Identification of the alternative sigma factor SigX regulon and its implications for Pseudomonas aeruginosa pathogenicity

We analyzed a deletion mutant of the ECF s factor SigX and applied mRNA profiling to define the SigX dependent regulon in P. aeruginosa in response to low osmolarity medium conditions. Furthermore, the combination of transcriptional data with chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing led to the identification of the DNA binding motif of SigX. Genome-wide mapping of SigX-binding regions revealed enrichment of downstream genes involved in fatty acid biosynthesis, type III secretion, swarming and c-di-GMP signaling. In accordance, a sigX deletion mutant exhibited an altered fatty acid composition of the cell membrane, reduced cytotoxicity, impaired swarming activity, elevated c-di-GMP levels and increased biofilm formation. In conclusion, a combination of ChIP-seq with transcriptional profiling and bioinformatic approaches to define consensus DNA binding sequences proved to be effective for the elucidation of the regulon of the alternative s factor SigX revealing its role in complex virulence-associated phenotypes in P. aeruginosa. Overall design: Transcriptome profiling of the SigX deletion mutant and overexpressing wildtype complemented by ChIP-seq