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2009 Fiscal Year Final Research Report

Fundamental Network of Genes and Proteins for Bacterial Cell Growth

Research Project

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Project/Area Number 17017026
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionNara Institute of Science and Technology

Principal Investigator

OGASAWARA Naotake  Nara Institute of Science and Technology, 情報科学研究科, 教授 (10110553)

Co-Investigator(Kenkyū-buntansha) MORI Hirotada  奈良先端科学技術大学院大学, バイオサイエンス研究科, 教授 (90182203)
KANAYA Shigehiko  奈良先端科学技術大学院大学, 情報科学研究科, 教授 (90224584)
OSHIMA Taku  奈良先端科学技術大学院大学, 情報科学研究科, 助教 (50346318)
ISHIKAWA Shu  奈良先端科学技術大学院大学, 情報科学研究科, 助教 (30359872)
Project Period (FY) 2005 – 2009
Keywords細菌細胞 / 枯草菌 / 大腸菌 / 転写制御 / ChIP-chip解析 / 必須タンパク質 / タンパク質複合体 / システム生物学
Research Abstract

Towards elucidation of fundamental networks of genes and proteins supporting growth of bacterial cells, we analyzed two model bacteria, Bacillus subtilis and Escherichia coli, using new methodologies, such as ChIP-chip analysis using a tiling chip and protein complex analysis using mass spectrometry. As the results, we obtained many new findings concerning new functions of essential genes, functional network of essential proteins, transcriptional regulatory network by transcription factors and nucleoid proteins, cell cycle regulation by nucleoid protein, and metabolome dynamics.

  • Research Products

    (35 results)

All 2009 2008 2007 2006

All Journal Article (24 results) (of which Peer Reviewed: 24 results) Presentation (7 results) Book (4 results)

  • [Journal Article] Update on the Keio collection of Escherichia coli single-gene deletion mutants.2009

    • Author(s)
      Yamamoto, N., Nakahigashi, K., Nakamichi, T., Yoshino, M., Takai, Y., Touda, Y., Furubayashi, A., Kinjo, S., Dose, H., Hasegawa, M., Datsenko, K.A., Nakayashiki, T., Tomita, M., Wanner, B.L., Mori H.
    • Journal Title

      Mol Syst Biol 5,335

    • Peer Reviewed
  • [Journal Article] Assessment of transcriptional responses in Bacillus subtilis cells to an antibiotic, Enduracidin, interfering with cell wall synthesis, by using a high-density tilling chip.2009

    • Author(s)
      Rukmana, A., Morimoto, T., Takahashi, H., Giyanto, Ogasawara, N.
    • Journal Title

      Gene Genet Sys 84

      Pages: 253-267

    • Peer Reviewed
  • [Journal Article] Noc protein binds to specific DNA sequences to coordinate cell division with chromosome segregation.2009

    • Author(s)
      Wu, L.J., Ishikawa, S., Kawai, Y., Oshima, T., Ogasawara, N., Errington, J.
    • Journal Title

      EMBO J 28

      Pages: 1940-1952

    • Peer Reviewed
  • [Journal Article] Systematic genome-wide scanning for genes involved in ATP generation in Escherichia coli.2009

    • Author(s)
      Hara, K.Y., Shimodate, N., Ito, M., Baba, T., Mori, H.
    • Journal Title

      Metab Eng 11

      Pages: 1-7

    • Peer Reviewed
  • [Journal Article] Differential binding profiles of StpA in wild-type and hns mutant cells: a comparative analysis of cooperative partners by ChIP-chip analysis.2009

    • Author(s)
      Uyar, E., Kurokawa, K., Yoshimura, M., Ishikawa, S., Ogasawara, N., Oshima, T.
    • Journal Title

      J Bacteriol 191

      Pages: 2388-2391

    • Peer Reviewed
  • [Journal Article] eSGA: E. coli synthetic genetic array analysis.2008

    • Author(s)
      Butland, G., Babu, M., Diaz-Mejia, J.J., Bohdana, F., Phanse, S., Gold, B., Yang, W., Li, J., Gagarinova, A.G., Pogoutse, O., Mori, H., Wanner, B.L., Lo, H., Wasniewski, J., Christopolous, C., Ali, M., Venn, P., Safavi-Naini, A., Sourour, N., Caron, S., Choi, J.Y., Laigle, L., Nazarians-Armavil, A., Deshpande, A., Joe, S., Datsenko, K.A.,Yamamoto, N., Andrews, B.J., Boone, C., Ding, H., Sheikh, B., Moreno-Hagelseib, G., Greenblatt, J.F., Emili, A.
    • Journal Title

      Nat Methods 5

      Pages: 789-795

    • Peer Reviewed
  • [Journal Article] High-throughput, quantitative analyses of genetic interactions2008

    • Author(s)
      Typas, A., Nichols, R.J., Siegele, D.A., Shales, M., Collins, S.R., Lim, B., Braberg, H., Yamamoto, N., Takeuchi, R., Wanner, B.L., Mori, H., Weissman, J.S., Krogan, N.J., Gross, C.A.
    • Journal Title

