Bacterial Strains and Culture Conditions
All strains used in this study are listed in Table 1. S. aureus cells22,47,48 were grown overnight in brain heart infusion (BHI) (VWR International Srl, Milan, Italy) or RPMI 1640 (Sigma-Aldrich, St. Louis, MO, USA) medium at 37°C with shaking. L. lactis cells carrying the expression vector alone (pNZ8037)49 or harboring the isdB gene (pNZ8037::isdB)21 were grown overnight in BHI medium supplemented with chloramphenicol (10 µg/ml) at 30°C without shaking. Cultures of L. lactis were diluted at 1:100 in the same medium and allowed to reach the exponential phase of growth. Nisin (6.4 ng/ml) was added, and cultures were allowed to grow overnight as above. In those experiments where a defined number of cells were used, bacteria were harvested from the cultures by centrifugation, washed, and suspended in phosphate-buffered saline (PBS), at OD600nm = 1.0. Escherichia coli BL21 (DE3) strain (Invitrogen, Carlsbad, CA, USA) transformed with vector pQE30 or pET28a (Integrated DNA Technologies, Leuven, Belgium) was grown in Luria agar and Luria broth (VWR International Srl) containing 100 µg/ml ampicillin or kanamycin, respectively, at 37°C with shaking.
Plasmid and DNA Manipulation
Plasmid DNA (Table 2) was isolated using the NucleoSpin Plasmid kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany), according to the manufacturer’s instructions, and transformed into E. coli XL1-Blue or BL21 (DE3) cells using standard procedures50. Transformants were screened by restriction analysis and verified by DNA sequencing (Eurofins Genomics, Milan, Italy). Cloning of IsdB NEAT1-NEAT2 (aa residues 48–480) was performed as reported by Miajlovic et al.51. Cloning of IsdB NEAT1 (aa residues 144–270) and IsdB NEAT2 (aa residues 334–458) domains was performed as reported previously22.
Table 2
Bacterial strain | Relevant properties | Reference |
S. aureus |
SH1000 WT | Laboratory strain. rsbU + derivative of S. aureus 8325-4 | 47 |
SH1000 spa | spa:: Tcr transduced from 8325-4 spa ::Tcr | 48 |
SH1000 isdB | isdB gene deleted by allelic exchange | 22 |
L. lactis |
NZ9800 (pNZ8037) | Expression vector with a nisin-inducible promoter, Cmr | 21 |
NZ9800 (pNZ8037::isdB) | isdB gene cloned in pNZ8037 Cmr | 22 |
E. coli |
XL1-Blue | E. coli cloning host | Stratagene |
BL21 (DE3) | E. coli cloning host | Invitrogen |
Abbreviations used as follows: AmpR, ampicillin resistance; KanR, kanamycin resistance. |
The synthetic gene fragment corresponding to the A1 domain (aa residues 460–730) of human vWF, modified based on the protocol of Chudapongse et al.52, was purchased by Eurofins Genomics. Cloning of the A1 domain was performed following the NEBuilder® HiFi DNA Assembly according to the manufacturer’s instructions (New England Biolabs, MA, USA). The primers used to amplify the A1 domain and the pET28a vector (Supplementary Table S1) were purchased from Integrated DNA Technologies.
Expression and purification of recombinant proteins
Recombinant A1 domain was expressed from pET28a (Millipore-Sigma, MA, USA) in E. coli BL21 (DE3) (Invitrogen). Recombinant proteins IsdB NEAT1-NEAT2, IsdB NEAT1, and IsdB NEAT2 were expressed as previously reported22. Overnight starter cultures were diluted at 1:40 in Luria broth containing the appropriate antibiotics (see above) and incubated with shaking until the culture reached the exponential phase (A600 = 0.4–0.6). Recombinant protein expression was induced by the addition of 1mM (final concentration) isopropyl 1-thio-β-D-galactopyranoside (IPTG) (Inalco, Milan, Italy) to the culture. After 4 h, bacterial cells were harvested by centrifugation and frozen at -80°C. Cells were re-suspended in lysis buffer (50 mM NaH2PO4, 300 mM NaCl, pH 8.0) containing 1 mM phenyl-methane-sulfonyl-fluoride (PMSF) (Sigma-Aldrich) and 20 µg/mL DNase (Sigma-Aldrich) and lysed by sonication (70% amplitude, 12 x 30″ on/off, 1′30″ interval between sonication steps). The cell debris was removed by centrifugation and proteins purified from the supernatants by Ni+ 2-affinity chromatography on a HiTrap chelating column (GE Healthcare, Buckinghamshire, UK). Protein purity was assessed by 10% SDS-PAGE and Coomassie Brilliant Blue staining. A bicinchoninic acid protein assay (Pierce, Rockford, IL, USA) was used to measure the concentration of purified proteins.
