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Understanding the core structures and dynamics of membrane protein complexes related in productions of valuable compounds from plants

Research Project

Project/Area Number 21H02115
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 38030:Applied biochemistry-related
Research InstitutionKanazawa University

Principal Investigator

YAMASHITA SATOSHI  金沢大学, 物質化学系, 准教授 (70361186)

Co-Investigator(Kenkyū-buntansha) 戸澤 譲  埼玉大学, 理工学研究科, 教授 (90363267)
Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥17,810,000 (Direct Cost: ¥13,700,000、Indirect Cost: ¥4,110,000)
Fiscal Year 2023: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2022: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2021: ¥10,530,000 (Direct Cost: ¥8,100,000、Indirect Cost: ¥2,430,000)
Keywords天然ゴム / フラボノイド / メタボロン / イソプレノイド / 植物特化代謝 / 二次代謝産物 / 結晶構造 / 脂溶性有用物質 / X線結晶構造解析 / ナノディスク / 無細胞翻訳系
Outline of Research at the Start

植物が生産するフラボノイドや天然ゴムなどの有用な二次代謝産物は、膜に結合する酵素が複合体をつくることにより効率的に合成していることが徐々にわかってきているが、この膜酵素複合体は壊れやすく、詳細に観察された例がない。本研究では、酵素複合体をナノスケールのディスク状膜構造へ乗せ、その機能に必要な最小単位(コア構造)を解明する。方法として、上記の膜構造に乗せた酵素を特殊な試薬で結び付けたり、同時に結晶化したりすることにより、複数の酵素がどのように相互作用しているかを解明する。また、ナノスケールの酵素の動きを観察できる原子間力顕微鏡(高速バイオAFM)を用いて、複合体のダイナミックな姿を明らかにする。

Outline of Final Research Achievements

Plant secondary metabolites (so called plant specialized metabolites) have been thought to be efficiently synthesized by a membrane-bound enzyme complex which is termed as metabolon. However, complex structures, stoichiometry and interface of the complex have not yet been clarified because of weak interactions between metabolon components on membrane environment. So far, no metabolon have been isolated and crystallized as a complex. In this project, flavonoid and isoprenoid (especially natural rubber) biosynthetic enzymes, that are known to form metabolon, were investigated. As a result, we successfully determined the stoichiometry and conditions that are required for the enzymatic activity of the core complex for natural rubber biosynthesis. Moreover, the core complex for flavonoid biosynthetic pathway were crystallized as a complex for the first time. This complex structure revealed the interface which was supported by crosslinking experiments.

Academic Significance and Societal Importance of the Research Achievements

植物が生産する二次代謝産物は、近年は植物特化代謝産物とよばれ、薬用化合物の宝庫である。また、植物特化代謝産物の一種である天然ゴムは、化学成分としては普遍的なイソプレンという繰り返しから合成されるものでありながら、ポリマーとしてのゴムは、特定のゴム生産植物しか合成できない。そのため、植物は奇跡の化学工場とも言われているが、そのキーとなるのが酵素複合体メタボロンの形成である。これらの作用機序、複合体構造、量論比、相互作用界面に関する知見を得ることは、基礎科学として新規性が高いが、微生物などの他の宿主で植物特化代謝の代替生産系を構築する応用上、必要不可欠な情報であり、大きな波及効果がある。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • Research Products

    (36 results)

All 2024 2023 2022 2021 Other

All Int'l Joint Research (1 results) Journal Article (9 results) (of which Peer Reviewed: 7 results,  Open Access: 1 results) Presentation (26 results) (of which Int'l Joint Research: 5 results,  Invited: 2 results)

  • [Int'l Joint Research] University of Tennessee, Knoxville(米国)

    • Related Report
      2023 Annual Research Report
  • [Journal Article] Cell-free translation system with artificial lipid-monolayer particles as a unique tool for characterizing lipid-monolayer binding proteins2024

    • Author(s)
      Kuroiwa Fu、Suda Hiraku、Yabuki Maho、Atsuzawa Kimie、Yamaguchi Haruhiko、Toyota Masatsugu、Kaneko Yasuko、Yamashita Satoshi、Takahashi Seiji、Tozawa Yuzuru
    • Journal Title

      Bioscience, Biotechnology, and Biochemistry

      Volume: 88 Issue: 5 Pages: 555-560

    • DOI

      10.1093/bbb/zbae026

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Front Cover: Structural‐Functional Correlations between Unique N‐terminal Region and C‐terminal Conserved Motif in Short‐chain <i>cis</i>‐Prenyltransferase from Tomato (ChemBioChem 7/2024)2024

