Global analysis of post-translational modifications in super-molecular protein complexes by targeted proteomics

• Project/Area Number: 22370042
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: The University of Tokushima
• Principal Investigator: TANIGUCHI Hisaaki 徳島大学, 疾患酵素学研究センター, 教授 (10257636)
• Co-Investigator(Kenkyū-buntansha): MAITA Nobuo 徳島大学, 疾患酵素学研究センター, 准教授 (00404046) ; IKEDA Kazuko 徳島大学, 疾患酵素学研究センター, 助教 (10108863) ; KOSAKO Hidetaka 徳島大学, 疾患酵素学研究センター, 准教授 (10291171)
• Project Period (FY): 2010 – 2013
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥18,980,000 (Direct Cost: ¥14,600,000、Indirect Cost: ¥4,380,000); Fiscal Year 2012: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2011: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2010: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
• Keywords: プロテオミクス / 巨大分子複合体 / 翻訳後修飾 / オルガネラ / 質量分析

Research Abstract

In this project, post-translational modifications were analyzed by targeted approach by isolating supra-molecular protein complexes and small organelles, and analyzing post-translational modifications using both top-down and bottom-up proteomic approaches. Reducing the complexity of the samples should increase the coverage and the extent of the modifications detected.

Research Products

• [Journal Article] Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor (2013)
  • Author(s): Hirose T, Maita N, Taniguchi H, Sharpless KB, Omura S, Sunazuka T
  • Journal Title: Proc.Natl.Acad.Sci. USA. Volume: 110 Issue: 40 Pages: 15892-15897
  • DOI: 10.1073/pnas.1315049110
  • Peer Reviewed
• [Journal Article] Human α-L-iduronidase uses its own N-glycan as a substrate-binding and catalytic module (2013)
  • Author(s): Maita N, Tsukimura T, Taniguchi T, Saito S, Ohno K, Taniguchi H, Sakuraba H
  • Journal Title: Proc. Natl. Acad. Sci. USA. Volume: 110 Issue: 36 Pages: 14628-14633
  • DOI: 10.1073/pnas.1306939110
  • Peer Reviewed
• [Journal Article] GRK6 deficiency in mice causes autoimmune disease due to impaired apoptotic cell clearance (2013)
  • Author(s): Nakaya M, Kosako H, Taniguchi H, Sato Kurose H
  • Journal Title: Nat Commun. Pages: 153-153
  • Peer Reviewed
• [Journal Article] Using Whole-Exome Sequencing to Identify Inherited Causes of Autism (2013)
  • Author(s): Yu TW, Okamura-Ikeda K, Taniguchi H, Walsh CA
  • Journal Title: Neuron Volume: 77 Issue: 2 Pages: 259-273
  • DOI: 10.1016/j.neuron.2012.11.002
  • Peer Reviewed
• [Journal Article] ADP Ribosylation Factor 1 Plays an Essential Role in the Replication of a Plant RNA Virus (2013)
  • Author(s): K Hyodo, et al.,
  • Journal Title: Journal of Virology Volume: 87 Issue: 1 Pages: 163-176
  • DOI: 10.1128/jvi.02383-12
  • Peer Reviewed
• [Journal Article] Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor. (2013)
  • Author(s): Hirose T
  • Journal Title: Proc Natl Acad Sci U S A. Volume: 110 Pages: 15892-15897
  • Peer Reviewed
• [Journal Article] Human α-L-iduronidase uses its own N-glycan as a substrate-binding and catalytic module. (2013)
  • Author(s): Maita N
  • Journal Title: Proc Natl Acad Sci U S A. Volume: 110 Pages: 14628-14633
  • Peer Reviewed
• [Journal Article] GRK6 deficiency in mice causes autoimmune disease due to impaired apoptotic cell clearance. (2013)
  • Author(s): Nakaya M
  • Journal Title: Nat Commun. Volume: 4 Issue: 1 Pages: 1532-1532
  • DOI: 10.1038/ncomms2410
