dorsal/arxiv
View SchemaEvolution of Protein Interaction Networks by Whole Genome Duplication and Domain Shuffling
| Authors | K. Evlampiev, H. Isambert |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0606036 |
| URL | https://arxiv.org/abs/q-bio/0606036 |
Abstract
Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. It is not clear, however, how such dramatic evolutionary process has contributed to shape the large scale topology of protein-protein interaction (PPI) networks. We propose and analytically solve a generic model of PPI network evolution under successive whole genome duplications. This demonstrates that the observed scale-free degree distributions and conserved multi-protein complexes may have concomitantly arised from i) intrinsic exponential dynamics of PPI network evolution and ii) asymmetric divergence of gene duplicates. This requirement of asymmetric divergence is in fact "spontaneously" fulfilled at the level of protein-binding domains. In addition, domain shuffling of multi-domain proteins is shown to provide a powerful combinatorial source of PPI network innovation, while preserving essential structures of the underlying single-domain interaction network. Finally, large scale features of PPI networks reflecting the "combinatorial logic" behind direct and indirect protein interactions are well reproduced numerically with only two adjusted parameters of clear biological significance.
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"abstract": "Successive whole genome duplications have recently been firmly established in\nall major eukaryote kingdoms. It is not clear, however, how such dramatic\nevolutionary process has contributed to shape the large scale topology of\nprotein-protein interaction (PPI) networks. We propose and analytically solve a\ngeneric model of PPI network evolution under successive whole genome\nduplications. This demonstrates that the observed scale-free degree\ndistributions and conserved multi-protein complexes may have concomitantly\narised from i) intrinsic exponential dynamics of PPI network evolution and ii)\nasymmetric divergence of gene duplicates. This requirement of asymmetric\ndivergence is in fact \"spontaneously\" fulfilled at the level of protein-binding\ndomains. In addition, domain shuffling of multi-domain proteins is shown to\nprovide a powerful combinatorial source of PPI network innovation, while\npreserving essential structures of the underlying single-domain interaction\nnetwork. Finally, large scale features of PPI networks reflecting the\n\"combinatorial logic\" behind direct and indirect protein interactions are well\nreproduced numerically with only two adjusted parameters of clear biological\nsignificance.",
"arxiv_id": "q-bio/0606036",
"authors": [
"K. Evlampiev",
"H. Isambert"
],
"categories": [
"q-bio.MN"
],
"title": "Evolution of Protein Interaction Networks by Whole Genome Duplication and Domain Shuffling",
"url": "https://arxiv.org/abs/q-bio/0606036"
},
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