Transcriptional Organization and Regulation of the l -Idonic Acid Pathway (GntII System) in Escherichia coli

Abstract

The genetic organization of the idn genes that encode the pathway for L-idonate catabolism was characterized. The monocistronic idnK gene is transcribed divergently from the idnDOTR genes, which were shown to form an operon. The 215-bp regulatory region between the idnK and idnD 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 idnD, and an UP element upstream of idnK. The genes of the L-idonate pathway were shown to be under catabolite repression control. Analysis of idnD-and idnK-lacZ fusions in a nonpolar idnD mutant that is unable to interconvert L-idonate and 5-ketogluconate indicated that either compound could induce the pathway. The L-idonate pathway was first characterized as a subsidiary pathway for D-gluconate catabolism (GntII), which is induced by D-gluconate in a GntI (primary gluconate system) mutant. Here we showed that the idnK and idnD operons are induced by D-gluconate in a GntI system mutant, presumably by endogenous formation of 5-ketogluconate from D-gluconate. Thus, the regulation of the GntII system is appropriate for this pathway, which is primarily involved in L-idonate catabolism; the GntII system can be induced by D-gluconate under conditions that block the GntI system.For three decades, there was thought to be two systems for D-gluconate catabolism, GntI and GntII (1). The GntI system consists of gntT, gntU, and gntK, which encode high-and lowaffinity D-gluconate transporters and a thermoresistant gluconate kinase, respectively (19)(20)(21)29). GntR negatively controls the GntI genes, as well as edd and eda of the EntnerDoudoroff pathway. The GntII system is composed of a thermosensitive gluconate kinase and a gluconate transporter, which provide for subsidiary catabolism of gluconate in GntI mutants (3,16). Recently, we discovered that the GntII system is, in fact, a pathway for catabolism of L-idonate, which proceeds via a D-gluconate intermediate (3). The discovery of this novel pathway solved the longstanding question of why there are two pathways for gluconate; GntI is primarily involved in gluconate catabolism, and GntII is responsible for idonate catabolism.The catabolic sequence for L-idonate is as follows: L-idonate is transported by the L-idonate transporter, IdnT; L-idonate is oxidized to 5-keto-gluconate (5KG) by L-idonate 5-dehydrogenase, IdnD; 5KG is reduced to D-gluconate by 5-keto-D-gluconate 5-reductase, IdnO; and D-gluconate is phosphorylated by a thermosensitive gluconate kinase, IdnK, to make 6-phosphogluconate (6PG), which is further catabolized via the Entner-Doudoroff pathway. Thus, IdnD and IdnO allow for the redox-coupled interconversion of L-idonate to D-gluconate via 5KG. The L-idonate catabolic pathway overlaps D-gluconate catabolism through the common intermediates D-gluconate and 6PG.While the biochemistry of the L...

Characterization and Use of Catabolite-Repressed Promoters from Gluconate Genes in Corynebacterium glutamicum

“…Both boxes matched the consensus CRP-binding site box (5Ј-TGTGA-N 6 -ACACT-3Ј) described previously by de Crombrugghe et al (12). No putative consensus binding sequences for GntR (5Ј-ATGTTA-N 4 -TAA CAT-3Ј) or IdnR (5Ј-ATGTTA-N 4 -TAACGT-3Ј) from E. coli (5,60) or for GntR interaction (the dyad symmetry sequence ATACTTGTA) from B. subtilis (22) were found upstream from the gntP or gntK genes. The absence of consensus GntR binding sites upstream from the gnt genes and the failure to find a gntR homolog on the chromosome of C. glutamicum might suggest a nonconventional mechanism for regulation of the gnt genes in this bacterium.…”

“…Both systems are transcriptionally regulated, i.e., induced by gluconate and repressed by glucose (9,58,60). In E. coli, another subsidiary gluconate system (GntII) has been previously described (30), but it is now considered the catabolic pathway for L-idonate where D-gluconate is an intermediary (4); the idn idonate operon (the former GntII) is repressed by a regulatory protein (IdnR) and globally repressed by the carbon source (5).…”

Mouse Intestine Selects Nonmotile flhDC Mutants of Escherichia coli MG1655 with Increased Colonizing Ability and Better Utilization of Carbon Sources

“…The MG1655 ⌬edd mutant therefore grows on gluconate as a sole carbon and energy source with a generation time of about 180 min, whereas wild-type MG1655 grows with a generation time of about 80 min. Expression of eda is not only required for the maximum rate of gluconate catabolism but is absolutely required for growth of E. coli on glucuronate as a sole carbon and energy source (4).…”

New insights into the regulatory networks of paralogous genes in bacteria

“…This evolutionary scenario can be observed in the regulation of the E. coli gntK and idnK gluconate kinase genes, involved in the 6-phosphogluconate synthesis which takes place in the Entner-Doudoroff and pentose phosphate pathways, respectively. Although these genes are regulated by the same TFs, CRP, GntR and IdnR, the last TF represses the transcription of gntK, whereas it activates the transcription of idnK (Bausch et al, 2004;Izu et al, 1997) (see Fig. 1b and Group 449 of Supplementary Tables S1 and S3).…”