Changes in Interaction Between Accessory Protein 8 and IL-17RA in UK Isolates Caused by Mutations in the SARS-CoV-2 Open Reading Frame 8

Year 2021, , 76 - 83, 31.07.2021

Ekrem Akbulut

https://doi.org/10.22399/ijcesen.935624

Abstract

SARS-CoV-2 is the infectous agent of Covid-19, one of the most important health problems of the twenty-first century. IL-17RA is an crucial receptor in the generation of the host immune response. ORF8 is the viral accessory protein of SARS-CoV-2 that suppresses the host immune response. Mutations can alter the viral properties and clinical course of SARS-CoV-2. In this study, we investigated the changes that SARS-CoV-2 ORF8 mutations may cause in the interaction of IL-17RA with ORF8. The study was carried out using 825 complete genome sequences from UK isolates. Mutation analyzes were performed using RDP4 and MEGAX. The protein model was created using the Swiss Model. Protein protein interaction was analyzed by Haddock ver 2.4. Analysis of changes in protein stability was performed using SDM2, mCSM stability and DUET tools. The change in ORF8 - IL-17RA binding affinity before and after the mutation was evaluated using mCSM-PPI2. We detected P30S, R52I, Y73C and L118V mutations in SARS-CoV-2 ORF8. Mutations have been shown to reduce protein stability and affinity. After the mutation, the binding dynamics of ORF8 to IL-17RA were changed. Molecular attachment scores were -78.0±3.4 kcal.mol-1 and -76.3±11.9 kcal.mol-1, for wild type and mutant, respectively. After the mutations, the hydrogen bond number and position between ORF8 and IL-17RA changed. While establishing ten hydrogen bonds between the wild type and IL-17RA, four hydrogen bonds were established between the mutant ORF8 and IL-17RA. The decreased affinity between ORF8 and IL-17RA can be seen as a stronger immune response and a milder clinical course. Although our results contain important data for understanding ORF8, which is an important drug target, it needs to be repeated with in-vivo and crystallgraphy studies.

Keywords

SARS-CoV-2, COVID19, Open Reading Frame 8, Accessory Protein 8, Mutation, IL-17RA

Thanks

We gratefully acknowledge the following Authors (See document S1 in Supplementary Material for authors and laboratories that provided genome data used in this study) from the Originating laboratories responsible for obtaining the specimens, as well as the Submitting laboratories where the genome data were generated and shared, on which this research is based. All submitters of data may be contacted directly via www.gisaid.org

