Systematic identification of molecular mediators underlying sensing of Staphylococcus aureus by Pseudomonas aeruginosa

ABSTRACT

Bacteria typically exist in dynamic, multispecies communities where polymicrobial interactions influence fitness. Elucidating the molecular mechanisms underlying these interactions is critical for understanding and modulating bacterial behavior in natural environments. While bacterial responses to foreign species are frequently characterized at the molecular and phenotypic level, the exogenous molecules that elicit these responses are understudied. Here we outline a systematic strategy based on transcriptomics combined with genetic and biochemical screens of promoter-reporters to identify the molecules from one species that are sensed by another. We utilized this method to study interactions between the pathogens Pseudomonas aeruginosa and Staphylococcus aureus that are frequently found in co-infections. We discovered that P. aeruginosa senses diverse staphylococcal exoproducts including the metallophore staphylopine, intermediate metabolites citrate and acetoin, and multiple molecules that modulate its iron starvation response. Further, we show that staphylopine inhibits biofilm formation and that P. aeruginosa can utilize citrate and acetoin for growth, revealing that these interactions have both antagonistic and beneficial effects. Our screening approach thus identified multiple S. aureus secreted molecules that are sensed by P. aeruginosa and affect its physiology, demonstrating the efficacy of this approach, and yielding new insight into the molecular basis of interactions between these two species.

INTRODUCTION

Bacteria frequently exist in multispecies communities in which cooperative and competitive interactions govern community composition and physiological outputs. Interactions among pathogenic bacterial species in multispecies infections can affect disease outcomes and antibiotic susceptibility (1, 2). Elucidating the molecules underlying these interactions is therefore critical to understand and modulate bacterial behavior in communities, and pairwise interaction studies using unbiased genetic and biochemical approaches are powerful tools for such analyses (3–5).

Previous studies on pairwise interspecies interactions have focused on the identification of molecules produced by one species and the effect of these molecules on specific phenotypes of another species, such as growth, biofilm formation, or antibiotic resistance (6–11). Recent work has described the genome-wide response of one species to another at the molecular level using either transcriptomics, proteomics, or metabolomics in multispecies conditions, revealing that these responses can be complex and affect numerous pathways (12–14), and are therefore likely mediated by multiple sensed secreted factors.

One powerful strategy to determine the cues being sensed by bacteria is to infer them from the cellular response. Examples include the SOS response indicating the sensing of DNA damage, or the heat shock response revealing the perception of high environmental temperature (15–17). In multispecies communities, specific bacterial responses have been used to identify the interspecific mediators. These include the upregulation of oxidative stress pathways in response to secreted redox-active molecules, alleviation of nutritional requirements due to sensing and use of secreted amino acids or other nutrients, and induction of iron starvation pathways by sensed iron competition caused by siderophores secreted by a foreign species (18–20). However, most such studies of interactions typically focus on a single response and the underlying molecules.

The goal of this work was to develop a comprehensive approach to define which exoproducts from one species are sensed by another and use this framework to study interspecies sensing in a model two-species system consisting of Pseudomonas aeruginosa and Staphylococcus aureus. Both are opportunistic pathogens that co-exist in wound infections, nosocomial pneumonia, as well as lung infections in cystic fibrosis (CF) patients (21–24), where co-infection with both pathogens has been associated with increased disease severity (25–27). Identifying the molecular determinants of interactions between these two co-infecting pathogens can thus provide novel insights into persistent infections and multispecies communities in general.

Interactions between these two species have been extensively studied (reviewed by (28–31)). P. aeruginosa affects the growth, metabolism, antibiotic resistance, and transcriptional state of S. aureus, mainly via the secretion of multiple antimicrobials (6, 32–35). S. aureus induces exploratory motility in P. aeruginosa via unknown exoproducts, and the quorum sensing molecule autoinducer-2 and cell wall precursor N-acetyl glucosamine which can be produced by S. aureus affect the regulation of P. aeruginosa virulence factors (36–41). However, characterization of the P. aeruginosa transcriptional response to S. aureus, and the comprehensive identification of the underlying sensed S. aureus secreted factors and their production pathways, have not been fully accomplished.

In this study, we outline a strategy to systematically identify the secreted molecules from one species that are sensed by another, utilizing transcriptomics in conjunction with genetic and biochemical screens of promoter-reporters. Our approach revealed that P. aeruginosa senses four distinct signals secreted by S. aureus: the metallophore staphylopine (StP) which induces zinc starvation, the intermediate metabolites citrate and acetoin which induce their uptake and catabolism, and unidentified molecules that affect iron-related pathways. Through the genome-wide screen, we also delineate the S. aureus genes that alter the production of these sensed molecules. Further, we find that these staphylococcal exoproducts mediate both antagonistic and beneficial effects on P. aeruginosa physiology. StP participates in metal competition and abrogates P. aeruginosa biofilm formation, while the intermediate metabolites can serve as sole carbon sources, and the iron-chelating secreted factors deliver iron to P. aeruginosa. Clinical isolates of S. aureus show similar production of sensed molecules, and other bacterial species can also induce some of the same pathways in P. aeruginosa, indicating the generality of these phenomena. Finally, we show that these S. aureus secreted molecules explain a major part of the P. aeruginosa response to S. aureus, demonstrating the utility of our approach to identify the secreted factors that underlie interspecies interactions.

RESULTS

Framework to comprehensively define the molecular mediators of bacterial interspecies sensing

We developed a systematic methodology within a two-species system to identify the sensed foreign molecules that underlie the global response of one species to the other (Fig. 1A). Our approach first defines the complex response resulting from exposure to a foreign species and identifies the different individual components of the response. Then, these individual responses are used to identify the respective causal foreign molecules via unbiased genetic and biochemical screens. Unlike previous approaches, our strategy does not focus on the effect of individual molecules on a foreign species, or on globally identifying all molecules that are produced by a species, rather each response is used to identify the respective specific foreign molecules that together make up the interspecies interaction.

FIGURE 1. P. aeruginosa differentially regulates metal deprivation and intermediate metabolite uptake pathways in the presence of S. aureus supernatant.

(A) Schematic for identification of molecular mediators of interspecies sensing in a two-species system. Global transcriptional response of one species to another species, or its secreted exoproducts, compared to monocultures, is determined by RNA-seq. Analysis of the differentially regulated genes and pathways may be used to identify the signaling molecules that are sensed. Promoter-reporters are constructed from representative upregulated genes and used to screen for the signaling molecules by two complementary methods. In the first method, a mutant library is screened for mutants that disrupt production or export of the signaling molecules, and therefore have lower reporter expression. In the second, the supernatant is biochemically fractionated and fractions are screened for induction of the promoter. (B) Venn diagrams of upregulated and downregulated genes (Log₂ fold change ≥ 1 or ≤ −1 and p < 0.05 cutoff) in P. aeruginosa after S. aureus supernatant exposure compared to media control after 20 min, 1 h, and 2 h. (C) Gene ontology (GO) enrichment of differentially expressed genes in P. aeruginosa after 20 min (2). Non-redundant categories for downregulated and upregulated biological processes are shown. (D) Scatterplot of mean expression levels of transcripts after S. aureus supernatant exposure compared to media control after 20 min. Genes annotated previously in P. aeruginosa strain PAO1 as being regulated by Fur, PvdS (IS box), or Zur are shown (3, 4). (E) Log₂ fold change of select transcripts in metabolite-uptake operons that increase in abundance over time.

