Quantitation analysis of pathway network analysis

• Project/Area Number: 17017042
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: NATSUME Tohru National Institute of Advanced Industrial Science and Technology, バイオメディシナル情報研究センター, 研究チーム長 (00357683)
• Co-Investigator(Kenkyū-buntansha): IEMURA Shun-ichiro 独立行政法人産業技術総合研究所, バイオメディシナル情報研究センター, 主任研究員 (90356410) ; NAKAYAMA hiroshi 独立行政法人理化学研究所, 中央研究所, 研究員 (80321793) ; SHIBUYA Kohji 東京医科歯科大学, 難治疾患研究所, 教授 (30261324)
• Project Period (FY): 2005 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥74,000,000 (Direct Cost: ¥74,000,000); Fiscal Year 2009: ¥15,200,000 (Direct Cost: ¥15,200,000); Fiscal Year 2008: ¥14,600,000 (Direct Cost: ¥14,600,000); Fiscal Year 2007: ¥14,100,000 (Direct Cost: ¥14,100,000); Fiscal Year 2006: ¥14,300,000 (Direct Cost: ¥14,300,000); Fiscal Year 2005: ¥15,800,000 (Direct Cost: ¥15,800,000)
• Keywords: タンパク質間相互作 / タンパク質ネットワーク解析 / プロテオミクス / 質量分析 / 動態解析 / マップキナーゼカスケー / シグナル伝達 / Erk / プロテミクス / タンパク質問相互作用 / マップキナーゼカスケード / ダイレクトナノLC / 古典的MAPキナーゼカスケ / Erkイフェクター / 安定同位体ラベル

Research Abstract

Cellular signaling comprises numerous numbers of proteins, which interact each other, Forming protein interaction network. To understand networks systematic andcomprehensively, we developed proteomic analytical platform to quantify proteininteractions. By the system, we found several novel signaling pathways.

Research Products

• [Journal Article] The selective autophagy substrate p62 activates the stress responsive transcription factor Nrf2 through inactivation of Keap1 (2010)
  • Author(s): Komatsu, M., H. Kurokawa, S. Waguri, K. Taguchi, A. Kobayashi, Y. Ichimura, Y.S. Sou, I. Ueno, A. Sakamoto, K.I. Tong, M. Kim, Y. Nishito, S.I. Iemura, T. Natsume, T. Ueno, E. Kominami, H. Motohashi, K. Tanaka, M. Yamamoto
  • Journal Title: Nat cell biology 12(3) Pages: 213-223
  • Peer Reviewed
• [Journal Article] The novel thioredoxin-related transmembrane protein TMX4 has reductase activity. (2010)
  • Author(s): Sugiura, Y., K.Araki, S.I.Iemura, T.Natsume, J.Hoseki, K.Nagata
  • Journal Title: J Biol Chem. 285 Pages: 7135-7142
  • Peer Reviewed
• [Journal Article] The selective autophagy substrate p62 activates the stress responsive transcription factor Nrf2 through inactivation of Keap1. (2010)
  • Author(s): Komatsu, M., H.Kurokawa, S.Waguri, K.Taguchi, A.Kobayashi, Y.Ichimura, Y.S.Sou, I.Ueno, A.Sakamoto, K.I.Tong, M.Kim, Y.Nishito, S.I.Iemura, T.Natsume, T.Ueno, E.Kominami, H.Motohashi, K.Tanaka, M.Yamamoto
  • Journal Title: Nat cell biology. 12 Pages: 213-223
  • Peer Reviewed
• [Journal Article] Assembly pathway of the Mammalian proteasome base subcomplex is mediated by multiple specific chaperones (2009)
  • Author(s): Kaneko, T., J. Hamazaki, S. Iemura, K. Sasaki, K. Furuyama, T. Natsume, K. Tanaka, S. Murata
  • Journal Title: Cell 137(5) Pages: 914-925
  • Peer Reviewed
• [Journal Article] CHD8 suppresses p53-mediated apoptosis through histone H1 recruitment during early embryogenesis (2009)
  • Author(s): Nishiyama, M., K. Oshikawa, Y. Tsukada, T. Nakagawa, S. Iemura, T. Natsume, Y. Fan, A. Kikuchi, A.I. Skoultchi, K.I. Nakayama
  • Journal Title: Nat cell biology 11(2) Pages: 863-876
  • Peer Reviewed
• [Journal Article] Assembly pathway of the Mammalian proteasome base subcomplex is mediated by multiple specific chaperones. (2009)
  • Author(s): Kaneko, T., J.Hamazaki, S.lemura, K.Sasaki, K.Furuyama, T.Natsume, K.Tanaka, S.Murata
  • Journal Title: Cell 137 Pages: 914-925
  • Peer Reviewed
• [Journal Article] Promotion of neurite extension by protrudin requires its interaction. (2009)
  • Author(s): Saita, S., Shirane, M., Natsume, T., lemura, S., Nakayama, K.
