Promoter selectivity of the RhlR quorum-sensing transcription factor receptor in Pseudomonas aeruginosa is coordinated by distinct and overlapping dependencies on C4-homoserine lactone and PqsE

Quorum sensing is a mechanism of bacterial cell-cell communication that relies on the production and detection of small molecule autoinducers, which facilitate the synchronous expression of genes involved in group behaviors, such as virulence factor production and biofilm formation. The Pseudomonas aeruginosa quorum sensing network consists of multiple interconnected transcriptional regulators, with the transcription factor, RhlR, acting as one of the main drivers of quorum sensing behaviors. RhlR is a LuxR-type transcription factor that regulates its target genes when bound to its cognate autoinducer, C4-homoserine lactone, which is synthesized by RhlI. RhlR function is also regulated by the metallo-β-hydrolase enzyme, PqsE. We recently showed that PqsE binds RhlR to alter its affinity for promoter DNA, a new mechanism of quorum-sensing receptor activation. Here, we perform ChIP-seq analyses of RhlR to map the binding of RhlR across the P. aeruginosa genome, and to determine the impact of C4-homoserine lactone and PqsE on RhlR binding to different sites across the P. aeruginosa genome. We identify 40 RhlR binding sites, all but three of which are associated with genes known to be regulated by RhlR. C4-homoserine lactone is required for maximal binding of RhlR to many of its DNA sites. Moreover, C4-homoserine lactone is required for maximal RhlR-dependent transcription activation from all sites, regardless of whether it impacts RhlR binding to DNA. PqsE is required for maximal binding of RhlR to many DNA sites, with similar effects on RhlR-dependent transcription activation from those sites. However, the effects of PqsE on RhlR specificity are distinct from those of C4-homoserine lactone, and PqsE is sufficient for RhlR binding to some DNA sites in the absence of C4-homoserine lactone. Together, C4-homoserine lactone and PqsE are required for RhlR binding at the large majority of its DNA sites. Thus, our work reveals three distinct modes of activation by RhlR: i) when RhlR is unbound by autoinducer but bound by PqsE, ii) when RhlR is bound by autoinducer but not bound by PqsE, and iii) when RhlR is bound by both autoinducer and PqsE, establishing a stepwise mechanism for the progression of the RhlR-RhlI-PqsE quorum sensing pathway in P. aeruginosa. AUTHOR SUMMARY Pseudomonas aeruginosa represents a serious threat to public health in the United States because of its intrinsic mechanisms of antimicrobial resistance. One of the primary drivers of its antimicrobial resistance profile is biofilm formation. Biofilms are multicellular communities that are formed in an ordered mechanism by the collective. In the case of P. aeruginosa, biofilm formation is controlled by a cell-cell communication process called quorum sensing. Quorum sensing underpins transcriptional changes in a bacterium that allows for the transition from individual, planktonic behaviors to group, sessile behaviors. Group behaviors are behaviors that are only beneficial to engage in once a critical threshold of kin population is reached. The transition to group behaviors is mediated by quorum sensing through an interconnected regulatory system, with the transcription factor receptor RhlR regulating the expression of hundreds of genes. RhlR-dependent transcription relies on the detection of a ligand produced by its partner synthase, RhlI, and an accessory binding protein that alters its affinity for promoter DNA, PqsE, resulting in a dual regulatory mechanism that was not previously observed in quorum sensing. The main goal of this study was to determine the molecular basis for promoter selection by RhlR using bacterial genetics and DNA-based sequencing methods for measuring site-specific protein binding. Our approach established the entirety of the RhlR direct regulon and the contributions of each of the known regulators to RhlR-dependent promoter binding and gene regulation.