Introduction OpenAI o3-deep-research-2025-06-26 121 citations 2026-03-20T23:42:28.617161

Introduction

FleQ (UniProt Q88ET0) is a transcriptional regulator in Pseudomonas putida KT2440 known as the master activator of flagellar biogenesis in pseudomonads (pmc.ncbi.nlm.nih.gov) (www.mdpi.com). It belongs to the NtrC family of enhancer-binding proteins – transcription factors that work with the alternative sigma factor RpoN (σ^54) to activate gene expression. FleQ’s domain architecture is characteristic of this family: an N-terminal REC (response regulator) domain, a central AAA+ ATPase domain that interacts with σ^54, and a C-terminal helix–turn–helix DNA-binding domain (www.mdpi.com). This design enables FleQ to bind specific promoter DNA sites and, upon activation, use ATP hydrolysis to remodel the RNA polymerase–σ^54 complex and initiate transcription. FleQ primarily functions in the bacterial cytoplasm/nucleoid, associating with target gene promoters to regulate their expression.

Key Concepts: By current understanding, FleQ is the master regulator orchestrating the switch between a motile lifestyle (flagellar motility) and a sessile lifestyle (surface attachment and biofilm formation) in P. putida and related species (pmc.ncbi.nlm.nih.gov) (www.mdpi.com). It was first characterized in Pseudomonas aeruginosa as the highest-level regulator in the flagellar gene hierarchy (pmc.ncbi.nlm.nih.gov), and P. putida FleQ plays a similar role (pmc.ncbi.nlm.nih.gov). Disruption of fleQ has dramatic effects: fleQ knockout mutants produce no flagellin (hence no flagella), are completely non-motile, and show severe defects in surface attachment and biofilm formation (www.mdpi.com) (pmc.ncbi.nlm.nih.gov). For example, a 2016 study reported that a P. putida fleQ mutant lost flagellar motility and formed significantly reduced biofilms on abiotic surfaces (pmc.ncbi.nlm.nih.gov). These phenotypes underscore FleQ’s central role in controlling motility structures and biofilm-related components in response to environmental and cellular signals.

Function and Domain Architecture

Functionally, FleQ acts as an enhancer-binding protein (EBP) that activates transcription of numerous genes, especially those required for building a functional flagellum. In P. aeruginosa and P. putida, FleQ governs a flagellar gene cascade with multiple classes of promoters (pmc.ncbi.nlm.nih.gov). It directly binds and activates σ^54-dependent class II promoters for flagellar structural and assembly genes, and thereby indirectly triggers class III promoters (whose activators are encoded by class II genes) (pmc.ncbi.nlm.nih.gov). Through this hierarchy, FleQ initiates production of the basal body, hook, and filament proteins of the polar flagellum. Another regulator, FliA (σ^28), works alongside FleQ for late-stage flagellin expression, but FleQ is the primary regulator setting the cascade in motion (pmc.ncbi.nlm.nih.gov) . Consistent with this role, fleQ mutants are non-flagellated and non-motile (www.mdpi.com). Electron microscopy and motility assays confirm that deleting fleQ abolishes flagellum formation in P. putida, rendering cells unable to swim (www.mdpi.com). Thus, FleQ is indispensable for activating the suite of flagellar genes necessary for motility.

Structurally, FleQ’s REC domain (N-terminus) suggests it evolved from a two-component response regulator, though a dedicated sensor kinase for FleQ has not been clearly identified in P. putida. This REC domain is similar to CheY-like receiver domains (www.mdpi.com) and likely serves as a regulatory switch—potentially controlled by phosphorylation or other signal binding. The central AAA+ ATPase domain provides ATP hydrolysis activity and contains the signature motifs (e.g. Walker A/B) for oligomerization and interaction with σ^54 (www.mdpi.com). In solution, FleQ can form oligomers (dimers to hexamers) and is thought to assemble as a hexamer on DNA to exert its ATPase-dependent remodeling of RNA polymerase (www.mdpi.com). Uniquely, FleQ’s AAA+ domain also binds the secondary messenger cyclic di-GMP (c-di-GMP) with high affinity (pmc.ncbi.nlm.nih.gov) (www.mdpi.com) – a crucial regulatory feature discussed below. Finally, a C-terminal helix–turn–helix (HTH) domain confers sequence-specific DNA binding (www.mdpi.com). FleQ recognizes specific enhancer sites in target promoters, typically located ~100 bp upstream of the transcription start (though in some cases binding sites can be downstream) (pubmed.ncbi.nlm.nih.gov). This allows FleQ to loop DNA and contact RNA polymerase. In summary, FleQ’s domain structure enables it to function as a signal-responsive, oligomerizing transcriptional activator, coupling chemical signals (ATP, c-di-GMP, possibly phosphorylation) to changes in gene expression.

Regulation of Motility and Biofilm Genes

One of FleQ’s most significant roles is coordinating the motile-to-sessile transition by inversely controlling flagellar genes and biofilm matrix genes in response to the second messenger c-di-GMP. Under low intracellular c-di-GMP (conditions favoring motility), FleQ actively promotes expression of flagellar and chemotaxis genes while suppressing certain biofilm-related genes (pmc.ncbi.nlm.nih.gov). As c-di-GMP levels rise (e.g. when the bacterium finds a surface to colonize or nutrient conditions change), c-di-GMP binds directly to FleQ’s AAA+ domain and alters its activity (pmc.ncbi.nlm.nih.gov) (www.mdpi.com). High c-di-GMP effectively inhibits FleQ’s ATPase activity and its activation of flagellar promoters (www.mdpi.com) (pmc.ncbi.nlm.nih.gov). In P. putida, several flagellar genes under FleQ control (class II/III promoters) are strongly down-regulated when c-di-GMP is artificially elevated (pmc.ncbi.nlm.nih.gov). Biochemically, structural models indicate that c-di-GMP lodges in the FleQ AAA+ domain, causing conformational changes that destabilize the active hexameric form and obstruct the ATP-binding site (www.mdpi.com). The current model is that c-di-GMP-bound FleQ can no longer properly interact with σ^54 or remodel RNAP, thereby silencing flagellar gene transcription (www.mdpi.com). This is an elegant mechanism by which rising c-di-GMP (a “stop swimming, start sticking” signal in bacteria) directly turns off the flagellar master activator.

