Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in <it>Pseudomonas </it>bacteria

<p>Abstract</p> <p>Background</p> <p>Catabolite repression control (CRC) is an important global control system in <it>Pseudomonas </it>that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in <it>Pseudomonas </it>spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in <it>Pseudomonas </it>spp. the Crc regulon has remained largely unexplored.</p> <p>Results</p> <p>In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced <it>Pseudomonas </it>genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits.</p> <p>Conclusions</p> <p>Catabolite repression control regulates a broad spectrum of genes in <it>Pseudomonas</it>. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how <it>Pseudomonas </it>bacteria integrate nutritional status cues with the regulation of traits that are of ecological, industrial and clinical importance.</p>