Towards comprehensive analysis of genetic interaction of E. coli

• Project/Area Number: 18201038
• 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: Nara Institute of Science and Technology
• Principal Investigator: MORI Hirotada Nara Institute of Science and Technology, バイオサイエンス研究科, 教授 (90182203)
• Research Collaborator: BARRY L. Wanner Purdue University, 教授
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥52,000,000 (Direct Cost: ¥40,000,000、Indirect Cost: ¥12,000,000); Fiscal Year 2008: ¥15,730,000 (Direct Cost: ¥12,100,000、Indirect Cost: ¥3,630,000); Fiscal Year 2007: ¥15,730,000 (Direct Cost: ¥12,100,000、Indirect Cost: ¥3,630,000); Fiscal Year 2006: ¥20,540,000 (Direct Cost: ¥15,800,000、Indirect Cost: ¥4,740,000)
• Keywords: 遺伝的相互作用 / 遺伝的ネットワーク / geneticinteraction / 合成致死 / 大腸菌 / 接合 / バーコード / システム生物学 / リソース / Hfr / GFP融合遺伝子 / 欠失株 / genetic network / 必須遺伝子 / 2重欠失株 / high throughput / 大腸菌リソース / ロバスト性 / GFP融合株 / 単一細胞遺伝子発現解析

Research Abstract

網羅的に遺伝的ネットワークを解明することを目的に、2重欠失株作製の系の開発と解析の評価を行った. 2重欠失の為の既存の欠失株ライブラリーにさらにもう1種類の欠失株ライブラリーの構築、単一欠失の接合による2重化のツールの開発、2重化のhighthroughput化、解析システムのそれぞれの開発を行った. 新規欠失株ライブラリーには、20ntのbarcodeを挿入し、創薬等のhighthroughputスクリーニングへの道も開いた.

Research Products

• [Journal Article] Systemat ic genome-wide scanning for genes involved in ATP generation in Escherichia coli. (2009)
  • Author(s): Hara, K. Y.
  • Journal Title: Metab Eng 11 Pages: 1-7
  • Peer Reviewed
• [Journal Article] High-throughput (2008)
  • Author(s): Typas, A., R.J. Nichols, D.A. Siegele, M.Shales, S.R. Collins, B. Lim, H. Braberg, N.Yamamoto, R. Takeuchi, B.L. Wanner, H. Mori, J.S. Weissman, N.J. Krogan, and C.A. Gross
  • Journal Title: quantitative analyses of genetic interactions in E. coli. Nat Methods 5 Pages: 781-7
  • Peer Reviewed
• [Journal Article] J.F. Greenblatt, and A. Emili. eSGA : E (2008)
  • Author(s): Butland, G., M. Babu, J.J. Diaz-Mejia, F.Bohdana, S. Phanse, B. Gold, W. Yang, J.Li, A.G. Gagarinova, O. Pogoutse, H. Mori, B . L . Wa n n e r , H.Lo, J.Wasniewski, C.Christopolous, M. Ali, P. Venn, A. Safavi-Naini, N. Sourour, S. Caron, J.Y. Choi, L. Laigle, A. Nazarians-Armavil, A. Deshpande, S. Joe, K.A. Datsenko, N. Yamamoto, B.J. Andrews,C. Boone, H. Ding, B. Sheikh, G. Moreno-Hagelseib
  • Journal Title: coli synthetic genetic array analysis. Nat Methods 5 Pages: 789-95
  • Peer Reviewed
• [Journal Article] The Applicat ions of Systematic In-Frame, Single-Gene Knockout Mutant Collection of Escherichia coli K-12. (2008)
  • Author(s): Baba, T
  • Journal Title: Methods Mol Biol 416 Pages: 183-94
  • Peer Reviewed
• [Journal Article] The Construction of Systematic In-Frame, Single-Gene Knockout Mutant Collection in Escherichia coli K-12. (2008)
  • Author(s): Baba, T., H. Mori.
