Comparative Genomic Analysis of the Hexuronate Metabolism Genes and Their Regulation in Gammaproteobacteria

Abstract

The hexuronate metabolism in Escherichia coli is regulated by two related transcription factors from the FadR subfamily of the GntR family, UxuR and ExuR. UxuR controls the D-glucuronate metabolism, while ExuR represses genes involved in the metabolism of all hexuronates. We use a comparative genomics approach to reconstruct the hexuronate metabolic pathways and transcriptional regulons in gammaproteobacteria. We demonstrate differences in the binding motifs of UxuR and ExuR, identify new candidate members of the UxuR/ExuR regulons, and describe the links between the UxuR/ExuR regulons and the adjacent regulons UidR, KdgR, and YjjM. We provide experimental evidence that two predicted members of the UxuR regulon, yjjM and yjjN, are the subject of complex regulation by this transcription factor in E. coli.D-Glucuronate and D-galacturonate can each serve as a sole carbon source for the growth of Escherichia coli. They are utilized via the Ashwell catabolic pathway (27). Hexuronates enter the cell using two different transport systems, GntP and ExuT (from the GntP and MFS families of transporters, respectively), which have dual specificity, importing D-tagaturonate/D-fructuronate and D-galacturonate/D-glucuronate, respectively. In addition, ␤-D-glucuronides can be utilized to form D-glucuronate using the UidB transporter and the UidA glucuronidase ( Fig. 1).D-Galacturonate and D-glucuronate are converted to the same metabolite, 2-keto-3-deoxy-D-gluconate, via parallel pathways, which involve one enzyme common for both pathways, D-glucuronate/D-galacturonate isomerase (UxaC), and two pairs of enzymes, D-mannonate and D-altronate hydrolases (UxuA and UxaA, respectively) and oxidoreductases (UxuB and UxaB, respectively), in each pathway (Fig. 1). The UxuB and UxaB proteins of E. coli are homologous (identity, 26%; positives, 42%; coverage, 95%) but may be confidently distinguished by the genome context analysis. The UxuA and UxaA demonstrate no discernible homology.The hexuronate metabolism in E. coli is regulated by two related transcription factors (TFs) from the FadR subfamily of the GntR family, UxuR and ExuR, whose amino acid sequences are 46% identical. UxuR controls the D-glucuronate metabolism by repressing uxuAB, uidABC, gntP, and its own gene uxuR (3,7,17,(24)(25)(26)(27). ExuR negatively controls most of the genes involved in the metabolism of both D-galacturonate and D-glucuronate, including exuT, uxaCA, uxaB, uxuAB, and exuR (6,22,[24][25][26][27].Understanding the regulation of the uidABC genes may have practical applications. Indeed, inhibiting ␤-glucuronidase produced by the gut flora can prevent the intestinal metabolism of the anticancer drug irinotecan, thereby diminishing life-threatening toxicity and conceivably allowing dose escalation that will enhance the drug's efficacy (33). It is also known that bacterial ␤-glucuronidase inhibitors can prevent a side effect of the common colon cancer chemotherapeutic CPT-11, severe diarrhea caused by ␤-glucuronidases from symbiotic bacteria that reactivate t...

Control of hexuronate metabolism in Escherichia coli by the two interdependent regulators, ExuR and UxuR: derepression by heterodimer formation

“…If glucuronate was added, two-fold molar excess of ExuR reproducibly trapped all the DNA fragments containing exuR promoter. This result was consistent with the prediction that ExuR is a glucuronate-sensitive repressor of ExuR synthesis (Suvorova et al, 2011). UxuR binding to the exuR regulatory region was also detected only in the presence of glucuronate, but the same molar excess of the protein left more unbound DNA as compared to ExuR (Fig.…”

“…It was previously predicted by bioinformatic analysis that UxuR represses expression of the divergent yjjM and yjjN genes that have been implicated in the metabolism of L-galactonate (Suvorova et al, 2011). YjjN (LgoD) is L-galactonate oxidoreductase, which converts L-galactonate to D-tagaturonate that is further converted to 2-keto-3-deoxygluconate by D-altronate oxidoreductase UxaB and the dehydratase UxaA (Fig.…”

“…Having established by gel-retardation assays that ExuR can bind to a promoter region that is known to be regulated by UxuR (Suvorova et al, 2011), two methods were used to determine the effects of ExuR on yjjM and yjjN transcription. First the yjjM and yjjN promoters were fused to lacZ in the promoter-probe vector, pRW224.…”

“…Bioinformatic analysis of the regulatory regions of genes known to be regulated by UxuR and ExuR led us to propose that they share similar target DNA-binding sites: aaatTGGTtaACCAattt for UxuR; and aAAgTgGTaTgAcAAcTtt for ExuR (Suvorova et al, 2011). As these consensus sequences are not identical, UxuR and ExuR might be expected to bind individual promoters with different affinities.…”

“…Other genes in the UxuR regulon include gntP, encoding a fructuronate transporter, uxuAB and uidABC, encoding enzymes (uxuA, uxuB and uidA) and transporters (uidB and uidC) involved in hexuronate metabolism, as well as the yjjN and yjjM genes encoding L-galactonate oxidoreductase and another putative transcription regulator of the GntR family, respectively (Bates Utz et al, 2004;Suvorova et al, 2011).…”