Conversely, FleQ also serves as a repressor for certain exopolysaccharide (EPS) and adhesin genes, and c-di-GMP relieves this repression (pmc.ncbi.nlm.nih.gov). In P. putida, FleQ binds to and represses the promoters of the cellulose biosynthesis operon (bcs genes) and at least one large adhesin gene (lapA), under low c-di-GMP conditions (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). FleQ prevents wasteful production of biofilm matrix when the cell is in a planktonic state. Strikingly, when c-di-GMP binds FleQ, this repression is lifted – and in some cases FleQ may even switch to activating those same genes at high c-di-GMP (pmc.ncbi.nlm.nih.gov). For example, FleQ directly controls the lapA adhesin gene needed for surface attachment: FleQ represses lapA when c-di-GMP is low, but upon c-di-GMP binding, FleQ’s conformation changes such that lapA transcription is activated (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Experimental evidence in P. putida shows FleQ binding at the lapA promoter in vivo and a requirement for FleQ (with elevated c-di-GMP) to induce lapA expression and robust biofilm formation (pmc.ncbi.nlm.nih.gov). In this way, FleQ exhibits a dual mode of action: it is an activator of motility and attachment factors under motile conditions, and a repressor–turned–activator of biofilm matrix genes under sessile conditions (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). This dual regulatory logic ensures a mutually exclusive expression of flagella vs. biofilm components. Genetic studies reinforce this: a fleQ mutant in P. putida is deficient in both swimming (no flagella) and in biofilm polysaccharide production control (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov), indicating FleQ is required both to enable flagellar gene expression and to properly regulate matrix gene expression.

FleN and accessory regulation: FleQ’s activity is modulated by protein partners as well. FleN is an “anti-activator” protein in Pseudomonas that binds to FleQ and inhibits its function (pmc.ncbi.nlm.nih.gov). FleN is thought to sequester FleQ or alter its oligomerization state, preventing excessive or untimely activation of flagellar genes. It also appears to enhance the effect of c-di-GMP on FleQ (pmc.ncbi.nlm.nih.gov). In P. aeruginosa, FleN binding to FleQ, together with c-di-GMP, strongly antagonizes FleQ-driven promoters (pmc.ncbi.nlm.nih.gov). Mutations in fleN can lead to hyperactive FleQ phenotypes (e.g., overproduction of flagella) or bypass of c-di-GMP signaling, underscoring FleN’s balancing role. Another regulatory input comes from transcriptional control of the fleQ gene itself. In P. aeruginosa, the global cAMP-responsive regulator Vfr (homolog of CRP) was shown to downregulate fleQ expression, linking nutrient/energy signals to motility regulation (pubmed.ncbi.nlm.nih.gov) (www.mdpi.com). And notably, an unrelated transcription factor AmrZ (see next section) directly represses fleQ transcription in P. putida/P. fluorescens (www.mdpi.com). Through these layers – second messenger binding, anti-activator protein interaction, and transcriptional regulation – FleQ is tightly controlled, ensuring flagella and biofilm genes are expressed only under suitable conditions.

Regulatory Network and Pathways Involving FleQ

Beyond flagellar genes, modern genomics has revealed FleQ to be a global regulator influencing numerous pathways. A ChIP-sequencing study (2018, Scientific Reports) mapped ~103 FleQ binding sites in the P. putida KT2440 genome (pmc.ncbi.nlm.nih.gov). These correspond to over 100 genes or operons under direct FleQ control in this organism (pmc.ncbi.nlm.nih.gov). Gene ontology analysis showed that while motility/chemotaxis genes are a major subset (~9% of FleQ-regulated genes), an even larger fraction (~16%) relate to iron acquisition and homeostasis (pmc.ncbi.nlm.nih.gov). Other functional categories enriched in the FleQ regulon include cell wall biogenesis (e.g. polysaccharide and adhesin production, ~6–8%) and signal transduction proteins (pmc.ncbi.nlm.nih.gov). This indicates FleQ’s influence extends beyond motility and biofilms into areas like nutrient uptake. For instance, FleQ was found to bind upstream of several iron siderophore receptor genes (pmc.ncbi.nlm.nih.gov), hinting that motile cells co-regulate iron scavenging, possibly to fuel the energetically costly flagella or adapt to new environments. Indeed, many of the FleQ-target genes were conserved between P. fluorescens F113 and P. putida KT2440, and introducing fleQ from one species could complement motility in the other (pmc.ncbi.nlm.nih.gov). This conservation underscores FleQ’s broad importance in pseudomonads as a central regulator of lifestyle adaptation.

A key emerging theme is the AmrZ–FleQ regulatory hub in environmental Pseudomonas. AmrZ is another global transcription factor (named for “alginate and motility regulator Z”) that often counter-balances FleQ. Recent studies show that AmrZ and FleQ have overlapping regulons and inversely regulate many of the same traits (www.mdpi.com). Notably, AmrZ directly represses the fleQ gene (lowering FleQ levels) and activates genes for diguanylate cyclases (enzymes that synthesize c-di-GMP) while repressing phosphodiesterases (which degrade c-di-GMP) (www.mdpi.com) (www.mdpi.com). The outcome is that AmrZ pushes the cell towards a high-c-di-GMP, non-motile, biofilm-friendly state, simultaneously reducing FleQ abundance. FleQ, in turn, was found to negatively regulate the amrZ gene in P. putida and P. fluorescens (pmc.ncbi.nlm.nih.gov), creating a reciprocal negative feedback. Thus, AmrZ and FleQ form a toggle-like circuit: FleQ promotes motility and suppresses certain biofilm functions, while AmrZ promotes biofilm and suppresses motility, each influencing the other’s expression or activity (www.mdpi.com) (www.mdpi.com). This AmrZ–FleQ hub is coordinated through c-di-GMP signaling – AmrZ’s effect on c-di-GMP levels is sensed by FleQ (which requires c-di-GMP binding for its biofilm gene regulation) (www.mdpi.com) (www.mdpi.com). Together, they allow Pseudomonas to finely tune its behavior in response to environmental cues. For example, in the rhizosphere (root environment), where bacteria must balance motility to reach new niches with adhesion to form microcolonies on roots, the AmrZ–FleQ system is critical (www.mdpi.com) (www.mdpi.com). Deletion of amrZ or fleQ alters production of extracellular matrix and flagella, respectively, and impairs the bacteria’s ability to adapt to the complex rhizosphere environment (www.mdpi.com) (www.mdpi.com). Researchers consider this duo a central regulatory hub for environmental adaptation in plant-associated pseudomonads (www.mdpi.com).

Another recent finding expands FleQ’s regulatory influence into the Gac/Rsm pathway, a major post-transcriptional control system. A 2023 study in P. fluorescens Pf0-1 discovered that FleQ not only controls transcription of adhesin genes (lapA, mapA encoding large surface adhesins), but also unexpectedly affects their post-transcriptional expression via the Gac/Rsm regulatory cascade (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). In a fleQ mutant, lapA/mapA mRNA levels were higher than wild-type, yet the adhesin proteins were present at lower levels (pmc.ncbi.nlm.nih.gov). This paradox was traced to the Rsm small RNA system: FleQ mutant strains had dysregulated activation of the Gac/Rsm pathway, which in turn caused more rapid turnover or reduced translation of LapA/MapA adhesins (pmc.ncbi.nlm.nih.gov). Over-activating the Gac/Rsm signals (through a suppressor mutation) partially rescued the biofilm defect of the fleQ mutant, indicating that FleQ normally helps optimize not just gene transcription but also the post-transcriptional stability of adhesin proteins (pmc.ncbi.nlm.nih.gov). This is an important insight: FleQ sits at a nexus of multiple regulatory layers – DNA-level control of gene expression and indirect RNA/protein-level control via global pathways. It underscores that FleQ’s influence on biofilm formation involves coordinating with other regulators to ensure adhesin proteins (like LapA, critical for sticking to surfaces) are produced in the right amount. These complex interconnections are an active area of research, revealing FleQ as a globally connected regulator rather than acting in isolation.

Recent Developments (2023–2024)

Research in the past two years has continued to shed light on FleQ’s role and potential applications. A 2023 comprehensive review of Pseudomonas ogarae F113 (formerly P. fluorescens F113) emphasized the AmrZ–FleQ hub as pivotal for adapting to life in the plant rhizosphere (www.mdpi.com) (www.mdpi.com). This work integrated new genomic and phenotypic data, concluding that FleQ and AmrZ co-regulate hundreds of genes and traits in opposite directions as discussed above. It highlighted that this regulatory hub operates not only in laboratory cultures but also in natural soil environments, making FleQ a key factor in Pseudomonas eco-physiology (www.mdpi.com). For instance, flagellar mutants (e.g. ΔfleQ) were shown to be severely handicapped in competitive root colonization – in mixed inocula, wild-type bacteria outcompete fleQ mutants on plant roots (www.mdpi.com). This finding from 2023 reinforces earlier observations that motility is vital for a bacterium’s success in colonizing the dynamic root ecosystem (www.mdpi.com). It also implies that FleQ-regulated traits (motility, adhesion, EPS) have real-world importance for beneficial plant-microbe interactions.

In 2023, new mechanistic insights were published regarding FleQ’s control of biofilm adhesins. Pastora et al. (Journal of Bacteriology, Sept 2023) found that in P. fluorescens, FleQ has a dual regulatory effect on LapA and MapA adhesins: it activates their transcription and also influences their post-translational retention on the cell surface (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). The study showed ΔfleQ mutants formed significantly less biofilm (quantitatively lower biomass) than wild-type, due in part to a reduction in cell-surface adhesin protein levels (pmc.ncbi.nlm.nih.gov). Intriguingly, the fleQ knockout had higher lapA/mapA mRNA levels, suggesting FleQ normally represses transcription slightly, but ensures protein production through some downstream mechanism (pmc.ncbi.nlm.nih.gov). The authors linked this to the global Gac/Rsm system: in the absence of FleQ, the Gac regulon may become overactive, producing excess small RNAs that bind and inhibit adhesin transcripts, or altering protease activity that degrades adhesins (pmc.ncbi.nlm.nih.gov). When they introduced mutations that dial down the Gac/Rsm pathway, the fleQ mutant’s biofilm formation improved (pmc.ncbi.nlm.nih.gov). This is a cutting-edge development showing FleQ’s integration with global signaling: it is not simply an on/off switch for genes, but part of a network that fine-tunes how much adhesin actually ends up on the cell surface. It highlights the complexity of FleQ’s role in biofilm development – an active area of research with implications for controlling biofilms.