  • Journal Title: Methods Mol Biol 416 Pages: 171-81
  • Peer Reviewed
• [Journal Article] Comprehensive analysis of the effects of Escherichia coli ORFson protein translation reaction. (2008)
  • Author(s): Kazuta, Y.
  • Journal Title: Mol Cell Proteoomics 7 Pages: 1530-40
  • Peer Reviewed
• [Journal Article] High-throughput, quantitative analyses of genetic interactions in E. coli. (2008)
  • Author(s): Typas, A.
  • Journal Title: Nat Methods(電子媒体)
  • Peer Reviewed
• [Journal Article] eSGA : E. coli synthetic genetic array analysis. (2008)
  • Author(s): Butland, G.
  • Journal Title: Nat Methods(電子媒体)
  • Peer Reviewed
• [Journal Article] The outer membrane TolC is involved in cysteine tolerance and overproduction in Escherichia coli. (2008)
  • Author(s): Wiriyathanawudhiwong
  • Journal Title: Appl Microbiol Biotechnol 81 Pages: 903-13
  • Peer Reviewed
• [Journal Article] Inhibitory effect of phosphoenolpyruvate on glycolytic enzymes in Escherichia coli. (2007)
  • Author(s): Ogawa T
  • Journal Title: Res Microbiol 158 Pages: 159-163
  • Peer Reviewed
• [Journal Article] A Genome-wide Approach to Identify the Genes Involved in Biofilm Formation in E. coli. (2007)
  • Author(s): Niba ETE
  • Journal Title: DNA Res 14 Pages: 237-246
  • Peer Reviewed
• [Journal Article] P-BOSS: A new filtering method for treasure hunting in metabolomics. (2007)
  • Author(s): Morohashi M
  • Journal Title: J Chromatogr 1159 Pages: 142-148
  • Peer Reviewed
• [Journal Article] Dynamic simulation of an in vitro multi-enzyme system. (2007)
  • Author(s): Ishii N
  • 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
  • Journal Title: Science 316 Pages: 593-597
  • Peer Reviewed
• [Journal Article] Genome-Wide Screening of Genes Required for Swarming Motility in Escherichia coli K-12. (2007)
  • Author(s): Inoue T,
  • Journal Title: J Bacteriol 189 Pages: 950-957
  • Peer Reviewed
• [Journal Article] B1500, a small membrane protein, connects the two-component systems EvgS/EvgA and PhoQ/PhoP in Escherichia coli. (2007)
  • Author(s): Eguchi Y
  • Journal Title: Proc Natl Acad Sci USA 104 Pages: 18712-18717
  • Peer Reviewed
• [Journal Article] Large-scale identification of protein-protein interaction of Escherichia coli K-12 (2006)
  • Author(s): M.Arifuzzaman
  • Journal Title: Genome Res. 16 Pages: 686-691
• [Journal Article] Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants : the Keio collection (2006)
  • Author(s): T.Baba
  • Journal Title: Mol Syst Biol. 2
• [Journal Article] Genome-Wide Screening of Genes Required for Swarming Motility in Escherichia coli K-12 (2006)
  • Author(s): T.Inoue
  • Journal Title: J Bacteriol. 189 Pages: 950-957
• [Journal Article] Experimental and computational assessment of conditionally essential genes in E. coli (2006)
  • Author(s): A.R.Joyce
  • Journal Title: J Bacteriol. 188 Pages: 8259-71
• [Journal Article] Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive) : Unique Resources for Biological Research (2006)
  • Author(s): M.Kitagawa
  • Journal Title: DNA Res. 12 Pages: 291-299
• [Journal Article] Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family (2006)
  • Author(s): E.Kuznetsova
  • Journal Title: J Biol Chem 281 Pages: 36149-36161
