Abstract
BackgroundDespite 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.ResultsWe 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.ConclusionResults from our analysis shed light on the mode and mechanism of the integration of horizontally transferred genes into operons and protein interaction networks.
Highlights
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
HGT genes evolve faster and have lower expression levels To investigate the selective pressure acting on organizational units, we classified E. coli genes according to their evolutionary conservation into three categories, namely, (i)
HGT Set: genes that are derived from putative recent horizontal gene transfer events after the divergence of E. coli and Salmonella
Summary
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. The extent of the evolutionary impact of HGT is still under debate [3], it is generally accepted that roughly 10–40% of the protein-coding genes are likely to have been introduced by HGT into the E. coli K12 genome (page number not for citation purposes). We envisage that successful incorporation of a horizontally transferred gene needs its successful transcription and translation, and its integration into the existing functional cellular network. We foresee a number of barriers that potentially exist against the incorporation and expression of horizontally transferred genes in a new recipient genome. The first step of integration for horizontally transferred genes is its incorporation into the host transcription machinery. Failure to achieve any of the above steps may result in eventual degradation and pseudogenization
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