Conservation and topology of protein interaction networks under duplication-divergence evolution
Conservation and topology of protein interaction networks under duplication-divergence evolution
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DOI：
10.1073/pnas.0804119105
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发表时间：
2008-07-22
影响因子：
11.1
通讯作者：
Isambert, Herve
中科院分区：
文献类型：
--
作者：
Evlampiev, Kirill;Isambert, Herve
基因组复制-分化过程是新蛋白质功能的主要来源，从而有助于功能分子网络的进化扩展。然而，目前尚不清楚这种复制分歧过程在多大程度上也通过构建分子网络的新兴特性而受到限制，无论任何特定的细胞功能如何。我们在这里解决这个问题，重点关注蛋白质-蛋白质相互作用（PPI）网络的进化。我们解决了一般的重复-分歧模型，该模型基于从单基因到全基因组重复的各种基因组规模的随机重复所产生的蛋白质-蛋白质相互作用的统计上必要的删除。主要的进化场景仅取决于两个全局参数：（i）控制 PPI 网络进化历史的蛋白质保守指数（M），以及（ii）控制其最终结构的独特拓扑指数（M'）。然后，我们证明，具有主要生物学相关性的保守的非稠密网络也必然是无标度的，无论模型参数的任何进化变化或波动如何。它被证明是由一般复制-发散进化下个体蛋白质保守性和网络拓扑之间的基本联系产生的。相比之下，我们发现，具有两个或多个蛋白质的网络基序的保守性不能在一般重复-趋异进化（独立于任何网络重新布线动态）下无限期地保留，这与系统发育上遥远物种之间的经验证据广泛一致。总而言之，这些重复分化过程固有的进化限制似乎在很大程度上控制了 PPI 网络的整体拓扑和尺度依赖性保护，无论任何特定的生物功能如何。
Genomic duplication-divergence processes are the primary source of new protein functions and thereby contribute to the evolutionary expansion of functional molecular networks. Yet, it is still unclear to what extent such duplication-divergence processes also restrict by construction the emerging properties of molecular networks, regardless of any specific cellular functions. We address this question, here, focusing on the evolution of protein-protein interaction (PPI) networks. We solve a general duplication-divergence model, based on the statistically necessary deletions of protein-protein interactions arising from stochastic duplications at various genomic scales, from single-gene to whole-genome duplications. Major evolutionary scenarios are shown to depend on two global parameters only: (i) a protein conservation index (M), which controls the evolutionary history of PPI networks, and (ii) a distinct topology index (M') controlling their resulting structure. We then demonstrate that conserved, nondense networks, which are of prime biological relevance, are also necessarily scale-free by construction, irrespective of any evolutionary variations or fluctuations of the model parameters. It is shown to result from a fundamental linkage between individual protein conservation and network topology under general duplication-divergence evolution. By contrast, we find that conservation of network motifs with two or more proteins cannot be indefinitely preserved under general duplication-divergence evolution (independently from any network rewiring dynamics), in broad agreement with empirical evidence between phylogenetically distant species. All in all, these evolutionary constraints, inherent to duplication-divergence processes, appear to have largely controlled the overall topology and scale-dependent conservation of PPI networks, regardless of any specific biological function.