Sato Yukuto, Nishida Mutsumi
Division of Molecular Marine Biology, Ocean Research Institute, The University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan.
BMC Evol Biol. 2007 Oct 29;7:204. doi: 10.1186/1471-2148-7-204.
The partitioning of ancestral functions among duplicated genes by neutral evolution, or subfunctionalization, has been considered the primary process for the evolution of novel proteins (neofunctionalization). Nonetheless, how a subfunctionalized protein can evolve into a more adaptive protein is poorly understood, mainly due to the limitations of current analytical methods, which can detect only strong selection for amino acid substitutions involved in adaptive molecular evolution. In this study, we employed a comparative evolutionary approach to this question, focusing on differences in the structural properties of a protein, specifically the electric charge, encoded by fish-specific duplicated phosphoglucose isomerase (Pgi) genes.
Full-length cDNA cloning, RT-PCR based gene expression analyses, and comparative sequence analyses showed that after subfunctionalization with respect to the expression organ of duplicate Pgi genes, the net electric charge of the PGI-1 protein expressed mainly in internal tissues became more negative, and that of PGI-2 expressed mainly in muscular tissues became more positive. The difference in net protein charge was attributable not to specific amino acid sites but to the sum of various amino acid sites located on the surface of the PGI molecule.
This finding suggests that the surface charge evolution of PGI proteins was not driven by strong selection on individual amino acid sites leading to permanent fixation of a particular residue, but rather was driven by weak selection on a large number of amino acid sites and consequently by steady directional and/or purifying selection on the overall structural properties of the protein, which is derived from many modifiable sites. The mode of molecular evolution presented here may be relevant to various cases of adaptive modification in proteins, such as hydrophobic properties, molecular size, and electric charge.
通过中性进化在重复基因间划分祖先功能，即亚功能化，被认为是新蛋白质（新功能化）进化的主要过程。然而，亚功能化蛋白质如何进化为更具适应性的蛋白质却鲜为人知，主要是由于当前分析方法的局限性，这些方法只能检测到对适应性分子进化中涉及的氨基酸替换的强烈选择。在本研究中，我们采用比较进化方法来解决这个问题，重点关注鱼类特异性重复磷酸葡萄糖异构酶（Pgi）基因编码的蛋白质的结构特性差异，特别是电荷。
全长cDNA克隆、基于RT-PCR的基因表达分析和比较序列分析表明，在重复的Pgi基因在表达器官方面发生亚功能化后，主要在内脏组织中表达的PGI-1蛋白的净电荷变得更负，而主要在肌肉组织中表达的PGI-2蛋白的净电荷变得更正。蛋白质净电荷的差异并非归因于特定的氨基酸位点，而是归因于PGI分子表面多个氨基酸位点的总和。
这一发现表明，PGI蛋白的表面电荷进化并非由对单个氨基酸位点的强烈选择驱动，导致特定残基的永久固定，而是由对大量氨基酸位点的弱选择驱动，进而由对蛋白质整体结构特性的稳定定向和/或纯化选择驱动，而蛋白质整体结构特性源自许多可修饰位点。这里呈现的分子进化模式可能与蛋白质适应性修饰的各种情况相关，如疏水性、分子大小和电荷。
