We describe a method for tracking the endomembrane rupture elicited by the intracellular bacteria Shigella flexneri and Mycobacterium tuberculosis upon host cell invasion. Our assay makes use of CCF4, a host cytoplasmic FRET probe in live or fixed cells. This reporter is degraded by an enzyme activity present on the bacterial surface.
Shigella flexneri are pathogenic bacteria that invade host cells entering into an endocytic vacuole. Subsequently, the rupture of this membrane-enclosed compartment allows bacteria to move within the cytosol, proliferate and further invade neighboring cells. Mycobacterium tuberculosis is phagocytosed by immune cells, and has recently been shown to rupture phagosomal membrane in macrophages. We developed a robust assay for tracking phagosomal membrane disruption after host cell entry of Shigella flexneri or Mycobacterium tuberculosis. The approach makes use of CCF4, a FRET reporter sensitive to β-lactamase that equilibrates in the cytosol of host cells. Upon invasion of host cells by bacterial pathogens, the probe remains intact as long as the bacteria reside in membrane-enclosed compartments. After disruption of the vacuole, β-lactamase activity on the surface of the intracellular pathogen cleaves CCF4 instantly leading to a loss of FRET signal and switching its emission spectrum. This robust ratiometric assay yields accurate information about the timing of vacuolar rupture induced by the invading bacteria, and it can be coupled to automated microscopy and image processing by specialized algorithms for the detection of the emission signals of the FRET donor and acceptor. Further, it allows investigating the dynamics of vacuolar disruption elicited by intracellular bacteria in real time in single cells. Finally, it is perfectly suited for high-throughput analysis with a spatio-temporal resolution exceeding previous methods. Here, we provide the experimental details of exemplary protocols for the CCF4 vacuolar rupture assay on HeLa cells and THP-1 macrophages for time-lapse experiments or end points experiments using Shigella flexneri as well as multiple mycobacterial strains such as Mycobacterium marinum, Mycobacterium bovis, and Mycobacterium tuberculosis.
Numerous bacterial pathogens are internalized in membrane-enclosed compartments of eukaryotic cells during their course of infection. Cell entry occurs either through phagocytosis by specialized host cells, as is the case for Mycobacterium tuberculosis that are ingested by macrophages, or the pathogens actively induce their uptake into typically non-phagocytic cells. In the case of induced uptake, for example for Shigella flexneri, the pathogen injects effector proteins into the host cytosol that hijack among other cell functions the tightly regulated endomembrane sorting machinery resulting in bacterial localization within an endosomal compartment 1,2. Subsequently, Shigella disrupts the enclosing membrane leading to vacuolar rupture and cytosolic access of the pathogen interfering with host membrane trafficking and avoiding delivery to the lysosome. More recently, phagolysosomal rupture has also been found as infection strategy used by Mycobacterium tuberculosis, a pathogen that was thought for a long time to be exclusively localized within a membrane-bound compartment 3,17.
To investigate dynamics of subcellular membrane trafficking of invasive pathogens, great improvements have been achieved since the transmission electron microscopy (TEM) based studies of the late 1980s 4,5. For example, fluorescence microscopy based methods using dyes, antibodies against bacterial surface components, or markers for co-localization with subcellular compartments took over 6,7. However, they still do not yield precise spatiotemporal resolution and robustness to measure vacuolar rupture by bacterial pathogens quantitatively.
This hurdle has been addressed with an assay based on the cephalosporin derived CCF4-AM FRET reporter that was first used to study gene expression 8. Then, it was used in the context of infection biology to investigate effector secretion and to follow the uptake of Neisseria into host cells 9,10,11. We developed an assay taking advantage of this reporter for studying vacuolar rupture induced by Shigella flexneri 12 and Mycobacterium tuberculosis17. The principle of our method is described in Figure 1 using Shigella flexneri. First, host cells are loaded with the FRET CCF4-AM substrate that is trapped inside the cytoplasm after cleaving off the AM ester moieties. Then, cells are infected with Shigella flexneri. β-lactamase present on the surface of the bacteria is able to cleave the CCF4 substrate as soon as vacuolar rupture occurs. This leads to a loss of FRET signal switching the emission peak from 535 nm to 450 nm upon excitation of the probe at 405 nm. The ratiometric measurement of the 450/535 nm intensities highlights vacuolar integrity: low ratios reflect membrane-enclosed or extracellular bacteria whereas high ratios reflect contact between the bacteria and the host cytosol. We also report an adaptation of this method for studying phagosomal rupture induced by Mycobacterium tuberculosis in THP-1 macrophages. The experimental principles remain the same although the sequence is reversed, CCF4-AM loading is applied only after bacterial infection.
