CdmR, a MarR family protein from Clostridioides difficile, binds with positive cooperativity in the predicted promoter region of a MATE efflux transporter

<i>Clostridioides difficile</i> is one of the most common causes of nosocomial infections worldwide and is responsible for a spectrum of conditions ranging from colitis to severe cases of sepsis, and even death. Of significant concern is the evolving antibiotic resistance of this pathogen, notably the recent emergence of strains with resistance to vancomycin and fidaxomicin, the first-line antibiotics currently used to treat <i>C. difficile</i> infections. Numerous members of the multiple antibiotic resistance regulator (MarR) protein family have been shown to play important roles in mediating drug-resistance in bacterial species, however very little is understood about their functions in <i>C. difficile</i>. Of the 14 MarR proteins predicted to be encoded in the <i>C. difficile</i> genome, only one has been functionally characterized to date, so the roles these proteins play in <i>C. difficile</i> pathogenicity are largely unknown. Here, we report the first biochemical study of the MarR homolog, CdmR, from <i>C. difficile</i>. CdmR binds with high sequence-specificity and high affinity at two DNA sites in the promoter region of an operon that encodes a predicted multidrug and toxic compound extrusion (MATE) family efflux transporter. The location of these sites strongly suggests that CdmR binding represses its own expression and that of the MATE gene. CdmR exhibits positive binding cooperativity at the two DNA sites, suggesting a highly sensitive and tightly controlled regulatory mechanism that may play an important role in the antibiotic resistance profile of <i>C. difficile</i>.