CopR is a global regulator of copper homeostasis in Pyrococcus furiosus

In several archaea, the Cu-transporting ATPase and the copper chaperone are arranged in a conserved copper resistance gene cluster (cop), which also contains an additional gene, encoding for a DNA-binding transcriptional regulator. In previous studies, pf0739 has been proposed to be the copper-dependent regulator CopR in P. furiosus.Here, we have characterised the metal-sensing transcriptional regulator CopR by describing the influence of different metal ions on the DNA-binding of wild-type and domain-depleted pf0739 mutants. To learn about the CopR-regulated gene network in P. furiosus, we performed differential gene expression analysis (DGE) and chromatin immunoprecipitation in combination with high-throughput sequencing (ChIP-seq) under normal and 20 microM copper-shock conditions. By integrating the transcriptome and genome-wide binding data, we found that CopR binds to the upstream regions of many copper-induced genes. Activation of the exporting ATPase (PF0740) was confirmed using in vitro transcription assays and DNase I footprinting. Negative-stain transmission electron microscopy and image analysis by 2D class averaging revealed an octameric assembly formed from a tetramer of dimers similar to the published crystal structures from LrpA from P. furiosus and FFRP, an orthologue of Pyrococcus sp. OT3.