Recombinant proteins FnBPA194 − 51153, FnBPB163 − 48054, IsdA47 − 31318, IsdH41 − 66020, ClfA221 − 55955, ClfB201 − 54256, CNA31 − 34457, SdrE53 − 60658, SdrD36 − 56858 were all expressed with His6 N-terminal affinity tags and purified as reported above.
Reagents, proteins, and antibodies
BSA (bovine serum albumin), Protease-free DNase I, Skim milk, von Willebrand factor, Heparin, Chondroitin sulphate, Heparan sulphate, Lysostaphin, Nisin, Protein A (SpA37 − 485), Biotin, Avidin-HRP, Trypsin, Calcium ionophore A23187 were purchased from Sigma-Aldrich. Collagens type I, type III, type IV, and type VI were purchased by Merck (Darmstadt, Germany). Ristocetin was from Hyphen BioMed (Neuville-sur-Oise, France). IgG were isolated from patients’ with infective endocarditis as previously reported34, all methods were carried out in accordance with relevant guidelines and regulations, all experimental protocols were approved by the ethical board of the University of Pavia and informed consent was obtained from all human participants. Anti-A1 6D1 monoclonal antibody was raised as previously described30. αThrombin and PPACK were bought from Haematologic Technologies (Essex Junction, VT, USA). Sensor Chip NTA and Ni2+ Sepharose 6 Fast Flow resin were purchased by Cytiva Lifesciences (Washington, USA). IsdB antibody was raised in rabbit by routine immunization procedure using purified IsdB NEAT1-NEAT2 as antigen. Anti-L. lactis antibody was raised in rabbit by routine immunization procedure using heat-inactivated L. lactis NZ9800 cells as antigen. Rabbit anti-human von Willebrand factor antibody and rabbit anti-mouse or goat anti-rabbit Horseradish Peroxidase (HRP)-conjugated secondary antibodies were purchased from Dako Cytomation (Glostrup, Denmark). Monoclonal mouse HRP-conjugated α-polyHistidine antibody were purchased from Abcam (Cambridge, UK).
Release of CWA proteins from S. aureus and detection of vWF-binding activity
Lysostaphin digestion. CWA proteins from S. aureus were released by following the protocol described by Pietrocola22. Briefly, bacteria were grown to the stationary phase, either in RPMI or BHI medium, harvested by centrifugation at 7000×g for 15 min at 4°C, washed three times with PBS, and resuspended to an A600 = 2.0 in lysis buffer (50 mM Tris-HCl, 20 mM MgCl2, pH 7.5) supplemented with 30% (w/v) raffinose. Cell wall proteins were solubilized from S. aureus by incubation with lysostaphin (200 µg/ml) for 20 min at 37°C in the presence of protease inhibitors (Complete Mini; Sigma-Aldrich). Protoplasts were recovered by centrifugation at 6000 ×g for 20 min, while the supernatant taken as the wall fraction was concentrated by treatment with 20% (v/v) trichloroacetic acid (TCA) for 30 min at 4°C. The precipitated proteins were washed twice with ice-cold acetone and dried overnight.
SDS-PAGE and Western blotting. Proteins released by lysostaphin digestion were boiled for 10 min in sample buffer (0.125 M Tris-HCl, 4% (w/v) SDS, 20% (v/v) glycerol, 10% (v/v) β-mercaptoethanol, 0.002% (w/v) bromophenol blue), separated by 10% (w/v) SDS-PAGE and electroblotted onto a nitrocellulose membrane (GE Healthcare). After blocking with 5% (w/v) skim milk (Sigma-Aldrich) in PBS overnight at 4°C, the membrane was probed with either 2 µg/ml of human vWF in PBS for 1h at 22°C followed by rabbit polyclonal anti-vWF antibody (1:5000) and HRP-conjugated goat anti-rabbit antibody (1:10000) in 1% (w/v) skim milk or with rabbit polyclonal anti-IsdB antibody (1:5000) and HRP-conjugated goat anti-rabbit antibody (1:10000) in 1% (w/v) skim milk. Blots were developed using the ECL Advance Western blotting detection kit (GE Healthcare), and images of the bands were captured by an ImageQuantTM LAS 4000 mini-biomolecular imager (GE Healthcare).
