State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China.
BMC Evol Biol. 2011 May 20;11:133. doi: 10.1186/1471-2148-11-133.
High-throughput screens have revealed large-scale protein interaction networks defining most cellular functions. How the proteins were added to the protein interaction network during its growth is a basic and important issue. Network motifs represent the simplest building blocks of cellular machines and are of biological significance.
Here we study the evolution of protein interaction networks from the perspective of network motifs. We find that in current protein interaction networks, proteins of the same age class tend to form motifs and such co-origins of motif constituents are affected by their topologies and biological functions. Further, we find that the proteins within motifs whose constituents are of the same age class tend to be densely interconnected, co-evolve and share the same biological functions, and these motifs tend to be within protein complexes.
Our findings provide novel evidence for the hypothesis of the additions of clustered interacting nodes and point out network motifs, especially the motifs with the dense topology and specific function may play important roles during this process. Our results suggest functional constraints may be the underlying driving force for such additions of clustered interacting nodes.
高通量筛选已经揭示了定义大多数细胞功能的大规模蛋白质相互作用网络。在蛋白质相互作用网络的生长过程中，蛋白质是如何被添加到网络中的，这是一个基本且重要的问题。网络基元代表了细胞机器的最简单构建块，具有生物学意义。
在这里，我们从网络基元的角度研究蛋白质相互作用网络的进化。我们发现，在当前的蛋白质相互作用网络中，具有相同年龄类别的蛋白质往往会形成基元，并且基元组成部分的这种共同起源受到它们的拓扑结构和生物学功能的影响。此外，我们发现，在具有相同年龄类别的组成部分的基元内的蛋白质往往彼此之间紧密地相互连接，共同进化并具有相同的生物学功能，这些基元往往位于蛋白质复合物内。
我们的研究结果为聚集相互作用节点的添加的假设提供了新的证据，并指出网络基元，特别是具有密集拓扑结构和特定功能的基元，可能在这一过程中发挥重要作用。我们的研究结果表明，功能约束可能是这种聚集相互作用节点添加的潜在驱动力。
