ZupT Facilitates Clostridioides difficile Resistance to Host-Mediated Nutritional Immunity.

During infection, pathogenic organisms must acquire essential transition metals from the host environment. Through the process of nutritional immunity, the host employs numerous strategies to restrict these key nutrients from invading pathogens. In this study, we describe a mechanism by which the important human pathogen Clostridioides difficile resists transition-metal limitation by the host. We report that C. difficile utilizes a zinc transporter, ZupT, to compete with the host protein calprotectin for nutrient zinc. Inactivation of this transporter in C. difficile renders this important pathogen sensitive to host-mediated metal restriction and confers a fitness disadvantage during infection. Our study demonstrates that targeting nutrient metal transport proteins in C. difficile is a potential avenue for therapeutic development.

T ransition metals, including iron (Fe), manganese (Mn), and zinc (Zn), are essential micronutrients for all living organisms. These metals are thus key resources in the battle between a host and pathogen during infection. Upon colonization of the mammalian host, pathogens must acquire transition metals from complex, diverse, and largely metal-restricted environments (1,2). Pathogens employ numerous strategies to scavenge metals from the host, including pirating metal from host proteins, releasing metal-chelating metallophores, and expressing high-affinity metal import systems (2). To combat this, vertebrates exploit the pathogen requirement for transition metals by producing factors that deplete the environment of free transition metals in a process termed nutritional immunity (3,4). One such factor is calprotectin, a heterodimer of S100A8 and S100A9 proteins. Calprotectin is abundant in the cytoplasm of neutrophils and chelates multiple transition metals, including Fe, Mn, and Zn (5). Calprotectinmediated metal limitation is antimicrobial to numerous pathogens and is critical to combating infection (6)(7)(8)(9). Defining the battle for transition metals between host and pathogen is important to understanding the factors that impact the outcome of infection, and has the potential to uncover novel therapeutic strategies for targeting pathogens.
The spore-forming bacterium Clostridioides difficile is the most commonly reported health care-associated pathogen in the United States and a global public health threat (10). The primary risk factor for C. difficile infection (CDI) is antibiotic treatment, which disturbs the resident microbial community in the gastrointestinal tract and reduces colonization resistance against the pathogen (11). Notably, the first-line therapy for C. difficile is also antibiotic treatment, which further perturbs the gut microbiota and increases risk for recurrent infection. Over the past decade, the rate, severity, and economic cost of CDI have risen dramatically in both children and adults (10,12). This highlights the urgent need for new antibiotic targets and novel therapeutic strategies for treating CDI.
Recent work from our group and others has demonstrated that fecal calprotectin is associated with CDI in humans and high levels of calprotectin are correlated with increased disease severity (7,(13)(14)(15). We have further demonstrated that calprotectin is antimicrobial against C. difficile and calprotectin-mediated metal limitation is an essential host immune response during CDI (7). Despite calprotectin's antimicrobial properties and high concentrations in the gastrointestinal tract during severe infections, C. difficile persists in this metal-limited environment. This suggests that C. difficile employs strategies to compete with the host for essential transition metals during infection, allowing for persistence. The mechanisms by which C. difficile combats host nutritional immunity have not been explored and may represent a new therapeutic target for treatment of CDI.
In this study, we investigated the role for a putative Zn transporter in C. difficile during host-mediated metal limitation. ZupT homologs in Salmonella enterica and Escherichia coli are important for metal scavenging in these organisms, but the role for ZupT in C. difficile has not been experimentally explored (16)(17)(18). We demonstrate that zupT is highly upregulated in the presence of recombinant calprotectin and is required for survival of calprotectin-mediated metal limitation in vitro. Furthermore, we show that ZupT imports Zn when C. difficile is metal starved and ZupT-deficient strains of C. difficile are less fit in a mouse model of infection. Together these results show that ZupT is an important factor used by C. difficile to combat host nutritional immunity during CDI.

RESULTS
C. difficile upregulates the putative Zn transporter ZupT during host-mediated metal limitation. Calprotectin is essential to the immune response to CDI and calprotectin-mediated metal limitation is antimicrobial to C. difficile (3,7). An RNA sequencing study by our group showed that the putative Zn transporter ZupT is one of the most highly upregulated genes in the presence of calprotectin in vitro (19). To begin to assess the contribution of ZupT to the response to host-mediated metal starvation, the transcriptional induction of zupT during treatment with recombinant calprotectin was validated using reverse transcription-quantitative PCR (qRT-PCR). In the presence of 0.35 mg/ml calprotectin, a Ͼ200-fold transcriptional increase of zupT was observed compared to the untreated controls (Fig. 1A). To confirm that this response was specific to metal limitation, C. difficile was treated with a chemical chelator N,N,N',N'-tetrakis (2-pyridinylmethyl)-1,2-ethanediamine (TPEN; 50 M). Exposure to TPEN-mediated metal starvation revealed a 500-fold increase in zupT transcripts compared to the untreated control (Fig. 1B). These results demonstrate that transcription of zupT is a robust response by C. difficile to metal limitation.