In the initial step, global transcriptional analysis is performed on one species exposed to another species or its cell-free supernatant compared to monocultures, to identify which pathways are differentially regulated by interspecies sensing. Next, promoter-reporter constructs are designed using representative genes from these upregulated classes. These promoter-reporter strains are then employed in two complementary approaches to identify the sensed interspecific molecules. First, an arrayed transposon mutant library in the species being sensed is screened to determine the mutants that are deficient in inducing reporter expression. The mutants are likely to be involved in the regulation, biosynthesis, or secretion of the cues, and mutant gene function is therefore used to identify the sensed molecules. Second, the sensed supernatant is fractionated to identify fractions that contain the active molecules inducing the promoters which can then be further analyzed by additional fractionation and mass spectrometry. This two-pronged unbiased approach can thus exhaustively reveal the molecules that lead to complex responses in a foreign species, irrespective of which pathways and mechanisms constitute the response. We applied this scheme to study the S. aureus secreted products that are sensed by P. aeruginosa.

P. aeruginosa senses S. aureus secreted products and upregulates metal- and metabolite-related pathways

We focused on the response of P. aeruginosa to S. aureus cell-free supernatant, as opposed to a co-culture model, since P. aeruginosa produces antimicrobials that may kill and lyse S. aureus cells (29, 42, 43), thus affecting the relative levels of staphylococcal secreted products that may be present. To determine the response of P. aeruginosa PA14 to S. aureus JE2, we performed RNA-seq on early-log phase P. aeruginosa cultures at 20 min, 1 h, and 2 h after the addition of 25% (v/v) S. aureus spent media or the same volume of media as a control. We found ∼100-200 genes that were significantly differentially expressed between these two conditions at each timepoint (Fig. 1B, Table S1, and S2).

We identified the major pathways that are induced in P. aeruginosa upon sensing S. aureus molecules to define candidate promoters for the screening strategy (Fig. 1A). First, we performed Gene Ontology (GO) enrichment analysis of the differentially regulated genes in P. aeruginosa after S. aureus exposure (Table S3). The downregulated genes showed enrichment of amino acid metabolism genes while upregulated genes indicated significant enrichment in genes involved in metal ion transport, as well as the biosynthesis of the siderophore pyoverdine, suggesting the sensing of metal deprivation (Fig. 1C and Table S3). Several genes previously reported to be controlled by the Zn-dependent repressor Zur, the Fe-dependent repressor Fur, and the Fe-specific sigma factor PvdS in P. aeruginosa PAO1 were upregulated 20 min after S. aureus supernatant exposure (Fig. 1D and Table S4) (44–46). Next, to identify additional robustly upregulated pathways that may not be well described by GO terms, we focused on all the upregulated genes that increased in fold change over time upon S. aureus supernatant exposure. Of the 461 total upregulated genes, 73 increased over time across the three time points (Fig. S1). We selected the operons that showed the highest terminal fold change, and these were associated with intermediate metabolite pathways, namely acetoin catabolism and tricarboxylic acids (TCA) uptake (Fig. 1E and Fig. S1).

The strongest P. aeruginosa response to S. aureus cell-free supernatant was thus represented by four pathways: Zn-deprivation, Fe-deprivation, TCA uptake, and acetoin catabolism. We selected one promoter from each of these four pathways whose respective transcripts had distinct patterns of expression in the RNA-seq analysis (PA14_11320, pvdG, opdH, acoR, respectively) (Fig. 2A) and designed promoter-reporters using the fluorescent protein mScarlet. Each reporter led to significantly higher levels of mScarlet expression in the presence of S. aureus supernatant, displaying dose-dependent responses compared to the media control (Fig. 2B). The two metal deprivation promoter-reporter strains induced the reporter earlier in the supernatant than the control, while the two intermediate metabolite reporter strains induced the reporter almost exclusively upon S. aureus supernatant exposure.

FIGURE 2. P. aeruginosa promoter-reporters are induced by S. aureus exoproducts.

(A) Expression levels from RNA-seq after exposure to S. aureus supernatant or media control for four transcripts as gene candidates for promoter-reporter construction. Gene annotations: PA14_11320, Zur-regulon putative lipoprotein in operon with ABC transporter; pvdG, pyoverdine biosynthesis thioesterase; opdH, TCA uptake porin; acoR, transcriptional regulator of acetoin catabolism genes. (B) Relative fluorescence units (RFU) of mScarlet normalized to OD₆₀₀ over time after exposure to S. aureus supernatant or media control in the indicated promoter-reporter strains. Slope calculated from 1.5-5 h (promoters of PA14_11320, opdH, and acoR) or 1-4 h (promoter of pvdG) after addition of supernatant, supernatant dilutions, or media control. Each strain had higher expression of mScarlet after supernatant addition compared with media control and displayed dose-dependent responses. Shaded regions and error bars show the standard deviation (SD).

The metallophore activity of staphylopine upregulates the Zn-deprivation response in P. aeruginosa

Each promoter-reporter strain was used to screen supernatants from the Nebraska Transposon Mutant Library (NTML) which contains over 1,800 ordered transposon mutants in methicillin-resistant S. aureus JE2 (47). We reasoned that transposon insertions in the genes involved in the expression, biosynthesis, or export of the sensed product(s) would result in altered promoter induction.

Using the promoter of a putative lipoprotein under control of the Zur regulon (PA14_11320) (44) to screen the NTML for mutants that were deficient in inducing mScarlet reporter expression, we found candidates with transposon insertions in the genes encoding the exporter (cntE) or biosynthetic enzymes (cntKLM) of the multi-metal binding molecule staphylopine (StP) (Fig. 3A, 3B, and Table S5). StP is a nicotianamine-like molecule that is exported out of the cell, where it binds zinc and imports it back into the cell (48). StP is generated from _L-histidine in three stepwise reactions by histidine racemase CntK, nicotianamine synthase CntL, and opine dehydrogenase CntM which incorporates pyruvate at the terminal step (48, 49). StP supports growth in zinc-deficient conditions, and mutants in the StP biosynthesis or export pathways show growth defects in the presence of the zinc chelator N,N,N′,N′-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine (TPEN) (Fig. S2A) (50, 51).

FIGURE 3. The S. aureus metallophore staphylopine is sensed by P. aeruginosa.

(A) Screening of the NTML identified mutants in the biosynthesis and secretion of staphylopine (StP) as deficient in the induction of the PA14_11320 promoter. Schematic shows StP (green pentagon) and pseudopaline (PsP) (blue pentagon) biosynthesis, export, binding to transition metals Zn, Co, Ni, and uptake. (B-F) RFU of mScarlet normalized to OD₆₀₀ over time from 1.5 to 5 h after exposure to media control or S. aureus WT or cnt supernatant and/or addition of the indicated concentrations of StP, Zn, or TPEN in the indicated P. aeruginosa WT or mutant promoter-reporter strains. (G) P. aeruginosa cultures were grown in medium alone or with the additives listed, and biofilm formation was assessed by crystal violet staining after 24 h of growth. Data shown for all panels are the means of three independent biological replicates. Datasets were analyzed by two-way ANOVA with Tukey’s test for multiple comparisons (significance shown for comparisons to: B, WT supernatant; F, respective WT sample, respectively) or one-way ANOVA with Dunnett’s test for multiple comparisons to the respective control (E, WT supernatant; C, D, and G, media control). The error bars denote the SD. *, p <0.05; **, p <0.01; ***, p <0.001; #, p <0.0001.

