Properties of peroxisomal and mitochondrial carnitine acetyltransferases purified from an alkane-grown yeast, Candida tropicalis, were compared each other. The molecular weight of both enzymes was estimated to be about 420000 by analytical ultracentrifugation and gel filtration chromatography with Sepharose 6B. However, each enzyme gave two subunits on the polyacrylamide slab gel electrophoresis in the presence of sodium dodecyl sulfate : the peroxisomal enzyme (64000 and 57000) and the mitochondrial enzyme (64000 and 52000). The subcellularly distinct enzymes gave a similar amino acid composition except for the contents of some amino acids : glycine, valine, glutamic acid and aspartic acid. Their isoelectric point was somewhat different: 5.11 for the peroxisomal enzyme and 5.22 for the mitochondrial enzyme. Both enzymes had the same amino-terminal residue (glutamic acid or glutamine) and the heat stability, and was indistinguishable immunochemically. These results suggest that peroxisomal and mitochondrial carnitine acetyltransferases of C. tropicalis cells may be products of the same nuclear gene. Differences in the molecular weight of the subunits of the enzymes would result from modification or processing of the common protein in the step of distribution to the respective organelles, that is, so-called posttranslational modification.Carnitine acetyltransferase, which catalyzes the reversible transfer of acetyl group between CoA and I -carnitine, has an important role in the metabolism of fatty acids in eukaryotic cells, because acetyl-CoA, a final product of j-oxidation of fatty acids, is not permeable through the various organelle membranes but acetylcarnitine is permeable through these membranes [l -41. This enzyme has been detected in peroxis o m a and microsomes as well as in mitochondria of mammalian cells, and isolated from pigeon breast muscle and rat liver mitochondria [I -61. However, there is no information about the molecular identity of peroxisomal and mitochondrial carnitine acetyltransferases isolated from the same cells.In this connection, a variety of interesting problems remain to be elucidated: whether or not peroxisomal and mitochondrial carnitine acetyltransferases are products encoded by the same gene; how these two enzymes are distributed into two subcellular compartment if they are the same gene products ; what relationships exist between these two enzymes and the biogenesis of organelles, especially peroxisomes and so on. To acquire useful information on these matters, it is necessary to compare the molecular properties of peroxisomal and mitochondrial carnitine acetyltransferases.In a previous paper [7], we have demonstrated that carnitine acetyltransferases induced in alkane-grown cells of Candida tropicalis are localized in peroxisomes and mitochondria and that both enzymes take an essential part in the transfer of acetyl units from peroxisomes to mitochondria for the complete operation of the glyoxylate cycle. These enzymes in both organelles were separated by DEAE-Sephacel column...