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Identification of the genes encoding biomass-degrading enzymes by microbial screening based on microdroplet deformability

Research Project

Project/Area Number 18K05330
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 37020:Chemistry and chemical methodology of biomolecules-related
Research InstitutionThe University of Tokyo

Principal Investigator

Iizuka Ryo  東京大学, 大学院理学系研究科(理学部), 助教 (90541954)

Project Period (FY) 2018-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2020: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2019: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords液滴 / マイクロ流体デバイス / 酵素 / スクリーニング
Outline of Final Research Achievements

Environmental microbes secrete enzymes capable of degrading macromolecules, such as agarose, into smaller molecules for cell growth. These enzymes can benefit the effective use of renewable natural resources such as biomass. However, most microbial cells remain unculturable and thus are inaccessible by culture-based methods. We then developed a culture-independent method for screening microbial cells that secrete polysaccharide hydrogel-degrading enzymes using deformability-based microfluidic microdroplet sorting. In this method, microbial cells are encapsulated as single cells in water-in-oil (W/O) microdroplets with hydrogel, whose shape becomes deformable as the hydrogel is progressively degraded into smaller molecules. Screening is achieved using a microfluidic device that passively sorts the deformed W/O microdroplets. Using this method, we successfully isolated single bacterial cells that hydrolyze agarose from seawater to identify agarase genes.

Academic Significance and Societal Importance of the Research Achievements

世界で6番目の広さの海洋に囲まれる我が国では,安定的に大量供給が可能で食糧と競合しないリグノセルロース系バイオマス(セルロース,ヘミセルロース,リグニンなど)とともに,海藻バイオマス(アガロース,アルギン酸,フコイダンなど海藻多糖類)の有効利用が重要である.海藻多糖類はエタノールなどのエネルギー原料のみならず,付加価値の高い生理活性分子に変換可能である.しかし,海藻多糖類を効率よく分解できる酵素の報告は少ない.本研究で確立したスクリーニング法を駆使することで,優れた海藻多糖類分解酵素の取得が可能となる.

Report

(5 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (53 results)

All 2022 2021 2020 2019 2018 Other

All Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 5 results,  Open Access: 3 results) Presentation (41 results) (of which Int'l Joint Research: 8 results,  Invited: 9 results) Book (2 results) Remarks (3 results)

  • [Journal Article] Inside or out? Clonal thiotrophic symbiont populations occupy deep-sea mussel bacteriocytes with pathways connecting to the external environment2021

    • Author(s)
      Tetsuro Ikuta, Yuka Amari, Akihiro Tame, Yoshihiro Takaki, Miwako Tsuda, Ryo Iizuka, Takashi Funatsu, Takao Yoshida
    • Journal Title

      ISME Communications

      Volume: 1 Issue: 1 Pages: 38-38

    • DOI

      10.1038/s43705-021-00043-x

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Heterogeneous dissociation process of truncated RNAs by oligomerized Vasa helicase.2021

    • Author(s)
      Yoshimi Kinoshita, Ryo Murakami, Nao Muto, Shintaro Kubo, Ryo Iizuka, Sotaro Uemura
    • Journal Title

      Communications Biology

      Volume: 4 Issue: 1 Pages: 1386-1386

    • DOI

      10.1038/s42003-021-02918-0

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Photo-reactive oligodeoxynucleotide-embedded nanovesicles (PROsomes) with switchable stability for efficient cellular uptake and gene knockdown2020

    • Author(s)
      Beob Soo Kim, Mitsuru Naito, Rimpei Kamegawa, Hyun Jin Kim, Ryo Iizuka, Takashi Funatsu, Shingo Ueno, Takanori Ichiki, Akihiro Kishimura, Kanjiro Miyata
    • Journal Title

      Chem. Commun.

      Volume: 56 Issue: 66 Pages: 9477-9480

    • DOI

      10.1039/d0cc01750g

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] ナノ・マイクロデバイスと1分子検出顕微鏡を用いた生体分子の機能解析と新機能創生2020

    • Author(s)
      飯塚 怜
    • Journal Title

      YAKUGAKU ZASSHI

      Volume: 140 Pages: 1299-1303

    • Related Report
      2020 Research-status Report
  • [Journal Article] Nascent SecM chain interacts with outer ribosomal surface to stabilize translation arrest2020

    • Author(s)
      Mikihisa Muta, Ryo Iizuka, Tatsuya Niwa, Yuanfang Guo, Hideki Taguchi, Takashi Funatsu
    • Journal Title

      Biochemical Journal

      Volume: 477 Issue: 2 Pages: 557-566

    • DOI

      10.1042/bcj20190723

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] ナノ・マイクロ構造体を利用した蛍光イメージング2019

    • Author(s)
      飯塚 怜
    • Journal Title

      化学工業

      Volume: 70 Pages: 228-233

    • Related Report
      2019 Research-status Report
  • [Journal Article] Construction of integrated gene logic-chip2018

    • Author(s)
      Takeya Masubuchi, Masayuki Endo, Ryo Iizuka, Ayaka Iguchi, Dong Hyun Yoon, Tetsushi Sekiguchi, Hao Qi, Ryosuke Iinuma, Yuya Miyazono, Shuichi Shoji, Takashi Funatsu, Hiroshi Sugiyama, Yoshie Harada, Takuya Ueda, Hisashi Tadakuma
    • Journal Title

      Nat. Nanotechnol.