P. aeruginosa produces a similar secreted opine metallophore, pseudopaline (PsP), that is also important for zinc uptake, and is produced by CntL and CntM with the addition of a terminal α-ketoglutarate instead of pyruvate (Fig. 3A) (49, 52–54). PsP is exported by CntI in the inner membrane and MexAB-OprM in the outer membrane and is imported back into the cell by CntO (52, 55). The entire cntOLMI operon was upregulated upon exposure to S. aureus supernatant (Table S1 and S2). Along with P’PA14_11320, we examined StP-mediated induction of two other Zur-regulated promoters: cntO (PA14_63960), the first gene in the cnt operon, and dksA2 (PA14_73020), which encodes a transcription factor in an operon with cobalamin synthesis genes (56). S. aureus cnt mutants lacking StP reduced mScarlet reporter expression from these three Zur-regulated promoters compared to wild type (WT) (Fig. 3B). The addition of increasing amounts of StP to the cntM::tn mutant supernatant restored P’PA14_11320 induction to WT levels at concentrations greater than 40 µM (Fig. 3C), indicating that similar concentrations are likely present in staphylococcal supernatant. Next, we sought to characterize if StP chelates metals from or delivers metals to P. aeruginosa. Addition of the zinc chelator TPEN increased promoter induction, with 0.5 µM mimicking the induction seen upon addition of S. aureus supernatant (Fig. 3D and Fig. S2B). Inversely, the induction was decreased by the addition of zinc, cobalt, or nickel (Fig. 3E and Fig. S2C) suggesting that StP chelates these metals, thereby inducing the zinc starvation response in P. aeruginosa.

To examine the role of the similar P. aeruginosa opine metallophore PsP in the response to StP, induction of P’PA14_11320 was measured in P. aeruginosa mutants lacking the genes encoding the importer (cntO), exporter (cntI), or entire cnt operon for PsP. Upon supernatant addition, induction of mScarlet reporter expression was increased in the ΔcntO and Δcnt mutants compared to the WT (Fig. 3F), demonstrating that the presence of PsP decreases StP-induced zinc starvation. Thus, in response to the opine metallophore StP, P. aeruginosa induces the Zur regulon which includes genes to synthesize its own zinc metallophore, PsP.

Higher levels of zinc availability are associated with increased P. aeruginosa biofilm formation and increased antagonism of S. aureus (57–59). We therefore explored the effects of StP, which we expect leads to zinc starvation, on P. aeruginosa biofilm formation and P. aeruginosa-S. aureus polymicrobial interactions. P. aeruginosa was grown in static conditions in medium with 0, 5, or 10 µM zinc added, and zinc addition increased biofilm formation (Fig. 3G). While the addition of 1 or 2 µM TPEN had only modest effects on biofilm formation, 80 µM StP reversed the effects of zinc addition and inhibited biofilm formation (Fig. 3G). A major component of P. aeruginosa-S. aureus interactions are P. aeruginosa-produced antimicrobials that inhibit S. aureus growth (29). To assess the role of StP on the inhibition of S. aureus growth by P. aeruginosa, cell-free supernatants were collected from P. aeruginosa cultures grown in 10 µM zinc, 1 µM TPEN, or 80 µM StP, and the growth of S. aureus in 50% (v/v) supernatant was determined. While supernatant from P. aeruginosa grown in zinc or TPEN inhibited S. aureus survival similar to the control, supernatant from P. aeruginosa cultured with StP showed lower inhibition of S. aureus, suggesting that StP may affect P. aeruginosa antimicrobial production (Fig. S2D).

Staphylococcal secreted products affect siderophore-biosynthesis responses in P. aeruginosa

To determine the secreted products affecting the iron starvation response, the S. aureus transposon library was screened with the promoter of a pyoverdine synthesis gene, pvdG, which is induced by low-iron conditions (46). Since the P. aeruginosa Zur regulon was responding to a metallophore, we hypothesized that the pvdG promoter would similarly respond to a siderophore but none of the S. aureus siderophore mutants reduced induction (Table S6). Instead, we identified more than 100 mutants each that had a higher (upregulating) or lower (downregulating) induction of the reporter compared to the WT (Fig. 4A and Table S6), and the relative iron chelation of the mutant supernatants did not correlate with their promoter induction (r = −0.04) (Fig. 4B, S3A, and Table S7). Several downregulating supernatants had significantly higher chelation than WT, including those from mutants of the ATP-dependent proteases ClpC and ClpP, suggesting that these proteases contribute to the regulation of the chelating factor(s) (Fig. 4B and Table S7).

FIGURE 4. P. aeruginosa pyoverdine promoter induction is affected by multiple S. aureus secreted factors.

(A) Transposon library screen with P’pvdG-reporter strain to determine mutations in S. aureus that increase or decrease induction in P. aeruginosa. For each mutant supernatant, the z-scores calculated from the mean slope (RFU/OD₆₀₀/hr) of each respective experiment for two replicates of the screen are shown. (z-score < −1, downregulating, red; z-score > 1, upregulating, blue). (B) Relative chelation of the downregulating and upregulating supernatants (r = −0.04 for correlation between the relative chelation and the z-score). Data was analyzed by one-way ANOVA with Dunnett’s test for multiple comparisons to the WT control. Supernatants with significantly different chelation compared to the WT control are labeled. Data shown represent three independent replicates. (C-E) WT S. aureus supernatant was fractionated by size-exclusion chromatography. Two independent biological replicates are shown. (C) RFU of mScarlet normalized to OD₆₀₀ over time from 1 to 4 h after exposure to media control, 1X whole S. aureus WT supernatant, water, or 10X fractions with or without proteinase K treatment (mixed 1:1 with medium). (D) Relative chelation of water control, whole supernatant, or 10X fractions. (E) Slope of OD₆₀₀ over time from 1 to 8 h of P. aeruginosa ΔpvdJ ΔpchE strain in medium control or medium with 200 µM BIP with the addition of whole WT S. aureus supernatant, media, or 10X fractions. Error bars denote the SD for panels B-E.

It has been reported that P. aeruginosa can utilize specific iron-chelating xenosiderophores such as deferoxamine (DFX) to obtain iron (60–63), and P’pvdG was repressed by DFX (Fig. S3B), showing iron delivery to P. aeruginosa. As a control, another iron chelator diethylene triamine penta-acetic acid (DTPA), which chelates iron away from P. aeruginosa, induced P’pvdG (Fig. S3B). Thus, the lack of correlation between P’pvdG induction and relative chelation by the S. aureus mutant supernatants may be due to a combination of iron competition and delivery to P. aeruginosa.

Next, we employed the second approach in our strategy to determine the sensed secreted products (Fig. 1A) where we biochemically fractionated S. aureus supernatant by size-exclusion chromatography and then screened concentrated fractions for their ability to induce the P’pvdG promoter-reporter. We also treated each fraction with proteinase K to determine if the active molecule(s) contain peptide bonds. Relative to the water control, fraction 4 increased promoter induction, but this was abolished by proteinase K treatment, while fraction 5 only induced the promoter after proteinase K treatment (Fig. 4C). Additionally, fractions 6-12 decreased induction regardless of proteinase K treatment (Fig. 4C). Similar to our observations with the mutant supernatants, fraction 4 did not have any chelating activity, whereas the fractions that decreased promoter induction (fractions 6-12) did (Fig. 4D). This suggests that the chelators present in the downregulating fractions repressed the expression of pyoverdine biosynthesis genes, possibly due to delivery of iron to P. aeruginosa.

To test if secreted staphylococcal molecules could deliver iron to P. aeruginosa, we used a P. aeruginosa ΔpvdJ ΔpchE mutant, which cannot produce the siderophores pyoverdine and pyochelin. The ΔpvdJ ΔpchE mutant is unable to grow in medium containing 200 µM of the iron chelator 2,2’-bipyridyl (BIP). The addition of DFX, but not DTPA, supports its growth in BIP media (Fig. S3C), confirming the ability of P. aeruginosa to utilize DFX to take up iron in the absence of its own siderophores. Interestingly, the ΔpvdJ ΔpchE mutant grew in BIP media after addition of whole S. aureus supernatant or individual fractions 5-12, but not media (Fig. 4E and Fig. S3C). Together with the promoter-reporter and iron chelation assays, these results indicate that one or more S. aureus chelators deliver iron to P. aeruginosa, while at least one staphylococcal exoproduct without chelating activity induces pyoverdine production.

