We thank Alejandro Brun from CISA-INIA for providing anti-Rift Valley fever Virus sera. Work in our laboratories is supported by Forschungsf&#246;rderung gem. &#167;2 Abs. 3 Kooperationsvertrag Universit&#228;tsklinikum Giessen und Marburg, the Leibniz Graduate School for Emerging viral diseases (EIDIS), the DFG Sonderforschungsbereich (SFB) 1021, and the DFG Schwerpunktprogramm (SPP) 1596.

1. Seeding of A549 Cells for Infection
<ol>
	<li>Cultivate a T75 flask of A549 cells at 37 &#176;C and 5% CO2 in cell culture medium (DMEM supplemented with 10% FCS, 526.6 mg/l L-glutamine, 50.000 U/l penicillin, and 50 mg/l streptomycin).</li>
	<li>Before starting to harvest the cells, warm up cell culture medium, PBS and 0.05% trypsin-EDTA in a waterbath heated to 37 &#176;C.</li>
	<li>Remove the medium and wash the cells with 10 ml PBS. Remove the PBS again.</li>
	<li>Add 3 ml of trypsin-EDTA and distribute equally in the flask. Transfer the flask in an incubator with 37 &#176;C and 5% CO2.</li>
	<li>When all cells are detached, add 7 ml of cell culture medium, resuspend the cells, and transfer the cell suspension into a 15 ml Falcon tube.</li>
	<li>Centrifuge the cells at 800 x g for 5 min at RT, remove the supernatant and resuspend the pellet in 10 ml fresh cell culture medium.</li>
	<li>Count the cells with a counting chamber.</li>
	<li>Add 2.5 x 106 cells in 5 ml of cell culture medium in two T25 flasks each. Incubate for 16 hr at 37 &#176;C and 5% CO2. One flask serves for the mock control and one for Cl 13 infection.</li>
</ol>
2. Infection with Rift Valley Fever Virus Clone 13 (Cl 13)
<ol>
	<li>NOTE: Cl 13 is an attenuated virus mutant which in Germany can be handled under BSL-2 conditions. Please refer to relevant national guidelines. Other typical IFN inducers would be Sendai virus (strain Cantell) or Newcastle disease virus.</li>
	<li>Pre-warm PBS, serum-free medium, and cell culture medium containing 5% FCS.</li>
	<li>Prepare 1.25 x 107 PFU/ml of Cl 13 in serum-free medium to infect 2.5 x 106 A549 cells with a multiplicity of infection (MOI) of 5. Prepare a slightly (roughly 10%) greater amount than needed to account for pipette errors.</li>
	<li>Wash the cells with PBS as described under 1.3.</li>
	<li>Add 1 ml of the Cl 13 dilution or of serum-free medium (uninfected control, mock) to the cells, and incubate for 1 hr at 37 &#176;C and 5% CO2. Move the flask carefully every 15 min to ensure equal distribution of Cl 13 dilution and serum-free medium, respectively.</li>
	<li>After 1 hr of infection, remove the inocula, add 5 ml of pre-warmed cell culture medium with 5% FCS, and incubate for 5 hr at 37 &#176;C and 5% CO2.</li>
</ol>
3. Preparation of Cell Lysates
<ol>
	<li>Prepare PBS / 0.5% Triton X-100 at 4 &#176;C. Do not add serine protease inhibitors.</li>
	<li>Wash the cells with cold PBS and add 10 ml of fresh PBS.</li>
	<li>Scrape the cells off, transfer the cell suspension in a falcon tube, and centrifuge at 800 x g for 5 min at RT.</li>
	<li>Remove the supernatant and resuspend the cell pellet in 30 &#181;l PBS / 0.5% Triton X-100. Transfer the lysate into a fresh 1.5 ml tube and incubate for at least 10 min at 4 &#176;C.</li>
	<li>Centrifuge the lysate at 10.000 x g for 10 min at 4 &#176;C and transfer the clarified cell lysate (supernatant) into a fresh tube.</li>
	<li>Determine the protein concentration by Bradford assay as described elsewhere33.</li>
	<li>Store at -20 &#176;C or proceed to trypsin digestion (4.1) or native PAGE (5.1).</li>
</ol>
4. Determination of Conformational Changes of Pattern Recognition Receptors
<ol>
	<li>TPCK-trypsin Treatment of Cell Lysates
	<ol>
		<li>Dilute L-1-tosylamido-2-phenylethyl chloromethyl ketone-treated (TPCK) trypsin in PBS to a final working concentration of 2 &#181;g/&#181;l.</li>
		<li>Adjust in two new tubes a final protein concentration of 25 &#181;g of each protein lysate (mock or Cl 13) in a final volume of 9 &#181;l with PBS. Hence, it should be four tubes with 25 &#181;g lysate each, two times mock and two times Cl 13 infection. One set as input control (untreated) and one set for treatment with TPCK-trypsin.</li>
