Introduction

P. aeruginosa is a Gram-negative bacterium that is a major cause of hospital-acquired infections and is a significant antibiotic resistance threat [1]. To survive in a broad range of conditions, this bacterium has evolved signaling pathways that relay information about changes in nutrients, chemical gradients, and mechanical forces such as those generated by fluid flow, and activates responses that promote its survival [2,3]. Understanding how extracellular-sensing pathways detect and respond to host cues is critical for improving treating bacterial infections.

Mammalian host immune systems respond to the presence of bacterial pathogens by recruiting immune cells that migrate rapidly through circulating blood to sites of infection [4]. Neutrophils are the first and most abundant immune cells recruited to inflamed or damaged tissues [5] and are stimulated into an activated state by bacterial components including the membrane constituent lipopolysaccharide. Activated neutrophils produce multiple products that are toxic to bacteria including reactive oxygen species (ROS) and reactive chlorine species (RCS) [6–9]. While the toxic effects of ROS on bacteria are understood, far less is known about how bacteria are affected by RCS [10,11]. Hypochlorous acid (HOCl) is a major neutrophil-produced RCS that is formed through the activity of myeloperoxidase with H₂O₂ and chlorine ions [6,7,12] and is strongly bactericidal [13–15]. P. aeruginosa is a potent activator of neutrophil respiratory bursts [16] but whether and how the bacteria detect and respond to these respiratory bursts, is not understood.

P. aeruginosa detects shear rate generated by the flow of fluids via the fro operon [3,17], which is upregulated in the bacterium during infection in humans [3,18] (Fig. 1A). In addition, fro is necessary for successful colonization of the gastrointestinal tract and lung infections [19,20], although the reasons for its necessity have been unclear. Because flow is ubiquitous in the pulmonary and circulatory systems, in principle the fro operon could be upregulated in flow-associated host environments. Given its important role in infection, it is possible that Fro could also respond to other immune-associated cues, such as the presence of neutrophils. The fro operon consists of froABCD (PA14_21570, PA14_21580, PA14_21590, PA14_21600), with FroC and FroD predicted to localize to the inner membrane, and FroB predicted to localize in the cytoplasm [21]. Expression of the operon is regulated by the sigma and anti-sigma factors froR (PA14_21550) and froI (PA14_21560), respectively [22]. Overexpression of froR upregulates fro, whereas overexpression of froI downregulates fro [3]. Flow activates FroR-dependent transcription of froABCD through an unknown mechanism [3].

Figure 1.

We show that the fro operon responds directly to HOCl, which is produced by neutrophils during immune response. Using a fluorescent reporter system in live cells and through quantitative measurements of transcription, we show that fro expression is upregulated in a mouse model of corneal infection and by activated neutrophils. Through transcriptional profiling, we determine that fro upregulation mitigates the toxic effects of HOCl by activating methionine sulfoxide reductases that relieve oxidative stress in bacteria. These data suggest a novel mechanism by which bacterial defense against host innate immunity is primed by a single system to detect host defense cues through both flow and the presence of the highly potent oxidative factor HOCl.

Results

Host cells stimulate fro expression in P. aeruginosa under non-flow conditions

We investigated whether the fro operon is activated directly by immune cells. To quantify fro expression, we used a P. aeruginosa strain that co-expresses the yellow fluorescent protein (YFP) under the transcriptional control of the fro promoter, and mCherry under the control of a constitutive promoter (Fig. 1B and [3]). While fro expression increases under flow (Fig. S1A in the Supplementary Information (SI) and [3]), experiments in this study were performed in the absence of flow in order to deconvolve the effects of flow from potential activation of fro by immune cells. Neutrophils and macrophages are among the first immune cells that are recruited to sites of infection. We co-incubated P. aeruginosa with neutrophils or macrophages for 30 minutes to determine whether they would elicit a response in the fro operon. Relative to P. aeruginosa that were incubated in host cell-free media, P. aeruginosa in close proximity to human neutrophils or that were engulfed in mouse macrophages appeared to increase fro expression (Fig. 1C), suggesting that close proximity to or direct interaction with these host cells stimulate fro expression in P. aeruginosa.

