Interaction of Receptor-Binding Domain of the SARS-CoV-2 Omicron Variant with hACE2 and Actin
Abstract
:1. Introduction
2. Materials and Methods
2.1. Preparation of Plasmid DNA
2.2. Protein Purification
2.3. Immunofluorescence and Confocal Microscopy
2.4. Mass Spectrometry (MS) Analysis
2.5. Western Blotting
2.6. FCCS
2.7. Protein Complex Prediction
2.8. Statistical Analyses
3. Results and Discussion
3.1. Increased Affinity between RBD of the Omicron Variant and hACE2
3.2. Co-Precipitation of β- and γ-Actin with Omicron RBD
3.3. Cytoplasmic RBDOmic Does Not Localize to Actin Filaments
3.4. Binding of RBD to Actin and Its Physiology
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Zhou, P.; Yang, X.L.; Wang, X.G.; Hu, B.; Zhang, L.; Zhang, W.; Si, H.R.; Zhu, Y.; Li, B.; Huang, C.L.; et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020, 579, 270–273. [Google Scholar] [CrossRef] [PubMed]
- Markov, P.V.; Ghafari, M.; Beer, M.; Lythgoe, K.; Simmonds, P.; Stilianakis, N.I.; Katzourakis, A. The evolution of SARS-CoV-2. Nat. Rev. Microbiol. 2023, 21, 361–379. [Google Scholar] [CrossRef] [PubMed]
- Yao, L.; Zhu, K.L.; Jiang, X.L.; Wang, X.J.; Zhan, B.D.; Gao, H.X.; Geng, X.Y.; Duan, L.J.; Dai, E.H.; Ma, M.J. Omicron subvariants escape antibodies elicited by vaccination and BA.2.2 infection. Lancet Infect. Dis. 2022, 22, 1116–1117. [Google Scholar] [CrossRef] [PubMed]
- Wang, Q.; Zhang, Y.; Wu, L.; Niu, S.; Song, C.; Zhang, Z.; Lu, G.; Qiao, C.; Hu, Y.; Yuen, K.Y.; et al. Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2. Cell 2020, 181, 894–904.E9. [Google Scholar] [CrossRef]
- Yan, R.; Zhang, Y.; Li, Y.; Xia, L.; Guo, Y.; Zhou, Q. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science 2020, 367, 1444–1448. [Google Scholar] [CrossRef]
- Belouzard, S.; Chu, V.C.; Whittaker, G.R. Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites. Proc. Natl. Acad. Sci. USA 2009, 106, 5871–5876. [Google Scholar] [CrossRef] [PubMed]
- Li, F.; Li, W.; Farzan, M.; Harrison, S.C. Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science 2005, 309, 1864–1868. [Google Scholar] [CrossRef]
- Laue, T.M.; Shire, S.J. The Molecular Interaction Process. J. Pharm. Sci. 2020, 109, 154–160. [Google Scholar] [CrossRef]
- Shum, M.H.; Lee, Y.; Tam, L.; Xia, H.; Chung, O.L.; Guo, Z.; Lam, T.T. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput. Struct. Biotechnol. J. 2024, 23, 759–770. [Google Scholar] [CrossRef]
- Li, L.; Liao, H.; Meng, Y.; Li, W.; Han, P.; Liu, K.; Wang, Q.; Li, D.; Zhang, Y.; Wang, L.; et al. Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Cell 2022, 185, 2952–2960.E10. [Google Scholar] [CrossRef]
- Harvey, W.T.; Carabelli, A.M.; Jackson, B.; Gupta, R.K.; Thomson, E.C.; Harrison, E.M.; Ludden, C.; Reeve, R.; Rambaut, A.; Consortium, C.-G.U.; et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat. Rev. Microbiol. 2021, 19, 409–424. [Google Scholar] [CrossRef] [PubMed]
- Shah, M.; Woo, H.G. Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Front. Immunol. 2021, 12, 830527. [Google Scholar] [CrossRef]
- Lan, J.; He, X.; Ren, Y.; Wang, Z.; Zhou, H.; Fan, S.; Zhu, C.; Liu, D.; Shao, B.; Liu, T.Y.; et al. Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction. Cell Res. 2022, 32, 593–595. [Google Scholar] [CrossRef] [PubMed]
- Wu, L.; Zhou, L.; Mo, M.; Liu, T.; Wu, C.; Gong, C.; Lu, K.; Gong, L.; Zhu, W.; Xu, Z. SARS-CoV-2 Omicron RBD shows weaker binding affinity than the currently dominant Delta variant to human ACE2. Signal Transduct. Target. Ther. 2022, 7, 8. [Google Scholar] [CrossRef] [PubMed]
- Jawad, B.; Adhikari, P.; Podgornik, R.; Ching, W.Y. Binding Interactions between Receptor-Binding Domain of Spike Protein and Human Angiotensin Converting Enzyme-2 in Omicron Variant. J. Phys. Chem. Lett. 2022, 13, 3915–3921. [Google Scholar] [CrossRef] [PubMed]
