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2004 Fiscal Year Final Research Report Summary

Frontier of genome biology toward understanding molecular systems supporting cellular life

Research Project

Project/Area Number 12205001
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, Graduate School of Information Science, Professor, 情報科学研究科, 教授 (10110553)

Co-Investigator(Kenkyū-buntansha) FUJITA Yasutaro  Fukuyama University, Faculty of Life Science and Biotechnology, Professor, 生命工学部, 教授 (40115506)
OHMORI Masayuki  Saitama University, Faculty of Science, Professor, 理学部, 教授 (80013580)
HAYASHI Tetsuya  Miyazaki University, Frontier Science Research Center, Professor, フロンティア科学実験総合センター, 教授 (10173014)
AIBA Hirofumi  Nagoya University, Graduate School of Bioagricultural Sciences, Associate Professor, 生命農学研究科, 助教授 (60211687)
KUHARA Satoru  kyushu University, Faculty of Agriculture, Professor, 農学研究院, 教授 (00153320)
Project Period (FY) 2000 – 2005
KeywordsGenome / Transcriptome / Proteome / Metabolome / Bioinformatics
Research Abstract

1) We have determined the essential gene sets for growth of model bacteria, B. subtilis and E. coli, to elucidate the universality and diversity of basic genes for cellular life.
2) We have also attempted to understand regulatory network of gene expression in model bacteria, and comprehensive view of two-component systems in E. coli, B. subtilis and cyanobacteria have been obtained.
3) We have developed a metabolome analysis system that has an ability to analyze quantitatively more than 1000 metabolites, and applied it for the analysis of metabolite dynamisms in B. subtilis and E. coli.
4) We have advanced the understanding of molecular mechanisms underlying the responses of cyanobacteria to various environmental signals.
5) We have revealed molecular mechanisms of pathogenisity of pathogenic bacteria and evolutional processes to acquire them, through analysis of pathogenic genes identified by genome sequencings.
6) We have determined the 16,520,305 bp sequence of the 20 chromosomes of the unicellular red alga Cyanidioschyzon merolae 10D as the first complete algal genome.
7) A large scale analysis of cDNA of Dictyostelium discoideum was performed to establish the genetic resources, and they then used for reverse-genetic and bioinformatic analyses, to understand the genetic control of development and differentiation of D. discoideum.
8) We have carried out bioinformatic studies in various aspects of genome biology; comparative analysis of genome sequences, prediction of higher order structure and function of proteins, network identification from microarray data sets, simulation of cellular functions, and the database development for structural and functional informations of B. subtilis and cyanobavteria.
9) Many proposed studies on genetic systems responsible for various cellular functions, systematic functional analysis of gene families and evolution and diversification of genes and genomes have been supported in the projects.

  • Research Products

    (42 results)

All 2005 2004 2003 2002 2001

All Journal Article (42 results)

  • [Journal Article] Prediction of transcriptional terminators in Bacillus subtilis and related species.2005

    • Author(s)
      de Hoon, M. J.
    • Journal Title

      PLoS Comput Biol 1

      Pages: e25

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Identification of Low-temperature-regulated ORFs in the cyanobacterium Anabaena sp. strain PCC 7120 : distinguishing the effects of low temperature from the effects of photosystem II excitation pressure.2005

    • Author(s)
      Ehira, S.
    • Journal Title

      Plant Cell Physiol 46

      Pages: 1237-1245

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Translocation of a long amino-terminal domain through ER membrane by following signal-anchor sequence.2005

    • Author(s)
      Kida, Y.
    • Journal Title

      EMBO J 24

      Pages: 3202-3213

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Large-scale prediction of cationic metabolite identity and migration time in capillary electrophoresis mass spectrometry using artificial neural networks.2005

    • Author(s)
      Sugimoto, M.
    • Journal Title

      Anal Chem 77

      Pages: 78-84

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] The genome of the social amoeba Dictyostelium discoideum.2005

    • Author(s)
      Eichinger, L.
    • Journal Title

      Nature 435

      Pages: 43-57

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Prediction of transcriptional terminators in Bacillus subtilis and related species.2005

    • Author(s)
      de Hoon, M.J., Makita, Y., Nakai, K., Miyano, S.
    • Journal Title

      PLoS Comput Biol 1

      Pages: e25

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Identification of Low-temperature-regulated ORFs in the cyanobacterium Anabaena sp. strain PCC 7120 : distinguishing the effects of low temperature from the effects of photosystem II excitation pressure.2005

    • Author(s)
      Ehira, S., Ohmori, M., Sato, N.
    • Journal Title

      Plant Cell Physiol 46

      Pages: 1237-1245

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Translocation of a long amino-terminal domain through ER membrane by following signal-anchor sequence.2005

