Name: identifying caspases and their motifs that cleave proteins during influenza a virus infection
Uploaded: 2022-07-21T15:00:00
Description: Watch this Scientific Journal Video about Identifying Caspases and their Motifs that Cleave Proteins During Influenza A Virus Infection at JoVE.com

The author acknowledges Jennifer Tipper, Bilan Li, Jesse vanWestrienen, Kevin Harrod, Da-Yuan Chen, Farjana Ahmed, Sonya Mros, Kenneth Yamada, Richard Webby, the BEI Resources (NIAID), the Health Research Council of New Zealand, the Maurice and Phyllis Paykel Trust (New Zealand), the H.S. and J.C. Anderson Trust (Dunedin), and the Department of Microbiology and Immunology and School of Biomedical Sciences (University of Otago).

Regulatory approvals were obtained from the University of Otago Institutional Biological Safety Committee to work with the IAV and mammalian cells. Madin-Darby Canine Kidney (MDCK) or human lung alveolar epithelial A549 cells and IAV H1N1 subtypes were used for the present study. IAV was grown in chicken eggs, as described elsewhere17. Sterile and aseptic conditions were used to work with mammalian cells, and a Biosafety Level 2 (or Physical Containment 2) facility and Class II biosafety cabinet w...

<ol>
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Y., Husain, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Caspase-mediated+cleavage+of+human+cortactin+during+influenza+A+virus+infection+occurs+in+its+actin-binding+domains+and+is+associated+with+released+virus+titres.">Caspase-mediated cleavage of human cortactin during influenza A virus infection occurs in its actin-binding domains and is associated with released virus titres.</a> Viruses. 12 (1), 87 (2020).</li><li>Zhirnov, O. P., Syrtzev, V. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Influenza+virus+pathogenicity+is+determined+by+caspase+cleavage+motifs+located+in+the+viral+proteins.">Influenza virus pathogenicity is determined by caspase cleavage motifs located in the viral proteins.</a> Journal of Molecular and Genetic Medicine. 3 (1), 124-132 (2009).</li><li>Zhirnov, O. P., Klenk, H. -. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alterations+in+caspase+cleavage+motifs+of+NP+and+M2+proteins+attenuate+virulence+of+a+highly+pathogenic+avian+influenza+virus.">Alterations in caspase cleavage motifs of NP and M2 proteins attenuate virulence of a highly pathogenic avian influenza virus.</a> Virology. 394 (1), 57-63 (2009).</li><li>Zhirnov, O. P., Konakova, T. E., Garten, W., Klenk, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Caspase-dependent+N-terminal+cleavage+of+influenza+virus+nucleocapsid+protein+in+infected+cells.">Caspase-dependent N-terminal cleavage of influenza virus nucleocapsid protein in infected cells.</a> Journal of Virology. 73 (12), 10158-10163 (1999).</li><li>Robinson, B. A., Van Winkle, J. A., McCune, B. T., Peters, A. M., Nice, T. 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S., Cieplak, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Caspase+cleavage+sites+in+the+human+proteome:+CaspDB,+a+database+of+predicted+substrates.">Caspase cleavage sites in the human proteome: CaspDB, a database of predicted substrates.</a> PLoS One. 9 (10), 110539 (2014).</li><li>Igarashi, Y., 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=CutDB:+A+proteolytic+event+database.">CutDB: A proteolytic event database.</a> Nucleic Acids Research. 35 (Database issue). 35, 546-549 (2007).</li><li>Crawford, E. 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It is established that viruses tailor the host factors and pathways to their benefit. In turn, the host cells resist that by employing various strategies. One of those strategies is PANoptosis, which host cells use as an antiviral strategy against virus infections. However, viruses like IAV have evolved their own strategies to counter PANoptosis and exploit it to their advantage1,3,6. This interplay involves the cleavage of vari...