- Vukojevic, V.; Papadopoulos, D.K.; Terenius, L.; Gehring, W.J.; Rigler, R. Quantitative study of synthetic Hox transcription factor-DNA interactions in live cells. Proc. Natl. Acad. Sci. USA 2010, 107, 4093–4098. [Google Scholar] [CrossRef] [PubMed]
- Bacia, K.; Kim, S.A.; Schwille, P. Fluorescence cross-correlation spectroscopy in living cells. Nat. Methods 2006, 3, 83–89. [Google Scholar] [CrossRef] [PubMed]
- Kitamura, A.; Kinjo, M. State-of-the-Art Fluorescence Fluctuation-Based Spectroscopic Techniques for the Study of Protein Aggregation. Int. J. Mol. Sci. 2018, 19, 964. [Google Scholar] [CrossRef] [PubMed]
- Iacobucci, I.; Monaco, V.; Cane, L.; Bibbo, F.; Cioffi, V.; Cozzolino, F.; Guarino, A.; Zollo, M.; Monti, M. Spike S1 domain interactome in non-pulmonary systems: A role beyond the receptor recognition. Front. Mol. Biosci. 2022, 9, 975570. [Google Scholar] [CrossRef] [PubMed]
- Zhou, Y.; Liu, Y.; Gupta, S.; Paramo, M.I.; Hou, Y.; Mao, C.; Luo, Y.; Judd, J.; Wierbowski, S.; Bertolotti, M.; et al. A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets. Nat. Biotechnol. 2023, 41, 128–139. [Google Scholar] [CrossRef] [PubMed]
- Surjit, M.; Jameel, S.; Lal, S.K. Cytoplasmic localization of the ORF2 protein of hepatitis E virus is dependent on its ability to undergo retrotranslocation from the endoplasmic reticulum. J. Virol. 2007, 81, 3339–3345. [Google Scholar] [CrossRef] [PubMed]
- Nie, Y.; Hui, L.; Guo, M.; Yang, W.; Huang, R.; Chen, J.; Wen, X.; Zhao, M.; Wu, Y. Rearrangement of Actin Cytoskeleton by Zika Virus Infection Facilitates Blood-Testis Barrier Hyperpermeability. Virol. Sin. 2021, 36, 692–705. [Google Scholar] [CrossRef] [PubMed]
- Taylor, M.P.; Koyuncu, O.O.; Enquist, L.W. Subversion of the actin cytoskeleton during viral infection. Nat. Rev. Microbiol. 2011, 9, 427–439. [Google Scholar] [CrossRef] [PubMed]
- Kloc, M.; Uosef, A.; Wosik, J.; Kubiak, J.Z.; Ghobrial, R.M. Virus interactions with the actin cytoskeleton-what we know and do not know about SARS-CoV-2. Arch. Virol. 2022, 167, 737–749. [Google Scholar] [CrossRef] [PubMed]
- Fujimoto, A.; Lyu, Y.; Kinjo, M.; Kitamura, A. Interaction between Spike Protein of SARS-CoV-2 and Human Virus Receptor ACE2 Using Two-Color Fluorescence Cross-Correlation Spectroscopy. Appl. Sci. 2021, 11, 10697. [Google Scholar] [CrossRef]
- Kitamura, A.; Nakayama, Y.; Shibasaki, A.; Taki, A.; Yuno, S.; Takeda, K.; Yahara, M.; Tanabe, N.; Kinjo, M. Interaction of RNA with a C-terminal fragment of the amyotrophic lateral sclerosis-associated TDP43 reduces cytotoxicity. Sci. Rep. 2016, 6, 19230. [Google Scholar] [CrossRef] [PubMed]
- Mirdita, M.; Schutze, K.; Moriwaki, Y.; Heo, L.; Ovchinnikov, S.; Steinegger, M. ColabFold: Making protein folding accessible to all. Nat. Methods 2022, 19, 679–682. [Google Scholar] [CrossRef]
- Li, G.; Tang, Z.; Fan, W.; Wang, X.; Huang, L.; Jia, Y.; Wang, M.; Hu, Z.; Zhou, Y. Atlas of interactions between SARS-CoV-2 macromolecules and host proteins. Cell Insight 2023, 2, 100068. [Google Scholar] [CrossRef]
- Gordon, D.E.; Jang, G.M.; Bouhaddou, M.; Xu, J.; Obernier, K.; White, K.M.; O‘Meara, M.J.; Rezelj, V.V.; Guo, J.Z.; Swaney, D.L.; et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020, 583, 459–468. [Google Scholar] [CrossRef]
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Fujimoto, A.; Kawai, H.; Kawamura, R.; Kitamura, A. Interaction of Receptor-Binding Domain of the SARS-CoV-2 Omicron Variant with hACE2 and Actin. Cells 2024, 13, 1318. https://doi.org/10.3390/cells13161318
Fujimoto A, Kawai H, Kawamura R, Kitamura A. Interaction of Receptor-Binding Domain of the SARS-CoV-2 Omicron Variant with hACE2 and Actin. Cells. 2024; 13(16):1318. https://doi.org/10.3390/cells13161318
Chicago/Turabian StyleFujimoto, Ai, Haruki Kawai, Rintaro Kawamura, and Akira Kitamura. 2024. "Interaction of Receptor-Binding Domain of the SARS-CoV-2 Omicron Variant with hACE2 and Actin" Cells 13, no. 16: 1318. https://doi.org/10.3390/cells13161318