Human cytomegalovirus evades ZAP detection by suppressing CpG dinucleotides in the major immediate early 1 gene

Lin, Y.-T., Chiweshe, S., McCormick, D., Raper, A., Wickenhagen, A., DeFillipis, V., Gaunt, E., Simmonds, P., Wilson, S. J. and Grey, F. (2020) Human cytomegalovirus evades ZAP detection by suppressing CpG dinucleotides in the major immediate early 1 gene. PLoS Pathogens, 16(9), e1008844. (doi: 10.1371/journal.ppat.1008844) (PMID:32886716) (PMCID:PMC7498042)

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Abstract

The genomes of RNA and small DNA viruses of vertebrates display significant suppression of CpG dinucleotide frequencies. Artificially increasing dinucleotide frequencies results in substantial attenuation of virus replication, suggesting that these compositional changes may facilitate recognition of non-self RNA sequences. Recently, the interferon inducible protein ZAP, was identified as the host factor responsible for sensing CpG in viral RNA, through direct binding and possibly downstream targeting for degradation. Using an arrayed interferon stimulated gene expression library screen, we identified ZAPS, and its associated factor TRIM25, as inhibitors of human cytomegalovirus (HCMV) replication. Exogenous expression of ZAPS and TRIM25 significantly reduced virus replication while knockdown resulted in increased virus replication. HCMV displays a strikingly heterogeneous pattern of CpG representation with specific suppression of CpG motifs within the IE1 major immediate early transcript which is absent in subsequently expressed genes. We demonstrated that suppression of CpG dinucleotides in the IE1 gene allows evasion of inhibitory effects of ZAP. We show that acute virus replication is mutually exclusive with high levels of cellular ZAP, potentially explaining the higher levels of CpG in viral genes expressed subsequent to IE1 due to the loss of pressure from ZAP in infected cells. Finally, we show that TRIM25 regulates alternative splicing between the ZAP short and long isoforms during HCMV infection and interferon induction, with knockdown of TRIM25 resulting in decreased ZAPS and corresponding increased ZAPL expression. These results demonstrate for the first time that ZAP is a potent host restriction factor against large DNA viruses and that HCMV evades ZAP detection through suppression of CpG dinucleotides within the major immediate early 1 transcript. Furthermore, TRIM25 is required for efficient upregulation of the interferon inducible short isoform of ZAP through regulation of alternative splicing.

Item Type:Articles
Additional Information:This project was funded by the Medical Research Council (https://mrc.ukri.org) MR/N001796/1 (FG), MR/K024752/1 (SJW), MC_UU_12014/10 (SJW) and MR/P022642/1 (SJW), the Biotechnology and Biological Sciences Research Council (https://bbsrc.ukri.org), BBS/E/D/ 20002172 (FG), Wellcome, https://wellcome.ac.uk, WT103767MA (PS) and through the Principal’s Career Development PhD scholarship from the University of Edinburgh (FG).
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Wilson, Professor Sam and Wickenhagen, Mr Arthur
Creator Roles:
Wickenhagen, A.Methodology
Wilson, S. J.Conceptualization, Funding acquisition, Resources, Writing – review and editing
Authors: Lin, Y.-T., Chiweshe, S., McCormick, D., Raper, A., Wickenhagen, A., DeFillipis, V., Gaunt, E., Simmonds, P., Wilson, S. J., and Grey, F.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:PLoS Pathogens
Publisher:Public Library of Science
ISSN:1553-7366
ISSN (Online):1553-7374
Copyright Holders:Copyright © 2020 The Authors
First Published:First published in PLoS Pathogens 16(9):e1008844
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
168748Identifying and characterising antiretroviral interferon stimulated genes (ISGs)Sam WilsonMedical Research Council (MRC)MR/K024752/1III - Centre for Virus Research
Medical Research Council (MRC)MC_UU_12014/10
301840Host and Viral Determinants of Interferon Resistance During HIV-1 TransmissionSam WilsonMedical Research Council (MRC)MR/P022642/1III - Centre for Virus Research