Structural organization of the gene for rat enoyl-CoA hydratase:3-hydroxyacyl-CoA dehydrogenase bifunctional enzyme.

Enoyl-CoA hydratase:3-hydroxyacyl-CoA dehydrogenase bifunctional enzyme is a monomeric protein which catalyzes the second and the third reactions of the peroxisomal beta-oxidation system. We cloned the gene for this enzyme from rat genomic libraries. The gene spans about 31 kilobases and consists of seven exons and six introns. The transcription initiation site was located 24 nucleotides upstream of the initiator methionine codon, ATG, determined by S1 nuclease mapping and primer extension analysis. The 5'-flanking region of the gene lacks typical TATA and CCAAT sequences, but contains G + C-rich sequences, including one CCGCCC ("GC" box) and two related GC hexanucleotides. Some of the structural features of the 5'-flanking region of this gene are shared by the 5'-upstream sequence of the gene for acyl-CoA oxidase, which catalyzes the first reaction of the peroxisomal beta-oxidation system and is induced coordinately with the bifunctional enzyme. Southern blot analysis of rat genomic DNA indicates that the bifunctional enzyme gene occurs once per haploid genome. The amino acid sequence of the carboxyl-terminal region of the bifunctional enzyme exhibits a significant level of homology to the sequence of pig mitochondrial 3-hydroxyacyl-CoA dehydrogenase. This region of the bifunctional enzyme is encoded mainly by the last exon (Exon VII) which codes for as much as 58% of the protein sequence. Based on the data plus our unpublished findings (N. Ishii, T. Osumi, and T. Hashimoto, unpublished data), we propose that the amino-terminal domain, which is principally encoded by Exons I-V, has enoyl-CoA hydratase activity, and the carboxyl-terminal one, which is mainly coded for by Exon VII, has a 3-hydroxyacyl-CoA dehydrogenase function.