CzcR regulon with ChIPseq
Pseudomonas aeruginosa is a versatile opportunistic pathogen that thrives in hostile environments by tightly regulating zinc (Zn) homeostasis. The CzcRS two-component system is pivotal for Zn resistance, primarily by activating the CzcCBA efflux pump, yet its basal activity and full regulon remain poorly defined. Here, we mapped the CzcR regulon under zinc-sufficient (ZS) and zinc-excess (ZE) conditions in P. aeruginosa PAO1 using ChIP-seq. Under ZE, we identified 38 CzcR binding sites, potentially regulating 42 genes, many of which are linked to virulence, antibiotic resistance, and stress response. Under ZS, 12 binding sites were detected, revealing a distinct basal regulon associated with metabolic, transport, and transcriptional regulatory functions. Motif analysis uncovered a specific CzcR binding motif under ZE, absent in most basal targets, suggesting a conformation-dependent DNA recognition mechanism. Integration of ChIP-seq data with transcriptomics identified eight novel CzcR-regulated genes mostly implicated in virulence and colistin resistance. Our findings demonstrate that CzcR exhibits dual functionality: its basal, potentially phosphorylation-independent activity maintains physiological robustness, while its activated form orchestrates Zn detoxification and virulence modulation. This study expands our understanding of how P. aeruginosa integrates metal sensing with clinically relevant phenotypes, highlighting CzcR as a key regulator at the intersection of metal homeostasis and pathogenicity.