PexR is a noncanonical regulator of the peroxide stress response in bacteria

Cells combat peroxide stress using peroxiredoxins and catalases. The paradigmatic H2O2-sensing OxyR or PerR transcription regulators typically control their expression in bacteria. Here, we report our discovery of a noncanonical mechanism for H2O2-signaled regulation of peroxiredoxin ahpC and catalase katB genes in Myxococcus xanthus by PexR, an ATP-binding bacterial enhancer binding protein that acts as a dual-function repressor-activator. PexR, a dimer capable of higher-order oligomerization, binds to dyad-symmetry repeats upstream of ahpC and katB, activating their H2O2-induced σ54-dependent expression. Under peroxide stress-free conditions, PexR downregulates housekeeping σA-dependent ahpC expression. Deleting ahpC causes pleiotropy, and synthetic lethality when eliminated with katB or pexR, indicating PexR-mediated co-regulation of AhpC and KatB as critical for normal growth. We show that resting state PexR is autoinhibited by its N-terminal Zn2+/Fe2+-binding GAF (cGMP-specific phosphodiesterases, adenylyl cyclases, and FhlA) domain, which senses H2O2 and releases its bound metal to trigger PexR-activated σ54-dependent expression. Our genomic analyses reveal conservation of PexR and its regulatory elements and, likely, mechanism across Myxococcota, frequently co-occurring with OxyR or PerR, showcasing this phylum's remarkable diversity of potential peroxide stress response regulatory mechanisms. Moreover, PexR likely operates in phyla beyond Myxococcota, and its discovery expands the toolkit for genetically encoded H2O2 sensors.