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タンパク質質量解析グループ

タンパク質質量解析チームでは、タンパク質プロファイルの比較・同定の為の、二次元電気ゲル電気泳動法、及び質量分析解析に関する新規手法の開発と、それらの技術を用いた研究の指導を行っています。

 

(fukao＠bs.naist.jp)

プロジェクト

1. プロテオミクスに関わる実験手法の確立

タンパク質質量解析チームでは、プロテオミクスに関わる実験手法の確立を行っています。
（１）磁気ビーズを用いた簡便な複合体精製法とその同定、（２）iTRAQ試薬を用いた相対定量解析、（３）リン酸化タンパク質の同定とリン酸化部位の同定（４）安定同位体ラベルしたペプチドを用いた絶対定量解析系の確立（５）SDSや不純物を除去することなく等電点電気泳動するための技術確立、などです。
この他、質量分析計による解析では、分析サンプルの調製がその成否を大きく左右するため、サンプルの前処理技術の確立に力を入れています。
（１）〜（３）の解析にはThermo Scientific LTQ-Orbitrap XLを、（４）の解析にはThermo Scientific TSQ-Vantageを、（５）の解析にはAnatech CoolPhoreStar IPG-IEF Type-Pをそれぞれ用いています。

2. 亜鉛恒常性維持機構における細胞内膜系の役割と機能解析

亜鉛は高等植物における必須微量元素であるため、その量が多すぎても少なすぎても成育を阻害します。
そのため植物は亜鉛を一定濃度に保つための恒常性維持機構を持っています。
我々はこの恒常性維持機構に細胞内膜系がどのような役割を持つのかに興味を持って研究を進めています。