Activated neutrophils induce fro expression

We focused on the potential activation of fro expression by neutrophils because P. aeruginosa triggers respiratory bursts in neutrophils [16], which generates ROS and RCS. We hypothesized that fro activation could be a response to respiratory burst products. P. aeruginosa were incubated in conditioned medium in which respiratory bursts were induced in human neutrophils using phorbol myristate acetate (PMA) [23,24] (Fig. 2A). The expression of fro was quantified by averaging the ratios of YFP to mCherry fluorescence for at least one hundred individual P. aeruginosa. In support of our hypothesis, conditioned medium from PMA-stimulated neutrophils increased expression of fro expression by 30-fold compared to conditioned medium from unstimulated neutrophils (Fig. 2B). The increased fro expression was not due to PMA alone, as PMA-treated medium without neutrophils had no effect on fro expression (Fig. 2B). Conditioned medium from unstimulated neutrophils had no significant effect on fro expression compared to medium alone (Fig. 2B), suggesting that the activation of fro is due to the products of respiratory bursts.

Figure 2.

HOCl but not H₂O₂ or HNO₃ induces fro expression

Activated neutrophils generate ROS and RCS through respiratory bursts (Fig. 2C), which have an inhibitory effect on bacterial growth [6,7,10,13,14]. To explore the hypothesis that these reactive species induce fro expression, we measured the effects of NaOCl, H₂O₂, and HNO₃ on fro expression at concentrations just below the minimum inhibitory concentrations (MICs) (Fig. 3A-B). NaOCl increased fro expression by up 74-fold at 1 µM (Fig. 3B). At 2 µM, NaOCl caused only a 3-fold increase in fro expression but these bacteria were noticeably smaller in size (Fig. S1B in the SI), raising the possibility that the treatment could have interfered with transcription. The activation of fro transcription by NaOCl was further assessed using reverse transcription quantitative PCR (RT-qPCR). In support of the fro-yfp reporter findings, a 200-fold increase in fro transcription was observed using 1 µM NaOCl (Fig. 3C).

Figure 3.

The increased fro expression was not due to sodium or chloride ions alone, as neither NaCl nor HCl affected fro expression in the absence of NaOCl (Fig. 3D). The fro response to NaOCl was not due to basic pH, as treatment with up to 6 mM of NaOH had no significant impact on fro activation (Fig. 3D). As fro activation is not due to sodium or chloride ions, nor changes in pH, we attributed the effects to hypochlorite (OCl^-), which is in equilibrium with the hypochlorous acid species (HOCl) at the pH of 7.1 used in our experiments.

Changes in fro expression were assessed using H₂O₂, a strong oxidizer. Small increases in fro expression were observed using the subinhibitory concentrations of 4 and 8 µM but these changes were not statistically significant compared to untreated cultures (Fig. 3A-B), and no significant changes in fro transcript abundance were observed using qRT-PCR (Fig. 3C). The fro response was also assessed using subinhibitory concentrations of HNO₃, for which no change in expression was detected up to near-MIC concentrations (Fig. 3A-B). Together, these results show that Fro expression is activated by HOCl and suggest that HOCl produced by stimulated neutrophils could activate fro expression.

Corneal infection activates fro expression

P. aeruginosa is a major cause of corneal ulcers and keratitis, which can cause visual impairment and blindness. Neutrophils are recruited within hours to infected corneal epithelia with neutrophil cell density peaking at 18 hours [25]. We tested the hypothesis that fro expression is upregulated during infection using a previously-established murine model of corneal infection in which P. aeruginosa strain PAO1F is inoculated at the site of a corneal abrasion [26]. Mice corneas were harvested 2 or 20 hours post-infection and fro transcripts were quantified using RT-qPCR. Transcription was normalized for number of P. aeruginosa using 5S ribosomal RNA. We confirmed that this strain of P. aeruginosa upregulates its fro transcription in response to NaOCl but not H₂O₂ (Fig. S1B in the SI), consistent with our previous results. In support of the hypothesis, fro expression increased significantly by 20 hours post-infection (Fig. 4A). Expression levels showed no significant change within the first two hours following infection, which we attribute to the low level of immune cell recruitment during this period.

Figure 4.

