Comprehensive analysis of protein interactions for determination of protein function in rice

• Project/Area Number: 16380010
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Breeding science
• Research Institution: YOKOHAMA CITY UNIVERSITY
• Principal Investigator: HIRANO Hisashi YOKOHAMA CITY UNIVERSITY, International Graduate School of Arts and Sciences, Professor, 大学院国際総合科学研究科生体超分子科学専攻, 教授 (00275075)
• Co-Investigator(Kenkyū-buntansha): KAWASAKI Hiroshi YOKOHAMA CITY UNIVERSITY, International Graduate School of Arts and Sciences, Associate Professor, 国際総合科学研究科, 准教授 (70169704) ; SASSA Hidenori Chiba University, Department of Horticulture, Associate Professor, 園芸学部, 准教授 (50295507) ; TANGA Michifumi Toyo Kohan Co., Director, 部長
• Project Period (FY): 2004 – 2006
• Project Status: Completed (Fiscal Year 2006)
• Budget Amount: ¥15,900,000 (Direct Cost: ¥15,900,000); Fiscal Year 2006: ¥1,500,000 (Direct Cost: ¥1,500,000); Fiscal Year 2005: ¥3,000,000 (Direct Cost: ¥3,000,000); Fiscal Year 2004: ¥11,400,000 (Direct Cost: ¥11,400,000)
• Keywords: proteome / protein interaction / DLC plate / protein chip / glycoprotein / rice / soybean / プロテオーム / 蛋白質間相互作用 / タンデムアフィニティー精製

Research Abstract

Protein chip has been one of the most promising tools for identification of expressed proteins and study of protein-protein interaction in proteome analysis. We developed a novel protein chip plate, which is made of diamond-like carbon-coated stainless steel (DLC), and modified with N-hydroxysuccinimide ester on the surface of plate. Proteins separated by SDS gel electrophoresis or two-dimensional electrophoresis (2-DE) were successfully electroblotted and immobilized covalently onto the DLC plate to produce easily and rapidly a high-density protein chip. High blotting efficiency (25-70 %) of proteins from the gels onto the DLC plate was obtained by improvement of electrophoresis and electroblotting techniques. Using the DLC plate, we established the techniques for identification of proteins immobilized on the DLC plate, for detection of proteins or peptides interacted with proteins immobilized on the plate using matrix-assisted laser desorption ionization/time-of-flight mass spectrometry, and also we developed the technique for identification of post-translational modification of proteins on the plate. In this study, we applied these techniques to identification of a number of proteins and N-linked glycoproteins of the rice calli and soybean seeds, which were separated by 2-DE. The developed techniques have a great potential to make possible the high-throughput proteome analysis in plants.

Research Products

• [Journal Article] On-chip identification and interaction analysis of gel-resolved proteins using a diamond-like carbon-coated plate. (2007)
  • Author(s): Iwafune, Y., Tan, J.Z., Ino, Y., Okayama, A., Ishigaki, Y., Saito, K., Suzuki, N., Arima, M., Oba, M., Kamei, S., Tanga, M., Okada, T., Hirano, H.
  • Journal Title: J. Proteome Res. 6 Pages: 2315-2322
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Slocus F-box brothers : Multiple and pollen-specific F-box genes with S haplotype-specific polymorphisms in apple and Japanese pear. (2007)
  • Author(s): Sassa, H., Kakui, H., Miyamoto, M., Suzuki, Y., Hanada, T., Ushijima, K., Kusaba, M., Hirano, H., Koba, T.
  • Journal Title: Genetics 175 Pages: 1869-1881
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] On-chip identification and interaction analysis of gel-resolved proteins using a diamond-like carbon-coated plate. (2007)
  • Author(s): Iwafune, Y., Tan, J.Z.Ino, Y., Okayama, A., Ishigaki, Y, Saito, K., Suzuki, N., Arima, M., Oba, M., Kamei, S., Tanga, M., Okada, T., Hirano, H.
  • Journal Title: J.Proteome Res. 6 Pages: 2315-2322
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] S locus F-box brothers : Multiple and pollen-specific F-box genes with S haplotype-specific polymorphisms in apple and Japanese pear. (2007)
  • Author(s): Sassa, H., Kakui, H., Miyamoto, M., Suzuki, Y, Hanada, T., Ushijima, K., Kusaba, M., Hirano, H., Koba, T.
