Prophage lambda induces terminal recombination in Escherichia coli by inhibiting chromosome dimer resolution: An orientation-dependent cis-effect lending support to bipolarization of the terminus

A prophage lambda inserted by homologous recombination near nif, the chromo some dimer resolution sire of Escherichia coli, is excised at a frequency t hat depends on irs orientation with respect to dif. In wild-type cells, ter minal hyper- (TH) recombination is prophage specific and undetectable by a test involving deletion of chromosomal segments between repeats identical t o those used for prophage insertion. TH recombination is, however, detected in both excision and deletion assays when Delta dif; xerC, ftsK mutations inhibit dimer resolution: lack of specialized resolution apparently results in recombinogenic lesions near dif. We also observed that the presence nea r dif of the prophage, in the orientation causing TH recombination, inhibit s dif resolution activity. By its recombinogenic effect, this inhibition ex plains the enhanced prophage excision in wild-type cells. The primary effec t of the prophage is probably an alteration of the dimer resolution regiona l control, which requires that dif is flanked by suitably oriented (polariz ed) stretches of DIVA. Our model postulates that the prophage inserted near dif in the deleterious orientation disturbs chromosome polarization on the side of the site where it is integrated, because lambda DNA, like the chro mosome, is polarized by sequence elements. Candidate sequences are oligomer s that display skewed distributions on each oriC-dif chromosome arm and on lambda DNA.