Identification of Regulation Targets and Analysis of Regulation Modes by Uncharacterized Transcription Factors from Escherichia coli

2008 Fiscal Year Final Research Report

• Project/Area Number: 18310133
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: 基礎ゲノム科学
• Research Institution: Hosei University
• Principal Investigator: ISHIHAMA Akira Hosei University, 生命科学部, 教授 (80019869)
• Project Period (FY): 2006 – 2008
• Keywords: ゲノム調節 / 転写 / 遺伝子 / 細菌 / 発現制御

Research Abstract

転写酵素RNAポリメラーゼの転写対象遺伝子群の選択は、転写因子との相互作用によって決定される。約300種類の大腸菌転写因子のうち、約100種は制御機能未知である。本研究では、機能未知転写因子が認識する配列から制御機能を同定するGenomic SELEX法を開発した。純化転写因子を利用した解析から、各転写因子の制御対象遺伝子群の同定に成功したことで、ゲノム転写包括制御の全貌解明の展望が開けた。

Research Products

• [Journal Article] Involvement of leucine-reponse transcription factor LeuO in regulation of the genes for sulfa-drug efflux (2009)
  • Author(s): Shimada, T., Yamamoto, K. and Ishihama, A.
  • Journal Title: J. Bacterlol 191(in press)
  • Peer Reviewed
• [Journal Article] A11R is the Allantoin/Glyoxylate-Sensing Master Regulator of the Genes for Degradation and Reutilization of Purines (2008)
  • Author(s): Hasegawa, A., Ogasawara, H., Kori, A. and Ishihama, A.
  • Journal Title: Microbiology 154 Pages: 3366-3378
  • Peer Reviewed
• [Journal Article] Involvement of RNA binding protein Hfq in the post-tanscriptional regulation of invE gene expression in Shigella sonnei (2008)
  • Author(s): Mitobe, J., Ishihara, T., Ishihama, A. and Watanabe, H.
  • Journal Title: J. Biol. Chem 283 Pages: 5738-5747
  • Peer Reviewed
• [Journal Article] The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions (2008)
  • Author(s): Shimada, T., Ishihama, A., Busby, S.J.W. and Grainger, D.C.
  • Journal Title: Nucleic Acids Res. 36 Pages: 3950-3955
  • Peer Reviewed
• [Journal Article] The uncharacterized YdhM is the regulator of the nemA gene, coding for N-ethylmaleimide reductase (2008)
  • Author(s): Umezawa, Y., Ogasawara, H., Shimada, T., Kori, A. and Ishihama, A.
  • Journal Title: J. Bacteriol 190 Pages: 5890-5897
  • Peer Reviewed
• [Journal Article] Involvement of multiple transcription factors for metal-induced spy gene expression in Escherichia coli (2008)
  • Author(s): Yamamoto, K., Ogasawara, H. and Ishihama, A.
  • Journal Title: J. Biotechnol 133(16) Pages: 6080-6084
  • Peer Reviewed
• [Journal Article] Genomic SELEX search for target genes under the control of PhoQP-RstBA signal relay cascade (2007)
  • Author(s): Ogasawara, H., Hasegawa, A., Kanda, E., Miki, T., Yamamoto, K. and Ishihama, A.
  • Journal Title: J. Bacteriol 189 Pages: 4791-4799
  • Peer Reviewed
• [Journal Article] PdhR(pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coll (2007)
  • Author(s): Ogasawara, H., Ishida, Y., Yamada, K., Yamamoto, K. and Ishihama, A.
  • Journal Title: J. Bacteriol 189 Pages: 5534-5541
  • Peer Reviewed
• [Journal Article] RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimdines (2007)
  • Author(s): Shimada, T., Hirao, K., Kori, A., Yamamoto, K. and Ishihama, A.
  • Journal Title: Mol. Microbic 66 Pages: 744-779
  • Peer Reviewed
• [Journal Article] The dynamic state of DNA topology is essential for genome condensation in bacteria (2006)
  • Author(s): Ohniwa, R. L. , Mirikawa, K., Kim, J., Ohta, T., Ishihama, A., Wada, C. and Takeyasu, K.
  • Journal Title: EMBO J. 25 Pages: 5591-5602
  • Peer Reviewed
• [Presentation] 大腸菌ゲノム転写の包括制御 (2009)
  • Author(s): 石浜明
  • Organizer: 2008年度「べん毛研究交流会」
  • Place of Presentation: 仙台、宮城
  • Year and Date: 20090309-11
• [Presentation] Genomic SELEX search for regulation targets by 100 species of uncharacterized transcription factors from E. coll. (2009)
  • Author(s): Ishihama, A.
  • Organizer: 12^<th> Transcription Assembly
  • Place of Presentation: Chandigarh, India