Inactivation of zupT decreases resistance to metal limitation. Based on the increased expression of zupT in the presence of calprotectin, we hypothesized that the encoded protein may play a central role in Zn acquisition during metal limitation by the host. To test this, a strain of C. difficile inactivated for zupT (zupT::CT) was generated using the ClosTron system (20). The lack of zupT rendered the bacteria more sensitive to calprotectin-mediated metal starvation, as growth was delayed over time in the presence of 0.35 mg/ml calprotectin and overall percent growth was reduced by 80% compared to the wild-type (WT) strain at 6 h ( Fig. 2A and B). Similar results were observed when the growth of the bacteria was assessed in 50 M TPEN, which led to a 40% reduction in growth of the mutant compared to the WT strain ( Fig. 2C and D). The growth of zupT::CT in either condition is recovered by expressing zupT in trans under the control of the predicted promoter-containing region upstream of zupT (ZupT::CT pJS116_zupT; Fig. 2A to D). Taken together, these data suggest that ZupT functions to obtain metals, such as Zn, in the face of host nutritional immunity and may play an important role in reducing the effect on C. difficile of nutrient metal starvation.
ZupT imports Zn during metal limitation. ZupT is highly expressed during competition with calprotectin and zinc uptake is essential to C. difficile survival during calprotectin-mediated metal starvation; however, it remains unknown if this putative metal transporter imports Zn into the cell (7,19). To investigate the ability of ZupT to take up Zn, cell cultures were grown in Zn-limited media and pulsed with a minor Zn stable isotope ( 70 Zn) prior to analysis of intracellular 70 Zn levels by inductively coupled plasma mass spectrometry (ICP-MS). The zupT::CT strain displayed a 10-fold reduction in intracellular 70 Zn compared to the WT strain in these experiments (Fig. 3). The uptake of 70 Zn was restored in the zupT::CT pJS116_pzupT-zupT complemented strain. These data demonstrate the direct contribution of ZupT to increasing intracellular Zn con- centrations as a strategy to combat Zn-limiting conditions (Fig. 3), and strongly support the assignment of ZupT as a Zn transporter.
ZupT mutants show a colonization defect in the gastrointestinal tract during infection. The reduced ability of zupT::CT to resist Zn starvation in the presence of the innate immune protein calprotectin suggests that ZupT may be required in a mouse model of CDI. To test this, mice were placed on a custom formulated diet that is Zn-free (7). This Zn-free diet was supplemented with standard levels of Zn (control diet: 29 mg/kg) and animals were fed the diet for 1 week prior to infection (7). Mice were then coinfected with WT and zupT::CT spores of C. difficile at a 1:1 ratio and disease was monitored for 4 days. Following treatment with the control diet, the WT strain colonized to ϳ10 8 CFU per gram of stool (Fig. 4A). The zupT::CT strain displayed a 1 log reduction in colonization compared to the WT strain ( Fig. 4A). Next, to examine the role of ZupT during conditions of Zn deficiency, we coinfected mice that were fed a custom formulated diet lacking Zn supplementation (low-Zn diet: 0 mg/kg). Following infection, we observed a 2 to 3 log defect in the zupT::CT strain under these extreme Zn-limited conditions (Fig. 4B). In both dietary conditions, the zupT::CT mutant showed a significant reduction in competitive index compared to WT and this reduction was increased in the low Zn diet (Fig. 4C). To ensure the zupT::CT strain does not contain an innate colonization defect, mice fed the control diet were mono-infected with either WT or zupT::CT strains. There were no signification differences in colonization between the WT or zupT::CT strain throughout the infection (Fig. 4D). Together, these data suggest that ZupT is required for C. difficile to overcome nutrient Zn limitation imposed by the host during CDI.

