Approaches to defining the ancestral eukaryotic protein complexome
Approaches to defining the ancestral eukaryotic protein complexome
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DOI：
10.1002/bies.20373
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发表时间：
2006-03-01
期刊：
影响因子：
4
通讯作者：
Bollen, M
中科院分区：
文献类型：
--
作者：
Ceulemans, H;Beke, L;Bollen, M
在本文中，我们整合和总结了目前关于真核生物祖先蛋白质复合物的信息，它被定义为现存真核生物从其最后共同祖先遗传的一组蛋白质复合物。从文献中，我们从真核模式生物中编译了具有三种或更多不同蛋白质成分的复合物列表。膜相关信号蛋白和特异性转录因子的组合复合物被忽略。一种严格但敏感的新型同源检测算法，加上人工序列相似性搜索和全基因组或片段和串联基因复制的已发表数据，使我们能够将绝大多数这些复合物映射到称为真核虚拟祖先（EVA）的虚拟原始真核生物。EVA旨在类似于最后一个共同的真核生物祖先，并在分子水平上模拟主要真核生物谱系的生物学共同点。然后将该数据集用于祖先真核生物络合物的功能和区域注释。此外，我们说明了它的有用性，以推断很少研究的真核生物的复合体和高度不同的同源物的识别。我们还讨论了大约1400个复合物相关的祖先蛋白质的进化。在所有13种被研究的自由生活的真核生物中，大约90%的这些蛋白质是保守的，复合物的进化减少和损失似乎是最小的。此外，现有的数据表明，一般来说，获得稳定的新设计复合物发生得太慢，不能成为进化创新的主要贡献者。最后，鉴于祖先真核复杂体的稳定性，我们建议在旨在模拟生物过程的数学系统的公式中使用它。我们的数据表明，这些简化的公式可以适用于大多数自由生活的真核生物模型。
In this paper, we integrate and summarize the currently available information on the ancestral eukaryotic protein complexome, which is defined as the set of protein complexes that extant eukaryotes inherited from their last common ancestor. From the literature, we compiled lists of complexes with three or more distinct protein components from well-studied eukaryotic model organisms. Combinatorial complexes of membrane-associated signalling proteins and specific transcription factors were disregarded. A stringent but sensitive novel orthology detection algorithm, complemented with manual sequence similarity searches and with published data on whole genome or segmental and tandem gene duplications, enabled us to map the vast majority of these complexes to a virtual primitive eukaryote termed Eukaryotic Virtual Ancestor (EVA). EVA is intended to resemble the last common eukaryotic ancestor and to emulate the biological common denominator of the major extent eukaryotic lineages at the molecular level. The dataset was then used for the functional and domain annotation of the ancestral eukaryotic complexome. Furthermore, we illustrate its usefulness for inferring complexes of poorly studied eukaryotes and for the recognition of highly divergent orthologs. We also discuss the evolution of the circa 1,400 complex-associated ancestral proteins. As about 90% of these proteins have been conserved in all thirteen studied free-living eukaryotes, the evolutionary reduction and loss of complexes seems minimal. Moreover, the available data suggest that, in general, the acquisition of stable complexes of novel design occurs too slowly to be a major contributor to evolutionary innovation. Finally, given the stability of the ancestral eukarotic complexome we propose its use in the formulation of the mathematical systems that aim to simulate biological processes. Our data suggest that these simplified formulations can apply to most free-living model eukaryotes.