Another important recent finding (Oladosu et al., 2024) concerns FleQ’s role in antibiotic tolerance in biofilms of P. aeruginosa. While P. putida is not a human pathogen, insights from P. aeruginosa biofilms are mechanistically relevant due to the conserved FleQ protein. Oladosu and colleagues showed that deleting fleQ in P. aeruginosa PAO1 leads to formation of thinner, less structured biofilms that are far more sensitive to antibiotics like tobramycin and norfloxacin (pmc.ncbi.nlm.nih.gov). In flow-cell experiments, wild-type PAO1 formed robust, towering microcolonies, whereas ΔfleQ mutants only formed flat, unstructured biofilm layers and failed to develop the typical tolerance to antibiotics (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Quantitatively, biofilm biomass and height were greatly reduced without FleQ, and the mutant biofilms were readily eradicated by antibiotic treatment compared to wild-type biofilms (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). This recent work suggests FleQ not only governs the initiation of biofilm formation but also fine-tunes the expression of biofilm-specific resistance factors. The study found that FleQ works in concert with another regulator, BrlR, which controls a set of efflux pumps and protective genes in mature biofilms (pmc.ncbi.nlm.nih.gov). FleQ “fine-tunes” a subset of these genes, ensuring the biofilm acquires full antibiotic tolerance (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). This is a significant development, as it positions FleQ as a potential target for anti-biofilm strategies – inhibiting FleQ could weaken biofilm structure and make bacteria more susceptible to antibiotics. While this result was in P. aeruginosa, it underscores FleQ’s broad importance in biofilm physiology. Future research may investigate if P. putida biofilms (in environmental or industrial settings) similarly rely on FleQ for resilience against stresses.

Biological Significance and Applications

Given FleQ’s central role in controlling motility and biofilm formation, it has important implications in both environmental and applied contexts. In agricultural biotechnology, certain P. putida and P. fluorescens strains are used as plant growth-promoting rhizobacteria (PGPR). For these beneficial bacteria, effective root colonization is essential for suppressing pathogens and aiding plant growth. FleQ-regulated traits – especially flagellar motility and initial adhesion – are critical for root colonization. Studies have shown that mutants lacking FleQ or flagella are severely impaired in competitive rhizosphere colonization (www.mdpi.com). They cannot swarm through soil as efficiently or reach nutrient-rich root zones, and thus are outcompeted by motile wild-type strains (www.mdpi.com) (www.mdpi.com). This can reduce their plant-beneficial effects (biocontrol and nutrient delivery), since colonization is a prerequisite for those activities (www.mdpi.com). Conversely, hypermotile variants of pseudomonads tend to colonize roots better (www.mdpi.com). These observations highlight FleQ as a key factor for environmental fitness: it enables the timely expression of motility when searching for new niches, and curbs motility in favor of adhesive growth once the bacterium finds a suitable site (like a root surface). Understanding this regulation has practical value – for example, PGPR strains might be engineered or induced to modulate FleQ activity to optimize root colonization. In one scenario, transiently suppressing FleQ (or increasing c-di-GMP) could promote strong biofilm-like microcolonies on roots for persistence, whereas boosting FleQ activity could enhance spreading to new root areas. Indeed, the concept of manipulating second messengers like c-di-GMP to alter bacterial behavior is being explored in microbial ecology. FleQ sits at the heart of that behavior switch in P. putida.

In industrial and environmental biotechnology, P. putida is a popular chassis for biodegradation and biotransformations. Controlling biofilm formation is often crucial in such settings – sometimes biofilms are desirable (e.g. in bioreactors or biofilters, where attached cells resist washout), and sometimes planktonic growth is preferred (to avoid clogs and fouling). FleQ, through c-di-GMP signaling, is a compelling target to modulate these states. For instance, if a robust biofilm is needed on a bioreactor surface, one could imagine elevating c-di-GMP levels (via a diguanylate cyclase or chemical inducer) to inactivate FleQ and promote EPS production. Conversely, if biofilm needs to be reduced, activating FleQ (or inhibiting c-di-GMP) would favor motile, planktonic growth. While direct industrial applications of FleQ manipulation are still speculative, the regulatory circuits are being unraveled to allow such control. A 2017 study demonstrated that FleQ is a multimeric c-di-GMP receptor that differentially regulates biofilm matrix components in P. putida (pubmed.ncbi.nlm.nih.gov). This knowledge opens the door to rationally tune the biofilm-forming capability of engineered P. putida by tweaking FleQ or its associated signaling pathways. In the medical domain, insights from FleQ in pseudomonads can translate into anti-biofilm approaches. Although P. putida is mostly non-pathogenic, the homologous FleQ in P. aeruginosa is essential for full biofilm development and antibiotic tolerance (pmc.ncbi.nlm.nih.gov). Compounds that destabilize FleQ’s interaction with c-di-GMP or with DNA could, in theory, force pathogenic biofilms into a state that is easier to eradicate. For example, if a drug kept FleQ in its active (apo) state when c-di-GMP is high, it might continuously repress polysaccharide genes and make biofilms fragile. Alternatively, locking FleQ in an inactive state might prevent flagellar gene expression, which could be useful to reduce the spread of infection by eliminating motility. These are conceptual strategies – current expert opinion suggests that targeting master regulators like FleQ or second messenger pathways is a promising angle in biofilm control (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov), though specific FleQ inhibitors are not yet available.

Expert Perspectives and Conclusion

Experts in microbial regulation consider FleQ a prime example of a global regulatory hub that integrates multiple signals to dictate bacterial lifestyle. As noted in a 2023 review, FleQ is “a central hub for environmental adaptation in pseudomonads”, coordinating motility, biofilm formation, and other traits in response to the intracellular c-di-GMP pool (www.mdpi.com). Its ability to bind c-di-GMP directly has been described as a groundbreaking discovery – FleQ was the first transcription factor identified to bind this second messenger without a dedicated PilZ domain (www.mdpi.com). This finding has spurred a broader appreciation that transcription programs can be tightly coupled to nucleotide signals. Research by Martínez-Granero, Rivilla and colleagues (2018) established FleQ as a global regulator impacting “probably more than one hundred genes” in P. putida, with binding sites spread across the genome (pmc.ncbi.nlm.nih.gov). They concluded that “together with AmrZ, FleQ is an important determinant for environmental adaptation”, underlining its dual role in motility and biofilm gene regulation (pmc.ncbi.nlm.nih.gov). Current opinions emphasize the sophistication of FleQ’s regulatory mechanism: rather than a simple on/off switch, FleQ works in concert with partner proteins (like FleN) and intersects with other regulatory systems (AmrZ, Rsm, etc.) to fine-tune outcomes (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). This multi-layered control is seen as essential for bacteria to rapidly adjust to changing conditions – for example, transitioning from free-swimming in water to attaching on a plant root involves rewiring dozens of genes, a feat accomplished in large part by the FleQ-centered network.