  • Journal Title: J Biol Chem. IF=5.58
  • Peer Reviewed
• [Journal Article] Atg 101, a novel mammalian autophagy protein interacting with A tg13. (2009)
  • Author(s): Hosokawa, N., T.Sasaki, S.I.lemura, T.Natsume, T.Hara, N.Mizushima
  • Journal Title: Autophagy 5 Pages: 973-979
  • Peer Reviewed
• [Journal Article] Nutrient-dependent mTORC1 association with the ULK1-Atg13-FIP200 complex required for autophagy. (2009)
  • Author(s): Hosokawa, N., T.Hara, T.Kaizuka, C.Kishi, A.Takamura, Y.Miura, S.lemura, T.Natsume, K.Takehana, N.Yamada, J.L.Guan, N.Oshiro, N.Mizushima
  • Journal Title: Molecular biology of the cell 20 Pages: 1981-1991
  • Peer Reviewed
• [Journal Article] Novel In Vitro Protein Fragment Complementation Assay Applicable to High-Throughput Screening in a 1536-Well Format. (2009)
  • Author(s): Hashimoto, J., T.Watanabe, T.Seki, S.Karasawa, M.lzumikawa, T.Seki, S.I.lemura, T.Natsume, N.Nomura, N.Goshima, A.Miyawaki, M.Takagi, K.Shin-Ya
  • Journal Title: J Biomol Screen. 14 Pages: 970-979
  • Peer Reviewed
• [Journal Article] A novel Grb2 associating protein (Gasp) is critical for positiveselection of thym ocytes,. (2009)
  • Author(s): Michael, P., Oda, H., Hayakawa, K., Sato, Y., Eshima, K., Kirikae, T., lemura, S., Shirai, M., Abe, T., Natsume, T., Sasazuki, T., Suzuki, H.
  • Journal Title: Proc Natl Acad Sci USA. MS2009-08593
  • Peer Reviewed
• [Journal Article] Gasp, a Grb2-associating protein, is critical for positive selection of thymocytes. (2009)
  • Author(s): Patrick, M.S., H.Oda, K.Hayakawa, Y.Sato, K.Eshima, T.Kirikae, S.Iemura, M.Shirai, T.Abe, T.Natsume, T.Sasazuki, H.Suzuki
  • Journal Title: Proc Natl Acad Sci USA 106 Pages: 16345-16350
  • Peer Reviewed
• [Journal Article] NLK, an essential effector of anterior formation, functions downstream of p38 MAP kinase. (2009)
  • Author(s): Ohnishi, E., T.Goto, A.Sato, M.S.Kim, S.I.Iemura, T.Ishitani, T.Natsume, J.Ohnishi, H.Shibuyaup
  • Journal Title: Mol cell Biol. 30 Pages: 675-683
  • Peer Reviewed
• [Journal Article] Mys protein regulates protein kinase A activity by interacting with regutatory type 1{alpha} subunit during vertebrate development. (2009)
  • Author(s): Kotani, T., S.I.Iemura, T.Natsume, K.Kawakami, M.Yamashita
  • Journal Title: J Biol Chem. 285 Pages: 5106-5116
  • Peer Reviewed
• [Journal Article] A novel type of E3-ligase for the Ufm1-conjugation system. (2009)
  • Author(s): Tatsumi, K., Y.S.Sou, N.Tada, E.Nakamura, S.I.Iemura, T.Natsume, S.H.Kang, C.H.Chung, M.Kasahara, E.Kominami, M.Yamamoto, K.Tanaka, M.Komatsu
  • Journal Title: J Biol Chem. 285 Pages: 5417-5427
  • Peer Reviewed
• [Journal Article] Asef2 and Neurabin2 cooperatively regulate actin cytoskeletal organization and are involved in HGF-induced cell migration. (2009)
  • Author(s): Sagara M、Kawasaki Y、家村俊一郎、夏目徹、Takai Y、秋山徹(東京大学分子細胞生物学研究所)
  • Journal Title: Oncogene 28 Pages: 1357-1365
  • Peer Reviewed
• [Journal Article] Inositol 1, 4, 5-triphosphate receptor-binding protein released with Inositol 1, 4, 5-triphosphate (IRBIT), associates with components of the mRNA 3' processing machinery in a phosphorylation-dependent manner and inhibits polyadenylation. (2009)
