2 functions with SPO11-1 in meiotic recombination. Plant J., 48: 206-216. Kuromori, T*., Wada, T*, Kamiya, A., Yuguchi. M., Yokouchi, T., Imura , Y., Takabe, H., Sakurai, T., Akiyama, K., Hirayama, T., Okada, K., and Shinozaki, K. (2006) A trial of phenome analysis using 4000Ds-insertional mutants in gene-coding regions of Arabidopsis. Plant J., 47: 640-651. * These authors contributed equally to this study. ■ Oral Presentations Sakai, T. (2007) Functions of photoreceptors on the hypocotyl growth. International Symposium on Light regulation of Plant Growth and Development. Nara, Japan. ● Invited Presentation in Domestic Meeting 1 invited Japanese presentation ● Presentations in International Meetings Tsuchida-Mayama, T., Nakano, M., Fujisawa, N., Okada, K., and Sakai, T. (2006) Phot1 controls post-transcriptional regulations of signal transducers of phototropism, NPH3 and RPT2. International Plant Photobiology Meeting. Paris, France. Selected oral presentation. Nagashima, A., Suzuki, G., Saji, K., Okada, K., Sakai, T. (2006) Phytochromes and cryptochromes regulate hypocotyl-bending through the action of PGP19 in Arabidopsis. International Plant Photobiology Meeting. Paris, France. ● Presentations in Domestic Meetings 4 Japanese presentations ● Presentations in Domestic Meeting ● Award 2 Japanese presentations Akitomo, NAGASHIMA: Best Poster Award in International Plant Photobiology Meeting. ■ Patent Application date: 2006. 10.12 Issued Date: NA Application Serial Number: 2006-278988 Patent No: NA Country: Japan Title of invention: Method of generating fast-growing plants by mutating the CPL3 gene. Growth Regulation Research Team Team Leader : Yuji KAMIYA ■ Publications ● Original Papers Zhu,Y., Nomura, N., Xu, Y., Zhang, Y., Peng, Y., Mao, B., Hanada, A., Zhou, H., Wang, H., Li, P., Zhu, Mander, L.W., Kamiya, Y., Yamaguchi, S., and He, Z. (2006) ELONGATED UPPERMOST INTERNODE Encodes a Cytochrome P450 Monooxygenase That Epoxidizes Gibberellins in a Novel Deactivation Reaction in Rice. Plant Cell, 18: 442-456. Umezawa, T., Okamoto, M., Kushiro, T., Nambara, E., Oono, Y., Seki, M., Kobayashi, M., Koshiba, T., Kamiya, Y., and Shinozaki, K. (2006) CYP707A3, a major ABA 8’-hydroxylase involved in dehydration response in Arabidopsis thaliana . The Plant J., 46:171-182. Okamoto, T., Kuwahara, A., Seo, M., Kushiro, T., Asami, T., Hirai, N., Kamiya, Y., Koshiba, T., and Nambara, E. (2006) CYP707A1 and CYP707A2, which encode ABA 8’-hydroxylases, are indispensable for a proper control of seed dormancy and germination in Arabidopsis. Plant Physiology, 141: 97-107. Oh, E., Yamaguchi, S., Kamiya, Y., Bae, G., Chung, W.I., and Choi, G. (2006) Light activates the degradation of PIL5 protein to promote seed germination through gibberellin in Arabidopsis. The Plant J., 47: 124-139. Chono, M., Honda, I., Shinoda, S., Kushiro, T., Kamiya, Y., Nambara, E., Kawakami, N., Kaneko, S., and Watanabe, Y. (2006) Field studies on the regulation of abscisic acid content and germinability during grain development of barely: molecular and chemical analysis of pre-harvest sprouting. J. Exp. Bot., 57:2421-2434. Saito, S., Okamoto, M., Shinoda, S., Kushiro, T., Koshiba, T., Kamiya, Y., Hirai, N., Todoroki, Y., Sakata, K., Nambara, E., and Mizutani, M. (2006) A plant growth retardant, uniconazole, is a potent inhibitor of ABA catabolism in Arabidopsis. Biosci. Biotechnol. Biochem., 70:1731-1739. Seo, M., Hanada, A., Kuwahara, A., Endo, A., Okamoto, M., Yamauchi, Y., North, H., Marion-Pall, A., Sun, T-p., Koshiba, T., Kamiya, Y., Yamaguchi, S., and Nambara, E. (2006) Regulation of hormone metabolism in Arabidopsis seeds: phytochrome regulation of abscisic acid metabolism and abscisic acid regulation of gibberellin metabolism.The Plant J., 48: 354-366. . ● Book Edition 神谷勇治、南原英司、山口信次郎 (2006) Molecular Cell Biology of Plant Hormones. 植物ホルモンの分子細胞生物学、講談社サ イエンティフィック ● Review Paper Yamaguchi, S., Nambara, E., and Kamiya, Y. (2006) Seed Development, dormancy and germination. Ann Plant Review Vol27 Chapter 9 RIKEN PSC 2007 Annual Report 73 Growth Regulation Research Group Matsuoka, K. (2006) Role of basic amino acid residues in the cytosolic region of type II membrane proteins on Golgi localization in plant cells. Gordon Research Conference on Plant Cell Walls, USA Shinya, T., Galis, I., Narisawa, T., Sasaki, M., Fukuda, H., Menard, R., Kauffmann, S., Kozone, I., Shibuya, N., Matsuoka, K., Hideaki, M., and Saito, M. (2007) Defense responses induced by a novel beta-1,3-, 1,6-oligoglucan elicitor from Alternaria alternata 102 in tobacco BY-2 cells. XIII International Congress on Molecular Plant-Microbe Interactions, Italy. Applicants: RIKEN Name of Inventors: Tominaga, R., and Wada, T. Gene Discovery Research Group Gene Discovery Research Group Galis, I., and Matsuoka, K. (2007) Chapter 13: Transcriptomic analysis of salicylic acid-responsive genes in tobacco BY-2 cells Salicylic acid: A plant hormone : 371-396. Shinya, T., Galis, I., Narisawa, T., Sasaki, M., Fukuda, H., Menard, R., Kauffmann, S., Kozone, I., Shibuya, N., Matsuoka, K., Hideaki, M., and Saito, M. (2007) Defense responses induced by a novel beta-1,3-, 1,6-oligoglucan elicitor from Alternaria alternata 102 in tobacco BY-2 cells. Meiji University International Symposium "Plant Immunity: From MAMPs/PAMPs Recognition to Gene-for-Gene Resistance", Japan. ■ Oral Presentations ● Invited Presentations in International Meetings 2 invited oral presentations ● Invited Presentation in Domestic Meeting are indispensable for a proper control of seed dormancy and germination in Arabidopsis . Plant Physiol., 141: 97-107. Umezawa, T. Okamoto, M., Kushiro, T., Nambara, E., Oono, Y., Kobayashi, M., Koshiba, T., Kamiya, Y., and Shinozaki, K. (2006). CYP707A3, a major ABA 8’-hydroxylase involved in dehydration and rehydration response in Arabidopsis thaliana . Plant J., 46: 171-182. 1 invited Japanese presentation ● Presentations in International Meetings 4 English presentations ● Presentations in Domestic Meetings ■ Press Release Rice EUI gene encodes gibberellin epoxidase Gibberellin methyltransferase from Arabidopsis. Dormancy and Adaptation Research Team Team Leader : Eiji NAMBARA ■ Publications ● Original Papers Saika, H., Okamoto, M., Miyoshi, K., Kushiro, T., Shinoda, S., Jikumaru, Y., Fujimoto, M., Arikawa, T., Takahashi, H., Ando, M., Arimura, S., Miyao, A., Hirochika, H., Kamiya, Y., Tsutsumi, N., Nambara, E., and Nakazono, M. (2007). Ethylene promotes submergence-induced expression of OsABA8ox1, a gene that encodes ABA 8’-hydroxylase in rice. Plant Cell Physiol., 48: 287-298. Seo, M., Hanada, A., Kuwahara, A., Endo, A., Okamoto, M., Yamauchi, Y., North, H., Marion-Poll, A., Sun, T.-p., Koshiba, T., Kamiya, Y., Yamaguchi, S., and Nambara, E. (2006). Regulation of hormone metabolism in Arabidopsis seeds: Phytochromeregulation of abscisic acid metabolism and abscisic acidregulation of gibberellin metabolism. Plant J., 48: 354-366. Chono, M., Honda, I., Shinoda, S., Kushiro, T., Kamiya, Y., Nambara, E., Kawakami, N., Kaneko, S., and Watanabe, Y. (2006). Field studies in the regulation of abscisic acid content and germinability during grain development of barley: molecular and chemical analysis of pre-harvest sprouting. J. Exp. Bot., 57: 2421-2434. ● Book Editions Yamaguchi, S., Kamiya, Y., and Nambara, E. (2007). Regulation of ABA and GA levels during seed development and germination in Arabidopsis . Annu. Plant Reviews In Seed Development, Dormancy and Germination. (Bradford, K., and Nonogaki, H. (eds)) . ISBN: 1405139838 / ISBN13: 9781405139830. Blackwell Publishing, Oxford, UK,Chapter 9: 224-247. Okamoto, M., Kuwahara, A., Seo, M., Kushiro, T., Asami, T., Hirai, N., Kamiya, Y., Koshiba, T., Nambara, E. (2006). CYP707A1 and CYP707A2, which encode ABA 8’-hydroxylases, 74 RIKEN PSC 2007 Annual Report ■ Publications ● Original Papers Oh, E., Yamaguchi, S., Hu, J., Jikumaru, Y., Jung, B., Pail, I., Lee, H., Sun, T.