References

• [1] Worldometer, "Coronavirus Cases" Worldometer (2020) 1–22. https://doi.org/10.1101/2020.01.23.20018549V2.
• [2] P. Zhou, X. Lou Yang, X.G. Wang, B. Hu, L. Zhang, W. Zhang, H.R. Si, Y. Zhu, B. Li, C.L. Huang, H.D. Chen, J. Chen, Y. Luo, H. Guo, R. Di Jiang, M.Q. Liu, Y. Chen, X.R. Shen, X. Wang, X.S. Zheng, K. Zhao, Q.J. Chen, F. Deng, L.L. Liu, B. Yan, F.X. Zhan, Y.Y. Wang, G.F. Xiao, Z.L. Shi, "A pneumonia outbreak associated with a new coronavirus of probable bat origin" Nature 579 (2020) 270–273. https://doi.org/10.1038/s41586-020-2012-7.
• [3] T.G. Flower, C.Z. Buffalo, R.M. Hooy, M. Allaire, X. Ren, J.H. Hurley, "Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion" Proceedings of the National Academy of Sciences 118 (2020) 1–6. https://doi.org/10.1101/2020.08.27.270637.
• [4] D.E. Gordon, D.E. Gordon, J. Hiatt, M. Bouhaddou, V. V Rezelj, S. Ulferts, "Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms" Science 9403 (2020) 1–38.
• [5] A. Fontanet, B. Autran, B. Lina, M.P. Kieny, S.S.A. Karim, D. Sridhar, "SARS-CoV-2 variants and ending the COVID-19 pandemic" The Lancet 397 (2021) 952–954. https://doi.org/10.1016/S0140-6736(21)00370-6.
• [6] M. Miao, E. De Clercq, G. Li, "Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective" Biomedicines 9 (2021) 412. https://doi.org/10.3390/biomedicines9040412.
• [7] F. Wu, S. Zhao, B. Yu, Y.M. Chen, W. Wang, Z.G. Song, Y. Hu, Z.W. Tao, J.H. Tian, Y.Y. Pei, M.L. Yuan, Y.L. Zhang, F.H. Dai, Y. Liu, Q.M. Wang, J.J. Zheng, L. Xu, E.C. Holmes, Y.Z. Zhang, "A new coronavirus associated with human respiratory disease in China" Nature 579 (2020) 265–269. https://doi.org/10.1038/s41586-020-2008-3.
• [8] F. Pereira, "Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene" Infection, Genetics and Evolution 85 (2020) 1–10. https://doi.org/10.1016/j.meegid.2020.104525.
• [9] C. Baruah, P. Devi, D.K. Sharma, "Sequence analysis and structure prediction of SARS-CoV-2 accessory proteins 9b and ORF14: Evolutionary analysis indicates close relatedness to bat coronavirus" BioMed Research International 2020 (2020) 1–13. https://doi.org/10.1155/2020/7234961.
• [10] Y. Zhang, J. Zhang, Y. Chen, B. Luo, Y. Yuan, F. Huang, T. Yang, F. Yu, J. Liu, B. Liu, Z. Song, J. Chen, T. Pan, X. Zhang, Y. Li, R. Li, W. Huang, F. Xiao, H. Zhang, "The ORF8 protein of SARS-CoV-2 mediates immune evasion through potently downregulating MHC-I" BioRxiv (2020) 1–41. https://doi.org/10.1101/2020.05.24.111823.
• [11] et al. Gordon DE, Jang GM, Bouhaddou M, "A SARS-CoV-2 protein interaction map reveals targets for drug repurposing" Nature 583 (2020) 1–13.
• [12] J.Y. Li, C.H. Liao, Q. Wang, Y.J. Tan, R. Luo, Y. Qiu, X.Y. Ge, "The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway" Virus Research 286 (2020) 198074. https://doi.org/10.1016/j.virusres.2020.198074.
• [13] L.K. Ely, S. Fischer, K.C. Garcia, "Structural basis of receptor sharing by interleukin 17 cytokines" Nature Immunology 10 (2009) 1245–1251. https://doi.org/10.1038/ni.1813.
• [14] D. Toy, D. Kugler, M. Wolfson, T. Vanden Bos, J. Gurgel, J. Derry, J. Tocker, J. Peschon, "Cutting Edge: Interleukin 17 Signals through a Heteromeric Receptor Complex" The Journal of Immunology 177 (2006) 36–39. https://doi.org/10.4049/jimmunol.177.1.36.
• [15] M. Kurte, P. Luz-Crawford, A.M. Vega-Letter, R.A. Contreras, G. Tejedor, R. Elizondo-Vega, L. Martinez-Viola, C. Fernández-O’Ryan, F.E. Figueroa, C. Jorgensen, F. Djouad, F. Carrión, "IL17/IL17RA as a novel signaling axis driving mesenchymal stem cell therapeutic function in experimental autoimmune encephalomyelitis" Frontiers in Immunology 9 (2018) 802. https://doi.org/10.3389/fimmu.2018.00802.