S. aureus secreted intermediate metabolites citric acid and acetoin induce uptake and catabolism in P. aeruginosa

To determine the staphylococcal secreted products that induce expression of the TCA uptake operon, the NTML transposon collection was screened with the opdH promoter-reporter strain. OpdH is a porin that uptakes TCAs, and is induced by the TCAs isocitrate, cis-aconitate, and citrate (64). Similar to the screen with the pvdG promoter, we obtained more than 100 mutants that upregulated or downregulated the opdH promoter (Fig. 5A and Table S8). GO enrichment analysis of these mutants indicated that aspartate family amino acid biosynthesis genes were enriched in the upregulating mutants and branched-chain amino acid biosynthesis, metabolism, and cellular respiration pathways were enriched in the downregulating mutants (Fig. 5B and Table S9) (65–67). Many of the identified genes encode proteins that catalyze enzymatic reactions within the TCA cycle and related pathways (Fig. 5C, Table S8, and Table S9). This included the downregulating supernatant from gltA::tn which encodes citrate synthase II which converts TCA intermediates to citrate, and the upregulating supernatant from acnA::tn encoding aconitate hydrase which breaks down citrate (Fig. 5A and Table S8), suggesting that S. aureus-secreted citrate may induce the opdH promoter-reporter. Exogenously added citrate induced the P’opdH reporter in a dose-dependent manner with between 100-200 µM having similar induction to S. aureus supernatant (Fig. 5D), and direct measurements showed that S. aureus supernatant contained 166.0 ± 13.0 µM citrate (Fig. 5E and Table S10). Citrate concentrations in the upregulating and downregulating mutant supernatants significantly correlated with induction of the P’opdH promoter (Pearson’s r = 0.6663, p < 0.0001) (Fig. 5E and Table S10). Therefore, S. aureus secretes the TCA intermediate metabolite citrate which is sensed by P. aeruginosa.

FIGURE 5. S. aureus-secreted citrate is sensed by P. aeruginosa.

(A) Transposon library screen with P’opdH-reporter strain to determine mutations in S. aureus that increase or decrease induction in P. aeruginosa. For each mutant supernatant, the z-scores calculated from the mean slope (RFU/OD₆₀₀/hr) of each respective experiment for two replicates of the screen are shown (z-score < −1, downregulating, red; z-score > 1, upregulating, blue). (B) GO enrichment analysis of downregulating and upregulating mutants. (C) Enzymatic reactions in central metabolism are shown, with the colors representing the effect of the mutant supernatants on promoter induction (downregulating, red; upregulating, blue; mutant not in library and/or no change, black). (D) RFU of P’opdH-mScarlet normalized to OD₆₀₀ over time from 1.5 to 5 h after exposure to media control, S. aureus supernatant, or dilutions of citric acid. (E) Citric acid measurements of the downregulating and upregulating supernatants correlate to their induction of the P’opdH promoter (r = 0.6663). Data was analyzed by one-way ANOVA with Dunnett’s test for multiple comparisons to the WT control. Data shown represent three independent replicates for panels D-E. Error bars denote the SD for panels D-E.

Recently, it was described that acetoin is released by S. aureus and in response, P. aeruginosa upregulates acetoin and butanoate pathways, including the acoR gene, which encodes a transcriptional regulator of the acetoin catabolism operon (68–70). We predicted that a transposon mutant screen of P’acoR induction may identify mutations in staphylococcal acetoin production and/or secretion. We identified nearly 200 mutants each that induced or repressed the promoter (Fig. 6A and Table S11); however, no significant pathways were identified by GO enrichment analysis. Two of the most downregulating mutant supernatants had transposon insertions in ilvB and ilvN, which encode enzymes that convert pyruvate into α-acetolactate, leading into the butanoate cycle where acetoin and 2,3-butanediol are synthesized and catabolized (Fig. 6A, C, and Table S11). The promoter of acoR is responsive to acetoin, 2,3-butanediol, and α-acetolactate, but not citrate (Fig. 6B and Fig. S4A), however 2,3-butanediol and α-acetolactate could not be detected in S. aureus supernatant in quantities that would be needed to induce the promoter (Fig. S4B). The acetoin concentration in the regulating mutant supernatants correlated with promoter induction in most supernatants (Pearson’s r = 0.2157, p < 0.0001), including those of genes leading into the butanoate cycle (Fig. 6C and D). However, a few select downregulating mutant supernatants contained significantly higher acetoin levels than WT, such as sucD encoding succinyl-CoA synthase and the clpC and clpP mutants (Fig. 6D and Table S12). Therefore, the main staphylococcal metabolite that induces acoR expression is acetoin.

FIGURE 6. Intermediate metabolites produced by S. aureus are sensed and utilized as carbon sources by P. aeruginosa.

(A) Transposon library screen with P’acoR-reporter strain to determine mutations in S. aureus that increase or decrease induction in P. aeruginosa. For each mutant supernatant, the z-scores calculated from the mean slope (RFU/OD₆₀₀/hr) of each respective experiment for two replicates of the screen are shown (z-score < −1, downregulating, red; z-score > 1, upregulating, blue). (B) RFU per OD₆₀₀ of P’acoR-mScarlet after addition of media, S. aureus supernatant, or the indicated concentrations of acetoin. (C) Enzymatic reactions of butanoate metabolism are shown, with the colors representing the effect of the mutant supernatants on promoter induction (downregulating, red; upregulating, blue; mutant not in library and/or no change, black). (D) Acetoin measurements of the upregulating and downregulating supernatants correlate with P’acoR induction (r = 0.2157). Acetoin concentration data was analyzed by one-way ANOVA with Dunnett’s test for multiple comparisons to the WT control. For panels B and D, data shown represent three independent replicates and error bars denote the SD. (E) Growth of P. aeruginosa was monitored at OD₆₀₀ after the addition of 1 mM glucose, citric acid, 2,3-butanediol, acetoin, or a mix of citric acid, 2,3-butanediol, and acetoin as the sole carbon sources. Two independent replicates are shown. Shaded regions denote the SD.

To ascertain if these intermediate metabolites can be utilized as carbon sources by P. aeruginosa, 1 mM citrate, 2,3-butanediol, and/or acetoin, or 1 mM glucose as a positive control, were added to the growth medium as the sole carbon source and P. aeruginosa growth was monitored for 16 h. As expected, in the absence of any carbon sources, P. aeruginosa was unable to grow (k = 0.003), while it grew with the addition of glucose (k = 1.057) (Fig. 6E). P. aeruginosa was also able to grow after addition of citric acid, 2-3-butanediol, and acetoin in combination (k = 0.781), or with just citric acid (k = 0.625), while slight growth was seen after the addition of 2,3-butanediol or acetoin alone (k = 0.273 and 0.270) (Fig. 6E). Thus, P. aeruginosa can utilize these secreted intermediate metabolites as energy sources.

S. aureus clinical isolates and other bacterial species also produce exoproducts that induce P. aeruginosa response pathways

Through the promoter-reporter screens, we identified four distinct pathways in P. aeruginosa that are induced by S. aureus JE2 secreted products. To test how widespread the production of these molecules is, we surveyed supernatants from four clinical isolates of S. aureus that were mono-isolated (CF049 strain) or co-isolated with P. aeruginosa (CF061, CF085, and CF089 strains) from cystic fibrosis patients. Supernatants from these strains induced all four promoter-reporters in P. aeruginosa (Fig. 7A), albeit to different degrees. While all the strains contained chelators, only CF049 and CF061 supported siderophore-deficient P. aeruginosa growth in iron-restricted medium (Fig. 7B and C). CF089, which showed the highest relative chelation, was unable to support the growth of the P. aeruginosa siderophore mutant, indicating that S. aureus likely produces multiple chelators, only some of which can deliver iron to P. aeruginosa, and the relative amounts of these may vary between strains. In addition, citrate and acetoin concentrations in the supernatants largely correlated with induction of the opdH and acoR promoters, respectively, except for CF061 and CF085 having lower levels of acetoin (Fig. 7D).

