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Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein-protein interaction network.

Abstract

Although gene duplications occur at a higher rate, only a small fraction of these are retained. The position of a gene's encoded product in the protein-protein interaction network has recently emerged as a determining factor of gene duplicability. However, the direction of the relationship between network centrality and duplicability is not universal: In Escherichia coli, yeast, fly, and worm, duplicated genes more often act at the periphery of the network, whereas in humans, such genes tend to occupy the most central positions. Herein, we have inferred duplication events that took place in the different branches of the primate phylogeny. In agreement with previous observations, we found that duplications generally affected the most central network genes, which is presumably the process that has most influenced the trend in humans. However, the opposite trend--that is, duplication being more common in genes whose encoded products are peripheral in the network--is observed for three recent branches, including, quite counterintuitively, the external branch leading to humans. This indicates a shift in the relationship between centrality and duplicability during primate evolution. Furthermore, we found that genes encoding interacting proteins exhibit phylogenetic tree topologies that are more similar than expected for random pairs and that genes duplicated in a given branch of the phylogeny tend to interact with those that duplicated in the same lineage. These results indicate that duplication of a gene increases the likelihood of duplication of its interacting partners. Our observations indicate that the structure of the primate protein-protein interaction network affects gene duplicability in previously unrecognized ways.

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  • Publisher Full Text

    • Authors

    Doherty A, Alvarez-Ponce D, McInerney JO

    Institution

    Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland.

    Source

    Molecular biology and evolution 29:11 2012 Nov pg 3563-73

    MeSH

    Animals
    Biological Evolution
    Gene Duplication
    Genes, Duplicate
    Genome
    Humans
    Phylogeny
    Primates
    Protein Interaction Maps

    Pub Type(s)

    Journal Article
    Research Support, Non-U.S. Gov't

    Language

    eng

    PubMed ID

    22723304