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1998 Fiscal Year Final Research Report Summary

Regulation of Translation Termination

Research Project

Project/Area Number 08044196
Research Category

Grant-in-Aid for international Scientific Research

Allocation TypeSingle-year Grants
SectionJoint Research
Research Field Molecular biology
Research InstitutionThe University of Tokyo

Principal Investigator

NAKAMURA Yoshikazu  Institute of Medical Science, University of Tokyo, Associate Professor, 医科学研究所, 助教授 (40114590)

Co-Investigator(Kenkyū-buntansha) ISAKSSON Leif  Dept.of Microbiology, Stockholm Univ., Professor, 微生物学部, 教授
BUCKINGHAM Richard  Institute de Biologie Physico-Chimique, Professor, 部長
TATE Warren P.  Dept.of Biochemistry, Univ.of Otago, Professor, 生化学部, 教授
KAJI Akira  Dept.Microbiolgy, Univ.of Pennsylvania School of Med.Professor, 医学部, 教授
YANOFSKY Charles  Dept.Biological Sciences, Stanford University, Professor, 生物科学部, 教授
Project Period (FY) 1996 – 1998
Keywordsprotein synthesis / translation termination / stop codon / polypeptide release factor / molecular mimicry / tRNA / ribosome / protein anticodon
Research Abstract

Termination of protein synthesis takes place on the ribosomes as a response to a stop, rather than a sense, codon in the 'decoding' site (A site). Translation termination requires two classes of polypeptide release factors (RFs) : a class-I factor, codon-specific RFs (RF1 and RF2 in prokaryotes ; eRF1 in eukaryotes), and a class-II actor, non-specific RFs (RF3 in prokaryotes ; eRF3 in eukaryotes) that bind guanine nucleotides and stimulate class-I RF activity. The model of 'release factor tRNA mimicry' (Cell 87 : 147, 1996) explains how protein reads the genetic code (stop codon) by assuming a potential anticodon mimicry. We identified crucial amino acids (and motifs) of RFs that contribute to stop codon recognition. First, a mutant was isolated by mutagenizing bacterial RF2 (specific to UGA/UAA) and then selecting a suppressor of a temperature-sensitive RF1 (specific to UAG/UAA) mutation. This mutant RF2 carried a single substitution of Lys for Glu at position 167, and acquired the ab … More ility to terminate protein synthesis at UAG, in addition to UGA and UAA, showing that position 167 and its vicinity are directly involved in stop codon recognition by means of discrimination at the third-base (motif I). Second, site-directed mutagenesis of RF2 highlighted residues at positions 205, 206, 207 and 213 ; their alterations are toxic to cells and induce abnormal termination at the sense codon(s) (motif II). These dominant lethal effects are frequently suppressed by mutations in motif I, revealing the functional interaction between the two regions. Third, the specificity of RF1 and RF2 can be converted by swapping these two motifs. These results demonstrate that RE protein encodes a protein. Fourth, the tethered radical footprinting data reveal the proximity of the tip of the predicted 'anticodon-stem mimicry domain' of RE1 to the 30S decoding site, providing the topological support for the proposed molecular mimicry of RF.
Analogous to the initiation and elongation steps of translation, the termination step involves hydrolysis of GTP to GDP by RF3 or eRF3. The model of RF-tRNA mimicry predicts that class-II GTP/GDP-binding proteins, RF3 and eRF3, may be an 'EF-Tu-like' vehicle protein to bring class-I proteins to the A site of the ribosome or an 'EF-G-like' translocase protein. We obtained the data to support that eRF3 is functionally closer to EF-Tu than EF-G in eukaryotes, while RF3 is closer to EF-G than EF-Tu in prokaryotes. Less

  • Research Products

    (56 results)

All Other

All Publications (56 results)

