Although the three enzymes unique to the glyoxylate cycle are expressed from a single ace operon in E. coli, the intracellular level of isocitrate lyase expressed from aceA is more than 100-fold higher than that of isocitrate dehydrogenase (IDH) kinase/phosphatase, the product of aceK. In an effort to elucidate the mechanism(s) for the differential expression, a sequence in the aceA/aceK intergenic region which can form a very stable secondary structure $({Delta}G=-54kcal/mol)$ when transcribed was deleted by site-directed mutagenesis. Determination of enzyme activities and maxicell labeling experiment with the deletion mutant and wild type operon clone indicated that the secondary structure plays little role in the downregulation of aceK expression. However, a comparison of ${eta}-galactosidase$ activities of several aceA::lacZ and aceK::lacZ fusion genes suggested that some 20-fold downshift occurs still in the aceA/aceK intergenic region, although the secondary structure-forming sequence within the region proved not to be involved. Another 8-fold drop in the expression of lacZ was observed from two fusion genes which had their fusion points within the coding sequence of aceK, suggesting one of the major determinants for the differential expression between aceA and aceK is located within the structural part of aceK.