In terms of data, our growing knowledge base quantifies FleQ’s impact. For instance, FleQ’s direct regulon in P. putida encompasses ~2% of the genome (pmc.ncbi.nlm.nih.gov), and its loss leads to a >80–90% reduction in swimming ability (measured by swim plate assays) and >50% reduction in biofilm biomass in lab assays (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). FleQ binding sites have been confirmed upstream of key genes like fliE, fliC (flagellar components), lapA (adhesin), bcsA (cellulose synthase), and multiple iron receptors (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). The regulation is intricately conditional: e.g., FleQ’s occupancy at the lapA promoter is strong regardless of c-di-GMP levels, but actual lapA expression is 3-fold higher when c-di-GMP is elevated (pmc.ncbi.nlm.nih.gov) (pmc.ncbi.nlm.nih.gov). Such data illustrate how FleQ can bind DNA constitutively yet require a signal to activate transcription – consistent with the notion that c-di-GMP triggers a switch in FleQ’s function at certain promoters. Another relevant statistic from competitive colonization experiments: in coinoculation trials on plant roots, wild-type Pseudomonas strains can outcompete fleQ mutants by an order of magnitude in recovered cell numbers (www.mdpi.com) (www.mdpi.com), demonstrating FleQ’s importance for survival in real-world ecosystems.

In summary, FleQ in P. putida KT2440 is a master transcriptional regulator that controls the expression of flagellar machinery, surface adhesins, and matrix polysaccharides, thereby governing the bacterium’s transition between motile and biofilm modes. It operates through a classic σ^54-enhancer binding mechanism, yet is uniquely modulated by the second messenger c-di-GMP and auxiliary proteins. FleQ sits at the intersection of multiple signaling pathways – integrating environmental cues (via c-di-GMP, two-component signals) and internal regulatory networks (FleN, AmrZ, Rsm) – to appropriately tune gene expression. Recent research (2023–2024) has expanded our understanding of FleQ’s regulon and revealed new layers of control, such as FleQ’s involvement in post-transcriptional regulation of adhesin proteins and in biofilm antibiotic tolerance. These findings position FleQ as a crucial node in Pseudomonas physiology and a potential target for interventions. Whether the goal is to enhance beneficial biofilms (e.g. for plant root colonization or bioremediation) or to disrupt harmful biofilms (in case of pathogenic relatives), insights into FleQ’s function and regulation provide a powerful knowledge base for guiding future applications. As our current understanding stands, FleQ exemplifies how bacteria leverage a single regulator to synchronously manage a broad suite of functions essential for adapting to life in diverse environments (pmc.ncbi.nlm.nih.gov) (www.mdpi.com). The continuing research and expert analyses underscore FleQ’s significance, making it a focal point in the study of bacterial lifestyle switching and signaling integration in pseudomonads.

References: (Key references are embedded above in text; publication dates and sources are provided in the citations. Primary sources include: Jiménez-Fernández et al., 2016, PLoS One ; Blanco-Romero et al., 2018, Sci. Reports (pmc.ncbi.nlm.nih.gov); Molina-Henares et al., 2017 (pubmed.ncbi.nlm.nih.gov); Oladosu et al., 2024, J. Bacteriol (pmc.ncbi.nlm.nih.gov); Pastora et al., 2023, J. Bacteriol (pmc.ncbi.nlm.nih.gov); and Blanco-Romero et al., 2023, Microorganisms (www.mdpi.com).)