  • Journal Title: Genetics 175 Pages: 1869-1881
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] On-chip identification and interaction analysis for gel-resolved proteins by mass spectrometry (2007)
  • Author(s): Iwafune Y, Tan J-Z, Ino Y, Okayama A, Ishigaki S, Saito K, Suzuki N, Arima M, Oba M, et al.
  • Journal Title: J. Proteome Res. (in press)
• [Journal Article] プロテインチップを用いた蛋白質間相互作用分析 (2006)
  • Author(s): 荒川憲昭, 岩船裕子, 平野 久
  • Journal Title: 臨床検査 50 Pages: 1467-1476
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] The analysis of N-glycolilneuraminic acid (NeuGc) of hepatoma tissue and K562 cell ferritins using HPLC and mass spectrometry. (2006)
  • Author(s): Asakawa, H., Sasabe, M., Miyazaki, R., Matsuda, H., Fukai, F., Hanada, K., Hirano, H., Takasaki, S.
  • Journal Title: Proc. Japan Acad. Sci. Ser. B, 82 Pages: 181-187
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Efficient electroblotting of gel-resolved proteins onto diamond-like carbon-coated plate for protein-chip. (2006)
  • Author(s): Ino, Y., Okayama, A., Iwafune, Y., Arakawa, N., Kikuchi, J., Kamita, M., Kawasaki, H., Okada, T., Hirano, H.
  • Journal Title: J. Electrophoresis 53 Pages: 33-37
  • NAID: 10018441577
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Proteomic search for potential diagnostic markers and therapeutic targets for ovarian clear cell adenocarcinoma. (2006)
  • Author(s): Morita, A., Miyagi, E., Yasumitsu, E., Kawasaki, H., Hirano, H., Hirahara, F.
  • Journal Title: Proteomics 6 Pages: 5880-5890
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Identification of a new class of pistil-specific proteins of Petunia inflata that is structurally similar to, but functionally distinct from, the self-incompatibility factor HT. (2006)
  • Author(s): Sassa, H., Hirano, H.
  • Journal Title: Mol Genet. Genomics 275 Pages: 97-104
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] A novel approach and protocol for discovering extremely low-abundance proteins in serum. (2006)
  • Author(s): Tanaka, Y., Akiyama.H., Kuroda.T., Jung, G., Tanahashi, K., Sugaya, H., Utsumi, J., Kawasaki, H., Hirano, H.
  • Journal Title: Proteomics 6 Pages: 4845-4855
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Identification of yeast aspartyl aminopeptidase gene by purifying and characterizing its product from yeast cells. (2006)
  • Author(s): Yokoyama, R., Kawasaki, H., Hirano, H.
  • Journal Title: FEBS J. 2173 Pages: 192-198
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] 4-kDa peptide. (2006)
  • Author(s): Hirano, H
  • Journal Title: Handbook of Biological Active Peptides (Kastin, A.J. ed.)(Academic Press, London) Pages: 1-4
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The analysis of N-glycolilneuraminic acid (NeuGc) of hepatoma tissue and K562 cell ferritins using HPLC and mass spectrometry. (2006)
  • Author(s): Asakawa, H., Sasabe, M., Miyazaki, R., Matsuda, H., Fukai, F., Hanada, K., Hirano, H., Takasaki, S.
  • Journal Title: Proc.Japan Acad.Sci.Ser.B 82 Pages: 181-187
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Efficient electroblotting of gel-resolved proteins onto diamond-like carbon-coated plate for protein-chip. (2006)
  • Author(s): Ino, Y., Okayama, A., Iwafune, Y, Arakawa, N., Kikuchi, J., Kamita, M., Kawasaki, H., Okada, T., Hirano, H.
  • Journal Title: J.Electrophoresis 53 Pages: 33-37
  • NAID: 10018441577
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Proteomic search for potential diagnostic markers and therapeutic targets for ovarian clear cell adenocarcinoma. (2006)
  • Author(s): Morita, A.Miyagi, E., Yasumitsu, E., Kawasaki, H., Hirano, H., Hirahara, F.
  • Journal Title: Proteomics 6 Pages: 5880-5890
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Identification of a new class of pistil-specific proteins of Petunia inflata that is structurally similar to, but functionally distinct from, the self-incompatibility factor HT. (2006)
  • Author(s): Sassa, H., Hirano, H.
  • Journal Title: Mol Genet.Genomics. 275 Pages: 97-104
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A novel approach and protocol for discovering extremely low-abundance proteins in serum. (2006)
  • Author(s): Tanaka, Y, Akiyama.H., Kuroda.T., Jung, G, Tanahashi, K., Sugaya, H., Utsumi, J., Kawasaki, H., Hirano, H.
