Unsuspected prophage‐like elements in Salmonella typhimurium

We present evidence for the existence of two large (≈50 kb) excisable segments in the chromosome of Salmonella typhimurium . The two elements — designated Gifsy ‐1 and Gifsy ‐2 — cover, respectively, the 57 units and the 24 units of the genetic map where they contribute indicative rare restriction sites. The two elements are closely interrelated and both contain a region of sequence similarity to the recE locus of the Rac prophage of Escherichia coli. Mutations within this region of Gifsy‐ 1 yield the classical ‘Sbc’ phenotype: they suppress the recombination defect of recB mutants, apparently by activating a normally silent recE ‐like gene. At the same time, these ‘ sbcE  ’ mutations activate a Xis‐type function that promotes excision of one or other of the two elements. Predictably, curing of Gifsy ‐1 results in the loss of recB mutant suppression. Surprisingly, the suppressor phenotype is also lost in cells cured for Gifsy ‐2 even though the Gifsy ‐1‐associated sbcE mutation is still present. Moreover, the excision frequency of Gifsy ‐1 drops dramatically in Gifsy ‐2‐cured cells. Thus, both elements must co‐operate in the activation of recombination and excision functions. Overall, the data presented here suggest that Gifsy‐ 1 and Gifsy‐ 2 are cryptic prophages. They are distinct from previously described Fels prophages. Unlike Fels , they are not specific to S. typhimurium strain LT2 since they are both also found in a virulent S. typhimurium isolate (ATCC 14028s).