SpoIVB is the critical determinant for intercompartmental signalling of pro-sigmaK processing during sporulation in Bacillus subtilis. We show here that the SpoIVB serine peptidase can cleave the SpoIVFA protein, which is one component of the pro-sigmaK processing complex. SpoIVFA has been shown elsewhere (Rudner, D.Z., and Losick, R., 2002, Genes Dev 16: 1007-1018) to tether BofA and SpoIVFB in a membrane-embedded heteroligomeric complex in which BofA directly inhibits the activity of SpoIVFB. Cleavage of SpoIVFA would provide the necessary signal to dissolve this complex and release BofA-mediated inhibition on the zinc metalloprotease, SpoIVFB, that is responsible for cleaving pro-sigmaK to its mature form. We also show that the SpoIVB PDZ domain is required for self-recognition and trans cleavage of SpoIVB and is probably also used to target an internal motif within the C-terminal region of SpoIVFA exposed in the space between the inner and outer forespore membranes. This work reveals the mechanism of intercompartmental signalling and provides a unified model as to how sigmaK-directed gene expression in the mother cell is co-ordinated with events in the forespore chamber.