To discover the role of the global regulatory protein CodY in Staphylococcus aureus, codY null mutations were created in two S. aureus clinical isolates, UAMS-1 and SA564. Transcriptional analysis revealed that the S. aureus CodY regulon is extensive and includes genes involved in metabolic adaptation, as well as genes encoding virulence factors. A total of 54 characterized and predicted virulence genes were differentially regulated in the codY mutant, including genes responsible for the production of capsule, biofilm, toxins, and several proteases. Most virulence genes were overexpressed in the codY mutant, but a few, associated with colonization, were underexpressed in the mutant. Additionally, a central regulator of S. aureus virulence, the accessory gene regulator (agr), was highly overexpressed in the codY mutants during exponential growth. Further transcript analysis showed that many of the virulence genes that are overexpressed in a codY mutant are dependent on agr for transcription or for maintaining stable transcript levels. Other virulence genes, however, were overexpressed both in the codY mutant and in an agr codY double mutant. One such locus, the icaADBC operon, is responsible for the production of polysaccharide intercellular adhesin, a major component of Staphylococcal biofilms. To understand the molecular mechanism of gene regulation by CodY in S. aureus, all CodY targets in the genome were identified by high throughput analysis of an in vitro pull-down assay. Purified S. aureus CodY proved to bind specifically to many sites within the S. aureus genome, including previously characterized metabolic targets, and several sequences within virulence genes. When tested in a murine model of foreign body infection, however, a codY mutant and the WT strain of UAMS-1 were equally fit at colonization of subcutaneously implanted catheters.

Like B. subtilis CodY, which senses nutrient availability by direct interaction with the branched-chain amino acids (BCAAs) and GTP, S. aureus CodY was activated synergistically by the BCAAs and GTP. Binding of these effectors increased the affinity of CodY for its target sites, allowing the protein to modulate gene expression according to nutrient availability. CodY potentially links induction of S. aureus virulence with conditions of nutrient starvation.