Identifying candidate genes whose expression is regulated by CbrAB and NtrBC in Pseudomonas fluorescens SBW25

Histidine is a good source of nutrient for many bacteria, but its utilization poses a significant challenge as it delivers excess nitrogen over carbon. The rate of histidine catabolism (hut) must thus be tightly regulated. Here, in Pseudomonas fluorescens SBW25, we show that the CbrAB two-component system directly activates the transcription of hut genes, while mediating succinate-induced carbon catabolite repression of hut at the translational level via the CbrAB-CrcYZ-Hfq/Crc regulatory cascade. When growing in minimal salt medium supplemented with histidine and succinate (the most preferred carbon source), the CbrAB-mediated promoter activity is weak; and the global nitrogen regulator NtrBC plays the dominant role in directly activating hut transcription. Overall design: Gene expression was compared between wild-type P. fluorescens SBW25 and each of the three mutants devoid of cbrB, ntrC and hutC, respectively. RNA-seq analyses of these four strains were performed in parellel. However, the data for wild type and the del-hutC mutant have been deposited in NCBI's Gene Expression Omnibus with accession number GSE146488.