Methionine sulfoxide reductase upregulation requires FroR

To understand how the HOCl response is regulated by fro, we performed transcriptional profiling of wild-type (WT) P. aeruginosa and a strain containing a deletion of FroR, which is the sigma factor that is required for fro activation [3]. The genes that were most upregulated by NaOCl in WT compared to the ΔfroR mutant were in the fro operon, the phosphate-specific and pyrophosphate-specific outer membrane porin genes oprO and oprP, and the methionine sulfoxide reductase genes msrB, msrQ and msrP (Fig. 4B). The methionine sulfoxide reductases (MSRs) have an essential role in bacterial survival and defense against RCS stress. HOCl oxidizes methionine residues 100-fold more rapidly than other cellular components, forming methionine sulfoxide, which impairs protein function [27–31]. MSRs restore proper protein function by reducing methionine sulfoxide back to methionine [11,32]. Our data suggest that froR is required for the upregulation of MSRs in response to HOCl stress. It is possible that oxidized methionine increases fro expression, which in-turn increases MSR expression.

We reasoned that if oxidized methionine upregulates fro, an excess of methionine should inhibit fro activation. In support of our interpretation, methionine co-treatment with NaOCl suppressed fro expression (Fig. 4C). We hypothesized that if fro expression is activated by HOCl oxidation, antioxidants such as cysteine and β-mercaptoethanol (βME) should suppress fro activation by functioning as alternative oxidation targets. Indeed, co-treatment of NaOCl with either cysteine or βME significantly suppressed NaOCl-activated fro expression (Fig. 4C and Fig. S2 in the SI).

We considered how fro could be upregulated by stimulated neutrophils in the context of these findings. RCS produced by neutrophils could oxidize methionine in P. aeruginosa, resulting in fro upregulation. Under this interpretation, supplying excess methionine should inhibit activation. Indeed, supplementing conditioned media from PMA-stimulated neutrophils with methionine completely suppressed fro expression (Fig. 4D). Together, these data suggest a model in which fro responds to HOCl-induced oxidation of methionine by upregulating MSRs.

FroR protects P. aeruginosa against HOCl

The upregulation of MSRs is expected to improve bacterial growth against HOCl stress. We measured the growth profiles of WT and ΔfroR strains of P. aeruginosa. Treatment with 16 µM NaOCl significantly inhibited the growth of the wild-type strain (Fig. 5A) but resulted in even greater growth inhibition in the ΔfroR strain. This observation suggests that the fro operon improves P. aeruginosa tolerance to HOCl stress.

Figure 5.

We considered other genes which may improve WT P. aeruginosa tolerance to HOCl. HOCl increased the expression of iron uptake genes (pvdA and pvdQ) and downregulated the expression of oxidative phosphorylation genes (cyoCDE) (Fig. 5B and Table S2 in the SI). These changes suggest that HOCl causes an iron deficiency and decreases oxidative phosphorylation. In order to compensate for decreased oxidative phosphorylation, P. aeruginosa may utilize amino acid catabolism as an alternative energy source, as evidenced by a concomitant upregulation of branched chain amino acid catabolism genes (hpd, bkdA1, bkdA2, and bkdB) by HOCl (Fig. 5B and Table S2 in the SI).

While the ΔfroR strain was sensitive to HOCl, the strain was tolerant (Fig. 5A), suggesting that additional mechanisms relieve HOCl stress. In the ΔfroR mutant, HOCl upregulated genes encoding multidrug efflux pumps (mexEF-oprN and mexXY) (Fig. 5C and Table S3 in the SI). While these pumps can relieve oxidative stress [33,34], they were not activated in the WT strain. This observation suggests that the response to HOCl may be hierarchical, in which Fro-regulated and Mex pathways could be first-line and second-line responses to HOCl stress, respectively. Supporting this interpretation, it has been reported that treatment of the WT strain using significantly higher (millimolar) HOCl concentrations upregulates mexEF-oprN [35] and the mexXY regulator mexT [36].

Discussion

Neutrophils are activated by the presence of bacteria that infect host tissue. In their activated state, neutrophils generate respiratory bursts that produce an abundance of HOCl. Whether and how bacteria respond to activated neutrophils has not been clear. We have demonstrated that P. aeruginosa responds to activated neutrophils by upregulating the transcriptional expression of the fro operon, which relieves HOCl stress. Our data suggest that the upregulation of fro could function as a bacterial defense mechanism against neutrophil attack, thus improving P. aeruginosa survival and colonization of human tissue during infection.

