Function-selective domain architecture plasticity potentials in eukaryotic genome evolution.
Function-selective domain architecture plasticity potentials in eukaryotic genome evolution.
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DOI：
10.1016/j.biochi.2015.05.003
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发表时间：
2015-12
期刊：
影响因子：
3.9
通讯作者：
Fang H
中科院分区：
文献类型：
--
作者：
Linkeviciute V;Rackham OJ;Gough J;Oates ME;Fang H
为了帮助评估蛋白质功能如何影响基因组进化，我们引入了“结构可塑性潜力”的新概念，即形成不同结构域结构的能力，既适用于单个结构域，也适用于按共享功能分组的一组结构域。我们设计了一个评分指标来衡量这些域集的可塑性潜力，并评估不同物种的功能如何随时间变化。将这一指标应用于真核生物基因组的系统发育树，我们发现每个功能的参与不是随机的，而是高度选择性的。对于某些谱系来说，有强烈的倾向于进化涉及与某些功能相关的领域。一般来说，真核生物的基因组，特别是动物，扩展了复杂的功能活动，如信号传导和调节，但代价是减少代谢过程。我们还观察到转录调控的差异进化和通道调控的独特进化作用；至关重要的是，这只能在建筑可塑性潜力方面观察到。我们的发现为理解功能在真核生物基因组进化中的意义提供了一个新的信息层面。一个网络搜索工具，可在http://supfam.org/Pevo上获得，为探索真核生物基因组进化中的功能重要性提供了广泛的选择。一种测量基因组结构域结构可塑性潜能的新概念。我们揭示了功能选择在真核生物基因组进化中的作用。真核基因组扩展信号和调控，但减少代谢。我们观察到反式和顺式调控之间的差异演化。我们观察到通道调节剂在分离真核生物王国中的独特作用。
To help evaluate how protein function impacts on genome evolution, we introduce a new concept of ‘architecture plasticity potential’ – the capacity to form distinct domain architectures – both for an individual domain, or more generally for a set of domains grouped by shared function. We devise a scoring metric to measure the plasticity potential for these domain sets, and evaluate how function has changed over time for different species. Applying this metric to a phylogenetic tree of eukaryotic genomes, we find that the involvement of each function is not random but highly selective. For certain lineages there is strong bias for evolution to involve domains related to certain functions. In general eukaryotic genomes, particularly animals, expand complex functional activities such as signalling and regulation, but at the cost of reducing metabolic processes. We also observe differential evolution of transcriptional regulation and a unique evolutionary role of channel regulators; crucially this is only observable in terms of the architecture plasticity potential. Our findings provide a new layer of information to understand the significance of function in eukaryotic genome evolution. A web search tool, available at http://supfam.org/Pevo, offers a wide spectrum of options for exploring functional importance in eukaryotic genome evolution. A new concept to measure domain architecture plasticity potential in a genome. We reveal the function-selective role in eukaryotic genome evolution. Eukaryotic genomes expand signalling and regulations but reduce metabolism. We observe differential evolution between trans- and cis-acting regulations. We observe a unique role of channel regulators in separating eukaryotic kingdoms.