  • Author(s): Kiefer H、Mizutani A、家村俊一郎、夏目徹、Ando H、Kuroda Y、御子柴克彦((独)理化学研究所)
  • Journal Title: J Biol Chem 284 Pages: 10694-10705
  • Peer Reviewed
• [Journal Article] Nutrient-dependent mTORC1 Association with the ULK1-Atg13-FIP200 Complex Required for Autophagy. (2009)
  • Author(s): Hosokawa N、Hara T、Kaizuka T、Kishi C、Takamura A、Miura Y、家村俊一郎、夏目徹、Takehana K、Yamada N、Guan JL、Oshiro N、水島 昇(東京医科歯科大学私学総合研究科)
  • Journal Title: Mol Biol Cell 20 Pages: 1981-1991
  • Peer Reviewed
• [Journal Article] Ankyrin repeat domain 28 (ANKRD28), a novel binding partnerof DOCK180, promotes cell migration by regulating focal adhesion formation. (2009)
  • Author(s): Tachibana M、Kiyokawa E、Hara S、家村俊一郎、夏目徹、Manabe T、松田道行(京都大学大学院生命科学研究科)
  • Journal Title: Exp Cell Res 315 Pages: 863-876
  • Peer Reviewed
• [Journal Article] CHD8 suppresses p53-mediated apoptosis through histone H1 recruitment during early embryogenesis. (2009)
  • Author(s): Nishiyama M、Oshikawa K、Tsukada Y、Nakagawa T、家村俊一郎、夏目徹、Fan Y、Kikuchi A、Skoultchi AI、中山敬一(九州大学 生態防御医学研究所)
  • Journal Title: Nat Cell Biol 11 Pages: 863-876
  • Peer Reviewed
• [Journal Article] FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells (2008)
  • Author(s): Hara, T., A. Takamura, C. Kishi, S. Iemura, T. Natsume, J.L. Guan, N. Mizushima
  • Journal Title: The Journal of cell biology 181(3) Pages: 497-510
  • Peer Reviewed
• [Journal Article] Activity-dependent synaptogenesis: regulation by a CaM-kinase kinase/CaM-kinase I/betaPIX signaling complex (2008)
  • Author(s): Saneyoshi, T., G. Wayman, D. Fortin, M. Davare, N. Hoshi, N. Nozaki, T. Natsume, T.R. Soderling
  • Journal Title: Neuron 57(1) Pages: 94-107
  • Peer Reviewed
• [Journal Article] The DHR1 domain of DOCK180 binds to SNX5 and regulates cation-independent mannose 6-phosphate receptor transport. (2008)
  • Author(s): 原重雄(大阪大学)、夏目徹、家村俊一郎、松田道行(京都大学)、清川悦子(京都大学)、Thomas Wassmer(University of Bristol)、Peter J. Cullen (University of Bristol)、日合弘(滋賀県立成人病センター)
  • Journal Title: J Biol Chem 19 Pages: 3823-3835
  • Peer Reviewed
• [Journal Article] CAATT/enhancer-binding proteins alpha and delta interact wit h NKX2-1 to synergistically activate mouse secretoglobin 3A2 gene expression. (2008)
  • Author(s): Takeshi Tomita(National Institutes of Health)、夏目徹、家村俊一郎、Taketomo Kido(National Institutes of Health)、黒谷玲子(横浜市立大学)、Esta Sterneck(National Institutes of Health)、Charles Vinson(National Institutes of Health)、Shioko Kimura(National Institutes of Health)
  • Journal Title: J Biol Chem 283 Pages: 25617-25627
  • Peer Reviewed
• [Journal Article] A parallel affinity purification method for selective isolation of polyubiquitinated proteins. (2008)
  • Author(s): 伊藤隆司(東京大学)、夏目徹、家村俊一郎、太田一寿(東京大学)、紀藤圭治(東京大学)
  • Journal Title: Proteomics 8 Pages: 3004-3007
  • Peer Reviewed
• [Journal Article] FIP200, a ULK-interacting protein, is required for autophago some formation in mammalian cells. (2008)
  • Author(s): Hara T, Takanlura A, Kishi C, 家村俊一郎, 夏目徹, Guan JL, Mizushima N.
