During mammalian embryogenesis, proteinases are important for both matrix remodeling and the activation of latent growth factors. As subtilisin-like prohormone convertases (SPCs) have recently been found to activate members of the matrix metalloproteinase and transforming growth factor-beta (TGF-beta) families, we sought to investigate the role of this gene family in murine implantation and embryogenesis. Using active site polymerase chain reaction (PCR) cloning, four members of the SPC family were identified at embryonic day 6.5: SPC1, SPC2, SPC3, and SPC6. In situ hybridization analysis of sectioned E6.5 embryos in utero demonstrated strong SPC6 expression in differentiated decidua, overlapping and extending beyond the region previously described for the metalloproteinase inhibitor TIMP-2. Lower levels of SPC6 expression were observed in trophoblasts and in the ectoplacental cone, suggesting multiple roles for this enzyme in implantation. Northern analysis showed that SPC6 mRNA in embryos is represented by two distinct sizes of message--the isoform SPC6-1 (3.0 kb) is most abundant at all stages, but significant levels of SPC6-b (6.0 kb) occur in E12.5 embryos. Whole mount in situ hybridization to E8.5 embryos demonstrated strong SPC6 expression in the most posterior somite. This somitic staining moved caudally with the developing embryo and by E10.5 became localized to the posterior of the tail, indicating that SPC6 is involved in somitogenesis. SPC6 was expressed at low levels throughout the embryo, except in the developing nervous system, and strong expression was observed in the first branchial arch and in skeletal regions of the developing vertebrae, limbs, and craniofacium, suggesting additional roles for SPC6 in skeletogenesis.