Identification of G-quadruplex-forming Sequences in Nucleocapsid Gene of SARS-CoV-2 Variants of Concern: An in silico Analysis

Document Type : Research Article

Author

Department of Cell and Molecular Biology, Faculty of Science, Kosar University of Bojnord, Bojnord, Iran

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as an enveloped RNA virus, has resulted in a global health threat. Recent studies emphasized that G-quadruplex structures are intrinsic obstacles to genome replication and targeting them in viral genomes could be a novel antiviral strategy to develop antiviral agents. The genomic RNA of SARS-CoV-2 codes for 29 proteins. One of them is the nucleocapsid protein with multiple functions, which is crucial for several steps of the viral life cycle. Here, we have analyzed putative G-quadruplex sequences (PQSs) in the Nucleocapsid gene of SARS-CoV2 and its variants of concern using a bioinformatics tool. The results showed that the number, position, and G-scores of PQSs were similar in Wuhan-hu-1 and Alpha, Beta, and Gamma variants. The main difference was observed in the Delta variant, in which a PQS was deleted at position 630 of the gene, which is the top-ranked highly conserved G-quadruplex. The Omicron variant had this PQS back at position 621 as it had acquired several mutations. In addition, there is also a unique R203M mutation, in the N protein of the Delta variant that leads to increased RNA packaging, replication, and severe COVID-19. We proposed that the R203M mutation has led to G˃T substitution and loss of the top-ranked highly conserved PQS in the N gene of the Delta variant. Therefore, due to the loss of this important PQS or indeed an obstacle to viral replication, the Delta variant could exhibit higher reproduction and pathogenicity than other variants of concern.

