Interactions between horizontally acquired genes create a fitness cost in Pseudomonas aeruginosa

Horizontal gene transfer (HGT) plays a central role in the evolution of microbes. Despite the benefits associated with HGT, newly acquired genetic material can also generate fitness costs that are likely to impose an important constraint on evolution by HGT. In this study, we use the interaction between Pseudomonas aeruginosa PAO1 and a costly small plasmid (pNUK73) as a model system to investigate the molecular basis of the cost of HGT. Using RNA-Seq, we show that the acquisition of pNUK73 results in a profound alteration of the transcriptional profile of the PAO1 chromosome, including the activation of the SOS response. Compensatory mutations in either a chromosomal helicase or kinase eliminate the fitness cost of plasmid carriage and reverse the changes in chromosomal gene expression associated with pNUK73 acquisition. Compensatory mutations also decrease the expression of the plasmid replication gene rep, and we experimentally demonstrate that high levels of rep expression drive the cost associated with pNUK73 carriage and the activation of the SOS response. Both genes involved in compensatory adaptation show multiple signatures of recent horizontal acquisition in the PAO1 genome and present no clear biological role in PAO1, implying that the cost of pNUK73 stems from intragenomic conflict between recently horizontally acquired genes. Our study provides new insights into the evolutionary and molecular mechanisms responsible for the cost of HGT, and we argue that interactions between mobile genetic elements may play an important role in the evolution of bacteria via HGT.