Reconstitution of prions and protein folding

2011 Fiscal Year Final Research Report

• Project Area: Protein community: organization and maintenance of protein functions
• Project/Area Number: 19058002
• 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 (2009-2011); The University of Tokyo (2007-2008)
• Principal Investigator: TAGUCHI Hideki 東京工業大学, 大学院・生命理工学研究科, 教授 (40272710)
• Co-Investigator(Kenkyū-buntansha): KOIKE Ayumi 神奈川工科大学, 応用バイオ科学部, 教授 (20454176)
• Project Period (FY): 2007 – 2011
• Keywords: タンパク質 / フォールディング / シャペロン / 酵母プリオン

Research Abstract

Protein must fold into unique tertiary structure to achieve its function. However, the folding often competes with intermolecular aggregation, which usually spoils the protein function. Protein aggregates include prions and amyloids, both of which cause fatal neurodegenerative diseases. We investigated following topics; 1) comprehensive aggregation analysis of more than 3,000 Escherichia coli proteins by using a reconstituted chaperone-free translation system, ii) global analysis of chaperone effects, iii) identification of in vivo chaperonin substrates, and iv) in vivo structure and dynamics of yeast prions.

Research Products

• [Journal Article] Biomolecular Robotics for Chemomechanically Driven Guest Delivery Fueled by Intracellular ATP (2013)
  • Author(s): Biswas, S., Kinbara, K., Niwa, T., Taguchi, H., Ishii, N., Watanabe, S., Miyata, K., Kataoka, K., Aida, T.
  • Journal Title: Nature Chemistry Volume: (published online)
  • Peer Reviewed
• [Journal Article] Nano-scale alignment of proteins on a flexible DNA back-bone (2012)
  • Author(s): Nojima, T., Konno, H., Kodera, N., Seio, K., Taguchi, H. and Yoshida, M
  • Journal Title: PLoS One Volume: 7 Pages: e52534
  • Peer Reviewed
• [Journal Article] Flexibility of GroES mobile loop is required for efficient chaperonin function (2012)
  • Author(s): Nojima, T., Ikegami, T., Taguchi, H. and Yoshida, M.
  • Journal Title: J. Mol. Biol Volume: 422 Pages: 291-299
  • Peer Reviewed
• [Journal Article] Global Analysis of Chaperone Effects Using a Reconstituted Cell-Free Translation System (2012)
  • Author(s): Niwa, T., Kanamori T., Ueda, T., Taguchi, H.
  • Journal Title: Proc. Natl. Acad. Sci. U.S.A Volume: 109 Pages: 8937-8942
  • Peer Reviewed
• [Journal Article] Mechanism of methionine synthase overexpression in chaperonin-depleted Escherichia coli (2012)
  • Author(s): Fujiwara K, Taguchi, H
  • Journal Title: Microbiology Volume: 158 Pages: 917-924
  • Peer Reviewed
• [Journal Article] Difference in the distribution pattern of substrate enzymes in the metabolic network of Escherichia coli, according to chaperonin requirement (2011)
  • Author(s): Takemoto K, Niwa T, Taguchi, H
  • Journal Title: BMC Syst Biol Volume: 5 Pages: 98
  • Peer Reviewed
• [Journal Article] Amphiphilic Polysaccharide Nanogels as Artificial Chaperones in Cell-Free Protein Synthesis (2011)
  • Author(s): Sasaki, Y, Asayama, W., Niwa, T., Sawada, S., Ueda, T., Taguchi, H., Akiyoshi, K.
  • Journal Title: Macromol. Biosci Volume: 11 Pages: 814-820
  • Peer Reviewed
• [Journal Article] Yeast prion protein New1 can break Sup35 amyloid fibrils into fragments in an ATP-dependent manner (2011)
  • Author(s): Inoue, Y., Kawai-Noma, S., Koike-Takeshita, A., Taguchi, H. and Yoshida, M.
  • Journal Title: Genes to Cells Volume: 16 Pages: 545-556
  • Peer Reviewed