-P., Kamiya, Y., and Choi, G. (2007) PIL5 regulates gibberellin responsiveness by directly binding to the GAI and RGA promoters in Arabidopsis seeds. Plant Cell, in press (E.O & S.Y. are co-first authors) Yamauchi, Y., Takeda-Kamiya, N., Hanada, A., Ogawa, M., Kuwahara, A., Seo, M., Kamiya, Y., and Yamaguchi, S. (2007) Contribution of gibberellin deactivation by AtGA2ox2 to the suppression of germination of dark-imbibed Arabidopsis thaliana seeds. Plant Cell Physiol, 48: 555-561. Jager, C.E., Symons, G.M., Nomura, T., Yamada, Y., Jennifer J. Smith, J.J., Yamaguchi, S., Kamiya, Y., Weller, J.L., Yokota, T., and Reid, J. B. (2007) Characterisation of two brassinosteroid C-6 oxidase genes in pea. Plant Physiol., 143: 1894-1904. Yamaguchi, S., and Nambara, E. (2006). Seed development and germination. Annu. Plant Reviews In Plant Hormone Signaling. (Hedden, P., and Thomas, S. (eds)). ISBN: 9781405138871/ ISBN10: 1405138874. Blackwell Publishing, Oxford, UK,Chapter 11: 311-338. Varbanova, M., Yamaguchi, S., Yang, Y., McKelvey, K., Hanada, A., Borochov, R., Yu, F., Jikumaru, Y., Ross, J., Cortes, D., Je Ma, C., Noel, JP., Mander, L., Shulaev, V., Kamiya, Y., Rodermel, S., Weiss, D., and Pichersky, E. (2007) Methylation of gibberellins by Arabidopsis GAMT1 and GAMT2. Plant Cell, 19: 32-45. ● Review Paper Asahina, M., Yamauchi, Y., Hanada, A., Kamiya, Y., Kamada, H., Satoh, S., and Yamaguchi, S. (2007) Effects of the removal of cotyledons on endogenous gibberellin levels in hypocotyls of young cucumber and tomato seedlings. Plant Biotechnol., 24: 99-106. Schroeder, J.I., and Nambara, E. (2006). A quick release mechanism for abscisic acid. Cell, 126: 1023-1025. ■ Oral Presentations ● Invited Presentations in International Meetings 2 invited presentations ● Invited Presentation in Domestic Meeting 1 invited Japanese presentation ● Presentations in International Meetings Seo, M., Hanada, A., Kuwahara, A., Endo, A., Okamoto, M., Yamauchi, Y., North, H., Marion-Poll, A., Sun, TP., Koshiba, T., Kamiya, Y., Yamaguchi, S., and Nambara,E. (2006) Regulation of hormone metabolism in Arabidopsis seeds: phytochrome regulation of abscisic acid metabolism and abscisic acid regulation of gibberellin metabolism. Plant J., 48: 354-366. Oh, E., Yamaguchi, S., Kamiya, Y., Bae, G., Chung, W., and Choi, G. (2006) Light activates the degradation of PIL5 protein to promote seed germination through gibberellin in Arabidopsis. Plant J., 47: 124-139. 3 presentations ● Presentations in Domestic Meetings 5 Japanese presentations Saito, S., Okamoto, M., Shinoda, S., Kushiro, T., Koshiba, T., Hirai, N., Sakata, K., Nambara, E., and Mizutani, M. (2006). A plant growth retardant uniconazole is a potent inhibitor of ABA catabolism in Arabidopsis . Biosci. Biotech. Biochem., 70: 1731-1739. Team Leader : Shinjiro YAMAGUCHI ■ Award Eiji NAMBARA: 2006 Japanese Society of Plant Physiologists Young Scientist Award ● Review Papers Yamaguchi, S., Kamiya, Y., and Nambara, E. (2006) Regulation of ABA and GA Levels during Seed Development and Germination in Arabidopsis. In “Seed development, Dormancy and Germination” (K. Bradford and H. Nonogaki eds., Blackwell Publishing, Oxford, UK), Annual Plant Reviews, 27: 224-247 Bishop, G., Nomura, T., Yokota, T., Montoya, T., Castle, J., Harrison, K., Kushiro, T., Kamiya, Y., Yamaguchi, S., Bancos, S., Szatmari, AM., and Szekeres, M. (2006) Dwarfism and cytochrome P450-mediated C-6 oxidation of plant steroid hormones. Biochem Soc Trans. 34: 1199-1201. Nomura,T., and Bishop, G. (2006) Cytochrome P450s in plant steroid hormone synthesis and metabolism. Phytochemistry Reviews, 5: 421-432. ■ Oral Presentations ● Invited Presentations in International Meetings Yamaguchi, S. (2006) Regulation of gibberellin biosynthesis and deactivation. The 6th Symposium on Plant Metabolism: Kyung Hee University, Suwon, Korea, August. Yamaguchi, S. (2006) Regulation of gibberellin deactivation reactions in plants. Crop Functional Genomics 2006: Seoul, Korea, June . ● Presentations in International Meetings Nomura, T., Zhu, Y., Yamauchi, Y., Magome, H., Kamiya, Y., He, Z., and Yamaguchi, S. (2006) A novel gibberellin deactivation enzyme in plants: International Congress on Plant Molecular Biology, Adelaide, Australia. Asahina, M., Satoh, S., Kamada, H., Yamauchi, Y., Hanada, A., Kamiya, Y., and Yamaguchi, S. (2006) Biosynthesis of gibberellins in cotyledons is required for tissue-reunion in cucumber and tomato hypocotyl: International Symposium on Tomato Genome Research, Tsukuba, Japan. Nomura, T., Kushiro, T., Yokota, T., Kamiya, Y., Bishop, G., and Yamaguchi, S. (2006) Cytochrome P450 enzymes that produce plant steroid hormone, brassinosteroid, in tomato fruits: International Symposium on Tomato Genome Research, Tsukuba, Japan. Yamazaki, T., Asahina, M., Yamaguchi, S., and Satoh, S. (2006) Morphological and gene expression analysis of tissue-reunion process in the Arabidopsis cut flowering stem: International Congress on Plant Molecular Biology, Adelaide, Australia. Toh, S., Imamura, A., Okamoto, M., Hanada, A., Yamaguchi, S., Kamiya, Y., Nambara, E., and Kawakami, N. (2006) Regulation of ABA and GA action by high temperature in Arabidopsis seeds: International Congress on Plant Molecular Biology, Adelaide, Australia. Magome, H., Yamaguchi, S., Kamiya, Y., and Oda, K. (2006)Overexpression of DDF1 , but not DREB1A , causes GA deficiency in Arabidopsis: International Congress on Plant Molecular Biology, Adelaide, Australia. ● Presentations in Domestic Meetings 10 Japanese presentations ■ Patents Application date : 2007. 3.27 Issued Date : NA Application Serial Number : 2007-82193 Patent No : NA RIKEN PSC 2007 Annual Report 75 Growth Regulation Research Group Growth Regulation Research Group 9 Japanese presentations Lefebvre,V., North, H., Frey, A., Sotta, B., Seo, M., Okamoto, M., Nambara, E., and Marion-Poll, A. (2006). Functional analysis of Arabidopsis NCED6 and NCED9 genes indicates that ABA synthesised in the endosperm is involved in the induction of seed dormancy. Plant J., 45: 309-319. Cellular Growth and Development Research Team Country : Japan Title of invention : Steviol biosynthesis enzyme Applicants : RIKEN Name of Inventors : Yamaguchi, S., Nomura, T., Magome, H., and Kamiya, Y. ■ Press Release Discovery of a new enzyme that inactivates a plant growth hormone: generation of mini-plants (Jan. 2007). Metabolic Function Research Team Team Leader : Kazuki SAITO ■ Publications Growth Regulation Research Group ● Original Papers Hatayama, M., Ono, E., Yonekura-Sakakibara, K., Tanaka, Y., Nishino, T., and Nakayama, T. (2006) Biochemical characterization and mutational studies of a chalcone synthase from yellow snapdragon (Antirrhinum majus ) flowers. Plant Biotech, 23: 373-378. Noji, M., Cintia Goulart Kawashima, Obayashi, T., and Saito, K.(2006) In Silico assessment of gene function involved in cysteine biosynthesis in Arabidopsis: Expression analysis of multiple isoforms of serine acetyltransferase. Amino Acids, 30: 163-171. Nakajima, J., Sato, Y., Hoshino, T., Yamazaki, M., and Saito, K. (2006) Mechanistic study on the oxidation of anthocyanidin synthase by quantum mechanical calculation. J. Biol. Chem., 281: 21387-21398. Higashi, Y., Hirai, M. Y., Fujiwara, T., Naito, S., Noji, M., and Saito, K. (2006) Proteomics and transcriptomic analysis of Arabidopsis seeds: Molecular evidence for successive processing of seed proteins and its implication in stress response to sulfur nutrition. Plant J., 48: 557-571. Yano, M., Kanaya, S., Altaf-Ul-Amin, Md., Kurokawa, K., Hirai, M. Y., and Saito, K. (2006) Integrated data mining of transcriptome and metabolome based on BL-SOM. J. Comp. Aid. Chem., 7: 125-136. Obayashi, T., Kinoshita, K., Nakai, K., Shibaoka, M., Hayashi, S., Saeki, M., Shibata, D., Saito, K., and Ohta, H. (2007) ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res., 35: D863-869. Li-Yang, J., Nakajima, J., Kimura, N., Saito, K., and Seo, S. (2007) Oleanane-type triterpene glycosides from Glychyrrhiza ularensis . Nat. Prod. Comm., 2, 243-248. 