2006 Fiscal Year Final Research Report Summary
Structural and functional study of translation apparatus from the viewpoint of molecular mimicry and prion transmission
Project/Area Number |
14035207
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Research Category |
Grant-in-Aid for Scientific Research on Priority Areas
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Allocation Type | Single-year Grants |
Review Section |
Biological Sciences
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Research Institution | The University of Tokyo |
Principal Investigator |
NAKAMURA Yoshikazu The University of Tokyo, Institute of Medical Science, Professor (40114590)
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Project Period (FY) |
2002 – 2006
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Keywords | molecular mimicry / translation termination / release factor / peptide anticodon / stop codon / ribosome recycling factor / yeast prion / ribosome |
Research Abstract |
Recent molecular and structural studies including those from this laboratory have revealed that proteins called translation factors mimic the shape of tRNA. One of them, a polypeptide release factor (RF), encodes a tripeptide that serves as an ‘anticodon' to decipher stop codons in mRNA. These findings let us to propose the novel concept of macromolecular mimicry between protein and RNA. Moreover, The [PSI^+] element of budding yeast represents the prion conformation of translation release factor eRF3 that is propagated and transmitted in the cytoplasm. On many levels, yeast prions are analogous to mammalian prions and much interest lies in understanding how prions are able to generate variation in isogenic strains. We have investigated RFs and ribosome-recycling-factor (RRF) from the viewpoint of molecular mimicry and prion transmission, and uncovered the following aspects. 1) Crystal structure and functional domain annotation of S. Pombe eRF3. 2) Functional interplay of EF-G and RRF at
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their tRNA-mimicry domains. 3) The critical role of the universally conserved A2602 of 23S rRNA for the peptide-release activity. 4) Part of the prion domain of yeast eRF3 masks the eRF3-binding site in eRF1. 5) The role of ribosomal protein L11 domains for the cooperative interaction with RF1 and RF2, responsible for translation termination. 6) The role of nonprion-state N-terminal domain of yeast eRF3 for functionality and stability of eRF3. 7) RRF disassembles the posttermination ribosomal complex independent of the ribosomal translocase activity of EF-G. 8) Discovery of a novel [PSI^+] prion variant that is independent of Hsp104. 9) Conformational memory preserved in a weak-to-strong or strong-to-weak [PSI^+] conversion during transmission to Sup35 prion variants. 10) The N-terminal 41-residue domain of S. cerevisiae Sup35 is a species-barrier determinant for [PSI^+] prion transmission. 11) Genome-wide screening and genetic selection for factors, including Hsp104 and other novel components, responsible for the maintenance of yeast prions. Less
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Research Products
(218 results)
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[Journal Article] Inhibition of midkine alleviates experimental autoimmune encephalomyelitis through the expansion of regulatory T cell population.2008
Author(s)
Wang, J, Takeuchi H., Sonobe, Y., Jin, S., Mizuno, T., Miyakawa, S., Fujiwara, M., Nakamura, Y., Kato, T., Muramatsu, H., Muramatsu, T., Suzumura. A.
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Journal Title
Proc. Natl. Acad. Sci. USA. 105
Pages: 3915-3920
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Structural and molecular basis for hyperspecificity of RNA aptamer to human immunoglobulin G.2008
Author(s)
Miyakawa, S., Nomura, Y., Sakamoto, T., Yamaguchi, Y., Kato, K., Yamazaki, S., Nakamura, Y.
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Journal Title
RNA (Apr 25[Epub ahead of print])
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Translation termination, the prion [psr」, and ribosome recycling. ln : Sonenberg N, Hershey JWB, Mathews MB, eds.2007
Author(s)
Ehrenberg, M., Hautyliuk V., Crist C. G., Nakamura, Y.
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Journal Title
Translational Control in Biology and Medicine. Cold Spring Harbor, New York : Cold Spring Harbor Laboratory Press.
Pages: 173-196
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Reduced activity or expression of polypeptide release factors induces mRNA cleavage and tmRNA tagging at, stop codons in E. coli.2007
Author(s)
Li, X., Yokota, T., Ito, K., Nakamura, Y., Aiba, H.