発表論文リスト

Articles

  • Zargar, S.M., Kurata, R., Inaba, S., Oikawa, A., Fukui, R., Ogata, Y., Agrawal, G.K., Rakwal, R., and Fukao Y.* (2015) Quantitative proteomics of Arabidopsis shoot microsomal proteins reveals a cross-talk between excess zinc and iron deficiency. Proteomics, in press.
    PubMed
  • Moro, C.F., Fukao, Y., Shibato, J., Rakwal, R., Timperio, A.M., Zolla, L., Agrawal, G.K., Shioda, S., Kouzuma, Y., and Yonekura, M. (2015) Unraveling the seed endosperm proteome of the lotus (Nelumbo nucifera Gaernt.) utilizing 1DE and 2DE separation in conjunction with tandem mass spectrometry. Proteomics, in press.
    PubMed
  • Huang, J., Fujimoto, M., Fujiwara, M., Fukao, Y., Arimura, S., and Tsutsumi, N. (2014) Arabidopsis dynamin-related proteins, DRP2A and DRP2B, function coordinately in post-Golgi trafficking. Biochem. Biophys. Res. Commun., 456 (1), 238-244.
    PubMed
  • Zargar, S.M., Fujiwara, M., Inaba, S., Kobayashi, M., Kurata, R., Ogata, Y., and Fukao, Y.* (2014) Correlation analysis of proteins responsive to Zn, Mn, or Fe deficiency in Arabidopsis roots based on iTRAQ analysis. Plant Cell Rep., 34 (1), 157-166.
    PubMed
  • Ido, K., Nield, J., Fukao, Y., Nishimura, T., Sato, F., and Ifuku, K. (2014) Cross-Linking Evidence for Multiple Interactions of the PsbP and PsbQ Proteins in a Higher Plant Photosystem II Supercomplex. J. Biol. Chem., 289(29):20150-7.
    PubMed
  • Sako, K., Yanagawa, Y., Kanai, T., Sato, T., Seki, M., Fujiwara, M., Fukao, Y., Yamaguchi, J. (2014) Proteomic analysis of the 26S proteasome reveals its direct interaction with transit peptides of plastid protein precursors for their degradation. J Proteome Res., 13(7):3223-30.
    PubMed
  • Goto, C., Tamura, K., Fukao, Y., Shimada, T., Hara-Nishimura, I. (2014) The Novel Nuclear Envelope Protein KAKU4 Modulates Nuclear Morphology in Arabidopsis. Plant Cell., 26(5):2143-2155.
    PubMed
  • Yasuda, S., Sato, T., Maekawa, S., Aoyama, S., Fukao, Y., and Yamaguchi, J. (2014) Phosphorylation of Arabidopsis ubiquitin ligase ATL31 is critical for plant carbon/nitrogen nutrient balance response and controls the stability of 14-3-3 proteins. J Biol Chem., 289(22):15179-93.
    PubMed
  • Entani, T., Kubo, K., Isogai, S., Fukao, Y., Shirakawa, M., Isogai, A., and Takayama, S.(2014) Ubiquitin-proteasome-mediated degradation of S-RNase in a solanaceous cross-compatibility reaction. Plant J., 78(6):1014-21.
    PubMed
  • Fujiwara, M., Uemura, T., Ebine, K., Nishimori, Y., Ueda, T., Nakano, A., Sato, M.H., Fukao, Y.* (2014) Interactomics of Qa-SNARE in Arabidopsis thaliana. Plant Cell Physiol., 55 (4), 781-789.
    PubMed
  • Tanaka, N., Kato, M., Tomioka, R., Kurata, R., Fukao, Y., Aoyama, T., and Maeshima, M. (2014) Characteristics of a root hair-less line of Arabidopsis thaliana under physiological stresses. J Exp Bot, 65 (6), 1497-1512.
    PubMed
  • Maekawa, S., Inada, N., Yasuda, S., Fukao, Y., Fujiwara, M., Sato, T., and Yamaguchi, J. (2014) The C/N regulator ATL31 controls papilla formation in response to powdery mildew fungi penetration by interacting with SNARE SYP121 in Arabidopsis. Plant Physiol., 164 (2), 879-887.
    PubMed
  • Shimada, TL., Takano, Y., Shimada, T., Fujiwara, M., Fukao, Y., Mori, M., Okazaki, Y., Saito, K., Sasaki, R., Aoki, K., and Hara-Nishimura, I.(2014) Leaf oil body functions as a subcellular factory for the production of a phytoalexin in Arabidopsis thaliana. Plant Physiol., 164 (1), 105-118.
    PubMed
  • Zargar, S.M., Kurata, R., Inaba, S., and Fukao, Y.* (2013) Unraveling the iron deficiency responsive proteome in Arabidopsis shoot by iTRAQ-OFFGEL approach. Plant Signal. Behav., 9 (1), e26892.
    PubMed
  • Hamada, T., Nagasaki-Tekeuchi, N., Kato, T., Fujiwara, M., Sonobe, S., Fukao, Y., and Hashimoto, T. (2013) Purification and characterization of novel microtubule-associated proteins from Arabidopsis cell suspension cultures. Plant Physiol., 163 (4), 1804-1816.
    PubMed
  • Takagi, J., Renna, L., Takahashi, H., Koumoto, Y., Tamura, K., Stefano, G., Fukao, Y., Kondo, M., Nishimura, M., Shimada, T., Brandizzi, F., and Hara-Nishimura, I. (2013) MAIGO5 Functions in Protein Export from Golgi-Associated Endoplasmic Reticulum Exit Sites in Arabidopsis. Plant Cell, 25 (11), 4658-4675.
    PubMed
  • Tamaki, T., Betsuyaku, S., Fujiwara, M., Fukao, Y., Fukuda, H., and Sawa, S. (2013) SUPPRESSOR OF LLP1 1-mediated C-terminal processing is critical for CLE19 peptide activity. Plant J., 76 (6), 970-981.
    PubMed
  • Sun, H.H., Fukao, Y., Ishida, S., Yamamoto, H., Maekawa, S., Fujiwara, M., Sato, T.,and Yamaguchi, J. (2013) Proteomics analysis reveals a highly heterogenous proteasome composition and the post-translational regulation of peptidase activity under pathogen signaling in plants. J. Proteome Res., 12 (11), 5084-5095.
    PubMed
