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1996 Fiscal Year Final Research Report Summary

Development of "Molecular Structural Phylogeny" on the Consideration of Protein 3D structure

Research Project

Project/Area Number 07304050
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section総合
Research Field 遺伝
Research InstitutionNational Institute of Genetics

Principal Investigator

TATENO Yoshio  National Institute of Genetics, Center for Information Biology, Professor, 生命情報研究センター, 教授 (00202424)

Co-Investigator(Kenkyū-buntansha) YAMAGUCHI Hiroshi  Osaka University, Institute for Protein Research, Division of Protein Crystallog, 蛋白質研究所・物理構造部門, 助手 (10252719)
MORIYAMA Hideaki  Tokyo Institute of Technology, Faculty of Bioscience and Biotechnology, Assistan, 生命理工学部, 助手 (50200457)
IKEO Kazuho  National Institute of Genetics, Center for Information Biology, Assistant Profes, 生命情報研究センター, 助手 (20249949)
GOJOBORI Takashi  National Institute of Genetics, Center for Information Biology, Professor, 生命情報研究センター, 教授 (50162136)
Project Period (FY) 1995 – 1996
Keywordsmolecular phylogeny / protein 3D structure / evolutionary motif / viral evolution / natural selection / cytochrome c oxidase / 3-isopropylmalate dehydrogenase
Research Abstract

With the advent of genome analysis, it has become clear that a gene is not a single entity but composed of subregions that have different evolutionary origins and histories. Consequently, it has been accepted that "one gene-multifunction, one gene-plural structures" is more realistic than "one gene-one function, one gene-one structure". This implies that a present gene has been formed by using smaller pieces in the course of the evolution. We call the piece the evolutionary motif (EM). To investigate the implication ;
(1)We aligned complete amino acid sequences which were translated from DNA sequences in the International DNA Databases, in view of molecular evolution. To carry out the alignment, we developed a method by which to repeat phylogenetic tree construction and multiple alignment alternaively until both gave consistent results. Then we searched for EMs by locating evolutionarily conserved residues among the aligned sequences. The average length of the EMs was estimated to be 60 residues which is a size of many functional and structural regions in a protein.
(2)EMs thus obtained were classified into hydrophilic, hydrophobic and intermediate ones. We think that hydrophilic EMs are located on the surface of a protein and play biological roles, and hydrophobic ones go inside it and something to do with its structure.
(3)Analyzing the aligned sequences by estimating the numbers of synonymous and nonsynonymous substitutions, we came to the conclusion that the evolutionary mechanism for more than 90% of the total sequences could be explained by the neutral mutation theory.
(4)We also elucidated three dimensional structures of cytochrome c oxidase and 3-isopropylmalate dehydrogenase, and confirmed that the structures were composed of substructures with different functions.
The above findings strongly support our idea that a present gene was created and evolved by taking up (and throwing away) EMs that were available then.

  • Research Products

    (32 results)

All Other

All Publications (32 results)

  • [Publications] QU,C.ら: "A mutation at the interface between domains causes rearrangement of domains in 3-isopropylmalate dehydrogenase" Protein Engineering. (in press).

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Igarashi,N.ら: "Detwinning of hemihedrally twinned crystals by the least squares method and its application to the crystal of hydroxylamine oxidoreductase from Nitrosomonas europaea" Applied Crystallography. (in press).

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Igarashi,N.ら: "The 2.8 Å structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium,Nitrosomonas europaea" Nature Structure Biology. (in press).