• [Journal Article] Role of phosphoenolpyruvate in the NADP-isocitrate dehydrogenate and isocitrate lyase reaction in Escherichia coli (2006)
  • Author(s): T.Ogawa
  • Journal Title: J Bacteriol. 189 Pages: 1176-1178
• [Journal Article] Escherichia coli K-12 : a cooperatively developed annotation anapshot--2005 (2006)
  • Author(s): M.Riley
  • Journal Title: Nucleic Acids Res 34 Pages: 1-9
• [Journal Article] Metabolomics approach for enzyme discovery (2006)
  • Author(s): N.Saito
  • Journal Title: J Proteome Res. 5 Pages: 1979-1987
• [Presentation] 多階層ネットワークの解明に向けて (2009)
  • Author(s): 森 浩禎
  • Organizer: システムバイオロジー研究会
  • Place of Presentation: 滋賀県
  • Year and Date: 2009-01-07
• [Presentation] EcoliHub : An Information Resource for ExperimentalistsAnd Modelers. (2008)
  • Author(s): 森 浩禎
  • Organizer: ISMB
  • Place of Presentation: Toronto, CANADA
  • Year and Date: 2008-07-21
• [Presentation] A computational Approach of Phenotype Microarray Data Finding Functional Units in Metabolic Networks. (2008)
  • Author(s): 森 浩禎
  • Organizer: ISMB
  • Place of Presentation: Toronto, CANADA
  • Year and Date: 2008-07-21
• [Presentation] Systematic Analysis of Genetic Interaction of Escherichia coli. (2008)
  • Author(s): 森 浩禎
  • Organizer: AMERICAN SCIETY FOR MICROBIOLOGY
  • Place of Presentation: Boston, USA
• [Presentation] EcoliHub : An Information Resource for ExperimentalistsAnd Modelers. (2008)
  • Author(s): 森 浩禎
  • Organizer: AMERICAN SCIETY FOR MICROBIOLOGY
  • Place of Presentation: Boston, USA
• [Presentation] EcoliHub : An Information Resource for Experimentalists And Modelers. (2008)
  • Author(s): 森 浩禎
  • Organizer: ICSB
  • Place of Presentation: Getheburg, Sweden
• [Presentation] Systematic Analysis of Genetic Interaction of Escberichia coll. (2008)
  • Author(s): 森 浩禎
  • Organizer: ICSB
  • Place of Presentation: Getheburg, Sweden
• [Presentation] New Genomic Tools for E. coli. (2008)
  • Author(s): 森 浩禎
  • Organizer: ARROWHEAD 2008
  • Place of Presentation: California, USA
• [Presentation] Development of the www. EcoliHub. org InformationResource. (2008)
  • Author(s): 森 浩禎
  • Organizer: IECA
  • Place of Presentation: Hixton, UK
• [Presentation] Towards Systerns Analysis of Escherichia coli. (2008)
  • Author(s): 森 浩禎
  • Organizer: Frontiers in Multi-Scale Systerms Biology
  • Place of Presentation: Atlanta, USA
• [Presentation] Phenotype Profiling of Single Gene Deletion Mutants Of E. Coli using Biolog Technoloy. (2008)
  • Author(s): 森 浩禎
  • Organizer: GIW2008
  • Place of Presentation: Gold Coast, Australia
• [Presentation] Development of the www. EcoliHub. org Information Resource. (2008)
  • Author(s): 森 浩禎
  • Organizer: GIW2008
  • Place of Presentation: Gold Coast, Australia
• [Presentation] Development of analytical methods to elucidate genetic Network from genetic interaction data. (2008)
  • Author(s): 森 浩禎
  • Organizer: 日本バイオインフォマティクス学会
  • Place of Presentation: 兵庫県
• [Presentation] 合成致死解析による大腸菌の遺伝的ネットワーク解析 (2008)
  • Author(s): 竹内 力矢, (Poster)
  • Organizer: 第2回日本ゲノム微生物学会年会
  • Place of Presentation: 大阪 日本
• [Presentation] Towards modeling and simulation of metabolic pathways (2007)
  • Author(s): 森 浩禎(oral)
  • Organizer: 2007日本バイオインフォマティクス学会年会
