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

Rhodobacter sphaeroides σE 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, σE 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 σE activity. We found that formation of the σE:ChrR complex inhibits the ability of σE to form a stable complex with core RNA polymerase. Since the σE:ChrR complex inhibits the ability of the sigma factor to bind RNA polymerase, we sought to identify amino acid substitutions in σE 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 σE that either increased or decreased the sensitivity of σE for inhibition by ChrR. Many of the amino acid residues that alter the sensitivity of σE to ChrR are located within regions known to be important for interacting with core RNA polymerase in other members of the σ70 superfamily. Our results suggest a model where solvent-exposed residues with region 2.1 of σE interact with ChrR to sterically occlude this sigma factor from binding core RNA polymerase and to inhibit target gene expression.