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Background  Despite the prevalence of horizontal gene transfer (HGT) in bacteria, to this date there were few studies on HGT in the context of gene expression, operons and protein-protein interactions. Using the recently available data set on the  E. coli  protein-protein interaction network, we sought to explore the impact of HGT on genome structure and protein networks.    Results  We classified the  E. coli  genes into three categories based on their evolutionary conservation: a set of 2158  Core  genes that are shared by all  E. coli  strains, a set of 1044  Non-core  genes that are strain-specific, and a set of 1053 genes that were putatively acquired by horizontal transfer. We observed a clear correlation between gene expressivity (measured by Codon Adaptation Index), evolutionary rates, and node connectivity between these categories of genes. Specifically, we found the  Core  genes are the most highly expressed and the most slowly evolving, while the  HGT  genes are expressed at the lowest level and evolve at the highest rate.  Core  genes are the most likely and  HGT  genes are the least likely to be member of the operons. In addition, we found the  Core  genes on average are more highly connected than  Non-core  and  HGT  genes in the protein interaction network, however the  HGT  genes displayed a significantly higher mean node degree than the  Core  and  Non-core  genes in the defence COG functional category. Interestingly,  HGT  genes are more likely to be connected to  Core  genes than expected by chance, which suggest a model of differential attachment in the expansion of cellular networks.    Conclusion  Results from our analysis shed light on the mode and mechanism of the integration of horizontally transferred genes into operons and protein interaction networks.

The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment