Interactions Between the Rhodobacter sphaeroides ECF Sigma Factor, σE, and its Anti-sigma Factor, ChrR

Abstract Rhodobacter sphaeroides σ E is a member of the extra cytoplasmic function sigma factor (ECF) family, whose members have been shown to regulate gene expression in response to a variety of signals. The functions of ECF family members are commonly regulated by a specific, reversible interaction with a cognate anti-sigma factor. In R. sphaeroides , σ E activity is inhibited by ChrR, a member of a newly discovered family of zinc containing anti-sigma factors. We used gel filtration chromatography to gain insight into the mechanism by which ChrR inhibits σ E activity. We found that formation of the σ E :ChrR complex inhibits the ability of σ E to form a stable complex with core RNA polymerase. Since the σ E :ChrR complex inhibits the ability of the sigma factor to bind RNA polymerase, we sought to identify amino acid substitutions in σ E that altered the sensitivity of this sigma factor to inhibition by ChrR. This analysis identified single amino acid changes in conserved region 2.1 of σ E that either increased or decreased the sensitivity of σ E for inhibition by ChrR. Many of the amino acid residues that alter the sensitivity of σ E to ChrR are located within regions known to be important for interacting with core RNA polymerase in other members of the σ 70 superfamily. Our results suggest a model where solvent-exposed residues with region 2.1 of σ E interact with ChrR to sterically occlude this sigma factor from binding core RNA polymerase and to inhibit target gene expression.