Chromosomal curing drives prophage evolution and bacterial epidemiology

Abstract

Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recombination (HR). This process may provide an evolutionary advantage to cells through enabling "chromosomal curing": the deletion of integrative mobile genetic elements (MGEs). However, many such MGEs are sensitive to RecA-DNA filaments, triggering activation of a lifecycle that may enable them to evade HR-mediated deletion. Despite >40% of isolates containing prophage integrated at a site that inhibits transformation, three representative prophage were identified in naturally-competent pneumococci to test this hypothesis. These encompassed representatives with C1-type and ImmAR-type regulatory systems, found in almost all pneumococcal prophage. All three prophage were deleted by HR with an efficiency similar to the transfer of base substitutions. Mutations that impaired a C1-regulated prophage increased this deletion rate, reflecting this element being activated by RecA-DNA filaments imported during transformation, likely preferentially killing cells that induce competence. ImmAR-regulated prophage instead responded to transient stimuli by excising as deletion-resistant pseudolysogens, only driving cell lysis in response to sustained stimuli. This was likely a consequence of these prophage reacting to multiple signals, as they differed in their response to both RecA and the DNA-binding protein and competence repressor DprA. One prophage constitutively elevated host DprA levels, thereby reducing transformation by preventing induction of the competence machinery. Hence these data are consistent with an evolutionary arms race between prophage and the competence machinery, resulting in bacterial diversification though HR being impeded by MGEs preventing their own elimination from the chromosome.