Evolution of protein domain promiscuity in eukaryotes
Evolution of protein domain promiscuity in eukaryotes
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DOI：
10.1101/gr.6943508
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发表时间：
2008-03-01
期刊：
影响因子：
7
通讯作者：
Koonin, Eugene V.
中科院分区：
文献类型：
--
作者：
Basu, Malay Kumar;Carmel, Liran;Koonin, Eugene V.
许多真核蛋白质含有多个结构域。某些域表现出出现在不同域体系结构中的趋势，并且可以被认为是“混杂的”。这些混杂的结构域通常参与蛋白质-蛋白质相互作用，并在相互作用网络中发挥关键作用，特别是那些有助于信号转导的网络。描述了真核生物中混杂结构域的系统比较基因组分析。引入了域混杂性的两种定量测量方法，并将其应用于不同真核生物的 28 个基因组的分析。总共有 215 个域被识别为严重混杂。动物中混杂结构域的比例明显高于真菌或植物中的比例。进化重建表明，结构域混杂是真核蛋白质的一个不稳定的、相对快速变化的特征，在真核生物的整个进化过程中，很少有结构域保持混杂。有些领域似乎在不同的谱系中独立地实现了混交，例如动物和植物。有人提出，混杂的域持续存在于相对较小的进化稳定域组合池中，在进化过程中从中出现了许多罕见的体系结构。域混杂与实验检测到的域相互作用的数量以及影响域的纯化选择的强度呈正相关。因此，混杂域的进化似乎受到其交互伙伴的多样性的限制。这组混杂结构域富含介导蛋白质-蛋白质相互作用的结构域，这些结构域涉及各种形式的信号转导，特别是在泛素系统和染色质中。因此，有限的混杂结构域对真核蛋白质组和信号网络的多样性和进化性做出了重大贡献。
Numerous eukaryotic proteins contain multiple domains. Certain domains show a tendency to occur in diverse domain architectures and can be considered "promiscuous." These promiscuous domains are, typically, involved in protein-protein interactions and play crucial roles in interaction networks, particularly those that contribute to signal transduction. A systematic comparative-genomic analysis of promiscuous domains in eukaryotes is described. Two quantitative measures of domain promiscuity are introduced and applied to the analysis of 28 genomes of diverse eukaryotes. Altogether, 215 domains are identified as strongly promiscuous. The fraction of promiscuous domains in animals is shown to be significantly greater than that in fungi or plants. Evolutionary reconstructions indicate that domain promiscuity is a volatile, relatively fast-changing feature of eukaryotic proteins, with few domains remaining promiscuous throughout the evolution of eukaryotes. Some domains appear to have attained promiscuity independently in different lineages, for example, animals and plants. It is proposed that promiscuous domains persist within a relatively small pool of evolutionarily stable domain combinations from which numerous rare architectures emerge during evolution. Domain promiscuity positively correlates with the number of experimentally detected domain interactions and with the strength of purifying selection affecting a domain. Thus, evolution of promiscuous domains seems to be constrained by the diversity of their interaction partners. The set of promiscuous domains is enriched for domains mediating protein-protein interactions that are involved in various forms of signal transduction, especially in the ubiquitin system and in chromatin. Thus, a limited repertoire of promiscuous domains makes a major contribution to the diversity and evolvability of eukaryotic proteomes and signaling networks.