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Incorpoation of biocitin into a protein by expanding the genetic code

Research Project

Project/Area Number 24710231
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field System genome science
Research InstitutionTokyo University of Science

Principal Investigator

UMEHARA Takuya  東京理科大学, 基礎工学部, 助教 (00415548)

Research Collaborator YANAGISAWA Tatsuo  
Project Period (FY) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2014: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2013: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2012: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywords非天然アミノ酸 / タンパク質翻訳 / tRNA / ピロリジン
Outline of Final Research Achievements

Since pyrrolysly-tRNA synthetase (PylRS)/pyrrolysine tRNA (tRNA(Pyl)) pair is orthogonal to aminoacyl-tRNA synthetase/tRNA pairs in various organisms, PylRS/tRNA(Pyl) pair has been used as one of the parental molecules to cotranslatinally incorporate an unnatural amino acid into a protein. In this project, I tried to develop the system to produce a biotinylated protein in E. coli by using PylRS/tRNA(Pyl) pair and biotinyl-L-lysine (biocitin). Although several challenges of in vivo selection to PylRS libraries with saturated mutations, many PylRS mutants recognizing natural amino acid were isolated as higher background. In addition to the selection, I constructed the PylRS mutant based on the docking model of PylRS and biocitin, which however showed the activity with very little. These results suggest that large modification of the active site in PylRS is required to obtain PylRS mutant that can charge biocitin onto tRNA(Pyl).

Report

(4 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • 2012 Research-status Report
  • Research Products

    (29 results)

All 2014 2013 2012

All Journal Article (6 results) (of which Peer Reviewed: 6 results,  Open Access: 2 results,  Acknowledgement Compliant: 2 results) Presentation (23 results)

  • [Journal Article] Development of a Functionally Minimized Mutant of the R3C Ligase Ribozyme Offers Insight into the Plausibility of the RNA World Hypothesis.2014

    • Author(s)
      Kurihara, E., Uchida, S., Umehara, T. and Tamura, K.
    • Journal Title

      Biology

      Volume: 3 Issue: 3 Pages: 452-465

    • DOI

      10.3390/biology3030452

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Proline might have been the first amino acid in the primitive genetic code2014

    • Author(s)
      2. Komatsu, R., Sawada, R., Umehara, T. and Tamura, K.
    • Journal Title

      J. Mol. Evol.

      Volume: 78 Issue: 6 Pages: 310-312

    • DOI

      10.1007/s00239-014-9629-9

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Pyrrolysyl-tRNA synthetase variants reveal ancestral aminoacylation function.2013

    • Author(s)
      Jae-Hyeong Ko, Yane-Shih Wang, Akiyoshi Nakamura, Li-Tao Guo, Dieter Soll and Takuya Umehara
    • Journal Title

      FEBS Letters

      Volume: 587 Issue: 19 Pages: 3243-3248

    • DOI

      10.1016/j.febslet.2013.08.018

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Glycols modulate terminator stem stability and ligand-dependency of a glycine riboswitch2013

    • Author(s)
      Hamachi, K., Hayashi, H., Shimamura, M., Yamaji, Y., Kaneko, A., Fujisawa, A., Umehara, T. and Tamura, K
    • Journal Title

      BioSystems

      Volume: 113 Issue: 2 Pages: 59-65

    • DOI

      10.1016/j.biosystems.2013.05.004

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Self-enhancement of hepatitis C virus replication by promotion of specific sphingolipid biosynthesis2012

    • Author(s)
      Hirata Y, Ikeda K, shimotohno K, et al.,
    • Journal Title

      PLoS Pathog

      Volume: PLoS Pathog Issue: 8 Pages: e1002860-e1002860

    • DOI

      10.1371/journal.ppat.1002860

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] RNA tetraplex as a primordial peptide synthesis scaffold2012

    • Author(s)
      Umehara, T., Kitagawa, T., Nakazawa, Y., Yoshino, H., Nemoto, R. and Tamura, K
    • Journal Title

      BioSystems

      Volume: 109 Issue: 2 Pages: 145-150

    • DOI

      10.1016/j.biosystems.2012.03.003

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Presentation] 脂質を用いたヌクレオチドの非酵素的重合2014

    • Author(s)
      松村 慎太郎, 楳原 琢哉, 田村 浩二
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] アロフェンを用いたヌクレオチドの重合2014

    • Author(s)
      櫻井 陽平, 樗木 政裕, 楳原 琢哉, 田村 浩二
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] Nanoarchaeum equitans由来グリシルtRNA合成酵素の原始型の探索2014

    • Author(s)
      藤沢 有磨, 土岐 梨彩子, 楳原 琢哉, 田村 浩二
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] R3C ligase ribozymeの反応機構の解明2014

    • Author(s)
      内田 小百合, 楳原 琢哉, 田村 浩二, 栗原 絵梨
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] 原始アミノ酸を用いたβシートの形成2014

    • Author(s)
      澤田 理沙, 楳原 琢哉, 田村 浩二
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] tRNA結合タンパク質 (Trbp) に結合するRNAアプタマーの取得2014

    • Author(s)
      大森 千里, 楳原 琢哉, 田村 浩二
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] グアニン四重鎖を足場としたアミノアシルミニヘリックスによるペプチド結合生成2014