ELISA-type solid-phase binding assays
Binding of vWF to IsdB and blocking experiments. The ability of soluble vWF to bind to immobilized recombinant CWA proteins (SpA37 − 485, FnBPA194 − 511, FnBPB163 − 480, IsdA47 − 313, IsdB48 − 480, IsdH41 − 660, ClfA221 − 559, ClfB201 − 542, CNA31 − 344, SdrE53 − 606, SdrD36 − 568) was determined by ELISA assay. Microtiter wells were coated overnight at 4°C with 1 µg/well of each protein in 0.1 M sodium carbonate, pH 9.5. The plates were washed three times with 0.5% (v/v) Tween 20 in PBS (PBST). To block additional protein-binding sites, the wells were treated for 1 h at 22°C with 2% (v/v) BSA in PBS and incubated for 1 h at 22°C with 1 µg/well of vWF in PBS. The plates were incubated with a rabbit polyclonal anti-human vWF IgG (1:1000 in 1% (v/v) BSA) and incubated for 1 h at 22°C. The wells were then incubated with an HRP-conjugated goat anti-rabbit antibody (1:1000 in 1% (v/v) BSA) for 45 min at 22°C. After washing, o-phenylenediamine dihydrochloride was added to the wells and the absorbance at 490 nm was determined using an ELISA plate reader (BioRad, Hercules, CA, USA).
To determine the effect of vWF ligands (heparin, and different types of collagens) on IsdB-vWF interaction, microtiter wells, coated with 1 µg of vWF, were incubated with 1 µg of IsdB in the presence or absence of 10 µg/well of each ligand. IsdB-binding to vWF was detected by the addition of a rabbit polyclonal anti-IsdB IgG (1:2000) followed by HRP-conjugated goat anti-rabbit antibody (1:1000).
The binding of 1 µg of IsdB to surface coated vWF (1 µg/well) in presence of increasing concentrations (from 0 to 10 µg/well) of heparin, chondroitin sulfate, or heparan sulfate was detected with IsdB antibody as reported above.
To assess the effect of ionic strength on the IsdB-vWF interaction, microtiter wells coated with 1 µg of vWF were incubated with 1 µg of IsdB in presence of increasing concentrations of NaCl (from 0 to 1 M). Complex formation was detected by incubation of the wells with the IsdB antibody.
The dose-dependent binding of IsdB to surface-coated human vWF or A1 domain (1 µg/well) was evaluated by incubation of the plates with increasing concentrations of IsdB (from 0 to 5 µg/well). Bound protein was revealed as reported before.
Binding of increasing concentrations of the A1 domain (from 0 to 5 µg/well) to immobilized IsdB NEAT1-NEAT2 or its subregions NEAT1 and NEAT2 (1 µg/well) was also assessed and detected by the addition of anti-human vWF IgG.
To assess the allosteric conformation change of vWF and the A1 domain exposure by ristocetin treatment, vWF (10 µg /ml) was treated with 0.5 mg/ml of ristocetin and the complex used to coat microtiter wells (100 µl). The A1 domain exposure was evaluated by the addition of the anti-A1 domain monoclonal antibody 6D1 (250 ng/well) followed by HRP-conjugated rabbit anti-mouse antibody (1:1000) to the wells.
The impact of the conformational change of the ristocetin-treated vWF was evaluated by measuring the binding of soluble vWF (1 µg/well) to immobilized IsdB (1 µg/well). The complex formation was detected using anti-human vWF IgG as previously reported.
Bacterial adhesion to surface-coated vWF. The ability of S. aureus or L. lactis ectopically expressing IsdB, to adhere to surface-coated vWF was evaluated by ELISA-based assay. Microtiter wells coated with vWF were incubated with cells (A600 = 1.0) of S. aureus SH1000 and its isdB mutant obtained from cultures grown to stationary phase in RPMI and suspended in 0.5% (v/v) BSA. The wells were extensively washed with PBST, blocked with 2% (v/v) BSA, and incubated with 100 µl bacterial suspensions for 1 h at 22°C. The expression of SpA on cell surface was exploited to detect bacteria adhesion by incubating the plates for 45 min with an HRP-conjugated rabbit anti-mouse antibody (1:1000). Adhesion of L. lactis to vWF was performed by incubating plates coated with vWF with cells of L. lactis expressing IsdB (L. lactis pNZ8037::isdB) and the strain carrying the empty vector (L.lactis pNZ8037) obtained from cultures grown in BHI. L. lactis binding to surface-coated vWF was detected by incubating 1 h at 22°C with a rabbit polyclonal anti-L. lactis IgG (1 µg/well) followed by an HRP-conjugated goat anti-rabbit antibody (1:1000).
