• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Genomic origin of chemodiversity in medicinal plants

Research Project

Project/Area Number 19H05652
Research Category

Grant-in-Aid for Scientific Research (S)

Allocation TypeSingle-year Grants
Review Section Broad Section H
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Saito Kazuki  国立研究開発法人理化学研究所, 環境資源科学研究センター, センター長 (00146705)

Co-Investigator(Kenkyū-buntansha) 吉本 尚子  千葉大学, 大学院薬学研究院, 講師 (10415333)
関 光  大阪大学, 大学院工学研究科, 准教授 (30392004)
庄司 翼  富山大学, 学術研究部薬学・和漢系, 教授 (40343272)
村中 俊哉  大阪大学, 大学院工学研究科, 教授 (60342862)
山崎 真巳  千葉大学, 大学院薬学研究院, 教授 (70222370)
高上馬 希重  北海道医療大学, 薬学部, 准教授 (80342781)
中林 亮  国立研究開発法人理化学研究所, 環境資源科学研究センター, 研究員 (30586160)
東 泰弘  国立研究開発法人理化学研究所, 環境資源科学研究センター, 研究員 (90634577)
榊原 圭子  国立研究開発法人理化学研究所, 環境資源科学研究センター, 上級研究員 (20360555)
Rai Amit (ライ アミット)  国立研究開発法人理化学研究所, 環境資源科学研究センター, 研究員 (60760535)
Project Period (FY) 2019-06-26 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥200,980,000 (Direct Cost: ¥154,600,000、Indirect Cost: ¥46,380,000)
Fiscal Year 2023: ¥31,330,000 (Direct Cost: ¥24,100,000、Indirect Cost: ¥7,230,000)
Fiscal Year 2022: ¥31,330,000 (Direct Cost: ¥24,100,000、Indirect Cost: ¥7,230,000)
Fiscal Year 2021: ¥31,330,000 (Direct Cost: ¥24,100,000、Indirect Cost: ¥7,230,000)
Fiscal Year 2020: ¥47,190,000 (Direct Cost: ¥36,300,000、Indirect Cost: ¥10,890,000)
Fiscal Year 2019: ¥59,800,000 (Direct Cost: ¥46,000,000、Indirect Cost: ¥13,800,000)
Keywords薬用植物 / ゲノム / トランスクリプトーム / メタボローム / 甘草 / 植物二次代謝
Outline of Research at the Start

医薬学や医療分野において重要性が増加し、主に国内で栽培されている薬用植物について、そのゲノムや化学成分に関連する研究を行う。有効成分の異なる甘草の複数種などについて、それらのゲノム配列とメタボロームデータ等を基に成分パターンなど関連している遺伝子などを推定する。さらに、甘草以外の重要な薬用植物についても薬用成分の生産に関与している遺伝子を推定する。さらに、これらの遺伝子や成分を応用する事により、新規の医薬成分の生産や薬用資源植物の持続的な有効利用などに利用する。

Outline of Final Research Achievements

In this study, we promoted integrated genomic science to enhance medicinal compound production in important plants like licorice, uncovering the genomic origins of plant chemical diversity. We successfully decoded the high-quality genome of Glycyrrhiza uralensis, identifying gene clusters for saponin and isoflavonoid biosynthesis. This research lays the groundwork for understanding the genomic basis of medicinal plant production and advancing metabolomic analysis for controlling compound production.

Academic Significance and Societal Importance of the Research Achievements

本研究は、重要生薬「甘草」を中心として医薬学や医療分野において重要性が増加する薬用資源植物の統合ゲノム科学を進展させ、植物成分生産のゲノム起源の解明に大きく貢献できた。これらの成果は将来的に植物製剤によって国民の健康や健康寿命の延伸に資するものであり、同時に「植物はなぜ、どのように薬となる多様な化学成分を作るのか?」という根源的な問いにも解答を与え人類の知の地平線を広げる事にもつながる。さらに、グローバル・コモンズとしての植物とその遺伝子資源など生物多様性の保全と利用という重要な社会的意義をも有する。

Assessment Rating
Ex-post Assessment Comments (Rating)

A: In light of the aim of introducing the research area into the research categories, expected outcomes of research have been produced.

