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

Date Published: August 3, 2018

Publisher: Public Library of Science

Author(s): Fangfang Li, Aiming Wang, John Carr.


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.

Partial Text

Among major infectious pathogens, viruses are the obligate intracellular agents that can infect all types of life forms from bacteria to plants and animals, and exclusively multiply in the host cells. The vast majority of known plant viruses are positive-sense single-stranded (+ss) RNA viruses that typically have a relatively small genome encoding no more than a dozen proteins. Since the genomic RNAs of +ss viruses are similar to the endogenous mRNAs, the regulation machinery of cellular RNA metabolism in the infected plants is unavoidably involved in viral infection.

In this study, we found that overexpression of any of four essential RNA decay components 5’RDGs including DCP1, DCP2, XRN4 and PARN failed to suppress GFP-induced S-PTGS and production of siRNAs, and instead enhanced S-PTGS in N. benthamiana (Fig 3). We also found that knock-down of any of the four 5’RDGs genes repressed GFP-induced S-PTGS and inhibited the generation of GFP-derived siRNAs (Fig 4). These data suggest that 5’RDGs seem to play an additive role to S-PTGS in N. benthamiana. Our data are consistent with a recent report that the poly(A) tail of mRNA blocks RDR6 from converting canonical mRNAs into substrates for gene silencing and AtRDR6 has an intrinsic preference for poly(A)-less mRNAs over polyadenylated mRNAs as templates in Arabidopsis [38]. However, several previous studies have concluded that both 5′–3′ and 3′–5′ cytoplasmic RNA decay pathways repress S-PTGS in Arabidopsis [28–31]. For example, it has been shown that impairing deadenylation and decapping enhance S-PTGS in Arabidopsis [30,39], possibly through restriction of RNA substrates from entry into the PTGS pathway. However, how deadenylation and decapping blocks the RNA substrate to access to PTGS is yet to be understood. It has also been suggested that RNA decay may compete for the same RNA substrates with RDRs-dependent RNA silencing to supress S-PTGS [28–30]. The assumption was based on the experimental evidence that the deficiency of RNA decay ribonucleases such as XRN4 enhances S-PTGS in Arabidopsis [28–30]. AtXRN4 does not play a significant role in controlling the degradation of unstable transcripts in A. thaliana, and it degrades predominantly the 5’ uncapped mRNA intermediates as well 3’ mRNA intermediates resulting from miRNA and possibly siRNA-mediated cleavage [37,40]. Moreover, XRN4-mediated decay also preferentially targets some transcripts such as those encoding nucleic acid–binding proteins and chloroplast proteins [40]. We speculate that rather than being competitive for substrates in Arabidopsis, NbXRN4 in N. benthamiana may degrade RNAs incompletely, generating RNA fragments, which facilitate RDRs-dependent dsRNA synthesis. Clearly, the interplay between RNA decay and RNA silencing is very complicated. The finding from this study may represent another example that not all findings from Arabidopsis can be simply extrapolated to other plant species such as N. benthamiana. The molecular mechanism by which the RNA decay pathway functions differently in relation to S-PTGS in Arabidopsis and N. benthamiana needs further study.