Details of the Researcher

PHOTO

Riki Imaizumi
Section
Graduate School of Engineering
Job title
Specially Appointed Assistant Professor(Research)
Degree

  • Doctor of Philosophy in Science (Kanazawa University)

Education 2

  • 金沢大学大学院　自然科学研究科　物質化学専攻

    2019/04 - 2024/03

  • Kanazawa University

    2015/04 - 2019/03

Professional Memberships 4

  • 日本植物バイオテクノロジー学会

    2024/08 - Present

  • 日本農芸化学会

    2021/03 - Present

  • 日本蛋白質科学会

    2021/04 - 2024/03

  • 日本生化学会

    2019/04 - 2024/03

Awards 2

  1. n

    2024/03

  2. 奨励賞（若手優秀発表賞）

    2022/09　イソプレノイド研究会　植物由来短鎖cPTの末端ランダム領域の構造解明と酵素機能への重要性

Papers 7

  1. Transient dynamics of flavonoid metabolons tune chalcone synthase specificity Peer-reviewed

    Riki Imaizumi, Toshiyuki Waki, Yoshikazu Hattori, Kohei Takeshita, Miru Sumita, Kazutomo Kawaguchi, Hiroyuki Kumeta, Kenichi Umeda, Kyohei Sato, Taro Yanai, Hiroaki Matsuura, Takeshi Yokoyama, Risa Omura, Kayo Nakatani, Naoki Sakai, Yukimura Kawagiwa, Yamato Doi, Aoi Yasuda, Takuya Nakano, Kaichi Uno, Kunihiro Yoshida, Misato Tsunashima, Tomohide Saio, Yoshikazu Tanaka, Seiji Takahashi, Noriyuki Kodera, Kunishige Kataoka, Masaki Yamamoto, Satoshi Yamashita, Toru Nakayama

    Nature Catalysis　2026/06/15

    DOI： 10.1038/s41929-026-01551-6 　

  2. Biosynthesis of unnatural polyisoprenes by engineered prenyltransferases on rubber particles

    Seiji Takahashi, Miki Suenaga-Hiromori, Tomoki Ishii, Nadia Nur Shazana Binti Abu Talib Khan, Tomoyo Mikami, Tomohiro Takahashi, Chiho Minakawa, Fumihiro Yanbe, Toshiyuki Waki, Toru Nakayama, Riki Imaizumi, Taro Yanai, Kunishige Kataoka, Satoshi Yamashita, Kohei Takeshita, Hiroaki Matsuura, Naoki Sakai, Masaki Yamamoto, Haruhiko Yamaguchi, Yukino Miyagi-Inoue, Kazuhisa Fushihara, Yuzuru Tozawa

    2024/07/03

    Publisher: Springer Science and Business Media LLC

    DOI： 10.21203/rs.3.rs-3615345/v1 　

    More details Close

    Abstract <p>Natural rubber (NR) is a sustainable biopolymer consisting mainly of cis-1,4-polyisoprene. Modifying an NR biosynthetic enzyme is a promising strategy to bioproduce novel polymers. Here, we have elucidated the NR biosynthetic mechanism and successfully developed novel enzymes that synthesise NR-sized polyisoprenes with unnatural substrates. NR is synthesised by a cis-prenyltransferase (cPT) on rubber particles (RPs), NR-harbouring lipid monolayer membrane organelles. However, the key to NR biosynthesis is not specialised cPTs, but the proper arrangement of cPTs on RPs since cPTs from various non-NR-producing organisms, such as humans, synthesise NR when introduced into the RPs. A tomato cPT, which condenses only one isoprene unit, was engineered to synthesise novel NR-sized polyisoprenes with artificial substrates by modifying residues for product size determination. Furthermore, the introduction of a modified trans-prenyltransferase into RPs led to the synthesis of NR-sized trans-1,4-polyisoprenes. This RP system could be used as a versatile platform for enzymatic polyisoprenoid synthesis.</p>