Influenza A virus (IAV) is the prototypic member of the Orthomyxoviridae family and is known to cause global epidemics and unpredictable pandemics. IAV causes human respiratory disease, influenza, commonly known as &#34;flu&#34;. The flu is an acute disease that results in the induction of host pro- and anti-inflammatory innate immune responses and the death of epithelial cells in the human respiratory tract. Both processes are governed by a phenomenon called programmed cell death1. The signaling for programmed cell death is induced as soon as various pathogen recognition receptors sense the incoming virus particles in host cells. This leads to the programming of the death of infected cells and signaling to the neighboring healthy cells by three interconnected pathways called pyroptosis, apoptosis, and necroptosis-recently coined as one process, PANoptosis1.
PANoptosis involves the proteolytic processing of many host and viral proteins from induction to execution. Such processing of proteins is primarily spearheaded by a family of cysteine proteases called caspases1,2. Up to 18 caspases (from caspase 1 to caspase 18) are known3. Most caspases are expressed as pro-caspases and activated by undergoing their own proteolytic processing either by autocatalysis or other caspases4 in response to a stimulus like a virus infection. The PANoptosis of IAV-infected cells was thought to be a host defense mechanism, but IAV has evolved ways to evade and exploit it to facilitate its replication1,2,5,6. One of them is to antagonize the host factors via caspase-mediated cleavage or degradation that are either inherently antiviral or interfere with one of the steps of the IAV life cycle. To this end, host factors, cortactin, HDAC4, and HDAC6 have been discovered to undergo caspase-mediated cleavage or degradation in IAV-infected epithelial cells7,8,9. The HDAC4 and HDAC6 are anti-IAV factors8,10, and cortactin interferes with IAV replication at a later stage of infection, potentially during viral assembly and budding11.
In addition, various caspases are also activated, which, in turn, cleave multiple proteins to activate the host inflammatory response during IAV infection1,2. Furthermore, nucleoprotein (NP), ion-channel M2 protein of IAV12,13,14, and various proteins of other viruses3,15,16 also undergo caspase-mediated cleavage during infection, which influences viral pathogenesis. Therefore, there is a continuous need to study caspase-mediated cleavage or degradation of host and viral proteins during IAV and other virus infections to understand the molecular basis of viral pathogenesis. Herein, the methods are presented to (1) assess the cleavage or degradation of such proteins by caspases, (2) identify those caspases, and (3) locate the cleavage sites.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>A549 cells</td>
			<td>ATCC</td>
			<td>CRM-CCL-185</td>
			<td>Human, epithelial, lung</td>
		</tr>
		<tr>
			<td>Ammonium chloride</td>
			<td>Sigma-Aldrich</td>
			<td>A9434</td>
			<td></td>
		</tr>
		<tr>
			<td>Caspase 3 Inhibitor</td>
			<td>Sigma-Aldrich</td>
			<td>264156-M</td>
			<td>Also known as &#39;InSolution Caspase-3 Inhibitor II - Calbiochem&#39;</td>
		</tr>
		<tr>
			<td>cOmplete, Mini Protease Inhibitor Cocktail</td>
			<td>Roche</td>
			<td>11836153001</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat anti-NP antibody</td>
			<td></td>
			<td></td>
			<td>Gift from Richard Webby (St Jude Children&#8217;s Research Hospital, Memphis, USA) to MH</td>
		</tr>
		<tr>
			<td>Lipofectamine 2000 Transfection Reagent</td>
			<td>ThermoFisher Scientific</td>
			<td>31985062</td>
			<td></td>
		</tr>
		<tr>
			<td>Lipofectamine RNAiMAX Transfection Reagent</td>
			<td>ThermoFisher Scientific</td>
			<td>13778150</td>
			<td></td>
		</tr>
		<tr>
			<td>MDCK cells</td>
			<td>ATCC</td>
			<td>CCL-34</td>
			<td>Dog, epithelial, kidney</td>
		</tr>
		<tr>
			<td>MG132</td>
			<td>Sigma-Aldrich</td>
			<td>M7449</td>
			<td></td>
		</tr>
		<tr>
			<td>Minimum Essential Medium (MEM)</td>
			<td>ThermoFisher Scientific</td>
			<td>11095080</td>
			<td>Add L-glutamine, antibiotics or other supplements as required</td>
		</tr>
		<tr>
			<td>MISSION siRNA Universal Negative Control #1</td>
			<td>Sigma-Aldrich</td>
			<td>SIC001</td>
			<td></td>
		</tr>
		<tr>
			<td>Odyssey Fc imager with Image Studio Lite software 5.2&#160;</td>
			<td>LI-COR</td>
			<td></td>
			<td>Odyssey Fc has been replaced with Odyssey XF and Image Studio Lite software has been replaced with Empiria Studio software.</td>
		</tr>
		<tr>
			<td>Pierce BCA Protein Assay Kit</td>
			<td>ThermoFisher Scientific</td>
			<td>23225</td>
			<td></td>
		</tr>
		<tr>
			<td>Plasmid expressing human cortactin-GFP fusion&#160;</td>
			<td>Addgene</td>
			<td>50728</td>
			<td>Gift from Kenneth Yamada to Addgene</td>
		</tr>
		<tr>
			<td>Pre-designed small interferring RNA (siRNA) to caspase 3</td>
			<td>Sigma-Aldrich</td>
			<td>NM_004346</td>
			<td>siRNA ID: SASI_Hs01_00139105</td>
		</tr>
		<tr>
			<td>Pre-designed small interferring RNA to caspase 6</td>
			<td>Sigma-Aldrich</td>
			<td>NM_001226</td>
			<td>siRNA ID: SASI_Hs01_00019062</td>
		</tr>
		<tr>
			<td>Pre-designed small interferring RNA to caspase 7</td>
			<td>Sigma-Aldrich</td>
			<td>NM_001227</td>
			<td>siRNA ID: SASI_Hs01_00128361</td>
		</tr>
		<tr>
			<td>Pre-designed SYBR Green RT-qPCR Primer pairs</td>
			<td>Sigma-Aldrich</td>
			<td>KSPQ12012</td>
			<td>Primer Pair IDs: H_CASP3_1; H_CASP6_1; H_CASP7_1</td>
		</tr>
		<tr>
			<td>Protran Premium nitrocellulose membrane</td>
			<td>Cytiva (Fomerly GE Healthcare)</td>
			<td>10600003</td>
			<td></td>
		</tr>
		<tr>
			<td>Rabbit anti-actin antibody</td>
			<td>Abcam</td>
			<td>ab8227</td>
			<td></td>
		</tr>
		<tr>
			<td>Rabbit anti-cortactin antibody</td>
			<td>Cell Signaling</td>
			<td>3502</td>
			<td></td>
		</tr>
		<tr>
			<td>Rabbit anti-GFP antibody</td>
			<td>Takara</td>
			<td>632592</td>
			<td></td>
		</tr>
		<tr>
			<td>SeeBlue Pre-stained Protein Standard</td>
			<td>ThermoFisher Scientific</td>
			<td>LC5625</td>
			<td></td>
		</tr>
		<tr>
			<td>Transfection medium, Opti-MEM</td>
			<td>ThermoFisher Scientific</td>
			<td>11668019</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris-HCl, NaCl, SDS, Sodium Deoxycholate, Triton X-100</td>
			<td>Merck</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin, TPCK-Treated</td>
			<td>Sigma-Aldrich</td>
			<td>4370285</td>
			<td></td>
		</tr>
	</tbody>
</table>

