Modular organization in the reductive evolution of protein-protein interaction networks

Background The variation in the size of the genome of distinct life forms remains somewhat puzzling. The organization of proteins into domains and the different mechanisms that regulate gene expression are two factors that potentially increase the capacity of genomes to create more complex systems. High-throughput protein interaction data now makes it possible to examine the additional complexity generated by the way that protein interactions are organized. Results We have studied the reduction in genome size of Buchnera from its common ancestor Escherichia coli. In this well defined evolutionary scenario, we found that among all the properties of the protein interaction networks, the organization of networks into modules is that which seems to be directly related with the evolutionary process of genome reduction. Conclusions The apparently non-random reduction of the modular structure of the networks and the retention of essential characteristics of the interaction network indicates that the role of proteins within the interaction network is important in the reductive process.