Global regulation of genome expression : Single cell analysis of environmental stress response

2009 Fiscal Year Final Research Report

• Project/Area Number: 17076016
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: Hosei University
• Principal Investigator: ISHIHAMA Akira Hosei University, 企画・戦略本部, 特任教授 (80019869)
• Co-Investigator(Kenkyū-buntansha): MAGARIYAMA Yukio 農業食品産業技術総合研究機構, 食品総合研究所, 上席研究員 (40343818) ; YAMAMOTO Kaneyoshi 法政大学, 生命科学部, 准教授 (40351580)
• Project Period (FY): 2005 – 2009
• Keywords: ナノバイオロジー / システム生物学 / ゲノム / 転写制御 / 一細胞観察 / プロモーター / 転写因子 / 大腸菌

Research Abstract

The model bacterium, Escherichia coli, is able to survive under various stressful conditions in nature by forming the bacterial community, in which each cell plays a different physiological role. For search of the role each plays, single-live cell observation systems were developed using newly constructed cell chips, and transcription in individual cells was analyzed. Towards understanding the regulation mechanism of genome transcription, we also performed the systematic analysis of regulatory roles of a to tal of 300 transcription factors from E. coli.

Research Products

• [Journal Article] Prokaryotic genome regulation: Multi-factor promoters, multi-target regulators and hierarchic networks. (2010)
  • Author(s): Ishihama, A.
  • Journal Title: FEMS Microbial Reviews (in press)
  • Peer Reviewed
• [Journal Article] Regulation of the Escherichia coli csgD promoter: Interplay between five transcription factors. (2010)
  • Author(s): Ogasawara, H., Kori, A., Yamada, K., Yamamoto, K., Ishihama, A.
  • Journal Title: Microbiology (in press)
  • 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., Ishihama, A.
  • Journal Title: Nucleic Acids Res (in press)
  • Peer Reviewed
• [Journal Article] Participation of regulator AscG of theβ-glucoside utilization operon in regulation of the propionate catabolism operon. (2009)
  • Author(s): Ishida, Y., Kori, A., Ishihama, A.
  • Journal Title: J. Bacteriol. 191(19) Pages: 6136-6144
  • Peer Reviewed
• [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., Watanabe, H.
  • Journal Title: BMC Microbiol 9 Pages: 110
  • Peer Reviewed
• [Journal Article] Involvement of leucine -response transcription factor LeuO in regulation of the genes for sulfa -drug efflux. (2009)
  • Author(s): Shimada, T., Yamamoto, K., Ishihama, A.
  • Journal Title: J. Bacteriol. 191(14) 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., Kashiwagi, K.
  • Journal Title: J. Baceriol. 191(17) Pages: 5348-5357
  • Peer Reviewed
• [Journal Article] AllR 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., Ishihama, A.
  • Journal Title: Microbiology 154 Pages: 366-3378
  • Peer Reviewed
• [Journal Article] Involvement of RNA binding protein Hfq in the post-transcriptional regulation of invE gene expression in Shigella sonnei. (2008)
  • Author(s): Mitobe, J., Ishihara, T., Ishihama, A., 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., Grainger, D.C.
  • Journal Title: Nucleic Acids Res. 36(12) 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., Ishihama, A.
  • Journal Title: J. Bacteriol. 190(17) Pages: 5890-5897
  • Peer Reviewed
• [Journal Article] Anaerobic regulation of citrate fermentation by CitAB in Escherichia coli. (2008)
  • Author(s): Yamamoto, K., Matsumoto, F., Oshima, T., Fujita, N., Ogasawara, N., Ishihama, A.
  • Journal Title: Biosci. Biotechnol. Biochem. 72(11) Pages: 3011-3014
  • 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., Ishihama, A.
  • Journal Title: J. Biotechnol. 133(16) Pages: 080-6084
  • Peer Reviewed
