The TLCΦ satellite phage harbors a Xer recombination activation factor

Significance Cholera toxin, the principal virulence factor of Vibrio cholerae, is encoded in the genome of an integrative mobile element exploiting Xer (IMEX), CTXΦ. Nontoxigenic strains generally lack a suitable CTXΦ attachment site. In addition, CTXΦ integration is intrinsically irreversible. Nevertheless, new epidemic clones carrying potentially more potent toxins are constantly created by CTXΦ excision and reintegration cycles. Previous studies suggested that these cycles depended on another IMEX, TLCΦ, whose integration corrected the attachment site of nontoxigenic strains and whose excision promoted the joint elimination of CTXΦ copies. Our work brings molecular understanding to the role played by TLCΦ and suggests how similar IMEXs might participate in the evolution of other pathogenic bacteria.

The circular chromosomes of bacteria can be concatenated into dimers by homologous recombination. Dimers are solved by the addition of a cross-over at a specific chromosomal site, dif, by 2 related tyrosine recombinases, XerC and XerD. Each enzyme catalyzes the exchange of a specific pair of strands. Some plasmids exploit the Xer machinery for concatemer resolution. Other mobile elements exploit it to integrate into the genome of their host. Chromosome dimer resolution is initiated by XerD. The reaction is under the control of a cell-division protein, FtsK, which activates XerD by a direct contact. Most mobile elements exploit FtsK-independent Xer recombination reactions initiated by XerC. The only notable exception is the toxin-linked cryptic satellite phage of Vibrio cholerae, TLCΦ, which integrates into and excises from the dif site of the primary chromosome of its host by a reaction initiated by XerD. However, the reaction remains independent of FtsK. Here, we show that TLCΦ carries a Xer recombination activation factor, XafT. We demonstrate in vitro that XafT activates XerD catalysis. Correspondingly, we found that XafT specifically interacts with XerD. We further show that integrative mobile elements exploiting Xer (IMEXs) encoding a XafT-like protein are widespread in gamma- and beta-proteobacteria, including human, animal, and plant pathogens.