    • Author(s)
      Imaizumi Riki、Matsuura Hiroaki、Yanai Taro、Takeshita Kohei、Misawa Shuto、Yamaguchi Haruhiko、Sakai Naoki、Miyagi‐Inoue Yukino、Suenaga‐Hiromori Miki、Waki Toshiyuki、Kataoka Kunishige、Nakayama Toru、Yamamoto Masaki、Takahashi Seiji、Yamashita Satoshi
    • Journal Title

      ChemBioChem

      Volume: 25 Issue: 7

    • DOI

      10.1002/cbic.202400160

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural insights into a bacterial β-glucosidase capable of degrading sesaminol triglucoside to produce sesaminol: toward the understanding of the aglycone recognition mechanism by the C-terminal lid domain2023

    • Author(s)
      Yanai Taro、Takahashi Yukino、Katsumura Eri、Sakai Naoki、Takeshita Kohei、Imaizumi Riki、Matsuura Hiroaki、Hongo Shuntaro、Waki Toshiyuki、Takahashi Seiji、Yamamoto Masaki、Kataoka Kunishige、Nakayama Toru、Yamashita Satoshi
    • Journal Title

      The Journal of Biochemistry

      Volume: 174 Issue: 4 Pages: 335-344

    • DOI

      10.1093/jb/mvad048

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Influence of distal glycan mimics on direct electron transfer performance for bilirubin oxidase bioelectrocatalysts2023

    • Author(s)
      Nishida Sayaka、Sumi Hinata、Noji Haruna、Itoh Akira、Kataoka Kunishige、Yamashita Satoshi、Kano Kenji、Sowa Keisei、Kitazumi Yuki、Shirai Osamu
    • Journal Title

      Bioelectrochemistry

      Volume: 152 Pages: 108413-108413

    • DOI

      10.1016/j.bioelechem.2023.108413

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 酵素の機能改変で自然界に存在しないポリイソプレノイドを合成2023

    • Author(s)
      高橋 征司, 竹下 浩平, 山口 晴彦, 山下 哲
    • Journal Title

      JETI = ジェティ : Japan energy & technology intelligence

      Volume: 70 Pages: 91-94

    • Related Report
      2023 Annual Research Report
  • [Journal Article] 天然ゴムの生合成コア酵素系の試験管内再構成2022

    • Author(s)
      黒岩風, 戸澤譲
    • Journal Title

      バイオサイエンスとインダストリー

      Volume: 80 Pages: 488-490

    • Related Report
      2022 Annual Research Report
  • [Journal Article] Reconstitution of prenyltransferase activity on nanodiscs by components of the rubber synthesis machinery of the Para rubber tree and guayule2022

    • Author(s)
      Kuroiwa Fu、Nishino Akira、Mandal Yasuko、Honzawa Masataka、Suenaga-Hiromori Miki、Suzuki Kakeru、Takani Yukie、Miyagi-Inoue Yukino、Yamaguchi Haruhiko、Yamashita Satoshi、Takahashi Seiji、Tozawa Yuzuru
    • Journal Title

      Scientific Reports

      Volume: 12 Issue: 1

    • DOI

      10.1038/s41598-022-07564-y

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure‐based engineering of a short‐chain <i>cis</i>‐prenyltransferase to biosynthesize nonnatural all‐ <i>cis</i> ‐polyisoprenoids: molecular mechanisms for primer substrate recognition and ultimate product chain‐length determination2022

    • Author(s)
      Kutsukawa Ryo、Imaizumi Riki、Suenaga‐Hiromori Miki、Takeshita Kohei、Sakai Naoki、Misawa Shuto、Yamamoto Masaki、Yamaguchi Haruhiko、Miyagi‐Inoue Yukino、Waki Toshiyuki、Kataoka Kunishige、Nakayama Toru、Yamashita Satoshi、Takahashi Seiji
    • Journal Title

      The FEBS Journal

      Volume: - Issue: 15 Pages: 4602-4621

    • DOI

      10.1111/febs.16392

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Catalytic promiscuity of rice 2-oxoglutarate/Fe(II)-dependent dioxygenases supports xenobiotic metabolism2021

    • Author(s)
      Takamura Natsuki、Yamazaki Akihiko、Sakuma Nozomi、Hirose Sakiko、Sakai Motonari、Takani Yukie、Yamashita Satoshi、Oshima Masahiro、Kuroki Makoto、Tozawa Yuzuru
    • Journal Title

      Plant Physiology

      Volume: 187 Issue: 2 Pages: 816-828

    • DOI

      10.1093/plphys/kiab293

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Presentation] Structural basis of short-chain cis-prenyltransferase from plants.2023

    • Author(s)
      Satoshi Yamashita
    • Organizer
      TERPNET 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Protein engineering, purification and characterization of a regulatory protein for cis-prenyltransferase from plant2023

