1996 Fiscal Year Final Research Report Summary
Development of "Molecular Structural Phylogeny" on the Consideration of Protein 3D structure
Grant-in-Aid for Scientific Research (A)
|Allocation Type||Single-year Grants |
|Research Institution||National Institute of Genetics |
TATENO Yoshio National Institute of Genetics, Center for Information Biology, Professor -> 国立遺伝学研究所, 生命情報研究センター, 教授 (00202424)
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
|Keywords||molecular phylogeny / protein 3D structure / evolutionary motif / viral evolution / natural selection / cytochrome c oxidase / 3-isopropylmalate dehydrogenase|
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)