76 RIKEN PSC 2007 Annual Report Hirai, M. Y., Sugiyama, K., Sawada, Y., Tohge, T., Obayashi, T., Suzuki, A., Araki, R., Sakurai, N., Suzuki, H., Aoki, K., Goda, H., Nishizawa, O. I., Shibata, D., and Saito, K. (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc. Natl. Acad. Sci., USA., 104: 6478-6483. Tohge, T., Yonekura-Sakakibara, K., Niida, R., and WatanabeTakahashi, A., and Saito, K. (2007) Phytochemical genomics in Arabidopsis thaliana : A case study for functional identification of flavonoid biosynthesis genes. Pure and Applied Chemistry, 79: 811-823. Yonekura-Sakakibara, K., Tohge, T., Niida, R., and Saito, K. (2007) Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression and reverse genetics. J Biol. Chem., 282: 14932-14941. ● Review Papers Yonekura- Sakakibara, K., and Saito, K. (2006) Review: Genetically modified plants for the promotion of human health. Biotech Lett, 28, 1983-1991 Yamazaki, M., and Saito, K. (2006) Isolation and characterization of anthocyanin 5-O -glucosyltransefrase in Perilla frutescens var. crispa by differential display. Methods in Molecular Biology, vol. 317: Differential Display Methods and Protocols. Eds by P. Liang, J.D. Meade and A.B. Pardee, Humana Press Inc. Totowa, NJ, 255-266. Asano, T., Sudo, H., Yamazaki, M., and Saito, K. (2007) Camptothecin production in cell cultures of Ophiorrhiza species. In “Medicinal Plant Biotechnology - From Basic Research to Industrial Applications” Vol. 2, Oliver Kayser and Wim Quax, eds: pp. 451-468, WILEY-VCH Verlag, Weinheim. Tohge, T., Nishiyama, Y., Hirai, M. Y., Yano, M., Nakajima, J., Awazuhara, M., Inoue, E., Takahashi, H., Goodenowe, D. B., Kitayama, M., Noji, M., Yamazaki, M., and Saito, K.(2007) Identification of Genes Involved in Anthocyanin Accumulation by Integrated Analysis of Metabolome and Transcriptome in Pap1 -Overexpressing Arabidopsis Plants. In “ Concepts in Plant Metabolomics” Basil J. Nikolau, Eve Syrkin Wurtele, eds: pp. 159-168, Springer, Heidelberg. Yonekura-Sakakibara, K., Nakayama, T., Yamazaki, M., and Saito, K. (2007) Modification and stabilization of anthocyanins. In Anthocyanin book, in press. 4 review chapters in Japanese. ■ Oral Presentations ■ Press Release ● Invited Presentations in International Meetings Journal of Biological Chemistry, Feb 22, 2007, Identification of a gene encoding an enzyme which determines flavonoid patterns in Arabidopsis. Saito,K. (2006) Integration of omics datasets towards metabolomics-based plant systems biology. 4th International Conference on Plant Metabolomics. Reading, Berkshire, UK, April 7-10. Metabolic Diversity Research Team Team Leader : Toshiya MURANAKA Saito,K. (2006) Metabolomics towards phytochemical genomics. The 53rd NIBB Conference. Dynamic Organelles in Plants. Okazaki, Japan, June 14-17. ■ Publications Saito,K. (2006) Integration of transcriptome and metabolome for study on plant natural product biosynthesis. ICOB-5& ISCNP-25 IUPAC International Conference on Biodiversity and Natural Products (IUPAC-2006). Kyoto, Japan, July 23-28. Kobayashi, K., Suzuki, M., Tang, J., Nagata, N., Ohyama, K., Seki, H., Kiuchi, R., Kaneko, Y., Nakazawa, M., Matsui, M., Matsumoto, M., Yoshida, S., and Muranaka, T. (2007) LOVASTATIN INSENSITIVE 1, a novel pentatricopeptide repeat protein, is a potential regulatory factor of isoprenoid biosynthesis in Arabidopsis. Plant Cell Physiol., 48:322-331. Saito,K., Asano,T., Sudo,H., Sirikantaramas,S., Kitayama,M., and Yamazaki,M. (2006) Gene discovery and pathway elucidation for camptothecin biosynthesis in Ophiorrhiza pumila. 8th International Congress of Plant Molecular Biology. Adelaide, Australia, August 20-25. Saito,K., Hirai,M.Y., Tohge,T., Yonekura-Sakakibara,K., Obayashi,T., Yano,M., Morioka,R., and Kanaya,S. (2006) Towards plant systems biology by metabolome-transcriptome integration. 8th International Congress of Plant Molecular Biology. Adelaide, Australia, August 20-25. Hirai,M.Y., and Saito,K. (2006) Comprehensive functional elucidation of the genes involved in glucosinolate biosynthesis. 1 st International meeting on glucosinolates. Jena, Germany, September 10-13. Saito,K. (2006) Metabolomics-based functional genomics highway in plants. International Workshop Plant Biotechnology for Production of Industrial Materials. Osaka, Japan, September 14. ● Original Papers Kohara, A., Nakajima, C., Yoshida, S., and Muranaka, T. (2007) Characterization and engineering of glycosyltransferases responsible for steroidal saponin biosynthesis in Solanaceous plants. Phytochem, 68: 478-486. Suzuki, M., and Muranaka, T. (2006) Molecular genetics of plant sterol backbone biosynthesis. Lipids, 42: 47-54. Rahman, L., Kitamura, Y., Yamaguchi, J., Mukai, M., Akiyama, K., Yamamoto, H., Muranaka, T., and Ikenaga, T. (2006) Exogenous plant H6H but not bacterial HCHL gene is expressed in Duboisia leichhardtii hairy roots and affects tropane alkaloid production. Enzyme and Microbial Technology, 39: 1183-1189. Suzuki, M., Xiang, T., Ohyama, K., Seki, H., Saito, K., Muranaka, T., Hayashi, H., Katsube, Y., Kushiro, T., Shibuya, M., and Ebizuka, Y. (2006) Lanosterol synthase in dicotyledonous plants. Plant Cell Physiol., 47: 565-571. Saito,K. (2006) Metabolomics-based plant functional genomics highway. The 4th Matsuyama International Symposium on CellFree Sciences. Matsuyama, Japan, October 6. Kojoma, M., Seki, H., Yoshida, S., and Muranaka, T. (2006) DNA polymorphisms in the tetrahydrocannabinolic acid (THCA) synthase gene in “drug-type” and “fiber-type” Cannabis sativa L. Forensic Science International, 159: 132-140. ● Invited Presentations in Domestic Meetings ● Review Papers 3 invited Japanese presentations 鈴木優志、村中俊哉 (2006) 植物ステロールの新しい生合成経 路 . 化学と生物 44: 806-807 ● Presentation in International Meeting Yonekura-Sakakibara K., Tohge T., Shibata M., Niida R., and Saito K. (2006) Functional Identification of Arabidopsis Flavonoid 7-O -Rhamnosyltransferase Gene by Co-expression Analysis. 17th International conference on Arabidopsis research, Madison USA, June 28-July 2. 關光、村中俊哉 (2006) 毛状根培養系の新展開∼物質生産研 究 20 年目に当たり . バイオサイエンスとインダストリー 64: 17-22 村中俊哉、小原淳子 (2006) 植物ステロイドの糖転移酵素 配 糖化に関わる遺伝子の解明により毒と薬の生産制御に期待 . 化 学と生物 44: 6-7 ● Presentation in Domestic Meeting 1 Japanese presentation RIKEN PSC 2007 Annual Report 77 Metabolic Function Research Group Metabolic Function Research Group Ono, E., Fukuchi-Mizutani, M., Nakamura, N., Fukui, Y., Yonekura-Sakakibara, K., Yamaguchi, M., Nakayama, T., Tanaka, T., Kusumi, T., and Tanaka, Y. (2006) Yellow flowers generated by expression of the aurone biosynthetic pathway. Proc Natl Acad Sci USA, 103: 11075-11080. Luo, J., Nishiyama, Y., Fuell, C., Taguchi, G., Elliott, K., Hill, L., Tanaka, Y., Kitayama, M., Yamazaki, M., Bailey, P., Parr, A., Michael, A. J., Saito, K., and Martin, C. (2007) Convergent evolution in the BAHD family of acyl transferases; identification and characterisation of anthocyanin acyl transferases from Arabidopsis thaliana . Plant J., in press. ■ Oral Presentations ● Invited Presentations in International Meetings Muranaka, T. (2007) “Comprehensive analysis of KO-mutants of sterol backbone synthesis toward understanding gametophyte development.” POSTECH Science Seminar, Pohang, Korea, February. Muranaka, T. (2006) “Strategy of RIKEN PSC to deal with GM plants: Study on metabolic systems from model plants to applied plants.” Bio2Biz Conference South Africa, Durban, South Africa, September. Muranaka, T. (2006) “Toward comprehensive understanding of sterol biosynthesis in higher plants.” 97th American Oil Chemical Society Annual Meeting, St. Louis, USA, April. ● Invited Presentations in Domestic Meetings 2 invited Japanese presentations ● Presentations in International Meetings contribution of AMT1;1 and AMT1;3 to ammonium uptake across the plasma membrane of nitrogen-deficient Arabidopsis roots. Plant J., 48: 522-534. Ishiyama, K., Inoue, E., Yamaya, T., and Takahashi, H. (2006). Gln-49 and Ser-174 residues play critical roles in determining the catalytic efficiencies of plant glutamine synthetase. Plant Cell Physiol., 47: 299-303. ● Review Papers Takahashi, H., and Saito, K. (2007). Molecular biology and functional genomics for identification of regulatory networks of plant sulfate uptake and assimilatory metabolism. in "Advances in Photosynthesis and Respiration - Sulfur Metabolism in Phototrophic Organisms" (Christiane Dahl, Rüdiger Hell, David Knaff, Thomas Leustek, eds., Springer) in press. Takahashi, H., Yoshimoto, N., and Saito, K. (2006). Anionic nutrient transport in plants: the molecular bases of sulfate transporter gene family. Genetic Engineering (J.K. Setlow, ed., Springer) 27, 67-80. 