RT Journal Article
SR Electronic
T1 Resurrected protein interaction networks reveal the strong rewiring that leads to network organisation after whole genome duplication
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 074989
DO 10.1101/074989
A1 Zhicheng Zhang
A1 Heleen Coenen
A1 Philip Ruelens
A1 Rashmi Hazarika
A1 Tareq Al Hindi
A1 Georgianna K. Oguis
A1 Vera Van Noort
A1 Koen Geuten
YR 2016
UL http://biorxiv.org/content/early/2016/09/13/074989.abstract
AB The evolution of plant genomes is characterized by several rounds of polyploidization or ancient whole genome duplication. While the consequences of these major events for genome structure and transcriptome expression have been investigated, the effects at the protein level remain unknown and yet will be functionally important. To understand how a plant protein-protein interaction network organizes itself after whole genome duplication, we studied the evolution of MADS-domain transcription factors. We accurately inferred, resurrected and tested the interactions of their ancestral proteins before and after the gamma triplication at the origin of core eudicots and directly compare these ancestral networks to the networks of Arabidopsis and tomato. We find that the gamma triplication generated a network constrained in size and saturated in possible number of interactions, which strongly rewired by the addition of many new interactions. The new interactions are surprisingly often established with related proteins, something we call neo-redundancy. The evolved networks are organized around hubs and into modules. The direct observation of preferential attachment of existing interactions to hubs through gene duplication explains the scale-free organization. The evolutionary optimal modular organization is favored by the addition of new interactions to the network and by the avoidance of mis-interactions, as shown by simulations. The resurrection of ancestral networks and the direct observation of ancestral rewiring events allowed us to elucidate the role of whole genome triplication, elementary processes and evolutionary mechanisms in the origin of a biological network.Author summary The complement of all DNA in an organism is called the genome, while the complement of all proteins is called the proteome. The cooperation between proteins in a proteome is organised in particular ways of which the origin and significance is not fully understood. Plants and — to a lesser extent — animals have undergone ancient and recent duplications of their genomes and corresponding proteomes in the course of evolutionary history. These are considered important events that may have coincided with the origin of important groups of species. However the consequences of such duplications for the organism are not well understood. Here we study ancient and current sample proteomes by resurrecting the ancestral proteins and comparing how they interacted with other proteins millions of years ago and now. We find that a genome duplication dramatically reorganised the proteome and the proteome acquired its organisation by the addition of new interactions and avoiding mis-interactions.