Life of proteins: maturation, translocation, quality control in the cell

• Project/Area Number: 13053101
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: YOSHIDA Masasuke Tokyo Institute of Technology, 資源化学研究所, 教授 (90049073)
• Co-Investigator(Kenkyū-buntansha): ENDO Toshiya Nagoya University, Grad.Sch.Science, Professor (70152014) ; 永田 和宏 京都大学, 再生医科学研究所, 教授 (50127114) ; 小椋 光 熊本大学, 発生医学研究センター, 教授 (00158825) ; 森 和俊 京都大学, 理学研究科, 教授 (70182194) ; 三原 勝芳 九州大学, 医学研究院, 教授 (40029963)
• Project Period (FY): 2001 – 2007
• Project Status: Completed (Fiscal Year 2007)
• Budget Amount: ¥205,100,000 (Direct Cost: ¥205,100,000); Fiscal Year 2007: ¥3,000,000 (Direct Cost: ¥3,000,000); Fiscal Year 2006: ¥31,800,000 (Direct Cost: ¥31,800,000); Fiscal Year 2005: ¥34,000,000 (Direct Cost: ¥34,000,000); Fiscal Year 2004: ¥53,000,000 (Direct Cost: ¥53,000,000); Fiscal Year 2003: ¥40,100,000 (Direct Cost: ¥40,100,000); Fiscal Year 2002: ¥36,000,000 (Direct Cost: ¥36,000,000); Fiscal Year 2001: ¥7,200,000 (Direct Cost: ¥7,200,000)
• Keywords: molecular chperone / ER stress / translocation / prion / ERAD / lipoprobin / disulfidebond formation / ATP dependent protease / 蛋白質の膜透過 / プリオン / ERAD / 外膜リポタンパク質 / ジスルフィド形成 / ATP依存性プロテアーゼ / ストレス / シャペロン / 成熟 / 輸送 / 生物物理 / 蛋白質 / フォールディング / シャペロニン / タンパク質の膜透過

Research Abstract

2003-2007年度の5年にわたる特定領域研究「蛋白質の一生」の成果取りまとめを以下のように行った。まず、研究成果報告書(250ページ)を作成した。これは、計画班員(12名)と公募班員(115名)の全員が各自の成果を述べて発表論文と海外の国際学会で口頭発表(招待講演、あるいはこれに準じる講演)をリストし、巻頭には顕著な成果を概括した。これを見れば、各班員の成果の内容だけでなく、その国際的な注目度もはっきりとわかる。また「キーワード:蛋白質の一生」(08年5月、共立出版)を上梓した。成果についてお互いに検討評価批判し今後の発展を議論するために、2007年11月22日-23日、成果発表会を行った。班員88名が参加した。時間を十分にとって、計画班員が5年間め研究の総括と今後の研究の方向について発表し、議論した。ついで、班員全員がポスター発表を行った。この5年間の進歩と次の課題について参加者の意見がおおむね一致したことを述べる。小胞体関連のストレス応答の理解は大きく進んだが不要蛋白質の認識や分解などまだ未解明の重要問題が残されている。ミトコンドリアやゴルジ体のストレス応答が次の目標として認識される。細胞の蛋白質のSS結合の管理の理解も大幅に進んだが次の課題は全体像と機構(構造)の解明である。蛋白質の分泌の理解はますます詳細に理解されるようになった。次の課題はその分子的理解と残された機構未知の分泌系の解明である。シャペロンの分子機構の理解の前進は地味であった。既存の分子機構モデルを再検討して研究する必要がある。細胞生理における重要な蛋白質分解の機能や新規の分子が多く発見された。さらに探索を続ける価値がある。一般に、さらに構造を知ることは大事であり、また動態を追求する新しいメソッドが求められている。そしてすべての分野において、病気との関連の究明も課題となる。

Research Products

• [Journal Article] SecY alterations that impair membrane protein folding and generate a membrane stress. (2007)
  • Author(s): Shimohata, N., Nagamori, S., Akiyama, Y., Kaback, H.R., Ito, K.
  • Journal Title: J. Cell Biol. 176 Pages: 307-317
• [Journal Article] Crystal structure of the DsbB-DsbA complex reveals a mechanism of disulfide bond generation. (2006)
  • Author(s): Inaba, K., Murakami, S., Suzuki, M., Nakagawa, A., Yamashita, E., Okada, K., Ito, K.
