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5.3.1 Infection of cells

Cells were seeded one day or few hours before infection. One colony of pathogenic S.aureus is grown in 1ml TSB medium overnight at 37°C. Prior to infection, bacteria are diluted 1:10 in fresh TSB medium and incubated for another 2 h to obtain bacteria in the logarithmic growth state minimizing toxin production.

After culture, bacteria are washed twice with PBS. For some experiments, bacteria are incubated with fluorescent dyes or fibronectin for 30 min to 1h at 37°C. Following this incubation, bacteria are washed three times again in PBS. The number of bacteria is photometrically determined at OD600 using a standard curve. Cells are infected at proper MOIs (for FACS or microscopic analysis: MOI 30, for gentamicin protection assay: MOI 20) depending on the experiment.

5.3.2 Gentamicin Protection Assay

2x105 HEK293T cells or 5x104 MEFs or 5x104 HeLa cells are seeded in 10μg/ml poly-lysine coated 24-well plates and infected at MOI 20 for 2 h at 37°C and 5% CO2. 2h later, to evaluate the number of intracellular bacteria, the medium is carefully removed and replaced by fresh medium containing 50 μg/ml gentamicin. After incubation for 1 h at 37°C, intracellular bacteria are released by treatment of 0.5% saponin for 15 min at 37°C. Samples are gradiently diluted (for S.aureus, first dilution: 100μl bacteria suspension in 900μl PBS; second dilution: 100μl of first dilution in 900μl PBS) and

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20μl suspension from second dilution is plated on TSB agar plates to determine the recovered colony forming units (cfu). Simultaneously, the parallel infected cells are directly lysed with 0.5% saponin without Gentamicin treatment and gradiently diluted (for S.aureus, first dilution: 40μl bacteria suspension in 960μl PBS; second dilution:

100μl of first dilution in 900μl PBS) and 20μl suspension from second dilution is plated on TSB agar plates to quantify cell adherent bacteria.

5.3.3 Extra- and intracellular bacteria staining and fluorescence microscopy examination

For PIP5KIγ90–/–and control MEF cells, 3 × 104 cells for each cell line are seeded on 10μg/ml poly-L-lysine coated, acid-washed glass cover slips in 24-well plate. Next day, cells are infected with S.aureus at MOI 30 for 2 h, then washed twice with PBS+/+ and fixed with 4% PFA for 20 min at RT. After this, cells are incubated in blocking buffer (PBS+/+ plus 10% FCS) for 10 min. Extracellular bacteria are detected by rabbit polyclonal α-staphylococcal serum diluted in blocking buffer (45 min at RT).

Afterwards, samples are washed three times with PBS+/+ and incubated with goat α-rabbit IgG-Cy5 in the dark for 30 min. Then, cells are washed three times and permeabilized by 0.5% Triton/PBS. 10 min later, cells are washed three times with PBS+/+, blocked for 10 min, and incubated with rabbit polyclonal α-staphylococcal serum at RT. 45min later, samples are washed three times with PBS+/+ and incubated with goat α-rabbit IgG coupled to Cy2 in the dark for 30 min. Finally, after three washes with PBS+/+, the cover slips are embedded in mounting medium (DaKo, Glostrup, Denmark) on glass slides and sealed with nail polish. Images are acquired with Leica

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AF6000LX fluorescence microscope and processed with ImageJ.

For the experiment performed with HEK293T cells, 2 x 105 transfected 293cells are seeded on poly-L-lysine coated cover slips in 24-well plate. 2 hours later, cells are infected with pacific-blue stained and biotin-labeled S.aureus at MOI 30 for 2 h, then washed twice with PBS+/+ and fixed with 4% PFA for 20 min at RT. After this, cells are incubated in blocking solution for 10min, afterwards, cells are incubated with streptavidin-AlexaFluor647 for 1h at RT in the dark. Finally, after three washes with PBS+/+, the cover slips are transferred to glass slides, embedded in mounting medium and sealed with nail polish. Images were acquired with Leica AF6000LX fluorescence microscope.