  • Journal Title: Proteomics 6 Pages: 4845-4855
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] S locus F-box brothers : Multiple and pollen-specific F-box genes with S haplotype-specific polymorphisms in apple and Japanese pear (2006)
  • Author(s): Sassa H, Kakui H, Miyamoto M, Suzuki Y, Hanada T, Ushijima K, KusabaM, Hirano H, Koba T
  • Journal Title: Genetics 175 Pages: 1869-1881
• [Journal Article] The analysis of N-glycolilneuraminicacid(NeuGc)ofhepatoma tissue and K562 cell ferritinsusingHPLCandmassspectrometry. (2006)
  • Author(s): Asakawa H, Sasabe M, Miyazaki R, Matsuda H, Fukai F, Hanada K, Hirano H, Takasaki S
  • Journal Title: Proc. Japan Cad. Ser. B 82 Pages: 181-187
• [Journal Article] Efficient electroblotting of gel-resolved proteins onto diamond-like carbon-coated plate for protein-chip. (2006)
  • Author(s): Ino Y, Okayama A, Iwafune Y, Arakawa N, Kikuchi J, Kamita M, Kawasaki H, Okada T, Hirano H
  • Journal Title: J. Electrophoresis 53 53 Pages: 33-37
  • NAID: 10018441577
• [Journal Article] Proteomic search for potential diagnostic markers and therapeutic targets for ovarian clear cell adenocarcinoma. (2006)
  • Author(s): Morita A, Miyagi E, Yasumitsu E, Kawasaki H, Hirano H, Hirahara F
  • Journal Title: Proteomics 6 Pages: 5880-5890
• [Journal Article] A novel approach and protocol for discovering extremely low-abundance proteins in serum. (2006)
  • Author(s): Tanaka Y, Akiyama H, Kuroda T, Jung G, Tanahashi K, Sugaya H, Utsumi J, Kawasaki H, Hirano
  • Journal Title: Proteomics 6 Pages: 4845-4855
• [Journal Article] プロテオミクスでみえてくる翻訳後修飾の機能 (2005)
  • Author(s): 川崎博史, 平野 久
  • Journal Title: 実験医学 Pages: 1043-1049
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] プロテオーム解析概論 (2005)
  • Author(s): 平野 久
  • Journal Title: ぶんせき 7 Pages: 348-353
  • NAID: 10016578205
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] プロテオミクスでみえてくる翻訳後修飾の機能,プロテアソームを例として (2005)
  • Author(s): 川崎博史, 平野 久
  • Journal Title: 実験医学 23 Pages: 1043-1049
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] The role of glycosylation in the function of a 48-kDa glycoprotein from carrot. Biochem. Biophys. Res. (2005)
  • Author(s): Shang, C, Sassa, H., Hirano, H.
  • Journal Title: Commun 328 Pages: 144-149
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] The role of glycosylation in the function of a 48-kDa glycoprotein from carrot. Biochem. Biophys. (2005)
  • Author(s): Shang, C., Sassa, H., Hirano, H.
  • Journal Title: Res.Commun. 328 Pages: 144-149
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Identification of yeast aspartyl aminopeptidase gene by purifying and characterizing its product from yeast cells. (2005)
  • Author(s): Yokoyama, R., Kawasaki, H., Hirano, H.
  • Journal Title: FEBS J. 2173 Pages: 144-149
• [Journal Article] プロテオーム解析技術,現状と課題 (2005)
  • Author(s): 平野 久
  • Journal Title: 遺伝子医学MOOK2 疾患プロテオミクスの最前線 Pages: 44-51
• [Journal Article] 二次元電気泳動とプロテオミクス (2004)
  • Author(s): 平野 久
  • Journal Title: 生化学 76 Pages: 1320-1327
  • NAID: 10013732819
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] トップダウンプロテオミクス (2004)
  • Author(s): 平野 久
  • Journal Title: BIO Clinica 19 Pages: 1154-1158
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] インタラクトミクス : タンパク質間相互作用のプロテオミクス (2004)
  • Author(s): 平野 久
  • Journal Title: バイオサイエンスとインダストリー 62 Pages: 732-736
  • NAID: 10014018655
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Technical aspects of functional proteomics in plants. (2004)
  • Author(s): Hirano, H., Islam, N., Kawasaki, H.
