Viral Suppressors of RNA Silencing in Plants (original) (raw)

An Overview of Antiviral RNA Silencing in Plant: Biogenesis, Host–Virus Interaction and Potential Applications

Approaches to Plant Stress and their Management, 2013

Small RNA molecules play a crucial regulatory role in maintaining genome stability as well as developmental regulations through a set of complex and partially overlapping pathways in a wide range of eukaryotic organisms. Active in both cytoplasm and nucleus, RNA interference regulates eukaryotic gene expression through transcriptional repression by epigenetic modification and interaction with transcription machinery. Small interfering RNAs (siRNAs/miRNAs) of 21-24 nucleotides constitute the innate defence arm against a variety of pathogens, especially viruses. Plant viruses with either DNA or RNA genomes are subjected to small RNA-directed RNA degradation. Additionally, DNA viruses are subjected to another line of defence through 'RNA-directed DNA methylations' (RdDM). On the other hand, viral-encoded proteins, called silencing suppressors (VSRs), are known to counter the defence machinery, and therefore the virus can evade the host surveillance system. Some plant viruses additionally adopt certain strategies like acquiring silencing resistant structures (some RNA virus) to evade the RNA silencing machinery and thereby shaping the viral as well as the host genome. Recently, it has been reported that particular viral proteins and viral siRNAs contribute directly to pathogenicity by interacting with certain host proteins or RNAs. Transcriptional regulation of host gene by small RNA of viral origin plays important role in pathogenesis and symptom development. Small regulatory RNAs of cellular rather than pathogen origin have also been found to play a broad role in improving the basal defence in the case of plant-virus interaction. This chapter provides key insights into the complex intricate machinery of diverse RNA silencing mechanisms, describes various evolutionary diverse strategies of viral

RNA Silencing and Plant Viral Diseases

Molecular Plant-Microbe Interactions®, 2012

RNA silencing plays a critical role in plant resistance against viruses, with multiple silencing factors participating in antiviral defense. Both RNA and DNA viruses are targeted by the small RNA-directed RNA degradation pathway, with DNA viruses being also targeted by RNA-directed DNA methylation. To evade RNA silencing, plant viruses have evolved a variety of counter-defense mechanisms such as expressing RNA-silencing suppressors or adopting silencing-resistant RNA structures. This constant defense–counter defense arms race is likely to have played a major role in defining viral host specificity and in shaping viral and possibly host genomes. Recent studies have provided evidence that RNA silencing also plays a direct role in viral disease induction in plants, with viral RNA-silencing suppressors and viral siRNAs as potentially the dominant players in viral pathogenicity. However, questions remain as to whether RNA silencing is the principal mediator of viral pathogenicity or if o...

Plant RNA-silencing immunity and viral counter-defence strategies

Molecular plant-microbe interactions, 2009

RNA silencing is a conserved eukaryotic process mediated by small RNA molecules that inhibit gene expression at the transcriptional, mRNA-stability or translational level through sequence-specific interactions. Diverse roles have been identified for RNA silencing such as genome defence against mobile DNA elements or downregulation of specific factors during plant and animal development. In plants, RNA silencing plays a crucial role in antiviral defence by inhibiting viral accumulation and sometimes preventing systemic infection. As a counter-defence mechanism, viruses have evolved a set of anti-silencing strategies, of which the most common is the production of viral suppressors of RNA silencing (VSRs). Here we review the different strategies underlying VSRs action including prevention of viral-derived small (vs)RNAs synthesis, vsRNAs sequestration or inhibition of vsRNA-guided effector complexes. We will also underline the consequences of this molecular arms race on the evolution of both viral and host genomes.

Identification of an RNA Silencing Suppressor from a Plant Double-Stranded RNA Virus

Journal of Virology, 2005

RNA silencing is a mechanism which higher plants and animals have evolved to defend against viral infection in addition to regulation of gene expression for growth and development. As a counterdefense, many plant and some animal viruses studied to date encode RNA silencing suppressors (RSS) that interfere with various steps of the silencing pathway. In this study, we report the first identification of an RSS from a plant double-stranded RNA (dsRNA) virus. Pns10, encoded by S10 of Rice dwarf phytoreovirus RDV), exhibited RSS activity in coinfiltration assays with the reporter green fluorescent protein (GFP) in transgenic Nicotiana benthamiana line 16c carrying GFP. The other gene segments of the RDV genome did not have such a function. Pns10 suppressed local and systemic silencing induced by sense RNA but did not interfere with local and systemic silencing induced by dsRNA. Expression of Pns10 also increased the expression of ␤-glucuronidase in transient assays and enhanced Potato virus X pathogenicity in N. benthamiana. Collectively, our results establish Pns10 as an RSS encoded by a plant dsRNA virus and further suggest that Pns10 targets an upstream step of dsRNA formation in the RNA silencing pathway.

