Regulatory Roles and Networks of the Whole Set of Transcription Factors in Escherichia coli

2011 Fiscal Year Final Research Report

• Project/Area Number: 21241047
• Research Category: Grant-in-Aid for Scientific Research (A)
• 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 法政大学, 企画戦略本部, 特任教授 (80019869)
• Project Period (FY): 2009 – 2011
• Keywords: ゲノム制御 / 転写制御 / 転写因子 / 大腸菌

Research Abstract

The genome expression is determined by controlling the distribution of a limited number of RNA polymerase within the genome through interaction with transcription factors. The aim of this research was to identify the regulatory role of all 300 transcription factors in the model prokaryote, Escherichia coli.
1) We developed the in vitro Genomic SELEX screening system and determined the regulation target genes for all 300 transcription factors.
2) We also developed the in vivo NIP-chip system and determined the intracellular distribution of transcription factors within the E. coli genome.
3) The regulation targets thus predicted were examined by measuring their expression in the presence and absence of transcription factors.
4) We determined the intracellular levels of all 300 transcription factors by using quantitative immune-blot analysis.
5) Taking all the results together, I have proposed :(1) the list of regulation targets for all 300 transcription factors ; and(2) the interaction network of 300 transcription factors, altogether forming complex hierarchic regulation networks.

Research Products

• [Journal Article] Prokaryotic genome regulation : Multi-factor promoters and multi-target regulators (2012)
  • Author(s): Ishihama, A.
  • Journal Title: Proc. Jpn. Acad Volume: (in press)
  • Peer Reviewed
• [Journal Article] Regulation targets of metal-response BasS-BasR two-component system in Escherichia coli : Modification of cell membrane (2012)
  • Author(s): Ogasawara, H., Shinohara, S. and Ishihama, A.
  • Journal Title: Microbiology Volume: 158 Pages: 1482-1492
  • Peer Reviewed
• [Journal Article] Induction of YdeO, a regulator for acid resistance gene, by ultraviolet irradiation in Escherichia coli (2012)
  • Author(s): Yamanaka, Y., Ishihama, A. and Yamamoto, K.
  • Journal Title: Biosci. Biotechnol. Biochem Volume: 76 Pages: 120041-1-2
  • Peer Reviewed
• [Journal Article] Increase in cell viability by polyamines through stimulation of the synthesis of ppGpp regulatory protein and protein in Escherichia coli. (2012)
  • Author(s): Terui, Y., Akiyama, M., Sakamoto, A., Tomitori, H., Yamamoto, K., Ishihama, A., Igarashi, K. and Kashiwagi, K.
  • Journal Title: J. Biochem. Cell Biol Volume: 44 Pages: 412-422
  • Peer Reviewed
• [Journal Article] RodZ(YfgA), a bacterial cytoskeletal protein, regulates expression of type III secretion system in Shigella sonnei through post-transcriptional processing (2011)
  • Author(s): Mitobe, J., Yanagihara, I., Ohnishi, K., Ishihama, A. and Watanabe, H.
  • Journal Title: EMBO Reports Volume: 12 Pages: 911-916
  • Peer Reviewed
• [Journal Article] Cross-regulation between biofilm formation and flagella synthesis : Role of biofilm master regulator CsgD (2011)
  • Author(s): Ogasaawara, H., Yamamoto, K. and Ishihama, A.
  • Journal Title: J. Bacteriol Volume: 193(10) Pages: 2587-2597
  • Peer Reviewed
• [Journal Article] Novel roles of LeuO in transcription regulation in E. coli : Antagonistic interplay with the universal silencer H-NS (2011)
  • Author(s): Shimada, T., Bridier, A., Briandet, R. and Ishihama, A.
  • Journal Title: Mol. Microbiol Volume: 81
  • Peer Reviewed
• [Journal Article] Novel roles of cAMP receptor protein(CRP) in regulation of transport and metabolism of carbon sources (2011)
  • Author(s): Shimada, T., Fujita, N., Yamamoto, K. and Ishihama, A.