• [Journal Article] The Role of omega subunit of RNA polymerase in expression of the relA Gene in Escherichia coli. (2007)
  • Author(s): Chatterji, D., Ozoline, O., Ogawa, Y. Shimada, T., Ishihama, A.
  • Journal Title: FEMS Microbiol. Lett. 267(1) Pages: 51-55
  • 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., Ishihama, A.
  • Journal Title: J. Bacteriol. 189(13) Pages: 4791-4799
  • Peer Reviewed
• [Journal Article] PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli. (2007)
  • Author(s): Ogasawara, H., Ishida, Y., Yamada, K., Yamamoto, K., Ishihama, A.
  • Journal Title: J. Bacteriol. 189(15) 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., Ishihama, A.
  • Journal Title: Mol. Microbiol. 66(3) Pages: 744-779
  • Peer Reviewed
• [Journal Article] Enhancement of the synthesis of RpoN, Cra and H -NS by polyamines at the level of translation Escherichia coli cultured with glucose and glutamate. (2007)
  • Author(s): Terui, Y., Higashi, K., Taniguchi, S., Shigemasa, A., Nishimura, K., Kashiwagi, K., Yamamoto, K., Ishihama, A., Igarashi, K.
  • Journal Title: J. Bacteriol 189(6) Pages: 2359-2368
  • Peer Reviewed
• [Journal Article] folA a new member of the TyrR regulon in Escherichia coli K-12. (2007)
  • Author(s): Yang, J., Ogawa, Y., Camakaris, H., Shimada, T., Ishihama, A., Pittard, A.J.
  • Journal Title: J. Bacteriol. 189(16) Pages: 6080-6084
  • Peer Reviewed
• [Journal Article] Enhancement of +1 frameshift by polyamines during translation of polypeptide release factor 2 in Escherichia coli. (2006)
  • Author(s): Higashi, K., Kashiwagi, K., Taniguchi, S., Terui, Y., Yamamoto, K., Ishihama, A., Igarashi, K.
  • Journal Title: J. Biol. Chem. 281 Pages: 9527-9537
  • Peer Reviewed
• [Journal Article] The dynamic state of DNA topology is essential for genome condensation in bacteria. (2006)
  • Author(s): Ohniwa, R.L., Morikawa, K., Kim, J., Ohta, T., Ishihama, A., Wada, C., Takeyasu, K.
  • Journal Title: EMBO J. 25 Pages: 5591-5602
  • Peer Reviewed
• [Journal Article] Characterization of copper -inducible promoters regulated by CpxA/CpxR in Escherichia coli. (2006)
  • Author(s): Yamamoto, K., Ishihama, A.
  • Journal Title: Bioscience, Biotechnology and Biochemistry 70 Pages: 1688-1695
  • Peer Reviewed
• [Journal Article] Systematic search for the Cra-binding promoters using genomic SELEX. (2005)
  • Author(s): Shimada, T., Fujita, N., Maeda, M., Ishihama, A.
  • Journal Title: Genes Cells 10(9) Pages: 907-918
  • Peer Reviewed
• [Journal Article] Transcriptional response of Escherichia coli to external copper. (2005)
  • Author(s): Yamamoto, K., Ishihama, A.
  • Journal Title: Mol. Microbiol. 55(1) Pages: 215-227
  • Peer Reviewed
• [Journal Article] Transcriptional response of Escherichia coli to external zinc. (2005)
  • Author(s): Yamamoto, K., Ishihama, A.
  • Journal Title: J. Bacteriol. 187(18) Pages: 6333-6340
  • Peer Reviewed
• [Journal Article] Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli. (2005)
  • Author(s): Yamamoto, K., Hirano, K., Ohshima, T., Aiba, H., Utsumi, R., Ishihama, A.
  • Journal Title: J. Biol. Chem. 280(2) Pages: 1448-1456
  • Peer Reviewed
• [Presentation] rokaryotic genome regulation: Multi-factor promoters, multi-target regulators and multi-factor networks. (2010)
  • Author(s): Ishihama, A.
  • Organizer: Japan -India Collaborative Science Program Seminar
  • Place of Presentation: Centre for Cellular and Molecular Biology (CCMB), 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「病原体抑制遺伝子の解明と感染症の制御」
  • Place of Presentation: 日大・オープンリサーチセンター, 東京
  • Year and Date: 2010-02-26
• [Presentation] 細菌細胞の個性:その分子基盤 (2010)