One of the striking features of the fro system is that it is finely tuned to activate at sub-lethal concentrations (1-2 µM) of NaOCl. Activated neutrophils produce HOCl concentrations as high as 50 µM [24]. The activation of fro at relatively low concentrations suggests that the system functions as an early and sensitive detector of HOCl. In hosts, fro may be upregulated in environments where HOCl is present in low concentrations, such as during early stages of neutrophil recruitment in the cornea or when P. aeruginosa is spatially distant from activated neutrophils. The early activation of fro could benefit P. aeruginosa by triggering a protective mechanism before HOCl reaches lethal concentrations. The ability of the Fro system to respond to the presence of fluid flow provides an additional layer of early activation, such as in the case of host circulatory systems. Shear rates that activate fro [3] could prime P. aeruginosa defenses against circulating neutrophils. Consistent with this interpretation, shear rate sensitizes Fro to H₂O₂ [17], which is also produced by neutrophils in response to the presence of bacteria [6].

Based on the observations that multi-drug efflux pumps only activate in the absence of FroR and at high HOCl concentrations [35], and that multiple systems repair RCS damage [1–3], the HOCl response is likely to follow a hierarchy of activation. Our data suggest a model in which the fro system is the first-line response that suppresses the toxic effects of HOCl towards methionine (Fig. 5D). FroR activates two distinct classes of reductases that repair RCS-oxidized methionine: MsrB reduces methionine sulfoxide with electrons provided by the thioredoxin system [37,38], and MsrPQ uses electrons from the respiratory chain [39]. The activation of both reductase classes enables P. aeruginosa to limit RCS stress in both the cytoplasmic and periplasmic spaces by utilizing multiple electron donor sources.

Bacteria that are exposed to low concentrations of HOCl have higher rates of horizontal gene transfer and can acquire antibiotic resistance genes more rapidly [40,41]. The fro system could thus facilitate antibiotic resistance through increasing P. aeruginosa tolerance to HOCl. Our findings thus suggest that the fro pathway could be an important defense mechanism to target in the development of novel antibiotic therapeutics. Inhibition of this pathway could increase P. aeruginosa susceptibility to neutrophil-mediated killing while minimizing antibiotic resistance.

Materials and methods

Strains, Growth Conditions, and Reagents

Experiments were performed using the P. aeruginosa strain AL143, which is strain PA14 strain that contains the yfp gene integrated between froA and froB and a constitutively-expressed mCherry gene [3], ΔfroR and ΔfroI mutant strains that were previously constructed [3], and P. aeruginosa strain PAO1F[42,43]. Strains were streaked onto LB-Miller (BD Biosciences, Franklin Lakes, NJ) petri dishes containing 2% Bacto agar (BD Biosciences, Franklin Lakes, NJ), incubated overnight at 37 °C, and single colonies were inoculated into 2mL of modified MinA minimal medium (60.3mM K₂HPO₄, 33.0mM KH₂PO4, 7.6mM (NH₄)₂SO_4, 1.0mM MgSO₄,) [44] containing 0.2% (w/v) sodium citrate as the carbon source. Strains were cultured in MinA minimal medium for 18 hours in a roller drum spinning at 200 rpm at 37 °C, diluted 1:1000 into fresh MinA minimal medium supplemented with oxidative or antioxidative agents, or were not supplemented and imaged using fluorescence microscopy. P. aeruginosa cultures were incubated with NaOCl, H₂O₂, HNO₃ for 3 hours unless otherwise stated at 37 °C before imaging.

Neutrophils were isolated from blood samples from healthy donors between 18 to 65 years old that were collected at the Institute for Clinical and Translational Science at the University of California, Irvine, through approved protocols with the UCI Institutional Review Board HS#2001-2058, and informed consent was obtained from all donors. Neutrophils were prepared as described in [45]. Briefly, 3% dextran (from Leuconostoc spp, M_r 450,000-650,000, Sigma-Aldrich, St. Louis, MO) in PBS (Gibco, ThermoFisher, Waltham, MA) was used to separate red blood cells (RBCs) from whole blood. Neutrophils were purified from the remaining cells by overlaying on a Ficoll density gradient (GE Healthcare, Chicago, IL) following centrifugation in Ficoll-Paque Centrifugation Media (GE Healthcare, Chicago, IL) for 25 minutes at 500 × g. The remaining RBCs were lysed using RBC Lysis Buffer (Fisher Scientific, Hampton, NH), and neutrophils were resuspended in RPMI 1640 medium (ATCC, Manassas, VA) and purity was assessed by flow cytometry using the ACEA NovoCyte Flow Cytometer and fluorescent antibodies APC-CD11b, FITC-CD16 and PE-CD66b (eBioscience, San Diego, CA). Neutrophils were immediately used for neutrophil stimulation or co-incubation experiments with P. aeruginosa. This procedure routinely yielded greater than 95% CD11B-positive neutrophil populations.

