Genome-wide transcriptional regulation by the flagellar sigma factor FliA in Pseudomonas putida

The sigma factor FliA (σ28) has been described to activate the expression of several chemoreceptor-encoding genes and the late flagellar genes in Pseudomonas putida, enabling synthesis of the filament, an stator complex and completion of the flagella-associated chemotaxis machinery. The activity of FliA is repressed in the cytoplasm by the anti-sigma factor FlgM upon completion of the flagellar hook. In this study we aim to identify genome-wide targets of regulation by FliA in P. putida KT2442 (a spontaneous rifampicin-resistant mutant of the reference strain KT2440) by performing RNA-seq experiments using a fliA deletion mutant and a constitutively active strain that combines the deletion of flgM with ectopic production of FliA. We introduced a miniTn7-derivative to express fliA under the salicylate-inducible nahR-Psal system into a P. putida KT2442-derivative ΔflgM mutant (ΔflgM/Psal-fliA), and a control miniTn7 cassette only bearing the nahR-Psal system into the ΔfliA strain. Three biological replicates of the control ΔfliA and ΔflgM/Psal-fliA strains were grown to exponential phase (OD600=0.3) in lysogeny broth (LB) supplemented with 2 mM sodium salicylate at 30ºC and 180 rpm shaking.