Effects of a Shift of the Signal Peptide Cleavage Site in Signal Peptide Variant on the Synthesis and Secretion of SARS-CoV-2 Spike Protein
Abstract
:1. Introduction
2. Results
2.1. Bioinformatics Analysis Signal Peptide of SARS-CoV-2 Spike(S) Protein
2.2. Signal Peptide Targets SARS-CoV-2 RBD Protein to the Endoplasmic Reticulum
2.3. Signal Peptide Promotes the Secretion Levels of SARS-CoV-2 RBD Protein
3. Discussion
4. Materials and Methods
4.1. Bacterial, Plasmids Construct and Cells Culture Conditions
4.2. RBD Proteins Expressed and Intracellular Fluorescence Assay in HEK293T Cell
4.3. RBD Protein Secretion Detection
- Rf: the relative fluorescence value;
- N: fluorescence value of negative control (HEK293T);
- P: fluorescence value of positive control (pEGFP-RBD);
- S: fluorescence value of target sample.
4.4. Statistical Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Perlman, S. Another Decade, Another Coronavirus. N. Engl. J. Med. 2020, 382, 760–762. [Google Scholar] [CrossRef] [PubMed]
- Zhu, N.; Zhang, D.; Wang, D.; Wang, W.; Li, X.; Yang, B.; Song, J.; Zhao, X.; Huang, B.; Shi, W.; et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N. Engl. J. Med. 2020, 382, 727–733. [Google Scholar] [CrossRef] [PubMed]
- Andersen, K.G.; Rambaut, A.; Lipkin, W.I.; Holmes, E.C.; Garry, R.F. The proximal origin of SARS-CoV-2. Nat. Med. 2020, 26, 450–452. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Lu, R.; Zhao, X.; Li, J.; Niu, P.; Yang, B.; Wu, H.; Wang, W.; Song, H.; Huang, B.; Zhu, N.; et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. Lancet 2020, 395, 565–574. [Google Scholar] [CrossRef] [Green Version]
- Steven, S.; Yen, T.L.; Chonggang, X.; Ethan, R.; Nick, H.; Ruian, K. High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2. Emerg. Infect. Dis. J. 2020, 26, 1470–1477. [Google Scholar]
- Coutard, B.; Valle, C.; de Lamballerie, X.; Canard, B.; Seidah, N.G.; Decroly, E. The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Antivir. Res. 2020, 176, 104742. [Google Scholar] [CrossRef]
- Tang, X.; Wu, C.; Li, X.; Song, Y.; Yao, X.; Wu, X.; Duan, Y.; Zhang, H.; Wang, Y.; Qian, Z.; et al. On the origin and continuing evolution of SARS-CoV-2. Natl. Sci. Rev. 2020, 7, 1012–1023. [Google Scholar] [CrossRef] [Green Version]
- Wang, Q.; Zhang, Y.; Wu, L.; Niu, S.; Song, C.; Zhang, Z.; Lu, G.; Qiao, C.; Hu, Y.; Yuen, K.; et al. Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2. Cell 2020, 181, 894–904. [Google Scholar] [CrossRef]
- Walls, A.C.; Park, Y.; Tortorici, M.A.; Wall, A.; McGuire, A.T.; Veesler, D. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell 2020, 181, 281–292. [Google Scholar] [CrossRef]
- Kumar, V.; Singh, J.; Hasnain, S.E.; Sundar, D. Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. Int. J. Mol. Sci. 2021, 22, 9131. [Google Scholar] [CrossRef] [PubMed]
- Escalera, A.; Gonzalez-Reiche, A.S.; Aslam, S.; Mena, I.; Laporte, M.; Pearl, R.L.; Fossati, A.; Rathnasinghe, R.; Alshammary, H.; van de Guchte, A.; et al. Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission. Cell Host Microbe 2022, 30, 373–387. [Google Scholar] [CrossRef]
- Biswas, S.; Dey, S.; Chatterjee, S.; Nandy, A. Combatting future variants of SARS-CoV-2 using an in-silico peptide vaccine approach by targeting the spike protein. Med. Hypotheses 2022, 161, 110810. [Google Scholar] [CrossRef]
