A model of large-scale proteome evolution

TL;DR

This paper introduces a simple evolutionary model for proteomes that explains their complex network topology through gene duplication and diversification under selection for robustness, matching observed yeast proteome data.

Contribution

It presents a novel model of proteome evolution that reproduces key statistical features of real proteome networks, highlighting the role of gene duplication and robustness.

Findings

Model reproduces statistical regularities of yeast proteome networks

Gene duplication and diversification explain network topology

Selection for robustness shapes proteome evolution

Abstract

The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have shown that its topology displays a number of surprising features shared by other complex networks, both natural and artificial. In order to understand the origins of this topology and its evolutionary implications, we present a simple model of proteome evolution that is able to reproduce many of the observed statistical regularities reported from the analysis of the yeast proteome. Our results suggest that the observed patterns can be explained by a process of gene duplication and diversification that would evolve proteome networks under a selection pressure, favoring robustness against failure of its individual components.