Bacterial protein interaction networks: connectivity is ruled by gene conservation, essentiality and function

TL;DR

This study investigates how gene conservation, essentiality, and function influence protein connectivity in bacterial PPI networks across 42 genomes, revealing a conserved core of highly connected, essential, and conserved proteins mainly involved in genetic information processing.

Contribution

It demonstrates that gene conservation, essentiality, and functional categories constrain protein connectivity in bacterial PPI networks, identifying a conserved core of highly connected proteins.

Findings

Highly connected proteins (k≥40) are conserved and essential.

A core of highly connected proteins is common across bacteria with small genomes.

Most core proteins are involved in ribosomal and genetic information processing functions.

Abstract

Protein-protein interaction (PPI) networks are the backbone of all processes in living cells. In this work we relate conservation, essentiality and functional repertoire of a gene to the connectivity $k$ (i.e., the number of interaction links) of the corresponding protein in the PPI network. On a set of 42 bacterial genomes of different sizes, and with reasonably separated evolutionary trajectories, we investigate three issues: i) whether the distribution of connectivities changes between PPI subnetworks of essential and nonessential genes; ii) how gene conservation, measured both by the evolutionary retention index (ERI) and by evolutionary pressures, is related to the the connectivity of the corresponding protein; iii) how PPI connectivities are modulated by evolutionary and functional relationships, as represented by the Clusters of Orthologous Genes (COGs). We show that conservation, essentiality and functional specialisation of genes constrain the connectivity of the corresponding proteins in bacterial PPI networks. In particular, we isolate a core of highly connected proteins (with connectivities $k\ge40$), which is ubiquitous among the species considered here -- though mostly visible in the degree distributions of bacteria with small genomes (less than 1000 genes). The genes that belong to this highly connected core are conserved, essential and, in most cases, belong to the COG cluster J, related to ribosomal functions and to the processing of genetic information.