Background
AmrZ, a RHH transcriptional regulator, regulates motility and alginate production in pseudomonads. Expression of amrZ depends on the environmental stress sigma factor AlgU. amrZ and algU mutants have been shown to be impaired in environmental fitness in different pseudomonads with different lifestyles. Considering the importance of AmrZ for the ecological fitness of pseudomonads and taking advantage of the full sequencing and annotation of the Pseudomonas fluorescens F113 genome, we have carried out a ChIP-seq analysis from a pool of eight independent ChIP assays in order to determine the AmrZ binding sites and its implication in the regulation of genes involved in environmental adaption.
Conclusions
The results presented here show that AmrZ is an important global transcriptional regulator involved in environmental sensing and adaption. It is also a new partner in the complex iron homeostasis regulation.
Results
154 enriched regions (AmrZ binding sites) were detected in this analysis, being 76% of them located in putative promoter regions. 18 of these peaks were validated in an independent ChIP assay by qPCR. The 154 peaks were assigned to genes involved in several functional classes such as motility and chemotaxis, iron homeostasis, and signal transduction and transcriptional regulators, including genes encoding proteins implicated in the turn-over of c-diGMP. A putative AmrZ binding site was also observed by aligning the 154 regions with the MEME software. This motif was present in 75% of the peaks and was similar to that described in the amrZ and algD promoters in P. aeruginosa. We have analyzed the role of AmrZ in the regulation of iron uptake genes, to find that AmrZ represses their expression under iron limiting conditions. Conclusions: The results presented here show that AmrZ is an important global transcriptional regulator involved in environmental sensing and adaption. It is also a new partner in the complex iron homeostasis regulation.