Involvement of sigma(54) in exponential silencing of the Pseudomonas putida TOL plasmid Pu promoter

The sigma(54)-dependent Pu promoter of the TOL plasmid pWWO of Pseudomonas putida becomes activated by the prokaryotic enhancer-binding XylR protein when cells encounter m-xylene in the medium. However, even in the presence of the aromatic inducer, Pu activity is silenced in vivo during rapid exponential growth of the cells in rich medium. Various elements known to be involved in the control of the transcriptional activity of the promoter were examined to ascertain the mechanism by which expression of Pu is limited during the exponential phase of growth. A truncated and fully constitutive XylR derivative deleted of its signal-reception N-terminal domain was found to be subjected to the same exponential silencing as the wildtype XylR when exposed to m-xylene. This indicated that the phenomenon is not due to a late activation of XylR by the aromatic effector. A Pu variant in which the integration host factor (IHF)-binding site had been functionally replaced by a statically curved DNA segment showed the same induction pattern, thus ruling out variations in the intracellular levels of IHF changes during growth as the element responsible for the inactivity of Pu in rapidly growing cells. On the contrary, overproduction of the sigma(54) factor allowed Pu expression during exponential phase. As sigma(54) protein levels remained approximately constant during growth, the exponential silencing of Pu could be caused ultimately by changes in the activity of the factor itself. This effect may not be exclusive to Pu, but could be a general co-regulation mechanism in sigma(54)-dependent promoters that connects transcription of a specific set of genes with the general physiological status of the cells.