Systems Level Analyses Reveal Multiple Regulatory Activities of CodY Controlling Metabolism, Motility and Virulence in <i>Listeria monocytogenes</i>

<div><p>Bacteria sense and respond to many environmental cues, rewiring their regulatory network to facilitate adaptation to new conditions/niches. Global transcription factors that co-regulate multiple pathways simultaneously are essential to this regulatory rewiring. CodY is one such global regulator, controlling expression of both metabolic and virulence genes in Gram-positive bacteria. Branch chained amino acids (BCAAs) serve as a ligand for CodY and modulate its activity. Classically, CodY was considered to function primarily as a repressor under rich growth conditions. However, our previous studies of the bacterial pathogen <i>Listeria monocytogenes</i> revealed that CodY is active also when the bacteria are starved for BCAAs. Under these conditions, CodY loses the ability to repress genes (<i>e</i>.<i>g</i>., metabolic genes) and functions as a direct activator of the master virulence regulator gene, <i>prfA</i>. This observation raised the possibility that CodY possesses multiple functions that allow it to coordinate gene expression across a wide spectrum of metabolic growth conditions, and thus better adapt bacteria to the mammalian niche. To gain a deeper understanding of CodY’s regulatory repertoire and identify direct target genes, we performed a genome wide analysis of the CodY regulon and DNA binding under both rich and minimal growth conditions, using RNA-Seq and ChIP-Seq techniques. We demonstrate here that CodY is indeed active (<i>i</i>.<i>e</i>., binds DNA) under both conditions, serving as a repressor and activator of different genes. Further, we identified new genes and pathways that are directly regulated by CodY (e.g., <i>sigB</i>, <i>arg</i>, <i>his</i>, <i>actA</i>, <i>glpF</i>, <i>gadG</i>, <i>gdhA</i>, <i>poxB</i>, <i>glnR and fla genes</i>), integrating metabolism, stress responses, motility and virulence in <i>L</i>. <i>monocytogenes</i>. This study establishes CodY as a multifaceted factor regulating <i>L</i>. <i>monocytogenes</i> physiology in a highly versatile manner.</p>