Reactivity of IgG from patients with infective endocarditis against IsdB. To test the reactivity of IgG from the collection of infective endocarditis sera IsdB NEAT1-NEAT2 was immobilized onto microtiter wells (1 µg/well). After blocking with BSA, the wells were incubated with antibodies (1 µg/well) from patients and healthy donors. The binding of antibodies was revealed by the addition of a polyclonal rabbit anti-human IgG (1:1000).
Capture of vWF by S. aureus cells
Cells of S. aureus strain SH1000 WT or the isdB mutant, grown to stationary phase in RPMI, were harvested by centrifugation at 7000×g at 4°C for 15 min, washed three times with PBS, and resuspended to an A600 = 1.0 in PBS. Cells were then incubated with human vWF (5 µg/mL) for 1 h at 22°C under constant shaking. The extraction of vWF captured by bacteria was conducted as previously described22. Briefly, bacteria were treated with the extraction buffer (125 mM Tris-HCl, pH 7.0, 2% (w/v) SDS) for 3 min at 95°C and finally centrifuged at 10.000 ×g for 3 min. The supernatants were subjected to 5% (w/v) SDS-PAGE under reducing conditions, and the proteins were electrotransferred to a nitrocellulose membrane. The membrane was incubated with a rabbit polyclonal vWF antibody followed by HRP-conjugated goat anti-rabbit IgG. The band intensities were quantified with Quantity One software (Bio-Rad).
Surface plasmon resonance
For performing SPR measurements on a NTA-Ni2+ sensor chip (see below), the recombinant 6xHis-tag-A1 was treated with α-thrombin to remove the 6xHis tag and yield vWF A1 sequence with an additional 17-amino acid segment at the N-terminus. The fused protein (1 mg/ml, 0.5 ml) was treated at an enzyme:substrate molar ratio of 1:200 in PBS, for 1h at 25°C. The reaction was quenched by adding 1 µM (D)-Phe-Pip-Arg-chloromethylketone, as an irreversible thrombin inhibitor, while A1 was purified by the batch mode procedure. Briefly, the reaction mixture was incubated with 25 µl of Ni2+−Sepharose-6 Fast Flow resin at 22°C for 1 h under gentle stirring on an orbital shaker. The supernatant, containing the purified A1, was then collected and protein purity and chemical identity assessed by nonreducing 4–12% (w/v) SDS-PAGE, high-resolution mass spectrometry and by Dot Blot analysis (not shown), using anti-His tag antibody as a probe, all conforming the removal of the 6xHis-tag.
SPR analyses were carried out on a dual flow-cell Biacore X-100 instrument (Cytiva, Uppsala, Sweden). 6xHis-tag-IsdB proteins (i.e. the ligands) were noncovalently immobilized onto a Ni2+-chelated nitrilotriacetate (NTA) carboxymethyldestrane sensor chip and incremental concentrations of A1 domain (i.e. the analyte) lacking the 6xHis-tag were loaded at incremental concentrations in the mobile phase, following the single-cycle operation mode. The Ni2+-NTA/6xHis-IsdB chip assembly was prepared as follows: the NTA chip (Cytiva) was first washed (flow-rate: 30 µl/min) with 0.35 M EDTA, pH 8.3 (contact time: 60 sec) and then loaded with 0.5 mM NiCl2 solution (120 µl, contact time: 240 sec); excess Ni2+ was removed by injecting 3 mM EDTA solution (contact time: 180 sec); finally, a solution of 6xHis-IsdB (130µl, 2µg/ml) was injected on the sensor chip (contact time: 180 sec) to yield a final immobilization level of 655 response units (RU). Next, the Ni2+-NTA/6xHis-IsdB chip was challenged (flow-rate: 30 µl/min; contact time: 120 sec) with increasing concentrations of vWF A1. All measurements were carried out at 25°C in HBS-EP + buffer (10 mM HEPES, pH 7.4, 0.15 M NaCl, 50 µM EDTA, 0.005% v/v polyoxyethylene sorbitan). After each set of measurements, the NTA chip was regenerated by a pulse of regeneration buffer (350 mM EDTA). Each sensogram was subtracted for the corresponding baseline, obtained on the reference flow cell and accounting for nonspecific binding, i.e. typically less than 2% of RUmax. The binding data were analyzed using the BIAevaluation software vs 2.0. The sensorgrams (Fig. 6, black curves) were fitted with theoretical curves obtained by simulations based on several different 1:1 stoichiometric binding models: i) simple analyte-ligand interaction, ii) bivalent analyte, and iii) heterogeneous ligand binding model31,32. The best fit, as evaluated from the χ2 values of experimental and simulated sensorgrams, was obtained using the heterogeneous ligand binding model, which assumes the existence of two populations/orientations (i.e., L1 and L2) of the immobilized ligand, allowing the exposure of different ligand surfaces which are variably accessible for interaction with the analyte. This is even more likely to occur with highly charged IsdB proteins bound on the NTA sensor chip, formed by the negatively charge chelating agent NTA and the positive Ni2+ ions. The relative abundance of L1 and L2 were estimated from their RUmax values, obtained as a fitting parameter, e.g. L1 = [RUmax1/(RUmax1 + RUmax2)] x 10031,32.