- Kannan, S.R.; Spratt, A.N.; Sharma, K.; Chand, H.S.; Byrareddy, S.N.; Singh, K. Omicron SARS-CoV-2 variant: Unique features and their impact on pre-existing antibodies. J. Autoimmun. 2022, 126, 102779. [Google Scholar] [CrossRef] [PubMed]
- Lan, J.; Ge, J.; Yu, J.; Shan, S.; Zhou, H.; Fan, S.; Zhang, Q.; Shi, X.; Wang, Q.; Zhang, L.; et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 2020, 81, 215–220. [Google Scholar] [CrossRef] [Green Version]
- Vankadari, N.; Wilce, J.A. Emerging WuHan (COVID-19) coronavirus: Glycan shield and structure prediction of spike glycoprotein and its interaction with human CD26. Emerg. Microbes Infect. 2020, 9, 601–604. [Google Scholar] [CrossRef] [Green Version]
- 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] [Green Version]
- Hoffmann, M.; Kleine-Weber, H.; Schroeder, S.; Krüger, N.; Herrler, T.; Erichsen, S.; Schiergens, T.S.; Herrler, G.; Wu, N.; Nitsche, A.; et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell 2020, 181, 271–280. [Google Scholar] [CrossRef] [PubMed]
- Song, H.; Seddighzadeh, B.; Cooperberg, M.R.; Huang, F.W. Expression of ACE2, the SARS-CoV-2 Receptor, and TMPRSS2 in Prostate Epithelial Cells. Eur. Urol. 2020, 78, 296–298. [Google Scholar] [CrossRef]
- Aatif, M.; Muteeb, G.; Alsultan, A.; Alshoaibi, A.; Khelif, B.Y. Dieckol and Its Derivatives as Potential Inhibitors of SARS-CoV-2 Spike Protein (UK Strain: VUI 202012/01): A Computational Study. Mar. Drugs 2021, 19, 242. [Google Scholar] [CrossRef]
- Wrapp, D.; Wang, N.; Corbett, K.S.; Goldsmith, J.A.; Hsieh, C.; Abiona, O.; Graham, B.S.; McLellan, J.S. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 2020, 367, 1260–1263. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Nothwehr, S.F.; Gordon, J.I. Targeting of proteins into the eukaryotic secretory pathway: Signal peptide structure/function relationships. Bioessays 1990, 12, 479–484. [Google Scholar] [CrossRef]
- Almagro Armenteros, J.J.; Tsirigos, K.D.; Sønderby, C.K.; Petersen, T.N.; Winther, O.; Brunak, S.; von Heijne, G.; Nielsen, H. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat. Biotechnol. 2019, 37, 420–423. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Guo, H.; Sun, J.; Li, X.; Xiong, Y.; Wang, H.; Shu, H.; Zhu, R.; Liu, Q.; Huang, Y.; Madley, R.; et al. Positive charge in the n-region of the signal peptide contributes to efficient post-translational translocation of small secretory preproteins. J. Biol. Chem. 2018, 293, 1899–1907. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Nilsson, I.; Lara, P.; Hessa, T.; Johnson, A.E.; von Heijne, G.; Karamyshev, A.L. The Code for Directing Proteins for Translocation across ER Membrane: SRP Cotranslationally Recognizes Specific Features of a Signal Sequence. J. Mol. Biol. 2015, 427, 1191–1201. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Lumangtad, L.A.; Bell, T.W. The signal peptide as a new target for drug design. Bioorganic. Med. Chem. Lett. 2020, 30, 127115. [Google Scholar] [CrossRef] [PubMed]
- Zhang, M.; Liu, L.; Lin, X.; Wang, Y.; Li, Y.; Guo, Q.; Li, S.; Sun, Y.; Tao, X.; Zhang, D.; et al. A Translocation Pathway for Vesicle-Mediated Unconventional Protein Secretion. Cell 2020, 181, 637–652. [Google Scholar] [CrossRef] [PubMed]
- Van Puyenbroeck, V.; Pauwels, E.; Provinciael, B.; Bell, T.W.; Schols, D.; Kalies, K.U.; Hartmann, E.; Vermeire, K. Preprotein signature for full susceptibility to the co-translational translocation inhibitor cyclotriazadisulfonamide. Traffic 2019, 21, 250–264. [Google Scholar] [CrossRef]