    • Author(s)
      Kida, Y., Mihara, K., Sakaguchi, M.
    • Journal Title

      EMBO J 24

      Pages: 3202-3213

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Large-scale prediction of cationic metabolite identity and migration time in capillary electrophoresis mass spectrometry using artificial neural networks.2005

    • Author(s)
      Sugimoto, M., Kikuchi, S., Arita, M., Soga, T., Nishioka, T., Tomita, M.
    • Journal Title

      Anal Chem 77

      Pages: 78-84

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] The genome of the social amoeba Dictyostelium discoideum.2005

    • Author(s)
      Eichinger, L., Pachebat, J.A., Glockner, G., Rajandream, M.A., Sucgang, R., Berriman, M., Song, J., Olsen, R., Szafranski, K., Xu, Q., et al.
    • Journal Title

      Nature 435

      Pages: 43-57

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Genome sequence of the ultra-small unicellular red alga Cyanidioschyzon merolae 10D2004

    • Author(s)
      Matsuzaki, M.
    • Journal Title

      Nature 428

      Pages: 653-657

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.2004

    • Author(s)
      De Hoon, M. J.
    • Journal Title

      Bioinformatics 20 Suppl 1

      Pages: I101-I108

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Protein network inference from multiple genomic data : a supervised approach.2004

    • Author(s)
      Yamanishi, Y.
    • Journal Title

      Bioinformatics 20 Suppl 1

      Pages: I363-I370

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Toward large-scale modeling of the microbial cell for computer simulation.2004

    • Author(s)
      Ishii, N.
    • Journal Title

      J Biotechnol 113

      Pages: 281-294

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.2004

    • Author(s)
      Matsuzaki, M., Misumi, O., Shin, I.T., Maruyama, S., Takahara, M., Miyagishima, S.Y., Mori, T., Nishida, K., Yagisawa, F., Nishida, K., et al.
    • Journal Title

      Nature 428

      Pages: 653-657

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.2004

    • Author(s)
      De Hoon, M.J., Makita, Y., Imoto, S., Kobayashi, K., Ogasawara, N., Nakai, K., Miyano, S.
    • Journal Title

      Bioinformatics 20 Suppl 1

      Pages: 1101-1108

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Protein network inference from multiple genomic data : a supervised approach.2004

    • Author(s)
      Yamanishi, Y., Vert, J.P., Kanehisa, M.
    • Journal Title

      Bioinformatics 20 Suppl 1

      Pages: 1363-1370

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Toward large-scale modeling of the microbial cell for computer simulation.2004

    • Author(s)
      Ishii, N., Robert, M., Nakayama, Y., Kanai, A., Tomita, M.
    • Journal Title

      J Biotechnol 113

      Pages: 281-294

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Dynamic recruitment of dynamin for final mitochondrial severance in a primitive red alga.2003

    • Author(s)
      Nishida, K.
    • Journal Title

      Proc Natl Acad Sci USA 100

      Pages: 2146-2151

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Essential Bacillus subtilis genes2003

    • Author(s)
      Kobayashi, K.
    • Journal Title

      Proc Natl Acad Sci USA 100

      Pages: 4678-4683

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA2003

    • Author(s)
      Soma, A.
    • Journal Title

      Mol Cell 12

      Pages: 689-698

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Genome sequence of Vibrio parahaemolyticus : a pathogenic mechanism distinct from that of V. cholerae.2003

    • Author(s)
      Makino, K.
    • Journal Title

      Lancet 361

      Pages: 743-749

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Quantitative metabolome analysis using capillary electrophoresis mass spectrometry.2003

    • Author(s)
      Soga, T.
    • Journal Title

      J Proteome Res 2

      Pages: 488-494

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Discovery of novel transcription control relationships with gene regulatory networks generated from multiple-disruption full genome expression libraries.2003

    • Author(s)
      Aburatani, S.
    • Journal Title

      DNA Res 10

      Pages: 1-8

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Genome-wide expression analysis of the responses to nitrogen deprivation in the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120.2003

    • Author(s)
      Ehira, S.
    • Journal Title

      DNA Res 10

      Pages: 97-113

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Dynamic recruitment of dynamic for final mitochondrial severance in a primitive red alga.2003

    • Author(s)
      Nishida, K., Takahara, M., Miyagishima, S.Y., Kuroiwa, H., Matsuzaki, M., Kuroiwa, T.
    • Journal Title

      Proc Natl Acad Sci U S A 100

      Pages: 2146-2151

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Essential Bacillus subtilis genes.2003

