4.1. Materials and Reagents
Reagents 2-amino-2-(hydroxymethyl)-1,3-propanediol hydrochloride (Tris-HCl), Triton X-100, Ethylenediaminetetraacetic acid disodium salt dihydrate (EDTA), sodium chloride (NaCl), and agarose low gelling temperature were purchased from Sigma-Aldrich (Bornem, Belgium). Formamide and 5-Cyano-2,3-ditolyl tetrazolium chloride (CTC) were obtained from VWR International. Tryptic soy agar (TSA), Tryptic soy broth (TSB), and Plate count agar (PCA) were purchased from Merck Millipore (Madrid, Spain). The NAM sequence was acquired from EUROGENTEC (Seraing, BELGIUM).
4.2. NAM Sequence
The sequence 5'6-FAM/lT*mG*mC*lC*mU*mC*lC*mC*mG*lT*mA*mG*lG*mA, where (FAM) represents fluorescein, l stands for LNA, m for 2´-OMe and * for PS internucleotide linkages, was used for this study. The sequence was complementary to a conserved 16S rRNA sequence in the domain Eubacteria 5. A stock solution of 500 µM was prepared in sterile ultrapure water and further diluted to 4 μM stock solutions. All stock aliquots were stored at -20 °C. The final concentration of 2 μM was achieved by diluting the 4 μM stock solution in hybridization solution (20% (v/v) formamide, 900 mM NaCl, 5 mM EDTA, 0.1% (v/v) Triton X-100, and 50 mM Tris-HCl) 5,44 and stored at 4 °C until use.
4.3. Bacterial Strains and Culture Conditions
Experiments were performed using E. coli JM109 (DE3) (Promega, Madison, USA) and E. coli K-12 MG1655. E. coli JM109 harboured the plasmid pFM23 for enhanced green fluorescent protein (eGFP) expression. This plasmid contained a kanamycin resistance gene for selection of plasmid containing bacteria 45. E. coli K-12 was cultivated on TSA 46, while E. coli JM109 was cultivated on PCA with kanamycin (20 µg/mL) 47. Both strains were grown overnight in TSB until the start of the stationary phase. E. coli K-12 was grown at 37 °C, whereas E. coli JM109 was grown at 30 °C, the optimal temperature for GFP internalization 48. Optical density (OD) at 600 nm was measured to guarantee that experiments would start with a similar initial concentration of bacterial cells (2.50E+10 CFU/mL).
Additionally, 1 mL of E. coli JM109 inoculum was centrifuged for 15 min at 16800 rcf in an Eppendorf Centrifuge 5418, and the bacterial pellet resuspended in fresh media. Two µL of 30 µg/mL cephalexin were added to the bacterial suspension of E. coli JM109, allowing it to grow for another 2 hours. Cephalexin, an antibiotic that blocks septation, elongates the cells, providing a larger non-bleached region that should contribute to fluorescence recovery after bleaching in the ROI and minimize overall photobleaching of the cell in FRAP experiments (described further ahead). The same antibiotic was not used for E. coli K-12 cells in the NAMs' diffusion assays to avoid compromising the wild-type bacterial envelope structure which could lead to an overestimation of NAMs diffusion. Finally, the inoculum of both strains was centrifuged for 15 min at 16800 rcf and the pellet resuspended in sterile NaCl saline solution at 0.15 M, corresponding to an osmolality of 300 mOsm (calculated by multiplying the sodium and potassium concentration by 2).
CTC was used to determine the respiratory activity of bacteria. CTC is a soluble crystal dye that competes with the final acceptor in the electron transport system. Respiring bacteria placed in CTC solution will take up the CTC and reduce it to insoluble formazan, which accumulates in the cells. On the other hand, dead or inactive cells show no accumulation of CTC formazan. To check for viability, 100 μL of 50 mM CTC were added to the saline bacterial suspension, gently vortexed and incubated for 30 minutes at 37 °C, protected from light.
4.4. Microslide Preparation
Agarose pads were prepared to function as bacterial traps and allow visualization of live bacterial cells without fixation. The solution was prepared by dissolving 2% low-melt agarose (w/v) in water. Thereafter, 60 μL were added on top of a glass slide and allowed to solidify at room temperature to a height of approximately one coverslip's thickness. A 5 μL drop of the saline bacterial suspension was then added onto the agarose pad. A coverslip was placed on top to spread the solution over the pad and left for 30 minutes for the bacteria to be immobilized in the agarose.
For the NAMs diffusion assays, the coverslip was removed, and a 5 μL drop of the 2 μM FAM-NAMs in hybridization solution was added to the agarose pad with trapped bacteria. This concentration of NAMs allows for a large surplus of probes when compared to the number of ribosomes in the cell 42. Cells in saline without the addition of NAMs served as negative control for autofluorescence. The samples were immediately visualized under a confocal microscope.