  • Journal Title: J Cell Biol. 181 Pages: 497-510
  • Peer Reviewed
• [Journal Article] Wnt signalling regulates paxillin ubiquitination essential for mesodermal cell motility (2007)
  • Author(s): Iioka, H., S. Iemura, T. Natsume, N. Kinoshita
  • Journal Title: Nat cell biology 9(7) Pages: 813-821
  • Peer Reviewed
• [Journal Article] Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice (2007)
  • Author(s): Komatsu, M., S. Waguri, M. Koike, Y.S. Sou, T. Ueno, T. Hara, N. Mizushima, J. Iwata, J. Ezaki, S. Murata, J. Hamazaki, Y. Nishito, S. Iemura, T. Natsume, T. Yanagawa, J. Uwayama, E. Warabi, H. Yoshida, T. Ishii, A. Kobayashi, M. Yamamoto, Z. Yue, Y. Uchiyama, E. Kominami, K. Tanaka
  • Journal Title: Cell 131(6) Pages: 1149-1163
  • Peer Reviewed
• [Journal Article] XRab40 and XCullin5 form a ubiquitin ligase complex essential for the noncanonical Wnt pathway (2007)
  • Author(s): Lee, R.H., H. Iioka, M. Ohashi, S. Iemura, T. Natsume, N. Kinoshita
  • Journal Title: The EMBO journal 26(15) Pages: 3592-3606
  • Peer Reviewed
• [Journal Article] Wnt signalling regulates paxillin ubiquitination essential for mesodermal cell motility (2007)
  • Author(s): Iioka H, Iemura S, Natsume T, Kinoshita N.
  • Journal Title: Nat Cell Biol 9 Pages: 813-821
  • Peer Reviewed
• [Journal Article] Anchoring of the 26S proteasome to the organellar membrane by FKBP38 (2007)
  • Author(s): Nakagawa T, Shirane M, Iemura S, Natsume T, Nakayama KI.
  • Journal Title: Genes Cells 12 Pages: 709-719
  • Peer Reviewed
• [Journal Article] XRab40 and XCullin5 form aubiquitin ligase complex essential for the noncanonical Wnt pathway (2007)
  • Author(s): Lee RH, Iioka H, Ohashi M, Iemura S, Natsume T, Kinoshita N.
  • Journal Title: EMBO J 26 Pages: 3592-3606
  • Peer Reviewed
• [Journal Article] Nemo-Like Kinase-Myocyte Enhancer Factor 2A Signaling Regulates Anterior Formation in Xenopus Development (2007)
  • Author(s): Satoh K, Ohnishi J, Sato A, Takeyama M, Iemura S, Natsume T, Shibuya H.
  • Journal Title: Mol Cell Biol 27 Pages: 7623-7630
  • Peer Reviewed
• [Journal Article] Nucleo-cytoplasmic shuttling of the zinc finger protein EZI is mediatedby importin-Independent nuclear import and CRMl-independent exportmechanisms (2007)
  • Author(s): Saijou E, Itoh T, Kim KW, Iemura SI, Natsume T, Miyajima A.
  • Journal Title: J Biol Chem 282 Pages: 32327-32337
  • Peer Reviewed
• [Journal Article] A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes (2006)
  • Author(s): Hamazaki, J., Iemura, S., Natsume, T., Yashiroda, H., Tanaka, K., Murata, S.
  • Journal Title: The EMBO journal 25(19) Pages: 4524-36
  • Peer Reviewed
• [Journal Article] XGAP, an ArfGAP, is required for polarized localization of PAR proteins and cell polarity in Xenopus gastrulation (2006)
  • Author(s): Hyodo-Miura, J., Yamamoto, T.S., Hyodo, A.C., Iemura, S., Kusakabe, M., Nishida, E., Natsume, T., Ueno, N.
  • Journal Title: Dev Cell 11(1) Pages: 69-79
  • Peer Reviewed
• [Journal Article] Shugoshin collaborates with protein phosphatase 2A to protect cohesin (2006)
  • Author(s): Kitajima, T.S., Sakuno, T., Ishiguro, K., Iemura, S., Natsume, T., Kawashima, S.A., Watanabe, Y.
  • Journal Title: Nature 441(7089) Pages: 46-52
  • Peer Reviewed
• [Journal Article] A novel ubiquitin-binding protein ZNF216 functioning in muscle atrophy (2006)
  • Author(s): Hishiya, A., Iemura, S., Natsume, T., Takayama, S., Ikeda, K., Watanabe, K.
