PS is a recipient of the Bill and Melinda Gates Grand Challenge Grant OPP1141322. PV was supported by a Swiss National Science Foundation Early Postdoc Mobility fellowship and a Roux-Cantarini postdoctoral fellowship. PJS is supported by an HHMI grant and ERC-2013-ADG 339579-Decrypt.

<ol>
	<li>Reineke, L. C., Lloyd, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diversion+of+stress+granules+and+P-bodies+during+viral+infection.">Diversion of stress granules and P-bodies during viral infection.</a> Virology. 436 (2), 255-267 (2013).</li><li>Kedersha, N., Ivanov, P., Anderson, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stress+granules+and+cell+signaling:+more+than+just+a+passing+phase.">Stress granules and cell signaling: more than just a passing phase.</a> Trends Biochem Sci. 38 (10), 494-506 (2013).</li><li>Vonaesch, P., Campbell-Valois, F. -. X., Dufour, A., Sansonetti, P. J., Schnupf, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Shigella+flexneri+modulates+stress+granule+composition+and+inhibits+stress+granule+aggregation.">Shigella flexneri modulates stress granule composition and inhibits stress granule aggregation.</a> Cell Microbiol. 18 (7), 982-997 (2016).</li><li>Kolobova, E., Efimov, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microtubule-dependent+association+of+AKAP350A+and+CCAR1+with+RNA+stress+granules.">Microtubule-dependent association of AKAP350A and CCAR1 with RNA stress granules.</a> Exp Cell Res. 315 (3), 542-555 (2009).</li><li>Anderson, P., Kedersha, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stress+granules:+the+Tao+of+RNA+triage.">Stress granules: the Tao of RNA triage.</a> Trends in biochemical sciences. 33 (3), 141-150 (2008).</li><li>Anderson, P., Kedersha, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stressful+initiations.">Stressful initiations.</a> J Cell Sci. 115, 3227-3234 (2002).</li><li>Mohr, I., Sonenberg, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Host+translation+at+the+nexus+of+infection+and+immunity.">Host translation at the nexus of infection and immunity.</a> Cell Host Microbe. 12 (4), 470-483 (2012).</li><li>Hu, S., Claud, E. C., Musch, M. W., Chang, E. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stress+granule+formation+mediates+the+inhibition+of+colonic+Hsp70+translation+by+interferon-+and+tumor+necrosis+factor.">Stress granule formation mediates the inhibition of colonic Hsp70 translation by interferon- and tumor necrosis factor.</a> Am J Physiol Gastointest Liver Physiol. 298 (4), 481-492 (2010).</li><li>Barry, E. M., Pasetti, M. F., Sztein, M. B., Fasano, A., Kotloff, K. L., Levine, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Progress+and+pitfalls+in+Shigella+vaccine+research.">Progress and pitfalls in Shigella vaccine research.</a> Nat Rev Gastroenterol Hepatol. 10 (4), 245-255 (2013).</li><li>Lanata, C. F., Fischer-Walker, C. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Global+Causes+of+Diarrheal+Disease+Mortality+in+Children.">Global Causes of Diarrheal Disease Mortality in Children.</a> PloS One. 8 (9), 72788 (2013).</li><li>Ashida, H., Ogawa, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Shigella+deploy+multiple+countermeasures+against+host+innate+immune+responses.">Shigella deploy multiple countermeasures against host innate immune responses.</a> Curr Opin Microbiol. 14 (1), 16-23 (2011).</li><li>Ashida, H., Ogawa, M., Mimuro, H., Kobayashi, T., Sanada, T., Sasakawa, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Shigella+are+versatile+mucosal+pathogens+that+circumvent+the+host+innate+immune+system.">Shigella are versatile mucosal pathogens that circumvent the host innate immune system.</a> Curr Opin Immunol. 23 (4), 448-455 (2011).</li><li>Kedersha, N., Anderson, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mammalian+stress+granules+and+processing+bodies.">Mammalian stress granules and processing bodies.</a> Methods Enzymol. 431, 61-81 (2007).</li><li>Ray, K., Marteyn, B., Sansonetti, P. J., Tang, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Life+on+the+inside:+the+intracellular+lifestyle+of+cytosolic+bacteria.">Life on the inside: the intracellular lifestyle of cytosolic bacteria.</a> Nat Re. Micro. 7 (5), 333-340 (2009).</li></ol>

The authors have nothing to disclose.

The protocol outlined here describes the induction, localization, and analysis of SGs in non-infected cells and cells infected with the cytosolic pathogen S. flexneri in the presence or absence of exogenous stress. Using free imaging software, the protocols allows for the precise qualitative and quantitative analysis of SG formation to identify and statistically address differences in given phenotypes.
There are several critical steps within the protocol for the infection, SG-inductio...

