RNA-seq analysis of Myxococcus xanthus wildtype and in-frame deletion mutants in epsW, epsZ and difE

Myxococcus xanthus is a model organism to study the biosynthesis and secretion of polysaccharides. The exopolysaccharide (EPS) is synthesized and exported via the Wzx/Wzy-dependent EPS pathway. The phosphoglycosyl transferase EpsZ initiates EPS biosynthesis by transferring galactose-1-P to undecaprenyl phosphate. EPS biosynthesis is stimulated by the Dif chemosensory system through the single-domain response regulator EpsW, which is activated through phosphorylation by the DifE kinase. Importantly, the mechanism by which EpsW~P activates EPS biosynthesis is unknown. To investigate if EpsW regulates EPS biosynthesis at the transcriptional level, we extracted total RNA from vegetative cells of the wildtype and the ?epsW mutant. Moreover, we extracted total RNA from vegetative cells of the ?epsZ and ?difE mutants to investigate the effects of EpsZ and DifE on the transcriptome.