Single-Gene and Whole-Genome Duplications and the Evolution of Protein-Protein Interaction Networks.

Proteins within a cell do not function in isolation, but instead physically interact with their molecular environment, either to transduce information from the external environment to the nucleus or to form multisubunit protein complexes that act as sophisticated molecular machines. Since the functionality of the cell depends on these physical interactions, it is no surprise that great effort is being made in cataloguing the interactome of a genome, that is, to identify and describe all protein–protein interactions (PPIs) a protein participates in. In this era of “omics” technologies and systems biology, researchers try to deal with the interactome of a given organism in a holistic approach, and try to reconstruct protein–protein interaction networks (PINs), using graph theory (Barabasi and Oltvai, 2004). In such networks, proteins are represented as nodes in a graph, and edges connect nodes that physically interact, or nodes that participate in the same complex. There is a significant amount of work on the principles of PINs, their statistical properties, and their significance for the cell (Barabasi and Oltvai, 2004), but the focus of this review is on the evolution of PPIs and more particularly the contribution of two major sources of molecular innovation, namely, single-gene and whole-genome duplications. It is important to understand the evolution of PPIs in order to address fundamental questions about molecular biology and to use the interactome correctly. First of all, we need to understand which molecular mechanisms are responsible for innovation and the evolution of PINs, and the extent of contribution of each one of those mechanisms. Also, PINs from different organisms need to be compared, in order to understand which are the universal core protein complexes, which protein complexes are specific to a certain clade of organisms, and which are unique to one species. In this way, wewill knowwhich experimentally determined interactions can be transferred from one organism to another and which interactions are not transferable. In addition, by studying the evolution of PPIs and PINs, we will better understand the components and types of interactions that are responsible for increasing biological complexity. It is well acknowledged that organismal complexity correlates with the number and coverage of PPI domains per protein (Xia et al., 2008). Complexity also seems to correlate with an expansion of certain gene families (van Nimwegen, 2003). We need to understand whether these particular families are linked to specific types of interactions and to improve our knowledge on the relationship between organismal complexity, the various modes of duplication, and PPIs. Here, we will first introduce the sources of molecular innovation in PINs, that is, through gene and genome duplications and mutations. Second, we will discuss and review studies from genome-scale data that provide a bird’s eye view about the importance of each source of molecular innovation, and finally, we will cite some medium-scale studies that use high-quality data and provide an in-depth view about the impact of gene/genome duplication on the evolution of PPIs.

Amoutzias, G., Van de Peer, Y. (2010) Single-Gene and Whole-Genome Duplications and the Evolution of Protein-Protein Interaction Networks. Evolutionary Genomics and Systems Biology (Book Chapter, Ed. Caetano-Anollés, G.),413-429.

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