    • Author(s)
      Taro YANAI, Kohei TAKESHITA, Riki IMAIZUMI, Natsumi TAMURA, Haruhiko YAMAGUCHI, Yukino MIYAGI-INOUE, Kunishige KATAOKA, Masaki YAMAMOTO, Toru Nakayama, Seiji TAKAHASHI, Satoshi YAMASHITA
    • Organizer
      TERPNET 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] n vitro reconstitution of core components of the rubber synthesis machinery based on a cell-free translation system.2023

    • Author(s)
      Fu Kuroiwa, Haruhiko Yamaguchi, Yukino Miyagi, Satoshi Yamashita, Seiji Takahashi, and Yuzuru Tozawa
    • Organizer
      TERPNET 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Structural and functional importance of the C-terminal conserved region of neryl diphosphate synthase from tomato2023

    • Author(s)
      Riki Imaizumi, Shuto Misawa, Taro Yanai, Kohei Takeshita, Hiroaki Matsuura, Haruhiko Yamaguchi, Yukino Miyagi-Inoue, Naoki Sakai, Kunishige Kataoka, Masaki Yamamoto, Toru Nakayama, Seiji Takahashi, Satoshi Yamashita
    • Organizer
      TERPNET 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 両親媒性コポリマーによる可溶化技術を用いたパラゴムノキ(Hevea brasiliensis)の天然ゴム生合成複合体単離2023

    • Author(s)
      KHAN Nadia Nur Shazana Binti Abu Talib, 小島幸治, 山口晴彦, 三上智世, 廣森美樹, 和氣駿之, 宮城ゆき乃, 山下哲, 戸澤譲, 中山亨、高橋征司
    • Organizer
      日本植物生理学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Biosynthesis of non-natural polyisoprenoids by functionally modified cis-prenyltransferases2022

    • Author(s)
      Haruhiko Yamaguchi, Yukino Miyagi-Inoue, Ryo Kutsukawa, Riki Imaizumi, Miki Suenaga-Hiromori, Syuto Misawa, Toshiyuki Waki, Toru Nakayama, Satoshi Yamashita, Seiji Takahashi
    • Organizer
      33rd Annual Association for Advancement of Industrial Crops (AAIC) meeting
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Structural basis and protein engineering of polyisoprenoid synthase2022

    • Author(s)
      山下哲
    • Organizer
      第3回天然ゴム研究会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Protein Engineering of the Regulatory Factor for Natural Rubber Synthase and its Structural Evaluation2022

    • Author(s)
      矢内太朗, 田村夏美, 山口晴彦, 宮城ゆき乃, 竹下浩平, 片岡邦重, 戸澤譲, 高橋征司, 山下哲
    • Organizer
      第3回天然ゴム研究会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Purification and Structural Analysis of a Membrane Protein Involved in Emulsification of Natural Rubber2022

    • Author(s)
      吉田城啓,黒澤悠太郎,林文晶,山口晴彦,島春奈,川端健太,竹下浩平, 宮城ゆき乃,片岡邦重,山下哲
    • Organizer
      第3回天然ゴム研究会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Structural determination and identification of regulation mechanisms of a natural rubber synthase homolog from plant2022

    • Author(s)
      今泉璃城,三沢柊人,山口晴彦,宮城ゆき乃,竹下浩平,廣森美樹,高橋征司,山下哲
    • Organizer
      第3回天然ゴム研究会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Enzymatic characterization of a trans-prenyltransferase from Manilkara zapota MztPT22022

    • Author(s)
      井澤大輔,三輪幸祐,廣森美樹,青木裕一,和氣駿之,小島幸治,山口晴彦,宮城ゆき乃,山下哲,戸澤譲,中山亨,高橋征司
    • Organizer
      第3回天然ゴム研究会
    • Related Report
      2022 Annual Research Report
  • [Presentation] olubilization of rubber particle membrane proteins by amphiphilic copolymers2022

    • Author(s)
      三上智世,NADIA NUR SHAZANA BINTI ABU TALIB KHAN,小島幸治,山口 晴彦,廣森 美樹,和氣 駿之,宮城 ゆき乃,山下 哲,戸澤 譲,中山 亨,高橋 征司
    • Organizer
      第3回天然ゴム研究会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 脂肪滴およびゴム粒子の構造維持に関わる膜タンパク質の比較解析2022

    • Author(s)
      中山隆司,開琢海,三輪 幸祐,廣森 美樹,和氣 駿之,山下哲,戸澤 譲,山口晴彦,宮城ゆき乃, 岩井 雅子,太田 啓之,中山 亨,高橋 征司
    • Organizer
      第95回日本生化学会大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Structural insight into the inhibition of chalcone synthase, the initial enzyme of flavonoid biosynthesis2022

