Host-directed Editing of the SARS-CoV-2 Genome

Overview

Journal Biochem Biophys Res Commun

Publisher Elsevier

Specialty Biochemistry

Date 2020 Nov 25

PMID 33234239

Citations 67

Authors

Tobias Mourier

Mukhtar Sadykov

Michael J Carr

Gabriel Gonzalez

William W Hall

Arnab Pain

Affiliations

Soon will be listed here.

Abstract

The extensive sequence data generated from SARS-CoV-2 during the 2020 pandemic has facilitated the study of viral genome evolution over a brief period of time. This has highlighted instances of directional mutation pressures exerted on the SARS-CoV-2 genome from host antiviral defense systems. In this brief review we describe three such human defense mechanisms, the apolipoprotein B mRNA editing catalytic polypeptide-like proteins (APOBEC), adenosine deaminase acting on RNA proteins (ADAR), and reactive oxygen species (ROS), and discuss their potential implications on SARS-CoV-2 evolution.

Citing Articles

Viral N protein hijacks deaminase-containing RNA granules to enhance SARS-CoV-2 mutagenesis.

Li Z, Luo L, Ju X, Huang S, Lei L, Yu Y EMBO J. 2024; 43(24):6444-6468.

PMID: 39567830 PMC: 11649915. DOI: 10.1038/s44318-024-00314-y.

Genomic epidemiology reveals the variation and transmission properties of SARS-CoV-2 in a single-source community outbreak.

Zhao N, He M, Wang H, Zhu L, Wang N, Yong W Virus Evol. 2024; 10(1):veae085.

PMID: 39493536 PMC: 11529616. DOI: 10.1093/ve/veae085.

C→U transition biases in SARS-CoV-2: still rampant 4 years from the start of the COVID-19 pandemic.

Simmonds P mBio. 2024; 15(12):e0249324.

PMID: 39475243 PMC: 11633203. DOI: 10.1128/mbio.02493-24.

MDA5 Is a Major Determinant of Developing Symptoms in Critically Ill COVID-19 Patients.

Maiti A Clin Rev Allergy Immunol. 2024; 67(1-3):58-72.

PMID: 39460899 DOI: 10.1007/s12016-024-09008-z.

Long COVID Definition, Symptoms, Risk Factors, Epidemiology and Autoimmunity: A Narrative Review.

Kozlowski P, Leszczynska A, Ciepiela O Am J Med Open. 2024; 11:100068.

PMID: 39034937 PMC: 11256271. DOI: 10.1016/j.ajmo.2024.100068.

References

Nakahama T, Kato Y, Kim J, Vongpipatana T, Suzuki Y, Walkley C . ADAR1-mediated RNA editing is required for thymic self-tolerance and inhibition of autoimmunity. EMBO Rep. 2018; 19(12). PMC: 6280791. DOI: 10.15252/embr.201846303. View

Salter J, Smith H . Modeling the Embrace of a Mutator: APOBEC Selection of Nucleic Acid Ligands. Trends Biochem Sci. 2018; 43(8):606-622. PMC: 6073885. DOI: 10.1016/j.tibs.2018.04.013. View

Smith E . The not-so-infinite malleability of RNA viruses: Viral and cellular determinants of RNA virus mutation rates. PLoS Pathog. 2017; 13(4):e1006254. PMC: 5407569. DOI: 10.1371/journal.ppat.1006254. View

Simmonds P . Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories. mSphere. 2020; 5(3). PMC: 7316492. DOI: 10.1128/mSphere.00408-20. View

Dalakas M . Guillain-Barré syndrome: The first documented COVID-19-triggered autoimmune neurologic disease: More to come with myositis in the offing. Neurol Neuroimmunol Neuroinflamm. 2020; 7(5). PMC: 7309518. DOI: 10.1212/NXI.0000000000000781. View

Chemudupati M, Kenney A, Bonifati S, Zani A, McMichael T, Wu L . From APOBEC to ZAP: Diverse mechanisms used by cellular restriction factors to inhibit virus infections. Biochim Biophys Acta Mol Cell Res. 2018; 1866(3):382-394. PMC: 6334645. DOI: 10.1016/j.bbamcr.2018.09.012. View

Li Q, Wu J, Nie J, Zhang L, Hao H, Liu S . The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Cell. 2020; 182(5):1284-1294.e9. PMC: 7366990. DOI: 10.1016/j.cell.2020.07.012. View

Fehr A, Perlman S . Coronaviruses: an overview of their replication and pathogenesis. Methods Mol Biol. 2015; 1282:1-23. PMC: 4369385. DOI: 10.1007/978-1-4939-2438-7_1. View

Sa Ribero M, Jouvenet N, Dreux M, Nisole S . Interplay between SARS-CoV-2 and the type I interferon response. PLoS Pathog. 2020; 16(7):e1008737. PMC: 7390284. DOI: 10.1371/journal.ppat.1008737. View

10.

Feng Y, Goubran M, Follack T, Chelico L . Deamination-independent restriction of LINE-1 retrotransposition by APOBEC3H. Sci Rep. 2017; 7(1):10881. PMC: 5589869. DOI: 10.1038/s41598-017-11344-4. View

11.

Gallo A, Vukic D, Michalik D, OConnell M, Keegan L . ADAR RNA editing in human disease; more to it than meets the I. Hum Genet. 2017; 136(9):1265-1278. DOI: 10.1007/s00439-017-1837-0. View

12.

Sadykov M, Mourier T, Guan Q, Pain A . Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction. J Mol Cell Biol. 2021; 13(3):225-227. PMC: 7928816. DOI: 10.1093/jmcb/mjab011. View

13.

Talarico R, Stagnaro C, Ferro F, Carli L, Mosca M . Symmetric peripheral polyarthritis developed during SARS-CoV-2 infection. Lancet Rheumatol. 2020; 2(9):e518-e519. PMC: 7357970. DOI: 10.1016/S2665-9913(20)30216-2. View

14.

Salter J, Bennett R, Smith H . The APOBEC Protein Family: United by Structure, Divergent in Function. Trends Biochem Sci. 2016; 41(7):578-594. PMC: 4930407. DOI: 10.1016/j.tibs.2016.05.001. View

15.

Savva Y, Rieder L, Reenan R . The ADAR protein family. Genome Biol. 2013; 13(12):252. PMC: 3580408. DOI: 10.1186/gb-2012-13-12-252. View

16.

Caudill V, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda E . CpG-creating mutations are costly in many human viruses. Evol Ecol. 2020; 34(3):339-359. PMC: 7245597. DOI: 10.1007/s10682-020-10039-z. View

17.

Kim D, Lee J, Yang J, Kim J, Kim V, Chang H . The Architecture of SARS-CoV-2 Transcriptome. Cell. 2020; 181(4):914-921.e10. PMC: 7179501. DOI: 10.1016/j.cell.2020.04.011. View

18.

Reshi M, Su Y, Hong J . RNA Viruses: ROS-Mediated Cell Death. Int J Cell Biol. 2014; 2014:467452. PMC: 4034720. DOI: 10.1155/2014/467452. View

19.

Pfaller C, Donohue R, Nersisyan S, Brodsky L, Cattaneo R . Extensive editing of cellular and viral double-stranded RNA structures accounts for innate immunity suppression and the proviral activity of ADAR1p150. PLoS Biol. 2018; 16(11):e2006577. PMC: 6264153. DOI: 10.1371/journal.pbio.2006577. View

20.

Moldovan J, Moran J . The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition. PLoS Genet. 2015; 11(5):e1005121. PMC: 4423928. DOI: 10.1371/journal.pgen.1005121. View