<jats:title>ABSTRACT</jats:title> <jats:p> The genetic organization of the <jats:italic>idn</jats:italic> genes that encode the pathway for <jats:sc>l</jats:sc> -idonate catabolism was characterized. The monocistronic <jats:italic>idnK</jats:italic> gene is transcribed divergently from the <jats:italic>idnDOTR</jats:italic> genes, which were shown to form an operon. The 215-bp regulatory region between the <jats:italic>idnK</jats:italic> and <jats:italic>idnD</jats:italic> genes contains promoters in opposite orientation with transcription start sites that mapped to positions −26 and −29 with respect to the start codons. The regulatory region also contains a single putative IdnR/GntR binding site centered between the two promoters, a CRP binding site upstream of <jats:italic>idnD</jats:italic> , and an UP element upstream of <jats:italic>idnK</jats:italic> . The genes of the <jats:sc>l</jats:sc> -idonate pathway were shown to be under catabolite repression control. Analysis of <jats:italic>idnD</jats:italic> - and <jats:italic>idnK</jats:italic> - <jats:italic>lacZ</jats:italic> fusions in a nonpolar <jats:italic>idnD</jats:italic> mutant that is unable to interconvert <jats:sc>l</jats:sc> -idonate and 5-ketogluconate indicated that either compound could induce the pathway. The <jats:sc>l</jats:sc> -idonate pathway was first characterized as a subsidiary pathway for <jats:sc>d</jats:sc> -gluconate catabolism (GntII), which is induced by <jats:sc>d</jats:sc> -gluconate in a GntI (primary gluconate system) mutant. Here we showed that the <jats:italic>idnK</jats:italic> and <jats:italic>idnD</jats:italic> operons are induced by <jats:sc>d</jats:sc> -gluconate in a GntI system mutant, presumably by endogenous formation of 5-ketogluconate from <jats:sc>d</jats:sc> -gluconate. Thus, the regulation of the GntII system is appropriate for this pathway, which is primarily involved in <jats:sc>l</jats:sc> -idonate catabolism; the GntII system can be induced by <jats:sc>d</jats:sc> -gluconate under conditions that block the GntI system.