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Development of a culture-independent method for the identification of microbial enzyme-encoding genes using water-in-oil microdroplets and its application

Research Project

Project/Area Number 15K18668
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Applied microbiology
Research InstitutionThe University of Tokyo

Principal Investigator

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

Project Period (FY) 2015-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2016: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2015: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywords液滴 / 微生物 / 酵素 / マイクロ流体デバイス
Outline of Final Research Achievements

Environmental microbes are a great source of industrially valuable enzymes with potent and unique catalytic activities. Unfortunately, the majority of microbes remain unculturable and thus are not accessible by culture-based methods. Then, I envisioned a culture-independent method for the identification of microbial enzyme-encoding genes using water-in-oil microdroplets. In this study, I established the method and demonstrated its practicality and usefulness. This method will facilitate the identification of genes encoding industrially valuable enzymes.

Report

(3 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • Research Products

    (26 results)

All 2017 2016 2015 Other

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Open Access: 2 results,  Acknowledgement Compliant: 1 results) Presentation (22 results) (of which Int'l Joint Research: 3 results,  Invited: 4 results) Remarks (2 results)

  • [Journal Article] Chaperonin GroEL uses asymmetric and symmetric reaction cycles in response to the concentration of non-native substrate proteins2016

    • Author(s)
      Ryo Iizuka, Takashi Funatsu
    • Journal Title

      Biophysics and Physicobiology

      Volume: 13 Issue: 0 Pages: 63-69

    • DOI

      10.2142/biophysico.13.0_63

    • NAID

      130005148429

    • ISSN
      2189-4779
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Culture-independent method for identification of microbial enzyme-encoding genes by activity-based single-cell sequencing using a water-in-oil microdroplet platform2016

    • Author(s)
      Kazuki Nakamura, Ryo Iizuka, Shinro Nishi, Takao Yoshida, Yuji Hatada, Yoshihiro Takaki, Ayaka Iguchi, Dong Hyun Yoon, Tetsushi Sekiguchi, Shuichi Shoji and Takashi Funatsu
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 22259-22259

    • DOI

      10.1038/srep22259

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 液滴を利用したバイオマス分解酵素産生微生物の探索法の開発2017

    • Author(s)
      鴫原 永之, 飯塚 怜, 川久保 渉, 尹 棟鉉, 関口 哲志, 庄子 習一, 船津 高志
    • Organizer
      第6回日本生物物理学会関東支部会
    • Place of Presentation
      早稲田大学 先端生命医科学センター(東京都新宿区)
    • Year and Date
      2017-03-13
    • Related Report
      2016 Annual Research Report
  • [Presentation] In vitro selection system to generate peptide agonists for G protein-coupled receptors using a water-in-oil microdroplet platform2017

    • Author(s)
      Ryo Iizuka, Takashi Sakurai, Yasuyuki Nakamura, Jun Ishii, Akihiko Kondo, Ayaka Iguchi, Dong Hyun Yoon, Tetsushi Sekiguchi, Shuichi Shoji, Takashi Funatsu
    • Organizer
      11th Annual Symposium on Nanobiotechnology 2017
    • Place of Presentation
      川崎市産業振興会館(神奈川県川崎市)
    • Year and Date
      2017-02-27
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] In vitro compartmentalization法を利用したGタンパク質共役型受容体作動性ペプチドリガンドの創出2016

    • Author(s)
      飯塚 怜,櫻井 貴志,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,船津 高志
    • Organizer
      第八回光塾
    • Place of Presentation
      東京工業大学 すずかけ台キャンパス(神奈川県横浜市)
    • Year and Date
      2016-12-17
    • Related Report
      2016 Annual Research Report
  • [Presentation] Culture-independent identification of genes encoding agarase from environmental bacteria using agarose gel microdroplets2016

    • Author(s)
      Eiji Shigihara, Ryo Iizuka, Takashi Sakurai, Yuji Hatada, Dong Hyun Yoon, Tetsushi Sekiguchi, Shuichi Shoji, Takashi Funatsu
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] A single integrated gene nano-chip functioning in an artificial cell2016