  • [Publications] Nakamura, Y., Ito, K., Isaksson, L.A.: "Emerging understanding of translation termination." Cell. 87. 147-150 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ito, K., Ebihara, K., Uno, M., Nakamura, Y.: "Conserved motifs of prokaryotic and eukaryotic polypeptide release factors : tRNA-protein mimicry hypothesis." Proc. Natl. Acad. Sci. USA. 93. 5443-5448 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Matsumura, K., Ito, K., Kawazu, Y., Mikuni, O., Nkamura, Y.: "Suppression of temperature-sensitive defects of polypeptide release factors RF-1 and RF-2 by mutations or by an excess of RF-3 in Escherichia coli." J. Mol. Biol.258. 588-599 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Yanofsky, C., Horn, V., Nakamura, Y.: "Loss or overproduction of polypeptide release factor 3 influences expression of the tryptophanase operon of Escherichia coli." J. Bacteiol.178. 3755-3762 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ito, K., Nakamura, Y.: "Localization of nusA-suppressing amino acid substitutions in the conserved regions of the β′ subunit of Escherichia coli RNA polymerase." Mol. Gen. Genet.251. 699-706 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Inada, T., Nakamura, Y.: "Autogenous coutrol of the suhB gene expression of Escherichia coli." Biochimie. 78. 209-212 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Wada, M., Nakamura, Y.: "Unique telomeric expression site of major-surface-glycoprotein genes of Pneumocystis carinii." DNA Res.3. 55-64 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Wada, M., Nakamura, Y.: "Antigenic varartion by telomeric recombination of major-surface-glycoprotein genes of Pneumocystis carinii." J. Euk. Microbiol.43. 85- (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Oshima, T., Aiba, H., Baba, T., Fujita, K., Hayashi, K., Honjo, A., Ikemoto, K., Inada, T., Itoh, T., Kajihara, M., Kanai, K., Kashimoto, K., Kimura, S., Kitagawa, M., Makino, K., Masuda, S., Miki, T., Mizobuchi, K., Mori, H., Motomura, K., Nakamura, Y., Nashimoto, H., Nishio, Y., Saito, N., Sampei, G., Seki, Y., Tagami, H., Takemoto, K., Wada, C., Yamamoto, Y., Yano, M., Horiuchi, T.: "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." DNA Res. 3. 137-155 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Aiba, H., Baba, T., Hayashi, K., Inada, T., Isono, K., Itoh, T., Kasai, H., Kshimoto, K., KItakawa, M., Kitagawa, M., Makino, K., Miki, T., Mizobuchi, K., Mori, H., Motomura, K., Nakade, S., Nakamura, Y., Nashimoto, H., Nishio, Y., Oshima, T., Saito, N., Sampei, G., Seki, Y., Sivasundaram, S., Tagami, H., Takeda, J., Takemoto, K., Wada, C., Yamamoto, Y., Horiuchi, T.: "A 570 kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 imn region on the linkage map." DNA Res.3. 363-377 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Itoh, T., Aiba, H., Baba, T., Hayashi, K., Inada, T., Isono, K., Kasai, H., Kashimoto, K., Kitakawa, M., Kitagawa, M., Makino, K., Miki, T., Mizobuchi, K., Mori, H., Mori, T., Motomura, K., Nakade, S., Nakamura, Y., Nashimoto, H., Nishio, Y., Oshima, T., Saito, N., Sampei, G., Seki, Y., Sivasundaram, S., Tagami, H., Takeda, J., Takemoto, K., Wada, C., Yamamoto, Y., Horiuchi, T.: "A 460 kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map." DNA Res.3. 370-392 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Uno, M., Ito, K., Nakamura, Y.: "Functional specificity of amino acid at position 246 in the tRNA mimicry domain of bacterial release factor 2." Biochimie. 78. 935-943 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Mita, K., Morimyo, M., Ito, K., Sugano, K., Ebihara, K., Hongo, E., Higashi, T., Hirayama, Y., Nakamura, Y.: "Comprehensive cloning of Schizosaccharamyces pombe genes encoding translation elongation factors." Gene. 187. 259-266 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ito, K., Nakamura, Y.: "Cloning and overexpression of polypeptide release factor 1 of Thermus thermophilus." Biochimie. 79. 287-292 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Yamamoto, Y., Aiba, A., Baba, T., Hayashi, K., Inada, T., Isono, K., Itoh, T., Kimura, S., Kitagawa, M., Makino, K., Miki, T., Mitsuhashi, N., Mizobuchi, K., Mori, H., Nakade, S., Nakamura, Y., Nashimoto, H., Oshima, T., Oyama, S., Saito, N., Sampei, G., Satoh, Y., Sivasundaram, S., Tagami, H., Takahashi, H., Takeda, J., Takemoto, K., Uehara, K., Wada, C., Yamagata, S., Horiuchi, T.: "Construction of a contiguous 874 kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min region on the linkage map and analysis of its sequence features." DNA Res.42. 91-113 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Wada, M., Nakamura, Y.: "Cloning and overexpression of cell surface subtilisin-like proteases (SSP) of Pneumocystis carinii." J. Euk. Microbiol.44. 54S- (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Wada, M., Nakamura, Y.: "Heterologous expression of Pneumocystis carinii genes in fission yeast." J. Euk. Microbiol.44. 55S-56S (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nakamura, Y., Wada, M.: "Molecular pathobiology and antigenic variation of Pneumocystis carinii." Adv. Parasitol.41. 