Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics
Unpredictable influenza pandemics, annual epidemics, and sporadic poultry-to-human avian influenza virus infections with high morbidity and mortality rates dictate a need to develop new antiviral approaches. Targeting cellular pathways and processes is a promising antiviral strategy shown to be effe...
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MDPI AG
2020-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/21/8294 |
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| author | Vera Ulyanova Raihan Shah Mahmud Alexander Laikov Elena Dudkina Maria Markelova Ahmed Mostafa Stephan Pleschka Olga Ilinskaya |
| author_facet | Vera Ulyanova Raihan Shah Mahmud Alexander Laikov Elena Dudkina Maria Markelova Ahmed Mostafa Stephan Pleschka Olga Ilinskaya |
| author_sort | Vera Ulyanova |
| collection | DOAJ |
| description | Unpredictable influenza pandemics, annual epidemics, and sporadic poultry-to-human avian influenza virus infections with high morbidity and mortality rates dictate a need to develop new antiviral approaches. Targeting cellular pathways and processes is a promising antiviral strategy shown to be effective regardless of viral subtypes or viral evolution of drug-resistant variants. Proteomics-based searches provide a tool to reveal the druggable stages of the virus life cycle and to understand the putative antiviral mode of action of the drug(s). Ribonucleases (RNases) of different origins not only demonstrate antiviral effects that are mediated by the direct RNase action on viral and cellular RNAs but can also exert their impact by signal transduction modulation. To our knowledge, studies of the RNase-affected cell proteome have not yet been performed. To reveal cellular targets and explain the mechanisms underlying the antiviral effect employed by the small extra-cellular ribonuclease of <i>Bacillus pumilus</i> (binase) both in vitro and in vivo, qualitative shotgun and quantitative targeted proteomic analyses of the influenza A virus (IAV) H1N1pdm09-infected A549 cells upon binase treatment were performed. We compared proteomes of mock-treated, binase-treated, virus-infected, and virus-infected binase-treated cells to determine the proteins affected by IAV and/or binase. In general, IAV demonstrated a downregulating strategy towards cellular proteins, while binase had an upregulating effect. With the help of bioinformatics approaches, coregulated cellular protein sets were defined and assigned to their biological function; a possible interconnection with the progression of viral infection was conferred. Most of the proteins downregulated by IAV (e.g., AKR1B1, AKR1C1, CCL5, PFN1, RAN, S100A4, etc.) belong to the processes of cellular metabolism, response to stimulus, biological regulation, and cellular localization. Upregulated proteins upon the binase treatment (e.g., AKR1B10, CAP1, HNRNPA2B1, PFN1, PPIA, YWHAB, etc.) are united by the processes of biological regulation, cellular localization, and immune and metabolic processes. The antiviral activity of binase against IAV was expressed by the inversion of virus-induced proteomic changes, resulting in the inhibition of virus-associated processes, including nuclear ribonucleoprotein export (NCL, NPM1, Nup205, and Bax proteins involved) and cytoskeleton remodeling (RDX, PFN1, and TUBB) induced by IAV at the middle stage of single-cycle infection in A549 cells. Modulation of the immune response could be involved as well. Overall, it seems possible that binase exerts its antiviral effects in multiple ways. |
| first_indexed | 2024-03-10T15:03:56Z |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T15:03:56Z |
| publishDate | 2020-11-01 |
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| spelling | doaj.art-53a28e6b8dbe436d955efa08b5296db02023-11-20T19:53:38ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-11-012121829410.3390/ijms21218294Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative ProteomicsVera Ulyanova0Raihan Shah Mahmud1Alexander Laikov2Elena Dudkina3Maria Markelova4Ahmed Mostafa5Stephan Pleschka6Olga Ilinskaya7Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, RussiaInstitute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, RussiaInstitute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, RussiaInstitute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, RussiaInstitute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, RussiaInstitute of Medical Virology, Justus Liebig University Giessen, 35392 Giessen, GermanyInstitute of Medical Virology, Justus Liebig University Giessen, 35392 Giessen, GermanyInstitute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, RussiaUnpredictable influenza pandemics, annual epidemics, and sporadic poultry-to-human avian influenza virus infections with high morbidity and mortality rates dictate a need to develop new antiviral approaches. Targeting cellular pathways and processes is a promising antiviral strategy shown to be effective regardless of viral subtypes or viral evolution of drug-resistant variants. Proteomics-based searches provide a tool to reveal the druggable stages of the virus life cycle and to understand the putative antiviral mode of action of the drug(s). Ribonucleases (RNases) of different origins not only demonstrate antiviral effects that are mediated by the direct RNase action on viral and cellular RNAs but can also exert their impact by signal transduction modulation. To our knowledge, studies of the RNase-affected cell proteome have not yet been performed. To reveal cellular targets and explain the mechanisms underlying the antiviral effect employed by the small extra-cellular ribonuclease of <i>Bacillus pumilus</i> (binase) both in vitro and in vivo, qualitative shotgun and quantitative targeted proteomic analyses of the influenza A virus (IAV) H1N1pdm09-infected A549 cells upon binase treatment were performed. We compared proteomes of mock-treated, binase-treated, virus-infected, and virus-infected binase-treated cells to determine the proteins affected by IAV and/or binase. In general, IAV demonstrated a downregulating strategy towards cellular proteins, while binase had an upregulating effect. With the help of bioinformatics approaches, coregulated cellular protein sets were defined and assigned to their biological function; a possible interconnection with the progression of viral infection was conferred. Most of the proteins downregulated by IAV (e.g., AKR1B1, AKR1C1, CCL5, PFN1, RAN, S100A4, etc.) belong to the processes of cellular metabolism, response to stimulus, biological regulation, and cellular localization. Upregulated proteins upon the binase treatment (e.g., AKR1B10, CAP1, HNRNPA2B1, PFN1, PPIA, YWHAB, etc.) are united by the processes of biological regulation, cellular localization, and immune and metabolic processes. The antiviral activity of binase against IAV was expressed by the inversion of virus-induced proteomic changes, resulting in the inhibition of virus-associated processes, including nuclear ribonucleoprotein export (NCL, NPM1, Nup205, and Bax proteins involved) and cytoskeleton remodeling (RDX, PFN1, and TUBB) induced by IAV at the middle stage of single-cycle infection in A549 cells. Modulation of the immune response could be involved as well. Overall, it seems possible that binase exerts its antiviral effects in multiple ways.https://www.mdpi.com/1422-0067/21/21/8294influenza virusribonucleasebinaseantiviral activityproteomicsliquid chromatography-tandem mass spectrometry (LC-MS/MS) |
| spellingShingle | Vera Ulyanova Raihan Shah Mahmud Alexander Laikov Elena Dudkina Maria Markelova Ahmed Mostafa Stephan Pleschka Olga Ilinskaya Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics International Journal of Molecular Sciences influenza virus ribonuclease binase antiviral activity proteomics liquid chromatography-tandem mass spectrometry (LC-MS/MS) |
| title | Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics |
| title_full | Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics |
| title_fullStr | Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics |
| title_full_unstemmed | Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics |
| title_short | Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics |
| title_sort | anti influenza activity of the ribonuclease binase cellular targets detected by quantitative proteomics |
| topic | influenza virus ribonuclease binase antiviral activity proteomics liquid chromatography-tandem mass spectrometry (LC-MS/MS) |
| url | https://www.mdpi.com/1422-0067/21/21/8294 |
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