Transcription inhibitors with XRE DNA-binding and cupin signal-sensing domains drive metabolic diversification in Pseudomonas

Abstract

Transcription factors (TFs) are instrumental in the bacterial response to new environmental conditions. They can act as direct signal sensors and subsequently induce changes in gene expression leading to physiological adaptation. Here, by combining RNA-seq and DAP-seq, we studied a family of eight TFs in Pseudomonas aeruginosa. This family, encompassing TFs with XRE-like DNA-binding and cupin signal-sensing domains, includes the metabolic regulators ErfA, PsdR and PauR and five so far unstudied TFs. The genome-wide delineation of their regulons identified 39 regulatory interactions with genes mostly involved in metabolism. We found that the XRE-cupin TFs are inhibitors of their neighboring genes, forming local, functional units encoding proteins with functions in condition-specific metabolic pathways. The phylogenetic analysis of this family of regulators across the Pseudomonas genus revealed a wide diversity of such metabolic regulatory modules and identified species with potentially higher metabolic versatility. Numerous uncharacterized XRE-cupin TFs were found near metabolism-related genes, illustrating the need of further systematic characterization of transcriptional regulatory networks in order to better understand the mechanisms of bacterial adaptation to new environments.IMPORTANCEBacteria of the Pseudomonas genus, including the major human pathogen P. aeruginosa, are known for their complex regulatory networks and high number of transcription factors, which contribute to their impressive adaptive ability. However, even in the most studied species, most of the regulators are still uncharacterized. With the recent advances in high-throughput sequencing methods, it is now possible to fill this knowledge gap and help understanding how bacteria adapt and thrive in new environments. By leveraging these methods, we provide an example of a comprehensive analysis of an entire family of transcription factors and bring new insights into metabolic and regulatory adaptation in the Pseudomonas genus.

Nitrogen metabolism in Pseudomonas putida: functional analysis using random barcode transposon sequencing

“…Based upon our fitness data and recently published DAP-Seq data from P. aeruginosa, we hypothesized that the transcription factor PP_5268 may regulate PP_5182 (132). However, no fluorescence signal was detected when testing the sequences upstream of PP_5182 or PP_5183 as promoters (data not shown).…”

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.…”

The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages

“…Homolog identification was performed by Reciprocal Best Blast Hit (RBBH) analysis 74 on the European Galaxy server 75 using all protein sequences from P. aeruginosa PA14 against all protein sequences from the other 191 genomes with minimum percentage alignment coverages of 90 and sequence identity of 50. The sequences from 66 core genes were concatenated for each genome and a multiple alignment was performed with MAFFT Galaxy version 7.221.3 using default settings 76 , as previously described 77 . The resulting alignment was used to build a Maximum-Likelihood phylogenetic tree using MEGA X 78 with 100 bootstraps, which was visualized and annotated using iTOL v5 79 .…”