Effects of the Noncoding Subgenomic RNA of Red Clover Necrotic Mosaic Virus in Virus Infection

dc.contributor.author Kanodia, Pulkit
dc.contributor.author Miller, W. Allen
dc.contributor.department Plant Pathology and Microbiology
dc.contributor.department Plant Sciences Institute
dc.date.accessioned 2022-02-28T19:14:48Z
dc.date.available 2022-02-28T19:14:48Z
dc.date.issued 2022-02
dc.description.abstract In recent years, a new class of viral noncoding subgenomic RNA (ncsgRNA) has been identified. This RNA is generated as a stable degradation product via an exoribonuclease-resistant RNA (xrRNA) structure, which blocks the progression of 5′→3′ exoribonuclease on viral RNAs in infected cells. Here, we assess the effects of the ncsgRNA of red clover necrotic mosaic virus (RCNMV), called SR1f, in infected plants. We demonstrate the following: (i) the absence of SR1f reduces symptoms and decreases viral RNA accumulation in Nicotiana benthamiana and Arabidopsis thaliana plants; (ii) SR1f has an essential function other than suppression of RNA silencing; and (iii) the cytoplasmic exoribonuclease involved in mRNA turnover, XRN4, is not required for SR1f production or virus infection. A comparative transcriptomic analysis in N. benthamiana infected with wild-type RCNMV or an SR1f-deficient mutant RCNMV revealed that wild-type RCNMV infection, which produces SR1f and much higher levels of virus, has a greater and more significant impact on cellular gene expression than the SR1f-deficient mutant. Upregulated pathways include plant hormone signaling, plant-pathogen interaction, MAPK signaling, and several metabolic pathways, while photosynthesis-related genes were downregulated. We compare this to host genes known to participate in infection by other tombusvirids. Viral reads revealed a 10- to 100-fold ratio of positive to negative strand, and the abundance of reads of both strands mapping to the 3′ region of RCNMV RNA1 support the premature transcription termination mechanism of synthesis for the coding sgRNA. These results provide a framework for future studies of the interactions and functions of noncoding RNAs of plant viruses.
dc.description.comments This article is published as Kanodia, Pulkit, and W. Allen Miller. "Effects of the noncoding subgenomic RNA of red clover necrotic mosaic virus in virus infection." Journal of virology 96 (2022): e01815-21. doi:10.1128/jvi.01815-21. Posted with permission. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/WwPgeX7z
dc.language.iso en
dc.publisher © 2022 Kanodia and Miller
dc.source.uri https://doi.org/10.1128/jvi.01815-21 *
dc.subject.keywords xrRNA
dc.subject.keywords SR1f
dc.subject.keywords XRN4
dc.subject.keywords RCNMV
dc.subject.keywords RNA-seq
dc.subject.keywords virus-host interactions
dc.subject.keywords Tombusviridae
dc.subject.keywords xrRNA
dc.title Effects of the Noncoding Subgenomic RNA of Red Clover Necrotic Mosaic Virus in Virus Infection
dc.type Article
dspace.entity.type Publication
relation.isOrgUnitOfPublication a26b5928-54bb-4a0b-a973-95d649d1ad83
relation.isOrgUnitOfPublication 4b65823e-e153-42b2-8a61-9d65df8a816e
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