Study of the regulons of alternative sigma factors RpoN and FliA in Xanthomonas campestris pv. campestris

[[abstract]]Xanthomonas campestris pv. campestris (XCC) is a Gram negative, rod-shaped bacterium, possessing a single polar flagellum, which is essential for swimming motility. The fully sequenced XCC genome has two homologues of the rpoN genes, rpoN1 and rpoN2. The two deduced RpoN sequences share 41 % of identity. An interaction with an NtrC-like activator is essential for the activation of the transcription initiation by a σ54-containing RNA polymerase. The results showed that 1) The two RpoN proteins has slight promoter specificity; 2) Both RpoN1 and RpoN2 may interact with NtrC to drive the expression of glnA gene; 3) Strength of an RpoN-dependent promoter is sependent on the sequences of RpoN binding site and activator binding site; 4) The the distance between the RpoN binding site and activator binding site determines the strength of glnA promoter. In XCC, the flagellar genes can be classified into three classes. Gene expressions are regulated in a three-tired hierarchy by RpoD (σ70), RpoN2 (σ54)/FleQ, and FliA (σ28), respectively. Using bioinformatic tools, we identified a FliA-dependent promoter consensus sequence in the promoter regions of late flagellar genes, some motility/chemotaxis and c-di-GMP-signaling-related genes. In this study, using promoter activity assay, we demonstrated that all the predicted promoters are positively regulated by FliA and indirectly positively regulated by RpoN2, FleQ, FlhA, genes of the upstream regulatory pathway. FlgM is an anti-FliA anti-sigma factor. It negatively regulates the expression of genes of FliA regulon