Citations

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  9. AnnotationURLCitation(end_index=2774, start_index=2603, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=transcriptional%20regulator%20FleQ%20and%20the,attachment%2C%20and%20the%20ability%20of')
  10. AnnotationURLCitation(end_index=3099, start_index=2928, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=transcriptional%20regulator%20FleQ%20and%20the,attachment%2C%20and%20the%20ability%20of')
  11. AnnotationURLCitation(end_index=3756, start_index=3593, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=match%20at%20L221%20regulatory%20elements%2C,activated%20by%20Class%20II%20gene')
  12. AnnotationURLCitation(end_index=4141, start_index=3978, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=match%20at%20L221%20regulatory%20elements%2C,activated%20by%20Class%20II%20gene')
  13. AnnotationURLCitation(end_index=4566, start_index=4418, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=FleQ%20has%20long%20been%20known,are%20regulated%20by%20a%20four')
  14. AnnotationURLCitation(end_index=4787, start_index=4646, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=mutants%20affected%20in%20fleQ%20and,polar%20flagella%2C%20a%2041%20kb')
  15. AnnotationURLCitation(end_index=5074, start_index=4933, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=mutants%20affected%20in%20fleQ%20and,polar%20flagella%2C%20a%2041%20kb')
  16. AnnotationURLCitation(end_index=5556, start_index=5432, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=pseudomonads%20,118%2C153%2C190%5D.%20The%20mode%20of')
  17. AnnotationURLCitation(end_index=5966, start_index=5842, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=pseudomonads%20,118%2C153%2C190%5D.%20The%20mode%20of')
  18. AnnotationURLCitation(end_index=6240, start_index=6132, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=antagonist%20,binding%20site%20domain')
  19. AnnotationURLCitation(end_index=6495, start_index=6361, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=polymerase,the%20synthesis%20of%20biofilm%20matrix')
  20. AnnotationURLCitation(end_index=6604, start_index=6496, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=antagonist%20,binding%20site%20domain')
  21. AnnotationURLCitation(end_index=6871, start_index=6747, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=pseudomonads%20,118%2C153%2C190%5D.%20The%20mode%20of')
  22. AnnotationURLCitation(end_index=7201, start_index=7051, title='FleQ, the major flagellar gene regulator in Pseudomonas aeruginosa, binds to enhancer sites located either upstream or atypically downstream of the RpoN binding site - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/12218010/#:~:text=to%20enhancer%20sites%20located%20either,FleQ.%20%28B%20to%20D%29%20Gel')
  23. AnnotationURLCitation(end_index=8052, start_index=7918, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=polymerase,the%20synthesis%20of%20biofilm%20matrix')
  24. AnnotationURLCitation(end_index=8378, start_index=8244, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=polymerase,the%20synthesis%20of%20biofilm%20matrix')
  25. AnnotationURLCitation(end_index=8487, start_index=8379, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=antagonist%20,binding%20site%20domain')
  26. AnnotationURLCitation(end_index=8718, start_index=8593, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=first%20TF%20known%20for%20its,binding%20site%20domain')
  27. AnnotationURLCitation(end_index=8853, start_index=8719, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=polymerase,the%20synthesis%20of%20biofilm%20matrix')
  28. AnnotationURLCitation(end_index=9160, start_index=9006, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=transcription%20of%20FleQ,genes%20involved%20in%20cyclic%20diguanylate')
  29. AnnotationURLCitation(end_index=9494, start_index=9369, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=first%20TF%20known%20for%20its,binding%20site%20domain')
  30. AnnotationURLCitation(end_index=9756, start_index=9648, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=antagonist%20,binding%20site%20domain')
  31. AnnotationURLCitation(end_index=10222, start_index=10062, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=AAA%2B%20ATPase%20domain%20of%20FleQ,the%20synthesis%20of%20biofilm%20matrix')
  32. AnnotationURLCitation(end_index=10532, start_index=10413, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=motility%20and%20adhesion%20,putida')
  33. AnnotationURLCitation(end_index=10667, start_index=10533, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=polymerase,the%20synthesis%20of%20biofilm%20matrix')
  34. AnnotationURLCitation(end_index=11085, start_index=10918, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=match%20at%20L230%20components%2C%20and,antagonize%20its%20activity%20and%20enhance')
  35. AnnotationURLCitation(end_index=11481, start_index=11321, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=AAA%2B%20ATPase%20domain%20of%20FleQ,the%20synthesis%20of%20biofilm%20matrix')
  36. AnnotationURLCitation(end_index=11650, start_index=11482, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=expression%20of%20the%20lapA%20gene%2C,and%20the%20transcriptional%20activation%20of')
  37. AnnotationURLCitation(end_index=12014, start_index=11846, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=expression%20of%20the%20lapA%20gene%2C,and%20the%20transcriptional%20activation%20of')
  38. AnnotationURLCitation(end_index=12365, start_index=12231, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=polymerase,the%20synthesis%20of%20biofilm%20matrix')
  39. AnnotationURLCitation(end_index=12542, start_index=12366, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=components%2C%20and%20repression%20is%20released,antagonize%20its%20activity%20and%20enhance')
  40. AnnotationURLCitation(end_index=12976, start_index=12805, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=transcriptional%20regulator%20FleQ%20and%20the,attachment%2C%20and%20the%20ability%20of')
  41. AnnotationURLCitation(end_index=13111, start_index=12977, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=polymerase,the%20synthesis%20of%20biofilm%20matrix')
  42. AnnotationURLCitation(end_index=13604, start_index=13428, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=components%2C%20and%20repression%20is%20released,antagonize%20its%20activity%20and%20enhance')
  43. AnnotationURLCitation(end_index=13974, start_index=13798, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=components%2C%20and%20repression%20is%20released,antagonize%20its%20activity%20and%20enhance')
  44. AnnotationURLCitation(end_index=14261, start_index=14085, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=components%2C%20and%20repression%20is%20released,antagonize%20its%20activity%20and%20enhance')
  45. AnnotationURLCitation(end_index=14862, start_index=14694, title='fleQ, the gene encoding the major flagellar regulator of Pseudomonas aeruginosa, is sigma70 dependent and is downregulated by Vfr, a homolog of Escherichia coli cyclic AMP receptor protein - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/12218009/#:~:text=aeruginosa%2C%20is%20sigma70%20dependent%20and,antiactivator%2C%20not%20much%20is%20known')
  46. AnnotationURLCitation(end_index=15020, start_index=14863, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=match%20at%20L448%20pseudomonads%2C%20Vfr,flagellar%20apparatus%20acting%20over%20KinB')