Computational methods
Electrostatic potential calculations were carried out using the APBS60 program, run on the crystallographic structure of IsdB_E chain (5vmm.pdb)15, after removal of Hb coordinates, and on the crystallographic structure of the A1 domain bound to platelets thrombin receptor GpIbα (1u0n.pdb)61, after removal of the receptor coordinates. Calculations were performed using a solvent dielectric of 78.14 and a protein dielectric of 2.0 at 310K in 150 mM NaCl.
Binding and adhesion assays to endothelial cells
IsdB binding to endothelial cells. Human umbilical vein endothelial cells (HUVEC) from a single donor (Lonza, Spain) were kindly provided by the Researchers of the Neonatal Unit and Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico S. Matteo, Pavia, Italy and cultured as previously reported36. To examine the binding of recombinant IsdB NEAT1-NEAT2 to endothelial cells, HUVEC were cultured onto 96-microtiter wells. Monolayers (8x104 cells/well) were treated with 0.1 mM calcium ionophore A23187 (Sigma-Aldrich) for 10 min at 22°C, washed three times with PBS, and then fixed with 3% (w/v) paraformaldehyde in PBS for 10 min. The wells were thoroughly rinsed with PBS, blocked with BSA (v/v) 2% in PBS for 1 h, and then incubated with increasing concentrations of recombinant IsdB (0.63–2.5 µg/well) in PBS for 1h. After extensive washing, IsdB binding to the wells was detected by addition to the wells of a rabbit polyclonal IsdB antibody followed by HRP-conjugated goat anti-rabbit IgG.
Bacterial adherence to endothelial cells. The ability of S. aureus cells to adhere to HUVEC cells was assessed by an ELISA-based assay. 100 µl of bacterial suspensions (A600 = 1.0) of S. aureus strain SH1000 WT and its isogenic isdB mutant obtained from cultures grown in RPMI were added to ionophore-treated HUVEC monolayers and the wells incubated for 1h. The attached bacteria were detected by incubating the wells with an HRP-conjugated rabbit anti-mouse antibody (1:1000) for 45 min at 22°C. To test the effect of the anti-A1 monoclonal antibody (mAb) 6D1 on the adhesion of S. aureus SH1000 to HUVEC monolayers, the assay was performed in the presence of 250 ng/well of the 6D1 or an unrelated mAb and bacterial attachment determined as above.
Inhibitory activity of patients’ IgG on the interaction of IsdB with vWF expressed on endothelial cells. The ability of the patients’ IgG to interfere with the binding of recombinant IsdB NEAT1-NEAT2 to ionophore-treated and fixed endothelial cells was determined by incubating the wells with 2.5 µg IsdB in the presence of the indicated IgG (10 µg/well) for 1h at 22°C. The binding of IsdB to the cells was detected as reported above. To analyse the effect of patients’ IgG on adherence of staphylococci to ionophore-treated HUVEC cells, 100 µl of a S. aureus SH1000 WT suspension (A600 = 1.0) were added to the monolayers and the wells incubated for 1 h at 22°C. Bacterial adherence was detected by incubating the wells with an HRP-conjugated rabbit anti-mouse antibody (1:1000). A similar adhesion protocol was used to test the effect of patients’ IgG on adhesion of L. lactispNZ8037::isdB and L. lactispNZ8037 to the monolayers. L. lactis adherence to the cells was determined by adding to the wells a rabbit anti-L. lactis IgG (1 µg/well) followed by an HRP-conjugated goat anti-rabbit antibody (1:1000).
Statistical methods.
Two-group comparisons were performed by Student's t-test. Analyses were performed using Prism 4.0 (GraphPad). Two-tailed P values < 0.05 were considered statistically significant.