NinR- and Red-Mediated Phage-Prophage Marker Rescue Recombination in Escherichia coli

We examined the requirement of λ recombination functions for marker rescue of cryptic prophage genes within the Escherichia coli chromosome. We infected lysogenic host cells with λimm434 phages and selected for recombinant immλ phages that had exchanged the imm434 region of the infecting phage for the heterologous 2.6-kb immλ region from the prophage. Phage-encoded activity, provided by either Red or NinR functions, was required for the substitution. Red− phages with ΔNinR, internal NinR deletions of rap-ninH, or orf-ninC were 117-, 12-, and 5-fold reduced for immλ rescue in a Rec+ host, suggesting the participation of several NinR activities. RecA was essential for NinR-dependent immλ rescue, but had slight influence on Red-dependent rescue. The host recombination activities RecBCD, RecJ, and RecQ participated in NinR-dependent recombination while they served to inhibit Red-mediated immλ rescue. The opposite effects of several host functions toward NinR- and Red-dependent immλ rescue explains why the independent pathways were not additive in a Rec+ host and why the NinR-dependent pathway appeared dominant. We measured the influence of the host recombination functions and DnaB on the appearance of oriλ-dependent replication initiation and whether oriλ replication initiation was required for immλ marker rescue.