FIGURE 7. Sensed exoproducts are secreted by S. aureus clinical isolates.

(A) RFU of mScarlet normalized to OD₆₀₀ over time (promoter of PA14_11320, opdH, and acoR calculated from 1.5 to 5 h; promoter of pvdG calculated from 1 to 4 h) of the indicated promoter-reporter strains after exposure to media control, or supernatants from S. aureus JE2 or clinical isolates CF049, CF061, CF085, and CF089. (B) Relative chelation of supernatants collected from S. aureus JE2 or the indicated clinical isolate. (C) Slope of OD₆₀₀ over time from 1 to 8 h of P. aeruginosa ΔpvdJ ΔpchE strain in medium control or medium with 200 µM BIP with the addition of medium or supernatant from S. aureus JE2 or the indicated clinical isolate. (D) Citrate and acetoin measurements of supernatants collected from S. aureus JE2 or the indicated clinical isolates. For panels A and C, datasets were analyzed by one-way ANOVA with Dunnett’s test for multiple comparisons to the media only control for A and no addition for C. Three independent replicates shown for all panels. Error bars denote the SD. *, p <0.05; **, p <0.01; ***, p <0.001; #, p <0.0001.

Since the sensing pathways in P. aeruginosa were induced by different strains of S. aureus, we wondered if other bacterial species could also induce similar responses in P. aeruginosa. Therefore, we tested cell-free supernatants from eight additional species: Bacillus subtilis, Staphylococcus epidermidis, Burkholderia cenocepacia, Escherichia coli, Klebsiella pneumoniae, Salmonella enterica Typhimurium, Stenotrophomonas maltophilia, and Vibrio cholerae. Induction of the P. aeruginosa response pathways varied among the species, with different combinations of two to four species inducing each pathway (Fig. S5). Notably, S. epidermidis, which is most closely related to S. aureus, did not induce zinc deprivation, pyoverdine production, or opdH in P. aeruginosa, whereas B. cenocepacia induced all four promoters (Fig. S5).

Identified secreted factors underlie a major part of the P. aeruginosa response to staphylococcal exoproducts

To determine if the identified molecules recapitulated the effect of S. aureus whole supernatant on P. aeruginosa, we added the individual molecules or a combination of all molecules to medium to P. aeruginosa cells and performed RNA-seq after 20 min and 2 h incubation (Table S13). The molecules were added at concentrations measured from the supernatant or that induced equivalent promoter activity: 80 µM StP, 150 µM citrate, and 150 µM acetoin. Since we did not identify the molecule(s) that induce the promoter of pvdG, we added a mixture of the iron chelators DTPA and DFX at concentrations that represented the induction of mScarlet reporter production (Fig. S3B). The mixture of the two chelators was added to mimic the dual phenotypes we observed, where DTPA induces the pvdG promoter, and DFX delivers iron to P. aeruginosa. As expected, each of the four products induced the respective response pathway in P. aeruginosa (Fig. 8A). Compared to the medium control, addition of the supernatant, the respectively paired identified products, or all products in combination led to upregulation of the metal starvation genes PA14_11320 and pvdG at 20 min and intermediate metabolite uptake and metabolism genes opdH and acoR at 2 h (Fig. 8A and Table S13). DTPA/DFX also induced PA14_11320, potentially due to chelation of zinc by DTPA (Fig. 8A) (71). We next determined what proportion of the P. aeruginosa response to S. aureus supernatant was explained by the identified products. Of the 417 genes that were upregulated upon exposure to S. aureus supernatant, 235 (56.3%) were also induced by at least one of the identified products, while 218 (52.3%) were induced upon exposure to the combination of all products (Fig. 8B). Despite the sensed products being identified using upregulated promoter-reporters, of the 263 genes that were downregulated upon exposure to S. aureus supernatant, 133 (50.6%) were also repressed by at least one of the identified products, while the combination of all molecules downregulated 77 genes (29.3%) (Fig. S6A). Thus, the four classes of identified sensed molecules account for a substantial part of both the upregulated and downregulated transcriptional responses of P. aeruginosa to S. aureus supernatant.

FIGURE 8. Identified sensed products recapitulate a major part of the P. aeruginosa response to S. aureus supernatant.

(A) Heatmap of fold change of the transcripts PA14_11320, pvdG, opdH, and acoR after addition of S. aureus supernatant, the indicated molecules, or all molecules in combination (+ Comb.) over media control, after 20 min or 2 h. (B) Inclusive intersection of all upregulated genes after addition of supernatant (+ Sup.) vs. at least one other condition (Overlap) or the combination of all molecules (+ Sup. / + Comb.). (C) Log₂ fold change of the upregulated genes that are non-intersecting (+ Sup. only) or intersecting among supernatant and at least one other condition (Overlap). Datasets were analyzed by a two-tailed t-test. #, p < 0.0001. (D) UpSet plot of exclusive intersections of upregulating genes between addition of S. aureus supernatant and the indicated molecules. (See Fig. S6 for full UpSet plot of all intersections.) (E) Model of P. aeruginosa sensing of S. aureus exoproducts. S. aureus secretes staphylopine, iron chelators, intermediate metabolites, and possibly proteinaceous molecules that are sensed by P. aeruginosa. In response, P. aeruginosa upregulates metal starvation and metabolite uptake pathways, which includes production of its own metal-binding molecules pseudopaline and pyoverdine.

Given that we selected our promoter-reporters based on significantly enriched pathways and genes with high fold change of gene expression (Fig. 1B and D), we posited that our identified sensed molecules likely underlie the upregulation of genes with higher fold change. In fact, the genes upregulated by both S. aureus supernatant and at least one of the identified molecules had a significantly higher fold change (mean log₂(fold change) = 2.38) when compared to the genes that are solely induced by S. aureus supernatant (mean log₂(fold change) = 1.50) (Fig. 8C). For the downregulated genes, the overlapping genes had a significantly lower fold change (mean log₂(fold change) = −1.83) when compared to the genes solely repressed by S. aureus supernatant (mean log₂(fold change) = −1.33) (Fig. S6B).

We determined which molecules explained what proportion of the response to staphylococcal supernatant by generating an UpSet plot to show intersections of upregulated genes in the supernatant with those among groups of the other conditions (Fig. 8D and Fig. S6C and D for expanded UpSet plots). The largest intersections were between the shared upregulated genes after addition of the combination of all molecules and the iron chelators DTPA/deferoxamine (130 genes), and these conditions and StP (42 genes) (Fig. 8D). These comparisons indicate that many of the genes induced by S. aureus supernatant are due to effects of exoproducts that induce iron-related pathways as well as zinc starvation, however intersections were found between the upregulated genes in S. aureus supernatant and each of the other conditions, showing their contribution to inducing distinct sensing pathways in P. aeruginosa. Taken together, we describe a model where P. aeruginosa senses the secreted staphylococcal molecules StP, iron chelators and unidentified proteins, and intermediate metabolites, and upregulates metal starvation pathways, thereby producing PsP and pyoverdine, and metabolite uptake and catabolism pathways to use citrate and acetoin as carbon sources (Fig. 8E).