		<li>Add 1 &#181;l of PBS (untreated) or 1 &#181;l of 2 &#181;g/&#181;l TPCK-trypsin (final concentration: 0.2 &#181;g/&#181;l) to the cell lysates and mix the reactions by pipetting. DO NOT freeze and thaw TPCK-trypsin aliquots, because it will compromise the efficiency of digestion.</li>
		<li>Incubate the lysates at 37 &#176;C for 25 min. Stop the reaction by adding 5x denaturing sample buffer (250 mM Tris-HCl pH 6.8, 10% SDS, 50% glycerol, 25% &#946;-mercaptoethanol, 0.5% bromphenol blue) and by boiling for 5 min at 95 &#176;C. It is important to NOT extend the trypsin incubation time. In case no protease-resistant fragments are detectable, the time of trypsin digestion must be shortened.</li>
		<li>After boiling, the samples can be stored at -20 &#176;C.</li>
	</ol>
	</li>
	<li>SDS Polyacrylamide Gel Electrophoresis (PAGE) and Western Blotting
	<ol>
		<li>Load the samples on a sodium dodecyl sulfate (SDS) polyacrylamide gel containing a 5% stacking over a 12% resolving gel. Separate the proteins at 25 mA per gel until the bromphenol blue runs out.</li>
		<li>Activate a polyvinylidene fluoride (PVDF) membrane for 30 sec with methanol and put it into transfer buffer (48 mM Tris, 39 mM glycin, 1.3 mM SDS, 20% methanol).</li>
		<li>Prepare the blotting with a semidry blotting system and allow the transfer of the proteins at 10 V for 1 hr. Take the membrane out, rinse it briefly with water, and let it dry.</li>
		<li>Reactivate the membrane by shortly transferring into methanol. Wash for 5 min with TBS. Block with 10% skim milk in TBS for 1 hr at RT or at 4 &#176;C O/N. Wash the membrane 3x for 5 min each with TBS.</li>
		<li>Prepare antibody dilution as recommended in table 1 and incubate the membrane for 1 hr at RT or at 4 &#176;C O/N.</li>
		<li>Wash the membrane 3x for 10 min each with TBS-T. Add the appropriate secondary antibody coupled with horseradish peroxidase at a 1:20,000 dilution in 1% skim milk in TBS. Incubate 45 min at RT.</li>
		<li>Wash the membrane 3x for 10 min each with TBS-T, and one additional time with TBS.</li>
		<li>For signal detection use a commercial chemiluminescense kit and a digital gel imaging system.</li>
	</ol>
	</li>
	<li>Coomassie Brilliant Blue G-250 Staining
	<ol>
		<li>Perform SDS-PAGE as described in 4.2.1. Load samples on an SDS polyacrylamide gel and run the gel at 25 mA per gel until bromphenol blue runs out.</li>
		<li>Perform Coomassie Brilliant Blue G-250 staining at RT. Do all incubations under constant shaking.</li>
		<li>Transfer the gel to the fixation solution containing 40% methanol and 10% acetic acid for 30 min.</li>
		<li>Exchange the buffer to destaining solution (25% ethanol and 8% acetic acid) and incubate for 5 min.</li>
		<li>Stain the gel with 0.2% Coomassie Brillant Blue G-250 in 40% methanol and 10% acetic acid for 1 hr.</li>
		<li>Destain the gel with the destaining solution and exchange the buffer after 10 min, 30 min, and 60 min.</li>
		<li>Store the gel in 25% ethanol, 8% acetic acid, and 4% glycerol at 4 &#176;C.</li>
		<li>Perform imaging and analysis as described under 4.2.8.</li>
	</ol>
	</li>
</ol>
5. Analysis of Oligomeric States of Pattern Recognition Receptors
<ol>
	<li>Native PAGE
	<ol>
		<li>Prepare 50 &#181;g of cell lysate in a final volume of 10 &#181;l with PBS and add 5&#215; native sample buffer (250 mM Tris-HCl pH 6.8, 1% sodium deoxycholate, 50% glycerol, 0.5% bromphenol blue) to a final concentration of 1x.</li>
		<li>Load the samples IMMEDIATELY on a native polyacrylamide gel with 5% as stacking and 8% as resolving gel. Any delay will result in a loss of native complexes34.</li>
		<li>Run the gel at 20 mA per gel at 4 &#176;C with 50 mM Tris-NaOH pH 9.0, 384 mM glycin as as anode and 50 mM Tris pH 8.3, 384 mM glycin, 1% sodium deoxycholate as cathode buffer. After 1.5-2 hr (bromphenol blue band has left the gel approximately 45 min earlier) the electrophoresis is finished.</li>
	</ol>
	</li>
	<li>Western Blotting
	<ol>
		<li>Activate a polyvinylidene fluoride (PVDF) membrane for 30 sec with methanol and put it into Towbin buffer (25 mM Tris, 192 mM glycin, 0.1% SDS, 20% methanol).</li>
		<li>Assemble a wet blot chamber according to the manufacturer&#8217;s instructions and fill the tank with Towin buffer.</li>
		<li>Perform the blotting with 250 mA for 1.5 hr at 4 &#176;C.</li>
		<li>When blotting is finished proceed as described from 4.2.3 on.</li>
	</ol>
	</li>
</ol>