    • Author(s)
      Kobayashi, K., Ehrlich, S.D., Albertini, A., Amati, G., Andersen, K.K., Arnaud, M., Asai, K., Ashikaga, S., Aymerich, S., Bessieres, P., et al.
    • Journal Title

      Proc Natl Acad Sci U S A 100

      Pages: 4678-4683

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA.2003

    • Author(s)
      Soma, A., Ikeuchi, Y., Kanemasa, S., Kobayashi, K., Ogasawara, N., Ote, T., Kato, J., Watanabe, K., Sekine, Y., Suzuki, T.
    • Journal Title

      Mol Cell 12

      Pages: 689-698

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Genome sequence of Vibrio parahaemolyticus : a pathogenic mechanism distinct from that of V cholerae.2003

    • Author(s)
      Makino, K., Oshima, K., Kurokawa, K., Yokoyama, K., Uda, T., Tagomori, K., Iijima, Y., Najima, M., Nakano, M., Yamashita, A., et al.
    • Journal Title

      Lancet 361

      Pages: 743-749

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Quantitative metabolome analysis using capillary electrophoresis mass spectrometry.2003

    • Author(s)
      Soga, T., Ohashi, Y., Ueno, Y., Naraoka, H., Tomita, M., Nishioka, T.
    • Journal Title

      J Proteome Res 2

      Pages: 488-494

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Discovery of novel transcription control relationships with gene regulatory networks generated from multiple-disruption full genome expression libraries.2003

    • Author(s)
      Aburatani, S., Tashiro, K., Savoie, C.J., Nishizawa, M., Hayashi, K., Ito, Y., Muta, S., Yamamoto, K., Ogawa, M., Enomoto, A., et al.
    • Journal Title

      DNA Res 10

      Pages: 1-8

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Genome-wide expression analysis of the responses to nitrogen deprivation in the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120.2003

    • Author(s)
      Ehira, S., Ohmori, M., Sato, N.
    • Journal Title

      DNA Res 10

      Pages: 97-113

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater.2002

    • Author(s)
      Shimizu, T.
    • Journal Title

      Proc. Natl. Acad. Sci. USA 99

      Pages: 996-1001

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Genomic diversity of Escherichia coli O157 revealed by whole genome PCR Scanning.2002

    • Author(s)
      Ohnishi, M.
    • Journal Title

      Proc. Natl. Acad. Sci. USA 99

      Pages: 17043-17048

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12.2002

    • Author(s)
      Oshima, T.
    • Journal Title

      Mol Microbiol 46

      Pages: 281-291

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] A transcriptional profile of multicellular development in Dictyostelium discoideum.2002

    • Author(s)
      Van Driessche, N.
    • Journal Title

      Development 129

      Pages: 1543-1552

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater.2002

    • Author(s)
      Shimizu, T., Ohtani, K., Hirakawa, H., Ohshima, K., Yamashita, A., Shiba, T., Ogasawara, N., Hattori, M., Kuhara, S., Hayashi, H.
    • Journal Title

      Proc Natl Acad Sci U S A 99

      Pages: 996-1001

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Genomic diversity of enterohemorrhagic Escherichia coli 0157 revealed by whole genome PCR scanning.2002

    • Author(s)
      Ohnishi, M., Terajima, J., Kurokawa, K., Nakayama, K., Murata, T., Tamura, K., Ogura, Y., Watanabe, H., Hayashi, T.
    • Journal Title

      Proc Natl Acad Sci U S A 99

      Pages: 17043-17048

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12.2002

    • Author(s)
      Oshima, T., Aiba, H., Masuda, Y., Kanaya, S., Sugiura, M., Wanner, B.L., Mori, H., Mizuno, T.
    • Journal Title

      Mol Microbiol 46

      Pages: 281-291

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] A transcriptional profile of multicellular development in Dictyostelium discoideum.2002

    • Author(s)
      Van Driessche, N., Shaw, C., Katoh, M., Morio, T., Sucgang, R., Ibarra, M., Kuwayama, H., Saito, T., Urushihara, H., Maeda, M., et al.
    • Journal Title

      Development 129

      Pages: 1543-1552

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems.2001

    • Author(s)
      Kobayashi, K.
    • Journal Title

      J Bacteriol 183

      Pages: 7365-7370

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems.2001

    • Author(s)
      Kobayashi, K., Ogura, M., Yamaguchi, H., Yoshida, K., Ogasawara, N., Tanaka, T., Fujita, Y.
    • Journal Title

      J Bacteriol 183

      Pages: 7365-7370

    • Description
      「研究成果報告書概要(欧文)」より

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Published: 2008-05-27  

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