DISCUSSION

In this study, we developed a systematic unbiased strategy using transcriptomics combined with genetics to determine the secreted exoproducts from one species that can be sensed by another in a model two-species system. We used this approach to study the sensing of S. aureus by P. aeruginosa. Unlike other strategies that focus on a single molecule or response pathway of interest, our genome-scale approach revealed multiple staphylococcal factors that are sensed by

P. aeruginosa, illustrating that interactions even between just two species can be complex and mediated by diverse molecules (Fig. 8E). Our genome-wide screen also determined the mutations in S. aureus that affect the regulation, biosynthesis, and/or secretion of the sensed exoproducts. The sensed molecules we identified explain most of the P. aeruginosa transcriptional response to S. aureus in our system, suggesting that this systematic genome-wide approach can be applied to other two-species systems to comprehensively identify the underlying molecules that affect bacterial sensing in multispecies communities. P. aeruginosa and S. aureus are commonly co-isolated from lung infections in CF patients and together contribute to worse disease outcomes compared to mono-infections (26, 27). It is therefore imperative to better understand their interactions and the molecular mediators involved. Here we found that P. aeruginosa senses multiple distinct S. aureus secreted molecules: the metallophore StP which affects zinc starvation and biofilm formation, unidentified molecules that affect pyoverdine production and/or deliver iron to P. aeruginosa, and the intermediate metabolites citrate and acetoin which are carbon sources for P. aeruginosa. Further, production of the sensed molecules was conserved in clinical isolates of S. aureus suggesting that these pathways and interactions are common between these two species.

Staphylococcal exoproducts affected P. aeruginosa metal homeostasis, and zinc and iron chelators defined >45% of the transcriptional response to S. aureus supernatant (Fig. 8D, Fig. S6, and Table S13). Zinc availability is required for virulence traits in both species, affecting P. aeruginosa motility, biofilm formation, and protease activity (58, 59, 72–74) and S. aureus biofilm formation and growth in vivo (50, 75–77). Interactions between P. aeruginosa and S. aureus in the context of zinc deprivation have been studied before in the presence of a neutrophil-derived metallophore, calprotectin, which binds zinc, manganese, nickel, and iron. Through metal chelation, calprotectin decreases anti-staphylococcal antimicrobial production and inhibits extracellular protease-mediated lysis of S. aureus thereby promoting coexistence between P. aeruginosa and S. aureus (57, 58). Moreover, it has been shown that the availability of zinc affects interactions between P. aeruginosa and the oral commensal species Streptococcus sanguinis SK36, likely due to zinc sequestration by P. aeruginosa (78). We found that S. aureus-secreted StP led to the upregulation of the biosynthesis genes of the metallophore PsP as well as other components of the Zur-dependent zinc starvation response in P. aeruginosa due to reduced availability of zinc. Additionally, StP inhibited P. aeruginosa biofilm formation and reduced P. aeruginosa antimicrobial killing of S. aureus. Our screen thus revealed a new interaction between S. aureus and P. aeruginosa through competition for and modulation of zinc availability by microbial opine metallophores. Zinc deprivation genes in P. aeruginosa are known to be induced in CF sputum (79–81), and our data suggest that competition with S. aureus may contribute to the induction.

P. aeruginosa and S. aureus are thought to compete for limited iron availability during infection via the secretion of iron-chelating siderophores and various iron uptake systems (28, 82). However, other studies have shown a downregulation of the P. aeruginosa iron starvation response in the presence of S. aureus or cell-free supernatant (35, 70, 83) and lysis of S. aureus liberates intracellular iron for acquisition by P. aeruginosa (35). The differences between studies could be due to variability in the iron content of the culture media as well as the S. aureus strains used. The results of our work support a complex effect of S. aureus on the P. aeruginosa iron response where on the whole S. aureus secreted products led to an induction of P. aeruginosa iron starvation responsive Fur- and PvdS-regulons, but P. aeruginosa obtains iron from specific staphylococcal chelators through xenosiderophore piracy, iron acquisition via uptake of a foreign siderophore (84). Characterization of this intriguing iron piracy, and identification of the likely novel underlying molecules, will be the subject of a future study.

Through the transposon screen with P’pvdG, we also described the mutations in S. aureus that affect production of these molecules and hence iron-responsive pathways in P. aeruginosa, including in genes encoding metabolic enzymes, transcriptional regulators, and proteases. Particularly, supernatant from S. aureus clpP and clpC mutants led to decreased pvdG promoter induction, but a large increase in relative chelation (Fig. 4B). Clp proteases comprise the main proteolytic system in S. aureus and are known to affect iron homeostasis (85, 86), and our data reinforce the idea that some S. aureus iron-related molecules may be direct or indirect targets of the Clp proteolysis machinery.

Our results also define a syntrophic relationship between P. aeruginosa and S. aureus where staphylococcal secreted intermediate metabolites citrate and acetoin can be used as carbon sources by P. aeruginosa. Costless secretion of valuable metabolites, especially of organic acids, is predicted to enable positive interspecies interactions through cross-feeding (87). It was reported previously that P. aeruginosa can take up both metabolites as carbon sources (64, 70, 88, 89), and acetoin was recently identified to participate in this cooperative interaction between P. aeruginosa and S. aureus in clinical co-isolates (70), which validates our screening approach in determining sensed exoproducts. Extracellular citrate has been detected in S. aureus cultures previously (90, 91), and our work shows that this staphylococcal secreted metabolite can be sensed by P. aeruginosa, thus defining another cooperative interaction between these two co-infecting pathogens. Higher concentrations of citrate affect quorum sensing and biofilm formation, and mediate iron uptake in P. aeruginosa (60, 92, 93). While citrate did not affect iron pathways in our study at the concentration found in S. aureus JE2 supernatant (Table S13), it is possible that higher concentrations that facilitate iron uptake may exist in communities with these two species. Our genome-wide screen identified mutations in S. aureus that affect production and/or secretion of these sensed intermediate metabolites, which is not only important for better understanding these cooperative interspecies interactions and general metabolism but also has implications for the effects of these metabolites on S. aureus such as acetoin affecting stress resistance or citrate influencing virulence (91, 94).

Previous studies have identified additional molecules that can be secreted by S. aureus, and are sensed by P. aeruginosa, such as N-acetyl glucosamine which induces the nag operon and autoinducer-2 which induces several virulence genes (36, 39, 95). However, these products were not identified during S. aureus co-culture and/or incubation with S. aureus supernatant, but rather with Gram-positive bacterial communities. We did not see these response pathways being induced in our study upon exposure to S. aureus cell-free supernatant, possibly due to differences in growth medium, experimental conditions, and timing of gene expression measurements between the studies, and/or insufficient amounts of these products being present in 25% (v/v) S. aureus supernatant.

There are limitations and considerations to using our screening approach. First, our study was conducted in a defined medium to avoid introduction of molecules from another species into the two-species system, such as culture media compositions that contain whole cell lysates, and it is important to consider that culture and growth conditions may affect either secreted molecule production and/or sensory responses. Next, the species being studied must have the necessary genetic tools available, such as reporter expression systems and random mutagenesis protocols, however these are becoming more widely accessible (96–98). The identification of sensed products using our approach was more straightforward when there was a primary sensory molecule driving the response, such as in the case of StP, citrate, or acetoin, although fractionation of WT and mutant supernatants can reveal the molecules underlying multifactor-driven responses as well. Another consideration is that there is significant strain to strain variability in bacteria, and studies should therefore utilize a panel of strains to interrogate interspecies sensing. While our screen was carried out in a single strain of each species, we validated that S. aureus clinical isolates from cystic fibrosis patients, including strains that were co-isolated with P. aeruginosa, retained production of molecules that induced the sensory pathways, albeit at varying levels.

Studies of interactions between P. aeruginosa and S. aureus have often focused on the effects of P. aeruginosa antimicrobials on staphylococcal growth and survival, however it is an active question if these species, which are often co-isolated, are more prone to competition or coexistence (31). Here by identifying the staphylococcal secreted products that are sensed by P. aeruginosa, we uncovered instances of both aspects: competition for metals, siderophore piracy, lifestyle alteration via inhibition of biofilm formation, and cooperation through release of intermediate metabolites used as carbon sources. Altering the production of these factors could potentially tip the balance in favor of a more beneficial or antagonistic interaction between these species.