  • Journal Title: Phytochemistry 65 Pages: 1487-1498
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] 2次元電気泳動を基礎としたプロテオーム解析システム (2004)
  • Author(s): 木村弥生, 平野 久
  • Journal Title: 蛋白質 核酸 酵素 49 Pages: 1866-1870
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Interaction of a 43-kDa receptor-like protein with a 4-kDa hormone-like peptide in soybean. (2004)
  • Author(s): Hanada, K., Hirano, H.
  • Journal Title: Biochemistry 43 Pages: 12105-12112
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Protein extraction from mature rice leaves for two-dimensional gel electrophoresis and its application in proteome analysis. (2004)
  • Author(s): Islam, N., Lonsdale, M., Upadhyaya, N.M., Higgins, T.J., Hirano, H., Akhurst, R.
  • Journal Title: Proteomics 4 Pages: 1903-1908
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Identification of three phosphorylation sites of alpha 7 subunit in yeast 20S proteasome in vivo using mass spectrometry. (2004)
  • Author(s): Iwafune, Y., Kawasaki, H., Hirano, H.
  • Journal Title: Arch. Biochem. Biophys. 431 Pages: 9-15
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Changes of protein profiles during pollen development in Lilium longiflorum. (2004)
  • Author(s): Miki-Hiroshige, H., Yamanaka, Y., Nakamura, S., Kurata, S., Hirano, H.
  • Journal Title: Sex Plant Reprod. 16 Pages: 209-214
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Mass spectrometric analysis of posttranslational modifications of a carrot extracellular glycoprotein. (2004)
  • Author(s): Shang, C., Shibahara, T., Hanada, K., Iwafune, Y., Hirano, H.
  • Journal Title: Biochemistry 43 Pages: 6281-6292
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Mass spectrometric analysis of expression of ATPase subunits encoded by duplicated genes in the 19S regulatory particle of rice 26S proteasome. (2004)
  • Author(s): Shibahara, T., Kawasaki, H., Hirano, H.
  • Journal Title: Arch. Biochem. Biophys. 421 Pages: 34-41
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Analyses of wheat seed proteome : exploring protein-protein interactions by manipulating genome composition. (2004)
  • Author(s): Islam, N., Hirano, H.
  • Journal Title: Proteome and Protein Analysis (Kamp, R.M., Calvete, J. and Choli-Papadopoulou, T. eds.)(Springer-Verlag, Berlin) Pages: 49-66
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Technical aspects of functional proteomics in plants. (2004)
  • Author(s): Hirano, H., Islam, N., Kawasaki, H.
  • Journal Title: Phytochemistry. 65 Pages: 1487-1498
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Identification of three phosphorylation sites of alpha 7 subunit in yeast 20S proteasome in vivo using mass spectrometry. (2004)
  • Author(s): Iwafune, Y., Kawasaki, H., Hirano, H.
  • Journal Title: Arch.Biochem.Biophys. 431 Pages: 9-15
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Changes of protein profiles during pollen development in Lilium longiflorum. (2004)
  • Author(s): Miki-Hiroshige, H., Yamanaka, Y, Nakamura, S., Kurata, S., Hirano, H.
  • Journal Title: Sex Plant Reprod. 16 Pages: 209-214
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Mass spectrometric analysis of expression of ATPase subunits encoded by duplicated genes in the 19S regulatory particle of rice 26S proteasome. (2004)
  • Author(s): Shibahara, T., Kawasaki, H., Hirano, H.
  • Journal Title: Arch.Biochem.Biophys. 421 Pages: 34-41
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] 2次元電気泳動を基礎としたプロテオーム解析システム (2004)
  • Author(s): 木村弥生, 平野 久
  • Journal Title: 蛋白質核酸酵素 49 Pages: 1866-1870
• [Book] Academic Press, London (Kastin, A. J. ed.) (2006)
  • Author(s): Hirano, H.
  • Total Pages: 4
  • Publisher: 4-kDa peptide. In : Handbook of Biological Active Peptides
  • Description: 「研究成果報告書概要(和文)」より
• [Book] プロテインチップと医療応用 バイオ解析・診断技術のテーラーメイド医療への応用,(山本重夫監修) (2006)
  • Author(s): 岩船裕子, 平野 久
  • Total Pages: 10
  • Publisher: シーエムシー出版
  • Description: 「研究成果報告書概要(和文)」より
• [Book] 4-kDa peptide. In : Handbook of Biological Active Peptide (2006)
  • Author(s): Hirano, H.