  • Place of Presentation: 東京お台場、日本
  • Year and Date: 2007-12-19
• [Presentation] Systems Biology of E. coli, Institute of Biomedical Sciences (2007)
  • Author(s): Mori Hirotda
  • Organizer: Fudan Universityほか3件
  • Place of Presentation: Shanghai, Republic of China
  • Year and Date: 2007-11-16
• [Presentation] Systems Approach Towards Understanding of E. coli Central Metabolism-Quantiatative Measerement of Transcription and Translation of Glycolytic and TCA Cycle Enzymes (2007)
  • Author(s): Mori Hirotada
  • Organizer: 2nd ASM Conference on Integrating Metabolism and Genomics(IMAGE2)ほか28件
  • Place of Presentation: Quebec, Canada
  • Year and Date: 2007-05-03
• [Presentation] Systems Approach Towards Understanding of E. coli Central Metabolism-Quantiatative Measerement of Transcription and Translation of Glycolytic and TCA Cycle Enzymes (2007)
  • Author(s): Mori H(Poster)
  • Organizer: 2nd ASM Conference on Integrating Metabolism and Genomics(IMAGE2)
  • Place of Presentation: Quebec, Canada
  • Year and Date: 2007-05-03
• [Presentation] Datsenko K.A.&Wanner B.L., Systems approach towards understanding of E (2007)
  • Author(s): Mori H., Dose H., Ikegami Y., Yamamotoya T.,Matsuno H., Narifusa Y., Nakahigashi K., Baba T.
  • Organizer: coli central metabolism- Quantitative measurement of transcription and translation of glycolytic and TCA cycle enzymes, IMAGE2(30-03)
  • Place of Presentation: Quebec, Canada
  • Year and Date: 2007-04-05
• [Presentation] 大腸菌のシステム生物学 (2007)
  • Author(s): 森 浩禎(oral)
  • Organizer: 21世紀大腸菌研究会
  • Place of Presentation: 藤枝、日本
• [Presentation] 大腸菌を用いたSystem biologyに向けて (2007)
  • Author(s): 森 浩禎(oral)
  • Organizer: 理研シンポジウム 第6回連携研究会
  • Place of Presentation: 兵庫、日本
• [Presentation] Towards a comprehensive analysis of the genetic network in Escherichia coli (2007)
  • Author(s): Mori H(oral)
  • Organizer: The 8th Analytical Genetics Meeting
  • Place of Presentation: Goethenburg, Sweden
• [Presentation] 遺伝的相互作用研究の展望, (2007)
  • Author(s): 森 浩禎(oral)
  • Organizer: 第17回システム生物学研究会
  • Place of Presentation: 奈良、日本
• [Presentation] 大腸菌の網羅的な二重欠損株の作製系の構築 (2007)
  • Author(s): 竹内 力矢(oral)
  • Organizer: 第17回システム生物学研究会
  • Place of Presentation: 奈良、日本
• [Presentation] 大腸菌の網羅的なSynthetic lethal/sicknessの解析法の開発 (2007)
  • Author(s): 柳原 芳充(oral)
  • Organizer: 第17回システム生物学研究会
  • Place of Presentation: 奈良、日本
• [Presentation] 大腸菌の必須遺伝子解析 (2007)
  • Author(s): 山本 奈津子(oral)
  • Organizer: 第17回システム生物学研究会
  • Place of Presentation: 奈良、日本
• [Presentation] Towards the systematic analysis of genetic interaction in E. coli. -Construction of second deletion library and the system to generate double knockout (2007)
  • Author(s): Mori H(Poster)
  • Organizer: Genomes 2007
  • Place of Presentation: Cambridge, UK
• [Presentation] Systems approach towards understanding of E. coli central metabolism-Quantitative measurement of transcription and translation of glycolytic and TCA cycle enzymes (2007)
  • Author(s): Mori H(Poster)
  • Organizer: IMAGE2
  • Place of Presentation: Quebec, Canada
• [Presentation] 遺伝的ネットワーク解明に向けて (2007)
  • Author(s): 竹内 力矢, (Poster)
  • Organizer: 第4回21世紀大腸菌研究会
  • Place of Presentation: 藤枝、日本
• [Presentation] 大腸菌遺伝的ネットワーク解明に向けた現状と解析 (2007)
