Temperate phages are able to integrate their genome into the host and replicate passively through a lysogenic state. Hosts frequently benefit from such a massive gene acquisition through lysogenic conversion, and as prophages may be beneficial to their hosts, we hypothesized that hosts adapted strategies to integrate that gene source. Since prophages integrate into and excise from the host chromosome through site-specific recombination (SSR), we investigated whether regulation of SSR at the level of gene expression could be involved in the maintenance process.
Our results show that lysogeny maintenance can be controlled by various host factors such as through different regulatory mechanisms in several Escherichia coli strains and in Salmonella enterica. We also show that defective or functional prophage maintenance can be controlled the same way, and in particular under stressful conditions. These newly characterized interactions reflect the co-evolution of host and viruses, allowing the acquisition of genes, and thus new properties, via horizontal transfer, while controlling the expression of deleterious genes.