2 Japanese review articles. Title of invention: Plant genetic engineering using a regulatory factor of sulfur assimilation. Applicants: RIKEN Name of Inventors : Maruyama-Nakashita, A., Nakamura, Y., Saito, K., and Takahashi, H. ■ Press Release Discovery of a transcription factor regulating plant sulfur metabolism - transcription factor “SLIM1” is essential for controlling production of sulfur metabolites beneficial for cancer prevention - (November, 2006). Biodynamics Research Team Team Leader : Hitoshi SAKAKIBARA ■ Publications ● Original Papers Unno, H., Uchida, T., Sugawara, H., Kurisu, G., Sugiyama, T., Yamaya, T., Sakakibara, H., Hase, T., and Kusunoki, M. (2006) Atomic structure of maize glutamine synthetase: a key enzyme for plant productivity. J. Biol. Chem., 281: 29287-29296. ● Presentations in Domestic Meetings ■ Oral Presentations 18 Japanese presentations ● Invited Presentation in International Meeting ■ Patent Takahashi, H. (2007). Molecular biology of plant sulfur nutrition. China-Japan Joint Workshop on Plant Molecular Breeding. Beijing, China, March. Plant Nutrition and Basal Metabolism Research Team Team Leader : Hideki TAKAHASHI ■ Publications ● Original Papers Maruyama-Nakashita, A., Inoue, E., Saito, K., and Takahashi, H. (2007). Sulfur-responsive promoter of sulfate transporter gene is potentially useful to detect and quantify selenate and chromate. Plant Biotechnol.,24: 261-263. Maruyama-Nakashita, A., Nakamura, Y., Tohge, T., Saito, K., and Takahashi, H. (2006). Arabidopsis SLIM1 is a central transcriptional regulator of plant sulfur response and metabolism. Plant Cell,18: 3235-3251. Loqué, D., Yuan, L., Kojima, S., Gojon, A., Wirth, J., Gazzarrini, S., Ishiyama, K., Takahashi, H., and von Wirén, N. (2006). Additive 78 RIKEN PSC 2007 Annual Report ● Presentations in International Meetings Maruyama-Nakashita, A., Nakamura, Y., Saito, K., and Takahashi, H. (2006). SLIM1, a novel transcription factor regulating sulfur limitation response. Keystone Symposia on Plant Responses to Abiotic Stress. Copper Mountain, Colorado, USA, April. Maruyama-Nakashita, A., Nakamura, Y., Tohge, T., Saito, K., and Takahashi, H. (2006). SLIM1/EIL3 transcription factor required for plant growth on low sulfur environment. 17th International Conference on Arabidopsis Research. Madison, Wisconsin, USA, July. Yuan, L., Loqué, D., Gojon, A., Takahashi, H., Kojima, S., and von Wirén, N. (2006). "Job sharing" among AMT-type ammonium transporters in Arabidopsis. 15th Congress of the Federation of European Societies in Plant Biology (FESPB 2006). Lyon, France, July. ● Presentations in Domestic Meetings 6 Japanese presentations ■ Patent Application date: 2006. 4. 7. Issued Date: NA Application Serial Number: 2006-106250 Patent No: NA Country: Japan Itouga, M., Suzuki, T., Komatsu, Y., Yamaguchi, I., Shiraishi, T., Ono, Y., and Sakakibara, H. (2006) Effect of some leaching waters from ashes of municipal waters on protonemal cell division of Funaria hygrometrica Hedw. Bryol. Res., 9: 78-83. (in Japanese with English abstract) Martin, A., Lee, J., Kichey, T., Gerentes, D., Zivy, M., Tatout, C., Dubois, F., Balliau, T., Valote, B., Davanture, M., Tercé-Laforgue, T., Quilleré, I., Coque, M., Gallais, A., Gonzalez-Moro, M., Bethencourt, L., Habash, D. Z., Lea, P. J., Charcosset, A., Perez, P., Murigneux, A., Sakakibara, H., Edwards, K. J., and Hirel, B. (2006) Two cytosolic glutamine synthetase isoforms of maize (Zea mays L.) are specifically involved in the control of grain production. Plant Cell, 18: 3252-3274. Itouga, M., Komatsu-Kato, Y., Yamaguchi, I., Ono, Y., and Sakakibara, H. (2006) Phytoremediation using bryophytes, 2.: Bryofiltration of copper in water using two species of Scopelophila. Hikobia, 14: 413-418. Sudo, E., Itouga, M., Yoshida, K., Ono, Y., and Sakakibara, H. (2006) Mitigation of Cu-toxicity through “bryo-filtration”: An evaluation with rice leaf photosynthesis and gene expression profile. Hikobia, 14: 419-429. Yokoyama, A., Yamashino, T., Amano, Y., Tajima, Y., Imamura, A., Sakakibara, H., and Mizuno, T. (2007) Type-B ARR transcription factors, ARR10 and ARR12, are implicated in cytokinin-mediated regulation of protoxylem differentiation in roots of Arabidopsis thaliana . Plant Cell Physiol., 48: 84-96. Hirose, N., Makita, N., Kojima, M.,Kamada-Nobusada, T., and Sakakibara, H. (2007) Over-expression of a type-A response regulator alters rice morphology and cytokinin metabolism. Plant Cell Physiol., 48: 523-539. ● Review Papers Sakakibara, H., Takei, K., and Hirose, N. (2006) Interactions between nitrogen and cytokinin in the regulation of metabolism and development. Trends in Plant Science, 11: 440-448. Sakakibara, H. (2006) Cytokinin. In Natural Chemistry: Plants (Ed. Yamamura, S., and Hasegawa, H.) 17-25. IPC Inc., Tokyo. (in Japanese) Takei, K., and Sakakibara, H. (2006) Nitrogen signaling mediated by cytokinin. In Plant Mimetics (Ed. Kai, M., and Morikawa, H.) 197-202. NTS Inc., Tokyo. (in Japanese) ■ Oral Presentations ● Invited Presentations in International Meetings Sakakibara, H., Hirose, N., Nobusada-Kamada, T., Takei, K., and Makita, N. (2006) Overview of genes involved in cytokinin metabolism in rice. The Third Rice Annotation Project Meeting (NIAS) Tsukuba, Japan, December Sakakibara, H. (2007) Regulation of cytokinin action: synthesis and activation. RIKEN Plant Science Center International Symposium-Trends in Plant Hormones- Yokohama, Japan, March Sakakibara, H. (2007) Regulation of cytokinin metabolism in Arabidopsis and rice. China-Japan Joint workshop on Plant Molecular Bleeding, Beijing, China, March ● Invited Presentations in Domestic Meetings 3 invited Japanese presentations ● Presentations in International Meetings Hirose, N., Makita, N., Kojima, M., and Sakakibara, H. (2006) Genomic analysis of the cytokinin response in Rice: analyses of a type-A response regulator, OsRR6. FESPB 2006, Lyon, France, July RIKEN PSC 2007 Annual Report 79 Plant Productivity Systems Research Group Application date : 2006. 7.13 Issued Date : NA Application Serial Number : 2006-192301 Patent No : NA Country : Japan Title of invention : Lanosterol synthase Applicants : RIKEN, Univ. Tokyo, Nihon Univ. Name of Inventors : Muranaka, T., Suzuki, M., Ebizuka, Y., Shibuya, M., Xiang, T., Aoki, T., and Ayabe, S. Sakamoto, T., Sakakibara, H., Kojima, M., Yamamoto, Y., Nagasaki, H., Inukai, Y., Sato, Y., and Matsuoka, M. (2006) Ectopic expression of KNOX homeodomain protein induces expression of cytokinin biosynthesis gene in rice. Plant Physiol., 142: 54-62. Iwama, A., Yamashino, T., Tanaka, Y., Sakakibara, H., Kakimoto, T., Hirayama, T., Sato, S., Kato, T., Tabata, S., Nagatani, A., and Mizuno, T. (2007) AHK5 His-kinase regulates root elongation through an ETR1-dependently integrated abscisic acid and ethylene signaling pathway in Arabidopsis thaliana . Plant Cell Physiol., 48: 375-380. Metabolic Function Research Group Metabolic Function Research Group 11 International presentations Kurakawa, T., Ueda, N., Maekawa, M., Kobayashi, K., Kojima, M., Nagato, Y., Sakakibara, H., and Kyozuka, J. (2007) Direct control of shoot meristem activity by a cytokinin activating enzyme. Nature, 445: 652-655. Kurakawa, T., Ueda, N., Maekawa, M., Kobayashi, K., Kojima, M., Nagato, Y., Sakakibara, H., and Kyozuka, J. (2007) Direct control of shoot meristem activity by a cytokinin activating enzyme. RIKEN Plant Science Center International Symposium-Trends in Plant Hormones- Yokohama, Japan, March Kuroha, T., and Sakakibara, H. (2007) Molecular