4.5. FRAP Microscope Setup
FRAP was performed on a Leica TCS SP8 confocal laser scanning inverted microscope equipped with an Argon Laser to measure the cytoplasmic DCs of eGFP and the 14-mer NAM. The sample was imaged with a PL APO 63x /1.40 oil-immersion objective and a pinhole of 1.0 Airy-disk units. The fluorophore or eGFP was excited using a 488 nm laser at 2% intensity, a speed of 1400 Hz, and a line average of 1 or 4 for E. coli JM109 expressing eGFP or E. coli K-12 cells, respectively. The microscope was enclosed in an environmental chamber and equipped with temperature control. The experiments with JM109 were performed at 30 °C, while those using K-12 were conducted at 37 °C, matching the bacterial growth temperatures. The same setup was used for the visualization of CTC-stained cells.
The ROI for FRAP was defined on one of the poles of the cell to ensure sufficient distance between the bleached region and the opposing pole. This arrangement reduces the effect of the intense bleaching laser on the fluorescent molecules in the latter area, facilitating subsequent fluorescence recovery. Five pre-bleaching images were taken, followed by a bleaching cycle of 10 frames with the 488 nm laser at 100% intensity, and 100 post-bleach images. Brightfield images were captured to identify the cells in which NAMs successfully internalised. FRAP movies were cropped using FIJI 49 to obtain individual movies for each cell, which were then analysed with PyFRAP 30 to derive the DCs.
4.6. PYFRAP Analysis
PyFRAP takes the first pre-bleach image and either perceives the cell in a two-dimensional (2D) geometry or interpolates it onto a three-dimensional (3D) mesh approximating the shape of the cell for numerical simulations of fluorescence recovery. The software also automatically detects the bleached area (i.e., the ROI).
4.6.1. Image analysis
Bacteria boundaries were automatically detected using Otsu thresholding 50, allowing for exact reinternalization of the bacterial geometry. Bleached ROIs were defined manually for each particular movie. After defining the ROIs, intensities were averaged across each ROI per timepoint:
Where r is the ROI of interest, and I(t,i) the intensity at pixel i and time t.
4.6.2. Fluorescence stability
To calculate the accurate DC of NAMs and ensure fluorescence stability, a pre-selection of datasets had to be undertaken. For this, cells were imaged in the same conditions described in the previous sections but skipping the bleaching step. Relative differences between maximum and minimum measured intensities for each dataset (d) were defined as:
Equation 1
where Ir (t) is the mean intensity in the ROI r at time t, t0 is the time of experiment start and T the final time point of the experiment.
Moreover, the mean relative intensity between start and end of the experiment (d ̃(r)) is given by:
Equation 2
Here, r represents a specific ROI, such as the complete bacterial cell or the bleached area, Δt denotes the time between two recorded frames, and n is the number of frames used to compute the means. Essentially, the mean intensity in a ROI over the last n = 20 timesteps is divided by the mean intensity in the first n time steps. Finally, 1 is subtracted from the results to extract the relative change. Values smaller than 0 indicate a decrease in fluorescence intensity at the end compared to the start of the experiment, while values larger than 0 suggest an increase in fluorescence over time. To further test if the data showed any significant trends, a Kwiatkowski-Phillips-Schmidt-Shin (KPSS) test was applied to each dataset 51.
4.6.3. 3D geometrical model interpolation
To accurately estimate diffusion in a 3D geometry, we approximated the bacteria as 3D ovals. For that, we used the 2D boundary estimated using Otsu thresholding and assumed the diameter of the bacteria to be equal the maximum width of the bacteria.
4.6.4. Fitting models and geometry for FRAP datasets
We simulated both the 2D as well as the 3D geometry using reaction-diffusion models. To obtain a good approximation of the initial state of bleaching, we applied the first image of the post-bleach movie as the initial condition onto the 2D or 3D mesh. Since the bleached region experiences the largest dynamics during a FRAP experiment, we refined the mesh using an attractor mesh centered around the center of mass of the bleached area. We chose a finite element size ranging from 0.07 µm2 to 0.34 µm2 and ca. 0.4 µm3 to 1.6 µm3 for the 2D and 3D mesh, respectively. The attractor then refined the mesh down to 25% of finite element size in the bleached area, resulting in average 2788 and 1515 finite elements for the 2D and 3D geometries, respectively.
Simulation results were fitted using a constrained Nelder-Mead algorithm. To mimic continuous internalisation of the fluorescent NAMs or loss of fluorescence due to efflux, we fitted additional models adding a linear influx and/or exponential efflux term, adding to the diffusion model, ultimately resulting in four distinct models. We forced the model to capture both the recovery process as well as the overall intensity in the cell by fitting both the simulation results in the bleached area and complete cell to the image intensities.