  • Peer Reviewed
• [Journal Article] Using Whole-Exome Sequencing to identify inherited causes of autism (2013)
  • Author(s): Yu TW
  • Journal Title: Neuron Volume: 77 Pages: 259-273
  • Peer Reviewed
• [Journal Article] The ADP-ribosylation factor 1 plays an essential role in the replication of a plant RNA virus. (2013)
  • Author(s): Hyodo K
  • Journal Title: J Virol. Volume: 87 Pages: 163-176
  • Peer Reviewed
• [Journal Article] Crystallization, X-ray diffraction analysis and SIRAS phasing of human α-L-iduronidase (2012)
  • Author(s): Maita N, Taniguchi H, and Sakuraba H
  • Journal Title: Acta Crystallographica Volume: Section F 68(Pt 11) Issue: 11 Pages: 1363-1366
  • DOI: 10.1107/s1744309112040432
  • Peer Reviewed
• [Journal Article] d-Dopachrome tautomerase promotes IL-6 expression and inhibits adipogenesis in preadipocytes (2012)
  • Author(s): Ishimoto K, Iwata T, Taniguchi H, Mizusawa N, Tanaka E, Yoshimoto K
  • Journal Title: Cytokine Volume: 60 Issue: 3 Pages: 772-777
  • DOI: 10.1016/j.cyto.2012.07.037
  • NAID: 120005755084
  • Peer Reviewed
• [Journal Article] PINK1 autophosphorylation upon membrane potential dissipation is essential for Parkin recruitment to damaged mitochondria (2012)
  • Author(s): 尾勝圭
  • Journal Title: Nature Communications Volume: 3 Issue: 1 Pages: 1016-1016
  • DOI: 10.1038/ncomms2016
  • Peer Reviewed
• [Journal Article] Differential Roles of Hsp70 and Hsp90 in the Assembly of the Replication Complex of a Positive-Strand RNA Plant Virus (2012)
  • Author(s): A Mine, K Hyodo, et al.,
  • Journal Title: Journal of Virology Volume: 86 Issue: 22 Pages: 12091-12104
  • DOI: 10.1128/jvi.01659-12
  • Peer Reviewed
• [Journal Article] Poly(A)-binding protein facilitates translation of an ncapped/nonpolyadenylated viral RNA by binding to the 3' untranslated region. (2012)
  • Author(s): Iwakawa HO, Tajima Y, Taniguchi T, Kaido M, Mise K, Tomari Y, Taniguchi H, Okuno T.
  • Journal Title: Journal of Virology Volume: 86(15) Issue: 15 Pages: 7836-7849
  • DOI: 10.1128/jvi.00538-12
  • Peer Reviewed
• [Journal Article] Derlin-1 and UBXD8 are engaged in dislocation and degradation of lipidated ApoB-100 at lipid droplets (2012)
  • Author(s): Suzuki M, Otsuka T, Ohsaki Y, Cheng J, Taniguchi T, Hashimoto H, Taniguchi H, Fujimoto T
  • Journal Title: Mol Biol Cell Volume: (印刷中)(in press) Issue: 5 Pages: 800-810
  • DOI: 10.1091/mbc.e11-11-0950
  • Peer Reviewed
• [Journal Article] Poly(A)-vinding protein facilitates translation of an uncapped/nonpoladenylated viral RNA by binding to the 3' untranslated region. (2012)
  • Author(s): Iwakawa HO
  • Journal Title: J. Virol. Volume: 86 Pages: 7836-7849
  • Peer Reviewed
• [Journal Article] Differential roles of Hsp70 and Hsp90 in the assembly of the replicase complex of a positive-strand RNA plant virus. (2012)
  • Author(s): Mine A
  • Journal Title: J Virol. Volume: 86 Pages: 12091-12104
  • Peer Reviewed
• [Journal Article] Derlin-1 and UBXD8 are engaged in dislocation and degradation of lipidated ApoB-100 at lipid droplets. (2012)
  • Author(s): Suzuki M
  • Journal Title: Mol. Biol. Cell Volume: 23 Pages: 800-810
  • Peer Reviewed
• [Journal Article] CrystallizationkX-ray diffraction analysis and SIRAS phasing of Human α-L-iduronidase. (2012)
  • Author(s): Maita N
  • Journal Title: Acta Crystallographica Section F 68 Volume: Pt 11 Pages: 1363-1366