J774.1 mouse macrophages (ATCC) were cultured in 10 mL DMEM (Gibco, ThermoFisher) in T75 flasks (VWR, Radnor, PA) at 37 °C with 5% CO₂. Macrophages were passaged every three days through scraping and were passaged every 5 days through trypsinization.

For P. aeruginosa size analysis experiments, cultures were incubated at 37 °C in 250 mL flasks for 3 hours with shaking at 225 rpm following the 1:1000 dilution. For methionine and antioxidant treatments, following the 1:1000 dilution, cultures were supplemented with NaOCl and the addition of methionine, β-mercaptoethanol (βME) or cysteine. 50 mL of each bacterial culture was incubated at 37 °C in 250 mL flasks for 3 hours with shaking at 225 rpm, imaged, and analyzed as described in the fluorescence microscopy section.

Fluorescence and Phase Contrast Microscopy

Bacteria were immobilized on 1% agarose pads containing minimal medium and imaged immediately. Cultures containing densities below 10 P. aeruginosa per frame were concentrated using a syringe filter with 0.2 or 0.8 µm pore sizes (Millipore, Burlington, MA). Images were acquired using a Nikon Eclipse Ti-E microscope (Nikon, Melville, NY) containing a Nikon 100X Plan Apo (1.45 N.A.) objective, a Nikon Ph3 phase contrast condenser annulus, a Sola light engine (Lumencor, Beaverton, OR), an LED-DA/FI/TX filter set (Semrock, Rochester, NY) for visualizing the mCherry fluorescence spectrum containing a 409/493/596 dichroic and 575/25 nm filters for excitation and 641/75 nm filters for emission, an LED-CFP/YFP/MCHERRY filter set (Semrock) for visualizing YFP fluorescence containing a 459/526/596 dichroic and 509/22 nm filters for excitation and 544/24 nm filters for emission, and a Hamamatsu Orca Flash 4.0 V2 camera (Hamamatsu, Bridgewater, NJ).

Images were acquired using Nikon NIS-Elements and analyzed using custom built software written previously [46] in Matlab (Mathworks, Natick, MA). See the “Data, code, and materials availability” section below to download code. Briefly, P. aeruginosa masks were determined from phase contrast images using an edge-detection algorithm. For size analysis, the total pixel area of each individual P. aeruginosa was determined by computing the mask area and converting from pixels to μm² by multiplying the mask area by a factor of 0.004225 μm²/pixel to account for the microscope camera pixel size and objective magnification. Fro expression was quantified by averaging computed ratios of YFP to mCherry fluorescence for at least one hundred individual P. aeruginosa. In each experiment, a minimum of 100 P. aeruginosa were imaged and used for analysis in which ratios were computed from the masked areas. To image P. aeruginosa under flow, microfluidic devices were fabricated using standard soft lithography techniques as established previously [47] with channel dimensions of 100 μm x 50 μm (width x height) and a flow rate of approximately 5 μL/min.

Co-incubation of Mammalian Cells with P. aeruginosa

P. aeruginosa were cultured for 18 hours in minimal medium, centrifuged at 4600 x g for 2 minutes and resuspended in DPBS (Gibco, ThermoFisher) three times, and diluted to a final OD₆₀₀ of 0.2. Macrophages that were harvested from growth flasks or freshly prepared neutrophils were washed three times by centrifuging at 300 x g for 5 minutes and resuspending in DPBS, and 1 mL aliquots containing 4×10⁵ cells/mL were transferred into flat-bottom dishes. P. aeruginosa culture was added to the cells at a multiplicity of infection of 10 and incubated at 37 °C with CO₂ for 30 minutes. Dishes were aspirated until approximately 20 µL of medium remained and pads consisting of 1% agarose containing DPBS were placed on top of the samples in the dishes to immobilize bacteria and cells. Samples were imaged immediately using microscopy.

