We cloned and characterized a cDNA encoding the Dictyostelium discoideum subunit of mitochondrial processing peptidase (Dd-MPP). Western blot analysis of the mitochondrial subfractions revealed that Dd-MPP is located in the mitochondrial matrix and membrane, whereas Dd-MPP, another subunit of DdMPP, is located only in the matrix. Although expression of Dd-MPP mRNA is down-regulated during early development, the level of the Dd-MPP protein is constant throughout the Dictyostelium life cycle. In a transformant expressing the antisense RNA of the -MPP gene, unexpectedly, the -MPP protein increased about 1.8-fold relative to the wild type, and its mRNA increased 4.5-fold. Expression of other mitochondrial proteins, -MPP and Cox IV, was also induced. These results suggest that antisense RNA inhibition of the -MPP gene induces gene expression of mitochondrial proteins, presumably in a retrograde signaling manner. This is the pathway of the transfer of information from the mitochondria to the nucleus.