  • 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: 2010-02-09
• [Presentation] Growth phase-dependent regulation of csgD, the master regulator of biofilm formation: Interplay between multiple transcription factors. (2009)
  • Author(s): Ishihama, A.
  • Organizer: 3 rd Internatl. Conf. Environ. Indust. Appl. Microbiol. (BioMicroWorld2009)
  • Place of Presentation: Lisbon, Portugal
  • Year and Date: 20091202-20091204
• [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: 20091021-20091024
• [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: 20091016-20091017
• [Presentation] Genomic SELEX search for regulation targets by 100 species of uncharacterized transcription factors from E. coli. (2009)
  • Author(s): Ishihama, A.
  • Organizer: 12th Transcription Assembly
  • Place of Presentation: Chandigarh, India
  • Year and Date: 20090302-20090305
• [Presentation] Transcription factor-promoter interaction networks. (2008)
  • Author(s): Ishihama, A.
  • Organizer: 2005 Internatl. Symp. Micro-Nano Mechatronics & Human Science
  • Place of Presentation: Nagoya, Japan.
  • Year and Date: 20081108-20051109
• [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: 20080316-20080317
• [Presentation] Multi-factor promoters and multi-factor networks. (2008)
  • Author(s): Ishihama, A.
  • Organizer: 20 th RNA Polymerase Workshop.
  • Place of Presentation: York, UK
  • Year and Date: 20080316-20080317
• [Presentation] Multi-scale genetics towards understanding the regulatory roles of all transcription factors from a single organism Escherichia coli. Asian Conference on Transcription (ACT) (2008)
  • Author(s): Ishihama, A.
  • Organizer: 10th Meeting, Jan.
  • Place of Presentation: Bangalore, India
  • Year and Date: 20080113-20080116
• [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: 20071200
• [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 Biology」
  • Place of Presentation: パシフィコ横浜、横浜
  • Year and Date: 20071200
• [Presentation] Multi-scale genetics of transcription network: Understanding the regulatory roles of all 300 transcription factors from a single organism Escherichia coli. (2007)
  • Author(s): Ishihama, A.
  • Organizer: 2007 Micro-Nano Mechatronics and Human Science Symp.
  • Place of Presentation: Nagoya Univ.
  • Year and Date: 20071100
• [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
  • 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
  • Year and Date: 2006-06-30
• [Presentation] ゲノム転写包括制御研究の戦略と戦術 (2005)
  • Author(s): 石浜明
  • Organizer: 東京大学化学生命工学セミナー
  • Place of Presentation: 東京大学、東京
  • Year and Date: 20051100
• [Presentation] ノム全遺伝子で対応する細菌の環境応答 (2005)
  • Author(s): 石浜明
  • Organizer: 特定領域研究「バイオ操作」第1回公開シンポジウム
  • Place of Presentation: 東京大学、東京
  • Year and Date: 20051000
• [Presentation] Genomic SELEX search for the genes and promoters under the control of E. (2005)
  • Author(s): Ishihama, A.
  • Organizer: coli transcription factors. Transcription Assembly
  • Place of Presentation: Hyderabad, India
  • Year and Date: 20050917-20050919
• [Presentation] Transcription in E. coli: the big picture. (2005)
  • Author(s): Ishihama, A.
  • Organizer: UK Integrated Biology of Escherichia coli Meeting
  • Place of Presentation: Birmingham, UK
  • Year and Date: 2005-12-30
• [Book] The Nucleoid:an Overview.(A. Beak, R .Curtiss III, J. B. Kaper, P. D. Karp, F. C. Neidhardt, T.Nystree, J. M. Slauch, C. L. Squires, and D. Ussery, eds., In:EcoSal-Escherichia coliand Salmonella:cellular and molecular biology., Chapter 2.6) (2009)
  • Author(s): Ishihama, A.
  • Publisher: ASM Press
  • URL: http://www.ecosal.org