  • Journal Title: Embo J 25(3) Pages: 554-64
  • Peer Reviewed
• [Journal Article] NARF, an Nemo-like Kinase (NLK)-associated Ring Finger Protein Regulates the Ubiquitylation and Degradation of T Cell Factor/Lymphoid Enhancer Factor (TCF/LEF). (2006)
  • Author(s): Yamada M, Ohnishi J, Ohkawara B, lemura S, Satoh K, Hyodo-Miura J., Kawachi K, Natsume T, Shibuya H
  • Journal Title: J Biol Chem. 281 (30) Pages: 20749-20760
• [Journal Article] Comparative genomic analysis of transcription regulation elements involved in human man kinase g-protein coupling pathway. (2006)
  • Author(s): Polouliakh N, Natsume T, Harada H, Fujibuchi W, Horton P
  • Journal Title: Bioinform Comput Biol. 4(2) Pages: 469-482
• [Journal Article] XGAP, an ArfGAP, is required for polarized localization of PAR proteins and cell polarity in Xenopus gastrulation. (2006)
  • Author(s): Hyodo-Miura J, Yamamoto TS, Hyodo AC, lemura S, Kusakabe M Nishida E, Natsume T, Ueno N
  • Journal Title: Dev Cell. 11 (1) Pages: 69-79
• [Journal Article] A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes. (2006)
  • Author(s): Hamazaki J, Iemura S, Natsume T, Yashiroda H, Tanaka K, Murata S
  • Journal Title: EMBO J 25 (19) Pages: 4524-4536
• [Journal Article] Protein phosphatase 6 down-regulates TAKI kinase activation in the IL-1 signaling pathway. (2006)
  • Author(s): Kaj ino T, Ren H, Iemura S, Natsume T, Stefansson B, Brautigan DL, Matsumoto K, Ninomiya-Tsuji J
  • Journal Title: J Biol Chem. 281 (52) Pages: 39891-39896
• [Journal Article] Cooperation of Multiple Chaperones Required for the Assembly of Mammalian 20S Proteasomes. (2006)
  • Author(s): Hirano Y, Hayashi H, Iemura S, Hendil KB, Niwa S, Kishimoto T, Kasahara M, Natsume T, Tanaka K, Murata S
  • Journal Title: Mol Cell. 24 (6) Pages: 977-984
• [Journal Article] A novel ubiquitin-binding protein ZNF216 functioning in muscle atrophy (2006)
  • Author(s): Akinori Hishiya
  • Journal Title: Embo J 2006, Feb 8 25(3) Pages: 554-564
• [Journal Article] A heterodimeric complex that promotes the assembly of mammalian 20S proteasomes. (2005)
  • Author(s): Hirano Y
  • Journal Title: Nature 2005, Oct 27 437(7063) Pages: 1381-1385
• [Journal Article] WNK1 regulates phosphorylation of cation-chloride-coupled cotransporters via the STE20-related kinases, SPAK and OSR1 (2005)
  • Author(s): Moriguchi T
  • Journal Title: J Biol Chem. 2005 Dec 30 280(52) Pages: 42685-42693
• [Presentation] タンパク質ネットワーク大規模解析から展開するケミカルバイオロジー (2009)
  • Author(s): 夏日徹
  • Organizer: 第68回日本癌学会学術総会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2009-10-02
• [Presentation] New generation proteomics (2009)
  • Author(s): 夏目徹
  • Organizer: 日本ヒトプロテオーム機構
  • Place of Presentation: 北里大学
  • Year and Date: 2009-07-30
• [Presentation] Systematic Analysis of Protein Interaction Networks Using Human Full Length cDNA. (2005)
  • Author(s): 夏目徹
  • Organizer: International chemical congress of pacific basin societies
  • Place of Presentation: Hilton Hawaiian Village
  • Year and Date: 2005-12-16
• [Presentation] Systematic analysis of protein interaction network using human full length cDNA (2005)
  • Author(s): 夏目徹
  • Organizer: VIth European Symposium of The Protein Society
  • Place of Presentation: Barcelona
  • Year and Date: 2005-05-01
• [Book] 明日を拓く新次元プロテオミクス超々高感度質量分析への道のり (2009)
  • Author(s): 夏目徹
  • Publisher: 学研メディカル秀潤社
• [Book] ストゲノム時代のタンパク質科学 (2006)
  • Author(s): 夏目徹
  • Publisher: 化学同人
• [Book] ゲノムから生命システムへ (2005)
  • Author(s): 夏目徹
  • Publisher: 共立出版