Visualizing host-pathogen interactions on a cellular level is a powerful method for gaining insights into pathogenic strategies and for identifying key cellular pathways. Indeed, pathogens can be used as tools to pinpoint important cellular targets or structures, as pathogens have evolved to subvert central cellular processes as a strategy for their own survival or propagation. Visualization of cellular components can be achieved by recombinantly expressing fluorescently-tagged host proteins. While this allows for real-time analysis, the generation of cell lines with specifically-tagged host proteins is highly laborious and may result in undesirable side effects. More convenient is the detection of cellular factors using specific antibodies, because multiple host factors can be analyzed simultaneously and one is not limited to a particular cell type. A drawback is that only a static view can be captured as immunofluorescence analysis necessitates host cell fixation. However, an important advantage of immunofluorescence imaging is that it readily lends itself to both qualitative and quantitative analysis. This in turn can be used to obtain statistically significant differences to provide new insights into host-pathogen interactions.
Fluorescent image analysis programs are powerful analytical tools for performing 3D and 4D analysis. However, the high cost of software and its maintenance make methods based on free open source software more widely attractive. Careful image analysis using bio-analysis software is valuable as it substantiates visual analysis and, when assigning statistical significances, increases confidence in the correctness of a given phenotype. Previously, SGs have been analyzed using the free ImageJ software, which necessitates the manual identification of individual SGs4. Here we provide a protocol for the induction and analysis of cellular SG formation in the context of bacterial infections using the free open source bio-image analysis software ICY (http://icy.bioimageanalysis.org). The bio-image analysis software has a built-in spot detector program that is highly suitable for SG analysis. It allows the fine-tuning of the automated detection process in specified Regions Of Interest (ROIs). This overcomes the need for manual analysis of individual SGs and removes sampling bias.
Many environmental stresses induce the formation of SGs, which are phase dense cytosolic, non-membranous structures of 0.2 - 5 &#181;m in diameter5,6. This cellular response is evolutionarily conserved in yeast, plants and mammals and occurs when global protein translation is inhibited. It involves aggregation of stalled translation initiation complexes into SGs, which are considered holding places for translationally-inactive mRNAs, allowing selective translation of a subset of cellular mRNAs. Upon removal of the stress, SGs dissolve and global rates of protein synthesis resume. SGs are composed of translation elongation initiation factors, proteins involved in RNA metabolism, RNA-binding proteins, as well as scaffolding proteins and factors involved in host cell signaling2, although the exact composition can vary depending on the stress applied. Environmental factors that induce SG formation include amino acid starvation, UV irradiation, heat shock, osmotic shock, endoplasmic reticulum stress, hypoxia and viral infection2,7,8. Much progress has been made in understanding how viruses induce and also subvert SG formation, while little is still known about how other pathogens, such as bacterial, fungal or protozoan pathogens, affect this cellular stress response1,7.
Shigella flexneri is a gram-negative facultative cytosolic pathogen of humans and the causative agent of severe diarrhea or shigellosis. Shigellosis is a major public health burden and leads to 28,000 deaths annually in children under 5 years of age9,10. S. flexneri infects the colonic epithelium and spreads cell-to-cell by hijacking the host&#39;s cytoskeletal components11,12. Infection of the epithelium supports the replication of S. flexneri within the cytosol but infected macrophages die through an inflammatory cell death process called pyroptosis. Infection leads to a massive recruitment of neutrophils and severe inflammation that is accompanied by heat, oxidative stress and tissue destruction. Thus, while infected cells are subject to internal stresses induced by infection, such as Golgi disruption, genotoxic stress and cytoskeletal rearrangements, infected cells are also subjected to environmental stresses due to the inflammatory process.
Characterization of the effect of S. flexneri infection on the ability of cells to respond to environmental stresses using a number of SG markers has demonstrated that infection leads to qualitative and quantitative differences in SG composition3. However, little is known about other bacterial pathogens. Here we describe a methodology for the infection of host cells with the cytosolic pathogen S. flexneri, the stressing of cells with different environmental stresses, the labeling of SG components, and the qualitative and quantitative analysis of SG formation and composition in the context of infected and non-infected cells. This method is widely applicable to other bacterial pathogens. In addition, the image analysis of the SG formation may be used for infections by viruses or other pathogens. It can be used to analyze SG formation upon infection or the effect of infection on SG formation in response to exogenous stresses.