Keywords

Main Subjects

References

Abiri, A., Lavigne, M., Rezaei, M., Nikzad, S., Zare, P., Mergny, J. L., & Rahimi, H. R. (2021). Unlocking G-quadruplexes as antiviral targets. Pharmacological Reviews, 73(3), 897-923. https://doi.org/10.1124/pharmrev.120.000230
Agarwala, P., Pandey, S., & Maiti, S. (2015). The tale of RNA G-quadruplex. Organic & Biomolecular Chemistry, 13(20), 5570-5585. https://doi.org/10.1039/c4ob02681k
Alsuwairi, F. A., Alsaleh, A. N., Alsanea, M. S., Al-Qahtani, A. A., Obeid, D., Almaghrabi, R. S., ... & Alhamlan, F. S. (2023). Association of SARS-CoV-2 nucleocapsid protein mutations with patient demographic and clinical characteristics during the Delta and Omicron waves. Microorganisms, 11(5), 1288. https://doi.org/10.3390/microorganisms11051288
Astuti, I. (2020). Severe Acute respiratory syndrome coronavirus 2 (SARS-CoV-2): an overview of viral structure and host response. Diabetes & Metabolic Syndrome: Clinical Research & Reviews, 14(4), 407-412. https://doi.org/10.1016/j.dsx.2020.04.020
Belmonte-Reche, E., Serrano-Chacon, I., Gonzalez, C., Gallo, J., & Banobre-Lopez, M. (2021). Potential G-quadruplexes and i-motifs in the SARS-CoV-2. PLoS One, 16(6), e0250654. https://doi.org/10.1371%2Fjournal.pone.0250654
Carvalho, J., Lopes-Nunes, J., Figueiredo, J., Santos, T., Miranda, A., Riscado, M., ... & Cruz, C. (2021). Molecular beacon assay development for severe acute respiratory syndrome coronavirus 2 detection. Sensors, 21(21), 7015. https://doi.org/10.3390/s21217015
Chan, J. F. W., Kok, K. H., Zhu, Z., Chu, H., To, K. K. W., Yuan, S., & Yuen, K. Y. (2020). Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerging Microbes & Infections, 9(1), 221-236. https://doi.org/10.1080/22221751.2020.1719902
Chang, C. K., Hou, M. H., Chang, C. F., Hsiao, C. D., & Huang, T. H. (2014). The SARS coronavirus nucleocapsid protein–forms and functions. Antiviral Research, 103, 39-50. https://doi.org/10.1016/j.antiviral.2013.12.009
Cui, H., & Zhang, L. (2020). G-quadruplexes are present in human coronaviruses including SARS-CoV-2. Frontiers in Microbiology, 11, 567317. https://doi.org/10.3389/fmicb.2020.567317
Díaz, J. (2020). SARS-CoV-2 molecular network structure. Frontiers in Physiology, 11, 870. https://doi.org/10.3389%2Ffphys.2020.00870
He, Y., Zhou, Y., Wu, H., Kou, Z., Liu, S., & Jiang, S. (2004). Mapping of antigenic sites on the nucleocapsid protein of the severe acute respiratory syndrome coronavirus. Journal of Clinical Microbiology, 42(11), 5309-5314. https://doi.org/10.1128/jcm.42.11.5309-5314.2004
Huston, N. C., Wan, H., Strine, M. S., Tavares, R. D. C. A., Wilen, C. B., & Pyle, A. M. (2021). Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. Molecular Cell, 81(3), 584-598. https://doi.org/10.1016/j.molcel.2020.12.041
Ji, D., Juhas, M., Tsang, C. M., Kwok, C. K., Li, Y., & Zhang, Y. (2021). Discovery of G-quadruplex-forming sequences in SARS-CoV-2. Briefings in Bioinformatics, 22(2), 1150-1160. https://doi.org/10.1093/bib/bbaa114
Khetran, S. R., & Mustafa, R. (2023). Mutations of SARS-CoV-2 structural proteins in the alpha, beta, gamma, and delta variants: bioinformatics analysis. JMIR Bioinformatics and Biotechnology, 4(1), e43906. https://doi.org/10.2196/43906
Kikin, O., D'Antonio, L., & Bagga, P. S. (2006). QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Research, 34(suppl_2), W676-W682. https://doi.org/10.1093/nar/gkl253
Li, B., Deng, A., Li, K., Hu, Y., Li, Z., Shi, Y., ... & Lu, J. (2022). Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant. Nature Communications, 13(1), 460. https://doi.org/10.1038/s41467-022-28089-y
Lyu, K., Chow, E. Y. C., Mou, X., Chan, T. F., & Kwok, C. K. (2021). RNA G-quadruplexes (rG4s): genomics and biological functions. Nucleic Acids Research, 49(10), 5426-5450. https://doi.org/10.1093/nar/gkab187
Machida, S., Depierre, D., Chen, H. C., Thenin-Houssier, S., Petitjean, G., Doyen, C. M., ... & Benkirane, M. (2020). Exploring histone loading on HIV DNA reveals a dynamic nucleosome positioning between unintegrated and integrated viral genomes. Proceedings of the National Academy of Sciences, 117(12), 6822-6830. https://doi.org/10.1073/pnas.1913754117
Maiti, A. K. (2022). Identification of G-quadruplex DNA sequences in SARS-CoV2. Immunogenetics, 74(5), 455-463. https://doi.org/10.1007/s00251-022-01257-6
Métifiot, M., Amrane, S., Litvak, S., & Andreola, M. L. (2014). G-quadruplexes in viruses: function and potential therapeutic applications. Nucleic Acids Research, 42(20), 12352-12366. https://doi.org/10.1093/nar/gku999
Miclot, T., Hognon, C., Bignon, E., Terenzi, A., Marazzi, M., Barone, G., & Monari, A. (2021). Structure and dynamics of RNA guanine quadruplexes in SARS-CoV-2 genome. original strategies against emerging viruses. The Journal of Physical Chemistry Letters, 12(42), 10277-10283. https://doi.org/10.1021/acs.jpclett.1c03071