identifying caspases and their motifs that cleave proteins during influenza a virus infection

Caspases, a family of cysteine proteases, orchestrate programmed cell death in response to various stimuli, including microbial infections. Initially described to occur by apoptosis, programmed cell death is now known to encompass three interconnected pathways: pyroptosis, apoptosis, and necroptosis, together coined as one process, PANoptosis. Influence A virus (IAV) infection induces PANoptosis in mammalian cells by inducing the activation of different caspases, which, in turn, cleave various host as well as viral proteins, leading to processes like the activation of the host innate antiviral response or the degradation of antagonistic host proteins. In this regard, caspase 3-mediated cleavage of host cortactin, histone deacetylase 4 (HDAC4), and histone deacetylase 6 (HDAC6) has been discovered in both animal and human epithelial cells in response to the IAV infection. To demonstrate this, inhibitors, RNA interference, and site-directed mutagenesis were employed, and, subsequently, the cleavage or resistance to cleavage and the recovery of cortactin, HDAC4, and HDAC6 polypeptides were measured by western blotting. These methods, in conjunction with RT-qPCR, form a simple yet effective strategy to identify the host as well as viral proteins undergoing caspase-mediated cleavage during an infection of IAV or other human and animal viruses. The present protocol elaborates the representative results of this strategy, and the ways to make it more effective are also discussed.

