Gene expression analysis indicates extensive genotype-specific crosstalk between the conjugative F-plasmid and the E-coli chromosome

Background: Plasmids are an important component of the bacterial genome, but the crosstalk between genes encoded on the chromosome and on the plasmid is still poorly understood. Results: We performed a large-scale survey for genes on the E. coli chromosome that are affected by the presence of the conjugative F-plasmid (crosstalk). The expression pattern of about 4% (107 genes) of the genes encoded by the chromosome was affected by the presence of the F-plasmid. Comparing two different Escherichia coli strains, MG1655 and DH5 alpha, we found a strong host genotype-specific crosstalk of the host chromosome with the F-plasmid. About 88% of the genes affected by the presence of the F-plasmid showed a significant plasmid by host genotype interaction, i.e. the presence of the F-plasmid resulted in a different gene expression in the two host genotypes. Less than 12% of the genes showed an additive effect of gene expression, i.e. host genotype independent crosstalk between plasmid and host chromosome. Conclusion: We propose that epistatic effects also contribute to the maintenance of F-plasmids in natural populations.