DISCUSSION
Transition metals are essential micronutrients for all living organisms, and invading pathogens must acquire these metals in the host environment to colonize and establish infection (2). This is complicated even further in the gastrointestinal tract, as enteric pathogens must also compete with resident microbiota for transition metals. Calprotectindependent nutritional immunity is essential to defend against CDI (7). However, recent studies have demonstrated that increased fecal calprotectin is a hallmark of severe CDI, suggesting that during severe infection, C. difficile must employ strategies to persist and thrive in the gastrointestinal tract despite nutritional immunity (7,(13)(14)(15). In this study, we explored a potential mechanism by which C. difficile competes with the host for transition metals during infection. Previously, our group demonstrated that calprotectin is an essential component of the innate immune response to CDI and calprotectin-mediated transition metal limitation is inhibitory to C. difficile growth (7). Furthermore, we showed that subinhibitory concentrations of calprotectin dramatically alter the transcriptional profile and metabolism of C. difficile in vitro (19).
Here, we explored the role of one of the most highly upregulated genes in the presence of calprotectin, zupT. Previous studies have shown that zupT is upregulated under metal stress, but this putative metal transporter has not been studied experimentally in C. difficile (19,21,22). We demonstrated that zupT expression was robustly induced in the presence of calprotectin or a chemical chelator, and that inactivation of zupT decreased the ability of C. difficile to grow in the presence of subinhibitory concentrations of calprotectin. Using ICP-MS, we further demonstrated that zupT mutant cells have a defect in heavy Zn uptake, suggesting that ZupT is indeed a bona fide Zn transporter in C. difficile. In mice fed standard Zn diets, as well as Zn-free diets, strains of C. difficile lacking functional ZupT showed decreased fitness compared to wild type. Taken together, this suggests that C. difficile employs strategies to compete with the host and the resident microbiota for metals during infection.
ZupT has been reported in several studies to be one of the most highly upregulated genes in C. difficile during metal stress, suggesting this importer plays a key role in metal homeostasis for this important pathogen (19,21,22). However, despite this strong transcriptional response, inactivation of zupT does not completely inhibit the ability of C. difficile to colonize the host or grow in the presence of lower concentrations of calprotectin ( Fig. 2 and 4). This suggests that C. difficile harbors additional metal import systems that may play similar roles in acquisition of Zn during. In support of this hypothesis, multiple putative Fe (CDR20291_1545-1548, CDR20291_1326-1328, CDR20291_2771-2774) and cation (CDR20291_0516-0157) transporters are transcriptionally increased in the presence of calprotectin (19). The phenomenon of functional redundancy in metal transport is shared among numerous enteric pathogens, including Enterococcus faecalis, E. coli, and multiple strains of Salmonella (16,(23)(24)(25). This has been specifically reported for ZupT homologs in several organisms. For example, the loss of ZupT in combination with the ZnuABC transporter in uropathogenic E. coli leads to a cumulative effect on fitness during urinary tract infections, whereas there was no decrease observed in a strain lacking only ZupT (24). In Salmonella enterica infection, strains lacking ZupT are attenuated in natural resistance-associated macrophage protein 1 (Nramp1) ϩ/ϩ mice, but strains lacking both ZnuABC and ZupT exhibit markedly pronounced attenuation during infection (16). Future studies that simultaneously interrogate multiple Zn-transport systems are needed to define the mechanisms of Zn import in C. difficile during host nutritional immunity.
Taken together, these data demonstrate that metal import in C. difficile is an important response to host-mediated nutritional immunity during infection. Future work is needed to characterize the response of C. difficile to transition metal limitation in the gut and to define the role for functional redundancy in metal transporters, as these pathways represent an intriguing target for therapeutic development.

MATERIALS AND METHODS
Ethics statement. All animal experiments under protocol M1700053 were reviewed and approved by the Institutional Animal Care and Use Committee of Vanderbilt University. Procedures were performed according to the institutional policies, NIH guidelines, Animal Welfare Act, and American Veterinary Medical Association guidelines on euthanasia.
Bacterial strains, growth conditions, and plasmids. Strains used in this study are listed in Table 1. C. difficile strains were grown at 37°C in an anaerobic chamber (85% nitrogen, 10% hydrogen, 5% carbon dioxide, Coy Lab Products) in brain heart infusion broth (BD Life Sciences) supplemented with 0.5% yeast extract (BD Life Sciences) and 0.1% cysteine (Sigma-Aldrich) (BHIS) or in C. difficile minimal media (CDMM) as described previously (26,27). Escherichia coli strains were grown in lysogeny broth (LB) or agar (LBA), supplemented with 50 g/ml kanamycin when necessary. Bacillus subtilis strains were grown on LBA or in BHI broth supplemented with 5 g/ml tetracycline or 2.5 g/ml chloramphenicol (27). All antibiotics were purchased from Sigma-Aldrich.