63-107 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Pel, H.J., Moffat, J.G., Ito, K., Nakamura, Y., Tate, W.P.: "Escherichia coli release factor-3 : resolving the paradox of a typical G protein structure and atypical function with guanine nucleotides." RNA. 4. 47-54 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nakamura, Y.: "The major surface antigen of Pneumocystis carinii." FEMS Immun. Med. Microbiol.22. 67-74 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nakamura, Y.: "Molecular microbiology of Pneumocystis carinii." Jps. J. Med. Mycol.39. 91-98 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Dasgupta, S., Fernandez, L., Kameyama, L., Inada, T., Nakamura, Y., Pappas, A., Court, D.: "Genetic uncoupling of the dsRNA-binding and RNA-cleavage activities of the Escherichia coli endoribonuclease RNaseIII-the effect of dsRNA binding on gene expression." Mol. Microbiol.28. 629-640 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ito, K., Ebihara, K., Nakamura, Y.: "The stretch of C-terminal acidic amino acids of translational release factor eRF1 is a primary binding site for eRF3 of fission yeast." RNA. 4. 958-972 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ito, K., Uno, M., Nakamura, Y.: "Single amino acid substitution in prokaryote polypeptide release factor 2 permits it to terminate translation at all three stop codons." Poc. Natl. Acad. Sci. USA. 95. 8165-8169 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nakamura, Y., Ito, K.: "How protein reads the stop codon and terminates translation (Review)." Genes Cells. 3. 263-278 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Mita, K., Morimyo, M., Hongo, E., Higashi, T., Sugaya, K., Ajimura, M., Ishihara, Y., Inoue, H., Sasanuma, S., Nohata, J., Kimura, T., Koike, Y., Ito, K., Nakamura, Y.: "The cDNA and intron catalog of ribosomal protein genes of Schizosaccharomyces pombe." Nucl. Acids Res, In Press. (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Crawford, D.-J.G., Ito, K., Nakamura, Y., Tate, W.P.: "Indirect regulation of termination efficiency at highly expressed genes and recoding sites by the factor recycling function of Escherichia coli release factor RF3." EMBO J.18. 727-732 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nakamura, Y.: "Posttranscriptional Contorol of Gene Expression" Springer-Verlag, 267 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nakamura, Y., Ito, K., Isaksson, L.A.: "Emerging understanding of translation termination." Cell. 87. 147-150 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ito, K., Ebihara, K., Uno, M., Nakamura, Y.: "Conserved motifs of prokaryotic and eukaryotic polypeptide release factors : tRNA-protein mimicry hypothesis." Proc.Natl.Acad.Sci.USA. 93. 5443-5448 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Matsumura, K., Ito, K., Kawazu, Y., Mikuni, O., Nakamura, Y.: "Suppression of temperature-sensitive defects of polypeptide release factors RF-1 and RF-2 by mutations or by an excess of RF-3 in Escherichia coli." J.Mol.Biol.258. 588-599 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Yanosky, C., Horn, V., Nakamura, Y.: "Loss or overproduction of polypeptide release factor 3 influences expression of the tryptophanase operon of Escherichia" J.Bacteriol.178. 3755-3762 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ito, K., Nakamura, Y.: "Localization of nusA-suppressing amino acid substitutions in the conserved regions of the beta' subunit of Escherichia coli RNA polymerase." Mol.Gen.Genet.251. 699-706 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Inada, T., Nakamura, Y.: "Autogenous control of the suhB gene expression of Escherichia coli." Biochimie. 78. 209-212 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Wada, M., Nakamura, Y.: "Unique telomeric expression site of major-surface-glycoprotein genes of Pneumocystis carinii." DNA Res.3. 55-64 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Wada, M., Nakamura, Y.: "Antigenic variation by telomeric recombination of major-surface-glycoprotein genes of Pneumocystis carinii." J.Euk.Microbiol.43. 8S (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nakamura, Y.: "Regulation of peptide chain termination (Review) ." Posttranscriptional Control of Gene Expression. 73-81 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Oshima, T., Aiba, H., Baba, T., Fujita, K., Hayashi, K., Honjo, A., Ikemoto, K., Inada, T., Itoh, T., Kajihara, M., Kanai, K..Kashimoto, K., Kimura, S., Kitagawa, M., Makino, K., Masuda, S., Miki, T., Mizobuchi, K., Mori, H., Motomura, K., Nakamura, Y., Nashimoto, H., Nishio, Y., Saito, N., Sampei, G., Seki, Y., Tagami, H., Takemoto, K., Wada, C., Yamamoto, Y., Yano, M., Horiuchi, T.: "A718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." DNA Res.3. 