  • Author(s): 竹内 力矢, (Poster)
  • Organizer: 理研シンポジウム 第6回連携研究会
  • Place of Presentation: 兵庫、日本
• [Presentation] 遺伝的ネットワーク解明に向けて (2007)
  • Author(s): 竹内 力矢, (Poster)
  • Organizer: 第30回日本分子生物学会年会
  • Place of Presentation: 横浜市、日本
• [Presentation] Systems approach towards understanding of E. coli central metabolism-Quantitative analyses of Glycolysis and TCA cycle- (2007)
  • Author(s): Dose H(Poster)
  • Organizer: 第30回日本分子生物学会年会
  • Place of Presentation: 横浜市、日本
• [Presentation] 条件致死性を示す機能未知遺伝子群の機能解析 (2007)
  • Author(s): 小口 瑞穂, (Poster)
  • Organizer: 第30回日本部分子生物学会年会
  • Place of Presentation: 横浜市、日本
• [Presentation] (2007)
  • Author(s): Mori H, (Poster)
  • Organizer: XV. International Conference on Intelligent Systems for Molecular Biology(ISMB)
  • Place of Presentation: Vienna, Austria
• [Presentation] EcoliHUB Information Resource for Experimentaion and Modeling (2007)
  • Author(s): Wanner B, (Poster)
  • Organizer: The Eighth International Conference on Systems Biology(ICSB)
  • Place of Presentation: Long Beach, USA
• [Presentation] An essential core of protein-protein interaction network in Escherichia coli (2007)
  • Author(s): Lin Chen-Ching, (Poster)
  • Organizer: The Eighth International Conference on Systems Biology(ICSB)
  • Place of Presentation: Long Beach, USA
• [Presentation] Towards modeling and simulation of Glycolysis and TCA cycle (2007)
  • Author(s): Dose H, (Poster)
  • Organizer: The Eighth International Conference on Systems Biology(ICSB)
  • Place of Presentation: Long Beach, USA
• [Presentation] EcoliHUB Information Resource for Experimentation and Modeling (2007)
  • Author(s): Wanner B, (Poster)
  • Organizer: The 18th International Conference on Genome Informatics(GIW2007)
  • Place of Presentation: Biopolis, Singapore
• [Presentation] 大腸菌のシステム生物学
  • Author(s): 森浩禎
  • Organizer: 21世紀大腸ほか28件
  • Place of Presentation: ポスター発表
• [Book] Single-Gene Knockout Mutant Collection in Escherichia coli K-12. Methods Mol Biol ; 416 (2008)
  • Author(s): Baba, T. and H. Mori
  • Publisher: The Construction of Systematic In-Frame
• [Book] Single-Gene Knockout Mutant Collection of Escherichia coli K-12. Methods Mol Biol ; 416 (2008)
  • Author(s): Baba, T., H.C. Huan, K. Datsenko, B.L. Wanner, and H. Mori
  • Publisher: The Applications of Systematic In-Frame
• [Book] The Construct ion of Systematic In-Frame, Single-Gene Knockout Mutant Collection of Escherichia coli K-12. Microbial Gene Essentiality Protocols and Bioinformatics (2008)
  • Author(s): Baba, T., H. Mori
  • Publisher: Humana Press
• [Book] The Applications of Systematic In-Frame, Single-Gene Knockout Mutant Collection of Eschericbia coli K-12. Microbial Gene Essentiality Protocols and Bioinformatics (2008)
  • Author(s): Baba, T.
  • Publisher: Humana Press
• [Book] Methods in Molecular Biology, Microbial Gene Essentiality: Protocols and Bioinformatics, Chapter 11 (2007)
  • Author(s): Baba T
  • Publisher: Human Press, Totowa, New Jersey.
• [Book] Methods in Molecular Biology, Microbial Gene Essentiality: Protocols and Bioinformatics, Chapter 12 (2007)
  • Author(s): Baba T
  • Publisher: Human Press, Totowa, New Jersey.
• [Remarks] データベース
  • URL: http://ecoli.naist.jp
• [Remarks]
  • URL: http://ecoli.naist.jp