      E. coli. Nat Methods 5

      Pages: 781-787

    • Peer Reviewed
  • [Journal Article] Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry2008

    • Author(s)
      Takahashi H, Kai K, Shinbo Y, Tanaka K, Ohta D, Oshima T, Altaf-Ul-Amin M, Kurokawa K, Ogasawara N, Kanaya S.
    • Journal Title

      Anal Bioanal Chem 391

      Pages: 2769-2782

    • Peer Reviewed
  • [Journal Article] The functional analysis of YabA, which interacts with DnaA and regulates initiation of chromosome replication in Bacillus subtils.2008

    • Author(s)
      Cho, E., Ogasawara, N., Ishikawa, S.
    • Journal Title

      Gene Genet Sys 83

      Pages: 111-125

    • Peer Reviewed
  • [Journal Article] Global regulation by horizontally transferred regulators establishes the pathogenicity of Escherichia coli.2008

    • Author(s)
      Abe, H., Miyahara, A., Oshima, T., Tashiro, K., Ogura, Y., Kuhara, S., Ogasawara, N., Hayashi, T., Tobe, T.
    • Journal Title

      DNA Res 15

      Pages: 25-38

    • Peer Reviewed
  • [Journal Article] Predicting state transitions in the transcriptome and metabolome using a linear dynamic system model.2007

    • Author(s)
      Morioka, R., Kanaya, S.,, Hirai, M., Yano, M., Ogasawara, N., Saito, K.
    • Journal Title

      BMC Bioinformatics 8,343

    • Peer Reviewed
  • [Journal Article] Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method.2007

    • Author(s)
      Ishikawa, S., Ogura, Y., Yoshimura, M., Okumura, H., Cho, E., Kawai, Y., Kurokawa, K., Oshima, T., Ogasawara, N.
    • Journal Title

      DNA Res 14

      Pages: 155-168

    • Peer Reviewed
  • [Journal Article] The GTP-binding protein YqeH participates in biogenesis of the 30S ribosome subunit in Bacillus subtilis.2007

    • Author(s)
      Loh, P.C., Morimoto, T., Matsuo, Y., Oshima, T., Ogasawara, N.
    • Journal Title

      Gene Genet Sys 82

      Pages: 281-289

    • Peer Reviewed
  • [Journal Article] Isolation and characterization of a dominant negative mutant of Bacillus subtilis GTP-binding protein, YlqF, essential for biogenesis and maintenance of the 50S ribosomal subunit.2007

    • Author(s)
      Matsuo, Y., Oshima, T., Loh, P.C., Morimoto, T., Ogasawara, N.
    • Journal Title

      J Biol Chem 282

      Pages: 25270-25277

    • Peer Reviewed
  • [Journal Article] Dynamic simulation of an in vitro multi-enzyme system.2007

    • Author(s)
      Ishii, N., Suga, Y., Hagiya, A., Watanabe, H., Mori, H., Yoshino, M., Tomita, M.
    • Journal Title

      FEBS Lett 581

      Pages: 413-420

    • Peer Reviewed
  • [Journal Article] Multiple high-throughput analyses monitor the response of E. coli to perturbations.2007

    • Author(s)
      Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P.Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M.
    • Journal Title

      Science 316

      Pages: 593-597

    • Peer Reviewed
  • [Journal Article] Involvement of the YneS/YgiH and PlsX proteins in phospholipid biosynthesis in both Bacillus subtilis and Escherichia coli.2007

    • Author(s)
      Yoshimura, M., Oshima, T., Ogasawara, N.
    • Journal Title

      BMC Microbiol 7,69

    • Peer Reviewed
  • [Journal Article] The entire organization of transcription units on the Bacillus subtilis genome.2007

    • Author(s)
      Kobayashi, H., Akitomi, J., Fujii, N., Kobayashi, K., Altaf-Ul-Amin, M., Kurokawa, K., Ogasawara, N., Kanaya, S.
    • Journal Title

      BMC Genomics 8,197

    • Peer Reviewed
  • [Journal Article] Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase.2006

    • Author(s)
      Oshima, T., Ishikawa, S., Kurokawa, K., Aiba, H., Ogasawara, N.
    • Journal Title

      DNA Res 13

      Pages: 141-153

    • Peer Reviewed
  • [Journal Article] A new FtsZ-interacting protein, YlmF, complements the activity of FtsA during progression of cell division in Bacillus subtilis.2006

    • Author(s)
      Ishikawa, S., Kawai, Y., Hiramatsu, K., Kuwano, M., Ogasawara, N.
    • Journal Title

      Mol Microbiol 60

      Pages: 1364-1380

    • Peer Reviewed
  • [Journal Article] Bacillus subtilis EzrA and FtsL synergistically regulate FtsZ ring dynamics during cell division.2006

