Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria

Abstract

The comparative approach is a powerful tool for the analysis of gene regulation in bacterial genomes. It can be applied to the analysis of regulons that have been studied experimentally as well as that of regulons for which no known regulatory sites are available. It is assumed that the set of co‐regulated genes and the regulatory signal itself are conserved in related genomes. Here, we use genomic comparisons to study the regulation of transport and utilization systems for sugar acids in gamma purple bacteria Escherichia coli, Salmonella typhi, Klebsiella pneumoniae, Yersinia pestis, Erwinia chrysanthemi, Haemophilus influenzae and Vibrio cholerae. The variability of the operon structure and the location of the operator sites for the main transcription factors are demonstrated. The common metabolic map is combined with known and predicted regulatory interactions. It includes all known and predicted members of the GntR, UxuR/ExuR, KdgR, UidR and IdnR regulons. Moreover, most members of these regulons seem to be under catabolite repression mediated by CRP. The candidate UxuR/ExuR signal is proposed, the KdgR consensus is extended, and new operators for all transcription factors are identified in all studied genomes. Two new members of the KdgR regulon, a hypothetical ATP‐dependent transport system OgtABCD and YjgK protein with unknown function, are detected. The former is likely to be the transport system for the products of pectin degradation, oligogalacturonides.

GntP Is the Escherichia coli Fructuronic Acid Transporter and Belongs to the UxuR Regulon

“…Derepression of gntP in an uxuR mutant strongly suggests that it is a new member of the UxuR regulon ( Table 2). UxuR is known to bind to a consensus operator site that is conserved in several species (27). We identified a putative UxuR binding site overlapping the gntP promoter and confirmed that this site is bound in vitro (Fig.…”

“…Since mutation of uxuR derepressed gntP expression, we measured binding of UxuR to the gntP regulatory region. Other researchers have searched all known genes involved in hexuronate catabolism to derive a putative UxuR operator consensus sequence, AAAT TGGTNNACCAATTT (27). The gntP UxuR operator lies within the promoter region, centered at Ϫ22 with respect to the transcriptional start site (10).…”

“…The gntP UxuR operator lies within the promoter region, centered at Ϫ22 with respect to the transcriptional start site (10). The UxuR operator of gntP (27). Bottom, proposed pathway for fructuronate metabolism in E. coli.…”

“…The pathways involve at least 26 known genes in six regulons that have been studied extensively (19,27). Still, there are some longstanding mysteries regarding the transport and catabolism of sugar acids by E. coli.…”

“…The uxuA and uxuB genes are negatively regulated by the product of the downstream gene, uxuR, and are induced for growth on glucuronate (1,2,8,(23)(24)(25)(26)(27). The gntP gene is predicted to be induced by glucuronate (27), but this has not been established experimentally. However, GntP does not appear to be involved in glucuronate catabolism: GntP is not homologous to the known glucuronate transporters, ExuT and KdgT, and GntP does not appear to transport glucuronate (10).…”