The flow of carbon metabolites between cellular compartments is an essential feature of fungal metabolism. During growth on ethanol, acetate, or fatty acids, acetyl units must enter the mitochondrion for metabolism via the tricarboxylic acid cycle, and acetyl coenzyme A (acetyl-CoA) in the cytoplasm is essential for the biosynthetic reactions and for protein acetylation. Acetyl-CoA is produced in the cytoplasm by acetyl-CoA synthetase during growth on acetate and ethanol while -oxidation of fatty acids generates acetyl-CoA in peroxisomes. The acetyl-carnitine shuttle in which acetyl-CoA is reversibly converted to acetyl-carnitine by carnitine acetyltransferase (CAT) enzymes is important for intracellular transport of acetyl units. In the filamentous ascomycete Aspergillus nidulans, a cytoplasmic CAT, encoded by facC, is essential for growth on sources of cytoplasmic acetyl-CoA while a second CAT, encoded by the acuJ gene, is essential for growth on fatty acids as well as acetate. We have shown that AcuJ contains an N-terminal mitochondrial targeting sequence and a C-terminal peroxisomal targeting sequence (PTS) and is localized to both peroxisomes and mitochondria, independent of the carbon source. Mislocalization of AcuJ to the cytoplasm does not result in loss of growth on acetate but prevents growth on fatty acids. Therefore, while mitochondrial AcuJ is essential for the transfer of acetyl units to mitochondria, peroxisomal localization is required only for transfer from peroxisomes to mitochondria. Peroxisomal AcuJ was not required for the import of acetyl-CoA into peroxisomes for conversion to malate by malate synthase (MLS), and export of acetyl-CoA from peroxisomes to the cytoplasm was found to be independent of FacC when MLS was mislocalized to the cytoplasm.The importance of understanding fungal carbon metabolism and its regulation has become increasingly apparent. This stems from studies of changes in metabolism accompanying fungal infections, development, and stress responses as well as the requirement for substrates for secondary metabolism (7,9,34,35,53). Furthermore, genome-wide studies of gene expression under different circumstances reveal the level of our ignorance of metabolic complexity. While carbon metabolism in the budding yeast, Saccharomyces cerevisiae, is best understood, it is widely recognized that this fungus is highly specialized in its preference for the fermentation of sugars to ethanol and the use of paralogous genes, derived from a whole-genome duplication in its evolutionary history, to encode different forms of enzymes for particular enzymatic reactions (20). The metabolism of another hemiascomycete, Candida albicans, has received attention recently because of its importance as a human pathogen, and there are many shared features with S. cerevisiae. Of special interest, however, is the extent to which the regulation of the expression of genes has been rewired such that the S. cerevisiae transcription factors used for controlling fundamental metabolic pathways may be different ...