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Georgia Fanouraki

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Open access Aug 2026

The FleQ-FleN circuit balances flagellar number against fitness in Pseudomonas aeruginosa

ABSTRACT Evolutionary constraints governing flagellar number in bacterial pathogens remain poorly understood. While related Pseudomonas species are hyperflagellated, Pseudomonas aeruginosa maintains strict monoflagellation through the FleQ-FleN regulatory circuit. Here, we demonstrate that FleN dosage is essential for maintaining monoflagellation and fitness. Confirming earlier reports, wild-type P. aeruginosa displayed unipolar monoflagellation, whereas ∆fleN mutants developed multiple flagella, frequently more than four, in unipolar or bipolar arrangements. These hyperflagellated cells showed marked fitness defects, including reduced growth, attenuated virulence in a nematode infection model, and a competitive disadvantage in co-culture. The virulence defect reflected hyperflagellation rather than the loss of motility, since a non-flagellated ∆fliC mutant retained full pathogenicity. Notably, ∆fleN cells rapidly evolved suppressor mutations in fleQ that partially restored growth and motility without always restoring monoflagellation. Five independent suppressor alleles mapped to key FleQ domains, four in the AAA+ ATPase domain, and one in the DNA-binding domain, consistent with reduced FleQ activity that rebalances the circuit. Single-cell holographic tracking showed that suppressor strains swim with heterogeneous dynamics, including subpopulations that reach wild-type (WT) speeds, despite carrying multiple flagella. Quantitative proteomics indicated that the fitness burden extends beyond flagellar components, with protein-abundance changes across metabolism, stress responses, and signaling. Conversely, selection under high-viscosity conditions drove wild-type cells to acquire enhanced spreading through a recurrent fleN mutation, fleNV178G; multiflagellation is therefore accessible. Together, these findings indicate that the FleQ-FleN circuit balances the flagellar number against fitness, holding P. aeruginosa at a single flagellum while retaining the latent capacity to reach multiflagellated states through single mutations. IMPORTANCE Bacterial flagella are extracellular appendages that rotate to propel the cell and enable swimming motility. While some bacteria have multiple flagella, many pathogenic species like Pseudomonas aeruginosa have just one. Surprisingly, mutants of P. aeruginosa with multiple flagella performed worse, that is, they grew more slowly, were less infectious in laboratory animals, and were outcompeted by wild-type bacteria. Even when some mutant bacteria evolved compensatory changes, they still struggled compared to single-flagellum bacteria. This reveals an important evolutionary trade-off: while multiple flagella might seem advantageous for movement, having just one flagellum allows the bacteria to grow faster and cause more severe infections. This plasticity likely explains why P. aeruginosa is so successful both in the environment and as a human pathogen. Bacterial flagella are extracellular appendages that rotate to propel the cell and enable swimming motility. While some bacteria have multiple flagella, many pathogenic species like Pseudomonas aeruginosa have just one. Surprisingly, mutants of P. aeruginosa with multiple flagella performed worse, that is, they grew more slowly, were less infectious in laboratory animals, and were outcompeted by wild-type bacteria. Even when some mutant bacteria evolved compensatory changes, they still struggled compared to single-flagellum bacteria. This reveals an important evolutionary trade-off: while multiple flagella might seem advantageous for movement, having just one flagellum allows the bacteria to grow faster and cause more severe infections. This plasticity likely explains why P. aeruginosa is so successful both in the environment and as a human pathogen.

Analí Migueles-Lozano, Merrill Asp, Sofia T Rocha et al. · 0 citations
Open access Jul 2026

Functional analysis of natural variation in the RNA-binding protein CsrA across the bacterial domain predicts regulatory activity

Abstract Bacteria employ sophisticated post-transcriptional regulatory mechanisms to adapt to environmental changes. Carbon storage regulator A (CsrA), a highly conserved RNA-binding protein, serves as a critical post-transcriptional regulator by typically recognizing GGA-containing hairpin loops in target mRNAs and repressing translation. However, how this conserved regulator evolved diverse species-specific regulatory networks remains unclear. We developed Swarm-seq, a high-throughput platform assessing CsrA homologs across the bacterial domain for regulating flagella-dependent swarming in Bacillus subtilis. Testing over five-hundred codon-optimized csrA homologs revealed functional divergence, partitioning CsrAs into two broad classes. Class I (CsrAHp, CsrASm, RsmNPa) strongly inhibited swarming, while Class II (CsrAEc, RsmAPa) failed despite sequence conservation. This differential activity occurred despite canonical GGA motifs in flagellin (hag) transcript, suggesting evolutionary plasticity in RNA-binding specificity beyond motif recognition. Leveraging this dataset, we trained machine learning algorithms to predict CsrA functionality, experimentally validating Bdellovibrio bacteriovorus CsrA (CsrABb) and Pseudomonas putida RsmA (RsmAPp) as Class I. Our findings establish Swarm-seq as a powerful platform for characterizing CsrA homologs from genetically intractable or unculturable bacteria and demonstrate the potential for machine learning-guided discovery of functional regulatory proteins, providing insights into post-transcriptional regulatory network evolution.

Jared T. Winkelman, Ethan Yarberry, Georgia Fanouraki et al. · 0 citations