  • Journal Title: Cell 127 Pages: 789-801
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structure of the Whole Cytosolic Region of ATP-Dependent Protease FtsH (2006)
  • Author(s): Suno R, Niwa H, Tsuchiya D, Zhang X, Yoshida M, Morikawa K.
  • Journal Title: Molecular Cell 22 Pages: 575-585
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structure of the Whole Cytosolic Region of ATP-Dependent Protease FtsH Molecular (2006)
  • Author(s): Suno R, Niwa H, Tsuchiya D, Zhang X, Yoshida M, Morikawa K.
  • Journal Title: Cell 22 Pages: 575-585
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of the whole cytosolic region of ATP-dependent protease FtsH (2006)
  • Author(s): Suno R, Niwa H, Tsuchiya D, Zhang X, Yoshida M, Morikawa K
  • Journal Title: Mol Cell. 22(5) Pages: 575-585
• [Journal Article] Identification of Tam41 maintaining integrity of the TIM23 protein translocator complex in mitochondria (2006)
  • Author(s): Y.Tamura, Y.Harada, K.Yamano, K.Watanabe, D.Ishikawa, C.Ohshima, S.Nishikawa, H.Yamamoto, T.Endo
  • Journal Title: J. Cell Biol. 174 Pages: 615-623
• [Journal Article] Derlin-2 and Derlin-3 are regulated by the mammalian unfolded protein response and are required for ER-associated degradation. (2006)
  • Author(s): Y.Oda, T.Okada, H.Yoshida, R.J.Kaufman, K.Nagata, K.Mori
  • Journal Title: J. Cell Biol. 172 Pages: 383-393
• [Journal Article] Cytosolic chaperonin prevents polyglutamine toxicity with altering the aggregation state. (2006)
  • Author(s): A.Kitamura, H.Kubota, C.Pack, G.Matsumoto, S.Hirayama, Y.Takahashi, H.Kimura, M.Kinjo, R.Morimoto, K.Nagata
  • Journal Title: Nature Cell Biol. 8(10) Pages: 1163-1169
  • NAID: 120005549596
• [Journal Article] Crytosolic chaperonin protects folding intermediates of Gβ from aggregation by recognizing hydrophobic β-strands (2006)
  • Author(s): S.Kubota, H.Kubota, K.Nagata
  • Journal Title: Proc. Natl. Acad. Sci. USA 103(22) Pages: 8360-8365
• [Journal Article] Leu-309 plays a critical role in the encapsulation of substrate protein into the internal cavity of GroEL (2006)
  • Author(s): Koike-Takeshita, A., Shimamura, T., Yokoyama, K., Yoshida, M., Taguchi, H.
  • Journal Title: J.Biol.Chem. 281 Pages: 962-967
• [Journal Article] An AAA protease FtsH can initiate proteolysis from internal sites of a model substrate, apo-flavodoxin (2006)
  • Author(s): Okuno, T., Yamanaka, K., Ogura, T.
  • Journal Title: Genes Cells 11(3) Pages: 261-268
• [Journal Article] Specific recognition of the collagen triple helix by chaperone HSP47 : minimal structural requirement and spatial molecular orientation. (2006)
  • Author(s): Koide, T., Asada, S., Takahara, Y., Nishikawa, Y., Nagata, K., Kitagawa, K.
  • Journal Title: J.Biol.Chem. 281(6) Pages: 3432-3438
• [Journal Article] pXBP1(U) encoded in XBP1 pre-mRNA negatively regulates unfolded protein response activator pXBP1(S) in mammalian ER stress response. (2006)
  • Author(s): Yoshida, H., Oku, M., Suzuki, M., Mori, K.
  • Journal Title: J.Cell Biol. 172(4) Pages: 565-575
• [Journal Article] Derlin-2 and Derlin-3 are regulated by the mammalian unfolded protein response and are required for ER-associated degradation. (2006)
  • Author(s): Oda, Y., Okada, T., Yoshida, H., Kaufman, R.J., Nagata, K., Mori, K.
  • Journal Title: J.Cell Biol. 172(3) Pages: 383-393
• [Journal Article] ATP-binding to NBD1 of the C1pB chaperone induces motion of the long coiled-coil, stabilizes the hexamer and activates NBD2 (2005)
  • Author(s): Watanabe, Y., Takano, M., Yoshida, M.