• [16] V. Ramirez-Carrozzi, A. Sambandam, E. Luis, Z. Lin, S. Jeet, J. Lesch, J. Hackney, J. Kim, M. Zhou, J. Lai, Z. Modrusan, T. Sai, W. Lee, M. Xu, P. Caplazi, L. Diehl, J. De Voss, M. Balazs, L. Gonzalez, H. Singh, W. Ouyang, R. Pappu, "IL-17C regulates the innate immune function of epithelial cells in an autocrine manner" Nature Immunology 12 (2011) 1159–1166. https://doi.org/10.1038/ni.2156.
• [17] B. Neupane, D. Acharya, F. Nazneen, G. Gonzalez-Fernandez, A.S. Flynt, F. Bai, "Interleukin-17A Facilitates Chikungunya Virus Infection by Inhibiting IFN-α2 Expression" Frontiers in Immunology 11 (2020) 2955. https://doi.org/10.3389/fimmu.2020.588382.
• [18] W.T. Ma, X.T. Yao, Q. Peng, D.K. Chen, "The protective and pathogenic roles of IL-17 in viral infections: Friend or foe?" Open Biology 9 (2019) 190109. https://doi.org/10.1098/rsob.190109.
• [19] V.K. Bhardwaj, R. Singh, P. Das, R. Purohit, "Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs" Computers in Biology and Medicine 128 (2021) 1–13. https://doi.org/10.1016/j.compbiomed.2020.104117.
• [20] GISAID, "GISAID - Next hCoV-19 App" Genomic Epidemiology of HCoV-19 (2020). https://www.gisaid.org (accessed April 1, 2021).
• [21] K. Katoh, "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform" Nucleic Acids Research 30 (2002) 3059–3066. https://doi.org/10.1093/nar/gkf436.
• [22] K. Katoh, J. Rozewicki, K.D. Yamada, "MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization" Briefings in Bioinformatics 20 (2018) 1160–1166. https://doi.org/10.1093/bib/bbx108.
• [23] D.W. Mount, "Using BLOSUM in sequence alignments" Cold Spring Harbor Protocols 3 (2008) pdb-top39. https://doi.org/10.1101/pdb.top39.
• [24] D.W. Mount, "Using PAM matrices in sequence alignments" Cold Spring Harbor Protocols 3 (2008) 1–9. https://doi.org/10.1101/pdb.top38.
• [25] D.P. Martin, B. Murrell, M. Golden, A. Khoosal, B. Muhire, "RDP4: Detection and analysis of recombination patterns in virus genomes" Virus Evolution 1 (2015). https://doi.org/10.1093/ve/vev003.
• [26] S. Kumar, G. Stecher, M. Li, C. Knyaz, K. Tamura, "MEGA X: Molecular evolutionary genetics analysis across computing platforms" Molecular Biology and Evolution 35 (2018) 1547–1549. https://doi.org/10.1093/molbev/msy096.
• [27] A. Waterhouse, M. Bertoni, S. Bienert, G. Studer, G. Tauriello, R. Gumienny, F.T. Heer, T.A.P. De Beer, C. Rempfer, L. Bordoli, R. Lepore, T. Schwede, "Swiss-Model: Homology modelling of protein structures and complexes" Nucleic Acids Research 46 (2018) W296–W303. https://doi.org/10.1093/nar/gky427.
• [28] M. Wiederstein, M.J. Sippl, "ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins" Nucleic Acids Research (2007). https://doi.org/10.1093/nar/gkm290.
• [29] V.B. Chen, W.B. Arendall, J.J. Headd, D.A. Keedy, R.M. Immormino, G.J. Kapral, L.W. Murray, J.S. Richardson, D.C. Richardson, "MolProbity: All-atom structure validation for macromolecular crystallography" Acta Crystallographica Section D: Biological Crystallography 66 (2010) 12–21. https://doi.org/10.1107/S0907444909042073.
• [30] D.W.A. Buchan, F. Minneci, T.C.O. Nugent, K. Bryson, D.T. Jones, "Scalable web services for the PSIPRED Protein Analysis Workbench." Nucleic Acids Research 41 (2013) W349–W357. https://doi.org/10.1093/nar/gkt381.
• [31] Y. Zhang, J. Skolnick, "Scoring function for automated assessment of protein structure template quality" Proteins: Structure, Function and Genetics 57 (2004) 702–710. https://doi.org/10.1002/prot.20264.