MATERIALS AND METHODS

Bacterial strains and growth conditions

Bacterial strains utilized in this study are listed in Table S14. P. aeruginosa UCBPP-PA14 (99) and S. aureus JE2 (47), other species listed, and their derivatives were grown in a modified M63 medium (100) (13.6 g·L^-1 KH₂PO₄, 2 g·L^-1 (NH₄)₂SO₄, 0.8 µM ferric citrate, 1 mM MgSO₄; pH adjusted to 7.0 with KOH) supplemented with 0.3% glucose, 1× ACGU solution (Teknova), 1× supplement EZ (Teknova), 70 ng·L^-1 biotin, and 7 mg·L^-1 nicotinamide, at 37°C, shaken at 300 rpm, except where noted. Vibrio cholerae was grown in M63 with the addition of 2% NaCl. For P. aeruginosa ΔpvdJ ΔpchE growth assays, 200 µM 2,2’-bipyridyl (BIP) (Sigma Aldrich) was added to M63 medium. For sole carbon source growth assays, EZ and glucose were not added in the formulation. For each growth assay, P. aeruginosa overnight cultures were diluted to an OD₆₀₀ of 0.05 before monitoring growth. The Nebraska Transposon Mutant Library (NTML) made up of 1,920 arrayed bursa aurealis transposon insertions in S. aureus JE2 was utilized for the transposon screen (47). For cloning and strain construction, strains were routinely cultured in Luria Bertani (Miller) broth or on agar plates with 20 g·L^-1 agar. For selection, antibiotics were added as 50 µg·mL^-1 gentamicin, 25 µg·mL^-1 irgasan, 50 µg·mL^-1 carbenicillin, and/or 10 µg·mL^-1 erythromycin as needed. Other additives include staphylopine (Santa Cruz Biotechnology), TPEN (Sigma Aldrich), ZnSO₄·7H₂O (Sigma Aldrich), NiCl₂·6H₂O (J. T. Baker Chemical Company), CoCl₂·6H₂O (Sigma Aldrich), DTPA (Sigma Aldrich), deferoxamine mesylate salt (Sigma Aldrich), and intermediate metabolites citric acid (Sigma Aldrich), acetoin (Sigma Aldrich), 2,3-butanediol (98% (v/v) solution, Sigma Aldrich), and (S)-α-acetolactic acid potassium salt (Toronto Research Chemicals).

Preparation of S. aureus cell-free supernatant

Overnight cultures of S. aureus strains were diluted to OD₆₀₀ of 0.05 in fresh media and grown for 24 h in flasks (or tubes or 96-well plates for NTML library supernatant preparation). Bacterial cultures grown in flasks were centrifuged at 4000 rpm for 20 minutes. The supernatant was applied to a Steriflip unit with a 0.2 μm polyethersulfone filter (MilliporeSigma). For supernatants prepared from the NTML library in 1-mL tube cultures or 96-well plates, culture was directly transferred to AcroPrep Advance 96-well 0.2 μm polyethersulfone filter plates (Pall) and centrifuged at 4000 rpm for 10 min to collect the sterile-filtered flow through. Supernatants were stored at −30°C until use.

RNA extraction and library preparation

P. aeruginosa overnight cultures were diluted to OD₆₀₀ of 0.05 in fresh media in flasks and grown to OD₆₀₀ of 0.50. Two milliliters were collected for RNA extraction immediately before addition of 5 mL (25% v/v) of either fresh media, supernatant, or additives in media and collected after 20 min, 1 h, and 2 h for the data described in Fig. 1 and after 20 min and 2 h for the data described in Fig. 8. Removed culture was mixed with 4 mL of RNAprotect Bacteria Reagent (Qiagen) for stabilization and incubated for 5 min at room temperature before centrifugation at 4000 rpm for 10 min. Supernatants were completely removed before storage of the pellets at −80°C. RNA was extracted using the Total RNA Purification Plus Kit (Norgen) according to the manufacturer’s instructions for Gram-negative bacteria. The extracted RNA was subjected to an additional genomic DNA removal by DNase I treatment in solution using the TURBO DNA-free Kit (Invitrogen) and checked by PCR for the absence of contaminating DNA. Integrity of the RNA preparation was confirmed by running on an agarose gel and observing intact rRNA bands. Next, rRNA was removed using the Ribo-Zero Depletion Kit for Gram Negative Bacteria (Illumina) or riboPOOLs (siTOOLs Biotech) before library preparation with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). The sequencing was performed at the Center for Cancer Research Genomics Core Facility. Two biological replicates were performed.

RNA-seq analysis

The sequencing files were processed with Cutadapt (101) and Trimmomatic (102). Alignment to the P. aeruginosa UCBPP-PA14 genome (NCBI) and pairwise comparisons were made using Rockhopper (Wellesley College) (103, 104). Upregulated and downregulated genes were based on transcripts that had p < 0.05 and log₂ fold change ≥ or ≤ 1. Venn diagrams were generated using matplotlib_venn package with venn3 using Python (105). All upregulated genes were evaluated for increasing fold change over time. UpSet plots were generated with ComplexUpset using R (106). For UpSet plots, all upregulated genes at 20 min and 2 h were combined and compared between datasets.

Construction of P. aeruginosa promoter-reporter strains and mutants

Bacterial strains and plasmids are listed in Table S14. Promoter sequences were amplified using the primers listed in Table S15. The amplified fragments were cloned by Gibson Assembly (NEB) into SpeI- and XhoI-digested pSEK109 (pLB3208), provided by the Dietrich lab (107). Plasmids were transformed into E. coli S17-1 λ-pir and confirmed by sequencing. Next, bi-parental conjugations were conducted as described previously between E. coli donor cells and P. aeruginosa recipients (20). For each conjugation, cells were collected and plated on LB + irgasan + gentamicin plates. The integration was then unmarked using Flp-FRT recombination by mating with an E. coli donor strain harboring the pFLP2 plasmid, selecting on LB + irgasan + carbenicillin, and further curing of this plasmid by selecting on LB plates (without NaCl) + 10% sucrose (108). All promoter-reporter strains were confirmed by PCR with the forward primer for the promoter and the reverse primer internal to mScarlet Pa094. For mutant construction, homologous downstream and upstream arms of cnt genes were amplified using the primers listed in Table S15. The amplified fragments were cloned into pDONRPEX18Gm attP sites using the Gateway BP Clonase II Enzyme mix (ThermoFisher). Plasmids were transformed into E. coli S17-1 λ-pir and confirmed by sequencing prior to conjugation as described above. Conjugants were streaked onto LB plates (without NaCl) + 10% sucrose, and then tested for gentamicin resistance. Gentamicin-sensitive strains were tested for the deletion by PCR and sequencing.

Plate reporter assay

P. aeruginosa overnight cultures were diluted to OD₆₀₀ of 0.05 in fresh media in flasks and grown to OD₆₀₀ of 0.5. At this time, 150 μL of culture was added to wells of a 96-well clear, flat-bottom polystyrene plate with 50 μL fresh media (control) or S. aureus supernatant with or without additives as described. Plates were incubated at 37°C with continuous orbital shaking at 807 cycles per minute (cpm) in a Synergy H1 microplate reader (BioTek) with fluorescence and optical density measurements every 30 minutes (mScarlet: 565 nm excitation and 600 nm emission; pyoverdine: 405 nm excitation and 460 nm emission (109); optical density at 600 nm). Measurements for duplicate wells were averaged, and the fluorescence was normalized to the growth (relative fluorescence units divided by the OD₆₀₀). Slopes were calculated from 1.5-5 h (promoters of PA14_11320, cntO, PA14_73020, opdH, and acoR) or 1-4 h (promoter of pvdG and pyoverdine).