<table border="0" cellpadding="0" cellspacing="0" width="1191">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:232px;">Primary Antibodies</td>
			<td style="width:211px;"></td>
			<td style="width:76px;"></td>
			<td style="width:672px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">eIF3b (N20), origin goat </td>
			<td>Santa Cruz</td>
			<td>sc-16377</td>
			<td>Robust and widely used SG marker. Cytosolic staining allows cell delineation. Dilution 1 in 300</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">eIF3b (A20), origin goat </td>
			<td>Santa Cruz</td>
			<td>sc-16378</td>
			<td>Same target as eIF3b (N20) and in our hands was identical to eIF3b (N20). Dilution 1 in 300</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">eIF3A (D51F4), origin rabbit (MC: monoclonal)</td>
			<td>Cell Signaling</td>
			<td>3411</td>
			<td>Part of multiprotein eIF3 complex with eIF3b . Dilution 1 in 800</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">eIF4AI, origin goat </td>
			<td>Santa Cruz</td>
			<td>sc-14211</td>
			<td>Recommended by (Ref # 13). Dilution 1 in 200</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">eIF4B, origin rabbit</td>
			<td>Abcam</td>
			<td>ab186856</td>
			<td>Good stress granule marker in our hands. Dilution 1 in 300</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">eIF4B, origin rabbit</td>
			<td>Cell Signaling</td>
			<td>3592</td>
			<td>Recommended by Ref # 13. Dilution 1 in 100</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">eIF4G, origin rabbit</td>
			<td>Santa Cruz</td>
			<td>sc-11373</td>
			<td>Widely used SG marker. (Ref # 13): may not work well in mouse cell lines. Dilution 1 in 300</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">G3BP1, origin rabbit (MC: monoclonal)</td>
			<td>BD Biosciences</td>
			<td>611126</td>
			<td>Widely used SG marker. Dilution 1 in 300</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Tia-1, origin goat </td>
			<td>Santa Cruz</td>
			<td>sc-1751</td>
			<td>Widely used SG marker. Can also be found in P bodies when SG are present (Ref # 13). Dilution 1 in 300</td>
		</tr>
		<tr height="21">
			<td colspan="2" height="21" style="height:21px;">Alexa-conjugated Secondary Antibodies</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">A488 anti-goat , origin donkey</td>
			<td>Thermo Fisher</td>
			<td>A-11055</td>
			<td>Cross absorbed. Dilution 1 in 500</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">A568 anti-goat, origin donkey</td>
			<td>Thermo Fisher</td>
			<td>A-11057</td>
			<td>Cross absorbed. Dilution 1 in 500</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">A488 anti-mouse, origin donkey</td>
			<td>Thermo Fisher</td>
			<td>A-21202</td>
			<td>Dilution 1 in 500</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">A568 anti-mouse, origin donkey</td>
			<td>Thermo Fisher</td>
			<td>A10037</td>
			<td>Dilution 1 in 500</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">A647 anti-mouse, origin donkey</td>
			<td>Thermo Fisher</td>
			<td>A31571</td>
			<td>Dilution 1 in 500</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">A488 anti-rabbit, origin donkey</td>
			<td>Thermo Fisher</td>
			<td>A-21206</td>
			<td>Dilution 1 in 500</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">A568 anti-rabbit, origin donkey</td>
			<td>Thermo Fisher</td>
			<td>A10042</td>
			<td>Dilution 1 in 500</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Other Reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Shigella flexneri</td>
			<td></td>
			<td></td>
			<td>Available from various laboratories by request</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Tryptone Casein Soya (TCS) broth</td>
			<td>BD Biosciences</td>
			<td>211825</td>
			<td>Standard growth medium for Shigella, application - bacterial growth</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TCS agar</td>
			<td>BD Biosciences</td>
			<td>236950</td>
			<td>Standard growth agar for Shigella, application - bacterial growth</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Congo red</td>
			<td>SERVA Electrophoresis GmbH</td>
			<td>27215.01</td>
			<td>Distrimination tool for Shigell that have lost the virulence plasmid, application - bacterial growth</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Poly L lysine</td>
			<td>Sigma-Aldrich</td>
			<td>P1274</td>
			<td>Useful to coating bacteria to increase infection, application - infection</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Gentamicin</td>
			<td>Sigma-Aldrich</td>
			<td>G1397</td>
			<td>Selective killing of extracellular but not cytosolic bacteria, application - infection</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HEPES</td>
			<td>Life Technologies</td>
			<td>15630-056</td>
			<td>PH buffer useful when cells are incubated at room-temperature, application - cell culture</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DMEM</td>
			<td>Life Technologies</td>
			<td>31885</td>
			<td>Standard culture medium for HeLa cells, application - cell culture</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fetal calf serum</td>
			<td>Biowest</td>
			<td>S1810-100</td>
			<td>5% supplementation used for HeLa cell culture medium, application - cell culture</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Non-essential amino acids</td>
			<td>Life Technologies</td>
			<td>11140</td>
			<td>1/100 dilution used for HeLa cell culture medium, application - cell culture</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DMSO</td>
			<td>Sigma-Aldrich</td>
			<td>D2650</td>
			<td>Reagent diluent, application - cell culture</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium arsenite</td>
			<td>Sigma-Aldrich</td>
			<td>S7400</td>
			<td>Potent stress granule inducer (Note: highly toxic, special handling and disposal required), application - stress inducer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Clotrimazole</td>
			<td>Sigma-Aldrich</td>
			<td>C6019</td>
			<td>Potent stress granule inducer (Note:health hazard, special handling and disposal required), application - stress inducer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PFA</td>
			<td>Electron Microscopy Scences</td>
			<td>15714</td>
			<td>4% PFA is used for standard fixation of cells, application - fixation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Triton X-100</td>
			<td>Sigma-Aldrich</td>
			<td>T8787</td>
			<td>Used at 0.03% for permeabilizationof host cells before immunofluorescent staining, application - permeabilization</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">A647-phalloidin</td>
			<td>Thermo Fisher</td>
			<td>A22287</td>
			<td>Dilution is at 1/40, best added during 2ary antibody staining, application - staining</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DAPI</td>
			<td>Sigma-Aldrich</td>
			<td>D9542</td>
			<td>Nucleid acid stain used to visualize both the host nucleus and bacteria, application - staining</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Parafilm</td>
			<td>Sigma-Aldrich</td>
			<td>BR701501</td>
			<td>Paraffin film useful for immunofluorescent staining of coverslips, application - staining</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Prolong Gold</td>
			<td>Thermo Fisher</td>
			<td>36930</td>
			<td>Robust mounting medium that works well for most fluorophores , application - mounting</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Mowiol</td>
			<td>Sigma-Aldrich</td>
			<td>81381</td>
			<td>Cheap and robust mounting medium that works well for most fluorophores, application - mounting</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">24-well cell culture plate</td>
			<td>Sigma-Aldrich</td>
			<td>CLS3527</td>
			<td>Standard tissue culture plates, application - cell culture</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">12-mm glass coverslips</td>
			<td>NeuVitro</td>
			<td>1001/12</td>
			<td>Cell culture support for immunofluorescent applications, application - cell support</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">forceps</td>
			<td>Sigma-Aldrich</td>
			<td>81381</td>
			<td>Cheap and obust mounting medium that works well for most fluorophores, application - mounting</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Programs and Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Prism</td>
			<td>GraphPad Software</td>
			<td></td>
			<td>Data analysisand graphing program with robust statistical test options, application - data analysis</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Leica SP5</td>
			<td>Leica Microsystems</td>
			<td></td>
			<td>Confocal microsope, application - image acquisition</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Imaris</td>
			<td>Bitplane</td>
			<td></td>
			<td>Professional image analysis program, application - data analysis</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Excel</td>
			<td>Microsoft</td>
			<td></td>
			<td>Data analysis and graphing program, application - data analysis</td>
		</tr>
	</tbody>
</table>