  3. Structural insights into catalytic promiscuity of chalcone synthase from Glycine max (L.) Merr.: Coenzyme A-induced alteration of product specificity Peer-reviewed

    Toshiyuki Waki, Riki Imaizumi, Kaichi Uno, Yamato Doi, Misato Tsunashima, Sayumi Yamada, Ryo Mameda, Shun Nakata, Taro Yanai, Kohei Takeshita, Naoki Sakai, Kunishige Kataoka, Masaki Yamamoto, Seiji Takahashi, Toru Nakayama, Satoshi Yamashita

    Biochemical and Biophysical Research Communications　150080-150080　2024/05

    Publisher: Elsevier BV

    DOI： 10.1016/j.bbrc.2024.150080 　

    ISSN： 0006-291X

  4. Structural‐Functional Correlations between Unique N‐terminal Region and C‐terminal Conserved Motif in Short‐chain cis‐Prenyltransferase from Tomato Peer-reviewed

    Riki Imaizumi, Hiroaki Matsuura, Taro Yanai, Kohei Takeshita, Shuto Misawa, Haruhiko Yamaguchi, Naoki Sakai, Yukino Miyagi‐Inoue, Miki Suenaga‐Hiromori, Toshiyuki Waki, Kunishige Kataoka, Toru Nakayama, Masaki Yamamoto, Seiji Takahashi, Satoshi Yamashita

    ChemBioChem　2024/01/29

    Publisher: Wiley

    DOI： 10.1002/cbic.202300796 　

    ISSN： 1439-4227

    eISSN： 1439-7633

    More details Close

    Abstract Neryl diphosphate (C10) synthase (NDPS1), a homodimeric soluble cis‐prenyltransferase from tomato, contains four disulfide bonds, including two inter‐subunit S−S bonds in the N‐terminal region. Mutagenesis studies demonstrated that the S−S bond formation affects not only the stability of the dimer but also the catalytic efficiency of NDPS1. Structural polymorphs in the crystal structures of NDPS1 complexed with its substrate and substrate analog were identified by employing massive data collections and hierarchical clustering analysis. Heterogeneity of the C‐terminal region, including the conserved RXG motifs, was observed in addition to the polymorphs of the binding mode of the ligands. One of the RXG motifs covers the active site with an elongated random coil when the ligands are well‐ordered. Conversely, the other RXG motif was located away from the active site with a helical structure. The heterogeneous C‐terminal regions suggest alternating structural transitions of the RXG motifs that result in closed and open states of the active sites. Site‐directed mutagenesis studies demonstrated that the conserved glycine residue cannot be replaced. We propose that the putative structural transitions of the order/disorder of N‐terminal regions and the closed/open states of C‐terminal regions may cooperate and be important for the catalytic mechanism of NDPS1.

  5. 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 domain Peer-reviewed

    Taro Yanai, Yukino Takahashi, Eri Katsumura, Naoki Sakai, Kohei Takeshita, Riki Imaizumi, Hiroaki Matsuura, Shuntaro Hongo, Toshiyuki Waki, Seiji Takahashi, Masaki Yamamoto, Kunishige Kataoka, Toru Nakayama, Satoshi Yamashita

