Modulating RssB activity: IraP, a novel regulator of σS stability in Escherichia coli

Abstract

The σS subunit of Escherichia coli RNA polymerase regulates the expression of stationary phase and stress response genes. σS is highly unstable in exponentially growing cells, whereas its stability increases dramatically upon starvation or under certain stress conditions. The degradation of σS is controlled by the phosphorylatable adaptor protein RssB and the ClpXP protease. RssB specifically directs σS to ClpXP. An unanswered question is how RssB-mediated degradation of σS is blocked by conditions such as glucose or phosphate starvation. We report here the identification and characterization of a new regulator of σS stability, IraP (inhibitor of RssB activity during phosphate starvation), that stabilizes σS both in vivo and in vitro. Deletion of iraP interferes with σS stabilization during phosphate starvation, but not during carbon starvation, and has a partial effect in stationary phase and nitrogen starvation. IraP interferes with RssB-dependent degradation of σS through a direct protein–protein interaction with RssB. A point mutant of IraP was isolated and found to be defective both for inhibition of σS degradation and interaction with RssB. Our results reveal a novel mechanism of regulation of σS stability through the regulation of RssB activity and identify IraP as a member of a new class of regulators, the anti-adaptor proteins.