      Volume: 13 Issue: 10 Pages: 933-940

    • DOI

      10.1038/s41565-018-0202-3

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] 変形能を利用した液滴ソーターによるアガロース分解酵素産_菌ゲノムの獲得2022

    • Author(s)
      牟田 幹悠,斉藤 開,飯塚 怜,川久保 渉,尹 棟鉉,関口 哲志,庄子 習一,伊藤 芽,秦田 勇二,船津 高志
    • Organizer
      第16回日本ゲノム微生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 深海性二枚貝シチヨウシンカイヒバリガイにおける化学合成細菌を共生させる鰓上皮細胞のユニークな構造2021

    • Author(s)
      甘利 友花, 多米 晃裕,高木 善弘,津田 美和子,飯塚 怜,船津 高志,吉田 尊雄,生田 哲朗
    • Organizer
      第92回日本動物学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] An efficient method to obtain fluorogenic RNA aptamers based on ability to activate fluorescence2021

    • Author(s)
      Keisuke Ito, Ryo Iizuka, Sotaro Uemura
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Screening of agarolytic microbial cells with a deformability-based microfluidic microdroplet sorting device2021

    • Author(s)
      Mikihisa Muta, Kai Saito, Ryo Iizuka, Wataru Kawakubo, Dong Hyun Yoon, Tetsushi Sekiguchi, Shuichi Shoji, Mei Ito, Yuji Hatada, Takashi Funatsu
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Development of a method for quantitative profiling of microRNAs in single exosomes2021

    • Author(s)
      Cinya Chung, Ryo Iizuka, Takashi Funatsu
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Deformability-based microfluidic microdroplet sorting as a platform for screening single agarolytic bacterial cells2021

    • Author(s)
      Ryo Iizuka, Mikihisa Muta, Kai Saito, Dong Hyun Yoon, Yuji Hatada, Tetsushi Sekiguchi, Shuichi Shoji, Takashi Funatsu
    • Organizer
      2021 International Chemical Congress of Pacific Basin Societies (PacifiChem 2021)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Isolation and analysis of cells, organelles and molecules using microfluidic microdroplets2021

    • Author(s)
      Ryo Iizuka
    • Organizer
      The 24th SANKEN International Symposium
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 油中水滴の変形能を利用した高分子ゲル分解微生物のスクリーニング2021

    • Author(s)
      飯塚 怜, 牟田 幹悠, 斉藤 開, 船津 高志, 川久保 渉, 庄子 習一, 尹 棟鉉, 関口 哲志, 伊藤 芽, 秦田 勇二
    • Organizer
      第32回高分子ゲル研究討論会
    • Related Report
      2020 Research-status Report
  • [Presentation] Isolation and analysis of specific cells and subcellular structures using microfluidic microdroplets2020

    • Author(s)
      Ryo Iizuka
    • Organizer
      Serendipity seminar
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] Direct observation of force-induced release of SecM translation arrest2020

    • Author(s)
      Zhuohao Yang, Ryo Iizuka, Takashi Funatsu
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Culture-independent method for screening macromolecule-degrading microbes using deformability-based microfluidic microdroplet sorting2020

    • Author(s)
      Mikihisa Muta, Kai Saito, Ryo Iizuka, Wataru Kawakubo, Hyun Yoon Dong, Tetsushi Sekiguchi, Shuichi Shoji, Mei Ito, Yuji Hatada, Takashi Funatsu
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] DEFORMABILITY-BASED MICROFLUIDIC MICRODROPLET SORTING AS A SCREENING METHOD FOR SINGLE AGAROLYTIC BACTERIAL CELLS2020

    • Author(s)
      Mikihisa Muta, Kai Saito, Ryo Iizuka, Wataru Kawakubo, Dong Hyun Yoon, Mei Ito, Yuji Hatada, Tetsushi Sekiguchi, Shuichi Shoji, Takashi Funatsu
    • Organizer
      The 24th International Conference on Miniaturized Systems for Chemistry and Life Sciences
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] ナノ・マイクロ空間を利用した生体分子の反応機構解析・探索2020