immunofluorescence analysis of stress granule formation after bacterial challenge of mammalian cells

Fluorescent imaging of cellular components is an effective tool to investigate host-pathogen interactions. Pathogens can affect many different features of infected cells, including organelle ultrastructure, cytoskeletal network organization, as well as cellular processes such as Stress Granule (SG) formation. The characterization of how pathogens subvert host processes is an important and integral part of the field of pathogenesis. While variable phenotypes may be readily visible, the precise analysis of the qualitative and quantitative differences in the cellular structures induced by pathogen challenge is essential for defining statistically significant differences between experimental and control samples. SG formation is an evolutionarily conserved stress response that leads to antiviral responses and has long been investigated using viral infections1. SG formation also affects signaling cascades and may have other still unknown consequences2. The characterization of this stress response to pathogens other than viruses, such as bacterial pathogens, is currently an emerging area of research3. For now, quantitative and qualitative analysis of SG formation is not yet routinely used, even in the viral systems. Here we describe a simple method for inducing and characterizing SG formation in uninfected cells and in cells infected with a cytosolic bacterial pathogen, which affects the formation of SGs in response to various exogenous stresses. Analysis of SG formation and composition is achieved by using a number of different SG markers and the spot detector plug-in of ICY, an open source image analysis tool.

To explain and demonstrate the protocol described in this manuscript, we characterized the image of clotrimazole-induced SGs in HeLa cells infected or not with the cytosolic pathogen S. flexneri. An outline of the procedure is presented in Figure 1, and includes virulent and avirulent S. flexneri streaked on Congo Red plates, bacteria preparation, infection, addition of environmental stress, sample fixation and staining, sample imaging and q...

Watch this Scientific Journal Video about Immunofluorescence Analysis of Stress Granule Formation After Bacterial Challenge of Mammalian Cells at JoVE.com

Immunofluorescence Analysis of Stress Granule Formation After Bacterial Challenge of Mammalian Cells

We describe a method for the qualitative and quantitative analysis of stress granule formation in mammalian cells after the cells are challenged with bacteria and a number of different stresses. This protocol can be applied to investigate the cellular stress granule response in a wide range of host-bacterial interactions.

Fluorescent imaging of cellular components is an effective tool to investigate host-pathogen interactions. Pathogens can affect many different features of ...

immunofluorescence-analysis-stress-granule-formation-after-bacterial

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Immunology and Infection

10.0K Views.  Institut Pasteur. We describe a method for the qualitative and quantitative analysis of stress granule formation in mammalian cells after the cells are challenged with bacteria and a number of different stresses. This protocol can be applied to investigate the cellular stress granule response in a wide range of host-bacterial interactions.

