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Classification of functionally unknown genes based on their transcriptional regulation

Research Project

Project/Area Number 22510208
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Genome biology
Research InstitutionThe Institute of Physical and Chemical Research

Principal Investigator

SHINKAI Akeo  独立行政法人理化学研究所, 機能解析第1研究チーム, チームリーダー (10391989)

Co-Investigator(Renkei-kenkyūsha) AGARI Yoshihiro  独立行政法人理化学研究所, 機能解析第1研究チーム, 特別研究員 (50469889)
Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2012: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2011: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2010: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywords遺伝子発現調節 / X線結晶構造 / 機能発見 / 高度好熱菌 / Thermus thermophilus / 蛋白質 / TetRファミリー / 転写因子 / 機能ゲノム科学 / 転写制御 / 機能未知遺伝子 / mRNA
Research Abstract

In order to find a clue to identify the function of the functionally unknown genes, we categorized them based on their transcriptional regulation, using Thermus thermophilus HB8 as a model organism. Genetic information in DNA is transcribed to mRNA, which is often regulated by protein called transcription factor. In many cases, the transcription reaction of several genes sharing similar cellular functions is simultaneously regulated by a transcription factor. Here, we investigated the function of four novel transcription factors, and identified six functionally unknown genes which were transcriptionally regulated together with functionally identified genes. This study may lead to identify the function of the functionally unknown genes.

Report

(5 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Products Report
  • Research Products

    (28 results)

All 2014 2013 2012 2011 2010 Other

All Journal Article (6 results) (of which Peer Reviewed: 6 results) Presentation (22 results) (of which Invited: 1 results)

  • [Journal Article] LdrP, a cAMP receptor protein/FNR family transcriptional regulator, serves as a positive regulator for the light-inducible gene cluster in the megaplasmid of Thermus thermophilus2014

    • Author(s)
      Hideaki Takano, Yoshihiro Agari, Kenta Hagiwara, Ren Watanabe, Ryuta Yamazaki, Teruhiko Beppu, Akeo Shinkai, Kenji Ueda
    • Journal Title

      Microbiology

      Volume: 160 Issue: 12 Pages: 2650-2660

    • DOI

      10.1099/mic.0.082263-0

    • Related Report
      Products Report
    • Peer Reviewed
  • [Journal Article] Structure and function of a TetR family transcriptional regulator, SbtR, from Thermus thermophilus HB82013

    • Author(s)
      Agari Y, Sakamoto K, Yutani K, Kuramitsu S, Shinkai A.
    • Journal Title

      Proteins

      Volume: (in press) Issue: 7 Pages: 1166-1178

    • DOI

      10.1002/prot.24266

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Transcriptional repression mediated by a TetR family protein, PfmR, from Thermus thermophilus HB82012

    • Author(s)
      Agari Y, Sakamoto K, Kuramitsu S, Shinkai A.
    • Journal Title

      J. Bacteriol

      Volume: 194(17) Issue: 17 Pages: 4630-4641

    • DOI

      10.1128/jb.00668-12

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Phenylacetyl-coenzyme A is an effector molecule of TetR family transcriptional repressor PaaR from Thermus thermophilus HB82011

    • Author(s)
      Sakamoto K, Agari Y, Kuramitsu S, Shinkai A
    • Journal Title

      J. Bacteriol

      Volume: 193(17) Issue: 17 Pages: 4388-4395

    • DOI

      10.1128/jb.05203-11

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] TetR family transcriptional repressor Thermus thermophilus FadR controls fatty acid degradation2011

    • Author(s)
      Agari Y, Agari K, Sakamoto K, Kuramitsu S, Shinkai A
    • Journal Title

      Microbiology

      Volume: 157(Pt 6) Issue: 6 Pages: 1589-1601

    • DOI

      10.1099/mic.0.048017-0

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] TetR family transcriptional repressor Thermus thermophilus FadR controls fatty acid degradation

    • Author(s)
      Yoshihiro Agari
    • Journal Title

      Microbiology

      Volume: (in press)

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] 高度好熱菌Thermus thermophilus HB8株における転写因子の機能解析と機能未知遺伝子の分類2013