Assessment Rating
Interim Assessment Comments (Rating)

A: In light of the aim of introducing the research area into the research categories, the expected progress has been made in research.

Report

(11 results)
  • 2024 Ex-post Assessment (Comments) ( PDF )
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Abstract (Interim Assessment) ( PDF )   Annual Research Report   Interim Assessment (Comments) ( PDF )
  • 2020 Annual Research Report
  • 2019 Abstract ( PDF )   Comments on the Screening Results ( PDF )   Annual Research Report
  • Research Products

    (39 results)

All 2023 2022 2021 2020 Other

All Journal Article (20 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 20 results,  Open Access: 17 results) Presentation (16 results) (of which Int'l Joint Research: 4 results,  Invited: 3 results) Book (2 results) Remarks (1 results)

  • [Journal Article] Downregulation of a cluster of genes encoding nitrate transporter 1/peptide transporter family proteins in tomato with a mutated JRE4 transcription factor2023

    • Author(s)
      Shoji Tsubasa、Saito Kazuki
    • Journal Title

      Plant Biotechnology

      Volume: 40 Issue: 1 Pages: 71-76

    • DOI

      10.5511/plantbiotechnology.22.1113a

    • ISSN
      1342-4580, 1347-6114
    • Year and Date
      2023-03-25
    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Induced production of specialized steroids by transcriptional reprogramming in <i>Petunia hybrida</i>2023

    • Author(s)
      Shoji Tsubasa、Sugawara Satoko、Mori Tetsuya、Kobayashi Makoto、Kusano Miyako、Saito Kazuki
    • Journal Title

      PNAS Nexus

      Volume: 2 Issue: 10

    • DOI

      10.1093/pnasnexus/pgad326

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genetic regulation and manipulation of nicotine biosynthesis in tobacco: strategies to eliminate addictive alkaloids2023

    • Author(s)
      Shoji Tsubasa、Hashimoto Takashi、Saito Kazuki
    • Journal Title

      Journal of Experimental Botany

      Volume: 75 Issue: 6 Pages: 1741-1753

    • DOI

      10.1093/jxb/erad341

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cultivation study of <i>Lithospermum erythrorhizon</i> to obtain “Shikon” as a purple dye and traditional medicine - root growth and shikonin derivatives content2023

    • Author(s)
      Kojoma M.
    • Journal Title

      Acta Horticulturae

      Volume: 1361 Issue: 1361 Pages: 13-20

    • DOI

      10.17660/actahortic.2023.1361.2

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Glycyrrhizin Production in Licorice Hairy Roots Based on Metabolic Redirection of Triterpenoid Biosynthetic Pathway by Genome Editing2023

    • Author(s)
      Chiyo Naoki、Seki Hikaru、Kanamoto Takuya、Ueda Hiroshi、Kojoma Mareshige、Muranaka Toshiya
    • Journal Title

      Plant And Cell Physiology

      Volume: 65 Issue: 2 Pages: 185-198

    • DOI

      10.1093/pcp/pcad161

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Disruption of a licorice cellulose synthase-derived glycosyltransferase gene demonstrates its in planta role in soyasaponin biosynthesis2023

    • Author(s)
      Sakanishi Manami、Chung Soo Yeon、Fujiwara Kentaro、Kojoma Mareshige、Muranaka Toshiya、Seki Hikaru
    • Journal Title

      Plant Cell Reports

      Volume: 43 Issue: 1

    • DOI

      10.1007/s00299-023-03095-6

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 甘草のゲノム解読から明らかになった薬効成分の生合成遺伝子クラスター2023

    • Author(s)
      Amit Rai, 斉藤和季
    • Journal Title

      バイオサイエンスとインダストリー

      Volume: 81 Pages: 310-311

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chromosome-scale genome assembly of Glycyrrhiza uralensis revealed metabolic gene cluster centred specialized metabolites biosynthesis2022

    • Author(s)
      Rai A, Hirakawa H, Rai M, Shimizu Y, Shirasawa K, Kikuchi S, Seki H, Yamazaki M, Toyoda A, Isobe S, Muranaka T, Saito K
    • Journal Title

      DNA Res.