Video: Immunofluorescence Analysis of Stress Granule Formation After Bacterial Challenge of Mammalian Cells

Invasion of Human Cells by a Bacterial Pathogen

Here we will describe how we study the invasion of human endothelial cells by bacterial pathogen Staphylococcus aureus . The general protocol can be applied to the study of cell invasion by virtually any culturable bacterium. The stages at which specific aspects of invasion can be studied, such as the role of actin rearrangement or caveolae, will be highlighted. Host cells are grown in flasks and when ready for use are seeded into 24-well plates containing Thermanox coverslips. Using coverslips allows subsequent removal of the cells from the wells to reduce interference from serum proteins deposited onto the sides of the wells (to which S. aureus would attach). Bacteria are grown to the required density and washed to remove any secreted proteins (e.g. toxins). Coverslips with confluent layers of endothelial cells are transferred to new 24-well plates containing fresh culture medium before the addition of bacteria. Bacteria and cells are then incubated together for the required amount of time in 5% CO2 at 37&deg;C. For S. aureus this is typically between 15-90 minutes. Thermanox coverslips are removed from each well and dip-washed in PBS to remove unattached bacteria. If total associated bacteria (adherent and internalised) are to be quantified, coverslips are then placed in a fresh well containing 0.5% Triton X-100 in PBS. Gentle pipetting leads to complete cell lysis and bacteria are enumerated by serial dilution and plating onto agar. If the number of bacteria that have invaded the cells is needed, coverslips are added to wells containing 500 &mu;l tissue culture medium supplemented with gentamicin and incubation continued for 1 h, which will kill all external bacteria. Coverslips can then be washed, cells lysed and bacteria enumerated by plating onto agar as described above. If the experiment requires direct visualisation, coverslips can be fixed and stained for light, fluorescence or confocal microscopy or prepared for electron microscopy.

A general protocol for the study of invasion of host cells by a bacterial pathogen, focusing on Staphylococcus aureus and human endothelial cells.

Here we will describe how we study the invasion of human endothelial cells by bacterial pathogen Staphylococcus aureus . The general protocol can be ...

In Vitro Assay of Bacterial Adhesion onto Mammalian Epithelial Cells

To cause infections, bacteria must colonize their host. Bacterial pathogens express various molecules or structures able to promote attachment to host cells1. These adhesins rely on interactions with host cell surface receptors or soluble proteins acting as a bridge between bacteria and host. Adhesion is a critical first step prior to invasion and/or secretion of toxins, thus it is a key event to be studied in bacterial pathogenesis. Furthermore, adhered bacteria often induce exquisitely fine-tuned cellular responses, the studies of which have given birth to the field of 'cellular microbiology'2. Robust assays for bacterial adhesion on host cells and their invasion therefore play key roles in bacterial pathogenesis studies and have long been used in many pioneer laboratories3,4. These assays are now practiced by most laboratories working on bacterial pathogenesis.
Here, we describe a standard adherence assay illustrating the contribution of a specific adhesin. We use the Escherichia coli strain 27875, a human pathogenic strain expressing the autotransporter Adhesin Involved in Diffuse Adherence (AIDA). As a control, we use a mutant strain lacking the aidA gene, 2787&Delta;aidA (F. Berthiaume and M. Mourez, unpublished), and a commercial laboratory strain of E. coli, C600 (New England Biolabs). The bacteria are left to adhere to the cells from the commonly used HEp-2 human epithelial cell line. This assay has been less extensively described before6.

In Vitro Assay of Bacterial Adhesion onto Mammalian Epithelial Cells

This protocol is a simple bacterial adhesion assay consisting in counting the numbers of bacterial colony forming units that are adhered onto cultured cells. The assay is robust, independent of the adhesin studied, and numerous variations are used in most laboratories working on bacterial pathogenesis.

To cause infections, bacteria must colonize their host. Bacterial pathogens express various molecules or structures able to promote attachment to host ...

Introducing Shear Stress in the Study of Bacterial Adhesion

During bacterial infections a sequence of interactions occur between the pathogen and its host. Bacterial adhesion to the host cell surface is often the initial and determining step of the pathogenesis. Although experimentally adhesion is mostly studied in static conditions adhesion actually takes place in the presence of flowing liquid. First encounters between bacteria and their host often occur at the mucosal level, mouth, lung, gut, eye, etc. where mucus flows along the surface of epithelial cells. Later in infection, pathogens occasionally access the blood circulation causing life-threatening illnesses such as septicemia, sepsis and meningitis. A defining feature of these infections is the ability of these pathogens to interact with endothelial cells in presence of circulating blood. The presence of flowing liquid, mucus or blood for instance, determines adhesion because it generates a mechanical force on the pathogen. To characterize the effect of flowing liquid one usually refers to the notion of shear stress, which is the tangential force exerted per unit area by a fluid moving near a stationary wall, expressed in dynes/cm2. Intensities of shear stress vary widely according to the different vessels type, size, organ, location etc. (0-100 dynes/cm2). Circulation in capillaries can reach very low shear stress values and even temporarily stop during periods ranging between a few seconds to several minutes 1. On the other end of the spectrum shear stress in arterioles can reach 100 dynes/cm2 2. The impact of shear stress on different biological processes has been clearly demonstrated as for instance during the interaction of leukocytes with the endothelium 3. To take into account this mechanical parameter in the process of bacterial adhesion we took advantage of an experimental procedure based on the use of a disposable flow chamber 4. Host cells are grown in the flow chamber and fluorescent bacteria are introduced in the flow controlled by a syringe pump. We initially focused our investigations on the bacterial pathogen Neisseria meningitidis, a Gram-negative bacterium responsible for septicemia and meningitis. The procedure described here allowed us to study the impact of shear stress on the ability of the bacteria to: adhere to cells 1, to proliferate on the cell surface 5and to detach to colonize new sites 6 (Figure 1). Complementary technical information can be found in reference 7. Shear stress values presented here were chosen based on our previous experience1 and to represent values found in the literature. The protocol should be applicable to a wide range of pathogens with specific adjustments depending on the objectives of the study.

During the infection process, a key step is the adhesion of pathogens with host cells. In most instances this adhesion step occurs in the presence of mechanical stress generated by flowing liquid. We describe a technique that introduces shear stress as an important parameter in the study of bacterial adhesion.

During bacterial infections a sequence of interactions occur between the pathogen and its host. Bacterial adhesion to the host cell surface is often the ...

Following Cell-fate in E. coli After Infection by Phage Lambda

The system comprising bacteriophage (phage) lambda and the bacterium E. coli has long served as a paradigm for cell-fate determination1,2. Following the simultaneous infection of the cell by a number of phages, one of two pathways is chosen: lytic (virulent) or lysogenic (dormant)3,4. We recently developed a method for fluorescently labeling individual phages, and were able to examine the post-infection decision in real-time under the microscope, at the level of individual phages and cells5. Here, we describe the full procedure for performing the infection experiments described in our earlier work5. This includes the creation of fluorescent phages, infection of the cells, imaging under the microscope and data analysis. The fluorescent phage is a "hybrid", co-expressing wild- type and YFP-fusion versions of the capsid gpD protein. A crude phage lysate is first obtained by inducing a lysogen of the gpD-EYFP (Enhanced Yellow Fluorescent Protein) phage, harboring a plasmid expressing wild type gpD. A series of purification steps are then performed, followed by DAPI-labeling and imaging under the microscope. This is done in order to verify the uniformity, DNA packaging efficiency, fluorescence signal and structural stability of the phage stock. The initial adsorption of phages to bacteria is performed on ice, then followed by a short incubation at 35&deg;C to trigger viral DNA injection6. The phage/bacteria mixture is then moved to the surface of a thin nutrient agar slab, covered with a coverslip and imaged under an epifluorescence microscope. The post-infection process is followed for 4 hr, at 10 min interval. Multiple stage positions are tracked such that ~100 cell infections can be traced in a single experiment. At each position and time point, images are acquired in the phase-contrast and red and green fluorescent channels. The phase-contrast image is used later for automated cell recognition while the fluorescent channels are used to characterize the infection outcome: production of new fluorescent phages (green) followed by cell lysis, or expression of lysogeny factors (red) followed by resumed cell growth and division. The acquired time-lapse movies are processed using a combination of manual and automated methods. Data analysis results in the identification of infection parameters for each infection event (e.g. number and positions of infecting phages) as well as infection outcome (lysis/lysogeny). Additional parameters can be extracted if desired.

Following Cell-fate in E. coli After Infection by Phage Lambda

This article describes the procedure for preparing a fluorescently-labeled version of bacteriophage lambda, infection of E. coli bacteria, following the infection outcome under the microscope, and analysis of infection results.

The system comprising bacteriophage (phage) lambda and the bacterium E. coli has long served as a paradigm for cell-fate determination1,2. Following the ...

Assessing Somatic Hypermutation in Ramos B Cells after Overexpression or Knockdown of Specific Genes

B cells start their life with low affinity antibodies generated by V(D)J recombination. However, upon detecting a pathogen, the variable (V) region of an immunoglobulin (Ig) gene is mutated approximately 100,000-fold more than the rest of the genome through somatic hypermutation (SHM), resulting in high affinity antibodies1,2. In addition, class switch recombination (CSR) produces antibodies with different effector functions depending on the kind of immune response that is needed for a particular pathogen. Both CSR and SHM are initiated by activation-induced cytidine deaminase (AID), which deaminates cytosine residues in DNA to produce uracils. These uracils are processed by error-prone forms of repair pathways, eventually leading to mutations and recombination1-3.
Our current understanding of the molecular details of SHM and CSR come from a combination of studies in mice, primary cells, cell lines, and cell-free experiments. Mouse models remain the gold standard with genetic knockouts showing critical roles for many repair factors (e.g. Ung, Msh2, Msh6, Exo1, and polymerase &eta;)4-10. However, not all genes are amenable for knockout studies. For example, knockouts of several double-strand break repair proteins are embryonically lethal or impair B-cell development11-14. Moreover, sometimes the specific function of a protein in SHM or CSR may be masked by more global defects caused by the knockout. In addition, since experiments in mice can be lengthy, altering expression of individual genes in cell lines has become an increasingly popular first step to identifying and characterizing candidate genes15-18.
Ramos &#x2013; a Burkitt lymphoma cell line that constitutively undergoes SHM &#x2013; has been a popular cell-line model to study SHM18-24. One advantage of Ramos cells is that they have a built-in convenient semi-quantitative measure of SHM. Wild type cells express IgM and, as they pick up mutations, some of the mutations knock out IgM expression. Therefore, assaying IgM loss by fluorescence-activated cell scanning (FACS) provides a quick read-out for the level of SHM. A more quantitative measurement of SHM can be obtained by directly sequencing the antibody genes. 
Since Ramos cells are difficult to transfect, we produce stable derivatives that have increased or lowered expression of an individual gene by infecting cells with retroviral or lentiviral constructs that contain either an overexpression cassette or a short hairpin RNA (shRNA), respectively. Here, we describe how we infect Ramos cells and then use these cells to investigate the role of specific genes on SHM (Figure 1).