    • Author(s)
      新海暁男
    • Organizer
      第13回日本蛋白質科学会年会
    • Place of Presentation
      とりぎん文化会館、鳥取
    • Year and Date
      2013-06-13
    • Related Report
      2012 Final Research Report
  • [Presentation] 分子間ジスルフィド結合を持つThermus thermophilus HB8由来TetRファミリー転写因子TTHA0167の構造と機能2012

    • Author(s)
      坂本恵子、上利佳弘、倉光成紀、新海暁男
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      マリンメッセ福岡、福岡
    • Year and Date
      2012-12-13
    • Related Report
      2012 Final Research Report
  • [Presentation] Thermus thermophilus HB8由来TetRファミリー転写調節因子 PfmRによる転写抑制2012

    • Author(s)
      上利佳弘、坂本恵子、倉光成紀、新海暁男
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      マリンメッセ福岡、福岡
    • Year and Date
      2012-12-13
    • Related Report
      2012 Final Research Report
  • [Presentation] Functional identification of transcriptional regulators from T. thermophilus HB82012

    • Author(s)
      新海暁男
    • Organizer
      第2回モデル生物丸ごと一匹学会
    • Place of Presentation
      SPring-8、兵庫
    • Year and Date
      2012-09-29
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [Presentation] Structural and functional analysis of TetR family transcriptional regulator PfmR from Thermus thermophilus HB82012

    • Author(s)
      上利佳弘、坂本恵子、新海暁男
    • Organizer
      第2回モデル生物丸ごと一匹学会
    • Place of Presentation
      Spring-8、兵庫
    • Year and Date
      2012-09-29
    • Related Report
      2012 Final Research Report
  • [Presentation] Structural and functional analysis of TetR family transcriptional regulator TTHA0167 from T. thermophilus HB82012

    • Author(s)
      坂本恵子、上利佳弘、新海暁男
    • Organizer
      第2回モデル生物丸ごと一匹学会
    • Place of Presentation
      SPring-8、兵庫
    • Year and Date
      2012-09-29
    • Related Report
      2012 Final Research Report
  • [Presentation] Thermus thermophilus PaaR, a TetR family transcriptional repressor, is involved in phenylacetic acid degradation2011

    • Author(s)
      坂本恵子、上利佳弘、倉光成紀、新海暁男
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜、横浜
    • Year and Date
      2011-12-15
    • Related Report
      2012 Final Research Report
  • [Presentation] Thermus thermophilus PaaR, a TetR family transcriptional repressor, is involved in phenylacetic acid degradation2011

    • Author(s)
      Keiko Sakamoto, Yoshihiro Agari, Seiki Kuramitsu, Akeo Shinkai
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川県)
    • Year and Date
      2011-12-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] 高度好熱菌Thermus thermophilus HB8株をモデル生物とし、転写制御の観点から機能未知遺伝子を分類する:転写因子の機能発見研究と機能未知遺伝子の分類2011

    • Author(s)
      新海暁男、上利佳弘、坂本恵子
    • Organizer
      第84回日本生化学大会
    • Place of Presentation
      京都国際会館、京都
    • Year and Date
      2011-09-23
    • Related Report
      2012 Final Research Report
  • [Presentation] 高度好熱菌Thermus thermophilus HB8株をモデル生物とし、転写制御の観点から機能未知遺伝子を分類する:転写因子の機能発見研究と機能未知遺伝子の分類2011

    • Author(s)
      新海暁男、上利佳弘、坂本恵子
    • Organizer
      第84回日本生化学大会シンポジウム
    • Place of Presentation
      京都国際会館(京都府)(招待講演)
    • Year and Date
      2011-09-23
    • Related Report
      2011 Annual Research Report
  • [Presentation] Study of transcriptional regulatory system of T. thermophilus HB8: Structure and function of two TetR family proteins2011

    • Author(s)
      新海暁男、上利佳弘、坂本恵子
    • Organizer
      第1回モデル生物丸ごと一匹学会
    • Place of Presentation
      SPring-8、兵庫
    • Year and Date
      2011-08-20
    • Related Report
      2012 Final Research Report
  • [Presentation] Functional and structural characterization of the TetR family transcriptional repressor PaaR from Thermus thermophilus HB82011