zupT::CT strain generation. Gene inactivation was achieved using the ClosTron system as described previously (20,27). Briefly, gBlocks containing specific modifications for insertion into the genome were generated using the TargeTronics algorithm (http://www.targetrons.com) and synthesized by Integrated DNA Technologies. The gBlocks were cloned into the pCR-Blunt vector using the Zero Blunt PCR cloning kit (Thermo Fisher Scientific) followed by restriction digest with BsrGI and HindIII (NEB) and ligation (NEB T4 ligase) into pJS107. Plasmids were transformed into the recA ϩ E. coli MG1655 through a standard heat shock protocol followed by transformation into B. subtilis JH2 using an established method (28). B. subtilis strains containing the pJS107_zupT plasmids were mated with C. difficile R20291 overnight at 37°C by plating and mixing together 100 l of each strain onto a BHIS plate in the anaerobic chamber. Plates were scraped and transferred into 2 ml of BHIS prior to plating 200 l onto BHIS plates containing 20 g/ml thiamphenicol and 50 g/ml kanamycin (BHIS thiamp20kan50 ). Colonies from these plates were patched onto new BHIS thiamp20kan50 and BHIS plates containing 5 g/ml tetracycline (BHIS tet5 ). Patched colonies that were tetracycline sensitive were patched again onto new BHIS thiamp20kan50 and BHIS tet5 plates. Colonies that remained tetracycline sensitive were streaked onto BHIS plates containing 20 g/ml lincomycin (BHIS linc20 ). Inactivation of the zupT gene was confirmed by performing PCR to identify a 1.5-kbp shift in gene size using gDNA extracted as previously described from colonies that were lincomycin resistant (27,28).
Complementation plasmids. Complementation plasmids (Table 1) were created by amplifying the zupT gene and intergenic region from C. difficile strain R20291. The amplicon was then cloned into the pJS116 plasmid backbone. C. difficile strains were transformed as described above with the removal of the lincomycin selection and were maintained on BHIS thiamp20 to ensure plasmid retention (28).
RNA extraction and quantitative qPCR. C. difficile cultures were grown anaerobically in triplicate in a 1:1 mixture of calprotectin buffer and BHIS with calprotectin or TPEN added in indicated concentrations at 37°C to an OD 600 of 0.3. After growth, a 1:1 solution of acetone:ethanol was added to an equal volume of the culture. Samples were stored at -80°C until used for RNA extraction. Samples were thawed on ice, pelleted, and resuspended in 750 l of LETS buffer (1 M LiCl, 0.5 M EDTA, 1 M Tris pH 7.4). Cells were transferred to tubes containing lysing matrix B beads (MP Biomedicals) and lysed by a FastPrep-24 (MP Biomedicals) bead beater for 45 s at 6 m/s. Lysed samples were heated for 5 min at 55°C and pelleted by centrifugation for 10 min. The supernatant was transferred to a fresh tube and 1 ml TRIzol (Thermo Fisher Scientific) was added. Chloroform (200 l) was added to each sample and vortexed prior to separation of the aqueous and organic layers by centrifugation for 15 min. The aqueous (upper) layer was transferred to a fresh tube and the RNA was precipitated through the addition of 1 ml isopropyl alcohol. Samples were incubated for 10 min and RNA was pelleted by centrifugation for 10 min. Supernatant was ClosTron plasmid (28) pJS107_zupT ClosTron plasmid with intron targeted to zupT This study pJS116 Stable C. difficile plasmid (28) pJS116_pzupT-zupT zupT::CT complementation plasmid This study removed and the RNA pellet was washed with 200 l of 70% ethanol. Samples were air dried for 1 min, then resuspended in 100 l RNase free water. DNA contamination was removed through the addition of 8 l RQ1 DNase, 12 l 10ϫ RQ1 buffer, and 2 l RNase inhibitor (Promega) to the purified RNA. Samples were DNase treated for 2 h and purified using the RNeasy miniprep RNA cleanup kit (Qiagen). RNA concentration was determined using the Synergy 2 with Gen 5 software (BioTek) and 2 g was reverse transcribed by M-MLV reverse transcriptase (Thermo Fisher Scientific) in the presence of RNase inhibitor (Promega) and random hexamers (Promega). Reaction mixtures lacking the reverse transcriptase were used to control for DNA contamination. Newly created cDNA was diluted 1:100 and was used in qRT-PCR using iQ SYBR green supermix (BIO-RAD) utilizing the primer pairs in Table 2. Amplification was achieved using a 3-step melt cure program on a CFX96 qPCR cycler (BIO-RAD). Transcript abundance was calculated using the ΔΔCT method normalized by the rpoB gene.