  • Journal Title: J.Biol.Chem. 280 Pages: 24562-24567
• [Journal Article] Comparison of the protein-unfolding pathways between mitochondrial protein import and atomic-force microscopy measurements. (2005)
  • Author(s): Sato, T., Esaki, M., Fernandez, J.M., Endo, T.
  • Journal Title: Proc.Natl.Acad.Sci.USA 102(50) Pages: 17999-18004
• [Journal Article] tRNA actively shuttles between the nucleus and cytosol in yeast (2005)
  • Author(s): Takano, A., Endo, T., Yoshihisa, T.
  • Journal Title: Science 309(5731) Pages: 140-142
• [Journal Article] The phosphate carrier has an ability to be sorted to either the TIM22 pathway or the TIM23 pathway for its import into yeast mitochondria (2005)
  • Author(s): Yamano, K., Ishikawa, D., Esaki, M., Endo, T.
  • Journal Title: J.Biol.Chem. 280(11) Pages: 10011-10017
• [Journal Article] Identification of a novel member of yeast mitochondrial Hsp70-associated motor and chaperone proteins that facilitates protein translocation across the inner membrane (2005)
  • Author(s): Yamamoto, H., Momose, T., Yatsukawa, Y., Ohshima, C., Ishikawa, D., Sato, T., Tamura,.Y., Ohwa, Y., Endo, T.
  • Journal Title: FEBS Lett. 579(2) Pages: 507-511
• [Journal Article] The maintenance of the endoplasmic reticulum network is regulated by p47, a cofactor of p97, through phosphorylation by cdc2 kinase. (2005)
  • Author(s): Kano, F., Kondo, H., Yamamoto, A., Tanaka, A.R., Hosokawa, N., Nagata, K., Murata, M.
  • Journal Title: Genes Cells 10(4) Pages: 333-344
• [Journal Article] A type I DnaJ homolog, DjA1, regulates androgen receptor signaling and spermatogenesis (2005)
  • Author(s): Terada, K., Yomogida, K., Imai, T., Kiyonari, H., Takeda, N., Kadomatsu, T., Yano, M., Aizawa, S., Mori, M.
  • Journal Title: EMBO J. 24 Pages: 611-622
• [Journal Article] GroEL Mediates Protein Folding with a Two Successive Timer Mechanism (2004)
  • Author(s): Ueno, T., Taguchi, H., Tadakuma, H., Yoshida, M., Funatsu, T
  • Journal Title: Mol.Cell 14 Pages: 423-434
• [Journal Article] Hsp 104 binds to yeast sup35 prion fiber but needs other factor(s) to sever it (2004)
  • Author(s): Yuji Inoue, Hideki Taguchi, Aiko Kishimoto, Masasuke Yoshida
  • Journal Title: J.Biol.Chem. 279 Pages: 52319-52323
• [Journal Article] Insufficient folding of type IV collagen and formation of abnormal basement membrane-like structure in embryoid bodies derived from HSP47-null ES cells. (2004)
  • Author(s): Y.MATSUOKA, H.KUBOTA, E.ADACHI, N.NAGAI, T.MARUTANI, N.HOSOKAWA, K.NAGATA
  • Journal Title: Mol.Biol.Cell. 15 Pages: 4467-4475
• [Journal Article] Accumulation of type IV collagen in dilated endoplasmic reticulum leads to apoptosis HSP47-knockout mouse embryos through the induction of CHOP. (2004)
  • Author(s): T.MARUTANI, A.YAMAMOTO, N.NAGAI, H.KUBOTA, K.NAGATA
  • Journal Title: J.Cell.Sci. 117 Pages: 5913-5922
• [Journal Article] Activation of mammalian unfolded protein response is compatible with the quality control system operating in the endoplasmic reticulum. (2004)
  • Author(s): S.Nadanaka, H.Yoshida, F.Kano, M.Murata, K.Mori
  • Journal Title: Mol.Biol.Cell 15 Pages: 2537-2548
• [Journal Article] XBP1 : a link between the unfolded protein response, lipid biosynthesis and biogenesis of the endoplasmic reticulum. (2004)
  • Author(s): R.Sriburi, S.Jackowski, K.Mori, J.W.Brewer
  • Journal Title: J.Cell Biol. 167 Pages: 35-41
• [Journal Article] Sorting of lipoproteins to the outer membrane in E.coli. (2004)
  • Author(s): Tokuda, H., Matsuyama, S.