  • Peer Reviewed
• [Journal Article] D-Dopachrome tautomerase promotes IL-6 expression and inhibits adipogenesis in preadipocytes. (2012)
  • Author(s): Ishimoto K
  • Journal Title: Cytokine Volume: 60 Pages: 772-777
  • Peer Reviewed
• [Journal Article] Vimentin binds IRAP and is involved in GLUT4 vesicle trafficking (2011)
  • Author(s): H irata Y, Iwata T, Le CTH, Jambaldorj B, Teshigawara K, Harada N, Sakaue H, Sakai T, Yoshimoto K, Nakaya Y
  • Journal Title: Biochem Biophys Res Commun Volume: 405(1) Issue: 3 Pages: 96-101
  • DOI: 10.1371/journal.pone.0033402
  • NAID: 120006631415
  • Peer Reviewed
• [Journal Article] Histone chaperone Spt6 is required for class switch recombination but not somatic hypermutation (2011)
  • Author(s): Okazaki IM, Okawa K, Kobayashi M, Yoshikawa K, Kawamoto S, Nagaoka H, Shinkura R, Kitawaki Y, Taniguchi H, Natsume T, Iemura S, and Honjo T
  • Journal Title: Proc Natl Acad Sci USA Volume: 108 Issue: 19 Pages: 920-925
  • DOI: 10.1073/pnas.1104423108
  • NAID: 120003163668
  • Peer Reviewed
• [Journal Article] Identification and localization of the sperm CRISP family protein CiUrabin involved in gamete interaction in the ascidian Ciona intestinalis (2011)
  • Author(s): Akira Yamaguchi, Takako Saito, Lixy Yamada, Hisaaki Taniguchi, Yoshito Harada, Hitoshi Sawada
  • Journal Title: Mol.Reprod.Dev. Volume: 78 Issue: 7 Pages: 488-497
  • DOI: 10.1002/mrd.21329
  • Peer Reviewed
• [Journal Article] CIPRO 2.5 : Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reniewing functionalit (2011)
  • Author(s): Endo, T., Ueno, K., Yonezawa, K., Mineta, K., Hotta, K., Satou, Y., Yamada, L., Ogasawara, M., Takahashi, H., Nakajima ,A., Nakachi, M., Nomura, M., Yaguchi, J., Sasakura, Y., Yamasaki, C., Sera, M., Yoshizawa, AC., Imanishi, T., Taniguchi ,H., and Inaba ,K.
  • Journal Title: Nicleic Acids Res Volume: 39 (Suppl.1) Issue: Database Pages: 807-814
  • DOI: 10.1093/nar/gkq1144
  • Peer Reviewed
• [Journal Article] Mechanical stress activates Smad pathway through PKCχto enhance interlukin-11 gene transcription in osteoblasts (2010)
  • Author(s): Kido S, Kuriwaka-Kido R, Matsumoto T, et al.
  • Journal Title: PLoS One Volume: 5(9) Issue: 9 Pages: e13090-e13090
  • DOI: 10.1371/journal.pone.0013090
  • Peer Reviewed
• [Journal Article] Induction of endosomal/ lysosomal pathways in differentiating osteoblasts as revealed by combined proteomic and transcriptomic analysis (2010)
  • Author(s): Taniguchi T, Kido S, Taniguchi H, et al.
  • Journal Title: FEBS Lett Volume: 584(18) Issue: 18 Pages: 3969-3974
  • DOI: 10.1016/j.febslet.2010.07.055
  • Peer Reviewed
• [Journal Article] New functional proteins identified by proteomic analysis in the epidermal growth factor receptor-mediated signaling pathway and application for practical use (2010)
  • Author(s): Tashiro K, Konishi H, Nabeshi H, Yamauchi E, and Taniguchi H
  • Journal Title: Yakugaku Zasshi (Review. Japanese) Volume: Apr;130(4) Pages: 471-477
  • NAID: 130000259533
  • Peer Reviewed
• [Journal Article] Dead time loss correction of mass errors occurring in high-throughput proteomics based on electrospray ionization time-of-flight tandem mass spectrometry (2010)
  • Author(s): Ishino Y, and Taniguchi H
  • Journal Title: Rapid Commun Mass Spectrom Volume: 24 Issue: 10 Pages: 1490-1495
  • DOI: 10.1002/rcm.4532
  • Peer Reviewed