  • Publisher: Academic Press, London
• [Book] プロテインチップと医療応用,バイオ解析・診断技術のテーラーメイド医療への応用 (2006)
  • Author(s): 岩船裕子, 平野 久
  • Publisher: シーエムシー出版,東京
• [Book] タンパク質研究なるほどQ＆A (2005)
  • Author(s): 戸田年総, 平野 久, 中村和行 編著
  • Total Pages: 1
  • Publisher: 羊土社
  • Description: 「研究成果報告書概要(和文)」より
• [Book] 植物医学事典(日本育種学会編) (2005)
  • Author(s): 平野 久
  • Total Pages: 1
  • Publisher: 培風館
  • Description: 「研究成果報告書概要(和文)」より
• [Book] プロテオーム解析技術,現状と課題 遺伝子医学MOOK2疾患プロテオミクスの最前線(戸田年総・荒木令江編) (2005)
  • Author(s): 平野 久
  • Total Pages: 8
  • Publisher: メヂカルドゥ
  • Description: 「研究成果報告書概要(和文)」より
• [Book] 最新疾患プロテオミクス研究の現状と展望,先端ラボ報告,横浜市立大学 遺伝子医学MOOK2疾患プロテオミクスの最前線(戸田年総・荒木令江編) (2005)
  • Author(s): 平野 久
  • Total Pages: 3
  • Publisher: メヂカルドゥ
  • Description: 「研究成果報告書概要(和文)」より
• [Book] タンパク質研究なるほどQ&A (2005)
  • Author(s): 戸田年総(平野 久, 中村和行)
  • Total Pages: 288
  • Publisher: 羊土社
• [Book] 一次構造決定 ゲノミクス・プロテオミクスの新展開(今中忠行監修) (2004)
  • Author(s): 平野 久, 岩船裕子
  • Publisher: エヌ・ティー・エス
  • Description: 「研究成果報告書概要(和文)」より
• [Book] Analyses of wheat seed proteome : exploring protein-protein interactions by manipulating genome composition. (2004)
  • Author(s): Islam, N., Hirano, H.
  • Total Pages: 18
  • Publisher: Springer-Verlag, Berlin
  • Description: 「研究成果報告書概要(和文)」より
• [Book] プロテアソームの翻訳後修飾の解析 ゲノミクス・プロテオミクスの新展開,(今中忠行監修) (2004)
  • Author(s): 岩船裕子, 平野 久
  • Total Pages: 6
  • Publisher: エヌ・ティー・エス
  • Description: 「研究成果報告書概要(和文)」より
• [Book] 試料前処理法 ゲノミクス・プロテオミクスの新展開,(今中忠行監修) (2004)
  • Author(s): 川崎博史, 平野 久
  • Total Pages: 5
  • Publisher: エヌ・ティー・エス
  • Description: 「研究成果報告書概要(和文)」より
• [Book] Proteome and Protein Analysis (2004)
  • Author(s): Islam, N., Hirano, H.
  • Publisher: Springer-Verlag
• [Patent(Industrial Property Rights)] 電気泳動ゲル膜処理装置 (2006)
  • Inventor(s): 平野久, 岡田毅, 三島圭太
  • Industrial Property Rights Holder: 横浜市立大学, SUS株式会社
  • Industrial Property Number: 2006-012599
  • Filing Date: 2006-01-20
  • Description: 「研究成果報告書概要(和文)」より
• [Patent(Industrial Property Rights)] 固体支持体及び該固体支持体上に複数の物質又は複合体を脱離/イオン化することにより質量分析する方法 (2004)
  • Inventor(s): 大場光芳, 山野博文, 亀井修一, 平野久
  • Industrial Property Rights Holder: 東洋鋼飯株式会社
  • Industrial Property Number: 2004-046881
  • Filing Date: 2004-02-23
  • Description: 「研究成果報告書概要(和文)」より
• [Patent(Industrial Property Rights)] 固体支持体上の生体分子を質量分析する方法およびそのための固体支持体 (2004)
  • Inventor(s): 大場光芳, 山野博文, 亀井修一, 平野久, 岩船裕子
  • Industrial Property Rights Holder: 東洋鋼鈑株式会社, 平野久, 財団法人木原記念横浜生命科学振興財団
  • Industrial Property Number: 2004-364934
  • Filing Date: 2004-12-16
  • Description: 「研究成果報告書概要(和文)」より