Protein Signatures That Promote Operator Selectivity among Paralog MerR Monovalent Metal Ion Regulators

Two paralog transcriptional regulators of the MerR family, CueR and GolS, are responsible for monovalent metal ion sensing and resistance in Salmonella enterica . Although similar in sequence and also in their target binding sites, these proteins differ in signal detection and in the set of target genes they control. Recently, we demonstrated that selective promoter recognition depends on the presence of specific bases located at positions 3′ and 3 within the operators they interact with. Here, we identify the amino acid residues within the N-terminal DNA-binding domain of these sensor proteins that are directly involved in operator discrimination. We demonstrate that a methionine residue at position 16 of GolS, absolutely conserved among GolS-like proteins but absent in all CueR-like xenologs, is the key to selectively recognize operators that harbor the distinctive GolS-operator signature, whereas the residue at position 19 finely tunes the regulator/operator interaction. Furthermore, swapping these residues switches the set of genes recognized by these transcription factors. These results indicate that co-evolution of a regulator and its cognate operators within the bacterial cell provides the conditions to avoid cross-recognition and guarantees the proper response to metal injury. Background: Two nucleotide bases distinguish promoters controlled by paralog MerR monovalent metalloregulators, avoiding cross-activation. Results: Specific residues within the DNA-binding region of the regulators were identified as responsible for the selectivity in the operator recognition. Conclusion: Co-evolution of both the regulator and its target operator sequences prevents cross-activation of paralog regulatory circuits. Significance: The basis for regulator/operator specificity among MerR monovalent metalloregulators is described.