• [Journal Article] Identification and Characterization of the 480 kDa Template-Specific RNA-Dependent RNA Polymerase Complex of Red Clover Necrotic Mosaic Virus (2010)
  • Author(s): Mine, A., Takeda, A., Taniguchi, T., Taniguchi, H., Kaido, M., Mise, K., and Okuno, T
  • Journal Title: J. Virol Volume: 84 Issue: 12 Pages: 6070-6081
  • DOI: 10.1128/jvi.00054-10
  • Peer Reviewed
• [Journal Article] Crystal structure of aminomethyltransferase in complex with dihydrolipoyl-H-protein of the glycine cleavage system : Implications for recognition of lipoyl protein substrate, disease-related mutations, and reaction mechanism (2010)
  • Author(s): Okamura-Ikeda, K. Hosaka, H. Maita, N. Fujiwara, K. Yoshizawa, A.C. Nakagawa, A. and Taniguchi, H
  • Journal Title: J. Biol. Chem. Volume: 85 Issue: 24 Pages: 18684-18692
  • DOI: 10.1074/jbc.m110.110718
  • NAID: 120006770863
  • Peer Reviewed
• [Journal Article] Global conformational change associated with the two step reaction catalyzed by Escherichia coli lipoate-protein ligase A (2010)
  • Author(s): Fujiwara, K. Maita, N. Hosaka, H. Okamura-Ikeda, K. Nakagawa, A. and Taniguchi, H
  • Journal Title: J. Biol. Chem. Volume: 285 Issue: 13 Pages: 9971-9980
  • DOI: 10.1074/jbc.m109.078717
  • NAID: 120006770865
  • Peer Reviewed
• [Journal Article] Crystal structure of aminomethyltransferase in complex with dihydrolipoyl-H-protein of the glycine cleavage system (2010)
  • Author(s): Okamura-Ikeda, K., et al.
  • Journal Title: Journal of Biological Chemistry Volume: 285 Pages: 18684-18692
  • Peer Reviewed
• [Journal Article] Identification and Characterization of the 480 kDa Template-Specific RNA-Dependent RNA Polymerase Complex of Red Clover Necrotic Mosaic Virus (2010)
  • Author(s): Mine, A., et al.
  • Journal Title: Journal of Virology Volume: 84 Pages: 6070-6081
  • Peer Reviewed
• [Journal Article] Induction of Endosomal/lysosomal Pathways in Differentiating Osteoblasts as Revealed by Combined Proteomic and Transcriptomic Analyses (2010)
  • Author(s): Taniguchi T, et al.
  • Journal Title: FEBS Letters Volume: 584 Pages: 3969-3974
  • Peer Reviewed
• [Journal Article] Dead time loss correction of mass errors occurring in high-throughput proteoinics based on electrospray ionization time-of-flight tandem mass spectrometry (2010)
  • Author(s): Taniguchi T, et al.
  • Journal Title: Rapid Commun Mass Spectrom Volume: 24 Pages: 1490-1495
  • Peer Reviewed
• [Journal Article] Mechanical stress activates Smad pathway through PKCδ to enhance in terleukin-11 gene transcription in osteoblasts (2010)
  • Author(s): Taniguchi T, et al.
  • Journal Title: PLoS Oae Volume: Sep 29;5(9) Pages: 1309-1309
  • Peer Reviewed
• [Presentation] ヒトα-L-イズロニダーゼの結晶構造解析 (2012)
  • Author(s): 真板 宣夫
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: 福岡国際会議場(福岡県)
  • Year and Date: 2012-12-14
• [Presentation] 腰部脊柱管狭窄症における肥厚黄色靱帯のプロテオーム解析 (2012)
  • Author(s): 合田 有一郎
  • Organizer: 第37回日本医用マススペクトル学会年会
  • Place of Presentation: ウインクあいち(愛知県)
  • Year and Date: 2012-10-26
• [Presentation] Wnt シグナル抑制因子sFRP4 の肥満・糖代謝との関連性についての検討 (2011)
  • Author(s): 藤中 雄一
  • Organizer: 第32回日本肥満学会
  • Place of Presentation: 淡路国際会議場(兵庫県)
  • Year and Date: 2011-09-23
• [Presentation] カタユウレイボヤ 8 細胞期胚におけるタンパク質局在のプロテオーム解析 (2011)
  • Author(s): 野田 武志
  • Organizer: 第82回日本動物学会
  • Place of Presentation: 東北大学(北海道)