  • Yamaoka, S., Shimono, Y., Shirakawa, M., Fukao, Y., Kawase, T., Hatsugai, N., Tamura, K., Shimada, T., and Hara-Nishimura I. (2013) Identification and dynamics of Arabidopsis AP-2 complex and its involvement in floral organ development. Plant Cell, 25 (8), 2958-2969.
    PubMed
  • Tamura, K., Iwabuchi, K., Fukao, Y., Kondo, M., Okamoto, K., Ueda, H., Nishimura, M., and Hara-Nishimura, I. (2013) Myosin XI-i links the nuclear membrane to the cytoskeleton to control nuclear movement and shape in Arabidopsis. Curr. Biol., 23 (18), 1776-1781.
    PubMed
  • Yoshida, K., Ohnishi, M., Fukao, Y., Okazaki, Y., Fujiwara, M., Song, C., Nakanishi, Y., Saito, K., Shimmen, T., Suzaki, T., Hayashi, F., Fukaki, H., Maeshima, M., and Mimura, T. (2013) Studies on vacuolar membrane microdomains isolated from Arabidopsis suspension-cultured cells: Local distribution of vacuolar membrane proteins. Plant Cell Physiol., 54 (10), 1571-1584.
    PubMed
  • Teh, O.K., Shimono, Y., Shirakawa, M., Fukao, Y., Tamura, K., Shimada, T., and Hara-Nishimura, I. (2013) The AP-1 μ adaptin is required for KNOLLE localization at the cell plate to mediate cytokinesis in Arabidopsis. Plant Cell Physiol., 54 (6), 838-847.
    PubMed
  • Hoshiyasu, S., Kohzuma, K., Yoshida, K., Fujiwara, M., Fukao, Y., Yokota, A., and Akashi, K. (2013) Potential involvement of N-terminal acetylation in the quantitative regulation of the ε subunit of chloroplast ATP synthase under drought stress. Biosci. Biotechnol. Biochem., 77 (5), 998-1007
    PubMed
  • Fukao, Y.*, Yoshida, M., Kurata, R., Kobayashi, M., Nakanishi, M., Fujiwara, M., Nakajima, K., and Ferjani, A. (2013) Peptide Separation Methodologies for In-depth Proteomics in Arabidopsis. Plant Cell Physiol., 54 (5), 808-815.
    PubMed
  • Cui, S., Fukao, Y., Mano, S., Yamada, K., Hayashi, M., and Nishimura, M. (2013) Proteomic Analysis Reveals that the Rab GTPase RabE1c is Involved in the Degradation of the Peroxisomal Protein Receptor PEROXIN 7. J. Biol. Chem., 288 (8), 6014-6023.
    PubMed
  • Nakano, R.T., Matsushima, R., Nagano, A.J., Fukao, Y., Fujiwara, M., Kondo, M., Nishimura, M., and Hara-Nishimura, I. (2012) ERMO3/MVP1/GOLD36 is involved in a cell type-specific mechanism for maintaining ER morphology in Arabidopsis thaliana. PLoS One, 7 (11), e49103.
    PubMed
  • Ido, K., Kakiuchi, S., Uno, C., Nishimura, T., Fukao, Y., Noguchi, T., Sato, F., and Ifuku, K. (2012) The conserved His144 in the PsbP protein is important for the interaction between the PsbP N-terminus and the Cyt B559 subunit of photosystem II. J. Biol. Chem., 287 (31), 26377-26387.
    PubMed
  • Nakasone, A., Fujiwara, M., Fukao, Y., Biswas, K.K., Kawai-Yamada, M., Narumi, I., Uchimiya, H., and Oono, Y. (2012) SMALL ACIDIC PROTEIN 1 acts with RUB modification components, the COP9 signalosome and AXR1, to regulate growth and development of Arabidopsis thaliana. Plant Physiol., 160 (1), 93-105
    PubMed
  • Henrichs, S., Wang, B., Fukao, Y., Zhu, J., Charrier, L., Bailly, A., Oehring, S.C., Linnert, M., Weiwad, M., Endler, A., Nanni, P., Pollmann, S., Mancuso, S., Schulz, A. and Geisler, M. (2012) Regulation of ABCB1/PGP1-catalysed auxin transport by linker phosphorylation. EMBO J., 31 (13), 2965-2980.
    PubMed
  • Peng, L., Fukao, Y., Fujiwara, M., and Shikanai, T. (2012) Multi-step Assembly of the Chloroplast NADH Dehydrogenase-Like Subcomplex A Requires Several Nucleus-encoded Proteins, Including CRR41 and CRR42, in Arabidopsis. Plant Cell, 24 (1), 202-214
    PubMed
  • Mano, S., Nakamori, C., Fukao, Y., Araki, M., Matsuda, A., Kondo, M., and Nishimura, M. (2011) The defect of peroxisomal membrane protein 38 causes enlargement of peroxisomes. Plant Cell Physiol. , 52 (12), 2157-2172.
    PubMed
  • Sato, T., Maekawa, S., Yasuda, S., Domeki, Y., Sueyoshi, K., Fujiwara, M., Fukao, Y., Goto, D.B., Yamaguchi, J. (2011) Identification of 14-3-3 proteins as a target of ATL31 ubiquitin ligase, a regulator of the C/N response in Arabidopsis. Plant J., 68 (1), 137-146.
    PubMed
  • Fukao, Y.*, and Ferjani, A. (2011) Dysfunction of V-ATPase under excess zinc mediates cell expansion compromise in Arabidopsis. Plant Signal. Behav., 6 (9), 1253-1255.
    PubMed
  • Yamamoto, H. Peng, L., Fukao, Y., and Shikanai, T. (2011) An Src homology 3 domain-like fold protein forms a ferredoxin-binding site for the chloroplast NADH dehydrogenase-like complex in Arabidopsis. Plant Cell, 23(4):1480-93
    PubMed
  • Peng, L., Fukao, Y., Myouga, F., Motohashi, R., Kazuo, S., and Shikanai, T. (2011) A Chaperonin Subunit with Unique Structures Is Essential for Folding of a Specific Substrate. PLoS Biol., 9(4):e1001040
    PubMed
  • Fukao, Y.*, Ferjani, A., Tomioka, R., Nagasaki, N., Kurata, R., Nishimori Y., Fujiwara, M., and Maeshima, M. (2011) iTRAQ Analysis Reveals Mechanisms of Growth Defects due to Excess Zinc in Arabidopsis. Plant Physiol., 155 (4), 1893-1907
    PubMed