characterization of Arabidopsis LOG family genes encoding cytokinin activating enzymes. RIKEN Plant Science Center International SymposiumTrends in Plant Hormones- Yokohama, Japan, March Takei, K., Kojima, M., and Sakakibara, H. (2007) Analysis of the genes encoding cytokinin hydroxylase in Arabidopsis. RIKEN Plant Science Center International Symposium-Trends in Plant Hormones- Yokohama, Japan, March Nobusada-Kamada, T., Takei, K., Hirose, N., Makita, N., Kojima, M., and Sakakibara, H. (2007) Identification of nitrogen-inducible isopentenyltransferase genes in rice. RIKEN Plant Science Center International Symposium-Trends in Plant Hormones- Yokohama, Japan, March ● Presentations in Domestic Meetings M., and Fukuda, H. (2006) Isolation and characterization of a novel peroxidase gene ZPO -C of which expression and function are closely associated with lignification during tracheary element differentiation. Plant Cell Physiol., 47: 493-503. Muto, H., Nagao, I., Demura, T., Fukuda, H., Kinjo, M., and Yamamoto, K. (2006) Fluorescence cross-correlation analyses of the molecular interaction between an Aux/IAA protein, MSG2/ IAA19, and protein-protein interaction domains of auxin response factors of Arabidopsis expressed in HeLa cells. Plant Cell Physiol., 47: 1095-1101. Zhou, G.-K., Kubo, M., Zhong, R., Demura, T., and Ye, Z.-H. (2007) Overexpression of miR165 affects apical meristem formation, organ polarity establishment, and vascular development in Arabidopsis . Plant Cell Physiol., 48: 391-404. Zhong, R., Demura, T., and Ye, Z.-H. (2006) SND1, a NAC domain transcription factor, is a key regulator of secondary wall synthesis in fibers of Arabidopsis . Plant Cell, 18: 3158-3170. Pyo, H., Demura, T., and Fukuda, H. (2006) Vascular cell expression patterns of Arabidopsis bZIP group I genes. Plant Biotech., 23: 497-501. formation, 2006 Gordon Research Conference on Plant Cell Walls, Biddeford USA, Jul. 30 - Aug. 4. Demura, T. (2006) Regulation of xylem cell differentiation in zinnia and Arabidopsis , JSPS-UPSC Colloquium on Frontiers in Plant Development, Umea Sweden, Jun. 2. Demura, T. (2007) Regulation of xylem cell differentiation, Plant Winter Conference 2007, Pohang Korea, Jan. 8-9. ■ Patents ■ Press Release Discovery of a key gene regulating activity of cytokinin, a productivity hormone, February, 2007. Morphoregulation Research Team Team Leader : Taku DEMURA Sasabe, M., Soyano, T., Takahashi, Y., Sonobe, S., Igarashi, H., Itoh, T., Hidaka, M., and Machida, Y. (2006) Phosphorylation of NtMAP65-1 by a MAP kinase down-regulates its activity of microtubule bundling and stimulates progression of cytokinesis of tobacco cells. Genes & Dev., 20: 1004-1014. Hamada, T., Igarashi, H., Yao, M., Hashimoto, T., Shimmen, T., and Sonobe, S. (2006) Purification and characterization of plant dynamin from tobacco BY-2 cells. Plant Cell Physiol., 47: 1175-1181. ● Review Papers Demura, T., and Fukuda, H. (2007) Transcriptional regulation in wood formation. Trends in Plant Sci., 12: 64-70. ■ Oral Presentations ● Original Papers ● Invited Presentations in International Meetings Sato, Y., Demura, T., Yamawaki, K., Inoue, Y., Sato, S., Sugiyama, Demura, T. (2006) Transcriptional regulation of xylem cell 80 RIKEN PSC 2007 Annual Report ■ Publications ● Original Papers 1 invited Japanese presentation Takahashi, F., Yoshida, R., Ichimura, K., Mizoguchi, T., Seo, S., Yonezawa, M., Maruyama, K., Yamaguchi-Shinozaki, K., and Shinozaki, K.(2007) A Dissecting the jasmonate signaling pathway by a novel MAP kinase cascade, MKK3–MPK6, in Arabidopsis . Plant Cell, in press. ● Presentations in International Meetings Demura, T. (2006) Transcription factors regulating xylem cell differentiation, Plant Vascular Development 2006, Vancouver, Canada, Jun. 9-11. Nishikubo, N., Araki, M., Fukuda, H., and Demura, T. (2006) Analysis of polygalacturonase for vessel formation, 2006 Gordon Research Conference on Plant Cell Walls, Biddeford, USA, Jul. 30 - Aug. 4. Demura, T. (2006) NAC-domain proteins regulating xylem vessel formation, 2006 FASEB Summer Research Conferences on Mechanisms of Plant Development, Saxtons River, USA, Aug. 5-9. Yamaguchi, M., Kubo, M., Fukuda, H., and Demura, T. (2006) Characterization of NAC-DOMAIN PROTEINS that negatively regulates xylem vessel differentiation, 8th International Congress of Plant Molecular Biology, Adelaide, Australia, Aug. 20-25. Maor, R., Jones, A., Nuhse, T.S., Studholme, D.J., Peck, S.C., and Shirasu, K. (2007) MudPIT analysis of ubiquitinated proteins in plants. Molecular & Cellular Proteomics, 6: 601-610. Heise, C.T., Duff, C.S., Boter, M., Casais, C., Airey, J.E., Leech, A.P., Amigues, B., Guerois, R., Moore, G.R., Shirasu, K., and Kleanthous, C. (2007) Biochemical characterization of RAR1 cycteine- and histidine-rich domains (CHORDs): A novel class of zinc-dependent protein-protein interaction modules. Biochemistry, 46: 1612-1623. Ichimura, K., Casais, C., Peck, S.C., Shinozaki, K., and Shirasu, K. (2006) MEKK1 is required for MPK4 activation and regulates tissue specific and temperature dependent cell death in Arabidopsis . J. Biol. Chem., 281: 36969-36976. Ohtani, M., Demura, T., and Sugiyama, M. (2006) Developmental significance of SRD2-mediated activation of snRNA transcription in Arabidopsis , RNA 2006 Izu: Functional RNAs and Regulatory Machinery, Izunokuni, Japan, Dec. 3-7. Noutoshi, Y., Kuromori, T., Wada, T., Hirayama, T., Kamiya, A., Imura, Y., Yasuda, M., Nakashita, H., Shirasu, K., and Shinozaki, K. (2006) Loss of NECROTIC SPOTTED LESIONS 1 associates with cell death and defense responses in Arabidopsis thaliana . Plant Mol. Biol., 62:29-42. Ito, J., Uemura, T., Saito, C., Motose Udagawa, M., Kubo, M., Demura, T., Fukuda, H., Nakano, A., and Ueda, T. (2007) A role of the vesicular traffic in xylem differentiation, Plant Winter Conference 2007, Pohang, Korea, Jan. 8-9. Azevedo, C., Betsuyaku, S., Peart, J., Takahashi, A., Noel, L., Sadanandom, A., Casais, C., Parker, J., and Shirasu, K. (2006) Role of SGT1 in resistance protein accumulation in plant immunity. EMBO J., 25: 2007-2016. Demura, T. (2007) Regulation of xylem cell differentiation in Arabidopsis and poplar revealed by transcriptome analysis, China-Japan Joint Workshop on Plant Molecular Breeding, Beijing, China, Mar. 12-13. Fujita, M., Fujita, Y., Noutoshi, Y., Takahashi, F., Narusaka, Y., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Crosstalk between abitoic and biotic stress responses: A current view from the points of convergence in the stress signaling networks. Curr. Opin. Plant Biol., 9: 436-432. Yamaguchi, M., Kubo, M., Fukuda, H., and Demura, T. (2007) NAC domain proteins involved in xylem vessel differentiation, Keystone Symposia on Plant Cell Biology, Coeur d'Alene, USA, Mar. 23-28. 2 Japanese reviews ■ Publications Team Leader : Ken SHIRASU ● Presentations in Domestic Meetings 10 Japanese presentations Gonzalez-Lamothe, R., Tsitsigiannis, D.I., Ludwig, A.A., Panicot, M., Shirasu, K., and Jones, J.D. (2006) The U-Box protein CMPG1 is required for efficient activation of defense mechanisms triggered by multiple resistance genes in tobacco and tomato. Plant Cell,18: 1067-1083. Nishiuchi, T., Masuda, D., Nakashita, H., Ichimura, K., Shinozaki, K., Yoshida, S., Kimura, M., Yamaguchi, I., and Yamaguchi, K. (2006) Fusarium phytotoxin trichothecenes have an elicitorlike activity in Arabidopsis thaliana , but the activity differed RIKEN PSC 2007 Annual Report 81 Plant Immunity Research Group Application date : 2007. 2.27 Issued Date : NA Application Serial Number : 2007-047520 Patent No : NA Country : Japan Title of invention : Clean-up of Pb-polluted water using protonema of bryophyte and its equipment. Applicants : RIKEN Name of Inventors : Itouga, M., Sakakibara, H., and Komatsu, Y. Geisler-Lee, J., Geisler, M., Coutinho, P., Segerman, B., Nishikubo, N., Takahashi, J., Aspeborg, H., Djerbi, S., Master, E., Andersson-Gunneras, S., Sundberg, B., Karpinski, S., Teeri, T., Kleczkowski, L., Henrissat, B., and Mellerowicz, E. (2006) Poplar carbohydrate-active enzymes. Gene identification and expression analyses. Plant Physiol., 140: 946-962. Plant Immunity Research Team Plant Productivity Systems Research Group Plant Productivity Systems Research Group Application date : 2006. 