- Van Puyenbroeck, V.; Vermeire, K. Inhibitors of protein translocation across membranes of the secretory pathway: Novel antimicrobial and anticancer agents. Cell Mol. Life Sci. 2018, 75, 1541–1558. [Google Scholar] [CrossRef] [Green Version]
- Zhou, Y.; Liu, P.; Gan, Y.; Sandoval, W.; Katakam, A.K.; Reichelt, M.; Rangell, L.; Reilly, D. Enhancing full-length antibody production by signal peptide engineering. Microb. Cell Factories 2016, 15, 47. [Google Scholar] [CrossRef] [Green Version]
- Aw, R.; McKay, P.F.; Shattock, R.J.; Polizzi, K.M. A systematic analysis of the expression of the anti-HIV VRC01 antibody in Pichia pastoris through signal peptide optimization. Protein Expr. Purif. 2018, 149, 43–50. [Google Scholar] [CrossRef]
- Shepard, B.D.; Natarajan, N.; Protzko, R.J.; Acres, O.W.; Pluznick, J.L. A cleavable N-terminal signal peptide promotes widespread olfactory receptor surface expression in HEK293T cells. PLoS ONE 2013, 8, e68758. [Google Scholar] [CrossRef]
- Yuan, M.; Wu, N.C.; Zhu, X.; Lee, C.D.; So, R.T.Y.; Lv, H.; Mok, C.K.P.; Wilson, I.A. A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV. Science 2020, 368, 630–633. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Song, Z.; Xu, Y.; Bao, L.; Zhang, L.; Yu, P.; Qu, Y.; Zhu, H.; Zhao, W.; Han, Y.; Qin, C. From SARS to MERS, Thrusting Coronaviruses into the Spotlight. Viruses 2019, 11, 59. [Google Scholar] [CrossRef] [Green Version]
- Steentoft, C.; Vakhrushev, S.Y.; Joshi, H.J.; Kong, Y.; Vester-Christensen, M.B.; Schjoldager, K.T.; Lavrsen, K.; Dabelsteen, S.; Pedersen, N.B.; Marcos-Silva, L.; et al. Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J. 2013, 32, 1478–1488. [Google Scholar] [CrossRef] [Green Version]
- Hargett, A.A.; Renfrow, M.B. Glycosylation of viral surface proteins probed by mass spectrometry. Curr. Opin. Virol. 2019, 36, 56–66. [Google Scholar] [CrossRef]
- Breiman, A.; Smith, G.L. Vaccinia virus B5 protein affects the glycosylation, localization and stability of the A34 protein. J. Gen. Virol. 2010, 91, 1823–1827. [Google Scholar] [CrossRef]
- Walski, T.; De Schutter, K.; Van Damme, E.J.M.; Smagghe, G. Diversity and functions of protein glycosylation in insects. Insect Biochem. Mol. Biol. 2017, 83, 21–34. [Google Scholar] [CrossRef]
- Eichler, J. Protein glycosylation. Curr. Biol. 2019, 29, R229–R231. [Google Scholar] [CrossRef] [Green Version]
- Tian, W.; Li, D.; Zhang, N.; Bai, G.; Yuan, K.; Xiao, H.; Gao, F.; Chen, Y.; Wong, C.; Gao, G.F. O-glycosylation pattern of the SARS-CoV-2 spike protein reveals an “O-Follow-N” rule. Cell Res. 2021, 31, 1123–1125. [Google Scholar] [CrossRef]
- McCallum, M.; Bassi, J.; De Marco, A.; Chen, A.; Walls, A.C.; Di Iulio, J.; Tortorici, M.A.; Navarro, M.J.; Silacci-Fregni, C.; Saliba, C.; et al. SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. Science 2021, 373, 648–654. [Google Scholar] [CrossRef]
- Zheng, J.; Yamada, Y.; Fung, T.S.; Huang, M.; Chia, R.; Liu, D.X. Identification of N-linked glycosylation sites in the spike protein and their functional impact on the replication and infectivity of coronavirus infectious bronchitis virus in cell culture. Virology 2018, 513, 65–74. [Google Scholar] [CrossRef]
- Tan, L.; Chen, Z.; Ma, X.; Huang, Q.; Sun, H.; Zhang, F.; Yang, S.; Xu, C.; Cui, N. Glycosylation of the hemagglutinin protein of H9N2 subtype avian influenza virus influences its replication and virulence in mice. J. Integr. Agric. 2019, 18, 1443–1450. [Google Scholar] [CrossRef]