      Volume: 29 Issue: 6 Pages: 1-14

    • DOI

      10.1093/dnares/dsac043

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Natural and induced variations in transcriptional regulator genes result in low‐nicotine phenotypes in tobacco2022

    • Author(s)
      Shoji Tsubasa、Moriyama Koki、Sierro Nicolas、Ouadi Sonia、Ivanov Nikolai V.、Hashimoto Takashi、Saito Kazuki
    • Journal Title

      The Plant Journal

      Volume: 111 Issue: 6 Pages: 1768-1779

    • DOI

      10.1111/tpj.15923

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A Jasmonate-Responsive ERF Transcription Factor Regulates Steroidal Glycoalkaloid Biosynthesis Genes in Eggplant2022

    • Author(s)
      Shoji Tsubasa、Saito Kazuki
    • Journal Title

      Plants

      Volume: 11 Issue: 23 Pages: 3336-3336

    • DOI

      10.3390/plants11233336

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus2021

    • Author(s)
      Rai Megha、Rai Amit、Mori Tetsuya、Nakabayashi Ryo、Yamamoto Manami、Nakamura Michimi、Suzuki Hideyuki、Saito Kazuki、Yamazaki Mami
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 22 Issue: 16 Pages: 8835-8835

    • DOI

      10.3390/ijms22168835

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Genetic divergence in transcriptional regulators of defense metabolism: insight into plant domestication and improvement2021

    • Author(s)
      Shoji Tsubasa、Umemoto Naoyuki、Saito Kazuki
    • Journal Title

      Plant Molecular Biology

      Volume: - Issue: 4-5 Pages: 401-411

    • DOI

      10.1007/s11103-021-01159-3

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] CRISPR/Cas9-mediated disruption of the <i>PYRROLIDINE KETIDE SYNTHASE</i> gene reduces the accumulation of tropane alkaloids in <i>Atropa belladonna</i> hairy roots2021

    • Author(s)
      Hasebe Fumihito、Yuba Honoka、Hashimoto Takashi、Saito Kazuki、Funa Nobutaka、Shoji Tsubasa
    • Journal Title

      Bioscience, Biotechnology, and Biochemistry

      Volume: 85 Issue: 12 Pages: 2404-2409

    • DOI

      10.1093/bbb/zbab165

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis2021

    • Author(s)
      Rai Amit、Hirakawa Hideki、Nakabayashi Ryo、Kikuchi Shinji、Hayashi Koki、Rai Megha、Tsugawa Hiroshi、Nakaya Taiki、Mori Tetsuya、Nagasaki Hideki、Fukushi Runa、Kusuya Yoko、Takahashi Hiroki、Uchiyama Hiroshi、Toyoda Atsushi、Hikosaka Shoko、Goto Eiji、Saito Kazuki、Yamazaki Mami
    • Journal Title

      Nature Communications

      Volume: 12 Issue: 1 Pages: 405-405

    • DOI

      10.1038/s41467-020-20508-2

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Allylic Hydroxylation Activity Is a Source of Saponin Chemodiversity in the Genus Glycyrrhiza2021

    • Author(s)
      Fanani Much Z、Sawai Satoru、Seki Hikaru、Ishimori Masato、Ohyama Kiyoshi、Fukushima Ery O、Sudo Hiroshi、Saito Kazuki、Muranaka Toshiya
    • Journal Title

      Plant and Cell Physiology

      Volume: in press Issue: 2 Pages: 262-271

    • DOI

      10.1093/pcp/pcaa173

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Seed-coat protective neolignans are produced by the dirigent protein AtDP1 and the laccase AtLAC5 in Arabidopsis2020

    • Author(s)
      Yonekura-Sakakibara Keiko、Yamamura Masaomi、Matsuda Fumio、Ono Eiichiro、Nakabayashi Ryo、Sugawara Satoko、Mori Tetsuya、Tobimatsu Yuki、Umezawa Toshiaki、Saito Kazuki
    • Journal Title