No conflicts of interest declared.

Sensing the presence of viruses and activation of the antiviral type I IFN system are crucial for successful innate immune responses22. Virus detection is thereby mediated by pathogen recognition receptors (PRRs) like RIG-I and PKR, enabling a rapid response and activation of antiviral defense mechanisms. Here, we describe two methods to directly evaluate the activation status of RIG-I and PKR.
Limited protease digestion as a tool to monitor conformational changes of RIG-I and PKR w...

A crucial event in antiviral host defense is the rapid detection of the pathogen by the so-called pattern recognition receptors (PRRs)1,2. Intracellular detection of RNA virus infection is dependent on two cytoplasmic RNA helicases, RIG-I (retinoic acid inducible gene I) and MDA5 (melanoma differentiation associated protein 5)3-5. RIG-I is composed of two N-terminal caspase recruitment domains (CARDs), a central DECH-box type RNA helicase domain, and a C-terminal domain (CTD)4,6. Whereas the CTD and the helicase domain are required for recognition of non-self (viral) RNAs, the CARDs mediate downstream signaling leading to establishment of an antiviral host status.
If RIG-I is in the silent state, i.e. in the absence of a specific RNA ligand, the second CARD interacts with the central helicase domain and keeps RIG-I in an auto-inhibitory conformation7-11. RIG-I binds to short double-strand (ds) RNA bearing a 5&#8217;-triphosphate (5&#8217;PPP), long dsRNA, and polyU/UC-rich RNA, classic signature structures which are present on the genomes of many RNA viruses12-16. Two major characteristics of RIG-I activation are a switch to a closed conformation6,17 and the homo-oligomerization6,18,19. The conformational switch enhances RNA binding, exposes the CARDs for downstream signaling, and reconstitutes an active ATPase site8,9,11,20. The formation of oligomeric RIG-I complexes leads to enhanced recruitment of downstream signaling adaptor molecules to form a platform for antiviral signal transduction11. The RIG-I-regulated signaling chain eventually activates the transcription factor IRF-3 for up-regulation of interferon (IFN-alpha/beta) genes and hence the gene expression of interferon stimulated genes (ISGs) for a full antiviral response21,22. One of the best characterized ISGs is the RNA-activated protein kinase (PKR) 23. PKR belongs to the family of eukaryotic translation initiation factor 2 alpha (eIF2&#945;) kinases and is composed of an N-terminal double-stranded RNA binding domain and a C-terminal kinase domain. The kinase domain constitutes the dimerization interface crucial for PKR activation and carries out the catalytic functions of the protein. Binding of PKR to viral dsRNA leads to its conformational change permitting dimerization and auto-phosphorylation at Thr 446 among other residues. PKR then mediates phosphorylation of eIF2&#945;, thereby blocking the translation of viral mRNAs23-27.
Both RIG-I and PKR undergo major structural rearrangements, form oligomeric complexes and are post-translationally modified by phosphorylation/dephosphorylation and ubiquitination10,11,19,23,24,26-29. For a better understanding of which viral RNA structures are activating RIG-I and PKR (and at what stage viral antagonists could be interfering), it is important to precisely determine the activation status. For both PRRs it was previously described that activation leads to the emergence of trypsin-resistant protein fragments6,17,30 and higher-order oligomers6,18,19. However, given the wealth of literature on these key factors of the antiviral host response1,2,24, application of direct methods seems comparatively rare. In the hope of stimulating broader usage, we provide convenient and sensitive protocols to robustly analyze the activation states of RIG-I and PKR. The IFN competent human cell line A549 is infected with an established activator of RIG-I and PKR, the attenuated Rift Valley fever virus mutant clone 13 (Cl 13)31,32. After a simple lysing procedure, the extracts of infected cells are tested by limited trypsin digestion/western blot analysis to evaluate conformational switching, and by blue native polyacrylamide gel electrophoresis (PAGE) /Western blot analysis to measure formation of oligomers.