  • Journal Title: PLoS ONE Volume: 6(6) Pages: e20081
  • Peer Reviewed
• [Journal Article] Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli (2011)
  • Author(s): Shimada, T., Yamamoto, K. and Ishihama, A.
  • Journal Title: J. Bacteriol Volume: 193(3) Pages: 649-659
  • Peer Reviewed
• [Journal Article] The Escherichia coli K-12 MntR mini-regulon includes dps that encodes the major stationary phase DNA-binding protein (2011)
  • Author(s): Yamamoto, K., Ishihama, A., Busby, S. J. W. and Brainger, D. C.
  • Journal Title: J. Bacteriol Volume: 193(6) Pages: 1477-1480
  • Peer Reviewed
• [Journal Article] Prokaryotic genome regulation : Multi-factor promoters, multi-target regulators and hierarchic networks (2010)
  • Author(s): Ishihama, A.
  • Journal Title: FEMS Microbial Reviews Volume: 34 Pages: 628-645
  • Peer Reviewed
• [Journal Article] The E. coli csgD promoter : Interplay between eight transcription factors (2010)
  • Author(s): Ogasawara, H., Yamada, K., Kori, A., Yamamoto, K. and Ishihama, A.
  • Journal Title: Microbiology Volume: 156(8) Pages: 2470-2483
  • Peer Reviewed
• [Journal Article] Regulatory role of MlrA in transcription activation of csgD, the master regulator of biofilm formation in Escherichia coli (2010)
  • Author(s): Ogasawara, H., Yamamoto, K. and Ishihama, A.
  • Journal Title: FEMS Microbiol. Lett Volume: 312 Pages: 160-168
  • Peer Reviewed
• [Journal Article] Single live-bacterial cell assay of promoter activity and regulat (2010)
  • Author(s): Teramoto, J., Yamanishi, Y., Magdy, E-S. H., Hasegawa, A., Kori, A., Nakajima, M., Arai, F., Fukuda, T. and Ishihama, A.
  • Journal Title: Genes Cells Volume: 15 Pages: 1111-1112
  • Peer Reviewed
• [Journal Article] A novel nucleoid protein of Escherichia coli induced under anaerobic growth conditions (2010)
  • Author(s): Teramoto, J., Yoshimura, S. H., Takeyasu, K. and Ishihama, A.
  • Journal Title: Nucleic Acids Res Volume: 38(11) Pages: 3605-3618
  • Peer Reviewed
• [Journal Article] Ribosome modulation factor, an important protein for cell viability encoded by the polymodulon modulon (2010)
  • Author(s): Terui, Y., Tabei, Y., Akiyama, M., Tomitori, H., Yamamoto, K., Ishihama, A., Igarashi, K. and Kashiwagi, K.
  • Journal Title: J. Biol. Chem Volume: 285 Pages: 28698-28707
  • Peer Reviewed
• [Journal Article] Participation of regulator AscG of the b. glucoside utilization operon in regulation of the propionate catabolism operon (2009)
  • Author(s): Ishida, Y., Kori, A. and Ishihama, A.
  • Journal Title: J. Bacteriol Volume: 191 Pages: 6136-6144
  • Peer Reviewed
• [Journal Article] Two modes of autoregulation of the murR repressor in Escherichia coli (2009)
  • Author(s): Ishii, D., Ishihama, A. and Yamamoto, K.
  • Journal Title: Biosci. Biotechnol. Biochem Volume: 73 Pages: 90421-1-3
• [Journal Article] Involvement of RNA-binding protein Hfq in the osmotic-response regulation of invE gene expression in Shigella sonnei (2009)
  • Author(s): Mitobe, J., Morita-Ishihara, T., Ishihama, A. and Watanabe, H.
  • Journal Title: BMC Microbiol Volume: 9 Pages: 110
  • Peer Reviewed
• [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. Bacteriol Volume: 191 Pages: 4562-4571
  • Peer Reviewed
• [Journal Article] Enhancement of the synthesis of RpoE and StpA by polyamines at the level of translation in Escherichia coli under heat shock conditions (2009)
  • Author(s): Terui, Y., Higashi, K., Tabei, Y., Tomitori, H., Yamamoto, K., Ishihama, A., Igarashi, K. and Kashiwagi, K.