    • Author(s)
      Takeya Masubuchi, Masayuki Endo, Ryo Iizuka, Ayaka Iguchi, Yoon Doung Hyun, Tetsushi Sekiguchi, Hao Qi, Ryosuke Iinuma, Yuya Miyazono, Shuichi Shoji, Takashi Funatsu, Hiroshi Sugiyama, Yoshie Harada, Takuya Ueda, Hisashi Tadakuma
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] In vitro selection of novel peptide agonists for human somatostatin receptor subtype-2 using water-in-oil microdroplets2016

    • Author(s)
      Takashi Sakurai, Ryo Iizuka, Yasuyuki Nakamura, Jun Ishii, Akihiko Kondo, Ayaka Iguchi, Dong Hyun Yoon, Tetsushi Sekiguchi, Shuichi Shoji, Takashi Funatsu
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] Construction and functional analysis of DNA origami base DNA-RNA hybrid nanomachine2016

    • Author(s)
      Takeya Masubuchi, Hisashi Tadakuma, Masayuki Endo, Ryo Iizuka, Hiroshi Sugiyama, Yoshie Harada, Takashi Funatsu, Takuya Ueda
    • Organizer
      情報計算化学生物学会(CBI学会)2016年大会
    • Place of Presentation
      タワーホール船堀(東京都江戸川区)
    • Year and Date
      2016-10-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] IN VITRO SELECTION OF NOVEL PEPTIDE AGONISTS FOR HUMAN SOMATOSTATIN RECEPTOR SUBTYPE-2 USING A WATER-IN-OIL MICRODROPLET PLATFORM2016

    • Author(s)
      T. Sakurai, R. Iizuka, Y. Nakamura, J. Ishii, A. Kondo, A. Iguchi, D. H. Yoon, T. Sekiguchi, S. Shoji, T. Funatsu
    • Organizer
      The 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2016)
    • Place of Presentation
      Convention Center Dublin (Dublin, Ireland)
    • Year and Date
      2016-10-09
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [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2016

    • Author(s)
      飯塚 怜
    • Organizer
      生物資源ゲノム解析拠点シンポジウム・研究発表会
    • Place of Presentation
      東京農業大学世田谷キャンパス(東京都世田谷区)
    • Year and Date
      2016-09-03
    • Related Report
      2016 Annual Research Report
  • [Presentation] マイクロ・ナノ空間を利用した糖質加水分解酵素の探索・機能解析2016

    • Author(s)
      飯塚 怜
    • Organizer
      第35回日本糖質学会年会
    • Place of Presentation
      高知市文化プラザ かるぽーと(高知県高知市)
    • Year and Date
      2016-09-01
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] マイクロ液滴を利用した標的微生物のシングルセルゲノミクス2016

    • Author(s)
      飯塚 怜
    • Organizer
      次世代シーケンス解析テクニカルセミナー(第6回 一細胞解析と次世代シーケンス)
    • Place of Presentation
      株式会社リバネス 知識創業研究センター(東京都新宿区)
    • Year and Date
      2016-07-28
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 液滴を利用した標的微生物のシングルセルゲノミクス2016

    • Author(s)
      飯塚 怜
    • Organizer
      生命機能研究グループセミナー
    • Place of Presentation
      海洋研究開発機構 横須賀本部(神奈川県横須賀市)
    • Year and Date
      2016-06-14
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] In vitro compartmentalization法を利用したGPCR作動性ペプチドリガンド創出法の開発2016

    • Author(s)
      飯塚 怜, 櫻井 貴志, 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, 船津 高志
    • Organizer
      第13回GPCR研究会
    • Place of Presentation
      日本科学未来館 みらいCANホール(東京都江東区)
    • Year and Date
      2016-05-13
    • Related Report
      2016 Annual Research Report
  • [Presentation] Directed evolution system to generate peptide agonists for G protein-coupled receptors using water-in-oil droplets2016

