Inhibition of Bacterial Gene Transcription with an RpoN-Based Stapled Peptide.

In response to environmental and other stresses, the σ(54) subunit of bacterial RNA polymerase (RNAP) controls expression of several genes that play a significant role in the virulence of both plant and animal pathogens. Recruitment of σ(54) to RNAP initiates promoter-specific transcription via the double-stranded DNA denaturation mechanism of the cofactor. The RpoN box, a recognition helix found in the C-terminal region of σ(54), has been identified as the component necessary for major groove insertion at the -24 position of the promoter. We employed the hydrocarbon stapled peptide methodology to design and synthesize stapled σ(54) peptides capable of penetrating Gram-negative bacteria, binding the σ(54) promoter, and blocking the interaction between endogenous σ(54) and its target DNA sequence, thereby reducing transcription and activation of σ(54) response genes.