Chain elongation of fatty acids is an important cellular process and is believed to occur in the endoplasmic reticulum of all eukaroytic cells. Herein we describe the cloning and characterization of a peroxisomal NADPHspecific trans-2-enoyl-CoA reductase, the key enzyme for a proposed peroxisomal chain elongation pathway. The reductase was solubilized and partially purified from guinea pig liver peroxisomes by affinity chromatography. On SDS-polyacrylamide gel electrophoresis, a 40-kDa band was identified as the enzyme, and its partial amino acid sequence (27 amino acids) was determined. A full-length cDNA for the reductase was cloned from a guinea pig liver cDNA library. The open reading frame of this nucleotide sequence encodes a 302-amino acid polypeptide with a calculated molecular mass of 32.5 kDa. Full-length mouse and human cDNA clones encoding homologous proteins have also been isolated. All of these translated polypeptides have the type I peroxisomal targeting signal, AKL, at the carboxyl terminus. The identity of the cloned enoyl-CoA reductase cDNAs was confirmed by expressing the guinea pig and human cDNAs in Escherichia coli. The His-tagged recombinant enzymes were found to have very high NADPH-specific 2-enoyl-CoA reductase activity with similar properties and specificity as the liver peroxisomal reductase. Both the natural and the recombinant enzyme catalyze the reduction of trans-2-enoyl-CoAs of varying chain lengths from 6:1 to 16:1, having maximum activity with 10:1 CoA. Northern blot analysis demonstrated that a single transcript of 1.3 kilobases is present in most mouse tissues, with particularly high concentrations in liver and kidney.In mammalian cells, the fatty acid chain elongation system has been shown to be present in both endoplasmic reticulum (ER) 1 and mitochondria (1). The ER pathway is similar to the fatty acid synthesis system. In this multistep process, malonylCoA first condenses with acyl-CoA to form a -keto acyl-CoA with two additional carbons with the release of CO 2 . The -keto acyl-CoA then undergoes reduction of the ketone group followed by dehydration to form a 2-enoyl-CoA, which is then reduced by NADH or NADPH to form the longer (ϩ2C) acylCoA. Chain elongation and other biotransformation of fatty acids have been shown to occur primarily in the ER (1, 2). The mitochondrial chain elongation system is a reversal of the fatty acid -oxidation system; thus, acetyl-CoA, instead of malonylCoA, is used for the condensation reaction, and the resulting -keto acyl-CoA undergoes the same series of reactions as described above (3). The physiological function of the mitochondrial chain elongation system is not clear (4). Contradictory findings have been reported regarding the presence of another cellular fatty acid chain elongation system in mammalian peroxisomes. Nagi et al. (5) initially reported the absence of an elongation system in rat liver peroxisomes. However, Horie et al. (6) later provided good evidence for the presence of an active peroxisomal chain elongation system in ...