The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks

TL;DR

This study reconstructs ancient protein-protein interaction networks from present-day data, revealing that PPI networks grow multiplicatively and support the duplication-divergence evolutionary model, enhancing understanding of cellular function evolution.

Contribution

It introduces a novel framework combining bioinformatics and theoretical modeling to reconstruct and analyze ancestral PPI networks, validating the duplication-divergence model.

Findings

PPI networks exhibit multiplicative growth over evolutionary time.

Ancient PPI networks support the duplication-divergence evolution model.

Networks display fractality and modularity consistent with theoretical predictions.

Abstract

Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale PPI networks of several model organisms were investigated. Methodological improvements now allow the analysis of PPI networks of multiple organisms simultaneously as well as the direct modeling of ancestral networks. This provides the opportunity to challenge existing assumptions on network evolution. We utilized present-day PPI networks from integrated datasets of seven model organisms and developed a theoretical and bioinformatic framework for studying the evolutionary dynamics of PPI networks. A novel filtering approach using percolation analysis was developed to remove low confidence interactions based on topological constraints. We then reconstructed the ancient PPI networks of different ancestors, for which the ancestral proteomes, as well as the ancestral interactions, were inferred. Ancestral proteins were reconstructed using orthologous groups on different evolutionary levels. A stochastic approach, using the duplication-divergence model, was developed for estimating the probabilities of ancient interactions from today's PPI networks. The growth rates for nodes, edges, sizes and modularities of the networks indicate multiplicative growth and are consistent with the results from independent static analysis. Our results support the duplication-divergence model of evolution and indicate fractality and multiplicative growth as general properties of the PPI network structure and dynamics.