The role of internal duplication in the evolution of multi-domain proteins
The role of internal duplication in the evolution of multi-domain proteins
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DOI：
10.1016/j.biosystems.2010.05.005
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发表时间：
2010-08-01
期刊：
影响因子：
1.6
通讯作者：
Akutsu, T.
中科院分区：
文献类型：
--
作者：
Nacher, J. C.;Hayashida, M.;Akutsu, T.
许多蛋白质由几个结构域组成。这些多结构域蛋白可能是在进化过程中通过选择性基因组生长动力学产生的，以执行新的功能，以及创造在生物学上可行的时间尺度上折叠的结构域单元经常通过各种遗传改组机制进化。在这里，我们检查了1000多个生物体，包括真核生物，古细菌和细菌物种的蛋白质结构域的统计分析扩展了早期的发现不对称的统计规律的蛋白质组，以更广泛的物种，而蛋白质是由广泛的结构域。显示幂律衰减，每个蛋白质的结构域家族的计算揭示了指数分布，表征了由少量独特家族组成的蛋白质宇宙。蛋白质组学中的结构研究表明，结构域重复或内部重复结构域代表了基因组中很小但很重要的一部分。尽管这一观察很重要，但直到最近才在很大程度上被忽视。我们模拟蛋白质组的进化动力学，并证明这些不同的分布实际上是植根于内部复制机制。这一过程产生了当代蛋白质结构域宇宙，决定了它的厚度减少，并驯服了它的增长这些发现具有重要的意义，从蛋白质相互作用网络建模到基于基因组扩展基本机制的进化研究（C）2010 Elsevier爱尔兰有限公司版权所有
Many proteins consist of several structural domains. These multi-domain proteins have likely been generated by selective genome growth dynamics during evolution to perform new functions as well as to create structures that fold on a biologically feasible time scale Domain units frequently evolved through a variety of genetic shuffling mechanisms. Here we examine the protein domain statistics of more than 1000 organisms including eukaryotic, archaeal and bacterial species The analysis extends earlier findings on asymmetric statistical laws for proteome to a wider variety of species While proteins are composed of a wide range of domains. displaying a power-law decay, the computation of domain families for each protein reveals an exponential distribution, characterizing a protein universe composed of a thin number of unique families Structural studies in proteomics have shown that domain repeats, or internal duplicated domains, represent a small but significant fraction of genome. In spite of its importance, this observation has been largely overlooked until recently. We model the evolutionary dynamics of proteome and demonstrate that these distinct distributions are in fact rooted in an internal duplication mechanism. This process generates the contemporary protein structural domain universe, determines its reduced thickness, and tames its growth These findings have important implications, ranging from protein interaction network modeling to evolutionary studies based on fundamental mechanisms governing genome expansion (C) 2010 Elsevier Ireland Ltd All rights reserved