    • Author(s)
      安田あおい,今泉璃城,中多舜,竹下浩平、坂井直樹、和氣駿之,片岡邦重,中山亨,山下哲
    • Organizer
      第95回日本生化学会大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Purification and characterization of N-terminally truncated HRBP, a regulatory protein for natural rubber synthase2022

    • Author(s)
      矢内太朗,今泉璃城,田村夏美,山口晴彦、宮城ゆき乃、片岡邦重,高橋征司,山下哲
    • Organizer
      第95回日本生化学会大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Functional study of putative catalytic residues of sesaminol glycoside hydrolyzing enzyme2022

    • Author(s)
      高橋由季乃、矢内太朗、勝村恵理、和氣駿之、片岡邦重、中山亨、山下哲
    • Organizer
      第95回日本生化学会大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 天然ゴム生合成に関与する膜結合型タンパク質の末端構造の解析2022

    • Author(s)
      吉田城啓,黒澤悠太郎,林文晶,山口晴彦,竹下浩平, 宮城ゆき乃,片岡邦重,山下哲
    • Organizer
      2022年度日本化学会北陸地区講演会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 植物由来トランス型プレニルトランスフェラーゼの精製と結晶化2022

    • Author(s)
      森麻人, 今泉璃城, 矢内太朗, 山口晴彦, 竹下浩平, 宮城ゆき乃, 片岡邦重, 高橋征司, 山下哲
    • Organizer
      2022年度日本化学会北陸地区講演会
    • Related Report
      2022 Annual Research Report
  • [Presentation] X線結晶構造に基づくシス型プレニルトランスフェラーゼの末端領域の機能解析2022

    • Author(s)
      三沢 柊人、今泉璃城、廣森美樹、片岡邦重、中山享、高橋征司、山下哲
    • Organizer
      日本生化学会北陸支部第40回大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 天然ゴム生合成機構の解明に向けた脂質単層膜ベシクルシステムの構築2022

    • Author(s)
      黒岩風, 矢吹眞帆, 山口晴彦, 宮城ゆき乃, 山下哲, 高橋征司, 戸澤譲
    • Organizer
      第3回天然ゴム研究会
    • Related Report
      2022 Annual Research Report
  • [Presentation] パラゴムノキの天然ゴム生合成酵素複合体におけるタンパク質間相互作用ドメインとその機能的意義の解析2022

    • Author(s)
      Nadia NUR SHAZANA BINTI ABU TALIB KHAN、廣森美樹、和氣駿之、山下哲、戸澤譲、山口晴彦、宮城ゆき乃、中山亨、高橋征司
    • Organizer
      日本農芸化学会2022年度大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] トマト由来ネリル二リン酸合成酵素NDPS1のX線結晶構造解析2022

    • Author(s)
      今泉璃城、三沢柊人、竹下浩平、坂井直樹、山口晴彦、宮城ゆき乃、片岡邦重、中山享、高橋征司、山下哲
    • Organizer
      日本農芸化学会2022年度大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 天然ゴム生合成マシナリーのコアサブユニットの解析2022

    • Author(s)
      黒岩風、西野輝、本澤正隆、廣森美樹、モンドル慶子、山口晴彦、宮城ゆき乃、山下哲、高橋征司、戸澤譲
    • Organizer
      日本農芸化学会2022年度大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] パラゴムノキおよびグアユール由来タンパク質によるナノディスク上へのプレニルトランスフェラーゼ活性の再構成2021

    • Author(s)
      黒岩風, 西野輝, 廣森美樹, モンドル慶子, 山口晴彦, 宮城ゆき乃, 山下哲, 高橋征司, 戸澤譲
    • Organizer
      イソプレノイド研究会例会
    • Related Report
      2021 Annual Research Report
  • [Presentation] サポジラ(Manilkara zapota)由来trans型プレニルトランスフェラーゼの酵素機能解析2021

    • Author(s)
      三輪幸祐, 廣森美樹, 青木裕一, 和氣駿之, 小島幸治, 山下哲, 山口晴彦, 宮城ゆき乃, 戸澤譲, 中山亨, 高橋征司
    • Organizer
      イソプレノイド研究会例会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 無細胞翻訳系を用いた脂肪滴への外来酵素導入によるイソプレノイドポリマー生産2021

    • Author(s)
      開琢海, 三輪幸祐, 廣森美樹, 和氣駿之, 山下哲, 戸澤譲, 山口晴彦, 宮城ゆき乃, 岩井雅子, 太田啓之, 中山亨, 高橋征司
    • Organizer
      イソプレノイド研究会例会
    • Related Report
      2021 Annual Research Report

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Published: 2021-04-28   Modified: 2025-01-30  

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