Antiviral strategies in plants based on RNA silencing

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2011

One of the challenges being faced in the twenty-first century is the biological control of plant viral infections. Among the different strategies to combat virus infections, those based on pathogen-derived resistance (PDR) are probably the most powerful approaches to confer virus resistance in plants. The application of the PDR concept not only revealed the existence of a previously unknown sequence-specific RNA-degradation mechanism in plants, but has also helped to design antiviral strategies to engineer viral resistant plants in the last 25 years. In this article, we review the different platforms related to RNA silencing that have been developed during this time to obtain plants resistant to viruses and illustrate examples of current applications of RNA silencing to protect crop plants against viral diseases of agronomic relevance. This article is part of a Special Issue entitled: MicroRNAs in viral gene regulation. Published by Elsevier B.V. j o u r n a l h o m e p a g e : w w w. e l s ev i e r. c o m / l o c a t e / b b a g r m

Three distinct suppressors of RNA silencing encoded by a 20-kb viral RNA genome

Proceedings of the National Academy of Sciences, 2004

virus-encoded function to block the RNA silencing antiviral defense. Here, we report the identification and characterization of three distinct suppressors of RNA silencing encoded by the Ϸ20-kb plus-strand RNA genome of citrus tristeza virus (CTV). When introduced by genetic crosses into plants carrying a silencing transgene, both p20 and p23, but not coat protein (CP), restored expression of the transgene. Although none of the CTV proteins prevented DNA methylation of the transgene, export of the silencing signal (capable of mediating intercellular silencing spread) was detected only from the F1 plants expressing p23 and not from the CP-or p20-expressing F1 plants, demonstrating suppression of intercellular silencing by CP and p20 but not by p23. Thus, intracellular and intercellular silencing are each targeted by a CTV protein, whereas the third, p20, inhibits silencing at both levels. Notably, CP suppresses intercellular silencing without interfering with intracellular silencing. The novel property of CP suggests a mechanism distinct to p20 and all of the other viral suppressors known to interfere with intercellular silencing and that this class of viral suppressors may not be consistently identified by Agrobacterium coinfiltration because it also induces RNA silencing against the infiltrated suppressor transgene. Our analyses reveal a sophisticated viral counter-defense strategy that targets the silencing antiviral pathway at multiple steps and may be essential for protecting CTV with such a large RNA genome from antiviral silencing in the perennial tree host.

Regulation of plant antiviral defense genes via host RNA-silencing mechanisms

Virology Journal

Background Plants in nature or crops in the field interact with a multitude of beneficial or parasitic organisms, including bacteria, fungi and viruses. Viruses are highly specialized to infect a limited range of host plants, leading in extreme cases to the full invasion of the host and a diseased phenotype. Resistance to viruses can be mediated by various passive or active mechanisms, including the RNA-silencing machinery and the innate immune system. Main text RNA-silencing mechanisms may inhibit viral replication, while viral components can elicit the innate immune system. Viruses that successfully enter the plant cell can elicit pattern-triggered immunity (PTI), albeit by yet unknown mechanisms. As a counter defense, viruses suppress PTI. Furthermore, viral Avirulence proteins (Avr) may be detected by intracellular immune receptors (Resistance proteins) to elicit effector-triggered immunity (ETI). ETI often culminates in a localized programmed cell death reaction, the hypersensi...

Inhibition of 3' modification of small RNAs in virus-infected plants require spatial and temporal co-expression of small RNAs and viral silencing-suppressor proteins.

