Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus [ChIP-seq]

Despite the well-known toxicity of uranium (U) to bacteria, little is known about how cells sense and respond to U. The recent finding of a U-specific stress response in Caulobacter crescentus has provided a foundation for studying the mechanisms of U- perception in bacteria. To gain insight into this process, we used a forward genetic screen to identify the regulatory components governing expression of the urcA promoter (PurcA) that is strongly induced by U. This approach unearthed a previously uncharacterized two-component system, UzcRS, which is responsible for U-dependent activation of PurcA. UzcRS is also highly responsive to zinc and copper, revealing a broader specificity than previously thought. Using ChIP-seq, we found that UzcR binds extensively throughout the genome in a metal-dependent manner and recognizes a non-canonical DNA binding site. Coupling the genome-wide occupancy data with RNA-seq analysis revealed that UzcR is a global regulator of transcription, predominately activating genes encoding proteins that are localized to the cell envelope; these include metallopeptidases, multidrug resistant efflux (MDR) pumps, TonB-dependent receptors and many proteins of unknown function. Collectively, our data suggest that UzcRS couples detection of U, Zn and Cu with a novel extracytoplasmic stress response. Mapping of UzcR occupancy of in the genome of Caulobacter crescentus NA1000 in PYE following spike-in with or without Zn for 1 hour. Immunoprecipitated DNA in wild type strain compared to Immunoprecipitated DNA in ΔuzcR strain.