The catabolism of fatty acids is important in the lifestyle of many fungi, including plant and animal pathogens. This has been investigated in Aspergillus nidulans, which can grow on acetate and fatty acids as sources of carbon, resulting in the production of acetyl coenzyme A (CoA). Acetyl-CoA is metabolized via the glyoxalate bypass, located in peroxisomes, enabling gluconeogenesis. Acetate induction of enzymes specific for acetate utilization as well as glyoxalate bypass enzymes is via the Zn 2 -Cys 6 binuclear cluster activator FacB. However, enzymes of the glyoxalate bypass as well as fatty acid beta-oxidation and peroxisomal proteins are also inducible by fatty acids. We have isolated mutants that cannot grow on fatty acids. Two of the corresponding genes, farA and farB, encode two highly conserved families of related Zn 2 -Cys 6 binuclear proteins present in filamentous ascomycetes, including plant pathogens. A single ortholog is found in the yeasts Candida albicans, Debaryomyces hansenii, and Yarrowia lipolytica, but not in the Ashbya, Kluyveromyces, Saccharomyces lineage. Northern blot analysis has shown that deletion of the farA gene eliminates induction of a number of genes by both short-and long-chain fatty acids, while deletion of the farB gene eliminates short-chain induction. An identical core 6-bp in vitro binding site for each protein has been identified in genes encoding glyoxalate bypass, beta-oxidation, and peroxisomal functions. This sequence is overrepresented in the 5 region of genes predicted to be fatty acid induced in other filamentous ascomycetes, C. albicans, D. hansenii, and Y. lipolytica, but not in the corresponding genes in Saccharomyces cerevisiae.It has become increasingly clear that the breakdown of fatty acids is important in the metabolism, development, and pathogenicity of many fungi. Catabolism occurs via the beta-oxidation pathway, in which fatty acids are activated to the corresponding acyl coenzyme A (CoA) and then oxidation by a series of enzyme steps releases acetyl-CoA and an acyl-CoA shortened by two carbons, which can undergo additional cycles of beta-oxidation. In mammals, beta-oxidation of long-chain fatty acids occurs in peroxisomes, while medium-and shortchain fatty acids undergo beta-oxidation in the mitochondria (reviewed in references 16 and 84). In contrast, in Saccharomyces cerevisiae fatty acids are metabolized entirely in peroxisomes (reviewed in reference 29). In fungi, where fatty acids can serve as sole sources of carbon and energy, the acetyl-CoA must be converted to C 4 compounds via the glyoxalate bypass, comprising the enzymes isocitrate lyase and malate synthase, allowing gluconeogenesis (40, 64). Isocitrate lyase and malate synthase are usually, but not always, located in peroxisomes. It has been found that mutations affecting isocitrate lyase, malate synthase, and peroxisomal functions can affect the pathogenicity of both plant and animal pathogens (33,37,45,46,66). Furthermore it has been found that genes encoding enzymes for fatty acid catabol...