Conditioned Medium from Neutrophils

Approximately 2×10⁶/mL of freshly harvested neutrophils were incubated at 37 °C in a roller drum spinning at a speed of 4 rotations per minute in PBGT medium (10 mM phosphate buffer pH 7.4 (2.46 mM monobasic with 7.54 mM dibasic sodium phosphate) containing 140 mM sodium chloride, 10 mM potassium chloride, 0.5 mM magnesium chloride, 1 mM calcium chloride, 1 mg/mL glucose, and 5 mM taurine [24]). To activate neutrophils, cultures were supplemented with 100 ng/mL of PMA for 1 hour and were separated from the supernatant by centrifugation for 5 minutes at 4,600 x g and 25 °C. The supernatant was isolated and used as conditioned medium. P. aeruginosa cultures were incubated for 3 hours in conditioned medium at 37 °C before imaging.

Growth Curves

Growth curve experiments were performed using a Synergy HTX multi-mode plate reader and sterile, tissue-culture treated, clear bottom, black polystyrene 96-well microplates (Corning, Corning, NY) containing 200 μL of culture in each well. The temperature set point was 37 °C and preheated before beginning measurements. For experiments performed with stationary phase bacteria, overnight cultures of bacteria were grown for 18 hours at 37 °C in the roller drum at 200 rpm to saturation, diluted into minimal medium to an optical density at 600 nm (OD₆₀₀) of 0.01 containing NaOCl, H₂O₂, HNO₃ or no supplement. Plates were incubated at 37 °C with continuous orbital shaking with an amplitude of 3 mm at the frequency of 180 cycles per minute and measured for OD₆₀₀ every 20 minutes.

Reverse Transcription Quantitative PCR (RT-qPCR)

Strains were cultured overnight, diluted 1:1000 into MinA medium, incubated in a shaker at 225 rpm at 37°C for 2.5 hours, treated with 1 µM NaOCl, 4 µM H₂O₂, or untreated for 30 minutes, concentrated using syringe filters, and centrifuged at 13,000 × g for 4 minutes to pellet P. aeruginosa. Pellets were either snap-frozen in liquid nitrogen or processed immediately for RNA extraction using the NucleoSpin RNA kit (Macherey-Nagel, Allentown, PA). cDNA was prepared using the High-Capacity cDNA Reverse Transcriptase Kit (ThermoFisher). Quantitative PCR was performed using the SsoAdvanced Universal SYBR Green Supermix (BioRad, Hercules, CA) using the C1000 Thermal Cycler with a CFX96 real-time detection system (Bio-Rad). froA transcripts were quantified using the primers 5’-TTTCCCTCGCTTCCTCCGTC-3’ and 5’-ACCTTCCTTGGCCTTCTCGG-3’, which target PA14_21570 or PA3284 in PA14 or PAO1, respectively. The transcript abundance for each sample was normalized by 5S rRNA abundance, which was determined using the primers 5’-TAGAGCGTTGGAACCACCTG-3’ and 5’-GAGACCCCACACTACCATCG-3’ [48], yielding normalized count thresholds (Cts). The average fold change in transcript abundance was determined by computing the ratio of the averaged normalized Cts and raising by the power of 2, as performed previously [49].

Murine Model of Corneal Infection

The expression of froA was assessed in a murine model of corneal infection as described previously[50,51]. Briefly, P. aeruginosa strain PAO1F was cultured to mid-exponential phase in modified MinA minimal medium containing 0.05% citrate, 0.1% casamino acids (Gibco) and 0.2% glucose as the carbon sources and resuspended in PBS (Gibco). Corneal epithelia of C57BL/6J mice aged 6-8 weeks (Jackson Laboratory, Bar Harbor, ME) were abraded with 3×5 mm scratches using a 25 g needle, and 2 µL of PBS containing 5×10⁴ of P. aeruginosa strain PAO1F was applied topically. Comparable numbers of male and female mice were used in each experimental group. Mouse eyeballs were collected and homogenized in 1 mL PBS at 2 hours post infection or 20 hours post infection. The homogenate was centrifuged for 5 minutes at 150 x g to remove corneal materials. Supernatant was centrifuged for 4 minutes at 13,000 x g. Pellets were suspended in lysis solution (10 mM Tris-HCl, 1 mM EDTA pH 8.0, 0.5 mg/mL lysozyme, 1% SDS) [49]. RNA was prepared using the NucleoSpin RNA kit (Macherey-Nagel) and assessed for mRNA expression using RT-qPCR.