9.4 Issued Date : NA Application Serial Number : 2006-238691 Patent No : NA Country : Japan Title of invention : Identification of cytokinin activating enzyme and its utilization. Applicants : RIKEN Name of Inventors : Sakakibara, H., and Ueda, N. Identification of a gene regulating production of most abundant biomass on land, Dec. 11, 2006. ● Invited Presentation in Domestic Meeting 10 Japanese presentations Haga, N., Kato, K., Murase, M., Araki, S., Kubo, M., Demura, T., Suzuki, K., Muller, I., Vob, U., Jurgens, G., and Ito, M. (2007) R1R2R3-Myb proteins positively regulate cytokinesis through activation of KNOLLE transcription in Arabidopsis thaliana . Development, 134: 1101-1110. ■ Press Release significantly among their molecular species. Mol. Plant Micro. Interact., 19:512-520. ● Review Papers Ichimura, K., Noutoshi, Y., and Shirasu, K. (2006) Role of MAP kinase cascade in plant immunity. Kagaku to Seibutsu 44: 466-471. (in Japanese) Noutoshi, Y., Ichimura, K., and Shirasu, K. (2006) Molecular mechanisms of plant disease resistance protein. Tanpakushitsu Kakusan Koso 51: 408-418. (in Japanese) ■ Oral Presentations ● Invited Presentations in International Meetings Ichimura, K., Casais, C., Peck, S.C., Shinozaki, K., and Shirasu, K. (2006) The RAR1-SGT1-HSP90 Complex and its Potential Link to a MAP Kinase Kinase Kinase in Plant Immunity. The 53rd NIBB Conference Dynamic Organelles in Plants. Okazaki, Japan, June. Ichimura, K., Casais, C., and Shirasu, K. (2006) MEKK1 negatively regulates defense responses in Arabidopsis . 8th International Congress of Plant Molecular Biology. Adelaide, Australia, August. Shirasu, K. (2006) Role of the RAR1-SGT1-HSP90 complex in Plant Immunity. The 18th Annual Meeting of the Korean Society for Molecular and Cellular biology. Seoul, Korea, October. Ichimura, K., Boter, M., and Shirasu, K. (2006) Functional analysis of R-gene mediated resistance. Iwate Plant Science Symposium 2006 The Frontier of Moleculat Plant Biology- Abiotic Stress Responses and Host-pathogen Interactions-. Iwate, Japan , October. Plant Immunity Research Group Shirasu, K., Boter, M., Amigues, B., Kadota, Y,. Peart, J., Breuer, C., Casais, C., Ochsenbein, F., and Guerois, R. (2007) Ternary chaperone complex formation in plant immunity. Meiji University International Symposium -Plant Immunity: From MAMPs/PAMPs Recognition to Gene-for-Gene Resistance-. Tokyo, Japan, March. ● Invited Presentations in Domestic Meetings 2 invited Japanese presentations Nakagami, H., Maor, R., and Shirasu, K. (2007) “2DLC-MS/MS based shotgun proteomic analysis of ubiquitinated proteins in Arabidopsis ” Keystone Symposia on Molecular and Cellular Biology, Montana, USA. Feb. Nakagami, H., Maor, R., and Shirasu, K. (2007) “2DLC-MS/MSbased shotgun proteomic analysis of ubiquitinated proteins in Arabidopsis ” Meiji University International Symposium - Plant Immunity: From MAMPs/PAMPs Recognition to Gene-for-Gene Resistance-, Tokyo, Japan, March. Noutoshi, Y., and Shirasu, K. (2007) “Chemical genomics approach to dissect the hypersensitive cell death signaling pathway in Arabidopsis” Meiji University International Symposium - Plant Immunity: From MAMPs/PAMPs Recognition to Gene-forGene Resistance-, Tokyo, Japan, March. Boter, M., Amigues, B., Kadota, Y., Guerois., Y., and Shirasu, K. (2007) “RAR1-SGT1-HSP90 complex in Plant immunity” Meiji University International Symposium - Plant Immunity: From MAMPs/PAMPs Recognition to Gene-for-Gene Resistance-, Tokyo, Japan, March. Ichimura, K., Casais, C., Peck, S.C., Shinozaki, K., and Shirasu, K. (2007) “MEKK1 Negatively Regulates Tissue Specific and Temperature Dependent Cell Death in Arabidopsis” Meiji University International Symposium - Plant Immunity: From MAMPs/PAMPs Recognition to Gene-for-Gene Resistance-, Tokyo, Japan, March. ● Orginal Papers Imai, K., Ohashi, Y., Tsuge, T., Yoshizumi, T., Matsui, M., Oka, A., and Aoyama, T.(2006)CYCA2;3 , a Key Regulator of Ploidy Levels in Arabidopsis Endoreduplication. Plant Cell 18: 382-396. Tsumoto, Y., Yoshizumi, T., Kuroda, H ., Kawashima, M ., Ichikawa, T., Nakazawa, M., Yamamoto, N., and Matsui, M. (2006) Light-dependent polyploidy control by a CUE protein variant in Arabidopsis . Plant Molecular Biology, 61:817-828 . Yoshizumi, T., Tsumoto, Y., Takiguchi, T., Nagata, N., Yamamoto, Y., Kawashima, M. Ichikawa, T., Nakazawa, M., Yamamoto, N., and Matsui, M. (2006) Increased level of polyploidy1, a conserved repressor of CYCLINA2 Transcription,controls endoreduplication in Arabidopsis , The Plant Cell, 18: 2452-2468. Ichikawa, T., Nakazawa, M., Kawashima, M., Iizumi, H., Kuroda, H., Kondou, Y., Tsuhara, Y., Suzuki, K., Ishikawa, A., Seki, M., Fujita, M., Motohashi, R ., Nagata, N., Takagi, T., Shinozaki, K., and Matsui, M.(2006) The FOX hunting system : An alternative gain-of- function gene hunting technique, The Plant J., 48: 974-985. Ichimura, K., Casais, C., Peck, S.C., Shinozaki, K., and Shirasu, K. (2007) MEKK1 Negatively Regulates Tissue Specific and Temperature Dependent Cell Death in Arabidopsis . The Japanese Society of Plant Physiologists, Matsuyama, Ehime, March. Yamamoto, Y. Y., Ichida, H., Matsui, M., Obokata, J., Sakurai, T., Satou, M., Seki, M., Shinozaki, K., and Abe, T. (2007)Identification of plant promoter constituents by analysis of local distribution of short sequence. BMC Genomics, 8: 67. Noutoshi, Y., and Shirasu, K. (2007) Chemical Genomics Approach to Study Hypersensitive Cell Death in Arabidopsis . The Japanese Society of Plant Physiologists, Matsuyama, Ehime, March. Yoshida, S., Gardner, S., Buettner, G., and Parniske, M.(2007) Analysis of Lotus japonicus ubiquitin E3 ligases interacting with Symbiosis-receptor kinase (SYMRK). The Japanese Society of Plant Physiologists, Matsuyama, Ehime, March. Boter, M., Kadota, Y., Guerois, R., and Shirasu, K. (2007) RAR1SGT1-HSP90 complex in disease resistance. The Japanese Society of Plant Physiologists, Matsuyama, Ehime, March. ● Review Paper Yoshizumi, T., and Matsui, M. (2007) Finding of a gene that controls endoreduplication -a cell cycle without cell division-. Bionics Feb. 74-76. ■ Oral Presentations ● Invited Presentations in International Meetings Matsui, M. (2006) ,Vitis-vinifera functional-genomics, RikenURGV joint project, Evry, France, December 26. Kuroda, H., Horii, Y., and Matsui, M., (2006) Large-scale ORF cloning and analysis of alternative pre-mRNA splicing events of F-box protein family in Arabidopsis, Vitis-vinifera functionalgenomics, Riken-URGV joint project, Evry, France, December 26. ● Invited Presentation in Domestic Meeting 1 invited Japanese presentation ● Presentations in International Meetings Kondou, Y., Kawashima, M., Ichikawa, T., Ishikawa,A., Muto, S., Hirochika, H., and Matsui, M.(2006) Isolation for Mutants of Higher Accumulated Elements and Pigments from Rice FOX Lines. 17th International Conference on Arabidopsis Research, Madison WI, June 28-July 2. (Poster) Motohashi, R., Okada, E., Kuroda, H., Nagata, N., Matsui, M., and Shinozaki,K. (2006) Functional analysis of ribosome binding factor (RBFA) homologue using Ac/Ds transposon system in Arabidopsis thaliana. Plant Biology 2006, Boston MA, August 4-9. (Poster) Yoshida, T., Nishimura, N., Kitahata, N., Kuromori, T., Kuroda, H., Matsui, M., Asami, T.,Shinozaki, K., and Hirayama, T. (2006) ABA-hypersensitive germination3 encodes a protein phosphatase 2C (AtPP2CA) that strongly regulates abscisic acid signaling during germination among Arabidopsis protein phosphatase 2Cs. Plant Biology 2006, Boston MA, August 4-9. (Poster) Kuroda, H., Horii, Y., and Matsui, M. (2006) ORF cloning of F-box protein genes of Arabidopsis reveals numerous transcript variants. Plant Genomics in China VII, Harbin, China, August 7-10. (Poster) Yoshizumi, T., Tsumoto, Y., Suzuki, K., Muto, S., Koshi, T., Yamamoto, Y., and Matsui, M.