    • Author(s)
      Ryo Iizuka, Takashi Sakurai, Yasuyuki Nakamura, Jun Ishii, Akihiko Kondo, Rui Sekine, Dong Hyun Yoon, Tetsushi Sekiguchi, Shuichi Shoji, Takashi Funatsu
    • Organizer
      The 8th Takeda Science Foundation Symposium on PharmaSciences Biomolecule-Based Medicinal Science: Featuring Mid-Size Drugs, Center for Learning and Innovation
    • Place of Presentation
      武田薬品研修所(大阪府吹田市)
    • Year and Date
      2016-01-21
    • Related Report
      2015 Research-status Report
  • [Presentation] CULTURE-INDEPENDENT METHOD FOR SCREENING AND IDENTIFYING MICROBIAL ENZYME-ENCODING GENES USING MICRODROPLET-BASED SINGLE CELL GENOMICS2015

    • Author(s)
      K. Nakamura, R. Iizuka, T. Yoshida, Y. Hatada, Y. Takaki, S. Nishi, A. Iguchi, D. H. Yoon, T. Sekiguchi, S. Shoji, T. Funatsu
    • Organizer
      The 19th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2015)
    • Place of Presentation
      Hwabaek International Convention Center (Gyeongju, Korea)
    • Year and Date
      2015-10-25
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] 液滴を利用した機能分子創出およびオミックス研究に資する基盤技術開発とその実践2015

    • Author(s)
      飯塚 怜
    • Organizer
      第59回脳科学セミナー
    • Place of Presentation
      埼玉大学工学部(埼玉県さいたま市)
    • Year and Date
      2015-10-16
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] Directed evolution system to generate peptide agonists for G protein-coupled receptors using water-in-oil droplets2015

    • Author(s)
      Takashi Sakurai, Ryo Iizuka, Yasuyuki Nakamura, Jun Ishii, Rui Sekine, Dong Hyun Yoon, Tetsushi Sekiguchi, Akihiko Kondo, Shuichi Shoji, Takashi Funatsu
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学 角間キャンパス 自然科学本館(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
  • [Presentation] An attempt to improve the method for directed evolution by in vitro compartmentalization2015

    • Author(s)
      Kentaro Tahara, Ryo Iizuka, Ayaka Iguchi, Dong Hyun Yoon, Tetsushi Sekiguchi, Shuichi Shoji, Takashi Funatsu
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学 角間キャンパス 自然科学本館(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
  • [Presentation] Culture-independent method for identifying microbial enzyme-encoding genes based on activity-driven single cell genomics2015

    • Author(s)
      Kazuki Nakamura, Ryo Iizuka, Takao Yoshida, Yuji Hatada, Yoshihiro Takaki, Shinro Nishi, Ayaka Iguchi, Dong Hyun Yoon, Tetsushi Sekiguchi, Shuichi Shoji, Takashi Funatsu
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学 角間キャンパス 自然科学本館(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
  • [Presentation] Rational design of orthogonal gene transcription nano device on DNA origami2015

    • Author(s)
      Takeya Masubuchi, Hisashi Tadakuma, Ryo Iizuka, Masayuki Endo, Takashi Funatsu, Hiroshi Sugiyama, Yoshie Harada, Takuya Ueda
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学 角間キャンパス 自然科学本館(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
  • [Presentation] 環境中の微生物を培養することなく「見える化」し,酵素遺伝子を取得する方法の開発2015

    • Author(s)
      飯塚 怜
    • Organizer
      第6回「光塾」
    • Place of Presentation
      広島大学東広島キャンパス(広島県広島市)
    • Year and Date
      2015-09-05
    • Related Report
      2015 Research-status Report
  • [Presentation] シングルセルゲノミクスを利用した微生物酵素遺伝子探索法2015

    • Author(s)
      飯塚 怜,中村 和貴,吉田 尊雄,秦田 勇二,高木 善弘,西 真郎,井口 彩香,尹 棟鉉,関口 哲志,庄子 習一,船津 高志
    • Organizer
      NGS現場の会 第四回研究会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2015-07-01
    • Related Report
      2015 Research-status 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
      2016 Annual Research Report
  • [Remarks] 東京大学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
      2015 Research-status Report

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Published: 2015-04-16   Modified: 2018-03-22  

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