Treatment with caspase 3 inhibitor 
It has been discovered that host cortactin, HDAC4, and HDAC6 polypeptides undergo degradation in response to IAV infection in both canine (MDCK) and human (A549, NHBE) cells7,8,9. By using the above approaches, it was uncovered that IAV-induced host caspases, particularly caspase 3, cause their degradation7,8...

Watch this Scientific Journal Video about Identifying Caspases and their Motifs that Cleave Proteins During Influenza A Virus Infection at JoVE.com

Identifying Caspases and their Motifs that Cleave Proteins During Influenza A Virus Infection

Influenza A virus (IAV) infection activates the caspases that cleave host and viral proteins, which, in turn, have pro- and antiviral functions. By employing inhibitors, RNA interference, site-directed mutagenesis, and western blotting and RT-qPCR techniques, caspases in infected mammalian cells that cleave host cortactin and histone deacetylases were identified.

Caspases, a family of cysteine proteases, orchestrate programmed cell death in response to various stimuli, including microbial infections. Initially ...

This method will help to determine and confirm whether a protein in influenza virus infected cells undergoes degradation or cleavage by caspases and identify the caspase cleavage sites. This method requires only basic molecular and cellular biology laboratory settings and research skills and do not require any specialized equipment or software training. This method can be adapted to achieve similar objectives involving infection with other animal viruses or microbes, and exposure to external stimuli, like toxins and chemicals.To begin, seed MDCK or A549 cells in a 12-well cell culture plate. Incubate the cells overnight at 37 degrees Celsius under a 5%carbon dioxide atmosphere. On the next day, remove the old culture medium from the cells and wash the cells in each well twice with one milliliter of serum-free MEM.Then, infect the cells by adding 400 microliters of influenza A virus inoculum, and place the plate for incubation for one hour. After incubation, remove the virus inoculum and wash the cells with MEM. Add one milliliter of serum-free MEM to each well and incubate the cells as shown in the previous step.After 24 hours, harvest the cells by scraping them with a one-milliliter syringe plunger and transfer them to a 1.5 milliliter tube. Centrifuge the tube at 12, 000G for two minutes at room temperature and collect the supernatant. Wash the cell pellet with 250 microliters of phosphate-buffered saline and centrifuge.Remove the supernatant and add 100 microliters of cell lysis buffer. Mix by vortex. Heat the tube at 98 degrees Celsius for 10 minutes to completely lyse the cells.Then, resolve equal amounts of protein from uninfected and infected samples by standard SDS polyacrylamide gel electrophoresis. After electrophoresis, transfer the protein gel to a nitrocellulose or PVDF membrane and perform Western blotting. Compare the protein levels in the mock-treated and inhibitor-treated infected sample lanes.In 100 microliters of appropriate medium, like Opti-MEM, dilute 100 nanomolars of control or caspase siRNA, or appropriate volume of transfection reagent. Incubate for five minutes at room temperature. Mix 100 microliters of each siRNA solution with 100 microliters of transfection reagent solution and incubate for 20 to 45 minutes at room temperature.Split and add 100, 000 MDCK or A549 cells in 800 microliters of the complete growth medium. Add 200 microliters of siRNA transfection reagent complex and add this suspension to a 12-well culture plate. Incubate the cells at 37 degrees Celsius under a 5%carbon dioxide atmosphere for 72 hours.Infect the cells with influenza A virus, but without inhibitors. Perform Western blotting, and compare the protein levels as shown previously. Locate the caspase cleavage motifs XXXD and DXXD on the polypeptide.Mutate the P1 aspartic acid, two glutamic acid, or alanine by site-directed mutagenesis and confirm by DNA sequencing. In 100 microliters of an appropriate medium, dilute two micrograms of wild-type or mutant plasma DNA or recommended volume of the transfection reagent and incubate the tubes for five minutes at room temperature. Mix 100 microliters of plasma DNA solution with 100 microliters of the transfection reagent solution and incubate for 20 to 45 minutes at room temperature.In the meantime, split and add 300, 000 MDCK or A549 cells to 800 microliters of complete growth medium. Add 200 microliters of DNA transfection reagent complex and add this suspension to a 12-well culture plate. Incubate the plate at 37 degrees Celsius under a 5%carbon dioxide atmosphere.After 48 hours, infect the cells with influenza A virus without inhibitors. Perform Western blotting, and compare the protein levels as shown previously. Using Western blotting, the degradation of host cortactin by influenza-induced host caspases was evaluated.Treatment of the influenza virus infected cells with a caspase-3 inhibitor resulted in the rescue of cortactin and viral NP degradation. Quantification of the intensity of cortactin bands and its normalization with the corresponding actin band showed that the level of cortactin in caspase-3 inhibitor treated infected cells was higher compared to untreated infected cells. In caspase-6 or caspase-7 depleted cells.No significant recovery in cortactin polypeptide levels was observed, whereas in caspase-3 depleted cells, cortactin recovered from the influenza virus induced degradation. Quantification and comparison of polypeptide levels showed that the cortactin polypeptide level in infected cells with depleted caspase-3 expression was higher than cells with normal caspase-3 expression. The mutation of aspartic acid at position 116 to glutamic acid rendered the cortactin polypeptide resistant to influenza virus induced degradation.Quantification and comparison of polypeptide levels showed that the level of mutant cortactin polypeptide in infected cells was higher than that of wild-type cortactin polypeptide. It is required to generate tens of mutants and perform repeated Western blotting to identify the caspase cleavage site in the polypeptide. An in vitro biochemical assay containing purified caspase and target polypeptide could be developed to confirm that the protein of interest is a direct gas-based substrate.This protocol will help to understand the significance, the degradation or cleavage of target protein in the system that is being studied, such as virus infection or a disease.

Research

JoVE Journal

Immunology and Infection

Generation of Recombinant Influenza Virus from Plasmid DNA

Efforts by a number of influenza research groups have been pivotal in the development and improvement of influenza A virus reverse genetics. Originally ...

Using Bioluminescent Imaging to Investigate Synergism Between Streptococcus pneumoniae and Influenza A Virus in Infant Mice

Using Bioluminescent Imaging to Investigate Synergism Between Streptococcus pneumoniae and Influenza A Virus in Infant Mice

During the 1918 influenza virus pandemic, which killed approximately 50 million people worldwide, the majority of fatalities were not the result of ...

High-throughput Detection Method for Influenza Virus

Influenza virus is a respiratory pathogen that causes a high degree of morbidity and mortality every year in multiple parts of the world. Therefore, ...

Peptide-based Identification of Functional Motifs and their Binding Partners

Specific short  peptides derived from motifs found in full-length proteins, in our case HIV-1  Nef, not only retain their biological function, but can ...

Influenza Virus Propagation in Embryonated Chicken Eggs

Influenza infection is associated with about 36,000 deaths and more than 200,000 hospitalizations every year in the United States. The continuous ...

Co-immunoprecipitation of the Mouse Mx1 Protein with the Influenza A Virus Nucleoprotein

Studying the interaction between proteins is key in understanding their function(s). A very powerful method that is frequently used to study interactions ...

Nasal Wipes for Influenza A Virus Detection and Isolation from Swine

Surveillance for influenza A viruses in swine is critical to human and animal health because influenza A virus rapidly evolves in swine populations and ...

Neutrophil Isolation and Analysis to Determine their Role in Lymphoma Cell Sensitivity to Therapeutic Agents

Neutrophils are the most abundant (40% to 75%) type of white blood cells and among the first inflammatory cells to migrate towards the site of ...

In Vitro Disassembly of Influenza A Virus Capsids by Gradient Centrifugation

In Vitro Disassembly of Influenza A Virus Capsids by Gradient Centrifugation

Acid-triggered molecular processes closely control cell entry of many viruses that enter through the endocytic system. In the case of influenza A virus ...

Fluorescence-based Neuraminidase Inhibition Assay to Assess the Susceptibility of Influenza Viruses to The Neuraminidase Inhibitor Class of Antivirals

The neuraminidase (NA) inhibitors are the only class of antivirals approved for the treatment and prophylaxis of influenza that are effective against ...