- Kotwal, G.J. Influence of glycosylation and oligomerization of vaccinia virus complement control protein on level and pattern of functional activity and immunogenicity. Protein Cell 2010, 1, 1084–1092. [Google Scholar] [CrossRef] [Green Version]
- Watanabe, Y.; Allen, J.D.; Wrapp, D.; McLellan, J.S.; Crispin, M. Site-specific glycan analysis of the SARS-CoV-2 spike. Science 2020, 369, b9983. [Google Scholar] [CrossRef]
- Snapp, E.L.; McCaul, N.; Quandte, M.; Cabartova, Z.; Bontjer, I.; Källgren, C.; Nilsson, I.; Land, A.; von Heijne, G.; Sanders, R.W.; et al. Structure and topology around the cleavage site regulate post-translational cleavage of the HIV-1 gp160 signal peptide. eLife 2017, 6, e26067. [Google Scholar] [CrossRef]
- Goh, E.; Lin, Z.; Ahn, B.Y.; Lopes-Rodrigues, V.; Dang, N.H.; Salim, S.; Berger, B.; Dymock, B.; Senger, D.L.; Ibanez, C.F. A Small Molecule Targeting the Transmembrane Domain of Death Receptor p75(NTR) Induces Melanoma Cell Death and Reduces Tumor Growth. Cell Chem. Biol. 2018, 25, 1485–1494. [Google Scholar] [CrossRef] [Green Version]
- Asada, H.; Inoue, A.; Ngako Kadji, F.M.; Hirata, K.; Shiimura, Y.; Im, D.; Shimamura, T.; Nomura, N.; Iwanari, H.; Hamakubo, T.; et al. The Crystal Structure of Angiotensin II Type 2 Receptor with Endogenous Peptide Hormone. Structure 2020, 28, 418–425. [Google Scholar] [CrossRef]
- Van Puyenbroeck, V.; Claeys, E.; Schols, D.; Bell, T.W.; Vermeire, K. A Proteomic Survey Indicates Sortilin as a Secondary Substrate of the ER Translocation Inhibitor Cyclotriazadisulfonamide (CADA). Mol. Cell. Proteom. 2017, 16, 157–167. [Google Scholar] [CrossRef]
Primers Name | Sequence (5′–3′) |
---|---|
pEGFP-F | CATCATCACCATCACCATGGATCCACCGGTCGCCACCATGGTG |
pEGFP-R | GGTGGCGAATTCGAAGCTTGAGCTC |
∆RBD-F | GAGCTCAAGCTTCGAATTCGCCACCATGAATATTACAAACTTGTGCCCTTTTG |
∆RBD-R | TGGATCCATGGTGATGGTGATGATGCTCAAGTGTCTGTGGATCACGGAC |
RBD-F | CTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATATTACAAACTTGTGCCCTTTTG |
RBD-R | CTAGAGACTAGTGGCAATAAAACAAGAAAAACAAACATGGTGGCGAATTCGAAGCTTGAGCTC |
L5F-F | TTGTTTTTTTTGTTTTATTGCCACTAGTCTCTAGTC |
L5F-R | CAATAAAACAAAAAAAACAAACATGGTGGCGAATTCG |
S13I-F | CTAGTCTCTATTCAGTGTGTTAATATTACAAACTTGT |
S13I-R | ACACACTGAATAGAGACTAGTGGCAATAAAACAAGA |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Zhang, Z.; Wan, X.; Li, X.; Wan, C. Effects of a Shift of the Signal Peptide Cleavage Site in Signal Peptide Variant on the Synthesis and Secretion of SARS-CoV-2 Spike Protein. Molecules 2022, 27, 6688. https://doi.org/10.3390/molecules27196688
Zhang Z, Wan X, Li X, Wan C. Effects of a Shift of the Signal Peptide Cleavage Site in Signal Peptide Variant on the Synthesis and Secretion of SARS-CoV-2 Spike Protein. Molecules. 2022; 27(19):6688. https://doi.org/10.3390/molecules27196688
Chicago/Turabian StyleZhang, Zhikai, Xuan Wan, Xinyue Li, and Chengsong Wan. 2022. "Effects of a Shift of the Signal Peptide Cleavage Site in Signal Peptide Variant on the Synthesis and Secretion of SARS-CoV-2 Spike Protein" Molecules 27, no. 19: 6688. https://doi.org/10.3390/molecules27196688
APA StyleZhang, Z., Wan, X., Li, X., & Wan, C. (2022). Effects of a Shift of the Signal Peptide Cleavage Site in Signal Peptide Variant on the Synthesis and Secretion of SARS-CoV-2 Spike Protein. Molecules, 27(19), 6688. https://doi.org/10.3390/molecules27196688