Misregulation of AUXIN RESPONSE FACTOR 8 Underlies the Developmental Abnormalities Caused by Three Distinct Viral Silencing Suppressors in Arabidopsis

Abstract

In Arabidopsis, micro (mi)RNAs and trans-acting (ta-si)RNAs synthesized directly or indirectly through the DICER-LIKE-1 (DCL1) ribonuclease have roles in patterning and hormonal responses, while DCL2,3,4-dependent small-interfering (si)RNAs are mainly involved in silencing of transposable elements and antiviral defense. Viral suppressors of RNA silencing (VSRs) produced by phytoviruses to counter plant defense may perturb plant developmental programs because of the collision of their inhibitory effects with the regulatory action of endogenous miRNAs and ta-siRNAs. This could explain the similar developmental aberrations displayed by Arabidopsis miRNA/ta-siRNA pathway mutants, including dcl1, and by some VSR-expressing plants. Nonetheless, the molecular bases for these morphological aberrations have remained mysterious, and their contribution to viral disease symptoms/virulence unexplored. The extent of VSR inhibitory actions to other types of endogenous small RNAs remains also unclear. Here, we present an in-depth analysis of transgenic Arabidopsis expressing constitutively HcPro, P19 and P15, three unrelated VSRs. We show that VSR expression has comparable, yet modest effects on known miRNA and ta-siRNA target RNA levels, similar to those observed using an hypomorphic dcl1 mutation. However, by combining results of transcriptome studies with deep-sequencing data from immuno-precipitated small RNAs, additional, novel endogenous targets of miRNA and ta-siRNA were identified, unraveling an unsuspected complexity in the origin and scope-of-action of these molecules. Other stringent analyses pinpointed misregulation of the miR167 target AUXIN RESPONSE FACTOR 8 (ARF8) as a major cause for the developmental aberrations exhibited by VSR transgenic plants, but also for the phenotypes induced during normal viral infection caused by the HcPro-encoding Turnip mosaic virus (TuMV). Neither RNA silencing, its suppression by VSRs, nor the virulence/accumulation of TuMV was altered by mutations in ARF8. These findings have important implications for our understanding of viral disease symptoms and small RNA-directed regulation of plant growth/development.

Author Summary

In the plant and animal RNA silencing pathways, small RNA molecules known as micro (mi)RNA and short-interfering (si)RNAs have key roles in development and antiviral defense, respectively. In turn, viruses counteract this defense by deploying specific virulence factors, referred to as Viral Suppressors of RNA silencing (VSRs), which target distinct steps of the host silencing machinery. In the model plant species Arabidopsis thaliana, transgenic expression of distinct VSRs often incurs a set of strikingly recurrent developmental anomalies that resemble those triggered by viral infections. While these defects have been assumed to result from a general interference of VSRs with silencing-based mechanisms controlling cellular growth, their exact molecular basis has remained largely elusive. Here, we address this issue by demonstrating that misregulation of a single transcript encoding the AUXIN RESPONSE FACTOR 8, a target of miR167, underlies most, if not all, of the defects caused by VSR expression, both in transgenic and in an authentic infection context. Our study also highlights the value of VSRs as generic tools for the discovery or validation of endogenous RNA silencing targets. These results also have implications for our understanding of small RNA-based regulations in plants, and shed light on the possible origin of some of the symptoms elicited by viral diseases.