Mourier, T., Shuaib, M., Hala, S., Mfarrej, S., Alofi, F., Naeem, R., ... & Pain, A. (2022). SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Nature Communications, 13(1), 601. https://doi.org/10.1038/s41467-022-28287-8
Mukherjee, S. K., Knop, J. M., & Winter, R. (2022). Modulation of the conformational space of SARS‐CoV‐2 RNA quadruplex RG‐1 by cellular components and the amyloidogenic peptides α‐Synuclein and hIAPP. Chemistry-A European Journal, 28(9), e202104182. https://doi.org/10.1002/chem.202104182
Narayanan, K., Kim, K. H., & Makino, S. (2003). Characterization of N protein self-association in coronavirus ribonucleoprotein complexes. Virus Research, 98(2), 131-140. https://doi.org/10.1016/j.virusres.2003.08.021
Panera, N., Tozzi, A. E., & Alisi, A. (2020). The G-quadruplex/helicase world as a potential antiviral approach against COVID-19. Drugs, 80(10), 941-946. https://doi.org/10.1007/s40265-020-01321-z
Perrone, R., Lavezzo, E., Riello, E., Manganelli, R., Palù, G., Toppo, S., ... & Richter, S. N. (2017). Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions. Scientific Reports, 7(1), 5743. https://doi.org/10.1038/s41598-017-05867-z
Ravi, V., Swaminathan, A., Yadav, S., Arya, H., & Pandey, R. (2022). SARS-CoV-2 variants of concern and variations within their genome architecture: does nucleotide distribution and mutation rate alter the functionality and evolution of the virus? Viruses, 14(11), 2499. https://doi.org/10.3390/v14112499
Rhodes, D., & Lipps, H. J. (2015). G-quadruplexes and their regulatory roles in biology. Nucleic Acids Research, 43(18), 8627-8637. https://doi.org/10.1093/nar/gkv862
Ruggiero, E., Zanin, I., Terreri, M., & Richter, S. N. (2021). G-quadruplex targeting in the fight against viruses: an update. International Journal of Molecular Sciences, 22(20), 10984. https://doi.org/10.3390%2Fijms222010984
Syed, A. M., Taha, T. Y., Tabata, T., Chen, I. P., Ciling, A., Khalid, M. M., ... & Doudna, J. A. (2021). Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles. Science, 374(6575), 1626-1632. https://doi.org/10.1126/science.abl6184
Telenti, A., Hodcroft, E. B., & Robertson, D. L. (2022). The evolution and biology of SARS-CoV-2 variants. Cold Spring Harbor Perspectives in Medicine, 12(5), a041390. https://doi.org/10.1101/cshperspect.a041390
Varshney, D., Spiegel, J., Zyner, K., Tannahill, D., & Balasubramanian, S. (2020). The regulation and functions of DNA and RNA G-quadruplexes. Nature Reviews Molecular Cell Biology, 21(8), 459-474. https://doi.org/10.1038/s41580-020-0236-x
Xu, J., Huang, H., & Zhou, X. (2021). G-quadruplexes in neurobiology and virology: functional roles and potential therapeutic approaches. Journal of the American Chemical Society Au, 1(12), 2146-2161. https://doi.org/10.1021/jacsau.1c00451
Zhai, L. Y., Liu, J. F., Zhao, J. J., Su, A. M., Xi, X. G., & Hou, X. M. (2022a). Targeting the RNA G-Quadruplex and protein interactome for antiviral therapy. Journal of Medicinal Chemistry, 65(15), 10161-10182. https://doi.org/10.1021/acs.jmedchem.2c00649
Zhai, L. Y., Su, A. M., Liu, J. F., Zhao, J. J., Xi, X. G., & Hou, X. M. (2022b). Recent advances in applying G-quadruplex for SARS-CoV-2 targeting and diagnosis: A review. International Journal of Biological Macromolecules. https://doi.org/10.1016/j.ij-biomac.2022.09.152
Zhan, Y., Yin, H., & Yin, J. Y. (2022). B. 1.617. 2 (Delta) Variant of SARS-CoV-2: features, transmission and potential strategies. International Journal of Biological Sciences, 18(5), 1844. https://doi.org/10.7150/ijbs.6-6881
Zhang, R., Xiao, K., Gu, Y., Liu, H., & Sun, X. (2020). Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2. Frontiers in Genetics, 11, 587829. https://doi.org/10.3389/fgene.2020.587829
Zhao, C., Qin, G., Niu, J., Wang, Z., Wang, C., Ren, J., & Qu, X. (2021). Targeting RNA G‐quadruplex in SARS‐CoV‐2: a promising therapeutic target for COVID‐19? Angewandte Chemie, 133(1), 436-442. https://doi.org/10.1002/anie.202011419
Zhao, L. P., Roychoudhury, P., Gilbert, P., Schiffer, J., Lybrand, T. P., Payne, T. H., ... & Geraghty, D. E. (2022). Mutations in viral nucleocapsid protein and endoRNase are discovered to be associated with COVID19 hospitalization risk. Scientific Reports, 12(1), 1206.  https://doi.org/10.1038/s41598-021-04376-4
Zidanloo, S. G., Hosseinzadeh Colagar, A., Ayatollahi, H., & Raoof, J. B. (2016). Downregulation of the WT 1 gene expression via TMPyP4 stabilization of promoter G-quadruplexes in leukemia cells. Tumor Biology, 37, 9967-9977. https://doi.org/10.1007/s13277-016-4881-9
 
Journal of Genetic Resources

Articles in Press, Accepted Manuscript
Available Online from 01 October 2023

Files

Share

How to cite

Statistics