Development of methods for quantitative description and perturbation of biomolecular pathways and networks

• Project/Area Number: 17017004
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The University of Tokyo
• Principal Investigator: ITO Takashi The University of Tokyo, 大学院・理学系研究科, 教授 (90201326)
• Co-Investigator(Kenkyū-buntansha): SUMIMOTO Hideki 九州大学, 大学院・医学系研究科, 教授 (30179303) ; KITO Keiji 明治大学, 農学部, 講師 (40345632)
• Project Period (FY): 2005 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥104,000,000 (Direct Cost: ¥104,000,000); Fiscal Year 2009: ¥21,700,000 (Direct Cost: ¥21,700,000); Fiscal Year 2008: ¥21,600,000 (Direct Cost: ¥21,600,000); Fiscal Year 2007: ¥21,400,000 (Direct Cost: ¥21,400,000); Fiscal Year 2006: ¥21,100,000 (Direct Cost: ¥21,100,000); Fiscal Year 2005: ¥18,200,000 (Direct Cost: ¥18,200,000)
• Keywords: 転写開始点 / 次世代シーケンサ / 定量プロテオミクス / ユビキチン化 / FRET / 遺伝子発現 / GIS-PET / ゲノム / トランスクリプトーム / プロテオーム / 定量性 / 454シークエンサ / 非コードRNA / 安定同位元素標識 / 質量分析 / 代謝物 / 蛋白質問相互作用 / リン酸化 / 質最分析 / 定量 / 蛋白質間相互作用

Research Abstract

As a basis for understanding dynamics of biomolecular pathways and networks, we developed novel methods for absolute quantification of gene expression using next generation DNA sequencing, absolute quantification of protein-protein interactions and quantitative analysis of ubiquitinated proteomes by mass spectrometry, and real-time monitoring of intracellular metabolites using FRET.