  • Journal Title: J. Baceriol Volume: 191 Pages: 5348-5357
  • Peer Reviewed
• [Journal Article] Characterization of CitA-CitB signal transduction activating genes involved in anaerobiccitrate catabolism in Escherichia coli (2009)
  • Author(s): Yamamoto, K., Matsumoto, F., Minagawa, S., Oshima, T., Fujita, N., Ogasawara, N. and Ishihama, A.
  • Journal Title: Biosci. Biotechnonl. Biochem Volume: 73 Pages: 346-350
  • Peer Reviewed
• [Presentation] Global Regulation of Prokaryotic Genome Transcription (2012)
  • Author(s): Ishihama, A.
  • Organizer: JN Centre for Advanced Scientific Research(JNCASR) Seminar
  • Place of Presentation: Bangalore
  • Year and Date: 2012-03-19
• [Presentation] 「細菌ゲノム転写の包括制御機構」ひとつの生物のすべての転写因子の制御機能の理解を目指して- (2012)
  • Author(s): 石浜明
  • Organizer: 東北大学グローバルCOE, Network Medicine創生拠点、NM高等教育セミナー
  • Place of Presentation: 東北大学医学部
  • Year and Date: 2012-03-08
• [Presentation] 大腸菌環境応答におけるゲノム転写の包括制御 (2011)
  • Author(s): 石浜明
  • Organizer: 第84回日本生化学会大会
  • Place of Presentation: 京都・国際会議場
  • Year and Date: 20110921-24
• [Presentation] Anaerobiosis-induced nucleoid associated protein Dan polymerizes along dsDNA to form rigid helical-like co-filament that is able to concatemarize (2011)
  • Author(s): Lim, C. J., Lee, S. Y., Ishihama, A. and Yan, J.
  • Organizer: Biophys. Soc. Meet."Dynamic DNA Packaging Across Kingdoms"
  • Place of Presentation: Asilomar, Californica, USA
  • Year and Date: 20110705-08
• [Presentation] 細菌細胞の個性:その分子基盤 (2011)
  • Author(s): 石浜明
  • Organizer: 九州大学G-COE「未来分子システム科学」公開セミナー
  • Place of Presentation: 九州大学先導物質化学研究所・福岡
  • Year and Date: 2011-02-09
• [Presentation] Multi-scale molecular genetics of prokaryotic genome regulation (2010)
  • Author(s): Ishihama, A., Ogasawara, H., Shimada, T. Teramoto, T., Kori, A., Yamada, K., Kobayashi, K., Katayama, T. and Yamamoto, K.
  • Organizer: 21st Internatl. Symp. Micro-NanoMechatronics Human Sci.
  • Place of Presentation: Nagoya Univ., Nagoya, Japan
  • Year and Date: 20101107-10
• [Presentation] Prokaryotic Genome Regulation : Multi-factor Promoters and Multi-target Regulators (2010)
  • Author(s): Ishihama, A.
  • Organizer: 2^<nd> Florence Conference on Phenotype Microarray
  • Place of Presentation: Internatl. Conf. Hall, Pisa, Italy
  • Year and Date: 20100913-15
• [Presentation] Prokaryotic Genome Regulation : Multi-factor Promoters and Multi-target Regulators (2010)
  • Author(s): Ishihama, A.
  • Organizer: 11^<th> Asian Conference on Transcription(ACT)
  • Place of Presentation: Nakijin Hall, Okinawa, Japan
  • Year and Date: 20100701-05
• [Presentation] 大腸菌ゲノム転写制御の新展開 (2010)
  • Author(s): 石浜明
  • Organizer: 第9回微生物研究会
  • Place of Presentation: 法政大学小金井キャンパス
  • Year and Date: 2010-06-26
• [Presentation] Genome-wide Genomic-SELEX Search of Regulation Targets by Transcription Factors (2010)
  • Author(s): Shimada, T., Fujita, N., Yamamoto, K. and Ishihama, A.