      The Plant Cell

      Volume: 33 Pages: 129-152

    • DOI

      10.1093/plcell/koaa014

    • NAID

      120006951677

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Multiomics-based characterization of specialized metabolites biosynthesis in Cornus Officinalis2020

    • Author(s)
      Rai Amit、Rai Megha、Kamochi Hidetaka、Mori Tetsuya、Nakabayashi Ryo、Nakamura Michimi、Suzuki Hideyuki、Saito Kazuki、Yamazaki Mami
    • Journal Title

      DNA Research

      Volume: 27 Issue: 2 Pages: 1-15

    • DOI

      10.1093/dnares/dsaa009

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Higher dimensional metabolomics using stable isotope labeling for identifying the missing specialized metabolism in plants2020

    • Author(s)
      Nakabayashi Ryo、Saito Kazuki
    • Journal Title

      Current Opinion in Plant Biology

      Volume: 55 Pages: 84-92

    • DOI

      10.1016/j.pbi.2020.02.009

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Metabolomics with 15N Labeling for Characterizing Missing Monoterpene Indole Alkaloids in Plants2020

    • Author(s)
      Nakabayashi Ryo、Mori Tetsuya、Takeda Noriko、Toyooka Kiminori、Sudo Hiroshi、Tsugawa Hiroshi、Saito Kazuki
    • Journal Title

      Analytical Chemistry

      Volume: 92 Issue: 8 Pages: 5670-5675

    • DOI

      10.1021/acs.analchem.9b03860

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Editorial: The Origin of Plant Chemodiversity - Conceptual and Empirical Insights2020

    • Author(s)
      Saito Kazuki
    • Journal Title

      Frontiers in Plant Science

      Volume: 11 Pages: 890-890

    • DOI

      10.3389/fpls.2020.00890

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] 植物二次代謝の転写因子:代謝制御の万能因子はあるのか?2023

    • Author(s)
      庄司翼
    • Organizer
      第40回日本植物バイオテクノロジー学会(千葉)大会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] ゲノム編集によるグリチルリチン高生産毛状根の作出2023

    • Author(s)
      千代直樹、關 光、金本拓也、上田大志、高上馬希重、村中俊哉
    • Organizer
      第40回日本植物バイオテクノロジー学会(千葉)大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 生薬シコンの基原植物ムラサキ(Lithospermum erythrorhizon)の北海道における栽培・生産の取り組み2023

    • Author(s)
      高上馬希重, 金尚永
    • Organizer
      第47回日本生薬学会北海道支部例会, 札幌
    • Related Report
      2023 Annual Research Report
  • [Presentation] ヒガンバナ科植物Tulbaghia violaceaの機能性含硫成分マラスミンの生合成に関わるS-酸化酵素の同定2023

    • Author(s)
      吉本尚子,王吉晨,鈴木秀幸,中嶋なな子,北島満里子,髙山廣光,斉藤和季,山崎真巳
    • Organizer
      日本生薬学会第69回年会(宮城)
    • Related Report
      2023 Annual Research Report
  • [Presentation] ネギ属植物およびカルスの含硫二次代謝物量に対するエリシター処理の影響の解析2023

    • Author(s)
      村田夏奈子、木佐貫あゆな、浅野孝、斉藤和季、山崎真巳、吉本尚子
    • Organizer
      第40回日本植物バイオテクノロジー学会(千葉)大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] The challenge of RIKEN CSRS for the establishment of Sustainable Resource Science2023

    • Author(s)
      Kazuki Saito
    • Organizer
      The 64th Annual Meeting of the Japanese Society of Plant Physiologists. ‘Japan-Singapore Binational Symposium: Plant Science & Precision Agriculture’
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Cultivation study for Shikon (Lithospermum erythrorhizon), purple dye and traditional medicine2022

    • Author(s)
      Mareshige Kojoma
    • Organizer
      31st International Horticultural Congress
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Phytochemical genomics - from Arabidopsis and beyond…2022

