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dc.contributor.authorIbrahim, Ahmad
dc.contributor.authorFros, Jelke
dc.contributor.authorBertran, Andre
dc.contributor.authorSechan, Ferdyansyah
dc.contributor.authorOdon, Valerie
dc.contributor.authorTorrance, Leslie
dc.contributor.authorKormelink, Richard
dc.contributor.authorSimmonds, Peter
dc.identifier.citationIbrahim , A , Fros , J , Bertran , A , Sechan , F , Odon , V , Torrance , L , Kormelink , R & Simmonds , P 2019 , ' A functional investigation of the suppression of CpG and UpA dinucleotide frequencies in plant RNA virus genomes ' , Scientific Reports , vol. 9 , 18359 .
dc.identifier.otherPURE: 272102354
dc.identifier.otherPURE UUID: 7d144f6b-50a7-4458-935a-f521543183d5
dc.identifier.otherScopus: 85075994434
dc.identifier.otherPubMed: 31797900
dc.description.abstractFrequencies of CpG and UpA dinucleotides in most plant RNA virus genomes show degrees of suppression comparable to those of vertebrate RNA viruses. While pathways that target CpG and UpAs in HIV-1 and echovirus 7 genomes and restrict their replication have been partly characterised, whether an analogous process drives dinucleotide underrepresentation in plant viruses remains undetermined. We examined replication phenotypes of compositionally modified mutants of potato virus Y (PVY) in which CpG or UpA frequencies were maximised in non-structural genes (including helicase and polymerase encoding domains) while retaining protein coding. PYV mutants with increased CpG dinucleotide frequencies showed a dose-dependent reduction in systemic spread and pathogenicity and up to 1000-fold attenuated replication kinetics in distal sites on agroinfiltration of tobacco plants (Nicotiana benthamiana). Even more extraordinarily, comparably modified UpA-high mutants displayed no pathology and over a million-fold reduction in replication. Tobacco plants with knockdown of RDP6 displayed similar attenuation of CpG- and UpA-high mutants suggesting that restriction occurred independently of the plant siRNA antiviral responses. Despite the evolutionary gulf between plant and vertebrate genomes and encoded antiviral strategies, these findings point towards the existence of novel virus restriction pathways in plants functionally analogous to innate defence components in vertebrate cells.
dc.relation.ispartofScientific Reportsen
dc.rightsCopyright © 2020 the Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit
dc.subjectQH301 Biologyen
dc.subjectQH426 Geneticsen
dc.titleA functional investigation of the suppression of CpG and UpA dinucleotide frequencies in plant RNA virus genomesen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews. School of Biologyen
dc.contributor.institutionUniversity of St Andrews. Biomedical Sciences Research Complexen
dc.description.statusPeer revieweden

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