Research Products

• [Journal Article] Remodeling of the SCF complex-mediated ubiquitination system by compositional alteration of incorporated F-box proteins (2010)
  • Author(s): Kato, M., Kito, K., Ota, K., Ito, T.
  • Journal Title: Proteomics 10 Pages: 115-123
  • Peer Reviewed
• [Journal Article] Remodeling of the SCF complex-mediated ubiquitination system by compositional alteration of incorporated F-box proteins. (2010)
  • Author(s): Kato, M., et al.
  • Journal Title: Proteomics Volume: 10 Pages: 115-123
  • Peer Reviewed
• [Journal Article] Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor (2009)
  • Author(s): Okada, S., Ota, K., Ito, T.
  • Journal Title: Protein Sci. 18 Pages: 2518-2527
  • Peer Reviewed
• [Journal Article] Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor. (2009)
  • Author(s): Okada, S., et al.
  • Journal Title: Protein Science Volume: 18 Pages: 2518-2527
  • Peer Reviewed
• [Journal Article] Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs (2008)
  • Author(s): Miura, F., Kawaguchi, N., Yoshida, M., Uematsu, C., Kito, K., Sakaki, Y., Ito, T.
  • Journal Title: BMC Genomics 9 Pages: 574-574
  • Peer Reviewed
• [Journal Article] A proteomic screen reveals the mitochondrial outer membrane protein Mdm34p as an essential target of the F-box protein Mdm30p (2008)
  • Author(s): Ota, K., Kito, K., Okada, S., Ito, T.
  • Journal Title: Genes Cells 13 Pages: 1075-1085
  • Peer Reviewed
• [Journal Article] Unexpected complexity of the budding yeast transcriptome (2008)
  • Author(s): Ito, T., Miura, F., Onda, M.
  • Journal Title: IUBMB Life 60 Pages: 775-781
  • Peer Reviewed
• [Journal Article] Mass spectrometry-based approaches toward absolute quantitative proteomics (2008)
  • Author(s): Kito, K., Ito, T.
  • Journal Title: Curr.Genomics 9 Pages: 263-274
  • Peer Reviewed
• [Journal Article] A parallel affinity purification method for selective isolation of polyubiquitinated proteins (2008)
  • Author(s): Ota, K., Kito, K., Iemura, S., Natsume, T, Ito, T.
  • Journal Title: Proteomics 8 Pages: 3004-3007
  • Peer Reviewed
• [Journal Article] Discrimination between stable and dynamic components of protein complexes by means of quantitative proteomics (2008)
  • Author(s): Kito, K., Kawaguchi, N., Okada, S., Ito, T.
  • Journal Title: Proteomics 8 Pages: 2366-2370
  • Peer Reviewed
• [Journal Article] A parallel affinity purification method for selective isolation of polyubiquitinated proteins (2008)
  • Author(s): Ota, K., Kito, K., Iemura, S., Natsume, T., Ito, T.
  • Journal Title: Proteomics 8 Pages: 3004-3007
  • Peer Reviewed
• [Journal Article] Absolute quantification of budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs (2008)
  • Author(s): Miura, F., Kawaguchi, N., Yoshida, M., Uematsu, C., Kito, K., Sakaki, Y., Ito, T.
  • Journal Title: BMC Genomics 9 Pages: 574-574
  • Peer Reviewed
• [Journal Article] Mass spectrometry-based approaches toward absolute quantitative proteomics (2008)
  • Author(s): Kito, K., Ito, T.
  • Journal Title: Curr. Genomics 9 Pages: 263-274
  • Peer Reviewed
• [Journal Article] Structure and function of the PB1 domain, a protein-interaction module conserved in animals, fungi, amoebas, and plants (2007)
  • Author(s): Sumimoto, H., Kamakura, S., Ito, T.
  • Journal Title: Sci.STKE 2007
  • Peer Reviewed
• [Journal Article] A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes (2007)
  • Author(s): Kito, K., Ota, K., Fujita, T., Ito, T.
  • Journal Title: J.Proteome Res. 6 Pages: 792-800
  • Peer Reviewed
• [Journal Article] A novel Cdc42-interacting domain of the yeast polarity establishment protein Beml : implications for modulation of mating pheromone signaling (2007)
  • Author(s): Yamaguchi, Y., Ota, K., Ito, T.
  • Journal Title: J.Biol.Chem. 282 Pages: 29-38
  • Peer Reviewed
• [Journal Article] Structure and function of the PB1 domain, a protein-interaction module conserved in animals, fungi, amoebas, and plants (2007)
  • Author(s): Sumimoto, H., Kamakura, S., & Ito, T.
  • Journal Title: Science's STKE 2007
• [Journal Article] Discrimination between stable and dynamic components of protein complexes by means of quantitative proteomics (2007)
  • Author(s): Kito, K., Kawaguchi, N., Okada, S., & Ito, T.
  • Journal Title: Proteomics 8(12) Pages: 2366-2370
• [Journal Article] A novel, Cdc42-interacting domain of the yeast polarity establishment protein Bem1 : implications for modulation of mating pheromone signaling. (2007)
  • Author(s): Yamaguchi, Y., Ota, K., Ito, T.
  • Journal Title: J. Biol. Chem. 282 Pages: 29-38
• [Journal Article] A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes. (2007)
  • Author(s): Kito, K., Ota, K., Fujita, T., Ito, T.
  • Journal Title: J. Proteome Res. 6 Pages: 792-800
• [Journal Article] A large-scale full-length cDNA analysis to explore the budding yeast transcriptome (2006)
  • Author(s): Miura, F., Kawaguchi, N., Sese, J., Toyoda, A., Hattori, M., Morishita, S., Ito, T.
  • Journal Title: Proc.Natl.Acad.Sci.USA 103 Pages: 17846-17851
  • Peer Reviewed
• [Journal Article] Transcriptional activators in yeast (2006)
  • Author(s): Titz, B., Thomas, S., Rajagopala, S., Chiba, T., Ito, T., Uetz, P.
  • Journal Title: Nucleic Acids Res. 34 Pages: 955-967
  • Peer Reviewed
• [Journal Article] A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 11q : comparison with chromosome 21q. (2006)
  • Author(s): Yamada, Y., ShiraKawa T., Taylor, T., Okamura, K., Soejima, H., Uchiyama, M., Iwasaka, T., Mukai, T., Muramoto, K., Sakaki, Y., Ito, T.
  • Journal Title: DNA Seq. 17(3) Pages: 300-306
• [Journal Article] Diverse DNA methylation status at alternative promoters of human genes in various normal tissues. (2006)
  • Author(s): Cheong, J., Yamada, Y., Yamashita, R., Irie, T., Kanai, A., Wakaguri, H., Nakai, K., Ito, T., Saito, I., Sugano, S., Suzuki, Y.
  • Journal Title: DNA Res. 13 Pages: 155-167
• [Journal Article] A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. (2006)
  • Author(s): Miura, F., Kawaguchi, N., Sese, J., Toyoda, A., Hattori, M., Morishita, S., Ito, T.
  • Journal Title: Proc. Natl. Acad. Sci. USA 103 Pages: 17846-17851
• [Journal Article] Lessons from comparative analysis of species-specific imprinted genes (2006)
  • Author(s): Okamura, K., Ito, T.
  • Journal Title: Cytogenet.Genome Res. 113(印刷中)
• [Journal Article] A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3' -end subsequences (2005)
  • Author(s): Miura, F., Uematsu, C., Sakaki, Y., Ito, T.
  • Journal Title: Bioinformatics 21 Pages: 4363-4370
  • Peer Reviewed
• [Journal Article] A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3'-end subsequences (2005)
  • Author(s): Miura, E, Uematsu, C., Sakaki, Y., Ito, T.
  • Journal Title: Bioinformatics 21 Pages: 4363-4370
• [Presentation] ペプチド連結型標準物質と質量分析(PCS-MS法)を用いたタンパク質の絶対量計測技術の開発 (2009)
  • Author(s): 紀藤圭治、伊藤隆司
  • Organizer: 日本ヒトプロテオーム機構第7回大会
  • Place of Presentation: 東京、北里大学薬学部
• [Presentation] Unexpected complexity of the budding yeast transcriptome (2008)
  • Author(s): Takashi Ito
  • Organizer: ASBMB (American Society of Biochemistry and Molecular Biology) 2008
  • Place of Presentation: Symposium "Global Systems Biology : Parts" SanDiego
  • Year and Date: 2008-04-06
• [Presentation] Unexpected complexity of the budding yeast transcriptome (2008)
  • Author(s): Takashi Ito
  • Organizer: ASBMB2008
  • Place of Presentation: San Diego, USA
  • Year and Date: 2008-04-06
• [Book] 明日を拓く新次元プロテオミクス(松本雅記、中山敬一:編) (2009)
  • Author(s): 紀藤圭治、伊藤隆司
  • Total Pages: 144
  • Publisher: 学研メディカル秀潤社
• [Book] Methods for protein-protein interaction analysis, Introduction to Systems Biology(Ed.Choi, S.) (2007)
  • Author(s): Kito, K., Ito, T.
  • Publisher: Humana Press
• [Book] Introduction to Systems Biology, Chapter 9 : Methods for Protein-Protein Interaction Analysis (2007)
  • Author(s): Kito, K. & Ito, T.
  • Publisher: Humana Press