We describe how to perform retroviral or lentiviral infections of overexpression or shRNA-containing constructs in the human Ramos B-cell line and how to measure somatic hypermutation in these cells.

B cells start their life with low affinity antibodies generated by V(D)J recombination.  However, upon detecting a pathogen, the variable (V) region of an ...

Fluorescence Microscopy Methods for Determining the Viability of Bacteria in Association with Mammalian Cells

Central to the field of bacterial pathogenesis is the ability to define if and how microbes survive after exposure to eukaryotic cells. Current protocols to address these questions include colony count assays, gentamicin protection assays, and electron microscopy. Colony count and gentamicin protection assays only assess the viability of the entire bacterial population and are unable to determine individual bacterial viability. Electron microscopy can be used to determine the viability of individual bacteria and provide information regarding their localization in host cells. However, bacteria often display a range of electron densities, making assessment of viability difficult. This article outlines protocols for the use of fluorescent dyes that reveal the viability of individual bacteria inside and associated with host cells. These assays were developed originally to assess survival of Neisseria gonorrhoeae in primary human neutrophils, but should be applicable to any bacterium-host cell interaction. These protocols combine membrane-permeable fluorescent dyes (SYTO9 and 4&#39;,6-diamidino-2-phenylindole [DAPI]), which stain all bacteria, with membrane-impermeable fluorescent dyes (propidium iodide and SYTOX Green), which are only accessible to nonviable bacteria. Prior to eukaryotic cell permeabilization, an antibody or fluorescent reagent is added to identify extracellular bacteria. Thus these assays discriminate the viability of bacteria adherent to and inside eukaryotic cells. A protocol is also provided for using the viability dyes in combination with fluorescent antibodies to eukaryotic cell markers, in order to determine the subcellular localization of individual bacteria. The bacterial viability dyes discussed in this article are a sensitive complement and/or alternative to traditional microbiology techniques to evaluate the viability of individual bacteria and provide information regarding where bacteria survive in host cells.

Central to the field of bacterial pathogenesis is the ability to define if and how microbes survive after exposure to eukaryotic cells. This article outlines protocols for the use of fluorescent dyes that reveal the viability of individual bacteria inside and associated with host cells.

Central to the field of bacterial pathogenesis is the ability to define if and how microbes survive after exposure to eukaryotic cells. Current protocols ...

Electroporation of Functional Bacterial Effectors into Mammalian Cells

The study of protein interactions in the context of living cells can generate critical information about localization, dynamics, and interacting partners. This information is particularly valuable in the context of host-pathogen interactions. Many pathogen proteins function within host cells in a variety of way such as, enabling evasion of the host immune system and survival within the intracellular environment. To study these pathogen-protein host-cell interactions, several approaches are commonly used, including: in vivo infection with a strain expressing a tagged or mutant protein, or introduction of pathogen genes via transfection or transduction. Each of these approaches has advantages and disadvantages. We sought a means to directly introduce exogenous proteins into cells. Electroporation is commonly used to introduce nucleic acids into cells, but has been more rarely applied to proteins although the biophysical basis is exactly the same. A standard electroporator was used to introduce affinity-tagged bacterial effectors into mammalian cells. Human epithelial and mouse macrophage cells were cultured by traditional methods, detached, and placed in 0.4 cm gap electroporation cuvettes with an exogenous bacterial pathogen protein of interest (e.g. Salmonella Typhimurium GtgE). After electroporation (0.3 kV) and a short (4 hr) recovery period, intracellular protein was verified by fluorescently labeling the protein via its affinity tag and examining spatial and temporal distribution by confocal microscopy. The electroporated protein was also shown to be functional inside the cell and capable of correct subcellular trafficking and protein-protein interaction. While the exogenous proteins tended to accumulate on the surface of the cells, the electroporated samples had large increases in intracellular effector concentration relative to incubation alone. The protocol is simple and fast enough to be done in a parallel fashion, allowing for high-throughput characterization of pathogen proteins in host cells including subcellular targeting and function of virulence proteins.

Electroporation was used to insert purified bacterial virulence effector proteins directly into living eukaryotic cells. Protein localization was monitored by confocal immunofluorescence microscopy. This method allows for studies on trafficking, function, and protein-protein interactions using active exogenous proteins, avoiding the need for heterologous expression in eukaryotic cells.

The study of protein interactions in the context of living cells can generate critical information about localization, dynamics, and interacting partners. ...

