Small protein modules dictate prophage fates during polylysogeny

DNA-damaging agents are the pervasive inducers of temperate phages in model bacteria. However, most bacteria in the biosphere are predicted to carry multiple prophages, a state called polylysogeny, making it unclear how co-residing prophages compete for host cell resources if they all respond to the identical trigger. We discover regulatory modules encoded on phage genomes that control prophage induction independently of the DNA damage cue. Genes specifying these pathways exist in linear plasmid-like phages at sites essential for phage propagation. The modules lack sequence similarity but display a shared regulatory logic of a transcription factor that activates expression of a neighboring gene encoding a small protein. The small protein inactivates the master repressor of lysis, leading to prophage induction. In some phages, the regulatory unit detects sensory information including quorum-sensing autoinducers, making lysis host-cell-density dependent. Exposure of the polylysogens studied here to different induction scenarios reveals that mixed phage populations emerge following DNA damage, however, induction through the SOS-independent module drives near-exclusive production of the phage sensitive to that specific cue. Considering the lack of potent DNA-damaging agents in natural habitats, we propose that additional phage-encoded sensory pathways that drive lysis play fundamental roles in phage-host biology and inter-prophage competition.