    • Author(s)
      Kawai, Y., Ogasawara, N.
    • Journal Title

      Microbiology 152

      Pages: 1129-1141

    • Peer Reviewed
  • [Journal Article] The GTP-binding Protein YlqF Participates in the Late Step of 50 S Ribosomal Subunit Assembly in Bacillus subtilis.2006

    • Author(s)
      Matsuo, Y., Morimoto, T., Kuwano, M., Loh, P.C., Oshima, T., Ogasawara, N.
    • Journal Title

      J Biol Chem 281

      Pages: 8110-8117

    • Peer Reviewed
  • [Journal Article] Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.2006

    • Author(s)
      Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M., Wanner, B.L., Mori, H.
    • Journal Title

      Mol Sys Biol 2

      Pages: 0008

    • Peer Reviewed
  • [Journal Article] Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus subtilis.2006

    • Author(s)
      Noirot-Gros, M.F., Velten, M., Yoshimura, M., McGovern, S., Morimoto, T., Ehrlich, S.D., Ogasawara, N., Polard, P., Noirot, P.
    • Journal Title

      Proc Natl Acad Sci USA 103

      Pages: 2368-2373

    • Peer Reviewed
  • [Presentation] Gene-to gene and gene-to-metabolite network analysis based on the time lag between gene and metabolite in Escherichia coli.2009

    • Author(s)
      Takahashi, H., Morikawa, R., Kai, K., Ohta, D., Oshima, T., Altaf-Ul-Amin, M., Ogasawara, N., Kanaya, S.
    • Organizer
      4th European Conference on Prokaryotic Genomics
    • Place of Presentation
      Gottingen, Germany
    • Year and Date
      20091004-20091007
  • [Presentation] Involvement of DnaA in the organization of B. subtilis nucleoid structure.2009

    • Author(s)
      Okumura, H., Yoshimura, M., Ishikawa, S., Ogasawara, N.
    • Organizer
      15th International Conference on Bacilli (5th International Conference on Gram-positive Microorganisms)
    • Place of Presentation
      San Diego, CA USA
    • Year and Date
      20090614-20090618
  • [Presentation] Distribution of StpA across the E. coli genome and functional relationship with H-NS.2008

    • Author(s)
      Uya, E., Oshima, T., Ogasawara, N.
    • Organizer
      XX International Congress of Genetics
    • Place of Presentation
      Berlin, Germany
    • Year and Date
      20080712-20080717
  • [Presentation] A novel regulation mechanism for the initiation of replication in Bacillus subtilis.2008

    • Author(s)
      Cho, E., Ishikawa, S., Ogasawara, N.
    • Organizer
      EMBO Conference on Replication and Segregation of Chromosomes
    • Place of Presentation
      Geilo, Norway
    • Year and Date
      20080616-20080620
  • [Presentation] Distribution of RNA polymerase on the Bacillus subtilis genome.2008

    • Author(s)
      Kusuya, Y., Oshima, T., Ishikawa, S., Kurokawa, K., Ogasawara, N.
    • Organizer
      Functional Genomics of Microorganisms
    • Place of Presentation
      Paris, France
    • Year and Date
      20080408-20080411
  • [Presentation] N-terminal deletion mutant of YlqF, which is essential GTP-binding protein, displays dominant negative phenotype in Bacillus subtilis.2007

    • Author(s)
      Matsuo, Y., Loh, P.C., Morimoto, T., Oshima, T., Ogasawara, N.
    • Organizer
      14th International Conference on Bacilli
    • Place of Presentation
      Pisa, Italy
    • Year and Date
      20070624-20070628
  • [Presentation] The GTP-binding protein YqeH participates in the biogenesis of 30S ribosome subunit in Bacillus subtilis.2006

    • Author(s)
      Loh, P.C., Morimoto, T., Matsuo, Y., Ogasawara, N.
    • Organizer
      Translational Control
    • Place of Presentation
      Cold Spring Harbor, NY USA
    • Year and Date
      20060906-20060909
  • [Book] 枯草菌でシステム生物学(吉川寛、堀寛編, 研究を支えるモデル生物)2009

    • Author(s)
      小笠原直毅
    • Total Pages
      231-233
    • Publisher
      化学同人
  • [Book] 大腸菌でシステム生物学(吉川寛、堀寛編, 研究を支えるモデル生物)2009

    • Author(s)
      森浩禎
    • Total Pages
      231-233
    • Publisher
      化学同人
  • [Book] 蛋白質核酸酵素(細菌の細胞分裂の分子メカニズム, 53)2008

    • Author(s)
      石川周、小笠原直毅
    • Total Pages
      1725-1731
    • Publisher
      共立出版
  • [Book] 細胞工学(タイリングチップを用いた細菌ゲノム機能研究の可能性, 25)2006

    • Author(s)
      大島拓、石川周、黒川顕、小笠原直毅
    • Total Pages
      1155-1160
    • Publisher
      秀潤社

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Published: 2011-06-18   Modified: 2016-04-21  

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