137-155 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Aiba, H., Baba, T., Hayashi, K., Inada, T., Isono, K., Itoh, T., Kasai, H., Kashimoto, K., Kitakawa, M., Kitagawa, M., Makino, K., Miki, T., Mizobuchi, K., Mori, H., Mori, T., Motomura, K., Nakade, S., Nakamura, Y., Nashimoto, H., Nishio, Y., Oshima, T., Saito, N., Sampei, G., Seki, Y., Sivasundaram, S., Tagami, H., Takeda, J., Takemoto, K., Wada, C., Yamamoto, Y., Horiuchi, T.: "A 460kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." DNA Res.3. 363-377 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Itoh, T., Aiba, H., Baba, T., Hayashi, K., Inada, T., Isono, K., Kasai, H., Kashimoto, K., Kitakawa, M., Kitagawa, M., Makino, K., Miki, T., Mizobuchi, K., Mori, H., Mori, T., Motomura, K., Nakade, S., Nakamura, Y., Nashimoto, H., Nishio, Y., Oshima, T., Saito, N., Sampei, G., Seki, Y., Sivasundaram, S., Tagami, H., Takeda, J., Takemoto, K., Wada, C., Yamamoto, Y., Horiuchi, T.: "A 460kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map." DNA Res.3. 370-392 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Uno, M., Ito, K., Nakamura, Y.: "Functional specificity of amino acid at position 246 in the tRNA mimicry domain of bacterial release factor2." Biochimie. 78. 935-943 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Mita, K., Morimyo, M., Ito, K., Sugano, K., Ebihara, K., Hongo, E., Higashi, T., Hirayama, Y., Nakamura, Y.: "Comprehensive cloning of Schizosaccharamycespombe genes encoding translation elongation factors." Gene. 187. 259-266 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ito, K., Nakamura, Y.: "Cloning and overexpression of polypeptide release factor 1 of Thermus thermophilus." Biochimie. 79. 287-292 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Yamamoto, Y., Aiba, H., Baba, T., Hayashi, K., Inada, T., Isono, K., Itoh, T., Kimura, S., Kitagawa, M., Makino, K., Miki, T., Mitsuhashi, N., Mizobuchi, K., Mori, H., Nakade, S., Nakamura, Y., Nashimoto, H., Oshima, T., Oyama, S., Saito, N., Sampei, G., Satoh, Y., Sivasundaram, S., Tagami, H., Takahashi, H., Takeda, J., Takemoto, K., Uehara, K., Wada, C., Yamagata, S., Horiuchi, T.: "Construction of a contiguous 874 kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min region on the linkage map and analysis of its sequence features." DNA Res.4. 91-113 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Wada, M., Nakamura, Y.: "Cloning and overexpression of cell surface subtilisin-like proteases (SSP) of Pneumocystis carinii." J.Euk.Microbiol.44. 54S (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Wada, M., Nakamura, Y.: "Heterologous expression of Pneunocystis carinii genes in fission yeast" J.Euk.Mircrobiol.44. 55S-56S (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nakamura, Y., Wada, M.: "Molecular pathobiology and antigenic variation of Pneumocystis carinii." Adv.Parasitol.41. 63-107 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Pel, H.J., Moffat, J.G,Ito, K., Nakamura, Y., Tate, W.P.: "Escherichia coli release factor-3 : resolving the paradox of a typical G protein structure and atypical function with guanine nucleotides." RNA. 4. 47-54 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nakamura, Y.: "The major surface antigen of Pneumocystis carinii." FEMS Immun.Med.Microbiol.22. 67-74 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nakamura, Y.: "Molecular microbiology of Pneumocystis carinii." Jps.J.Med.Mycol.39. 91-98 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Dasgupta, S., Fernandez, L., Kameyama, L., Inada, T., Nakamura, Y., Pappas, A., Court, D.: "Genetic uncoupling of the dsRNA-binding and RNA-cleavage activities of the Escherichia coli endoribonuclease RNaseIII-the effect of dsRNA binding on gene expression." Mol.Microbiol.28. 629-640 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ito, K., Ebihara, K., Nakamura, Y.: "The stretch of C-terminal acidic amino acids of translational release factor eRF1 is a primary binding site for eRF3 of fission yeast." RNA. 4. 958-972 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ito, K., Uno, M., Nakamura, Y.: "Single amino acid substitution in prokaryote polypeptide release factor 2 permits it to terminate translation at all three stop codons." Proc.Natl.Acad.Sci.USA. 95. 8165-8169 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nakamura, Y., Ito, K.: "How protein reads the stop codon and terminates translation (Review)." Genes Cells. 3. 263-278 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Mita, K., Morimyo, M., Hongo, E., Higashi, T., Sugaya, K., Ajimura, M., Ishihara, Y., Inoue, H., Sasanuma, S., Nohata, J., Kimura, T., Koike, Y., Ito, K., Nakamura, Y.: "The cDNA and intron catalog of ribosomal protein genes Schizosaccaromyces pombe." Nucl.Acids Res. In press. (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Crawford, D.-J.G., Ito, K., Nakamura, Y., Tate, W.P.: "Indirect regulation of termination efficiency at highly expressed genes and recoding sites by the factor recycling function of Escherichia coli release factor RF3." EMBO J.18. 727-732 (1998)

    • Description
      「研究成果報告書概要(欧文)」より

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Published: 1999-12-08  

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