Arabidopsis FIERY1, XRN2, and XRN3 Are Endogenous RNA Silencing Suppressors

Abstract

The eukaryotic defense response posttranscriptional gene silencing (PTGS) is directed by short-interfering RNAs and thwarts invading nucleic acids via the RNA slicing activity of conserved ARGONAUTE (AGO) proteins. PTGS can be counteracted by exogenous or endogenous suppressors, including the cytoplasmic exoribonuclease XRN4, which also degrades microRNA (miRNA)-guided mRNA cleavage products but does not play an obvious role in development. Here, we show that the nuclear exoribonucleases XRN2 and XRN3 are endogenous PTGS suppressors. We also identify excised MIRNA loops as templates for XRN2 and XRN3 and show that XRN3 is critical for proper development. Independently, we identified the nucleotidase/ phosphatase FIERY1 (FRY1) as an endogenous PTGS suppressor through a suppressor screen in a hypomorphic ago1 genetic background. FRY1 is one of six Arabidopsis thaliana orthologs of yeast Hal2. Yeast hal2 mutants overaccumulate 39-phosphoadenosine 59-phosphate, which suppresses the 59!39 exoribonucleases Xrn1 and Rat1. fry1 mutant plants recapitulate developmental and molecular characteristics of xrn mutants and likely restore PTGS in ago1 hypomorphic mutants by corepressing XRN2, XRN3, and XRN4, thus increasing RNA silencing triggers. We anticipate that screens incorporating partially compromised silencing components will uncover additional PTGS suppressors that may not be revealed using robust silencing systems.

Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis

“…3B, Middle), similar to that described previously in a study based on the infection of a different xrn4/ein5 mutant by a different CMV isolate (40). We found that ein5 plants were also more resistant to CMV-Δ2b than WT plants and that CMVΔ2b accumulated to the highest level in rdr1 plants (Fig.…”

Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs

“…In animals, some of these complexes are associated with components of the RNA silencing machinery (Leung et al, 2006), and there is evidence that Drosophila P-bodies are involved in miRNA-directed target decay through deadenylation and decapping, whereas translational repression is P-body independent (Eulalio et al, 2007). In plants, components of the RNA decapping machinery were found involved in RNA silencing (Gazzani et al, 2004;Gy et al, 2007), and the existence of P-bodies was recently demonstrated (Xu et al, 2006). Thus, it will be interesting to investigate which type of proteins, such as other members of the large AGO family, are linked to miRNAs and their mRNA targets in nonpolysomal fractions.…”

The role of decapping proteins in the miRNA accumulation inArabidopsis thaliana

“…[46][47][48] The accumulation of miR164 does not decrease in the xrn4 null mutant. 48 It is thought that the lethality of dcp1, dcp2 and vcs arise from defects in decapping and subsequent 5'-3' mRNA decay, although the null xrn4 mutant is not lethal.…”

“…[46][47][48] The accumulation of miR164 does not decrease in the xrn4 null mutant. 48 It is thought that the lethality of dcp1, dcp2 and vcs arise from defects in decapping and subsequent 5'-3' mRNA decay, although the null xrn4 mutant is not lethal. [46][47][48] Our results suggest that defects in the miRNA pathway are a major cause of the lethal phenotypes in dcp1, dcp2 and vcs mutants.…”

“…48 It is thought that the lethality of dcp1, dcp2 and vcs arise from defects in decapping and subsequent 5'-3' mRNA decay, although the null xrn4 mutant is not lethal. [46][47][48] Our results suggest that defects in the miRNA pathway are a major cause of the lethal phenotypes in dcp1, dcp2 and vcs mutants. To further examine how DCP1, DCP2 and VCS act in the miRNA pathway is important to comprehensively characterize mRNA decay mechanisms and the roles of P-bodies.…”