  • Year and Date: 2011-09-22
• [Presentation] D-dopachrome tautomerase は脂肪細胞での脂質代謝を制御する (2011)
  • Author(s): 岩田 武男
  • Organizer: 第54回日本糖尿病学会年次学術集会
  • Place of Presentation: 札幌教育文化会館(北海道)
  • Year and Date: 2011-05-19
• [Presentation] Heat shock protein 70 (Hsp70)はRed clover necrotic mosaic virus (RCNMV) のRNA 複製酵素複合体の形成を制御している (2011)
  • Author(s): 峯 彰
  • Organizer: 日本植物病理学会大会
  • Place of Presentation: ルミエール府中(東京都)
  • Year and Date: 2011-03-27
• [Presentation] Heat shock protein 70 (Hsp70)はRed clover necrotic mosaic virus (RCNMV)のRNA複製酵素複合体の形成を制御している (2011)
  • Author(s): 峯彰
  • Organizer: 日本植物病理学会大会
  • Place of Presentation: 東京(ルミエール府中)
  • Year and Date: 2011-03-27
• [Presentation] Establishment of a Method for Proteomic Analysis of Human Achilles Tendon (2011)
  • Author(s): Sato Nori
  • Organizer: Annual meeting of the Orthopaedic Research Society
  • Place of Presentation: Long Beach Convention Center, 米国ロングビーチ
  • Year and Date: 2011-01-13
• [Presentation] Development of a Method for Proteomic Analysis of Human Yellow Ligament (2011)
  • Author(s): Sato Nori
  • Organizer: Annual meeting of the Orthopaedic Research Society
  • Place of Presentation: Long Beach Convention Center, 米国ロングビーチ
  • Year and Date: 2011-01-13
• [Presentation] 仮想ゲルを用いたLC/MS データの表示とタンパク質修飾の探索プログラム (2010)
  • Author(s): 吉沢 明康
  • Organizer: BMB2010
  • Place of Presentation: 神戸国際会議場(兵庫県)
  • Year and Date: 2010-12-07
• [Presentation] 仮想ゲルを用いたLC/MSデータの表示とタンパク質修飾の探索プログラム (2010)
  • Author(s): 吉沢明康
  • Organizer: BMB2010
  • Place of Presentation: 神戸(神戸国際展示場)
  • Year and Date: 2010-12-07
• [Presentation] CIPRO 2.5 : Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments (2010)
  • Author(s): Toshinori Endo
  • Organizer: Biocuration 2010
  • Place of Presentation: Tokyo(東京国際交流館)
  • Year and Date: 2010-10-12
• [Presentation] カタユウレイボヤにおける精子膜タンパク質のプロテオーム解析 (2010)
  • Author(s): 横田直人
  • Organizer: 第81回日本動物学会
  • Place of Presentation: 東京(東京大学)
  • Year and Date: 2010-09-25
• [Presentation] カタユウレイボヤにおける精子膜タンパク質のプロテオーム解析 (2010)
  • Author(s): 横田 直人
  • Organizer: 第81回日本動物学会
  • Place of Presentation: 東京大学(東京都)
  • Year and Date: 2010-09-23
• [Presentation] Poly(A)結合タンパク質(PABP)はRed clovernecrotic mosaic virus (RCNMV) RNA1の3'非翻訳領域(UTR)に結合しcap/poly(A)非依存的翻訳を促進する (2010)
  • Author(s): 岩川弘宙
  • Organizer: 日本植物病理学会大会
  • Place of Presentation: 京都(国立京都国際会館)
  • Year and Date: 2010-04-18
• [Presentation] Red clover necrotic mosaic virusのRNA合成を担う480 kDa複合体の同定と性状解析 (2010)
  • Author(s): 峯彰
  • Organizer: 日本植物病理学会大会
  • Place of Presentation: 京都(国立京都国際会館)
  • Year and Date: 2010-04-18
• [Presentation] CIONA INTESTINALIS PROTEIN DATABASE CIPRO SHOWS A VARIETY OF PROTEOMES FOR A SINGLE SPECIES (2010)
  • Author(s): Toshinori Endo
  • Organizer: Computational Biology Research Center Workshop 2010
  • Place of Presentation: Tokyo (Computational Biology Research Center)
• [Presentation] CIPRO 2.5 : Ciona intestinalis Protein Database, a unique integrated repository of large-scale omics data, bioinformatic analyses, and curated annotation, with ability for user rating and comments (2010)
  • Author(s): Toshinori Endo
  • Organizer: Beyond the Genome
  • Place of Presentation: Boston
• [Remarks]
  • URL: http://www.tokushima-u.ac.jp/ier/divisions/proteomics.html
• [Remarks]
  • URL: http://www.tokushima-u.ac.jp/ier/
• [Remarks]
  • URL: http://www.ier.tokushima-u.ac.jp/