RNA-seq Library Preparation and Data Analysis

P. aeruginosa was cultured and RNA was prepared as described in the RT-qPCR section. RNA yield was measured using a Nanodrop 2000 (Thermo Fisher, Waltham, MA). Samples were depleted of ribosomal RNA using the NEBNext rRNA Depletion kit (New Enland Biolabs, Ipswich, MA), from which cDNA libraries were constructed using the NEBNext Ultra II Directional Library kit (NEB), which were sequenced by the UC Irvine Genomics Research & Technology Hub (Irvine, CA) using an Illumina NovaSeq X Plus (Illumina, San Diego, CA) using paired-end 150 bp reads at a depth of approximately 10 M read per sample. Raw reads were checked with fastQC [52] (version 0.21.1), and trimmed and filtered into paired and unpaired reads using Trimmomatic [53] (version 0.39) in Java (1.8.0) using the ‘PE’ setting. Paired and unpaired reads were aligned to the PA14 genome (NCBI accession NC_008463.1) using Bowtie2 [54] (version 2.5.4) using the default ‘sensitive’ mode, were counted using the featureCounts program in Subread [55] (version 2.0.8) with the ‘countReadPairs’ option enabled for paired-end reads, and were fit into a negative binomial model to compute fold-change in gene expression using DeSeq2 [56] (version 1.40.2). The statistical significance of the changes were computed using the Wald test in DeSeq2. Gene Ontology enrichment analysis for Fig. 1A was performed using GOEnrichment [57] (version 2.0.1). The msrQ (PA14_62100), msrP (PA14_62110) genes were annotated at Pseudomonas.com [21] as yedZ and yedY, respectively, but are referred to here with their updated names [58].

Statistical Analysis

Statistical analysis and figures were generated in R (The R Foundation, Vienna, Austria) (version 4) and RStudio (Posit Software, Boston, MA).

Data, Code and Materials Availability

Raw data for all figures that contain statistical analyses are available in the Supplementary Information Source Data file. RNA-seq data is available at the National Center for Biotechnology Information Gene Expression Omnibus (GEO) (accession number GSE290217, accessible during review period using the token: whcbicwsvnmjdqj). The custom Matlab scripts used to process and analyze fluorescence microscopy data are freely available at https://github.com/asirya/AVIassembleGUI.

Acknowledgements

The authors thank Michael Z. Zulu and Stephanie Matsuno for their feedback on prior drafts of this article, Hew Yeng Lai for imaging of bacteria in microfluidic devices, and Hanjuan Shao for assistance with RNA preparation.

Additional information

Author Contributions

I.P.F., R.S. and A.S. conceived and designed the experiments. L.A.U. prepared neutrophils from human samples. S.A. and M.E.M. performed mouse corneal infection experiments and L.D. homogenized tissue. A.H. performed growth curves. S.J.K. prepared cDNA libraries from RNA samples for RNA-seq. R.S. performed RT-qPCR experiments and analyzed RNA-seq data. I.P.F. performed all other experiments and analyzed data. I.P.F. and L.A.U. wrote the initial draft of the manuscript. S.J.K., R.S. and A.S. revised it. All authors edited the paper.

Funding

This work was supported by the Stanley Behrens Fellows in Medicine Award to L.U., and grants from the National Institutes of Health (NIH) National Institute of Biomedical Imaging and Bioengineering (NIBIB) (R21EB027840-01), the National Cancer Institute (NCI) (DP2CA250382-01), the National Science Foundation (NSF) (DMS1763272), and the Simons Foundation (594598QN) to T.L.D. I.P.F received funding from the Horizon Europe Research and Innovation Program through the Marie Skłodowska-Curie grant #847413 and from the Program of the Ministry of Science and Higher Education #5005/H2020-MSCA-COFUND/2019/2.

Funding

HHS | NIH | National Cancer Institute (NCI) (DP2CA250382-01)

National Science Foundation (NSF) (DMS1763272)

HHS | NIH | National Institute of Biomedical Imaging and Bioengineering (NIBIB) (R21EB027840-01)

Simons Foundation (SF) (594598QN)

EC | Horizon Europe | Excellent Science | HORIZON EUROPE Research Infrastructures (RI) (847413)

Program of the Ministry of Science and Higher Education (5005/H2020-MSCA-COFUND/2019/2)

Additional files

Supplementary Figures and Tables

Supplementary Source Data Spreadsheet