  47. AnnotationURLCitation(end_index=15312, start_index=15167, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=the%20expression%20of%20fleQ%20in,related%20proteins%20with%20a%20putative')
  48. AnnotationURLCitation(end_index=15962, start_index=15831, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=In%20this%20work%2C%20we%20have,Gene%20ontology')
  49. AnnotationURLCitation(end_index=16188, start_index=16057, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=In%20this%20work%2C%20we%20have,Gene%20ontology')
  50. AnnotationURLCitation(end_index=16525, start_index=16381, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=categories%20according%20to%20the%20Gene,in%20both%20species')
  51. AnnotationURLCitation(end_index=16842, start_index=16698, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=categories%20according%20to%20the%20Gene,in%20both%20species')
  52. AnnotationURLCitation(end_index=17179, start_index=17035, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=categories%20according%20to%20the%20Gene,in%20both%20species')
  53. AnnotationURLCitation(end_index=17664, start_index=17503, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=binding%20sites%20is%20similar%20in,FleQ%20binding%20sites%20identified%20are')
  54. AnnotationURLCitation(end_index=18259, start_index=18114, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=F113%2C%20AmrZ%20and%20FleQ%20are,regulate%20traits%20such%20as%20motility')
  55. AnnotationURLCitation(end_index=18630, start_index=18482, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=match%20at%20L435%20the%20expression,related%20proteins%20with%20a%20putative')
  56. AnnotationURLCitation(end_index=18778, start_index=18631, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=represses%20the%20expression%20of%20fleQ,is%20the%20opposed%20lifestyle%20to')
  57. AnnotationURLCitation(end_index=19141, start_index=19022, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=motility%20and%20adhesion%20,putida')
  58. AnnotationURLCitation(end_index=19558, start_index=19406, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=match%20at%20L80%20regulated%20by,adaption%20to%20the%20rhizosphere%20environment')
  59. AnnotationURLCitation(end_index=19704, start_index=19559, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=the%20expression%20of%20fleQ%20in,related%20proteins%20with%20a%20putative')
  60. AnnotationURLCitation(end_index=20038, start_index=19886, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=match%20at%20L80%20regulated%20by,adaption%20to%20the%20rhizosphere%20environment')
  61. AnnotationURLCitation(end_index=20163, start_index=20039, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=levels%20of%20c,its%20interaction%20with%20FleQ%20and')
  62. AnnotationURLCitation(end_index=20602, start_index=20451, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=regulated%20by%20AmrZ%20and%20it,adaption%20to%20the%20rhizosphere%20environment')
  63. AnnotationURLCitation(end_index=20767, start_index=20603, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=flagellar%20master%20regulator%20FleQ%20as,for%20environmental%20adaption%20in%20pseudomonads')
  64. AnnotationURLCitation(end_index=21048, start_index=20951, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=matrix%20components,ogarae')
  65. AnnotationURLCitation(end_index=21190, start_index=21049, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=mutants%20affected%20in%20fleQ%20and,polar%20flagella%2C%20a%2041%20kb')
  66. AnnotationURLCitation(end_index=21469, start_index=21309, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=match%20at%20L646%20flagellar%20master,for%20environmental%20adaption%20in%20pseudomonads')
  67. AnnotationURLCitation(end_index=22027, start_index=21870, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=both%20transcriptionally%20and%20post,abundance%20of%20LapA%20and%20MapA')
  68. AnnotationURLCitation(end_index=22165, start_index=22028, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=and%20mapA%20transcripts%20compared%20to,fluorescens')
  69. AnnotationURLCitation(end_index=22450, start_index=22293, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=both%20transcriptionally%20and%20post,expression%20of%20the%20lapA%20and')
  70. AnnotationURLCitation(end_index=22783, start_index=22663, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=type%20,transcriptionally%20enhance')
  71. AnnotationURLCitation(end_index=23186, start_index=23049, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=and%20mapA%20transcripts%20compared%20to,fluorescens')
  72. AnnotationURLCitation(end_index=24193, start_index=24048, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=F113%2C%20AmrZ%20and%20FleQ%20are,regulate%20traits%20such%20as%20motility')
  73. AnnotationURLCitation(end_index=24354, start_index=24194, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=match%20at%20L646%20flagellar%20master,for%20environmental%20adaption%20in%20pseudomonads')
  74. AnnotationURLCitation(end_index=24852, start_index=24701, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=regulated%20by%20AmrZ%20and%20it,adaption%20to%20the%20rhizosphere%20environment')
  75. AnnotationURLCitation(end_index=25189, start_index=25048, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=mutants%20affected%20in%20fleQ%20and,polar%20flagella%2C%20a%2041%20kb')
  76. AnnotationURLCitation(end_index=25480, start_index=25336, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=match%20at%20L359%20are%20amongst,that%20variants%20isolated%20from%20the')
  77. AnnotationURLCitation(end_index=26151, start_index=25978, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=about%20the%20underlying%20mechanisms%20that,in%20the%20%CE%94fleQ%20mutant%20background')
  78. AnnotationURLCitation(end_index=26289, start_index=26152, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=and%20mapA%20transcripts%20compared%20to,fluorescens')
  79. AnnotationURLCitation(end_index=26626, start_index=26469, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=both%20transcriptionally%20and%20post,expression%20of%20the%20lapA%20and')
  80. AnnotationURLCitation(end_index=26979, start_index=26822, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=both%20transcriptionally%20and%20post,expression%20of%20the%20lapA%20and')
  81. AnnotationURLCitation(end_index=27359, start_index=27222, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=and%20mapA%20transcripts%20compared%20to,fluorescens')
  82. AnnotationURLCitation(end_index=27610, start_index=27473, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=and%20mapA%20transcripts%20compared%20to,fluorescens')
  83. AnnotationURLCitation(end_index=28605, start_index=28469, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=biofilms,BfiSR%20and%20antibiotic%20tolerance%20via')
  84. AnnotationURLCitation(end_index=28950, start_index=28814, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=biofilms,BfiSR%20and%20antibiotic%20tolerance%20via')
  85. AnnotationURLCitation(end_index=29088, start_index=28951, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=Biofilm%20formation%20was%20evaluated%20post,COMSTAT')
  86. AnnotationURLCitation(end_index=29407, start_index=29271, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=biofilms,BfiSR%20and%20antibiotic%20tolerance%20via')