• [32] J. Xu, Y. Zhang, "How significant is a protein structure similarity with TM-score = 0.5?" Bioinformatics 26 (2010) 889–895. https://doi.org/10.1093/bioinformatics/btq066.
• [33] G.C.P. Van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. Van Dijk, S.J. De Vries, A.M.J.J. Bonvin, "The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes" Journal of Molecular Biology 428 (2016) 720–725. https://doi.org/10.1016/j.jmb.2015.09.014.
• [34] A.P. Pandurangan, B. Ochoa-Montaño, D.B. Ascher, T.L. Blundell, "SDM: A server for predicting effects of mutations on protein stability" Nucleic Acids Research 45 (2017) W229–W235. https://doi.org/10.1093/nar/gkx439.
• [35] D.E. V Pires, D.B. Ascher, T.L. Blundell, "DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach" Nucleic Acids Research 42 (2014) W314–W319.
• [36] C.H.M. Rodrigues, Y. Myung, D.E.V. Pires, D.B. Ascher, "MCSM-PPI2: predicting the effects of mutations on protein-protein interactions" Nucleic Acids Research 47 (2019) W338–W344. https://doi.org/10.1093/nar/gkz383.
• [37] D. Davis, Ö.N. Yaveroʇlu, N. Malod-Dognin, A. Stojmirovic, N. Pržulj, "Topology-function conservation in protein-protein interaction networks" Bioinformatics 31 (2015) 1632–1639. https://doi.org/10.1093/bioinformatics/btv026.
• [38] Y. Liu, C. Zhang, F. Huang, Y. Yang, F. Wang, J. Yuan, Z. Zhang, Y. Qin, X. Li, D. Zhao, S. Li, S. Tan, Z. Wang, J. Li, C. Shen, J. Li, L. Peng, W. Wu, M. Cao, L. Xing, Z. Xu, L. Chen, C. Zhou, W.J. Liu, L. Liu, C. Jiang, "Elevated plasma levels of selective cytokines in COVID-19 patients reflect viral load and lung injury" National Science Review 7 (2020) 1003–1011. https://doi.org/10.1093/nsr/nwaa037.
• [39] C. Huang, Y. Wang, X. Li, L. Ren, J. Zhao, Y. Hu, L. Zhang, G. Fan, J. Xu, X. Gu, Z. Cheng, T. Yu, J. Xia, Y. Wei, W. Wu, X. Xie, W. Yin, H. Li, M. Liu, Y. Xiao, H. Gao, L. Guo, J. Xie, G. Wang, R. Jiang, Z. Gao, Q. Jin, J. Wang, B. Cao, "Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China" The Lancet 395 (2020) 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5.
• [40] C. Qin, L. Zhou, Z. Hu, S. Zhang, S. Yang, Y. Tao, C. Xie, K. Ma, K. Shang, W. Wang, D.S. Tian, "Dysregulation of immune response in patients with coronavirus 2019 (COVID-19) in Wuhan, China" Clinical Infectious Diseases 71 (2020) 762–768. https://doi.org/10.1093/cid/ciaa248.
• [41] G. Chen, D. Wu, W. Guo, Y. Cao, D. Huang, H. Wang, T. Wang, X. Zhang, H. Chen, H. Yu, X. Zhang, M. Zhang, S. Wu, J. Song, T. Chen, M. Han, S. Li, X. Luo, J. Zhao, Q. Ning, "Clinical and immunological features of severe and moderate coronavirus disease 2019" Journal of Clinical Investigation 130 (2020) 2620–2629. https://doi.org/10.1172/JCI137244.
• [42] B.E. Young, S.W. Fong, Y.H. Chan, T.M. Mak, L.W. Ang, D.E. Anderson, C.Y.P. Lee, S.N. Amrun, B. Lee, Y.S. Goh, Y.C.F. Su, W.E. Wei, S. Kalimuddin, L.Y.A. Chai, S. Pada, S.Y. Tan, et al., "Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study" The Lancet 396 (2020) 603–611. https://doi.org/10.1016/S0140-6736(20)31757-8.
• [43] A. Goepfert, S. Lehmann, J. Blank, F. Kolbinger, J.M. Rondeau, "Structural Analysis Reveals that the Cytokine IL-17F Forms a Homodimeric Complex with Receptor IL-17RC to Drive IL-17RA-Independent Signaling" Immunity 52 (2020) 499-512.e5. https://doi.org/10.1016/j.immuni.2020.02.004.
• [44] M. Veldhoen, "Interleukin 17 is a chief orchestrator of immunity" Nature Immunology 18 (2017) 612–621. https://doi.org/10.1038/ni.3742.
• [45] L. Zinzula, "Lost in deletion: The enigmatic ORF8 protein of SARS-CoV-2" Biochemical and Biophysical Research Communications 538 (2021) 116–124. https://doi.org/10.1016/j.bbrc.2020.10.045.