How the global structure of protein interaction networks evolves

TL;DR

This paper investigates how protein interaction networks evolve through interaction changes and gene duplications, showing these processes shape network structure independently of natural selection.

Contribution

It provides estimates of interaction turnover rates in yeast and explains the evolution of network degree distribution without invoking natural selection.

Findings

Over 100 interactions added per million years in yeast

Highly connected proteins have higher interaction turnover

Distribution P(d) remains broad-tailed regardless of experimental method

Abstract

Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can be estimated from available Saccharomyces cerevisiae genome data and are sufficiently high to affect network structure on short time scales. For instance, more than 100 interactions may be added to the yeast network every million years, a substantial fraction of which adds previously unconnected proteins to the network. Highly connected proteins show a greater rate of interaction turnover than proteins with few interactions. From these observations one can explain ? without natural selection on global network structure ? the evolutionary sustenance of the most prominent network feature, the distribution of the frequency P(d) of proteins with d neighbors, which is a broad-tailed distribution. This distribution is independent of the experimental approach providing nformation on network structure.