  • Tamura, K., Fukao, Y., Iwamoto, M., Haraguchi, T., and Hara-Nishimura, I. (2010) Identification and characterization of nuclear pore complex components in Arabidopsis thaliana. Plant Cell, 22 (12), 4084-4097
    PubMed
  • Igawa, T., Fujiwara, M., Tanaka, I., Fukao, Y., and Yanagawa, Y. (2010) Characterization of bacterial-type phosphoenolpyruvate carboxylase expressed in male gametophyte of higher plants. BMC Plant Biol., 14 (10) 200
    PubMed
  • Okuda, T., Hammani, K., Tanz, S., Peng, L., Fukao, Y., Myouga, F., Motohashi, R., Shinozaki, K., Small, I., and Shikanai, T. (2010) The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts. Plant J., 61 (2), 339-349
    PubMed
  • Fukao, Y.*, Ferjani, A., Fujiwara, M., Nishimori Y., and Ohtsu, I. (2009) Identification of Zinc-Responsive Proteins in the Roots of Arabidopsis thaliana using a Highly Improved Method of Two-Dimensional Electrophoresis., Plant Cell Physiol., 50 (12), 2234-2239
    PubMed
  • Sato, A., Sato, Y., Fukao, Y., Fujiwara, M., Umezawa, T., Shinozaki, K., Hibi, T., Taniguchi, M., Miyake, H., Goto, D.B., and Uozumi, N. (2009) Threonine at position 306 of the KAT1 potassium channel is essential for channel activity and is a target site for ABA-activated SnRK2/OST1/SnRK2.6 protein kinase., Biochem J., 424 (3), 439-448
    PubMed
  • Peng, L., Fukao, Y., Fujiwara M., and Shikanai. T. (2009) Efficient operation of NAD(P)H dehydrogenase-dependent cyclic electron flow requires the supercomplex formation with photosystem I via minor LHCI in Arabidopsis. Plant Cell, 21 (11), 3623-3640
    PubMed
  • Fujiwara, M., Hamada, S., Hiratsuka, M., Fukao, Y., Kawasaki, T., and Shimamoto, K. (2009) Proteome analysis of detergent-resistant membranes (DRMs) associated with OsRac1-mediated innate immunity in rice. Plant Cell Physiol., 50 (7), 1191-1200
    PubMed
  • Igawa, T., Fujiwara, M., Takahashi, H., Sawasaki, H., Endo, Y., Seki, M., Shinozaki, K., Fukao, Y., and Yanagawa, Y. (2009) Isolation and identification of ubiquitin-related proteins from Arabidopsis seedlings. J. Exp. Bot., 60 (11), 3067-3073
    PubMed
  • Hamada, Y., Igarashi, H., Taguchi, R., Fujiwara, M., Fukao, Y., Shimmen, T., Yokota E., and Sonobe, S. (2009) The Putative RNA-Processing Protein, THO2, is a Microtubule-Associated Protein in Tobacco. Plant Cell Physiol.50 (4), 801-811
    PubMed
  • Minami, A., Fujiwara, M., Furuto A., Fukao, Y., Yamashita, T., Kamo, M., Kawamura, Y., and Uemura, M. (2009) Alterations in Detergent-Resistant Plasma Membrane Microdomains in Arabidopsis thaliana During Cold Acclimation. Plant Cell Physiol., 50 (2), 341-359
    PubMed
  • Shimada, T.L., Shimada, T., Takahashi, H., Fukao, Y., and Hara-Nishimura, I. (2008) A novel role for oleosins in freezing tolerance of oilseeds in Arabidopsis thaliana. Plant J., 55 (5), 798-809
    PubMed
  • Nagano, A.J., Fukao, Y., Fujiwara, M., Nishimura, M., and Hara-Nishimura, I. (2008) Antagonistic Jacalin-Related Lectins Regulate the Size of ER Body-Type β-Glucosidase Complexes in Arabidopsis thaliana. Plant Cell Physiol., 49 (6), 969-980
    PubMed
  • Yamada, K., Fukao, Y., Hayashi, M., Fukazawa, M., Suzuki, I., and Nishimura, M. (2007) Cytosolic HSP90 regulates the heat shock response that is responsible for heat acclimation in Arabidopsis thaliana. J. Biol. Chem., 282 (52), 37794-37804
    PubMed
  • Li, L., Shimada, T., Takahashi, H., Ueda, H., Fukao, Y., Kondo, M., Nishimura, M., and Hara-Nishimura, I. (2006) MAIGO2 is involved in exit of seed storage proteins from the endoplasmic reticulum in Arabidopsis thaliana. Plant Cell, 18 (12), 3535-3547
    PubMed
  • Santelia, D., Vincenzetti, V., Azzarello, E., Bovet, L., Fukao, Y., Duchtig, P., Mancuso, S., Martinoia, E., and Geisler, M. (2005) MDR-like ABC transporter AtPGP4 is involved in auxin-mediated lateral root and root hair development. FEBS Letter, 579 (24), 5399-5406
    PubMed
  • Matsushima, R., Fukao, Y., Nishimura, M., and Hara-Nishimura, I. (2004) NAI1 gene encodes a basic-helix-loop-helix-type putative transcription factor that regulates the formation of an endoplasmic reticulum-derived structure, the ER body. Plant Cell, 16 (6), 1536-1549.
    PubMed
  • Fukao, Y., Hayashi, M., Hara-Nishimura, I., and Nishimura, M. (2003) Novel glyoxysomal protein kinase, GPK1, identified by proteomic analysis of glyoxysomes in etiolated cotyledons of Arabidopsis thaliana (Rapid paper). Plant Cell Physiol., 44 (10), 1002-1012.
    PubMed
  • Fukao, Y., Hayashi, M., and Nishimura, M. (2002) Proteomic analysis of leaf peroxisomal proteins in greening cotyledons of Arabidopsis thaliana (Rapid paper). Plant Cell Physiol., 43 (7), 689-696.
    PubMed
  • Fukao, Y., Hayashi, Y., Mano, S., Hayashi, M., and Nishimura, M. (2001) Developmental analysis of a putative ATP/ADP carrier protein localized on glyoxysomal membranes during the peroxisome transition in pumpkin cotyledons. Plant Cell Physiol., 42 (8), 835-841.
    PubMed

