Determination of the Two-Component Systems regulatory network reveals core and accessory regulations across Pseudomonas aeruginosa lineages

Abstract

Pseudomonas aeruginosa possesses one of the most complex bacterial regulatory networks, which largely contributes to its success as a human opportunistic pathogen. However, most of its transcription factors (TFs) are still uncharacterized and the potential intra-species variability in regulatory networks has been mostly ignored so far. Here, to provide a first global view of the two-component systems (TCSs) regulatory network in P. aeruginosa, we produced and purified all DNA-binding TCS response regulators (RRs) and used DAP-seq to map the genome-wide binding sites of these 55 TFs across the three major P. aeruginosa lineages. The resulting networks encompass about 40% of all genes in each strain and contain numerous new important regulatory interactions across most major physiological processes, including virulence and antibiotic resistance. Strikingly, the comparison between the three representative strains shows that about half of the detected targets are specific to only one or two of the tested strains, revealing a previously unknown large functional diversity of TFs within a single species. Three main mechanisms were found to drive this diversity, including differences in accessory genome content, as exemplified by the strain-specific plasmid in the IHMA87 outlier strain which harbors numerous binding sites of chromosomally-encoded RRs. Additionally, most RRs display potential auto-regulation or RR-RR cross-regulation, bringing to light the vast complexity of this network. Overall, we provide the first complete delineation of the TCS regulatory network in P. aeruginosa that will represent an important resource for future studies on this pathogen.

Zinc homeostasis in Pseudomonas

“…Importantly, the structure shows that zinc is directly recognized by CzcS, without the need for additional periplasmic proteins. In P. aeruginosa, twelve response regulators of TCS might bind the intergenic region between czcRS and czcCBA forming CzcR as the "key downstream node of RR network" (Trouillon et al 2021). Besides, CzcR exhibits a dual role: in addition to promoting zinc, cadmium, and cobalt resistance via the activation of the czcCBA efflux pump, it downregulates the expression of oprD by directly binding the promoter region.…”

A Zur-mediated transcriptional regulation of the zinc export system

“…Zur could also compete with binding of a transcriptional repressor in this region, revealing an alternative start of transcription. For example, numerous TCS RRs have recently been detected in the intergenic region between czcR and czcC (27). Alternatively, Zur could modify a secondary structure at the DNA limits the full transcription of czcR .…”

BysR, a LysR-type Pleiotropic Regulator, Controls Production of Occidiofungin by Activating the LuxR-type transcriptional regulator AmbR1 in Burkholderia sp. JP2-270

“…DAP-seq has been successfully applied to identify TFBSs in several organisms, especially in eukaryotes, such as Arabidopsis thaliana (26), rice (39, 40) and maize (41). However, DAP-seq was not widely used in prokaryotes, and only several reports have been reported in the study of TFs in Pseudomonas , such as the studies on XRE-like family TFs and two-component systems response regulators in Pseudomonas aeruginosa (42, 43). More studies in different species will be encouraged to evaluate the applicability of DAP-seq in prokaryote.…”