    • Author(s)
      飯塚 怜
    • Organizer
      第1343回生物科学セミナー
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] Nascent SecM chain stabilizes the translation arrest by interacting with the outer surface of the ribosome2019

    • Author(s)
      牟田 幹悠, 飯塚 怜, 丹羽 達也, 田口 英樹, 船津 高志
    • Organizer
      第19回東京大学生命科学シンポジウム
    • Related Report
      2019 Research-status Report
  • [Presentation] Gタンパク質共役型受容体ペプチドアゴニスト創出法の開発2019

    • Author(s)
      飯塚 怜
    • Organizer
      第12回ナノバイオ若手ネットワーキングシンポジウム
    • Related Report
      2019 Research-status Report
  • [Presentation] 微生物一細胞の酵素活性を見える化してその遺伝子を取得する2019

    • Author(s)
      飯塚 怜,牟田 幹悠,斉藤 開,川久保 渉, 尹 棟鉉, 関口 哲志, 庄子 習一, 伊藤 芽, 秦田 勇二, 船津 高志
    • Organizer
      環境バイオテクノロジー学会2019年度大会
    • Related Report
      2019 Research-status Report
  • [Presentation] 油中水滴を利用した標的微生物のシングルセルゲノミクス2019

    • Author(s)
      飯塚 怜,船津 高志
    • Organizer
      シングルセルゲノミクス研究会2019
    • Related Report
      2019 Research-status Report
  • [Presentation] ナノ・マイクロデバイスと1分子検出顕微鏡を用いた生体分子の機能解析と新機能創生2019

    • Author(s)
      飯塚 怜
    • Organizer
      第63回日本薬学会関東支部大会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] Isolation and analysis of specific cells, organelles and supramolecular complexes using microfluidic microdroplets2019

    • Author(s)
      Ryo Iizuka
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] Development of a method for quantitative profiling of microRNAs in single exosomes2019

    • Author(s)
      Cinya Chung, Ryo Iizuka, Takashi Funatsu
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] Feasibility study of the method to obtain peptide agonists for G protein-coupled receptors using water-in-oil microdroplets2019

    • Author(s)
      Anna Matsueda, Takashi Sakurai, Ryo Iizuka, Yasuyuki Nakamura, Jun Ishi, Akihiro Kondo, Dong Hyun Yoon, Tetsushi Sekiguchi, Syuichi Syoji, Soichiro Tsuda, Takashi Funatsu
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] Deformability-based microfluidic droplet screening to obtain microbes producing macromolecule-degrading enzymes2019

    • Author(s)
      Mikihisa Muta, Kai Saito, Ryo Iizuka, Wataru Kawakubo, Dong Hyun Yoon, Tetsushi Sekiguchi, Shuichi Shoji, Mei Ito, Yuji Hatada, Takashi Funatsu
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] Releasing SecM translation arrest and observing resumed translation using magnetic tweezers2019

    • Author(s)
      Zhuohao Yang, Ryo Iizuka, Takashi Funatsu
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] 微生物1細胞の酵素活性を検出してその遺伝子を取得する2019

    • Author(s)
      飯塚 怜, 船津 高志
    • Organizer
      第37回農薬環境科学研究会
    • Related Report
      2019 Research-status Report
  • [Presentation] Emerged nascent SecM chain stabilizes the translation arrest by interacting with the exoerior surface of the ribosome2019

    • Author(s)
      Mikihisa Muta, Ryo Iizuka, Tatsuya Niwa, Hideki Taguchi, Takashi Funatsu
    • Organizer
      63rd Annual Meeting of the Biophysical Society (BPS19)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 望む形質・形態を有する細胞・小器官・分子複合体を単離して解析する2019

    • Author(s)
      飯塚 怜
    • Organizer
      形態解析ワークショップ - 多様な顕微鏡を用いて
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Gタンパク質共役型受容体ペプチドアゴニスト創出法のハイスループット化2019

    • Author(s)
      松枝 杏奈,櫻井 貴志,飯塚 怜,中村 泰之,石井 純,近藤 昭彦,井口 彩香,尹 棟鉉,関口 哲志,庄子 習一,藤村 祐,赤木 仁,石毛 真行,船津 高志
    • Organizer
      日本薬学会第139年会
    • Related Report
      2018 Research-status Report
  • [Presentation] 油中水滴内の微生物の酵素活性を見える化してその遺伝子を取得する2019

    • Author(s)
      飯塚 怜,牟田 幹悠,斉藤 開,川久保 渉, 尹 棟鉉, 関口 哲志, 庄子 習一, 伊藤 芽, 秦田 勇二, 船津 高志
    • Organizer
      日本薬学会第139年会
    • Related Report
      2018 Research-status Report
  • [Presentation] 油中水滴の変形能を利用したバイオマス分解酵素微生物のスクリーニング2018