• [Journal Article] Single-particle tracking of quantum dot-conjugated prion proteins inside yeast cells (2011)
  • Author(s): Tsuji, T., Kawai-Noma, S., Pack, C-G., Terajima, H., Yajima, J., Nishizaka, T., Kinjo, M. & Taguchi, H.
  • Journal Title: Biochem. Biophys. Res. Commun Volume: 405 Pages: 638-643
  • Peer Reviewed
• [Journal Article] Single molecule imaging of the trans-translation entry process via anchoring of the tagged ribosome (2011)
  • Author(s): Zhou, Z-P., Shimizu, Y., Tadakuma, H., Taguchi, H., Ito, K. and Ueda, T
  • Journal Title: J. Biochem Volume: 149 Pages: 609-618
  • Peer Reviewed
• [Journal Article] A. In vivo evidence for the fibrillar structures of Sup35 prions in yeast cells (2010)
  • Author(s): Kawai-Noma, S., Pack, C-G., Kojidani, T., Asakawa, H., Hiraoka, Y., Kinjo, M., Haraguchi, T., Taguchi, H., and Hirata
  • Journal Title: J. Cell Biol Volume: 190 Pages: 223-231
  • Peer Reviewed
• [Journal Article] A systematic survey of in vivo obligate chaperonin-dependent substrates (2010)
  • Author(s): Fujiwara, K., Ishihama, Y., Nakahigashi, K., Soga, T. and Taguchi, H.
  • Journal Title: EMBO J Volume: 29 Pages: 1552-1564
  • Peer Reviewed
• [Journal Article] Diffuse oligomer-based transmission of yeast prions. (Review) (2010)
  • Author(s): Taguchi, H. and Kawai-Noma, S
  • Journal Title: FEBS J Volume: 277 Pages: 1359-1368
  • Peer Reviewed
• [Journal Article] D-loop of actin differently regulates the motor function of myosins II And V (2009)
  • Author(s): Kubota, H., Mikhailenko, S. V., Okabe, H., Taguchi, H., and Ishiwata, S.
  • Journal Title: J. Biol. Chem Volume: 284 Pages: 35251-35258
  • Peer Reviewed
• [Journal Article] Single mother-daughter pair analysis to analyze the diffusion properties of yeast prion Sup35 in guanidine-HCl treated [PSI+] cells (2009)
  • Author(s): Kawai-Noma, S., Pack, C-G., Tsuji, T., Kinjo, M., Taguchi, H.
  • Journal Title: Genes to Cells Volume: 14 Pages: 1045-1054
  • Peer Reviewed
• [Journal Article] A tubular biocontainer: Metal ion-induced 1D assembly of a molecularly engineered chaperonin (2009)
  • Author(s): Biswas, S., Kinbara, K., Oya, N., Ishii, N., Taguchi, H., Aida, T.
  • Journal Title: J. Am. Chem. Soc Volume: 131 Pages: 7556-7557
  • Peer Reviewed
• [Journal Article] Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins (2009)
  • Author(s): Niwa, T., Ying, B.-W., Saito, K., Jin, W. Z., Takada, S., Ueda, T. Taguchi, H.
  • Journal Title: Proc. Natl. Acad. Sci. U.S.A. Volume: 106 Pages: 4201-4206
  • Peer Reviewed
• [Journal Article] Cryo-EM structure of the native GroEL-GroES complex from Thermus thermophilus encapsulating substrate inside the cavity (2009)
  • Author(s): Kanno, R., Koike-Takeshita, A., Yokoyama, K., Taguchi, H., Mitsuoka, K.
  • Journal Title: Structure Volume: 17 Pages: 287-293
  • Peer Reviewed
• [Journal Article] Kinetic analysis of conformational changes of GroEL based on the fluorescence of tyrosine 506 (2008)
  • Author(s): Hosono, K., Ueno, T., Taguchi, H., Motojima, F., Zako, T., Yoshida, M., Funatsu, T.
  • Journal Title: Protein J Volume: 27 Pages: 461-468
  • Peer Reviewed
• [Journal Article] Revisiting the GroEL-GroES reaction cycle via the symmetrical intermediate implied by novel aspects of the GroEL (D398A) mutant (2008)
  • Author(s): Koike-Takeshita, A., Yoshida, M., Taguchi, H.
  • Journal Title: J. Biol. Chem Volume: 283 Pages: 23774-23781
  • Peer Reviewed