(2006) Gene trapping of the Arabidopsis genome with a firefly luciferase reporter. Plant Genomics in China VII, Harbin China , August 7-10. (Poster) Takahashi, S., Ichikawa, T., Kondou, Y., Ishikawa, A., Kawashima, M., Hirochika, H., and Matsui, M. (2006) Screening of useful rice genes concerned with Ultraviolet-B tolerance mechanisms by the Rice FOX hunting system. 8th International Congress of Plant Molecular Biology, Adelaide Australia, August 20-25. (Poster) Higuchi, M., Matsui, K., Ichikawa, T., Kondou, Y., Ishikawa, A., Kawashima, M., Hirochika, H., and Matsui, M. (2006) Isolation of high-light resistant mutants using rice FOX lines. 8th International Congress of Plant Molecular Biology, Adelaide Australia, August 20-25. (Poster) Kuroda, H., Horii, Y., and Matsui, M. (2006) F-box protein families in rice and Arabidopsis. RAP3 meeting, Tsukuba Japan, December 9-10. (Poster) Yoshizumi, T., Tsumoto, Y., Suzuki, K., Muto, S., Koshi, T., Yamamoto, Y., and Matsui, M. (2007) Gene trapping of the Arabidopsis genome with a firefly luciferase reporter. Cold Spring Harbor Laboratory Meeting on Plant Genomes, New York NY. March 15-18.(Poster) Ichikawa, T., Nakazawa, M., Kawashima, M., Iizumi, H., Kuroda, H., Kondou, Y., Ishikawa, A., Seki, M., Fujita, M., Shinozaki, K., and Matsui, M. (2007) The FOX hunting system : An, alternative gain-of- function gene hunting technique. Cold Spring Harbor RIKEN PSC 2007 Annual Report 83 Plant Functional Genomics Research Group Ichimura, K., Casais, C., Peck, S.C., Shinozaki, K., and Shirasu, K. (2006) “MEKK1 negatively regulates tissue specific and temperature dependent cell death in Arabidopsis.” 17th International Conference on Arabidopsis Research, Madison, USA, Jun. RIKEN PSC 2007 Annual Report ■ Publications Yoshida, S. (2006) Nuclear signaling components in root symbiosis. US-Japan joint seminar at Tokyo University, Tokyo, August. ● Presentations in Domestic Meetings ● Presentations in International Meetings 82 Team Leader : Minami MATSUI Kobayashi, K., Suzuki, M., Tang, J., Nagata, N., Ohyama, K., Seki, H., Kiuchi, R., Kaneko, Y., Nakazawa, M., Matsui, M., Matsumoto, S., Yoshida, S., and Muranaka, T. (2007) LOVASTATIN INSENSITIVE 1, a Novel Pentatricopeptide Repeat Protein, is a Potential Regulatory Factor of Isoprenoid Biosynthesis in Arabidopsis . Plant Cell Phisiol. : 322-331. Nakagami, H., M, Maor, R., and Shirasu, K. (2007) 2DLC-MS/ MS-based shotgun proteomic analysis of ubiquitinated proteins in Arabidopsis . The Japanese Society of Plant Physiologists, Matsuyama, Ehime, March. Boter, M., Peart, J., Amigues, B., Breuer, C., Kadota, Y., Guerois, R., and Shirasu, K. (2006) “RAR1-SGT1-HSP90 interactions in R-gene mediated resistance” 3rd international conference on The Hsp90 Chaperone Machine, Munich, Germany, Sept. Plant Functional Genomics Research Team Laboratory Meeting on Plant Genomes, New York NY, March 15-18. (Poster) ● Presentations in Domestic Meetings 8 Japanese Presentations 18 Japanese presentations (Poster) ■ Patents Application date: September 21,2006 Issued Date: NA Application Serial Number: 2006-256034 Patent No: NA Country: Japan Title of invention: Dwarf genes of Arabidopsis. Applicants: RIKEN Name of Inventors : Ichikawa,T., Kawashima,M., Iizumi,H., Kuroda, H., Kondou, Y., Seki, M., Hasegawa,Y.,Matsui,M., Ishikawa, A., Nakazawa,M., and Suzuki,K. ,N.,Sakai, H., Sakai, Y., Sakata, K., Sakurai, T., Sato, F., Sato, Y., Schoof, H., Seki, M., Shibata, M., Shimizu, Y., Shinozaki, K., Shinso, Y., Singh, N.K., Smith-White, B., Takeda, J., Tanino, M., Tatusova, T., Thongjuea, S., Todokoro, F., Tsugane, M., Tyagi, A.K., Vanavichit, A., Wang, A., Wing, R.A., Yamaguchi, K., Yamamoto, M., Yamamoto, N., Yu, Y., Zhang, H., Zhao, Q., Higo, K., Burr, B., Gojobori, T., and Sasaki, T. (2007) Curated Genome Annotation of Oryza sativa ssp. Japonica and Comparative Genome Analysis with Arabidopsis thaliana . Genome Res., 17:175-183. Mitsuda, N., Iwase, A., Yamamoto, H., Yoshida, M., Seki, M., Shinozaki, K., and Ohme-Takagi, M. (2007) NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis . Plant Cell, 19: 270-280. Yamamoto, Y.Y., Ichida, H., Matsui, M., Obokata, J., Sakurai, T., Satou, M., Seki, M., Shinozaki, K., and Abe, T. (2007) Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics, 8: 67. Application date : August 14,2006 Issued Date : NA Application Serial Number:2006-221061 Patent No: NA Country : Japan Title of invention : Early growth genes of Arabidopsis. Applicants : RIKEN Name of Inventors : Ichikawa,T., Kawashima,M., Iizumi,H., Kuroda, H., Kondou, Y., Seki, M., Hasegawa,Y., Matsui,M., Ishikawa, A., Nakazawa,M., and Suzuki,K. Oono, Y., Seki, M., Satou, M., Iida, K., Akiyama, K., Sakurai, T., Fujita, M., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays. Funct. Integr. Genomics, 4: 1-23. ■ Press Releases Matsuda, T., Kigawa, T., Koshiba, S., Inoue, M., Aoki, M., Yamasaki, K., Seki, M., Shinozaki, K., and Yokoyama, S. (2006) Cell-free synthesis of zinc-binding proteins. J. Struct. Funct. Genomics, 7: 93-100. Identification of a gene that controls specific cell cycle. Oct. 26, 2006 Rapid identification of useful genes, "Fox hunting System". Dec. 26, 2006 Plant Genomic Network Research Team Team Leader : Motoaki SEKI ■ Publications ● Original Papers 84 RIKEN PSC 2007 Annual Report Hasegawa, Y., Seki, M., Mochizuki, Y., Heida, N., Okamoto, K., Sakurai, T., Satou, M., Akiyama, K., Iida, K., Lee, K., Kanaya, S., Demura, T., Shinozaki, K., Konagaya, A., and Toyoda, T. (2006) A flexible representation of omic knowledge for thorough analysis of microarray data. Plant Methods, 2: 5. Nakashima, K., Fujita, Y., Katsura, K., Maruyama, K., Narusaka, Y., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006) Transcriptional Regulation of ABI3- and ABA-responsive Genes Including RD29B and RD29A in Seeds, Germinating Embryos, and Seedlings of Arabidopsis . Plant Mol. Biol., 60: 51-68 and S.M. Jain, eds, Springer Publishing, Dordrecht, in press. Sakuma, Y., Maruyama, K., Osakabe, Y., Feng, Q., Seki, M., Shinozaki K., and Yamaguchi-Shinozaki, K. (2006) Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell, 18: 1292-1309. ■ Oral Presentations Yamasaki, K., Kigawa, T., Inoue, M., Yamasaki, T., Yabuki, T., Aoki, M., Seki, E., Matsuda, T., Tomo, Y., Terada, T., Shirouzu, M., Tanaka, A., Seki, M., Shinozaki, K., and Yokoyama, S. (2006) Disruption of the Second Zinc-Binding Site of an Arabidopsis SBP-Family Transcription Factor Retains Its Tertiary Structure. FEBS Lett., 580: 2109-2116. Umezawa, T., Okamoto, M., Kushiro, T., Nambara, E., Oono, Y., Seki, M., Kobayashi, M., Koshiba, T., Kamiya, Y., and Shinozaki, K. (2006) CYP707A3, a major ABA 8’-hydroxylase involved in dehydration and rehydration response in Arabidopsis thaliana . Plant J., 46: 171-182. Ito, Y., Katsura, K., Maruyama, K., Taji, T., Kobayashi, M., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006) Functional Analysis of Rice DREB1/CBF-Type Transcription Factors Involved in Cold-Responsive Gene Expression in Transgenic Rice. Plant Cell Physiol., 47:141-153. Myouga, F., Motohashi, R., Kuromori, T., Nagata, N., and Shinozaki, K. (2006) An Arabidopsis chloroplast-targeted Hsp101 homolog, APG6, has an essential role in choloroplast development as well as heat stress response. Plant J., 48: 249-260. Kuromori, T., Wada, T., Kamiya, A., Yuguchi, M., Yokouchi, T., Imura, Y., Takabe, H., Sakurai, T., Akiyama, K., Hirayama, T., Okada, K., and Shinzoaki, K. (2006) A trial of phenome analysis using 4000 Ds -insertional mutants in gene-coding regions of Arabidopsis . Plant J., 47: 640-651. Yoshida, T., Nishimura, N., Kitahata, N., Kuromori, T., Ito, T., Asami, T., Shinozaki, K., and Hirayama T. (2006) ABA Hypersensitive Germination3 encodes a protein phosphatase 2C (AtPP2CA) that strongly regulates ABA signaling during germination among Arabidopsis PP2Cs . Plant Physilol., 140: 115-126. ● Review Papers Seki, M., Umezawa, T., Urano, K., and Shinozaki, K. (2007) Regulatory