    • Author(s)
      坂本恵子、上利佳弘、倉光成紀、新海暁男
    • Organizer
      第1回モデル生物丸ごと一匹学会
    • Place of Presentation
      SPring-8、兵庫
    • Year and Date
      2011-08-20
    • Related Report
      2012 Final Research Report
  • [Presentation] Study of transcriptional regulatory system of T.thermophilus HB8 : Structure and function of two TetR family proteins2011

    • Author(s)
      Akeo Shinkai, Yoshihiro Agari, Keiko Sakamoto
    • Organizer
      第1回モデル生物丸ごと一匹学会(高度好熱菌丸ごと一匹プロジェクト第10回連携研究会共催)
    • Place of Presentation
      スプリング-8(兵庫県)(招待講演)
    • Year and Date
      2011-08-20
    • Related Report
      2011 Annual Research Report
  • [Presentation] Functional and structural characterization of the TetR family transcriptional repressor PaaR from Thermus thermophilus HB82011

    • Author(s)
      Keiko Sakamoto, Yoshihiro Agari, Seiki Kuramitsu, Akeo Shinkai
    • Organizer
      第1回モデル生物丸ごと一匹学会(高度好熱菌丸ごと一匹プロジェクト第10回連携研究会共催)
    • Place of Presentation
      スプリング-8(兵庫県)
    • Year and Date
      2011-08-20
    • Related Report
      2011 Annual Research Report
  • [Presentation] Structural and functional genomics of a model organism Thermus thermophilus HB8: toward functional discovery of functionally unknown proteins2011

    • Author(s)
      Shinkai A, Bessho Y, Agari Y, Iino H, Fukui K, Kitamura A, Sakamoto K, Kim K, Masui R, Yokoyama S, Kuramitsu S
    • Organizer
      International Conference on Structural Genomics
    • Place of Presentation
      Chestnut Conference Centre、トロント、カナダ
    • Year and Date
      2011-05-13
    • Related Report
      2012 Final Research Report
  • [Presentation] 脂肪酸の分解を制御する、高度好熱菌Thermus thermophilus HB8 由来TetR ファミリー転写因子FadR の構造と機能"BMB20102010

    • Author(s)
      上利佳弘、上利和子、坂本恵子、倉光成紀、新海暁男
    • Organizer
      第33回日本分子生物学会・第83回日本生化学会大会合同大会
    • Place of Presentation
      神戸ポートアイランド、神戸
    • Year and Date
      2010-12-07
    • Related Report
      2012 Final Research Report
  • [Presentation] 脂肪酸分解を制御する、高度好熱菌Thermus thermophilus HB8由来TetRファミリー転写因子FadRの構造と機能2010

    • Author(s)
      上利佳弘、上利和子、坂本恵子、倉光成紀、新海暁男
    • Organizer
      BMB2010
    • Place of Presentation
      神戸
    • Year and Date
      2010-12-07
    • Related Report
      2010 Annual Research Report
  • [Presentation] 高度好熱菌Thermus thermophilus HB8株における転写因子の機能解析と機能未知遺伝子の分類

    • Author(s)
      新海暁男
    • Organizer
      第13回日本蛋白質科学会年会ワークショップ
    • Place of Presentation
      とりぎん文化会館、鳥取
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 分子間ジスルフィド結合を持つThermus thermophilus HB8由来TetRファミリー転写因子TTHA0167の構造と機能

    • Author(s)
      坂本恵子
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      マリンメッセ福岡、福岡
    • Related Report
      2012 Annual Research Report
  • [Presentation] Thermus thermophilus HB8由来TetRファミリー転写調節因子 PfmRによる転写抑制

    • Author(s)
      上利佳弘
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      マリンメッセ福岡、福岡
    • Related Report
      2012 Annual Research Report
  • [Presentation] Structural and functional analysis of TetR family transcriptional regulator PfmR from Thermus thermophilus HB8

    • Author(s)
      上利佳弘
    • Organizer
      第2回モデル生物丸ごと一匹学会
    • Place of Presentation
      SPring-8、兵庫
    • Related Report
      2012 Annual Research Report
  • [Presentation] Structural and functional analysis of TetR family transcriptional regulator TTHA0167 from T. thermophilus HB8

    • Author(s)
      坂本恵子
    • Organizer
      第2回モデル生物丸ごと一匹学会
    • Place of Presentation
      SPring-8、兵庫
    • Related Report
      2012 Annual Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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