Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing

TLDR

Plants use DICER‑LIKE proteins to mediate RNA silencing, regulating gene expression and defending against viruses. The study investigates why Arabidopsis expresses four distinct DCLs, a diversity not seen in other kingdoms. The authors find that DNA viruses generate 21‑, 22‑, and 24‑nt siRNAs via all four DCLs, with DCL1 producing 21‑nt siRNAs from the CaMV leader, while RNA virus infection is mainly governed by DCL4, which together with RDR6 and HEN1 drives extensive virus‑induced silencing; additionally, CaMV and ORMV disrupt RDR6 processing and HEN1 methylation, respectively, underscoring the role of DCL diversity in plant antiviral defense.

Abstract

Like other eukaryotes, plants use DICER-LIKE (DCL) proteins as the central enzymes of RNA silencing, which regulates gene expression and mediates defense against viruses. But why do plants like Arabidopsis express four DCLs, a diversity unmatched by other kingdoms? Here we show that two nuclear DNA viruses (geminivirus CaLCuV and pararetrovirus CaMV) and a cytoplasmic RNA tobamovirus ORMV are differentially targeted by subsets of DCLs. DNA virus-derived small interfering RNAs (siRNAs) of specific size classes (21, 22 and 24 nt) are produced by all four DCLs, including DCL1, known to process microRNA precursors. Specifically, DCL1 generates 21 nt siRNAs from the CaMV leader region. In contrast, RNA virus infection is mainly affected by DCL4. While the four DCLs are partially redundant for CaLCuV-induced mRNA degradation, DCL4 in conjunction with RDR6 and HEN1 specifically facilitates extensive virus-induced silencing in new growth. Additionally, we show that CaMV infection impairs processing of endogenous RDR6-derived double-stranded RNA, while ORMV prevents HEN1-mediated methylation of small RNA duplexes, suggesting two novel viral strategies of silencing suppression. Our work highlights the complexity of virus interaction with host silencing pathways and suggests that DCL multiplicity helps mediate plant responses to diverse viral infections.