  87. AnnotationURLCitation(end_index=29545, start_index=29408, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=Biofilm%20formation%20was%20evaluated%20post,COMSTAT')
  88. AnnotationURLCitation(end_index=30037, start_index=29860, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=The%20transcription%20factor%20FleQ%20contributes,involved%20in%20biofilm%20formation%20when')
  89. AnnotationURLCitation(end_index=30274, start_index=30138, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=biofilms,BfiSR%20and%20antibiotic%20tolerance%20via')
  90. AnnotationURLCitation(end_index=30452, start_index=30275, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=The%20transcription%20factor%20FleQ%20contributes,involved%20in%20biofilm%20formation%20when')
  91. AnnotationURLCitation(end_index=31757, start_index=31613, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=match%20at%20L359%20are%20amongst,that%20variants%20isolated%20from%20the')
  92. AnnotationURLCitation(end_index=32034, start_index=31893, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=mutants%20affected%20in%20fleQ%20and,polar%20flagella%2C%20a%2041%20kb')
  93. AnnotationURLCitation(end_index=32183, start_index=32035, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=are%20amongst%20the%20most%20severely,that%20variants%20isolated%20from%20the')
  94. AnnotationURLCitation(end_index=32470, start_index=32326, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=match%20at%20L359%20are%20amongst,that%20variants%20isolated%20from%20the')
  95. AnnotationURLCitation(end_index=32699, start_index=32551, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=are%20amongst%20the%20most%20severely,that%20variants%20isolated%20from%20the')
  96. AnnotationURLCitation(end_index=34771, start_index=34627, title='FleQ of Pseudomonas putida KT2440 is a multimeric cyclic diguanylate binding protein that differentially regulates expression of biofilm matrix components - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/27503246/#:~:text=FleQ%20of%20Pseudomonas%20putida%20KT2440,Gonz%C3%A1lez%5E%7B%202')
  97. AnnotationURLCitation(end_index=35325, start_index=35189, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=biofilms,BfiSR%20and%20antibiotic%20tolerance%20via')
  98. AnnotationURLCitation(end_index=36138, start_index=35994, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=known%20to%20contribute%20to%20biofilm,This%20was%20further')
  99. AnnotationURLCitation(end_index=36316, start_index=36139, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=The%20transcription%20factor%20FleQ%20contributes,involved%20in%20biofilm%20formation%20when')
  100. AnnotationURLCitation(end_index=36938, start_index=36778, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=match%20at%20L646%20flagellar%20master,for%20environmental%20adaption%20in%20pseudomonads')
  101. AnnotationURLCitation(end_index=37250, start_index=37142, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=antagonist%20,binding%20site%20domain')
  102. AnnotationURLCitation(end_index=37715, start_index=37584, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=In%20this%20work%2C%20we%20have,Gene%20ontology')
  103. AnnotationURLCitation(end_index=38054, start_index=37890, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=current%20investigation,important%20determinant%20for%20environmental%20adaption')
  104. AnnotationURLCitation(end_index=38487, start_index=38311, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=components%2C%20and%20repression%20is%20released,antagonize%20its%20activity%20and%20enhance')
  105. AnnotationURLCitation(end_index=38625, start_index=38488, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=and%20mapA%20transcripts%20compared%20to,fluorescens')
  106. AnnotationURLCitation(end_index=39199, start_index=39068, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=In%20this%20work%2C%20we%20have,Gene%20ontology')
  107. AnnotationURLCitation(end_index=39518, start_index=39347, title='Complex Interplay between FleQ, Cyclic Diguanylate and Multiple σ Factors Coordinately Regulates Flagellar Motility and Biofilm Development in Pseudomonas putida - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC5026340/#:~:text=transcriptional%20regulator%20FleQ%20and%20the,attachment%2C%20and%20the%20ability%20of')
  108. AnnotationURLCitation(end_index=39655, start_index=39519, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=biofilms,BfiSR%20and%20antibiotic%20tolerance%20via')
  109. AnnotationURLCitation(end_index=39954, start_index=39835, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=motility%20and%20adhesion%20,putida')
  110. AnnotationURLCitation(end_index=40119, start_index=39955, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=genes%20included%20fliE%2C%20lapA%2C%20algD%2C,peaks%2C%20as%20in%20some%20peaks')
  111. AnnotationURLCitation(end_index=40442, start_index=40323, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=iron%20homeostasis,GMP%20does%20not')
  112. AnnotationURLCitation(end_index=40611, start_index=40443, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=expression%20of%20the%20lapA%20gene%2C,and%20the%20transcriptional%20activation%20of')
  113. AnnotationURLCitation(end_index=41182, start_index=41041, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=mutants%20affected%20in%20fleQ%20and,polar%20flagella%2C%20a%2041%20kb')
  114. AnnotationURLCitation(end_index=41331, start_index=41183, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=are%20amongst%20the%20most%20severely,that%20variants%20isolated%20from%20the')
  115. AnnotationURLCitation(end_index=43028, start_index=42867, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=binding%20sites%20is%20similar%20in,FleQ%20binding%20sites%20identified%20are')
  116. AnnotationURLCitation(end_index=43189, start_index=43029, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=match%20at%20L646%20flagellar%20master,for%20environmental%20adaption%20in%20pseudomonads')
  117. AnnotationURLCitation(end_index=43754, start_index=43623, title='Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440 - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC6120874/#:~:text=In%20this%20work%2C%20we%20have,Gene%20ontology')
  118. AnnotationURLCitation(end_index=43930, start_index=43786, title='FleQ of Pseudomonas putida KT2440 is a multimeric cyclic diguanylate binding protein that differentially regulates expression of biofilm matrix components - PubMed', type='url_citation', url='https://pubmed.ncbi.nlm.nih.gov/27503246/#:~:text=FleQ%20of%20Pseudomonas%20putida%20KT2440,Gonz%C3%A1lez%5E%7B%202')
  119. AnnotationURLCitation(end_index=44107, start_index=43971, title='FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC12096822/#:~:text=biofilms,BfiSR%20and%20antibiotic%20tolerance%20via')
  120. AnnotationURLCitation(end_index=44305, start_index=44148, title='The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens - PMC', type='url_citation', url='https://pmc.ncbi.nlm.nih.gov/articles/PMC10521353/#:~:text=both%20transcriptionally%20and%20post,expression%20of%20the%20lapA%20and')
  121. AnnotationURLCitation(end_index=44507, start_index=44360, title='Adaption of Pseudomonas\xa0ogarae F113 to the Rhizosphere Environment—The AmrZ-FleQ Hub', type='url_citation', url='https://www.mdpi.com/2076-2607/11/4/1037/xml#:~:text=FleQ%20has%20long%20been%20known,regulator%20of%20flagellar%20synthesis%20in')