    • Author(s)
      飯塚 怜
    • Organizer
      第11回ナノバイオ若手ネットワーキングシンポジウム
    • Related Report
      2018 Research-status Report
  • [Presentation] Photocontrol of ribosome movement on mRNA using reversible photocrosslinking strategy2018

    • Author(s)
      Ryo Iizuka, Shunsuke Yamashiro, Takashi Funatsu
    • Organizer
      International Symposium on Proteins; from the Cradle to the Grave
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Releasing SecM translation arrest and observing resumed translation using optical tweezers2018

    • Author(s)
      Zhuohao Yang, Ryo Iizuka, Takashi Funatsu
    • Organizer
      International Symposium on Proteins; from the Cradle to the Grave
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Identification of a +1 frameshift observed during TnaC-mediated ribosome stalling2018

    • Author(s)
      Tomoki Shinozawa, Ryo Iizuka, Takashi Funatsu
    • Organizer
      International Symposium on Proteins; from the Cradle to the Grave
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Stabilization mechanism of SecM translation arrest2018

    • Author(s)
      Mikihisa Muta, Ryo Iizuka, Tatsuya Niwa, Hideki Taguchi, Takashi Funatsu
    • Organizer
      International Symposium on Proteins; from the Cradle to the Grave
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] イメージングを基軸としたタンパク質の機能解析および探索2018

    • Author(s)
      飯塚 怜
    • Organizer
      第27回日本バイオイメージング学会学術集会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Analysis of the frameshift depending on TnaC-mediated ribosome stalling2018

    • Author(s)
      Tomoki Shinozawa, Ryo Iizka, Takashi Funatsu
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] Analysis of the stabilization mechanism of SecM-mediated translation arrest2018

    • Author(s)
      Mikihisa Muta, Ryo Iizuka, Takashi Funatu
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] Single-molecule analysis of actin polymerization using linear zero-mode waveguides2018

    • Author(s)
      Soichiro Fujii, Ryo Iizuka, Masamichi Yamamoto, Makoto Tsunoda, Takashi Tanii, Takashi Funatsu
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] Droplet-based microfluidic screening for obtaining microbes producing macromolecule-degrading enzymes2018

    • Author(s)
      Ryo Iizuka, Kai Saito, Eiji Shigihara, Wataru Kawakubo, Daiki Tanaka, Dong Hyun Yoon, Tetsushi Sekiguchi, Shuichi Shoji, Mei Ito, Yuji Hatada, Takashi Funatsu
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] High-throughput in vitro selection method for obtaining peptide agonists of G protein-coupled receptors2018

    • Author(s)
      Anna Matsueda, Takashi Sakurai, Ryo Iizuka, Yasuyuki Nakamura, Jun Ishii, Akihiko Kondo, Ayaka Iguchi, Dong Hyun Yoon, Tetsushi Sekiguchi, Shuichi Shoji, Yuu Fujimura, Jin Akagi, Masayuki Ishige, Takashi Funatsu
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] 微生物の酵素活性を「見える化」して酵素を取得する2018

    • Author(s)
      飯塚 怜
    • Organizer
      リバネスStartup Factoryセミナー(小さな生き物による大きな世界貢献 未来を作る微生物応用技術)
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] マイクロ・ナノ空間を利用した酵素の探索・反応機構解析2018

    • Author(s)
      飯塚 怜
    • Organizer
      酵素工学研究会 第80回講演会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Book] 先端の分析法 第2版 第9節 その他 第1項 次世代シーケンサー2022

    • Author(s)
      飯塚 怜,上村 想太郎
    • Total Pages
      1072
    • Publisher
      エヌ・ティー・エス
    • ISBN
      9784860437374
    • Related Report
      2021 Annual Research Report
  • [Book] 固定化リボソームを用いたタンパク質合成の一分子イメージング (In 細胞・生体分子の固定化と機能発現)2018

    • Author(s)
      飯塚 怜, 船津 高志
    • Publisher
      シーエムシー出版
    • ISBN
      9784781313269
    • Related Report
      2018 Research-status Report
  • [Remarks] Researchmap

    • URL

      https://researchmap.jp/ryoiizuka

    • Related Report
      2021 Annual Research Report 2020 Research-status Report 2019 Research-status Report
  • [Remarks] ORCiD

    • Related Report
      2021 Annual Research Report
  • [Remarks] 東京大学大学院薬学系研究科生体分析化学教室ホームページ

    • URL

      http://www.f.u-tokyo.ac.jp/~funatsu/

    • Related Report
      2019 Research-status Report 2018 Research-status Report

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Published: 2018-04-23   Modified: 2023-01-30  

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