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Journal Title
Mol. Micro. 63
Pages: 116-126
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Translation termination, the prion [PSI^+], and ribosome recycling.2007
Author(s)
Ehrenberg, M., Hauryliuk V., Crist C. G., Nakamura, Y.
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Journal Title
In : Sonenberg N, Hershey JWB, Mathews MB, eds. Translational Control in Biology and Medicine. Cold Spring Harbor, New York : Cold Spring Harbor Laboratory Press
Pages: 173-196
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] RNA aptamers to mammalian initiation factor 4G inhibit cap- dependent translation by blocking the formation of initiation factor complexes.2006
Author(s)
Miyakawa, S., Oguro, A., Ohtsu, T., Imataka, H., Sonenberg, N., Nakamura, Y.
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Journal Title
Description
「研究成果報告書概要(和文)」より
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[Journal Article] RNA aptamers to mammalian initiation factor 4G inhibit cap-dependent translation by blocking the formation of initiation factor complexes.2006
Author(s)
Miyakawa, S., Oguro, A., Ohtsu, T., Imataka, H., Sonenberg, N., Nakamura, Y.
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Journal Title
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A.2005
Author(s)
Sakamoto, T., Oguro, A., Kawai, G., Sonenberg, N., Ohtsu, T., Nakamura, Y.
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Journal Title
Nucl. Acids Res. 33
Pages: 745-754
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Crystal Structure and Functional Analysis of the Eukaryotic Class II Release Factor eRF3 from S. Pombe.2004
Author(s)
Kong, C., Ito, K., Walsh, M., Wada, M., Liu, Y., Kumar, S., Barford, D., Nakamura, Y., Song, H.
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Journal Title
Mol. Cell 14
Pages: 233-245
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Crystal Structure and Functional Analysis of the Eukaryotic Class II Release Factor eRF3 from S. Pombe.2004
Author(s)
Kong, C, Ito, K., Walsh, M., Wada, M., Liu, Y., Kumar, S., Barford, D., Nakamura, Y., Song, H.
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Journal Title
Mol. Cell 14
Pages: 233-245
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Crystal Structure and Functional Analysis of the Eukaryotic Class II Release Factor eRF3 from S. Pombe.2004
Author(s)
Kong., C, Ito, K., Walsh, M., Wada, M., Liu, Y., Kumar, S., Barford, D., Nakamura, Y., Song, H.
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Journal Title
Mol. Cell 14
Pages: 233-245
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Antizyme frameshifting as a functional probe of eukaryotic translational termination.2003
Author(s)
Karamysheva, Z. N., Karamyshev, A. L., Ito, K., Yokogawa, T., Nishikawa, K., Nakamura, Y., Matsufuji, s.
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Journal Title
Nucl. Acids Res. 31
Pages: 5949-5956
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] The critical role of the universally conserved A2602 of 23S ribosomal RNA in the release of the nascent peptide during translation termination.2003
Author(s)
Polacek, N., Gomez, M., Ito, K., Xiong, L., Nakamura, Y., Mankin, A.
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Journal Title
Mol. Cell 11
Pages: 103-112
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Characterization of mutations in the GTP-binding domain of IF2 resulting in cold-sensitive growth of Escherichia coli.2003
Author(s)
Laursen, B. S., Siwanowicz, I., Larigauderie, G., Hedegaard, J., Ito, K., Nakamura, Y., Kenney, J., Mortensen, K. K., Sperling-Petersen, H. U.
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Journal Title
J. Mol. Bid. 326
Pages: 543-551
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Antizyme frameshifting as a functional probe of eukaryotic translational termination.2003
Author(s)
Karamysheva, Z. N., Karamyshev, A. L., Ito, K., Yokogawa, T., Nishikawa, K., Nakamura, Y., Matsufuji, S.
