Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires.
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires.
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DOI：
10.1186/gb-2011-12-1-r4
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发表时间：
2011
期刊：
影响因子：
12.3
通讯作者：
Godzik A
中科院分区：
文献类型：
--
作者：
Zmasek CM;Godzik A
基因组的大小和复杂性，以基因或蛋白质结构域的数量来衡量，在大多数现存的真核生物中是非常相似的，并且通常与它们的形态复杂性无关。不同真核生物基因组的功能含量和能力进化的潜在趋势可能被基因的同时获得和丢失所掩盖。我们在主要的分歧点重建了假定的祖先物种的域谱，包括最后的真核共同祖先（LECA）。我们表明，令人惊讶的是，在真核生物进化过程中，结构域损失通常超过结构域增益。只有在动物和脊椎动物子树的基础上，领域的获得多于领域的损失。观察到的得失平衡具有明显的功能偏差，在动物进化过程中最为明显，其中大多数增益代表与调节有关的域，而大多数损失代表与代谢功能有关的域。这种趋势是如此一致，以至于根据它们的功能概况对基因组进行聚类，形成了一个类似于生命之树的组织。此外，我们的研究结果表明，在动物进化过程中失去的代谢功能可能被肠道微生物等共生生物的代谢能力所取代。虽然蛋白质结构域的获得和损失在真核生物进化过程中很常见，但损失往往大于收益，并导致功能谱的显着差异。这里提出的结果为复杂的最后真核共同祖先提供了额外的论据，但也显示了在动物崛起过程中代谢能力的丧失和调节复杂性的增加的总体趋势。
Genome size and complexity, as measured by the number of genes or protein domains, is remarkably similar in most extant eukaryotes and generally exhibits no correlation with their morphological complexity. Underlying trends in the evolution of the functional content and capabilities of different eukaryotic genomes might be hidden by simultaneous gains and losses of genes. We reconstructed the domain repertoires of putative ancestral species at major divergence points, including the last eukaryotic common ancestor (LECA). We show that, surprisingly, during eukaryotic evolution domain losses in general outnumber domain gains. Only at the base of the animal and the vertebrate sub-trees do domain gains outnumber domain losses. The observed gain/loss balance has a distinct functional bias, most strikingly seen during animal evolution, where most of the gains represent domains involved in regulation and most of the losses represent domains with metabolic functions. This trend is so consistent that clustering of genomes according to their functional profiles results in an organization similar to the tree of life. Furthermore, our results indicate that metabolic functions lost during animal evolution are likely being replaced by the metabolic capabilities of symbiotic organisms such as gut microbes. While protein domain gains and losses are common throughout eukaryote evolution, losses oftentimes outweigh gains and lead to significant differences in functional profiles. Results presented here provide additional arguments for a complex last eukaryotic common ancestor, but also show a general trend of losses in metabolic capabilities and gain in regulatory complexity during the rise of animals.
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