<table border="0" cellpadding="0" cellspacing="0" width="320">
	<tbody>
		<tr height="43" style="height:32.25pt">
			<td class="xl66" height="43" style="height:32.25pt;width:60pt" width="80">Name</td>
			<td class="xl67" style="width:60pt" width="80">Company</td>
			<td class="xl67" style="width:60pt" width="80">Catalog Number</td>
			<td class="xl67" style="width:60pt" width="80">Comments</td>
		</tr>
		<tr height="22" style="height:16.5pt">
			<td class="xl68" height="22" style="height:16.5pt;width:60pt" width="80">cell culture</td>
			<td class="xl76" colspan="3" style="border-right:1.0pt solid black;
 border-left:none;width:180pt" width="240"></td>
		</tr>
		<tr height="106" style="height:79.5pt">
			<td class="xl69" height="106" style="height:79.5pt;width:60pt" width="80">Dulbecco&#8217;s modified Eagle&#8217;s medium (DMEM)</td>
			<td class="xl70" style="width:60pt" width="80">Gibco</td>
			<td class="xl65" style="width:60pt" width="80">21969-035</td>
			<td class="xl71" style="width:60pt" width="80"></td>
		</tr>
		<tr height="22" style="height:16.5pt">
			<td class="xl72" height="22" style="height:16.5pt;width:60pt" width="80">OptiMEM</td>
			<td class="xl70" style="width:60pt" width="80">Gibco</td>
			<td class="xl65" style="width:60pt" width="80">31985-47</td>
			<td class="xl71" style="width:60pt" width="80"></td>
		</tr>
		<tr height="22" style="height:16.5pt">
			<td class="xl72" height="22" style="height:16.5pt;width:60pt" width="80">L-glutamine</td>
			<td class="xl70" style="width:60pt" width="80">PAA</td>
			<td class="xl65" style="width:60pt" width="80">25030-024</td>
			<td class="xl71" style="width:60pt" width="80"></td>
		</tr>
		<tr height="61" style="height:45.75pt">
			<td class="xl72" height="61" style="height:45.75pt;width:60pt" width="80">penicillin-streptomycin</td>
			<td class="xl70" style="width:60pt" width="80">PAA</td>
			<td class="xl65" style="width:60pt" width="80">15070-063</td>
			<td class="xl71" style="width:60pt" width="80"></td>
		</tr>
		<tr height="64" style="height:48.0pt">
			<td class="xl73" height="64" style="height:48.0pt;width:60pt" width="80">fetal calf serum (FCS)</td>
			<td class="xl70" style="width:60pt" width="80">PAA</td>
			<td class="xl65" style="width:60pt" width="80">10270</td>
			<td class="xl71" style="width:60pt" width="80"></td>
		</tr>
		<tr height="64" style="height:48.0pt">
			<td class="xl69" height="64" style="height:48.0pt;width:60pt" width="80">0.05% trypsin-EDTA</td>
			<td class="xl70" style="width:60pt" width="80">Gibco</td>
			<td class="xl65" style="width:60pt" width="80">25300-054</td>
			<td class="xl71" style="width:60pt" width="80"></td>
		</tr>
		<tr height="22" style="height:16.5pt">
			<td class="xl68" height="22" style="height:16.5pt;width:60pt" width="80">chemicals</td>
			<td class="xl76" colspan="3" style="border-right:1.0pt solid black;
 border-left:none;width:180pt" width="240"></td>
		</tr>
		<tr height="190" style="height:142.5pt">
			<td class="xl73" height="190" style="height:142.5pt;width:60pt" width="80">L-1-tosylamido-2-phenylethyl chloromethyl ketone-treated (TPCK) trypsin</td>
			<td class="xl65" style="width:60pt" width="80">Sigma Aldrich</td>
			<td class="xl65" style="width:60pt" width="80">T1426</td>
			<td class="xl65" style="width:60pt" width="80"></td>
		</tr>
		<tr height="22" style="height:16.5pt">
			<td class="xl68" height="22" style="height:16.5pt;width:60pt" width="80">antibodies</td>
			<td class="xl78" colspan="3" style="border-right:1.0pt solid black;
 border-left:none;width:180pt" width="240"></td>
		</tr>
		<tr height="106" style="height:79.5pt">
			<td class="xl69" height="106" style="height:79.5pt;width:60pt" width="80">mouse monoclonal anti-RIG-I antibody (ALME-1)</td>
			<td class="xl74" style="width:60pt" width="80">Enzo Life Sciences</td>
			<td class="xl65" style="width:60pt" width="80">ALX-804-849-C100</td>
			<td class="xl65" style="width:60pt" width="80">WB: 1:500 in 1% skim milk in TBS</td>
		</tr>
		<tr height="85" style="height:63.75pt">
			<td class="xl69" height="85" style="height:63.75pt;width:60pt" width="80">mouse monoclonal anti-PKR (B10)</td>
			<td class="xl65" style="width:60pt" width="80">Santa Cruz</td>
			<td class="xl65" style="width:60pt" width="80">sc-6282</td>
			<td class="xl65" style="width:60pt" width="80">WB: 1:500 in 1% skim milk in TBS</td>
		</tr>
		<tr height="85" style="height:63.75pt">
			<td class="xl69" height="85" style="height:63.75pt;width:60pt" width="80">rabbit monoclonal anti-P-PKR (Thr446)</td>
			<td class="xl65" style="width:60pt" width="80">Epitomics</td>
			<td class="xl65" style="width:60pt" width="80">1120-1</td>
			<td class="xl65" style="width:60pt" width="80">WB: 1:1.000 in 5% BSA in TBS</td>
		</tr>
		<tr height="64" style="height:48.0pt">
			<td class="xl69" height="64" style="height:48.0pt;width:60pt" width="80">rabbit polyclonal anti-IRF-3</td>
			<td class="xl65" style="width:60pt" width="80">Santa Cruz</td>
			<td class="xl65" style="width:60pt" width="80">sc-9082</td>
			<td class="xl65" style="width:60pt" width="80">WB: 1:500 in 1% skim milk in TBS</td>
		</tr>
		<tr height="85" style="height:63.75pt">
			<td class="xl69" height="85" style="height:63.75pt;width:60pt" width="80">rabbit monoclonal anti-P-IRF-3 (Ser386)</td>
			<td class="xl65" style="width:60pt" width="80">IBL</td>
			<td class="xl65" style="width:60pt" width="80">og-413</td>
			<td class="xl65" style="width:60pt" width="80">WB: 1:100 in 1% skim milk in TBS</td>
		</tr>
		<tr height="126" style="height:94.5pt">
			<td class="xl81" height="211" rowspan="2" style="border-bottom:1.0pt solid black;
 height:158.25pt;border-top:none;width:60pt" width="80">rabbit anti-RVFV hyperimmune serum &#34;C2&#34; (MP-12)</td>
			<td class="xl82" rowspan="2" style="border-bottom:1.0pt solid black;
 border-top:none;width:60pt" width="80"></td>
			<td class="xl82" rowspan="2" style="border-bottom:1.0pt solid black;
 border-top:none;width:60pt" width="80"></td>
			<td class="xl75" style="width:60pt" width="80">Kindly provided by Alejandro Brun (CISA-INIA)</td>
		</tr>
		<tr height="85" style="height:63.75pt">
			<td class="xl65" height="85" style="height:63.75pt;width:60pt" width="80">WB: 1:2.000 in 1% skim milk in TBS</td>
		</tr>
		<tr height="106" style="height:79.5pt">
			<td class="xl69" height="106" style="height:79.5pt;width:60pt" width="80">mouse monoclonal anti-beta-actin (8H10D10)</td>
			<td class="xl65" style="width:60pt" width="80">Cell Signalling</td>
			<td class="xl65" style="width:60pt" width="80">3700</td>
			<td class="xl65" style="width:60pt" width="80">WB: 1:1.000 in 1% skim milk in TBS</td>
		</tr>
		<tr height="106" style="height:79.5pt">
			<td class="xl69" height="106" style="height:79.5pt;width:60pt" width="80">polyclonal peroxidase-conjugated goat anti-rabbit</td>
			<td class="xl65" style="width:60pt" width="80">Thermo Fisher</td>
			<td class="xl65" style="width:60pt" width="80">0031460 1892914</td>
			<td class="xl65" style="width:60pt" width="80">WB: 1:20.000 in 1% skim milk in TBS</td>
		</tr>
		<tr height="106" style="height:79.5pt">
			<td class="xl64" height="106" style="height:79.5pt;width:60pt" width="80">polyclonal peroxidase-conjugated goat anti-mouse</td>
			<td class="xl63" style="width:60pt" width="80">Thermo Fisher</td>
			<td class="xl63" style="width:60pt" width="80">0031430 1892913</td>
			<td class="xl63" style="width:60pt" width="80">WB: 1:20.000 in 1% skim milk in TBS</td>
		</tr>
	</tbody>
</table>

