Structure of cryptic λ prophages

Abstract

When Escherichia coli cells lysogenic for bacteriophage λ are induced with ultraviolet light, cells carrying cryptic λ prophages are occasionally found among the apparently cured survivors. The λ variant crypticogen ( λcrg) carries an insertion of the transposable element IS2, which increases the frequency of cryptic lysogens to about 50% of cured cells: 43 of these cryptic prophages have been characterized. They all contain substitutions that replace the early segment of the prophage genome (from the IS2 to near the cos site) with a duplicate copy of a large segment of the host chromosome. The right end of the substitution always results from recombination between the nin- QSR- cos region of the prophage and the homologous incomplete lambdoid prophage Qsr′ at 12.5 minutes in the E. coli chromosome. The left end of the substitution is usually a crossover that recombines the IS2 element in the prophage with an E. coli IS2 at 8.5 minutes, near the lac gene, or with a second IS2 located counterclockwise from leu at 2 minutes, generating duplications of at least 200,000 bases. Five cryptic lysogens derived from cells lysogenic for a reference strain of λ (which lacks the IS2 present in λcrg) have been characterized. They contain substitutions whose right termini are generated by a crossover with the Qsr′ prophage. The left termini of these substitutions are formed either by a crossover between the λ exo gene and a short exo-homologous segment of Qsr′ ( 2 5 ), or by a crossover between sequences to the left of attL and an unmapped distant region of the host chromosome ( 3 5 ). The large duplications carried by these cryptic lysogens are stable, unlike tandem duplications, and so may significantly influence the cell's evolutionary potential.