Role of Virus-Derived Small RNAs in Plant Antiviral Defense: Insights from DNA Viruses

In plants and some animals, viral infection triggers production of virus-derived short interfering (si)RNAs (vsRNAs) by the host gene-silencing machinery, which is thought to restrict virus replication and spread. To counter the silencing-based host defense and thereby establish successful infection, viruses encode suppressor proteins that block different steps of siRNA biogenesis or action. Plants infected with DNA viruses accumulate three major size classes of vsRNAs that are processed from double-stranded RNA precursors by Dicer-like (DCL) proteins. In a model plant Arabidopsis thaliana possessing four DCLs, DCL4 and DCL1 generate 21-nt vsRNAs, DCL2 generates 22-nt vsRNAs, and DCL3 generates 24-nt vsRNAs. In contrast, RNA virus infections are associated with production of DCL4-dependent 21-nt vsRNAs and DCL2-dependent 22-nt vsRNAs. This reflects the difference in life cycles of plant DNA and RNA viruses: the former are transcribed in the nucleus where DCL1 and DCL3 normally generate endogenous miRNAs and heterochromatic siRNAs, respectively, whereas the latter are generally restricted to the cytoplasm. To function in silencing, like endogenous miRNAs and siRNAs, vsRNAs must get associated with Argonaute (AGO) family proteins and guide the resulting RNA-induced silencing complexes to complementary RNA or DNA targets. The nuclear-localized AGO proteins act in transcriptional gene silencing and heterochromatin formation through siRNA-directed DNA methylation, whereas the cytoplasmic AGOs act in posttranscriptional gene silencing through miRNA/siRNA-directed mRNA cleavage and/or translational repression. The plant silencing machinery has a remarkable ability to mediate siRNA amplification and systemic spread; these processes involve RNA-dependent RNA polymerases and plant-specific DNA-dependent RNA polymerases Pol IV and Pol V. Thus, amplification and spread of vsRNAs may also play a role in plant antiviral defense. Here we review the accumulating evidence on the role of nuclear and cytoplasmic components of the plant silencing machinery in the biogenesis and action of vsRNAs. We also describe silencing suppression and evasion strategies evolved by plant viruses and illustrate how viruses and their suppressor proteins could be used as a tool to discover novel features of the plant silencing system.