Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440

Abstract

Bacterial motility plays a crucial role in competitiveness and colonization in the rhizosphere. In this work, Chromatin ImmunoPrecipitation Sequencing (ChIP-seq) analysis has been used to identify genes putatively regulated by the transcriptional regulatory protein FleQ in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440. This protein was previously identified as a master regulator of flagella and biofilm formation in both strains. This work has demonstrated that FleQ from both bacteria are conserved and functionally equivalent for motility regulation. Furthermore, the ChIP-seq analysis has shown that FleQ is a global regulator with the identification of 121 and 103 FleQ putative binding sites in P. fluorescens F113 and P. putida KT2440 respectively. Putative genes regulated by FleQ included, as expected, flagellar and motility-related genes and others involved in adhesion and exopolysaccharide production. Surprisingly, the ChIP-seq analysis also identified iron homeostasis-related genes for which positive regulation was shown by RT-qPCR. The results also showed that FleQ from P. fluorescens F113 shares an important part of its direct regulon with AmrZ, a global regulator also implicated in environmental adaption. Although AmrZ also regulates motility and iron uptake, the overlap occurred mostly with the iron-related genes, since both regulators control a different set of motility-related genes.

Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance

“…The GacS/GacA two-component regulatory system is implicated in biofilm formation ( Martinez-Gil et al., 2014 ) and flagellar transport ( Kim et al., 2014 ), suggesting alternate regulation of these functions may be generally beneficial in well-mixed planktonic cultivations, as has been previously reported ( Bentley et al., 2020 ). Genes related to flagellar transport ( fleQ and fliQ ( Blanco-Romero et al., 2018 )) were also mutated in several TALE/ALE conditions ( Fig. 2 , Supplementary Data File 1 ), further strengthening the argument that a deregulation of flagellar transport improves growth under the experimental conditions applied here due to conservation of resources as has been demonstrated previously ( Martínez-García et al., 2014b ; Utrilla et al., 2016 ).…”

The Wsp intermembrane complex mediates metabolic control of the swim‐attach decision of Pseudomonas putida

“…Those confined alterations produce the desired response using specific modulators that respond to heterogeneous variations (Dahlstrom and O'Toole, 2017;Dahlstrom et al, 2018). To shed some light on the way that cdGMP formed from WspR interacts with certain TFs and regulators to form biofilm in P. putida, the same type of experiments were performed using combined deletions of three regulators that respond to cdGMP in this context: for one side, we focused on FleQ and FleN, TFs that are clearly involved in the regulation of motility and sesility (Baraquet et al, 2012;Jimenez-Fernandez et al, 2016;Blanco-Romero et al, 2018). On a different side, FlgZ, also known in E. coli as YgcR, is a protein that harbours a cdGMP recognizing PilZ domain, which has been determined as a motility regulator through certain flagellar parts (Martinez-Granero et al, 2014).…”

“…FleQ is the most important transcription factor (TF) and master regulator of biofilm formation and motility responsive to cdGMP. The same TF is also related to other functions, including iron homeostasis (Blanco-Romero et al, 2018) and the control of Type 6 secretion system (Wang et al, 2018). In P. putida in conditions of low cdGMP, FleQ can interact with σ 54 to regulate a high number of promoters related to motility and flagella.…”

Crosstalk between the Type VI Secretion System and the Expression of Class IV Flagellar Genes in the Pseudomonas fluorescens MFE01 Strain

“…The promoters that control expression of flagellar genes have been divided into three classes for enterobacteria [30], whereas in Pseudomonas, flagellar gene expression is controlled in a four-tiered hierarchy of transcriptional regulation (called classes I to IV) [31]. Transcriptional regulators, including RpoN, FliA, FleR, and FleQ, finely control expression of the flagellar genes needed for the coordinated assembly of flagella [32].…”