  • Year and Date: 20090302-05
• [Presentation] 細菌の金属ストレスに対する転写応答の包括的な制御機構 (2008)
  • Author(s): 山本兼由、石浜明
  • Organizer: 日本農芸化学会大会
  • Place of Presentation: 名城大学・名古屋
  • Year and Date: 20080326-29
• [Presentation] 20 years of progress with RNA polymerase (2008)
  • Author(s): Ishihama, A.
  • Organizer: 20^<th> RNA Polymerase Workshop
  • Place of Presentation: York, UK
  • Year and Date: 20080316-17
• [Presentation] Multi-factor promoters and multi-factor networks (2008)
  • Author(s): Ishihama, A. et.al.
  • Organizer: 20^<th> RNA Polymerase Workshop
  • Place of Presentation: York, UK
  • Year and Date: 20080316-17
• [Presentation] Multi-Scale Genetics towards Understanding the Regulatory Roles of All Transcription Factors from a Single Organism Escherichia coll. Asian Conference on Transcription (ACT) (2008)
  • Author(s): Ishihama, A.
  • Organizer: 10^<th> Meeting
  • Place of Presentation: Bangalore, India
  • Year and Date: 20080113-16
• [Presentation] ゲノムの転写制禦 : ひとつの生物のすべての転写因子の調節機能同定の試み (2007)
  • Author(s): 石浜明
  • Organizer: 第30回日本分子生物学会・第80回日本生化学会マスターズレクチャー
  • Place of Presentation: パシフィコ横浜、横浜
  • Year and Date: 20071210-14
• [Presentation] 細菌の環境金属応答の転写包括制御 (2007)
  • Author(s): 石浜明・山本兼由・小笠原寛・島田友裕・寺本潤
  • Organizer: 第30回日本分子生物学会・第80回日本生化学会ワークショップ「金属イオンのChemical Bio10gy」
  • Place of Presentation: パシフィコ横浜、横浜
  • Year and Date: 20071210-14
• [Presentation] Multi-Scale Genetics of Transcription Network : Understanding the Regulatory Roles of All 300 Transcription Factors from a Single Organism (2007)
  • Author(s): Ishihama, A., et.al.
  • Organizer: Escherichia coll
  • Place of Presentation: Nagoya, Japan
  • Year and Date: 20071100
• [Presentation] RutR is the uracil/thymine sensing regulator of a set of genes for synthesis and degradation of pyrimidines (2007)
  • Author(s): Shimada, T., Hirao, K., Kori, A., Yamamoto, K., Grainger, D. C. , Busby, S.J.W. and Ishihama, A.
  • Organizer: RNA Polymerase Workshop
  • Place of Presentation: London, UK
  • Year and Date: 20070300
• [Presentation] The bacterial nucleoid (2006)
  • Author(s): Ishihama, A.
  • Organizer: The 1^<st> Symp Nuclear Architecture : Chromosome-Chromatin Dynamics
  • Place of Presentation: Bangalrore, India
  • Year and Date: 20061200
• [Presentation] Systemacic search for regulatory roles of putative transcription factors with unidentified functions (2006)
  • Author(s): Ishihama, A.
  • Organizer: The 10^<th> Transcription Assembly
  • Place of Presentation: Kolkata, India
  • Year and Date: 20061200
• [Presentation] 大腸菌機能未知転写因子の機能解析 : 制御標的遺伝子の探索 (2006)
  • Author(s): 石浜明、小笠原寛、島田友裕、寺本潤、郡彩子、山田佳代子、平尾貴世、長谷川明子、梅澤喜正、矢吹光史郎、成瀬みなみ、石田雄司、稲葉達也、松井勝、鍛代悠一、田中邦貴
  • Organizer: 第6回日本蛋白質科学会年会
  • Place of Presentation: 京都
  • Year and Date: 20060424-26
• [Presentation] RNAポリメラーゼ : ゲノム転写の包括制御機構 (2006)
  • Author(s): 石浜明
  • Organizer: シンポジウム"The Origins of Trendy RNAs"
  • Place of Presentation: 北里大学、東京
  • Year and Date: 2006-07-15
• [Presentation] マルチスケール遺伝学 : 大腸菌全転写因子の機能同定 (2006)
  • Author(s): 石浜明、小笠原寛、島田友裕、寺本潤、郡彩子、山田佳代子、平尾貴世、長谷川明子、梅澤喜正、矢吹光史郎、石田雄司、稲葉達也、松井勝、鍛代悠一、加藤大策
  • Organizer: シンポジウム「マルチスケール操作によるシステム細胞工学」
  • Place of Presentation: 名古屋大学野依学術交流館、名古屋
  • Year and Date: 2006-06-30
• [Book] The nucleoid : an overview. In : Escherichia coil and Salmonella (Neidhardt, F.C., eds.) (2009)
  • Author(s): Ishihama, A.
  • Publisher: American Society of Microbiology Washington, USA
• [Book] Multi-scale genetics towards understanding the regulatory roles of all 300 transcription factors from a single organism Escherichia coli (2007)
  • Author(s): Ishihama, A. et.al
  • Total Pages: 35-39
  • Publisher: In : Micro Uano Mechatronics and Human Science (Fukuda, T. eds.)
• [Remarks]
  • URL: http://www.k.hosei.ac.jp/ceng/fb/teacher/ishihama.html