NsrR Represses σ-Dependent Small RNAs and Interacts with RpoE via a Noncanonical Mechanism in .

The envelope stress response in is primarily governed by the sigma factor RpoE (σ), which activates protective genes upon membrane perturbation. Under non-stress conditions, σ is sequestered by its anti-sigma factor RseA. In this study, we identify an unexpected role for the nitric-oxide-sensing repressor NsrR in dampening σ activity and repressing σ-dependent small RNAs, including , , and . Overexpression of represses transcription from σ-dependent promoters and phenocopies σ inactivation, resulting in filamentous morphology and growth defects. Conversely, Δ de-represses σ targets, with additive effects in mutants-supporting an RseA-independent regulatory role. Time-course analysis shows NsrR represses σ activity, with kinetics comparable to those of RseA. While in vitro assays failed to detect robust NsrR binding to σ target promoters, NsrR directly interacts with σ in bacterial two-hybrid assays. Structural modeling using AlphaFold3 supports a plausible NsrR-RpoE interaction interface. These findings suggest that NsrR functions as a noncanonical anti-sigma-like modulator of σ, integrating redox and envelope stress signals to maintain membrane homeostasis.