  • Journal Title: BBA-Molecular Cell Research 1693 Pages: 5-13
• [Journal Article] Effects of lipoprotein overproduction on the induction of DegP (HtrA) involved in the quality control of Escherichia coli periplasm. (2004)
  • Author(s): Miyadai, H., Tanaka-Masuda, K., Matsuyama, S., Tokuda, H.
  • Journal Title: J.Biol.Chem. 279 Pages: 39807-39813
• [Journal Article] Translation arrest of SecM is essential for the basal and regulated expression of SecA. (2004)
  • Author(s): Murakami, A., Nakatogawa, K., Ito, K.
  • Journal Title: Proc.Natl.Acad.Sci.USA 101 Pages: 12330-12335
• [Journal Article] RseP (YaeL), an E.coli RIP protease, cleaves transmembrane sequences. (2004)
  • Author(s): Akiyama, Y., Kanehara, K., Ito, K.
  • Journal Title: EMBO J. 23 Pages: 4434-4442
• [Journal Article] Identification of a cysteineresidue important for the ATPase activity of C.elegans fidgetin homologue. (2004)
  • Author(s): Yakushiji, Y., Yamanaka, K., Ogura, T.
  • Journal Title: FEBS Lett. 578 Pages: 191-197
• [Journal Article] Analysis of the two p97/VCP/Cdc48p proteins of Caenorhabditis elegans and their suppression of polyglutamine-induced protein aggregation. (2004)
  • Author(s): Yamanaka, K., Okubo, Y., Suzaki, T., Ogura, T.
  • Journal Title: J.Struct.Biol. 146 Pages: 242-250
• [Journal Article] Mitochondrial import receptors Tom20 and Tom22 have chaperone-like activity (2004)
  • Author(s): Yano, M., Terada, K., Mori, M.
  • Journal Title: J.Biol.Chem. 279 Pages: 10808-10813
• [Journal Article] EDEM as an acceptor of terminally misfolded glycoproteins released from calnexin. (2003)
  • Author(s): Y. ODA, N. HOSOKAWA, I. WADA & K. NAGATA
  • Journal Title: Science 299(5611) Pages: 1394-1397
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] EDEM as an acceptor of terminally misfolded glycoproteins released from calnexin. (2003)
  • Author(s): Y. ODA, N. HOSOKAWA, I. WADA & K. NAGATA
  • Journal Title: Science 299 (5611) Pages: 1394-1397
  • Description: 「研究成果報告書概要(欧文)」より
• [Presentation] Import and sorting of mitochondrial proteins (2005)
  • Author(s): Toshiya Endo
  • Organizer: International Symposium on Membrane Dynamics and Cell Regulation
  • Place of Presentation: 福岡市
  • Year and Date: 2005-06-29
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] Import and sorting of mitochondrial proteins (2005)
  • Author(s): Toshiya Endo
  • Organizer: International Symposium on Membrane Dynamics and Cell Regulation
  • Place of Presentation: Fukuoka, JAPAN
  • Year and Date: 2005-06-29
  • Description: 「研究成果報告書概要(欧文)」より
• [Book] タンパク質の一生集中マスター (2007)
  • Author(s): 編集/遠藤斗志也, 森和俊, 田口英樹
  • Total Pages: 146
  • Publisher: 羊土社
• [Book] 蛋白質の一生 蛋白質拡散酵素増刊号 (2006)
  • Author(s): 監修代表 吉田 賢右
  • Total Pages: 1152
  • Publisher: 共立出版
  • Description: 「研究成果報告書概要(和文)」より
• [Book] of proteins (protein, nucleicacid and enzyme) (2004)
  • Author(s): M. Yoshida, et al.