Review

  • Fukao, Y.* (2012) Protein-Protein Interactions in Plants. Plant Cell Physiol., 53 (4), 617-625 PubMed

Book

  • Zargar, S.M., Kurata, R., Rakwal, R., and Fukao, Y.* (2015) Peptide separation methodologies for in-depth proteomics. Plant Cell Growth and Expansion - Methods and Protocols. Book Chapter, Edited by Jose M. Estevez, Springer., 1242, 195-209.
    PubMed
  • Zargar, S.M., Bhattacharjee, C., Rai, R., Fukao, Y., Agarwal, G.K., and Rakwal, R.(2014) Omics based approaches for improvement of common bean - Omics technologies and crops improvement - Book Chapter, Edited by Noureddine Benkeblia, pp. 271-302, CRC press
  • Arai, Y., Fukao, Y., Hayashi, M., and Nishimura, M. (2008) Plant proteomics: technologies, strategies, and applications. Edited by Agrawal, G.K., and Rakwal, R. pp.377-389. John Wiley & Sons, Inc., Hoboken, New Jersey.
  • 深尾　陽一朗、西村　幹夫 (2003) プロテオーム解析から見たペルオキシソーム代謝（総説）、蛋白質核酸酵素,　増刊号、45 (15 Suppl), 2176-2183.

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