Closer inspection of the intra-species Crc candidates, however, shows that some genes linked to carbohydrate metabolism could also be directly regulated by Crc (Additional file 1). For example, in P. aeruginosa and P. fluorescens species, the gene, zwf, encoding glucose-6-phosphate dehydrogenase has a Crc motif, whereas in P. putida

and P. syringae species, the gene, gap-1, encoding glyceraldehyde-3-phosphate dehydrogenase has a Crc motif. When viewed in an integrated way, it is seen that there are two distinct patterns to the regulation of genes in this class (Figure 2). When present, sugar transporters are generally subject to CRC control, whereas the regulation of Cisplatin downstream sugar metabolism is species-specific with respect to genes encoding catabolic enzymes. Interestingly, the same trend is observed for amino acid metabolism where most of the interspecies Crc candidates are involved in transport (Table 1), whereas intraspecies candidates are involved in metabolism (Additional file 1). Figure 2 Predicted Crc regulon of carbohydrate metabolism in Pseudomonas. Selected genes

involved Sepantronium cost in carbohydrate transport and metabolism are shown along with their status vis a vis (predicted) Crc regulation. Genes from P. aeruginosa (squares), P. fluorescens (circles), P. putida (triangles) and P. syringae (diamonds) are shown, with filled/unfilled symbols indicating that the target in that species is/is not predicted to be regulated by

Crc. An asterisk (*) after a symbol indicates where an orthologous locus is absent in the relevant species. OM – outer membrane; PP – periplasm; IM – inner membrane; ED – Entner-Doudoroff pathway; EMP – Embden-Meyerhoff pathway; 2-K-3-DG-6-P – 2-keto-3-deoxygluconate-6-phosphate. OprB – carbohydrate porin B; GlpF – glycerol transporter; FruAB – fructose phosphotransferase system; many Mtr – mannitol transporter SP600125 supplier subunit; GtsA – glucose transporter subunit; GntP – gluconate transporter; KguT – 2-ketogluconate transporter; Mdh – mannitol dehydrogenase; AlgA – mannose-6-P isomerase; Zwf – glucose-6-P dehydrogenase; Edd – gluconate-6-P dehydratase; KguE – xylose isomerase; GapA – glyceraldehyde-3-P dehydrogenase; Eno – phosphopyruvate hydratase. Some steps of the Embden-Meyerhoff pathway are abbreviated with a dashed line for clarity. It is notable that another gene, cstA, with a predicted role in carbon starvation stress alleviation was also implicated as a Crc candidate. The CstA protein is involved in peptide transport that would assist the cell in escaping carbon starvation [47]. In Escherichia coli, induction of the cstA gene depends on cAMP and Crp [48] indicating that this locus is subject to CCR in E. coli.