Animals and experimental models of Clostridioides difficile infection.
All animal experiments were approved by the Animal Care and Use Committee of Vanderbilt University (protocol M1700053). C57BL/6 male mice at 6 to 8 weeks old were purchased from Jackson Laboratories and given one week to equilibrate their microbiota prior to experimentation. Mice were housed with autoclaved water, food, and bedding and all experimental manipulations were performed in a biosafety level 2 laminar flow hood. Mice were housed in individual cages under the same conditions during the experiment and all mice were culture negative for C. difficile prior to infection. One week prior to infection, mice were placed on diets containing altered metal levels as previously described (7). For the C. difficile infection model, mice were given cefoperazone at 0.5 mg/ml in drinking water ad libitum for 5 days followed by a 2-day recovery period and subsequent infection. Mice were infected via oral gavage with a 1:1 mixture of 1 ϫ 10 5 spores of C. difficile (NAP1/BI/027 strain R20291) and zupT::CT or 1 ϫ 10 5 spores of each individual strain resuspended in phosphate-buffered saline (PBS). Mice were monitored for survival or were euthanized after reaching a terminal endpoint of appearing moribund or experiencing weight loss of Ͼ20% from baseline. C. difficile CFU were quantified daily from fecal samples. Samples were diluted and homogenized in PBS and serial plated onto taurocholate cycloserine cefoxitin fructose agar (TCCFA) with or without lincomycin for enumeration as CFU per gram of feces. Competitive index (zupT::CT/WT) was measured for each dietary condition.
Uptake of 70 Zn isotope. C. difficile strains were grown anaerobically in BHIS or BHIS thiamp20 containing 50 M TPEN to an OD 600 of 0.5. 70 ZnO (Cambridge Isotope Laboratories) was added to each sample at a final concentration of 25 M and samples were incubated at 37°C for 1 h. A 1:1 mixture of acetone:ethanol was added and the cells were pelleted by centrifugation (4000 ϫ g for 10 min). Cells were subsequently washed twice and resuspended in 1ϫ PBS. Samples were transferred to metal-free 15 ml conical tubes (VWR), digested overnight in 50% Optima-grade nitric acid (Thermo Fisher Scientific) and 12.5% hydrogen peroxide at 50°C prior to 1:10 dilution in Millipore water for inductively coupled plasma mass spectrometry analysis.
Inductively coupled plasma mass spectrometry. Elemental quantification on acid-digested liquid samples was performed using an Agilent 7700 inductively coupled plasma mass spectrometer (Agilent, Santa Clara, CA) attached to a Teledyne CETAC Technologies ASX-560 autosampler (Teledyne CETAC Technologies, Omaha, NE). The following settings were fixed for the analysis: Cell Entrance ϭ Ϫ40 V; Cell Exit ϭ Ϫ60 V; Plate Bias ϭ Ϫ60 V; OctP Bias ϭ Ϫ18 V; and collision cell Helium Flow ϭ 4.5 ml/min. Optimal voltages for Extract 2, Omega Bias, Omega Lens, OctP RF, and Deflect were determined empirically before each sample set was analyzed. Element calibration curves were generated using ARISTAR ICP Standard Mix (VWR, Radnor, PA). Samples were introduced by peristaltic pump with 0.5 mm internal diameter tubing through a MicroMist borosilicate glass nebulizer (Agilent). Samples were initially taken up at 0.5 rps for 30 s followed by 30 s at 0.1 rps to stabilize the signal. Samples were analyzed in Spectrum mode at 0.1 rps, collecting three points across each peak and performing three replicates of 100 sweeps for each element analyzed. The sampling probe and tubing were rinsed for 20 s at 0.5 rps with 2% nitric acid between every sample. Data were acquired and analyzed using the Agilent Mass Hunter Workstation Software version A.01.02. Data of the investigated metal ion were normalized to the 34 S abundance of each sample.
Statistical analyses. Statistical analyses were performed using GraphPad Prism version 8. Specific statistical tests, replicate numbers, calculated errors, and other information for each experiment are reported in the figure legends.

ACKNOWLEDGMENTS
We thank Joseph A. Sorg for providing plasmids and strains utilized in this study and for advice and critical feedback related to this work.