Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria

In Bacillus subtilis, utilisation of xylose, arabinose and ribose is controlled by the transcriptional factors XylR, AraR and RbsR, respectively. Here we apply the comparative approach to the analysis of these regulons in the Bacillus/Clostridium group. Evolutionary variability of operon structures is demonstrated and operator sites for the main transcription factors are predicted. The consensus sequences for the XylR and RbsR binding sites vary in different subgroups of genomes. The functional coupling of gene clusters and the conservation of regulatory sites allow for detection of non-orthologous gene displacement of ribulose kinase in Enterococcus faecium and Clostridium acetobutylicum. Moreover, candidate catabolite responsive elements found upstream of most pentose-utilising genes suggest CcpA-mediated catabolite repression.