A prophage intercepts pathogenic activity of infecting phage for defense.

Bacteria counter bacteriophage threats using diverse anti-phage systems often encoded on prophages within hotspots for accessory genes. These prophages must ensure that encoded defense systems do not inhibit their spread. Here, we discover two anti-phage defense elements, RemS and PokE, encoded within the Gifsy-3 prophage of Salmonella enterica Typhimurium 14028 that restrict phage infection without affecting the lytic cycle of Gifsy-3. RemS, an ATPase, is expressed from a hotspot for accessory genes in lambdoid phages. PokE is a small membrane-depolarizing protein/peptide encoded within the Gifsy-3 lysis cassette. During infection by phage BTP1, pokE transcription is specifically driven by the Q antiterminator of BTP1, as the infecting phage prepares to express its lysis genes. PokE then disrupts the BTP1 lytic cycle through abortive infection. Altogether, this work uncovers how a prophage repurposes an essential feature of phage lytic cycles to both detect and respond to a phage-specific essential pathogenic activity.