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

随着基因组分析的出现，人们已经清楚地认识到，基因不是一个单一的实体，而是由具有不同进化起源和历史的子区域组成。因此，“一基因多功能，一基因多结构”比“一基因一功能，一基因一结构”更符合实际。这意味着现在的基因是在进化过程中由更小的片段形成的。我们称之为进化基序（EM）。为了探讨其意义：（1）从分子进化的角度，我们从国际DNA数据库中的DNA序列翻译的完整氨基酸序列进行了比对。为了进行比对，我们开发了一种方法，通过该方法交替重复系统发育树构建和多重比对，直到两者给出一致的结果。然后，我们通过在比对序列中定位进化上保守的残基来搜索EM。EM的平均长度估计为60个残基，这是蛋白质中许多功能和结构区域的大小。（2）将所得EM分为亲水性EM、疏水性EM和中间型EM。我们认为，亲水性EM位于蛋白质的表面并发挥生物学作用，而疏水性EM则进入蛋白质内部并与其结构有关。（3）通过对比对序列的同义和非同义替换数目的估计，我们发现90%以上的序列的进化机制可以用中性突变理论来解释。(4)We进一步阐明了细胞色素c氧化酶和3-异丙基苹果酸脱氢酶的三维结构，并证实了这些结构是由不同功能的亚结构组成的，这些结果有力地支持了我们的观点，即现在的基因是通过吸收（和丢弃）当时可用的EM而产生和进化的。

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.