    The Journal of Biochemistry　174　(4)　335-344　2023/06/29

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/jb/mvad048 　

    ISSN： 0021-924X

    eISSN： 1756-2651

    More details Close

    Abstract The sesaminol triglucoside (STG)-hydrolyzing β-glucosidase from Paenibacillus sp. (PSTG1), which belongs to glycoside hydrolase family 3 (GH3), is a promising catalyst for the industrial production of sesaminol. We determined the X-ray crystal structure of PSTG1 with bound glycerol molecule in the putative active site. PSTG1 monomer contained typical three domains of GH3 with the active site in domain 1 (TIM barrel). In addition, PSTG1 contained an additional domain (domain 4) at the C-terminus that interacts with the active site of the other protomer as a lid in the dimer unit. Interestingly, the interface of domain 4 and the active site forms a hydrophobic cavity probably for recognizing the hydrophobic aglycone moiety of substrate. The short flexible loop region of TIM barrel was found to be approaching the interface of domain 4 and the active site. We found that n-heptyl-β-D-thioglucopyranoside detergent acts as an inhibitor for PSTG1. Thus, we propose that the recognition of hydrophobic aglycone moiety is important for PSTG1-catalyzed reactions. Domain 4 might be a potential target for elucidating the aglycone recognition mechanism of PSTG1 as well as for engineering PSTG1 to create a further excellent enzyme to degrade STG more efficiently to produce sesaminol.

  6. Structure‐based engineering of a short‐chain cis‐prenyltransferase to biosynthesize nonnatural all‐ cis ‐polyisoprenoids: molecular mechanisms for primer substrate recognition and ultimate product chain‐length determination International-journal Peer-reviewed

    Ryo Kutsukawa and Riki Imaizumi, Miki Suenaga‐Hiromori, Kohei Takeshita, Naoki Sakai, Shuto Misawa, Masaki Yamamoto, Haruhiko Yamaguchi, Yukino Miyagi‐Inoue, Toshiyuki Waki, Kunishige Kataoka, Toru Nakayama, Satoshi Yamashita, Seiji Takahashi

    The FEBS Journal　289　(15)　4602-4621　2022/02/22

    Publisher: Wiley

    DOI： 10.1111/febs.16392 　

    ISSN： 1742-464X

    eISSN： 1742-4658

    More details Close

    Most cis-prenyltransferases (cPTs) use all-trans-oligoprenyl diphosphate, such as (E,E)-farnesyl diphosphate (FPP, C15 ), but scarcely accept dimethylallyl diphosphate (DMAPP, C5 ), as an allylic diphosphate primer in consecutive cis-condensations of isopentenyl diphosphate. Consequently, naturally occurring cis-1,4-polyisoprenoids contain a few trans-isoprene units at their ω-end. However, some Solanum plants have distinct cPTs that primarily use DMAPP as a primer to synthesize all-cis-oligoprenyl diphosphates, such as neryl diphosphate (NPP, C10 ). However, the mechanism underlying the allylic substrate preference of cPTs remains unclear. In this study, we determined the crystal structure of NDPS1, an NPP synthase from tomato, and investigated critical residues for primer substrate preference through structural comparisons of cPTs. Highly conserved Gly and Trp in the primer substrate-binding region of cPTs were discovered to be substituted for Ile/Leu and Phe, respectively, in DMAPP-preferring cPTs. An I106G mutant of NDPS1 exhibited a low preference for DMAPP, but a higher preference for FPP. However, an I106G/F276W mutant preferred not only DMAPP but also all-trans-oligoprenyl diphosphates, with 15-fold higher catalytic efficiency than WT. Surprisingly, the mutant synthesized longer polyisoprenoids (~C50 ). Furthermore, one of the helix domains that constitute the hydrophobic cleft for accommodating elongating prenyl chains was also demonstrated to be critical in primer substrate preference. An NDPS1 I106G/F276W mutant with a chimeric helix domain swapped with that of a medium-chain cPT synthesizing C50-60 polyisoprenoids showed over 94-fold increase in catalytic efficiency for all primer substrates tested, resulting in longer products (~C70 ). These NDPS1 mutants could be used in the enzymatic synthesis of nonnatural all-cis-polyisoprenoids.

