RNA decay is an antiviral defense in plants that is counteracted by viral RNA silencing suppressors

Abstract

Exonuclease-mediated RNA decay in plants is known to be involved primarily in endogenous RNA degradation, and several RNA decay components have been suggested to attenuate RNA silencing possibly through competing for RNA substrates. In this paper, we report that overexpression of key cytoplasmic 5’–3’ RNA decay pathway gene-encoded proteins (5’RDGs) such as decapping protein 2 (DCP2) and exoribonuclease 4 (XRN4) in Nicotiana benthamiana fails to suppress sense transgene-induced post-transcriptional gene silencing (S-PTGS). On the contrary, knock-down of these 5’RDGs attenuates S-PTGS and supresses the generation of small interfering RNAs (siRNAs). We show that 5’RDGs degrade transgene transcripts via the RNA decay pathway when the S-PTGS pathway is disabled. Thus, RNA silencing and RNA decay degrade exogenous gene transcripts in a hierarchical and coordinated manner. Moreover, we present evidence that infection by turnip mosaic virus (TuMV) activates RNA decay and 5’RDGs also negatively regulate TuMV RNA accumulation. We reveal that RNA silencing and RNA decay can mediate degradation of TuMV RNA in the same way that they target transgene transcripts. Furthermore, we demonstrate that VPg and HC-Pro, the two known viral suppressors of RNA silencing (VSRs) of potyviruses, bind to DCP2 and XRN4, respectively, and the interactions compromise their antiviral function. Taken together, our data highlight the overlapping function of the RNA silencing and RNA decay pathways in plants, as evidenced by their hierarchical and concerted actions against exogenous and viral RNA, and VSRs not only counteract RNA silencing but also subvert RNA decay to promote viral infection.

A Novel Interaction Network Used by Potyviruses in Virus–Host Interactions at the Protein Level

“…However, the same mutations in the 4E-binding motif of HCpro also affect other HCpro functions, i.e., the mutations reduce the formation of PVA-induced cytoplasmic granules and reduce viral RNA accumulation resulting from VPg and HCpro co-expression [70]. The functions of the RNA-silencing and RNA decay pathways partly overlap and may co-operate with respect to virus defense in plants based on recent data [32]. Both VPg and HCpro bind essential components of the RNA decay system, decapping protein 2 (DCL2) and exoribonuclease 4 (XRN4), respectively, and suppress RNA decay in N. benthamiana [32].…”

“…HCpro contains the canonical 4E-binding motif found in eIF4G, and mutations in this motif in HCpro of PVA abolish viral infectivity [25]. HCpro is involved in viral genome amplification [26], RNA binding [27], viral cell-to-cell and long-distance movement [28], and suppression of the basal antiviral defense mechanism based on RNA interference (RNAi) [29][30][31], and RNA decay [32]. VPg is also involved in these functions during the viral infection cycle [2,27,[32][33][34][35][36].…”

“…HCpro is involved in viral genome amplification [26], RNA binding [27], viral cell-to-cell and long-distance movement [28], and suppression of the basal antiviral defense mechanism based on RNA interference (RNAi) [29][30][31], and RNA decay [32]. VPg is also involved in these functions during the viral infection cycle [2,27,[32][33][34][35][36]. Furthermore, both VPg and HCpro are multifunctional potyviral proteins that form homodimers [3,37] and interact with each other [38,39].…”

Alterations in cellular RNA decapping dynamics affect tomato spotted wilt virus cap snatching and infection in Arabidopsis

“…S3) mutant plants showed increased tobacco rattle virus‐ Phytoene Desaturase (TRV‐PDS) virus‐induced gene silencing (VIGS), indicating an increase in production of siRNAs leading to the silencing of endogenous genes. THe observation herein that XRN4 has activity against TSWV, Plantago asiatica mosaic virus (PlAMV) and turnip mosaic virus (TuMV) (Figs , ) is consistent with other reports investigating the interaction between XRN4 and several positive sense single‐stranded (ss)RNA viruses in yeast (where RNA silencing is not a factor) and plants (Cheng et al ., ; Peng et al ., ; Jiang et al ., ; Li & Wang, ). In plants, XRN4 activity is thought to have two opposing outcomes in viral RNA infection: increasing viral infection by degrading aberrant RNAs and reducing viral infection by degrading the viral RNAs directly.…”

Antiviral RNAi mediated Plant defense versus its suppression by viruses

“…In another example, a potyvirus, namely Turnip mosaic virus (TuMV) has been allowed to infect Nicotiana benthamiana plant and the viral RNA has been found to be subjected to both antiviral silencing and RNA decay pathways. However, the two viral suppressors, namely Hc-Pro and VPg, interact with host XRN4 and DCP2 respectively and compromise the antiviral function [23].…”