Gene ontology (GO) enrichment analysis

For P. aeruginosa PA14 pathway analysis, the open reading frame designations for the corresponding PAO1 orthologs of P. aeruginosa UCBPP-PA14 genes were obtained using the Pseudomonas Genome Database (www.pseudomonas.com/rbbh/pairs) (110). Similarly, for S. aureus JE2 pathway analysis, the open reading frame designations for the corresponding NCTC8325 orthologs of S. aureus JE2 USA300_FPR3757 genes were obtained using the AureoWiki repository (http://aureowiki.med.uni-griefswalk.de/Downloads) (111). The list of designations from the RNA-seq analysis (P. aeruginosa) or selected transposon mutants (S. aureus) were analyzed at the Gene Ontology Resource (www.geneontology.org) by the PANTHER Overrepresentation Test (released 20210224) (Annotation Version and Release Date: GO Ontology database DOI: 10.5281/zenodo.5228828 Released 2021-08-18) or (released 20200728) (Annotation Version and Release Date: GO Ontology database DOI: 10.5281/zenodo.4081749 Released 2020-10-09), respectively, for enriched biological processes by Fisher’s exact test with Bonferroni correction.

Biochemical fractionation

Five milliliters of S. aureus supernatant were frozen and lyophilized before resuspension in 500 μL of filtered water. The resuspension was separated using a Superdex 30 10/300 GL size exclusion column (GE Healthcare) with filtered water as buffer at a flow rate of 0.7 mL·min^-1 for 1.5 column volumes at 2.6 MPa for a total of 36.5 mL with 18 fractions collected after every 2 mL. Fractions were frozen, lyophilized, and resuspended in 500 μL of water. For protease digestion, 60 μL of each fraction was treated with 1 μL of thermolabile proteinase K (New England Biolabs) for 1 h at 37°C followed by inactivation for 10 min at 55°C.

Biofilm formation assay

P. aeruginosa was grown overnight in modified M63 medium. Overnight culture was diluted to a starting OD₆₀₀ of 0.05 in fresh medium mixed with the indicated additives as described. One hundred μL of culture was added to eight replicate wells of a 96-well plate. Biofilms were allowed to form in static conditions for 24 h at 37°C and assessed for biofilm formation using crystal violet staining (112).

Supernatant survival assay

To prepare cell-free supernatant, P. aeruginosa was inoculated from an overnight culture at an OD₆₀₀ of 0.05 and allowed to grow for 16 h in medium with the indicated additives. The culture was centrifuged, and the supernatant was filtered with a Steriflip unit with a 0.2 μm polyethersulfone filter (MilliporeSigma). For the survival assay, S. aureus was inoculated from an overnight culture at an OD₆₀₀ of 0.05 and grown to an OD₆₀₀ of 0.5. Next, 500 μL of culture was added to 500 μL (50% v/v final concentration) of either P. aeruginosa cell-free supernatant or M63 salts control. After 16 h, S. aureus was plated on LB agar plates and enumerated after growth.

Chromeazurol S (CAS) assay for iron chelation

Solutions were prepared exactly as described and assay was performed as described with some changes (113). One hundred microliters of M63 media reference or 75 μL M63 with 25 μL of S. aureus supernatant (1X concentration) were added to plate and mixed with 100 μL CAS shuttle solution. Plates were incubated for 1 h at room temperature. The absorbance was measured at OD₆₃₀. The absorbance ratio was calculated by dividing the average absorbance for the sample by the absorbance of the media reference. Next, this ratio was normalized to a standard log-based curve of WT supernatant to return the relative chelation.

Citrate measurements

Citrate concentrations were measured in S. aureus supernatant using the Citric Acid Assay Kit (Megazyme) according to the microplate assay instructions. Absorbances after the enzymatic reaction were compared to a standard log-based curve of citric acid concentrations to determine the concentration in supernatant.

Acetoin and α-acetolactate measurements

Acetoin was measured by the Voges-Proskauer test adapted for microtiter plates essentially as described (70, 114). In order, 35 μL 0.5% (m/v) creatine (Sigma), 50 μL 5% (m/v) α-naphthol (Sigma), 50 μL 40% (v/v) KOH, and 50 μL S. aureus supernatant was added to each well. The reaction was incubated at room temperature for 15 min and absorbance was measured at OD₅₆₀. Concentrations were calculated based on a linear standard curve. To quantify α-acetolactate, 5 µl 2M H₂SO₄ was added to supernatant and incubated for 15 min at 60°C for decarboxylation of α-acetolactate to acetoin before adding to the above reagents as described (115). Due to precipitation in the wells, each mixture was transferred to a new well before reading absorbance.

Quantification of 2,3 butanediol by mass spectrometry

Stock solution of 50 mM 2,3-butanediol (Sigma Aldrich) and calibration standards from 0 to 40 µM were prepared in water. The isotopic standard (IS) solution of 5 µM 2,3-butanediol (Toronto Research Chemicals) was prepared in water. 2,3-Butanediol in the samples were determined by LC-MS/MS after derivatization with trichloroacetyl isocyanate (Sigma Aldrich) according to Chen et al. (116) with slight modification. In a 1.5 mL plastic vial, 5 µL of standard or sample was mixed with 5 µL IS, 250 µL acetonitrile and 20 µL trichloroacetyl isocyanate. After 5 min, 250 µL water was added to the vials and the mixture were analyzed by liquid chromatography-mass spectrometry LC-MS/MS. LC were performed with a Shimadzu 20AC-XR system with a 2.1 x 100 mm, Cortecs C8 column (Waters). Mobile phase A was 10 mM ammonium formate with 0.15% (v/v) formic acid in water and mobile phase B was methanol. The flow rate was 300 µL·min^-1 and the injection volume was 5 µL. 2,3-Butanediol was eluted from the column using a gradient (0-0.2 min/55% (v/v) B; 5 min/70% (v/v) B; 5.1-6 min/95% (v/v) B; 6.1-8 min/55% (v/v) B). MS/MS was performed with a TSQ Vantage triple quadrupole mass spectrometer (Thermo Fisher Scientific) operating in selected reaction monitoring mode with positive ionization. The derivatized peaks were detected using the following mass-to-charge ratio (m/z) precursor > product ions: 2,3-butanediol (484 > 262); 2,3-butanediol-d8 (492 > 270). 2,3-Butanediol concentrations in the samples were determined by a linear calibration curve with 1/x weighting generated by the Thermo Xcalibur software. The curve was constructed by plotting the peak area ratios vs. standard concentrations. The peak area ratio was calculated by dividing the peak area of 2,3-butanediol by the peak area of the IS.

Accession number(s)

The RNA-seq data have been deposited at NCBI Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/) under accession numbers GSE185963 and GSE186138.

COMPETING INTERESTS

No competing interests declared.

ACKNOWLEDGMENTS

We would like to acknowledge the Center for Cancer Research Genomics Core for RNA-sequencing, King Chan at the Protein Characterization Laboratory at Frederick National Laboratory for Cancer Research for quantifying 2,3-butanediol, the Cystic Fibrosis Foundation Isolate Core for providing clinical isolate strains, and the Dietrich lab (Columbia University) for providing the pSEK109 (pLD3208) plasmid. We thank Susan Gottesman, Kumaran Ramamurthi, Gisela Storz, and Saaed Tavazoie for comments on the manuscript, and members of the Gottesman, Ramamurthi, and Khare labs for discussion and feedback throughout this study. This work utilized the computational resources of the NIH High Performance Computing Biowulf cluster (http://hpc.nih.gov). Diagrams in Figures 1, 3, 5, and 8 were created with BioRender (http://biorender.com). This work was supported by the Intramural Research Program of the NIH, National Cancer Insitute, Center for Cancer Research. TMZ was supported by a Postdoctoral Research Associate Training (PRAT) Fellowship award 1FI2GM137843-01 from the National Institute of General Medical Sciences.

Footnotes

• The authors declare no conflict of interest.