  7. Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean International-journal Peer-reviewed

    Riki Imaizumi, Ryo Mameda, Kohei Takeshita, Hiroki Kubo, Naoki Sakai, Shun Nakata, Seiji Takahashi, Kunishige Kataoka, Masaki Yamamoto, Toru Nakayama, Satoshi Yamashita, Toshiyuki Waki

    Proteins: Structure, Function, and Bioinformatics　89　(1)　126-131　2021/01

    Publisher: Wiley

    DOI： 10.1002/prot.25988 　

    ISSN： 0887-3585

    eISSN： 1097-0134

    More details Close

    Isoflavonoid is one of the groups of flavonoids that play pivotal roles in the survival of land plants. Chalcone synthase (CHS), the first enzyme of the isoflavonoid biosynthetic pathway, catalyzes the formation of a common isoflavonoid precursor. We have previously reported that an isozyme of soybean CHS (termed GmCHS1) is a key component of the isoflavonoid metabolon, a protein complex to enhance efficiency of isoflavonoid production. Here, we determined the crystal structure of GmCHS1 as a first step of understanding the metabolon structure, as well as to better understand the catalytic mechanism of GmCHS1.

Show all ︎Show first 5

Misc. 18

  1. チクル生合成に関与するtrans型プレニルトランスフェラーゼの構造的基盤とダイマー間架橋の意義

    中切亮我, 矢内太朗, 今泉璃城, 山口晴彦, 竹下浩平, 竹下浩平, 坂口祐美, 戸澤譲, 高橋征司, 山下哲

    イソプレノイド研究会例会講演要旨集(CD-ROM)　35th　2025

  2. Investigating the mechanism of higher-order structure formation and X-ray crystallography of chalcone isomerase from snapdragon

    隅田深瑠, 宮原一真, 矢内太郎, 竹下浩平, 今泉璃城, 和氣駿之, 片岡邦重, 山本雅貴, 中山亨, 山下哲

    日本農芸化学会大会講演要旨集(Web)　2025　2025

    ISSN： 2186-7976

  3. Structural studies to elucidate substrate recognition mechanisms of sesaminol glycoside hydrolases

    荒井杏美, 矢内太郎, 高橋由季乃, 竹下浩平, 今泉璃城, 山本雅貴, 片岡邦重, 中山亨, 山下哲

    日本農芸化学会大会講演要旨集(Web)　2025　2025

    ISSN： 2186-7976

  4. 短鎖シス型プレニルトランスフェラーゼダイマーのサブユニット間相互作用およびC末端の二次構造変化が関与する触媒機構

    今泉璃城, 今泉璃城, 松浦滉明, 矢内太朗, 山口晴彦, 竹下浩平, 廣森美樹, 宮城ゆき乃, 山本雅貴, 中山亨, 高橋征司, 山下哲

    イソプレノイド研究会例会講演要旨集(CD-ROM)　34th　2024

  5. 天然ゴム合成コア酵素を構成するHRBPのN末端およびC末端ドメインに関する研究

    田村夏美, 矢内太朗, 今泉璃城, 山口晴彦, 宮城ゆき乃, 竹下浩平, 片岡邦重, 高橋征司, 山下哲

    日本生化学会大会(Web)　97th　2024

  6. The Crystal Structure of Chalcone Synthase Complexd with Chalcone Isomerase-like Protein

    今泉璃城, 和氣駿之, 竹下浩平, 安田あおい, 松浦滉明, 中多舜, 坂井直樹, 片岡邦重, 高橋征司, 山本雅貴, 山下哲, 中山亨

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  7. The Crystal Structure of Sesame Lignan Glycoside Hydrolase and the Novel Function of its C-terminal Domain

