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The strict anaerobe  Clostridium difficile  is the most common cause of nosocomial diarrhea, and the oxygen-resistant spores that it forms have a central role in the infectious cycle. The late stages of sporulation require the mother cell regulatory protein σ K . In  Bacillus subtilis , the onset of σ K  activity requires both excision of a prophage-like element ( skin   Bs  ) inserted in the  sigK  gene and proteolytical removal of an inhibitory pro-sequence. Importantly, the rearrangement is restricted to the mother cell because the  skin   Bs   recombinase is produced specifically in this cell. In  C .  difficile , σ K  lacks a pro-sequence but a  skin   Cd   element is present. The product of the  skin   Cd   gene  CD1231  shares similarity with large serine recombinases. We show that CD1231 is necessary for sporulation and  skin   Cd   excision. However, contrary to  B .  subtilis , expression of  CD1231  is observed in vegetative cells and in both sporangial compartments. Nevertheless, we show that  skin   Cd   excision is under the control of mother cell regulatory proteins σ E  and SpoIIID. We then demonstrate that σ E  and SpoIIID control the expression of the  skin   Cd   gene  CD1234 , and that this gene is required for sporulation and  skin   Cd   excision. CD1231 and CD1234 appear to interact and both proteins are required for  skin   Cd   excision while only CD1231 is necessary for  skin   Cd   integration. Thus, CD1234 is a recombination directionality factor that delays and restricts  skin   Cd   excision to the terminal mother cell. Finally, while the  skin   Cd   element is not essential for sporulation, deletion of  skin   Cd   results in premature activity of σ K  and in spores with altered surface layers. Thus,  skin   Cd   excision is a key element controlling the onset of σ K  activity and the fidelity of spore development.

A Recombination Directionality Factor Controls the Cell Type-Specific Activation of σK and the Fidelity of Spore Development in Clostridium difficile