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

The comparative approach is a powerful tool for the analysis of gene regula tion in bacterial genomes. It can be applied to the analysis of regulons th at have been studied experimentally as well as that of regulons for which n o known regulatory sites are available. It is assumed that the set of co-re gulated genes and the regulatory signal itself are conserved in related gen omes, Here, we use genomic comparisons to study the regulation of transport and utilization systems for sugar acids in gamma purple bacteria Escherich ia coli, Salmonella typhi, Klebsiella pneumoniae, Yersinia pestis, Erwinia chrysanthemi, Haemophilus influenzae and Vibrio cholerae, The variability o f the operon structure and the location of the operator sites for the main transcription factors are demonstrated. The common metabolic map is combine d with known and predicted regulatory interactions, It includes all known a nd predicted members of the GntR, UxuR/ExuR, KdgR, UidR and IdnR regulons, Moreover, most members of these regulons seem to be under catabolite repres sion 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 h ypothetical ATP-dependent transport system OgtABCD and YjgK protein with un known function, are detected. The former is likely to be the transport syst em for the products of pectin degradation, oligogalacturonides.