monitoring activation of the antiviral pattern recognition receptors rig-i and pkr by limited protease digestion and native page

Host defenses to virus infection are dependent on a rapid detection by pattern recognition receptors (PRRs) of the innate immune system. In the cytoplasm, the PRRs RIG-I and PKR bind to specific viral RNA ligands. This first mediates conformational switching and oligomerization, and then enables activation of an antiviral interferon response. While methods to measure antiviral host gene expression are well established, methods to directly monitor the activation states of RIG-I and PKR are only partially and less well established.
Here, we describe two methods to monitor RIG-I and PKR stimulation upon infection with an established interferon inducer, the Rift Valley fever virus mutant clone 13 (Cl 13). Limited trypsin digestion allows to analyze alterations in protease sensitivity, indicating conformational changes of the PRRs. Trypsin digestion of lysates from mock infected cells results in a rapid degradation of RIG-I and PKR, whereas Cl 13 infection leads to the emergence of a protease-resistant RIG-I fragment. Also PKR shows a virus-induced partial resistance to trypsin digestion, which coincides with its hallmark phosphorylation at Thr 446. The formation of RIG-I and PKR oligomers was validated by native polyacrylamide gel electrophoresis (PAGE). Upon infection, there is a strong accumulation of RIG-I and PKR oligomeric complexes, whereas these proteins remained as monomers in mock infected samples.
Limited protease digestion and native PAGE, both coupled to western blot analysis, allow a sensitive and direct measurement of two diverse steps of RIG-I and PKR activation. These techniques are relatively easy and quick to perform and do not require expensive equipment.

Recognition of a viral agonist by RIG-I or PKR triggers conformational switching6,17,30 and oligomerization6,18,27. We assayed these two activation markers by limited protease digestion and native polyacrylamide gel electrophoresis (PAGE), respectively.
Human A549 cells were infected with Rift Valley fever virus clone 13 (Cl 13), which is characterized by a mutation of the IFN antagonist NSs35,36. Due to the absence of functional NSs, Clone 13 strongly induces ...

Watch this Scientific Journal Video about Monitoring Activation of the Antiviral Pattern Recognition Receptors RIG-I And PKR By Limited Protease Digestion and Native PAGE at JoVE.com

Monitoring Activation of the Antiviral Pattern Recognition Receptors RIG-I And PKR By Limited Protease Digestion and Native PAGE

Innate defenses to virus infections are triggered by pattern recognition receptors (PRRs). The two cytoplasmic PRRs RIG-I and PKR bind to viral signature RNAs, change conformation, oligomerize, and activate antiviral signaling. Methods are described which allow to conveniently monitor the conformational switching and the oligomerization of these cytoplasmic PRRs.

Host defenses to virus infection are dependent on a rapid detection by pattern recognition receptors (PRRs) of the innate immune system. In the cytoplasm, ...

monitoring-activation-antiviral-pattern-recognition-receptors-rig-i

Research

JoVE Journal

Immunology and Infection

12.0K Views.  Philipps-University Marburg. Innate defenses to virus infections are triggered by pattern recognition receptors (PRRs). The two cytoplasmic PRRs RIG-I and PKR bind to viral signature RNAs, change conformation, oligomerize, and activate antiviral signaling. Methods are described which allow to conveniently monitor the conformational switching and the oligomerization of these cytoplasmic PRRs.