  • Organizer: Jacques Monod Commemorative Minisymposium : Gene Expression and Signalling in Bacteria
  • Place of Presentation: Institut Pasteur, Paris, France
  • Year and Date: 2010-05-31
• [Presentation] Prokaryotic Genome Regulation. Japan-India Collaborative Science Program Seminar (2010)
  • Author(s): Ishihama, A.
  • Organizer: Centre for Cellular and Molecular Biology(CCMB)
  • Place of Presentation: Hyderabad, India
  • Year and Date: 2010-03-17
• [Presentation] 細菌ゲノム制御全体像解明のための戦略戦術 (2010)
  • Author(s): 石浜明
  • Organizer: 日本大学学術研究高度化推進事業公開シンポジウム
  • Place of Presentation: 日大・オープンリサーチセンター
  • Year and Date: 2010-02-26
• [Presentation] Regulatory roles of nucleoid-associated proteins in Escherichia coli (2009)
  • Author(s): Ishihama, A., Teramoto, J., Ogasawara, H., Shimada, T. and Yamamoto, K.
  • Organizer: 32nd Ann. Meet. Mol. Biol. Soc. Jpn
  • Place of Presentation: Pacifico Yokohama, Japan
  • Year and Date: 20091209-12
• [Presentation] Growth phase-dependent regulation of csgD, the master regulator of biofilm formation (2009)
  • Author(s): Ishihama, A., Ogasawara, H., Shimada, T., Teramoto, J., Kori, A., Yamada, K., and Yamamoto, K.
  • Organizer: 3^<rd> Internatl. Conf. Environmental, Industrial and Applied Microbiology, BioMicroWorld
  • Place of Presentation: Lisbon, Portugal
  • Year and Date: 20091202-04
• [Presentation] 細菌の生存戦略としてのバイオフィルム形成:遺伝子制御ネットワークと転写因子群 (2009)
  • Author(s): 石浜明
  • Organizer: 日本生化学会第82回大会シンポジウム"細菌の生存戦略をめぐる新たな展開"
  • Place of Presentation: 神戸ポートアイランド、神戸
  • Year and Date: 20091021-24
• [Presentation] 細菌の環境金属応答のゲノム制御 (2009)
  • Author(s): 石浜明, 小笠原寛、島田友祐、寺本潤
  • Organizer: メタロチオネインおよびメタルバイオサイエンス研究会2009
  • Place of Presentation: 東京大学・山上会館
  • Year and Date: 20091016-17
• [Presentation] 大腸菌における環境金属応答のゲノム転写制御 (2009)
  • Author(s): 石浜明
  • Organizer: メタルバイオサイエンス研究会2009
  • Place of Presentation: 東京大学、東京
  • Year and Date: 20091016-17
• [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: 秋保グランドホテル、宮城
  • Year and Date: 20090309-11
• [Presentation] Genomic SELEX search for regulation targets by 100 species of uncharacterized transcription factors from E. coli (2009)
  • Author(s): Ishihama, A.
  • Organizer: 12^<th> Transcription Assembly
  • Place of Presentation: Chandigarh, India
  • Year and Date: 20090302-05
• [Book] Detection of bacterial bahits : Single planktonic cells and assembled Detection of bacterial bahits : Single planktonic cells and assembled biofilm. In : Nanomedicine in Diagnostics (2012)
  • Author(s): Ishihama, A.
  • Total Pages: 191-216
  • Publisher: Science Publishes
• [Book] Transcription factors and transcriptional apparatus in bacteria. In : Encyclopedia of Systems Biology (2012)
  • Author(s): Ishihama, A.
  • Publisher: Springer
• [Book] Prokaryotic genome regulation : Multi-factor promoters, multi-target regulators and hierarchic networks (2010)
  • Author(s): Ishihama, A.
  • Total Pages: 628-645
• [Book] Chapter 2.6, The Nucleoid : an Overview. In : EcoSal. Escherichia coli and Salmonella : cellular and molecular biology (2010)
  • Author(s): Ishihama, A.
  • Publisher: インターネット出版
  • URL: http://www.ecosal.org.
• [Book] 原核生物RNAポリメラーゼ.「生化学事典」 (2010)
  • Author(s): 石浜明
  • Total Pages: 788
  • Publisher: 朝倉書店