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Tateno,Y.ら: "Evolutionary Motif and Its Biological and Structural Significance" J.Mol.Evol.44. S38-S43 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Tateno,Y.ら: "DNA Data Bank of Japan in the age of information biology" Nucleic Acids Res.25. 14-17 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Yamaguchi,Y.ら: "Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts" Proc.Natl.Acad.Sci.USA. 94. 1264-1269 (1997)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Akishinonomiya F.ら: "Monophyletic origin and unique dispersal patterns of domestic fowls." Proc.Natl.Acad.Sci.USA. 93. 6792-6795 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Endo,T.ら: "Large-Scale Search for Genes on Which Positive Selection May Operate" Mol.Biol.Evol.13. 685-690 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nagata,C.ら: "Cryocrystallography of 3-Isopropylmalate Dehydrogenase from Thermus thermophilus and its Chimeric Enzyme" Acta Cryst.D52. 623-630 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Tsukihara,T.ら: "The Whole Structure of the 13-Subunit Oxidized Cytochrome c Oxidase at 2.8 Å" Science. 272. 1136-1144 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Oda,Y.ら: "Crystallization and preliminary X-ray diffraction analysis of two lysinal derivatives of Achromobacter protease I" Acta Cryst.D52. 1027-1029 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Moriyama,H.ら: "Crystal sturcture of mutated 3-isopropylmalate dehydrogenease from Thermus thermophilus HB8 and their relationship to the thermostability of the enzyme" J.Biochem.117. 408-413 (1995)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Kitakami,H.ら: "YAMATO and ASUKA : DNA Database Management Systems." Proceedings of the Twenty-Eighth Annual Hawaii International Conference on System Sciences. 72-80 (1995)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Tateno,Y.: "Development of information biology" Protein,Nucleic Acid,and Enzyme. 40. 102-108 (1995)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Tateno,Y.: "Gene" Dictionary of Mathematics,Physics,and Information Science. 39-42 (1995)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Tsukihara,T.ら: "Structures of Metal Sites of Oxidized Bovine Heart Cytochrome c Oxidase at 2.8 Å" Science. 269. 1069-1704 (1995)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Qu, C.et al.: "A mutation at the interface between domains causes rearrangement of domains in 3-isopropylmalate dehydrogenase" Protein Engineering. (in press).

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Igarashi, N.et al.: "Detwinning of hemihedrally twinned crystals by the least squares method and its application to the crystal of hydroxylamine oxidoreductase from Nitrosomonas europaea" Applied Crystallography. (in press).

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Igarashi, N.et al.: "The 2.8 * structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea" Nature Structure Biology. (in press).

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Tateno, Y.et al: "Evolutionary Motif and Its Biological and Structural Significance" J.Mol.Evol.44. S38-43 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Tateno, Y.et al.: "DNA Data Bank of Japan in the age of information biology" Nucleic Acids Res.25. 14-17 (1977)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Yamaguchi, Y.et al.: "Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts" Proc.Natl.Acad.Sci.USA,94. 1264-1269 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Akishinonomiya F.et al.: "Monophyletic origin and unique dispersal patterns of domestic fowls" Proc.Natl.Acad.Sci.USA. Vol.93. 6792-6795 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Endo, T.et al.: "Large-Scale Search for Genes on Which Positive Selection May Operate" Mol.Biol.Evol.13. 685-690 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nagata, C.et al.: "Cryocrystallography of 3-Isopropylmalate Dehydrogenase from Thermus thermophilus and its Chimeric Enzyme" Acta Cryst.D52. 623-630 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Tsukihara, T.et al.: "The Whole Structure of the 13-Subunit Oxidized Cytochrome c Oxidase at 2.8*" Science. 272. 1136-1144 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Oda, Y.et.al.: "Crystallization and preliminary X-ray diffraction analysis of two lysinal derivatives of Achromobacter protease I" Acta Cryst.D52. 1027-1029 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Moriyama, H.et al.: "Crystal structure of mutated 3-isopropylmalate dehydrogenease from Thermus thermophilus HB8 and their relationship to the thermostability of the enzyme" J.Biochem.117. 408-413 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kitakami, H.et al.: "YAMATO and ASUKA : DNA Database Management Systems" Proceedings of the Twenty-Eighth Annual Hawaii International Conference on System Sciences. 72-80 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Tateno, Y.: "Development of information biology" Protein, Nucleic Acid, and Enzyme. 40. 102-108 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Tateno, Y.: "Gene" Dictionary of Mathematics, Physics, and Information Science. 39-42 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Tsukihara T.et al.: "Structures of Metal Sites of Oxidized Bovine Heart Cytochrome c Oxidase at 2.8*" Science. Vol.269. 1069-1704 (1995)

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

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Published: 1999-03-09  

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