Video: Monitoring Activation of the Antiviral Pattern Recognition Receptors RIG-I And PKR By Limited Protease Digestion and Native PAGE

Recognition of Epidermal Transglutaminase by IgA and Tissue Transglutaminase 2 Antibodies in a Rare Case of Rhesus Dermatitis

Tissue transglutaminase 2 (tTG2) is an intestinal digestive enzyme which deamidates already partially digested dietary gluten e.g. gliadin peptides. In genetically predisposed individuals, tTG2 triggers autoimmune responses that are characterized by the production of tTG2 antibodies and their direct deposition into small intestinal wall 1,2. The presence of such antibodies constitutes one of the major hallmarks of the celiac disease (CD). Epidermal transglutaminase (eTG) is another member of the transglutaminase family that can also function as an autoantigen in a small minority of CD patients. In these relatively rare cases, eTG triggers an autoimmune reaction (a skin rash) clinically known as dermatitis herpetiformis (DH). Although the exact mechanism of CD and DH pathogenesis is not well understood, it is known that tTG2 and eTG share antigenic epitopes that can be recognized by serum antibodies from both CD and DH patients 3,4.
In this study, the confocal microscopy examination of biopsy samples from skin lesions of two rhesus macaques (Macaca mulatta) with dermatitis (Table 1, Fig. 1 and 2) was used to study the affected tissues. In one animal (EM96) a spectral overlap of IgA and tTG2 antibodies (Fig. 3) was demonstrated. The presence of double-positive tTG2+IgA+ cells was focused in the deep epidermis, around the dermal papillae. This is consistent with lesions described in DH patients 3. When EM96 was placed on a gluten-free diet, the dermatitis, as well as tTG2+IgA+ deposits disappeared and were no longer detectable (Figs. 1-3). Dermatitis reappeared however, based on re-introduction of dietary gluten in EM96 (not shown). In other macaques including animal with unrelated dermatitis, the tTG2+IgA+ deposits were not detected. Gluten-free diet-dependent remission of dermatitis in EM96 together with presence of tTG2+IgA+ cells in its skin suggest an autoimmune, DH-like mechanism for the development of this condition. This is the first report of DH-like dermatitis in any non-human primate.

Recognition of Epidermal Transglutaminase by IgA and Tissue Transglutaminase 2 Antibodies in a Rare Case of Rhesus Dermatitis

Dermatitis herpetiformis (DH) is a chronic inflammatory condition characterized by an autoimmune reaction between IgA and epidermal transglutaminase (eTG). DH develops in a very small portion of gluten-sensitive and/or celiac patients. The results of this study indicate that DH can also develop in a rhesus monkey host with symptoms of idiopatic dermatitis.

Tissue transglutaminase 2 (tTG2) is an intestinal digestive enzyme which deamidates already partially digested dietary gluten e.g. gliadin peptides. In ...

Immunofluorescence to Monitor the Cellular Uptake of Human Lactoferrin and its Associated Antiviral Activity Against the Hepatitis C Virus

Immunofluorescence is a laboratory technique commonly used to study many aspects of biology. It is typically used to visualize the distribution and/or localization of a target molecule in cells and tissues. Immunofluorescence relies on the specificity of fluorescent-labelled antibodies against their corresponding antigens within a cell. Both direct and indirect immunofluorescence approaches can be used which rely on the use of antibodies linked with a fluorochrome. Direct immunofluorescence is less frequently used because it provides lower signal, involves higher cost and less flexibility. In contrast, indirect immunofluorescence is more commonly used because of its high sensitivity and provides an amplified signal since more than one secondary antibody can attach to each primary antibody. In this manuscript, both epifluorescence microscopy and confocal microscopy were used to monitor the internalization of human lactoferrin, an important component of the immune system, into hepatic cells. Moreover, we monitored the inhibitory potential of hLF on the intracellular replication of the Hepatitis C virus using immunofluorescence. Both the advantages and disadvantages associated with these approaches are discussed.

The human lactoferrin (hLF) is a component of the immune system. In this study, immunofluorescence assays are used to demonstrate both the hepatocellular uptake of hLF and a qualitative reduction in the hepatitis C virus replication upon treatment with hLF.

Immunofluorescence is a laboratory technique commonly used to study many aspects of biology. It is typically used to visualize the distribution and/or ...

Early Viral Entry Assays for the Identification and Evaluation of Antiviral Compounds

Cell-based systems are useful for discovering antiviral agents. Dissecting the viral life cycle, particularly the early entry stages, allows a mechanistic approach to identify and evaluate antiviral agents that target specific steps of the viral entry. In this report, the methods of examining viral inactivation, viral attachment, and viral entry/fusion as antiviral assays for such purposes are described, using hepatitis C virus as a model. These assays should be useful for discovering novel antagonists/inhibitors to early viral entry and help expand the scope of candidate antiviral agents for further drug development.

Here, we present a protocol that examines specific steps of the viral entry to identify and evaluate novel antiviral agents.

Cell-based systems are useful for discovering antiviral agents. Dissecting the viral life cycle, particularly the early entry stages, allows a mechanistic ...