• [Journal Article] Single molecule imaging of full protein synthesis by immobilized ribosomes (2008)
  • Author(s): Uemura, S., Iizuka, R., Ueno, T., Shimizu, Y., Taguchi, H., Ueda, T., Puglisi, J., Funatsu, T.
  • Journal Title: Nucleic Acids Research Volume: 36 Pages: e70
  • Peer Reviewed
• [Journal Article] Comparison of refolding activities between nanogel artificial chaperone and GroEL systems (2008)
  • Author(s): Asayama, W., Sawada, S., Taguchi, H., Akiyoshi, K.
  • Journal Title: Int. J. Biol. Macromol Volume: 42 Pages: 241-246
  • Peer Reviewed
• [Presentation] In vivo structure and dynamics of yeast prion protein (2013)
  • Author(s): Hideki Taguchi
  • Organizer: SPIE 2013: Nano-Bio Sensing, Imaging & Spectroscopy
  • Place of Presentation: Jeju-do, Korea
  • Year and Date: 20130220-22
• [Presentation] Global analyses of protein aggregation and chaperone effects (2012)
  • Author(s): Hideki Taguchi
  • Organizer: SFB 3rd International symposium "Molecular Machines in Protein Folding and Protein Transport"
  • Place of Presentation: Munich, Germany
  • Year and Date: 20120723-25
• [Presentation] Global analysis of chaperone action using a reconstituted cell-free translation system (2011)
  • Author(s): Hideki Taguchi
  • Organizer: EMBO Conference "The Biology of Molecular Chaperones"
  • Place of Presentation: Grundlsee, Austria
  • Year and Date: 20110519-24
• [Presentation] A systematic survey of in vivo obligate chaperonin GroE-dependent substrates (2010)
  • Author(s): Hideki Taguchi
  • Organizer: 3rd International Symposium on Protein Society
  • Place of Presentation: ホテル日航奈良、奈良
  • Year and Date: 20100913-16
• [Presentation] A comprehensive survey of in vivo obligate GroEL/ES substrates (2009)
  • Author(s): Hideki Taguchi
  • Organizer: 4th International Congress on Stress Responses in Biology and Medicine, Symposium "From chaperones to Translocators"
  • Place of Presentation: 札幌
  • Year and Date: 20091006-09
• [Presentation] Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins (2009)
  • Author(s): Hideki Taguchi
  • Organizer: EMBO Conference "The Biology of Molecular Chaperones"
  • Place of Presentation: Dubrovnik, Croatia
  • Year and Date: 20090523-26
• [Presentation] Mechanism of yeast prion propagation revealed by direct observation of prion protein dynamics (2009)
  • Author(s): Hideki Taguchi
  • Organizer: International Conference "Protein Folding and Neurodegenerative Diseases"
  • Place of Presentation: 平安会館、京都
  • Year and Date: 20090406-07
• [Presentation] Direct observation of yeast prion dynamics in single-living cells (2008)
  • Author(s): Hideki Taguchi
  • Organizer: 2nd Pacific Rim International Conference on Protein Science
  • Place of Presentation: Cairns convention centre, Cairns, Australia
  • Year and Date: 20080622-26
• [Presentation] Direct observation of yeast prion Sup35 dynamics in single-living cells (2008)
  • Author(s): Hideki Taguchi
  • Organizer: Cold Spring Harbor Laboratory meeting on Molecular Chaperones and Stress Responses
  • Place of Presentation: Cold Spring Harbor Laboratory, New York, USA
  • Year and Date: 20080430-0504
• [Book] キーワード:蛋白質の一生 (2008)
  • Author(s): 編集・遠藤斗志也、小椋光、永田和宏、森 和俊、田口 英樹、吉田 賢右
  • Publisher: 共立出版
• [Remarks] 大腸菌蛋白質可溶性データベース:eSol
  • URL: http://www.tanpaku.org/tp-esol
• [Remarks] 田口研究室ウェブサイト
  • URL: http://www.taguchi.bio.titech.ac.jp
• [Remarks] 田口英樹の補足情報
  • URL: http://taguchi-hideki.blogspot.jp