For immunofluorescence staining of transfected PIP5KIγ90–/– orNIH3T3 SYNJ1 KO cells, 5 × 104 cells are seeded on poly-L-lysine coated cover slips in 24-well plate. Next day, cells are transfected with indicated plasmid DNA. 24h or 48h after transfection, cells were infected with pacific-blue stained and biotin-labeled S.aureus at MOI 30 for 2 h. After the infection, the same staining procedure as described above for the transfected 293 cells was used.

5.3.4 Invasion assay by flow cytometry

This method is based on the paper from Hauck lab (Pils, Stefan, et al. 2006). 1x106 HEK293T cells or 2 x105 NIH3T3 cells are seeded in poly-lysine coated wells of 6-well plate. One colony of S.aureus is cultured in 1ml TSB medium overnight. Next day, Bacterial culture is transferred to 9ml fresh TSB medium and cultured for another 2h.

Afterwards, S.aureus is stained with FITC and the OD600 is measured. Cells are

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infected at MOI30 and incubated for 2h at 37°C. After 2h infection, medium is aspirated and cells are washed once with PBS. 1ml Trypsin/EDTA is added to each well and incubated for 2min at 37°C. 3ml fresh cell culture medium is added to stop trypsinization and cells are separated via pipetting up and down several times. Then, cells are transferred into 15ml tubes and centrifuged. The cell pellet is re-suspended in 1ml ice cold FACS buffer and transferred to 1.5 ml Eppendorf tubes, then washed twice again. The cells are re-suspended in 1ml FACS buffer and distributed to 2 FACS tubes (one tube 600μl and the other 400μl) and placed on ice, under dark. The samples containing 600μl cell suspension are measured by Flow cytometry. To quench the fluorescence from adhering bacteria on cell surface, 400μl trypan blue is added and the signal is measured again. The fluorescence intensity is analyzed to compare the invasion efficiency.

5.3.5 live-cell imaging

Cells are seeded in poly-lysine coated 3.5cm dishes (with integrated coverslip), eg. 1 x 105 cells/dish. Next day, exchange of DMEM medium with colorless DMEM and preparation of the CLSM (heating of incubation chamber to 37°C and connection of CO2 supply) followed. If bacterial infection is investigated, cells are directly infected with the fluorescence stained S.aureus at MOI60. First of all, appropriate cells are searched (for example, the transfected cells). Then the settings are adjusted and finally the movie is started to record. Afterwards, images and movies are analyzed by LAS software and Image J.

5.3.6 Scanning-Electron-Microscopy (SEM)

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Cells are seeded on poly-lysine coated coverslips in a 24-well plate (3 x 104 cells/well).

Next day, cells are infected at MOI 50. Subsequently cells are fixed with SEM fixation solution for 1h at RT. Afterwards samples are gradually dehydrated via an ethanol dilution range. The critical point drying by liquid CO2 followed and samples are sputtered with 10 nm gold-palladium. Samples are analyzed by a Philips SEM 505.

5.3.7 Measurement of FAK phosphorylation upon S.aureus infection

Cells are starved in starvation medium (DMEM plus 0.5% FCS) overnight. Next day, cells are detached by Trypsin/EDTA and the trypsinization is stopped via the addition of trypsin inhibitor. After centrifugation, cells are re-suspended in suspension medium (DMEM plus 0.25% BAS) and further incubated for 45min at 37°C. Meanwhile, 6 cm dishes are coated with poly-lysine for 45min and later blocked by suspension medium for another 45min, afterwards, 2 x 106 cells are seeded in each coated dish and incubated for 45min to let cells attach. Then cells are infected with 2μg/ml Fn coated bacteria at MOI 100for indicated time. Whole cell lysate is prepared with the modified RIPA buffer and FAK phosphorylation is analyzed via western blotting.

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