Originally published as Genetics Published Articles Ahead of Print on June 14, 2005.

Genetics, Vol. 170, 1485-1499, August 2005, Copyright © 2005
doi:10.1534/genetics.105.042341

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

Recovery of a Nonhomologous imm{lambda} DNA Segment by Infecting {lambda}imm434 Phages

Sidney Hayes1, Kengo Asai, Audrey M. Chu and Connie Hayes

Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada

1 Corresponding author: Department of Microbiology and Immunology, College of Medicine, Health Sciences Bldg., Room A227, 107 Wiggins Rd., University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
E-mail: hayess{at}duke.usask.ca

We examined the requirement of {lambda} recombination functions for marker rescue of cryptic prophage genes within the Escherichia coli chromosome. We infected lysogenic host cells with {lambda}imm434 phages and selected for recombinant imm{lambda} phages that had exchanged the imm434 region of the infecting phage for the heterologous 2.6-kb imm{lambda} region from the prophage. Phage-encoded activity, provided by either Red or NinR functions, was required for the substitution. Red– phages with {Delta}NinR, internal NinR deletions of rap-ninH, or orf-ninC were 117-, 12-, and 5-fold reduced for imm{lambda} rescue in a Rec+ host, suggesting the participation of several NinR activities. RecA was essential for NinR-dependent imm{lambda} 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 imm{lambda} rescue. The opposite effects of several host functions toward NinR- and Red-dependent imm{lambda} 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 ori{lambda}-dependent replication initiation and whether ori{lambda} replication initiation was required for imm{lambda} marker rescue.