PaeR is a Copper‐Sensing MarR Homolog from Clostridium difficile that Binds Cooperatively to its Promoter DNA Region

Abstract

Multiple antibiotic resistance regulator (MarR) proteins are widely found in prokaryotes and archaea. Most characterized MarR homologs function as transcriptional repressors of genes involved in metabolic and stress response pathways. MarR proteins regulate transcription through sequence-specific DNA binding interactions and many respond allosterically to small molecule ligands or metal ions. In this report, we describe the DNA and ligand binding properties of PaeR (putative antibiotic efflux regulator), a previously uncharacterized MarR homolog from the pathogen, Clostridium difficile. Biophysical characterization of PaeR indicates that it exists predominantly as a homodimer with a thermal unfolding temperature of 59.3°C. Electrophoretic mobility shift assays (EMSAs) reveal PaeR to be a sequence-specific DNA binding protein that associates with DNA as a homodimer with very high binding affinity (Kd = 3.2 ± 0.6 nM) at a pseudo-palindromic site in its promoter region. Interestingly, our data indicates that PaeR binds to at least one additional site in its promoter/operator region with positive binding cooperativity. Initial screens to identify potential effectors of PaeR binding to DNA indicate that this protein is responsive to low concentrations of copper ions. Homology modeling of the PaeR homodimer suggests a possible mechanism for copper-induced effects on DNA binding. These data, in conjunction with the genetic context of the paeR gene, suggest a possible role of PaeR in regulating antibiotic resistance in C. difficile.