    • Author(s)
      富岡 慎忠, 楳原 琢哉, 田村 浩二
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] キャピラリー電気泳動を用いた核酸・アミノ酸重合の分析2014

    • Author(s)
      長坂 倫, 楳原 琢哉, 田村 浩二
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] Evolutionary process of tRNA and riboswitches2014

    • Author(s)
      Hamachi, K., Umehara, T. and Tamura, K
    • Organizer
      Origins 2014
    • Place of Presentation
      Nara Prefecture New Public Hall
    • Year and Date
      2014-07-06 – 2014-07-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] tRNAとリボスイッチから見たRNAの進化2014

    • Author(s)
      浜地 心、楳原琢哉、 田村浩二
    • Organizer
      生命の起原および進化学会第39回学術講演会
    • Place of Presentation
      広島修道大学
    • Related Report
      2013 Research-status Report
  • [Presentation] 新規アミノアシル化法を用いたin vitro 非天然タンパク質創製法の最適化2013

    • Author(s)
      那須元太郎、楳原琢哉、田村浩二、上田 淳
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド
    • Related Report
      2013 Research-status Report
  • [Presentation] Nanoarchaeum equitans 由来MetRSのtRNA結合機構の解明2013

    • Author(s)
      金子明弘、山本太郎、楳原琢哉、田村浩二
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド
    • Related Report
      2013 Research-status Report
  • [Presentation] 原始環境下におけるリボソームモデルの探索2013

    • Author(s)
      川端 舞、楳原琢哉、田村浩二
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド
    • Related Report
      2013 Research-status Report
  • [Presentation] R3C ligase ribozymeの反応機構と最小活性単位の解明2013

    • Author(s)
      栗原絵梨、楳原琢哉、田村浩二
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド
    • Related Report
      2013 Research-status Report
  • [Presentation] Nanoarchaeum equitans由来フェレドキシンの構造と進化2013

    • Author(s)
      野呂雄樹、篠塚晃一郎、岩崎俊雄、楳原琢哉、田村浩二
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド
    • Related Report
      2013 Research-status Report
  • [Presentation] Domain structures and evolution of tRNA, aminoacyl tRNA synthetases, and riboswitches2013

    • Author(s)
      Kokoro Hamachi, Takuya Umehara, and Koji Tamura
    • Organizer
      AARS2013 2013 9th International Symposium on Aminoacyl-tRNA Synthetases
    • Place of Presentation
      The Prince Hakone
    • Related Report
      2013 Research-status Report
  • [Presentation] Evolution of riboswitches conjectured from a glycine-independent glycine riboswitch2013

    • Author(s)
      Kokoro Hamachi, Takuya Umehara, Koji Tamura
    • Organizer
      第86回日本生化学会大会
    • Place of Presentation
      パシフィコ横浜
    • Related Report
      2013 Research-status Report
  • [Presentation] グリシン非依存的グリシンリボスイッチから見たリボスイッチの進化2013

    • Author(s)
      浜地心、楳原琢哉、田村浩二
    • Organizer
      第86回日本生化学会大会
    • Place of Presentation
      パシフィコ横浜
    • Related Report
      2013 Research-status Report
  • [Presentation] 鋳型非依存的RNAの重合における触媒物質の探索2013

    • Author(s)
      松村慎太郎、根本遼平、楳原琢哉、田村浩二
    • Organizer
      東京理科大学総合研究機構・RNA科学総合研究センター公開シンポジウム「RNA world への階梯」
    • Place of Presentation
      東京理科大学・葛飾キャンパス
    • Related Report
      2013 Research-status Report
  • [Presentation] グリコールがグリシンリボスイッチのグリシン依存性を変調する2013

    • Author(s)
      浜地 心、楳原琢哉、田村浩二
    • Organizer
      東京理科大学総合研究機構・RNA科学総合研究センター公開シンポジウム「RNA world への階梯」
    • Place of Presentation
      東京理科大学・葛飾キャンパス
    • Related Report
      2013 Research-status Report
  • [Presentation] アセチルリジル-tRNA 合成酵素の機能解析2013

    • Author(s)
      楳原琢哉、田村浩二
    • Organizer
      東京理科大学総合研究機構・RNA科学総合研究センター公開シンポジウム「RNA world への階梯」
    • Place of Presentation
      東京理科大学・葛飾キャンパス
    • Related Report
      2013 Research-status Report
  • [Presentation] ナノ古細菌チロシルtRNA合成酵素によるtRNATyrのチロシル化2013

    • Author(s)
      藤沢有麿、堀越達也、楳原琢哉、田村浩二
    • Organizer
      東京理科大学総合研究機構・RNA科学総合研究センター公開シンポジウム「RNA world への階梯」
    • Place of Presentation
      東京理科大学・葛飾キャンパス
    • Related Report
      2013 Research-status Report
  • [Presentation] 大腸菌遺伝暗号拡張によるリン酸化セリン導入タンパク質の生産2012

    • Author(s)
      楳原琢哉、田村浩二、Dieter Soll
    • Organizer
      東京理科大学総合研究機構・RNA科学総合研究センター公開シンポジウム「RNA科学の現状と将来」
    • Place of Presentation
      東京理科大学
    • Related Report
      2012 Research-status Report

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Published: 2013-05-31   Modified: 2019-07-29  

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