The Ex Vivo Culture and Pattern Recognition Receptor Stimulation of Mouse Intestinal Organoids

Primary intestinal organoids are a valuable model system that has the potential to significantly impact the field of mucosal immunology. However, the complexities of the organoid growth characteristics carry significant caveats for the investigator. Specifically, the growth patterns of each individual organoid are highly variable and create a heterogeneous population of epithelial cells in culture. With such caveats, common tissue culture practices cannot be simply applied to the organoid system due to the complexity of the cellular structure. Counting and plating based solely on cell number, which is common for individually separated cells, such as cell lines, is not a reliable method for organoids unless some normalization technique is applied. Normalizing to total protein content is made complex due to the resident protein matrix. These characteristics in terms of cell number, shape and cell type should be taken into consideration when evaluating secreted contents from the organoid mass. This protocol has been generated to outline a simple procedure to culture and treat small intestinal organoids with microbial pathogens and pathogen associated molecular patterns (PAMPs). It also emphasizes the normalization techniques that should be applied when protein analysis are conducted after such a challenge.

The Ex Vivo Culture and Pattern Recognition Receptor Stimulation of Mouse Intestinal Organoids

Here, a protocol to harvest, maintain, and treat mouse small intestinal organoids with pathogen associated molecular patterns (PAMPs) and Listeria monocytogenes is described, as well as emphasis on gene expression and proper normalization techniques for protein.

Primary intestinal organoids are a valuable model system that has the potential to significantly impact the field of mucosal immunology. However, the ...

Generating De Novo Antigen-specific Human T Cell Receptors by Retroviral Transduction of Centric Hemichain

T cell receptors (TCRs) are used clinically to direct the specificity of T cells to target tumors as a promising modality of immunotherapy. Therefore, cloning TCRs specific for various tumor-associated antigens has been the goal of many studies. To elicit an effective T cell response, the TCR must recognize the target antigen with optimal affinity. However, cloning such TCRs has been a challenge and many available TCRs possess sub-optimal affinity for the cognate antigen. In this protocol, we describe a method of cloning de novo high affinity antigen-specific TCRs using existing TCRs by exploiting hemichain centricity. It is known that for some TCRs, each TCR&#945; or TCR&#946; hemichain do not contribute equally to antigen recognition, and the dominant hemichain is referred to as the centric hemichain. We have shown that by pairing the centric hemichain with counter-chains differing from the original counter-chain, we are able to maintain the antigen specificity, while modulating its interaction strength for the cognate antigen. Thus, the therapeutic potential of a given TCR can be improved by optimizing the pairing between the centric and counter hemichains.

Generating De Novo Antigen-specific Human T Cell Receptors by Retroviral Transduction of Centric Hemichain

Herein we describe a novel method to generate antigen-specific T cell receptors (TCRs) by pairing the TCR&#945; or TCR&#946; of an existing TCR, possessing the antigen-specificity of interest, with complementary hemichain of the peripheral T cell receptor repertoire. The de novo generated TCRs retain antigen-specificity with varying affinity.

T cell receptors (TCRs) are used clinically to direct the specificity of T cells to target tumors as a promising modality of immunotherapy. Therefore, ...

Arbovirus Infections As Screening Tools for the Identification of Viral Immunomodulators and Host Antiviral Factors

RNA interference- and genome editing-based screening platforms have been widely used to identify host cell factors that restrict virus replication. However, these screens are typically conducted in cells that are naturally permissive to the viral pathogen under study. Therefore, the robust replication of viruses in control conditions may limit the dynamic range of these screens. Furthermore, these screens may be unable to easily identify cellular defense pathways that restrict virus replication if the virus is well-adapted to the host and capable of countering antiviral defenses. In this article, we describe a new paradigm for exploring virus-host interactions through the use of screens that center on naturally abortive infections by arboviruses such as vesicular stomatitis virus (VSV). Despite the ability of VSV to replicate in a wide range of dipteran insect and mammalian hosts, VSV undergoes a post-entry, abortive infection in a variety of cell lines derived from lepidopteran insects, such as the gypsy moth (Lymantria dispar). However, these abortive VSV infections can be &#34;rescued&#34; when host cell antiviral defenses are compromised. We describe how VSV strains encoding convenient reporter genes and restrictive L. dispar cell lines can be paired to set-up screens to identify host factors involved in arbovirus restriction. Furthermore, we also show the utility of these screening tools in the identification of virally encoded factors that rescue VSV replication during coinfection or through ectopic expression, including those encoded by mammalian viruses. The natural restriction of VSV replication in L. dispar cells provides a high signal-to-noise ratio when screening for the conditions that promote VSV rescue, thus enabling the use of simplistic luminescence- and fluorescence-based assays to monitor the changes in VSV replication. These methodologies are valuable for understanding the interplay between host antiviral responses and viral immune evasion factors.

Here, we present the protocols to identify 1) virus-encoded immunomodulators that promote arbovirus replication and 2) eukaryotic host factors that restrict arbovirus replication. These fluorescence- and luminescence-based methods allow researchers to rapidly obtain quantitative readouts of arbovirus replication in simplistic assays with low signal-to-noise ratios.

RNA interference- and genome editing-based screening platforms have been widely used to identify host cell factors that restrict virus replication. ...

Co-immunoprecipitation Assay for Studying Functional Interactions Between Receptors and Enzymes

Receptor-associated enzymes are the major mediators of cellular activation. These enzymes are regulated, at least in part, by physical interactions with cytoplasmic tails of the receptors. The interactions often occur through specific protein domains and result in activation of the enzymes. There are several methods to study interactions between proteins. While co-immunoprecipitation is commonly used to study domains that are required for protein-protein interactions, there are no assays that document the contribution of specific domains to activity of the recruited enzymes at the same time. Accordingly, the method described here combines co-immunoprecipitation and an on-bead enzymatic activity assay for simultaneous evaluation of interactions between proteins and associated enzymatic activation. The goal of this protocol is to identify the domains that are critical for physical interactions between a protein and enzyme and the domains that are obligatory for complete activation of the enzyme. The importance of this assay is demonstrated, as certain receptor protein domains contribute to the binding of the enzyme to the cytoplasmic tail of the receptor, while other domains are necessary to regulate the function of the same enzyme.