    矢内太朗, 高橋由季乃, 坂井直樹, 竹下浩平, 今泉璃城, 松浦滉明, 和氣駿之, 高橋征司, 山本雅貴, 片岡邦重, 中山亨, 山下哲

    日本農芸化学会大会講演要旨集(Web)　2024　2024

    ISSN： 2186-7976

  8. サポジラ(Manilkara zapota)由来トランス型プレニルトランスフェラーゼのタンパク質工学とX線結晶構造解析の試み

    矢内太朗, 森麻人, 中切亮我, 今泉璃城, 山口晴彦, 竹下浩平, 松浦滉明, 宮城ゆき乃, 片岡邦重, 和氣駿之, 中山亨, 高橋征司, 山下哲

    イソプレノイド研究会例会講演要旨集(CD-ROM)　33rd　2023

  9. セサミノール配糖体加水分解酵素のX線結晶構造解析によって示されたC末端ドメインの新奇機能

    矢内太朗, 高橋由季乃, 坂井直樹, 竹下浩平, 今泉璃城, 松浦滉明, 宮原一真, 和氣駿之, 高橋征司, 山本雅貴, 片岡邦重, 中山亨, 山下哲

    日本生化学会大会(Web)　96th　2023

  10. 天然ゴム合成酵素の活性調節タンパク質HRBPのN末端欠損型の精製とキャラクタリゼーション

    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

    日本生化学会大会(Web)　95th　2022

  11. フラボノイド生合成の初発酵素であるカルコン合成酵素の阻害に関する構造的研究

    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

    日本生化学会大会(Web)　95th　2022

  12. 銅中心遠位部位の変異により高活性化した一価銅酸化酵素の構造

    今泉璃城, 中多舜, 河野天太, 山下哲, 片岡邦重

    ビタミン　96　(3)　2022

    ISSN： 0006-386X

  13. 指向性進化法による高活性型マルチ銅オキシダーゼの結晶構造解析

    中多舜, 河野天太, 高田修平, 今泉璃城, 坂井直樹, 竹下浩平, 山下哲, 櫻井武, 片岡邦重

    日本生化学会大会(Web)　94th　2021

  14. Exploring catalytically omportant amino acid residues of a soybean isoflavone glucosyltransferase

    中山亨, 佐藤誠哉, 伊藤圭介, 高橋征司, 和氣駿之, 高橋厚人, 大山拓次, 楠木正巳, 今泉璃城, 山下哲

    日本農芸化学会大会講演要旨集(Web)　2021　2021

    ISSN： 2186-7976

  15. ダイズイソフラボノイド生合成に関与するカルコン合成酵素の結晶構造解析

    中多舜, 和氣駿之, 今泉璃城, 久保大樹, 竹下浩平, 片岡邦重, 中山亨, 山下哲

    日本生化学会大会(Web)　93rd　2020

  16. X-ray crystallography of soybean isoflavone biosynthetic enzyme

    山下哲, 今泉璃城, 中多舜, 竹下浩平, 和氣駿之, 山本雅貴, 高橋征司, 片岡邦重, 中山亨

    日本農芸化学会大会講演要旨集(Web)　2020　2020

    ISSN： 2186-7976

  17. 長鎖シス型プレニルトランスフェラーゼのパートナーであるNogo-B receptorファミリーのタンパク質構造について

    矢内太朗, 今泉璃城, 高畑佳佑, 山口晴彦, 宮城ゆき乃, 竹下浩平, 戸澤譲, 高橋征司, 山下哲

    イソプレノイド研究会例会講演要旨集　30th　2020

  18. パラゴムノキの天然ゴム生合成に関与するcis-prenyltransferaseとパートナータンパク質間の相互作用解析

    今泉璃城, 山口晴彦, 宮城ゆき乃, 片岡邦重, 戸澤譲, 伏原和久, 高橋征司, 山下哲

    日本生化学会大会(Web)　92nd　2019

Show all ︎Show first 5

Presentations 7

  1. Structural dynamics narrowing chalcone synthase specificity in a flavonoid metabolon

    Riki Imaizumi, Toshiyuki Waki, Kohei Takeshita, Taro Yanai, Hiroaki Matsuura, Miru Sumita, Naoki Sakai, Yukimura Kawagiwa, Aoi Yasuda, Seiji Takahashi, Kunishige Kataoka, Masaki Yamamoto, Toru Nakayama, Satoshi Yamashita