    • Author(s)
      Kazuki Saito
    • Organizer
      Kyoto University ERATO International Symposium: Chemistry and Plant Biology
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Identification of an S-oxygenase involved in the biosynthesis of marasmin, an antibacterial component in Tulbaghia violacea2021

    • Author(s)
      2.Wang Jichen, Hideyuki Suzuki, Nanako Nakashima, Mariko Kitajima, Kazuki Saito, Mami Yamazaki, Naoko Yoshimoto
    • Organizer
      第65回日本薬学会関東支部大会(オンライン)
    • Related Report
      2021 Annual Research Report
  • [Presentation] ネギ属植物のカルスの誘導と硫黄二次代謝能の解析2021

    • Author(s)
      木佐貫あゆな、浅野孝、藤井勲、斉藤和季、吉本尚子
    • Organizer
      日本薬学会 第141年会(広島)
    • Related Report
      2020 Annual Research Report
  • [Presentation] カンプトテシン生合成解明を目指した統合オミクス科学2021

    • Author(s)
      山崎真巳、ライ アミット、北村智、齊藤和季
    • Organizer
      日本薬学会 第141年会(広島)
    • Related Report
      2020 Annual Research Report
  • [Presentation] ディリジェントタンパク質AtDP1 とラッカーゼAtLAC5 はシロイヌナズナの種子特異的ネオリグナンの生合成に関わる2021

    • Author(s)
      榊原圭子、山村正臣、松田史生、小埜栄一郎、中林 亮、菅原聡子、森 哲哉、飛松裕基、梅澤俊明、斉藤和季
    • Organizer
      第62回日本植物生理学会(島根)
    • Related Report
      2020 Annual Research Report
  • [Presentation] 液体クロマトグラフィータンデム質量分析とイメージング質量分析を用いたマルチメタボロミクスによる根浸出性代謝物の空間的蓄積様式の特定2021

    • Author(s)
      中林 亮、武田(神谷)紀子、森 哲哉、韮澤 崇、豊岡公徳、斉藤和季
    • Organizer
      第62回日本植物生理学会(島根)
    • Related Report
      2020 Annual Research Report
  • [Presentation] ネギ属植物のカルスにおける硫黄二次代謝能の解析2021

    • Author(s)
      木佐貫あゆな、浅野孝、藤井勲、斉藤和季、吉本尚子
    • Organizer
      第62回日本植物生理学会(島根)
    • Related Report
      2020 Annual Research Report
  • [Presentation] 薬用植物クララにおける二次代謝産物の生合成機構の解明 Elucidation of biosynthetic mechanism of secondary metabolisms in Sophora flavescens2020

    • Author(s)
      清水陽平, Rai Amit, 中村道美, 鈴木秀幸, 斉藤和季, 山崎真巳
    • Organizer
      第61回日本植物生理学会年会(大阪)
    • Related Report
      2019 Annual Research Report
  • [Presentation] Genome Assembly and Characterization of Medicinal Plant Sophora Flavescens2020

    • Author(s)
      Amit Rai , Yohei Shimizu , Hideki Hirakawa , Mami Yamazaki, Kazuki Saito
    • Organizer
      Plant and Animal Genome Conference XXVIII; San Diego, USA
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Book] Volume 7: New Methods in Natural Products Chemistry. in: Comprehensive Natural Products III: Chemistry and Biology2020

    • Author(s)
      Kazuki Saito
    • Publisher
      Elsevier
    • ISBN
      9780081026915
    • Related Report
      2020 Annual Research Report
  • [Book] The Origin of Plant Chemodiversity - Conceptual and Empirical Insights2020

    • Author(s)
      Kazuki Saito
    • Publisher
      Frontiers Media SA
    • Related Report
      2020 Annual Research Report
  • [Remarks] 理化学研究所 環境資源科学研究センター 統合メタボロミクス研究グループ

    • URL

      http://metabolomics.riken.jp/

    • Related Report
      2023 Annual Research Report

URL: 

Published: 2019-06-27   Modified: 2025-02-04  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi