Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics
Abstract
:1. Introduction
2. Results
2.1. Confirmation of Viral Infection of A549 Cells and Antiviral Action of Binase
2.2. Qualitative Shotgun Proteomic Profiling of Virus-Infected and Binase-Treated Cells
2.3. Quantitative Proteomic Profiling of Virus-Infected and Binase-Treated Cells
3. Discussion
4. Materials and Methods
4.1. Materials and Methods Cell Culture, Virus, and Binase
4.2. Determination of Virus Titers by Focus Forming Assay (FFA)
4.3. Cell Treatment and Lysis
4.4. Qualitative Shotgun Proteomics
4.4.1. “In-Solution” Protein Digestion
4.4.2. LC-MS/MS Analysis
4.4.3. Database Search
4.5. Quantitative Targeted Proteomics
4.5.1. “In-gel” Protein Digestion
4.5.2. “In-Silico” Protein Digestion
4.5.3. Targeted LC-MS/MS Analysis (LC-MRM/MS)
4.6. Protein Networks and Pathway Analysis
4.7. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Binase or IAV Effect | GO Term | Biological Process or Cellular Component | Proteins |
---|---|---|---|
Downregulated by IAV | |||
GO:0051186 | Cofactor metabolic process | PKM, ENO1, PGK1, LDHA, GPI, PGAM, G6PD, TKT, AKR1B1, AKR1B10, AKR1C3, AKR1C1, HSP90AA1 | |
GO:0044281 | Small-molecule metabolic process | SORL1, ALDH1A1, ACSS3, RAN, HSPA8, TARS, MAPK1, MAPK3 | |
GO:0006955 | Immune response | CCL5, MDA5, PPIA, HSPA8, HSP90AA1, EEF1A1, MAPK1, MAPK3, TUBB4B, TUBB, PKM, ACTB, GPI, PGAM1, G6PD | |
GO:0007010 | cytoskeleton organization | TUBB3, TUBA4A, TUBB4B, ACTB, PFN1 | |
GO:0006810, GO:0051179 | transport and localization | SORL1, RDX, RAN, YWHAB, TOMM5 | |
Upregulated by IAV | |||
GO:0045321 | leucocyte activation | SPTAN1, DDX3X, HSPD1, RAB10, ANXA2, TXNDC5 | |
GO:0065003 | protein-containing complex assembly | ATL3, EIF3A, NDUFS8, ANXA2, HSPD1, DDX3X | |
Downregulated by binase | |||
GO:0016020 | Membrane | LRPPRC, TRAP1, HSPD1, PHB2, SURF4, NDUFS8, KRT10, PON2, MYOF, RAP1A | |
Upregulated by binase | |||
GO:0010468 | regulation of gene expression | PFN1, DNAJB1, EEF1A1, PPP2CA, PRKDC, XRCC6, NCL, RDX, MSN, ACTB, MAPK1, MAPK2, YWHAB, HSPA8, RAN, RPS2, RPSA, RPL15, EIF3K, EIF2A, EIF3E, EIF3H, HNRNPA2B1, CAND1, CCL5, TRAP1, C14ORF166, ENO1 | |
GO:0006887 | exocytosis | CAND1, CCL5, PGAM1, GPI, PKM, ANXA2, PYGB, CAP1, TUBB, TUBB4B, TUBB4A, TXNDC5, PPI, MAPK1, RAP1A, HSP90AA1, HSPA8, ANXA5, EEF1A1, SPTAN, PSMD13, XRCC6 | |
GO:0006897 | endocytosis | MAPK3, MAPK1, HSP90AA1, CLTC, ACTB, CAP1, SORL1, TXNDC5 | |
GO:0051641 | cellular localization | RAN, IPO4, HNRNPA2B1, HNRNPA1L2, KIF5B, C14orf166, RDX, MSN, SRP68, RPSA, RPS2, RPL25, BAX, YWHAB, TUBB4A, TUBB, TUBB4B, ACTB, CLTC, ANXA2, ANXA5, SORL1, AKR1C1, AKR1C3, TXNDC5, PPIA | |
GO:0042786 | immune process | MDA5, CCL5, PGAM1, PKM, HSPA8, PSMD3, CAND1, KIF5B, XRCC6, RAP1A, HSP90AA1, EEE1A1, MAPK1, PPIA, GPI, PYGB, CAP1, ANXA2, SPTAN1, BAX, TUBB4B, TXNDC5, TUBB, MSN | |
GO:0055114, GO:0008152 | oxidation-reduction and metabolic processes | AKR1C3, AKR1C1, AKR1B10, ALDH16A1, ALDH18A1, ALDH1A1, ALDH3A1, FASN, PYGB, GPI, G6PD, LDHA, ENO1, PGAM1, PKM, PGK1 | |
Upregulated by binase in IAV-infected cells | |||
GO:0051186, GO:1901135, GO:0001523, GO:0006629, GO:0050896 | cofactor metabolic process, carbohydrate derivative metabolic process, retinoid metabolic process, lipid metabolic process, response to stimulus | AKR1B1, AKR1B10, AKR1C1, AKR1C3, ANXA5, ENO1, PFN1, PGAM1, PGK1, PPIA | |
GO:0022406 | membrane docking | TUBB, TUBB4A, TUBB4B, HSP90AA1 | |
GO:0006955 | immune response | MDA5, CCL5, CAP1, KIF5B, MAPK3, TUBB, TUBB4A, TUBB4B, HSP90AA1 | |
Downregulated by binase in IAV-infected cells | |||
GO:0016032 | viral process | NPM1, HSPD1, EIF3L, EIF3A | |
GO:0007029 | endoplasmic reticulum organization | RAB10, ATL3 | |
GO:0043066 | negative regulation of apoptosis | TXNDC5, KRAS, NPM1, HSPD1, and HTATIP2 | |
GO:0061028 | establishment of endothelial barrier | RDX, EZR, RAP1A, FASN | |
GO:0006413 | translational initiation | RPL15, RPSA, EIF3H, EIF3E, RPS2 | |
GO:0032272 | negative regulation of protein polymerization | MAPRE1, SRTAN1, RDX | |
GO:0034470 | ncRNA processing | SSB, C14orf166, RPSA, RPS2, SKIV2L2 | |
GO:0045321, GO:0042119 | leukocyte and neutrophil activation | BAX, CCL5, SPTAN1, RAP1A, CAP1, SURF4, PRKDC | |
GO:0044056 | symbiont process | CCL5, NUP205, BAX, C14orf166, RPSA, SSB | |
GO:0006913 | nucleocytoplasmic transport | PHB2, RPSA, NUP205, SSB | |
GO:0070372 | regulation of ERK1 and ERK2 cascade | PHB2, RAP1A, CCL5, EZR | |
GO:0010467, GO:0006349 | gene expression and its regulation | PRKDC, TRAP1, DNAJB1, YLPM1, C14orf166, SSB, RDX, EZR, CCL5, RPSA, RPL15, RPS2, EIF3H, EIF3E, PHB2, SNRNP200, SKIV2L2, BAX, NUP205 | |
GO:0051234 | establishment of localization | CLINT1, CCL5, NUP205, BAX, MAPRE1, C14orf166, RPL15, RPSA, RPS2, SSB, RAP1A, SPTAN1, EZR, RDX, CAP1, SURF4, PHB2 |
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Ulyanova, V.; Shah Mahmud, R.; Laikov, A.; Dudkina, E.; Markelova, M.; Mostafa, A.; Pleschka, S.; Ilinskaya, O. Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics. Int. J. Mol. Sci. 2020, 21, 8294. https://doi.org/10.3390/ijms21218294
Ulyanova V, Shah Mahmud R, Laikov A, Dudkina E, Markelova M, Mostafa A, Pleschka S, Ilinskaya O. Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics. International Journal of Molecular Sciences. 2020; 21(21):8294. https://doi.org/10.3390/ijms21218294
Chicago/Turabian StyleUlyanova, Vera, Raihan Shah Mahmud, Alexander Laikov, Elena Dudkina, Maria Markelova, Ahmed Mostafa, Stephan Pleschka, and Olga Ilinskaya. 2020. "Anti-Influenza Activity of the Ribonuclease Binase: Cellular Targets Detected by Quantitative Proteomics" International Journal of Molecular Sciences 21, no. 21: 8294. https://doi.org/10.3390/ijms21218294