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Journal Title
Nucl. Acids Res. 31
Pages: 5949-5956
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Characterization of mutations in the GTP-binding domain of IF2 resulting in cold-sensitive growth of Escherichia coli. J. Mol. Biol.2003
Author(s)
Laursen, B. S., Siwanowicz, I., Larigauderie, G., Hedegaard, J., Ito, K., Nakamura, Y., Kenney, J., Mortensen, K. K., Sperling-Petersen, H. U.
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Journal Title
J. Mol. Biol. 326
Pages: 543-551
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Isolation and expression of two genes encoding eukaryotic release factor 1 (eRFl)from Paramedum tetraurelia.2002
Author(s)
Kervestin, S., Gamier, O. A., Karamyshev, A. L., Ito, K., Nakamura, Y., Meyer, E., Jean-Jean, O.
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Journal Title
J. Euk. Microbiol. 49
Pages: 374-382
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Structure of ribosomal protein LI from Methanococcus thermolithotrophicus. Functionally important structural invariants on L1 surface.2002
Author(s)
Nevskaya, N., Tishchenko, S., Paveliev, M., Smolinskaya, Y., Fedorov, R., Piendl, W., Nakamura, Y., Toyoda, T., Garber, M., Nikonov, s.
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Journal Title
Acta Cryst. D58
Pages: 1023-1029
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Omnipotent decoding potential resides in eukaryotic translation termination factor eRFl of variant-code organisms and is modulatedby the interactions of amino acid sequences within the domain 1.2002
Author(s)
Ito, K., Frolova, L., Seit-Nebi, A., Karamyshev, A. L., Kisselev, L., Nakamura, Y.
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Journal Title
Proc. Natl. Acad. Sci. USA. 99
Pages: 8494-8499
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Isolation and expression of two genes encoding eukaryotic release factor 1 (eRF1) from Paramecium tetraurelia.2002
Author(s)
Kervestin, S., Garnier, O. A., Karamyshev, A. L., Ito, K., Nakamura, Y., Meyer, E., Jean-Jean, O. J. Euk. Microbiol.
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Journal Title
J. Euk. Microbiol. 49
Pages: 374-382
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Structure of ribosomal protein L1 from Methanococcus thermolithotrophicus. Functionally important structural invariants on L1 surface.2002
Author(s)
Nevskaya, N., Tishchenko, S., Paveliev, M., Smolinskaya, Y., Fedorov, R., Piendl, W., Nakamura, Y., Toyoda, T., Garber, M., Nikonov, S.
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Journal Title
Acta Cryst. D58
Pages: 1023-1029
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Omnipotent decoding potential resides in eukaryotic translation termination factor eRF1 of variant-code organisms and is modulated by the interactions of amino acid sequences within the domain 1.2002
Author(s)
Ito, K., Frolova, L., Seit-Nebi, A., Karamyshev, A. L., Kisselev, L., Nakamura, Y.
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Journal Title
Proc. Natl. Acad. Sci. USA. 99
Pages: 8494-8499
Description
「研究成果報告書概要(欧文)」より
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[Presentation] N-terminal prion domain of yeast release factor eRF3 : functionality and biogenesis.2007
Author(s)
Nakamura, Y., Kurahashi, H., Kodama。H., Takahashi, A., Hara, H., Ito, K.
Organizer
International Symposium "Milestones in the Life of Proteins"
Place of Presentation
Kyoto
Year and Date
20070315-20070316
Description
「研究成果報告書概要(和文)」より
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[Presentation] RNAと創薬2006
Author(s)
中村義一
Organizer
第65回日本癌学会学術総会シンポジウム
Place of Presentation
横浜
Year and Date
20060928-20060930
Description
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[Presentation] High affinity RNA for mammalian initiation factor 4E interferes with mRNA-cap binding and inhibits translation.2005
Author(s)
Mochizuki, K., Oguro, A., Ohtsu, T., Sonenberg, N., Nakamura, Y.
Organizer
10th Annual RNA Conference.