Thus, by quantitative ratiometric fluorescence measurements at the single cell level, the vacuolar rupture of Shigella flexneri can be tracked in real time and in fixed samples from different cell types 12,13,14. Furthermore, this method can be adapted to a number of other invasive pathogens as shown in this study using Mycobacterium bovis and Mycobacterium tuberculosis. Finally, the miniaturization of our protocol to 96 well (or 384 well) formats allows screening of numerous conditions at high throughput.
The CCF4-AM/β-lactamase assay is a straightforward method to track vacuolar disruption induced by intracellular Shigella flexneri and mycobacteria in different cell types. It makes use of a lactamase sensitive cytoplasmic FRET reporter that is cleaved by an enzyme active on the surface of the bacteria.
Loss of the CCF4-AM substrate can easily be avoided by adding probenecid to all solutions after loading of the substrate. As demonstrated, the assay can be adapted to multiple cell types (epithelial cells, phagocytic cells) and formats (96 well, 35 mm glass bottom dishes, 6/12/24 well plates). For the use of the 6/12/24 well plate, sterile coverslips are distributed at the bottom of each well before seeding the cells. At the end of the experiment, coverslips are transferred on slides in mounting medium, such as Prolong Gold Antifade Reagent (Invitrogen). This way the signal is stable for longer time periods after the assay compared to the 96 wells format where samples are preserved in PBS after fixation. The high cost of the CCF4-AM substrate should be taken into account before determination of the sample volume. This is why we recommend scaling them down. Experiments are more expensive in 6/12/24 well format but the signals are stable for days. On the contrary, experiments are cheaper in the 96 well format, but samples have to be analyzed on the day of the experiment. It is noteworthy that live experiments can also be performed at the 96 well or 384 well format. This allows performing live experiment using dozens of conditions at the same time (mutant bacteria, MOI, plasmid or siRNA transfection, chemicals etc.) with numbers of positions per well. Although suited for Shigella flexneri, we highlight that “true” real time or time-lapse experiments are not feasible for mycobacteria studies since the infection cycle exceeds measurable concentrations of CCF4 that can be retained in the cytosol. For this reason, the CCF4-AM substrate is applied on cells only after invasion is achieved.
In case MetaMorph software is used for the acquisition and analysis, we recommend using the module “screen acquisition” that allows acquiring an entire 96/384 well plate with a specified number of pictures per well. Further, the module “review screen data” allows (i) visualizing the stitched picture mosaic of each well for any channel at the same time on a big “poster” and (ii) looping a specialized algorithm for measuring the intensities in the 535 and the 450 nm channels. Even though, we have been able to measure vacuolar rupture by single bacteria using time-lapse microscopy, we would like to caution that the enzymatic activity on the surface of individual bacteria varies rendering it difficult to precisely correlate number of intracellular bacteria and effectiveness of vacuolar rupture.
Given the robustness of the assay, it is suited for high throughput approaches in 96 or 384 well formats. We also have successfully adapted this protocol for FACS analysis to study the infection of cells in suspension 16. The assay can also be used for the investigation of other bacteria or carriers presenting lactamase on their surface, leading to a wide range of applications. For example, this approach can be used to study vacuolar rupture induced by other pathogens such as β-lactamase expressing Legionella pneumophila, Listeria monocytogenes or Salmonella typhimurium 12. Since Listeria monocytogenes has a short infection cycle comparable to Shigella flexneri, time-lapse experiments are possible. In contrast, because Legionella pneumophila and Salmonella typhimurium display long infection cycles, we suggest to perform end point experiments.
The variety of possible applications makes the CCF4-AM/β-lactamase assay an interesting fluorometric method for tracking vacuolar rupture induced by intracellular pathogens in fixed samples or in real time.
The authors have nothing to disclose.
This work was funded by the Agence Nationale pour la Recherche and by the European Research Council.
Name of the reagent | Company | Catalogue number | Comments (optional) |
LiveBlazer FRET-B/G Loading Kit (CCF4-AM) | Invitrogen | K1089 | Protect from light, stock in – 80 ° aliquots |
Draq5 | Biostatus | DR50050 | |
Poly-L-lysine | Sigma | P9155 | |
μCLEAR-PLATE, BLACK, 96 well | Greiner Bio-One | 655090 | |
35 mm glass bottom dishes | MatTek corp. | P35G-1.5-10-C | |
Probenecid | Sigma | P8761 | |
β-lactamase | Sigma | P0389 |