2004 Fiscal Year Final Research Report Summary
Frontier of genome biology toward understanding molecular systems supporting cellular life
| Project/Area Number |
12205001
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| Research Category |
Grant-in-Aid for Scientific Research on Priority Areas
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| Allocation Type | Single-year Grants |
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| Review Section |
Biological Sciences
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| Research Institution | Nara Institute of Science and Technology |
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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)
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| 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)
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| Project Period (FY) |
2000 – 2005
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| Keywords | Genome / Transcriptome / Proteome / Metabolome / Bioinformatics |
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| 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.
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[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.
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Journal Title
Anal Chem 77
Pages: 78-84
Description
「研究成果報告書概要(欧文)」より
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[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.
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Journal Title
Description
「研究成果報告書概要(欧文)」より
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[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.
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Journal Title
Nature 428
Pages: 653-657
Description
「研究成果報告書概要(欧文)」より
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[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.
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Journal Title
Bioinformatics 20 Suppl 1
Pages: 1101-1108
Description
「研究成果報告書概要(欧文)」より
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[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.
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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
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[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.
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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
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[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.
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Journal Title
Mol Cell 12
Pages: 689-698
Description
「研究成果報告書概要(欧文)」より
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[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.
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Journal Title
Lancet 361
Pages: 743-749
Description
「研究成果報告書概要(欧文)」より
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[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.
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Journal Title
J Proteome Res 2
Pages: 488-494
Description
「研究成果報告書概要(欧文)」より
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[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.
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Journal Title
Description
「研究成果報告書概要(欧文)」より
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[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.
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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
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[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.
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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
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[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.
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Journal Title
Mol Microbiol 46
Pages: 281-291
Description
「研究成果報告書概要(欧文)」より
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[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.
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Journal Title
Development 129
Pages: 1543-1552
Description
「研究成果報告書概要(欧文)」より
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[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.
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Journal Title
J Bacteriol 183
Pages: 7365-7370
Description
「研究成果報告書概要(欧文)」より