Plant viruses are inducers and targets of RNA silencing. Viruses counteract with RNA silencing by expressing silencing-suppressor proteins. Many of the identified proteins bind siRNAs, which prevents assembly of silencing effector complexes, and also interfere with their 3’ methylation, which protects them against degradation. Here, we investigated the 3’ modification of silencing-related small RNAs in Nicotiana benthamiana plants infected with viruses expressing RNA silencing suppressors, the p19 protein of Carnation Italian ringspot virus (CIRV) and HC-Pro of Tobacco etch virus (TEV). We found that CIRV had only a slight effect on viral siRNA 3’ modification, but TEV significantly inhibited the 3’ modification of si/miRNAs. We also found that p19 and HC-Pro were able to bind both 3’ modified and non-modified small RNAs in vivo. The findings suggest that the 3’ modification of viral siRNAs occurs in the cytoplasm, though miRNA 3’ modification likely takes place in the nucleus as well. Both silencing suppressors inhibited the 3’ modification of si/miRNAs when they and small RNAs were transiently co-expressed, suggesting that the inhibition of si/miRNA 3’modification requires spatial and temporal co-expression. Finally, our data revealed that a HEN1-like methyltransferase might account for the small RNA modification at the their 3’-terminal nucleotide in N. benthamiana.

A plant RNA virus suppresses RNA silencing through viral RNA replication

The EMBO Journal, 2005

RNA interference (RNAi) is a post-transcriptional generegulatory mechanism that operates in many eukaryotes. RNAi is induced by double-stranded RNA (dsRNA) and is mainly involved in defence against transposons and viruses. To counteract RNAi, viruses have RNAi suppressors. Here we show a novel mechanism of RNAi suppression by a plant virus Red clover necrotic mosaic virus (RCNMV). To suppress RNAi, RCNMV needs multiple viral components, which include viral RNAs and putative RNA replicase proteins. A close relationship between the RNA elements required for negative-strand RNA synthesis and RNAi suppression suggests a strong link between the viral RNA replication machinery and the RNAi machinery. In a transient assay, RCNMV interferes with the accumulation of small-interfering RNA (siRNAs) in RNAi induced by a hairpin dsRNA and it also interferes with microRNA (miRNA) biogenesis. An Arabidopsis dcl1 mutant showed reduced susceptibility to RCNMV infection. Based on these results, we propose a model in which, to replicate, RCNMV deprives the RNAi machinery of Dicer-like enzymes that are involved in both siRNA and miRNA biogenesis. The EMBO Journal VOL 24 | NO 17 | 2005 EMBO THE EMBO JOURNAL THE EMBO JOURNAL Viral RNA replication complex suppresses RNAi A Takeda et al &

Plants Encode a General siRNA Suppressor That Is Induced and Suppressed by Viruses

PLOS Biology, 2015

Small RNAs play essential regulatory roles in genome stability, development, and responses to biotic and abiotic stresses in most eukaryotes. In plants, the RNaseIII enzyme DICER-LIKE1 (DCL1) produces miRNAs, whereas DCL2, DCL3, and DCL4 produce various size classes of siRNAs. Plants also encode RNASE THREE-LIKE (RTL) enzymes that lack DCL-specific domains and whose function is largely unknown. We found that virus infection induces RTL1 expression, suggesting that this enzyme could play a role in plantvirus interaction. To first investigate the biochemical activity of RTL1 independent of virus infection, small RNAs were sequenced from transgenic plants constitutively expressing RTL1. These plants lacked almost all DCL2-, DCL3-, and DCL4-dependent small RNAs, indicating that RTL1 is a general suppressor of plant siRNA pathways. In vivo and in vitro assays revealed that RTL1 prevents siRNA production by cleaving dsRNA prior to DCL2-, DCL3-, and DCL4-processing. The substrate of RTL1 cleavage is likely long-perfect (or near-perfect) dsRNA, consistent with the RTL1-insensitivity of miRNAs, which derive from DCL1-processing of short-imperfect dsRNA. Virus infection induces RTL1 mRNA accumulation, but viral proteins that suppress RNA silencing inhibit RTL1 activity, suggesting that RTL1 has evolved as an inducible antiviral defense that could target dsRNA intermediates of viral replication, but that a broad range of viruses counteract RTL1 using the same protein toolbox used to inhibit antiviral RNA silencing. Together, these results reveal yet another level of complexity in the evolutionary battle between viruses and plant defenses.