Here, we present a protocol for co-immunoprecipitation and an on-bead enzymatic activity assay to simultaneously study the contribution of specific protein domains of plasma membrane receptors to both enzyme recruitment and enzyme activity.

Receptor-associated enzymes are the major mediators of cellular activation. These enzymes are regulated, at least in part, by physical interactions with ...

Digestion of the Murine Liver for a Flow Cytometric Analysis of Lymphatic Endothelial Cells

Within the liver, lymphatic vessels are found within the portal triad, and their described function is to remove interstitial fluid from the liver to the lymph nodes where cellular debris and antigens can be surveyed. We are very interested in understanding how the lymphatic vasculature might be involved in inflammation and immune cell function within the liver. However, very little has been published establishing digestion protocols for the isolation of lymphatic endothelial cells (LECs) from the liver or specific markers that can be used to evaluate liver LECs on a per cell basis. Therefore, we optimized a method for the digestion and staining of the liver in order to evaluate the LEC population in the liver. We are confident that the method outlined here will be useful for the identification and isolation of LECs from the liver and will strengthen our understanding of how LECs respond to the liver microenvironment.

The goal of this protocol is to identify lymphatic endothelial cell populations within the liver using described markers. We utilize collagenase IV and DNase and a gentle mincing of tissue, combined with flow cytometry, to identify a distinct population of lymphatic endothelial cells.

Within the liver, lymphatic vessels are found within the portal triad, and their described function is to remove interstitial fluid from the liver to the ...

Confocal Imaging of Double-Stranded RNA and Pattern Recognition Receptors in Negative-Sense RNA Virus Infection

Double-stranded (ds) RNA is produced as a replicative intermediate during RNA virus infection. Recognition of dsRNA by host pattern recognition receptors (PRRs) such as the retinoic acid (RIG-I) like receptors (RLRs) RIG-I and melanoma differentiation-associated protein 5 (MDA-5) leads to the induction of the innate immune response. The formation and intracellular distribution of dsRNA in positive-sense RNA virus infection has been well characterized by microscopy. Many negative-sense RNA viruses, including some arenaviruses, trigger the innate immune response during infection. However, negative-sense RNA viruses were thought to produce low levels of dsRNA, which hinders the imaging study of PRR recognition of viral dsRNA. Additionally, infection experiments with highly pathogenic arenaviruses must be performed in high containment biosafety level facilities (BSL-4). The interaction between viral RNA and PRRs for highly pathogenic RNA virus is largely unknown due to the additional technical challenges that researchers need to face in the BSL-4 facilities. Recently, a monoclonal antibody (Mab) (clone 9D5) originally used for pan-enterovirus detection has been found to specifically detect dsRNA with a higher sensitivity than the traditional J2 or K1 anti-dsRNA antibodies. Herein, by utilizing the 9D5 antibody, we describe a confocal microscopy protocol that has been used successfully to visualize dsRNA, viral protein and PRR simultaneously in individual cells infected by arenavirus. The protocol is also suitable for imaging studies of dsRNA and PRR distribution in pathogenic arenavirus infected cells in BSL4 facilities.

Double-stranded RNA produced during RNA virus replication can be recognized by pattern recognition receptors to induce an innate immune response. For negative-sense RNA viruses, the interaction between the low-level dsRNA and PRRs remains unclear. We have developed a confocal microscopy method to visualize arenavirus dsRNA and PRR in individual cells.

Double-stranded (ds) RNA is produced as a replicative intermediate during RNA virus infection. Recognition of dsRNA by host pattern recognition receptors ...

Image Processing Protocol for the Analysis of the Diffusion and Cluster Size of Membrane Receptors by Fluorescence Microscopy

Particle tracking on a video sequence and the posterior analysis of their trajectories is nowadays a common operation in many biological studies. Using the analysis of cell membrane receptor clusters as a model, we present a detailed protocol for this image analysis task using Fiji (ImageJ) and Matlab routines to: 1) define regions of interest and design masks adapted to these regions; 2) track the particles in fluorescence microscopy videos; 3) analyze the diffusion and intensity characteristics of selected tracks. The quantitative analysis of the diffusion coefficients, types of motion, and cluster size obtained by fluorescence microscopy and image processing provides a valuable tool to objectively determine particle dynamics and the consequences of modifying environmental conditions. In this article we present detailed protocols for the analysis of these features. The method described here not only allows single-molecule tracking detection, but also automates the estimation of lateral diffusion parameters at the cell membrane, classifies the type of trajectory and allows complete analysis thus overcoming the difficulties in quantifying spot size over its entire trajectory at the cell membrane.

Here, we present a protocol for single particle tracking image analysis that allows quantitative evaluation of diffusion coefficients, types of motion and cluster sizes of single particles detected by fluorescence microscopy.

Particle tracking on a video sequence and the posterior analysis of their trajectories is nowadays a common operation in many biological studies. Using ...