metabolic network in drought stress responses. Curr. Opin. Plant Biol., in press. Machida, M., Takechi, K., Sato, H., Chung, S.J., Kuroiwa, H., Takio, S., Seki, M., Shinozaki, K., Fujita, T., Hasebe, M., and Takano, H. (2006) Genes for the peptidoglycan synthesis pathway are essential for chloroplast division in moss. Proc. Natl. Acad. Sci. USA, 103: 6753-6758. Seki,M., Kamiya, A., Carninci, P., Hayashizaki, Y., and Shinozaki, K. (2006) Generation of full-length cDNA libraries from plant materials. In Methods in Molecular Biology. Edited by John Parkinson, Humana Press Inc., NJ., in press. Gross, J., Cho, W.K., Lezhneva, L., Falk, J., Krupinska, K., Shinozaki, K., Seki, M., Herrmann, R.G., and Meurer, J. (2006) A plant locus essential for phylloquinone (vitamin k1) biosynthesis originated from a fusion of four eubacterial genes. J. Biol. Chem., Seki, M., Umezawa, T., Kim, J.M., Matsui, A., To, T., and Shinozaki, K. (2006) Transcriptome analysis of plant drought and salt stress response. In Advances in Molecular Breeding toward Drought and Salt Tolerant Crops. M.A. Jenks, P.M. Hasegawa ● Invited Presentations in International Meetings and Seminars Seki, M. (2006) Arabidopsis whole-genome expression profiling under abiotic stress conditions, Gordon Research Conference on Salt & Water Stress in Plants, Oxford, UK, Sep. 3-8. Seki, M., Ishida, J., Morosawa, T., Matsui, A., Kim, J.M., Nakajima, M., Enju, A., To, T., Iida, K., Go, M., Mochizuki, Y., Hasegawa, Y., Kaminuma, E., Toyoda, T., and Shinozaki K. (2006) Arabidopsis whole-genome expression profiling under abiotic stress conditions, 8th International Congress of Plant Molecular Biology, Adelaide, Australia, Aug. 20-25. Seki, M. (2006) Arabidopsis whole-genome expression profiling under abiotic stress conditions, Molecular, Cellular & Developmental Biology (MCDB) Seminar in the Ohio State University, Ohio, USA, May 22. ● Invited Presentation in Domestic Meeting 1 invited Japanese presentation ● Presentations in International Meetings Seki, M., Matsui, A., Kim, J.M., Ishida, J., Nakajima, M., Morosawa, T., Kawashima, M., Satou, M., To, T., Kurihara, Y., Kaminuma, E., Endo, T., Mochizuki, Y., Kobayashi, N., Toyoda, T., and Shinozaki, K. (2007) Arabidopsis whole-genome transcriptome analysis under drought, cold, high-salinity, and ABA treatment conditions using tiling array and 454 sequencing technology, 24th Symposium in Plant Biology on Gene Silincing: The Biology of Small RNAs and the Epigenome, Riverside, USA, Jan. 18-20. Seki, M., Ishida, J., Morosawa, T., Matusi, A., Kim, J.M., Nakajima, M., Enju, A., To, T., Iida, K., Go, M., Mochizuki, Y., Hasegawa, Y., Toyoda, T., and Shinzoaki, K. (2006) Arabidopsis whole-genome transcriptome analysis under abiotic stress conditions, The 16th Penn Atate Symposium in Plant Physiologyon RNA Biology: Novel Insights from Plant Systems, Penn State, USA, May 18-20. Kim, J.M., Kuromori, T., To, T., Hirayama, T., Seki, M., and Shinozaki, K.(2006) Functional analysis of AtORC1a in a phase progression, 8th International Congress of Plant Molecular Biology, Adelaide, Australia, Aug. 20-25. Myouga, F., Akiyama, K., Sakurai, T., Motohashi, R., and Shinozaki, K. (2006) Gene discovery for chloroplast proteins involved in drought tolerance in Arabidopsis using the rarge database, 8th International Congress of Plant Molecular Biology, Adelaide, Australia, Aug. 20-25. Ichikawa, H., Nakamura, H., Hakata, M., Kajikawa, M., Ando, S., Amano, S., Toki, N., Higashi, N., Fujita, M., Enju, A., Seki, M., Nakazawa, M., Ichikawa, T., Matsui, M., Shinozaki, K., Miyao, A., Toki, T., and Hirochika H. (2006) FOX hunting system: a genomewide functional analysis of rice genes using transgenic plants, RIKEN PSC 2007 Annual Report 85 Plant Functional Genomics Research Group Plant Functional Genomics Research Group Itoh, T., Tanaka, T., Barrero, R.A., Yamasaki, C., Fujii, Y., Hilton, P.B., Antonio, B.A., Aono, H., Apweiler, R., Bruskiewich, R., Bureau, T., Burr, F., Fuks, G., Habara, T., Haberer, G., Han, B., Harada, E., Hiraki, A.T., Hirochika, H., Hoen, D., Hokari, H., Hosokawa, S., Hsing, Y.I., Ikawa, H., Ikeo, K., Imanishi, T., Ito, Y., Jaiswal, P., Kanno, M., Kawahara, Y., Kawamura, T., Kawashima, H., Khurana, J.P., Kikuchi, S., Komatsu, S., Koyanagi, K.O., Kubooka, H., Lieberherr, D., Lin, Y.C., Lonsdale, D., Matsumoto, T., Matsuya, A., McCombie, W.R., Messing, J., Miyao, A., Mulder, N., Nagamura, Y., Nam, J., Namiki, N., Numa, H., Nurimoto, S., O'Donovan, C., Ohyanagi, H., Okido, T., de Oliveira, A.C., Oota, S., Osato, N., Palmer, L.E., Quetier, F., Raghuvanshi,S.,Saichi Ichikawa, T., Nakazawa, M., Kawashima, M., Iizumi, H., Kuroda, H., Kondou, Y., Tsuhara, Y., Suzuki, K., Ishikawa, A., Seki, M., Fujita, M., Motohashi, R., Nagata, N., Takagi, T., Shinozaki, K., and Matsui, M. (2006) The FOX hunting system: an alternative gain-of-function gene hunting technique. Plant J., 45: 974-985. 281: 17189-17196. 8th International Congress of Plant Molecular Biology WorkShop, Adelaide, Australia, Aug. 20-25. Hakata, M., Nakamura, H., Asano, T., Kajikawa, M., Amano, K., Toki, N., Higashi, N., Fujita, M., Enju, A., Seki, M., Nakazawa, M., Ichikawa, T., Shinozaki, K., Matsui, M., Komatsu, S., Miyao, A., Toki, S., Hirochika, H., and Ichikawa H. (2006) Genomewide functional analysis of rice genes using fox hunting system 2. Analysis and identificaiton of introduced cDNAs in the foxrice lines, 8th International Congress of Plant Molecular Biology, Adelaide, Australia, Aug. 20-25. Nakamura, H., Hakata, M., Kajikawa, M., Ando, S., Amano, K., Toki, N., Higashi, N., Fujita, M., Enju, A., Seki, M., Nakazawa, M., Ichikawa, T., Matsui, M., Shinzoaki, K., Miyao, A., Toki, T., Hirochika, H., and Ichikawa, H. (2006) Genome-wide functional analysis of rice genes using foc hunting system 1. Overview and current status, 8th International Congress of Plant Molecular Biology, Adelaide Australia, Aug. 20-25. Umezawa, T., Todaka, D., Totoki, Y., Sakurai, T., Seki, M., Toyoda, A., Maruyama, K., Nakashima, K., Mizukado, S., Kasuga, M., Ahmed, S, Sado, H., Harada, K., Tsubokura, Y., Sato, S., Anai, T., Ishimoto, M., Funatsuki, H., Teraishi, M., Shinano, T., Akashi, R., Sakaki, Y., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Construction of a soybean full-length cDNA library and oligonucleotide microarray, The KAZUSA Conference on legume Genetics and Genomics in Asia, Kisarazu, Japan, Nov. 27-28. Fujita, Y., Fujita, M., Satoh, R., Maruyama, K., Sayama, H., Seki, M., Hiratsu, K., Ohme-Takagi, M., Shinzoaki, K., and YamaguchiShinozaki, K. (2006) AREB1 mediates novel ABRE-dependent ABA-signaling that enhances drought stress tolerance in Arabidopsis thaliana, Gordon Research Conference on Salt & Water Stress in Plants, Oxford, UK, Sep. 3-8. Ichikawa, T., Nakazawa, M., Kondou, Y., Ishikawa, A., Kawashima, M., Iizumi, H., Seki, M., Fujita, M., Muto, S., Shinozaki, K., and Matsui, M. (2006) Evaluation of Arabidopsis FOX line: T2 phenotype and phenotype recapitulation by transformation, 17th International Conference on Arabidopsis Research, Wisconsin-Madison, USA, June 28- July 2. ● Presentations in Domestic Meetings 26 Japanese presentations ■ Patents Plant Functional Genomics Research Group Application date: Nov. 27, 2006 Issued Date: NA Application Serial Number: 2006-318803 Patent No: NA Country: Japan Title of invention: Environmental stress-responsive promoters and transcription factors Applicants: RIKEN Name of Inventors: Shinozaki, K., Seki, M., and Fujita, M. Application date: Oct. 20, 2006 Issued Date: NA Application Serial Number: 2006-286326 Patent No: NA Country: Japan Title of invention: Environmental stress-responsive promoters and 86 RIKEN PSC 2007 Annual Report the methods to drive the tissue-specific gene expression using the promoters Applicants: RIKEN Name of Inventors: Seki, M., Kim, J.M., Shinozaki, K., Fujita, M., Enju, A., Kobayashi, H., and Nakajima, M. ■ Press Release Opening the observable traits of 4000 Arabidopsis mutants to the public (July 27, 2006).