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 of the corresponding protein in the PPI networks. Focusing on a set of 42 bacterial species with reasonably separated evolutionary trajectories, we investigate three issues: i) whether the distribution of connectivity values 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 (evaluated through the ratio K_a/K_s and ENC plots) 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 Proteins (COGs). We show that conservation, essentiality and functional specialization of genes control in a quite universal way the topology of the emerging bacterial PPI networks. Noteworthy, a structural transition in the network is observed such that, for connectivities k\ge40 , bacterial PPI networks are mostly populated by genesthat are conserved, essential and which , in most cases, belong to the COG cluster J, related to ribosomal functions and to the processing of genetic information.
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.
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