Generation and Multi-phenotypic High-content Screening of Coxiella burnetii Transposon Mutants

Invasion and colonization of host cells by bacterial pathogens depend on the activity of a large number of prokaryotic proteins, defined as virulence factors, which can subvert and manipulate key host functions. The study of host/pathogen interactions is therefore extremely important to understand bacterial infections and develop alternative strategies to counter infectious diseases. This approach however, requires the development of new high-throughput assays for the unbiased, automated identification and characterization of bacterial virulence determinants. Here, we describe a method for the generation of a GFP-tagged mutant library by transposon mutagenesis and the development of high-content screening approaches for the simultaneous identification of multiple transposon-associated phenotypes. Our working model is the intracellular bacterial pathogen Coxiellaburnetii, the etiological agent of the zoonosis Q fever, which is associated with severe outbreaks with a consequent health and economic burden. The obligate intracellular nature of this pathogen has, until recently, severely hampered the identification of bacterial factors involved in host pathogen interactions, making of Coxiella the ideal model for the implementation of high-throughput/high-content approaches.

Generation and Multi-phenotypic High-content Screening of Coxiella burnetii Transposon Mutants

Coxiella burnetii is an obligate intracellular Gram-negative bacterium responsible for the zoonotic disease Q fever. Here we describe methods for the generation of Coxiella fluorescent transposon mutants as well as the automated identification and analysis of the resulting internalization, replication and cytotoxic phenotypes.

Invasion and colonization of host cells by bacterial pathogens depend on the activity of a large number of prokaryotic proteins, defined as virulence ...

Methods to Inhibit Bacterial Pyomelanin Production and Determine the Corresponding Increase in Sensitivity to Oxidative Stress

Pyomelanin is an extracellular red-brown pigment produced by several bacterial and fungal species. This pigment is derived from the tyrosine catabolism pathway and contributes to increased oxidative stress resistance. Pyomelanin production in Pseudomonas aeruginosa is reduced in a dose dependent manner through treatment with 2-[2-nitro-4-(trifluoromethyl)benzoyl]-1,3-cyclohexanedione (NTBC). We describe a titration method using multiple concentrations of NTBC to determine the concentration of drug that will reduce or abolish pyomelanin production in bacteria. The titration method has an easily quantifiable outcome, a visible reduction in pigment production with increasing drug concentrations. We also describe a microtiter plate method to assay antibiotic minimum inhibitory concentration (MIC) in bacteria. This method uses a minimum of resources and can easily be scaled up to test multiple antibiotics in one microtiter plate for one strain of bacteria. The MIC assay can be adapted to test the affects of non-antibiotic compounds on bacterial growth at specific concentrations. Finally, we describe a method for testing bacterial sensitivity to oxidative stress by incorporating H2O2 into agar plates and spotting multiple dilutions of bacteria onto the plates. Sensitivity to oxidative stress is indicated by reductions in colony number and size for the different dilutions on plates containing H2O2 compared to a no H2O2 control. The oxidative stress spot plate assay uses a minimum of resources and low concentrations of H2O2. Importantly, it also has good reproducibility. This spot plate assay could be adapted to test bacterial sensitivity to various compounds by incorporating the compounds in agar plates and characterizing the resulting bacterial growth.

Bacterial pyomelanin production results in increased resistance to oxidative stress and virulence. We report on techniques that can be used to determine inhibition of pyomelanin production and assay the resulting increase in sensitivity to oxidative stress in bacteria, as well as determine antibiotic minimum inhibitory concentration (MIC).

Pyomelanin is an extracellular red-brown pigment produced by several bacterial and fungal species. This pigment is derived from the tyrosine catabolism ...

Implementation of a Permeable Membrane Insert-based Infection System to Study the Effects of Secreted Bacterial Toxins on Mammalian Host Cells

Many bacterial pathogens secrete potent toxins to aid in the destruction of host tissue, to initiate signaling changes in host cells or to manipulate immune system responses during the course of infection. Though methods have been developed to successfully purify and produce many of these important virulence factors, there are still many bacterial toxins whose unique structure or extensive post-translational modifications make them difficult to purify and study in in vitro systems. Furthermore, even when pure toxin can be obtained, there are many challenges associated with studying the specific effects of a toxin under relevant physiological conditions. Most in vitro cell culture models designed to assess the effects of secreted bacterial toxins on host cells involve incubating host cells with a one-time dose of toxin. Such methods poorly approximate what host cells actually experience during an infection, where toxin is continually produced by bacterial cells and allowed to accumulate gradually during the course of infection. This protocol describes the design of a permeable membrane insert-based bacterial infection system to study the effects of Streptolysin S, a potent toxin produced by Group A Streptococcus, on human epithelial keratinocytes. This system more closely mimics the natural physiological environment during an infection than methods where pure toxin or bacterial supernatants are directly applied to host cells. Importantly, this method also eliminates the bias of host responses that are due to direct contact between the bacteria and host cells. This system has been utilized to effectively assess the effects of Streptolysin S (SLS) on host membrane integrity, cellular viability, and cellular signaling responses. This technique can be readily applied to the study of other secreted virulence factors on a variety of mammalian host cell types to investigate the specific role of a secreted bacterial factor during the course of infection.

Here, a method using a permeable membrane insert-based infection system to study the effects of Streptolysin S, a secreted toxin produced by Group A Streptococcus, on keratinocytes is described. This system can be readily applied to the study of other secreted bacterial proteins on various host cell types during infection.

Many bacterial pathogens secrete potent toxins to aid in the destruction of host tissue, to initiate signaling changes in host cells or to manipulate ...