Short-chain acyl-CoA oxidases are -oxidation enzymes that are active on short-chain acyl-CoAs and that appear to be present in higher plant peroxisomes and absent in mammalian peroxisomes. Therefore, plant peroxisomes are capable of performing complete -oxidation of acyl-CoA chains, whereas mammalian peroxisomes can perform -oxidation of only those acyl-CoA chains that are larger than octanoyl-CoA (C 8 ). In this report, we have shown that a novel acyl-CoA oxidase can oxidize short-chain acyl-CoA in plant peroxisomes. A peroxisomal short-chain acyl-CoA oxidase from Arabidopsis was purified following the expression of the Arabidopsis cDNA in a baculovirus expression system. The purified enzyme was active on butyryl-CoA (C 4 ), hexanoyl-CoA (C 6 ), and octanoyl-CoA (C 8 ). Cell fractionation and immunocytochemical analysis revealed that the short-chain acyl-CoA oxidase is localized in peroxisomes. The expression pattern of the short-chain acylCoA oxidase was similar to that of peroxisomal 3-ketoacyl-CoA thiolase, a marker enzyme of fatty acid -oxidation, during post-germinative growth. Although the molecular structure and amino acid sequence of the enzyme are similar to those of mammalian mitochondrial acyl-CoA dehydrogenase, the purified enzyme has no activity as acyl-CoA dehydrogenase. These results indicate that the short-chain acyl-CoA oxidases function in fatty acid -oxidation in plant peroxisomes, and that by the cooperative action of long-and short-chain acylCoA oxidases, plant peroxisomes are capable of performing the complete -oxidation of acyl-CoA.Oilseed plants convert reserve oil to sucrose after germination. This unique type of gluconeogenesis occurs in the storage tissues of oilseeds, such as endosperms or cotyledons (1). The metabolic pathway involves many enzymes in several subcellular compartments, including lipid bodies, glyoxysomes (a specialized peroxisome), mitochondria, and the cytosol. Within the entire gluconeogenic pathway, the conversion of a fatty acid to succinate takes place within the glyoxysomes, which contain enzymes for fatty acid -oxidation and the glyoxylate cycle.Glyoxysomes and leaf peroxisomes are members of a group of organelles called peroxisomes (2). In glyoxysomes, fatty acids are first activated to fatty acyl-CoA by fatty acyl-CoA synthetase (3). Fatty acyl-CoA is the substrate for fatty acid -oxidation, which consists of four enzymatic reactions (4). The first reaction is catalyzed by acyl-CoA oxidase. The second and third enzymatic reactions are catalyzed by a single enzyme that possesses enoyl-CoA hydratase and -hydroxyacyl-CoA dehydrogenase activities (5). The fourth reaction is catalyzed by 3-ketoacyl-CoA thiolase (referred to as thiolase below) (6). Acetyl-CoA, an end product of fatty acid -oxidation, is metabolized further to produce succinate by the glyoxylate cycle.In mammalian cells, both peroxisomes and mitochondria contain a functional fatty acid -oxidation system. In peroxisomes, the first enzyme of fatty acid -oxidation, acyl-CoA oxidase, donates...