Rules of Expansion: an Updated Consensus Operator Site for the CopR-CopY Family of Bacterial Copper Exporter System Repressors

Abstract

Copper is broadly toxic to bacteria. As such, bacteria have evolved specialized copper export systems (<i>cop</i> operons) often consisting of a DNA-binding/copper-responsive regulator (which can be a repressor or activator), a copper chaperone, and a copper exporter. For those bacteria using DNA-binding copper repressors, few studies have examined the regulation of this operon regarding the operator DNA sequence needed for repressor binding. In <i>Streptococcus pneumoniae</i> (the pneumococcus), CopY is the copper repressor for the <i>cop</i> operon. Previously, homologs of pneumococcal CopY have been characterized to bind a 10-base consensus sequence T/GACANNTGTA known as the <i>cop</i> box. Using this motif, we sought to determine whether genes outside the <i>cop</i> operon are also regulated by the CopY repressor, which was previously shown in <i>Lactococcus lactis</i> We found that <i>S. pneumoniae</i> CopY did not bind to <i>cop</i> operators upstream of these candidate genes <i>in vitro</i> During this process, we found that the <i>cop</i> box sequence is necessary but not sufficient for CopY binding. Here, we propose an updated operator sequence for the <i>S. pneumoniae</i><i>cop</i> operon to be ATTGACAAATGTAGAT binding CopY with a dissociation constant (<i>K_d</i> ) of ∼28 nM. We demonstrate strong cross-species interaction between some CopY proteins and CopY operators, suggesting strong evolutionary conservation. Taken together with our binding studies and bioinformatics data, we propose the consensus operator RNYKACANNYGTMRNY for the bacterial CopR-CopY copper repressor homologs.<b>IMPORTANCE</b> Many Gram-positive bacteria respond to copper stress by upregulating a copper export system controlled by a copper-sensitive repressor, CopR-CopY. The previous operator sequence for this family of proteins had been identified as TACANNTGTA. Here, using several recombinant proteins and mutations in various DNA fragments, we define those 10 bases as necessary but not sufficient for binding and in doing so, refine the <i>cop</i> operon operator to the 16-base sequence RNYKACANNTGTMRNY. Due to the sheer number of repressors that have been said to bind to the original 10 bases, including many antibiotic resistance repressors such as BlaI and MecI, we feel that this study highlights the need to reexamine many of these sites of the past and use added stringency for verifying operators in the future.