    Pacifichem2025　2025/12/19

  2. セイヨウトウキ由来モノテルペン合成酵素の 生成物特異性決定要因に関する研究

    今泉 璃城, 天野博之, 栗栖尚嗣, 角掛陽, 茂木大介, 菊池洋平, 廣森美樹, 和氣駿之, 中山亨, 高橋征司

    第35回イソプレノイド研究会　2025/09/16

  3. 両親媒性コポリマーを用いた天然ゴム生合成酵素含有 ゴム粒子膜マイクロドメインの可溶化

    三上 智世, 今泉 璃城, NADIA NUR, SHAZANA ABU TALIB KHAN, 小島 幸治, 廣森 美樹, 和氣 駿之, 山下 哲, 戸澤 譲, 山口 晴彦, 坂口 祐美, 中山 亨, 高橋 征司

    日本農芸化学会 2025年度札幌大会　2025/03/06

  4. Structural Insights into the Mechanism of Chalcone isomerase-like protein that Rectifies Chalcone Synthase Activity

    2024/09/01

  5. テルペノイド生合成に関与するシス型プレニルトランスフェラーゼの先端的立体構造解析と酵素機能改変 Invited

    今泉 璃城

    日本ビタミン学会第76回大会　2024/06/08

  6. Structural and functional importance of the C-terminal conserved region of neryl diphosphate synthase from tomato

    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

    terpnet 2023　2023/08/02

  7. Studies on allylic substrate recognition and prenyl-chain elongation mechanism in cis-prenyltransferase from plant

    Riki Imaizumi, Ryo Kutsukawa, Miki Suenaga, Haruhiko Yamaguchi, Yukino Miyagi-Inoue, Kazuhisa Fushihara, Toru Nakayama, Satoshi Yamashita, Seiji Takahashi

    Pacifichem 2021　2021/12/18

Show all Show first 5

Research Projects 2

  1. 膜環境を維持した膜結合型酵素の単離法の確立と構造解析

    今泉 璃城

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 研究活動スタート支援

    Institution: 東北大学

    2024/07/31 - 2026/03/31

  2. 植物二次代謝の高効率な生合成の鍵となるメタボロンの構造解析と膜上動態イメージング

    今泉 璃城

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業 特別研究員奨励費

    Category: 特別研究員奨励費

    Institution: 金沢大学

    2021/04/28 - 2024/03/31

    More details Close

    本研究は，植物のイソフラボン及び天然ゴム生合成において、進化の過程でつくりだした酵素複合体がダイナミックに動く姿と，分子レベルでの詳細な構造を捉え、高効率な生合成の謎を解明することを目的としている．本年度は，分子レベルでの詳細な構造を捉えるため，発現・精製・結晶化条件の最適化を行った．イソフラボンを含むフラボノイド生合成の初発段階を担い，酵素複合体(メタボロン)の構成因子の一つであるダイズ由来カルコン合成酵素(CHS)の反応特異性低下の原因であると考えられる補因子A(CoA)との複合体構造を原子分解能で決定した．この構造からCoA結合サイトを決定し，CoAによるCHSに対する反応阻害様式を明らかにした．この知見を代謝工学的に応用できれば，様々な生理活性を有するフラボノイド類の高効率な発酵生産系構築につなげられる可能性がある．さらに，天然ゴム生合成酵素類似酵素であるトマト由来ネリル二リン酸合成酵素(NDPS1)の結晶構造を1.9Å分解能で決定した．さらに，NDPS1を一部改変することにより酵素活性の上昇ならびに生成物特性の変換が可能であることを示した．本成果は，査読付き国際学術雑誌であるThe FEBS Journalにアクセプトされ，オンライン公開された．この知見は，超長鎖のポリマー分子である天然ゴムの生合成機構解明へ向けた重要な知見であるのみならず，酵素改変により創出した非天然型の全シス型イソプレンポリマーをテルペンサイクラーゼ等により修飾することで非天然型新規化合物を生み出すことができる可能性がある．現在，決定した結晶化条件を元にNDPS1と生成物アナログとの複合体構造を決定するため，再度条件の最適化及びX線回折実験を進めている．また，高速バイオAFMによる動的な構造解析についても，採用時の年度計画を元に条件検討を進めている．