  • Total Pages: 1152
  • Publisher: Kyoristu-shuppan
  • Description: 「研究成果報告書概要(欧文)」より
• [Remarks] 「研究成果報告書概要(和文)」より
  • URL: http://www.res.titech.ac.jp/~seibutu/lifeofproteins/
• [Publications] Lee, S., Sowa, M.E., Watanabe, Y., Sigler, P.B., Chiu, W., Yoshida, M., Tsai, F.T.F.: "The Structure of ClpB : A Molecular Chaperone that Rescues Proteins from an Aggregated State"Cell. 115. 229-240 (2003)
• [Publications] Kanehara, K., Ito, K., Akiyama, Y.: "YaeL proteolysis of RseA is controlled by the PDZ domain of YaeL and a Gln-rich region of RseA"EMBO J.. 22. 6389-6398 (2003)
• [Publications] S.Nishikawa et al.: "Nep98p is a component of the yeast spindle pole body and essential for nuclear division and fusion"J.Biol.Chem. 278. 9938-9943 (2003)
• [Publications] Yano, M. et al.: "Mitochondrial import receptors Tom20 and Tom22 have chaperone-like activity"J.Biol.Chem. (2004)
• [Publications] Higurashi, T., Hiragi, Y., Ichimura, K., Seki, Y., Soda, K., Mizobata, T., Kawata, Y.: "Structural Stability and Solution Structure of Chaperonin GroES Heptamer Studied by Synchrotron Small-Angle X-Ray Scattering"J.Mol.Biol.. 333(3). 605-620 (2003)
• [Publications] Motojima, F., Yoshida, M.: "Discrimination of ATP, ADP, and AMPPNP by Chaperonin GroEL : hwxokinase treatment revealed the exclusive role of ATP"J.Biol.Chem.. 2278. 26648-26654 (2003)
• [Publications] Y.Oda, N.Hosokawa, I.Wada, K.Nagata: "EDEM as an acceptor of terminally misfolded glycoproteins released from calnexin"Science. 299. 1394-1397 (2003)
• [Publications] H.Yamamoto, M.Esaki, T.Kanamori, Y.Tamura, S.Nishikawa, T.Endo: "Tim50 is a subunit of the TIM23 complex that links protein translocation across the outer and inner mitochondrial membranes"Cell. 111. 519-528 (2002)
• [Publications] Nakatogawa, H., Ito, K.: "The ribosomal exit tunnel functions as a discriminating gate"Cell. 108. 629-636 (2002)
• [Publications] Masuda, K., S.Matsuyama, H.Tokuda: "Elucidation of the function of lipoprotein-sorting signals that determine membrane localization"Proc.Natl.Acad.Sci.USA. 99. 7390-7395 (2002)
• [Publications] Krzywda, S., A.M.Brzozowski, C.Verma, K.Karata, T.Ogura, A.J.Wilkinson: "The crystal structure of the AAA domain of the-ATP-dependent protease FtsH of Escherichia coli at 1.5Å resolution"Structure. 10. 1073-1083 (2002)
• [Publications] Niwa, H.Tsuchiya, D.Makyio, H.Yoshida, M.Morikawa, K.: "Hexameric Ring Structure of the ATPase Domain of the Membrane-Integrated Metalloprotease FtsH from Thermus thermophilus HB8"Structure. 10. 1415-1423 (2002)
• [Publications] Inoue, Y.: "Strong Growth Polarity of Yeast Prion-Fiber Revealed by Single Fiber Imaging"J.Biol.Chem.. 276. 35227-35230 (2001)
• [Publications] Taguchi, H: "Single-molecule observation of protein-protein interactions in the chaperonin system"Nat.Biotechnol.. 19. 861-865 (2001)
• [Publications] Nishikawa, S.: "Molecular chaperones in the yeast ER maintain the solubility of proteins for retro-translocation and degradation"J.Cell.Biol. 153. 1061-1070 (2001)
• [Publications] Shiseki, K.: "Synchronized Domain Opening Motion of GroEL is Essential for Communication between the Two Rings"J.Biol.Chem.. 276. 11335-11338 (2001)
• [Publications] Nakatsukasa, K.: "Mnllp, an mannosidase-like protein in yeast, is required for ER-associated degradation of glycoproteins"J.Biol.Chem.. 276. 8635-8638 (2001)
• [Publications] Abe, Y.: "Structural basis of presequence recognition by the mitochondrial protein receptor Tom20"Cell. 100. 551-560 (2000)
• [Publications] 吉田 賢右(分担): "分子シャペロンによる細胞機能制御"シュプリンガー・フェアラーク東京. 219 (2001)