Place of Presentation
Banff, Canada
Year and Date
20050524-20050529
Description
「研究成果報告書概要(和文)」より
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[Presentation] High affinity RNAs against eukaryotic initiation factor 4G inhibit translation in vitro : Potential tools to control translation initiation.2005
Author(s)
Miyakawa, S., Oguro, A., Ohtsu, T., Imataka, H., Sonenberg, N., Nakamura, Y.
Organizer
10th Annual RNA Conference.
Place of Presentation
Banff, Canada
Year and Date
20050524-20050529
Description
「研究成果報告書概要(和文)」より
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[Presentation] RNA aptamers targeting C-termini of KRAS oncoprotein.2005
Author(s)
Tanaka, Y., Oguro, A., Ohtsu, T., Akagi, K., Nakamura, Y., Kozu, T.
Organizer
10th Annual RNA Conference.
Place of Presentation
Banff, Canada
Year and Date
20050524-20050529
Description
「研究成果報告書概要(和文)」より
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[Presentation] 酵母プリオン2003
Author(s)
中村義一
Organizer
大阪大学微生物病研究所 感染症フォーラム
Place of Presentation
大阪
Year and Date
20030218-20030219
Description
「研究成果報告書概要(和文)」より
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[Presentation] リボソーム再生因子の構造遺伝学2002
Author(s)
中村義一, 藤原俊伸, 豊田友彦, 伊藤耕一
Organizer
第75回日本生化学会大会シンポジウム
Place of Presentation
東京
Year and Date
20021014-20021017
Description
「研究成果報告書概要(和文)」より
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[Presentation] Ominipotent decoding potential of release factor eRFl from variant-code organisms and modulation by TAS tripeptide in domain 1.2002
Author(s)
Nakamura, Y., Ito, K., Frolova, L., Seit-Nebi, A., Kisselev, L.
Organizer
CSH Translational Control meeting
Place of Presentation
Cold Spring Harbor Laboratory, NY
Year and Date
20020910-20020915
Description
「研究成果報告書概要(和文)」より
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[Presentation] High affinity RNA for initiation factor 4A helicase binds selectively compact form of eIF4A and hinders cap dependent translaiton by blocking ATP hydrolysis.2002
Author(s)
Oguro, A., Ohtsu, T., Svitkin, Y., Sonenberg, N., Nakamura, Y.
Organizer
CSH Translational Control meeting.
Place of Presentation
Cold Spring Harbor Laboratory, NY
Year and Date
20020910-20020915
Description
「研究成果報告書概要(和文)」より
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[Presentation] Ominipotent decoding potential of release factor eRF1 from variant-code organisms and modulation by TAS tripeptide in domain 1.2002
Author(s)
Nakamura, Y., Ito, K., Frolova, L., Seit-Nebi, A., Kisselev, L.
Organizer
CSH Translational Control meeting
Place of Presentation
Cold Spring Harbor Laboratory, NY
Year and Date
20020910-20020915
Description
「研究成果報告書概要(欧文)」より
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[Presentation] 翻訳系における分子擬態2002
Author(s)
中村義一
Organizer
日本農芸化学会シンポジウム
Place of Presentation
仙台
Year and Date
20020324-20020327
Description
「研究成果報告書概要(和文)」より
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[Presentation] U50HG, an intronic U50 snoRNA host gene isolated from human malignant lymphoma ; structural analysis of mouse U50HG homologue, mU50HG.2001
Author(s)
Tanaka, R., Satoh, H., Morishita, Y., Watanabe, T., Nakamura, Y., Mori, S.
Organizer
17th Wilhelm Berahard's Workshop
Place of Presentation
Arcachon, France
Year and Date
20010901-20010905
Description
「研究成果報告書概要(和文)」より
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[Presentation] U50HG, an intronic U50 snoRNA host gene isolated from human malignant lymphoma ; structural analysis of mouse U50HG homologue, mU50HG.2001
Author(s)
Tanaka, R., Satoh, H., Morishita, Y., Watanabe, T., Nakamura, Y., Mori, S.
Organizer
17th Wilhelm Bemhard's Workshop
Place of Presentation
Arcachon, France
Year and Date
20010901-20010905
Description
「研究成果報告書概要(欧文)」より
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