Gene regulation by translational inhibition is determined by Dicer partnering proteins

Abstract

MicroRNAs (miRNAs) are small regulatory RNAs produced by Dicer proteins that regulate gene expression in development and adaptive responses to the environment(1-4). In animals, the degree of base pairing between a miRNA and its target messenger RNA seems to determine whether the regulation occurs through cleavage or translation inhibition(1). In contrast, the selection of regulatory mechanisms is independent of the degree of mismatch between a plant miRNA and its target transcript(5). However, the components and mechanism(s) that determine whether a plant miRNA ultimately regulates its targets by guiding cleavage or translational inhibition are unknown(6). Here we show that the form of regulatory action directed by a plant miRNA is determined by DRB2, a DICER-LIKE1 (DCL1) partnering protein. The dependence of DCL1 on DRB1 for miRNA biogenesis is well characterized(7-9), but we show that it is only required for miRNA-guided transcript cleavage. We found that DRB2 determines miRNA-guided translational inhibition and represses DRB1 expression, thereby allowing the active selection of miRNA regulatory action. Furthermore, our results reveal that the core silencing proteins ARGONAUTE1 (AGO1) and SERRATE (SE) are highly regulated by miRNA-guided translational inhibition. DRB2 has been remarkably conserved throughout plant evolution, raising the possibility that translational repression is the ancient form of miRNA-directed gene regulation in plants, and that Dicer partnering proteins, such as human TRBP, might play a similar role in other eukaryotic systems.

mRNA Decay of Most Arabidopsis miRNA Targets Requires Slicer Activity of AGO1

“…PCA plots with r-log normalized counts data and differential expression analysis (Wald test, multiple testing adjustment of P values with Benjamini-Hochberg procedure) were performed in the Bioconductor environment (Gentleman et al, 2004) using DESeq2 version 1.4.5 (Love et al, 2014) workflow. The list of validated and predicted miRNA and tasiRNAs targets used for data analyses (Supplemental Table S10) was updated from Reis et al (2015).…”

“…In animals, there is good evidence for the existence of mechanisms of repression both at initiation and postinitiation levels (Olsen and Ambros, 1999;Seggerson et al, 2002;Pillai et al, 2005;Maroney et al, 2006;Nottrott et al, 2006;Petersen et al, 2006;Fukaya et al, 2014), but the precise molecular nature of these mechanisms has not been clearly defined. In plants, mechanisms of translational repression by miRNAs remain nearly completely unknown, and although genetic screens have identified some genes required for the process (Brodersen et al, 2008;Yang et al, 2012a;Li et al, 2013;Reis et al, 2015), none of them provides clear insight into how AGO1 recruitment to an mRNA may bring about its translational repression. mRNA degradation is another common outcome of AGO recruitment.…”

Missing Pieces in the Puzzle of Plant MicroRNAs

“…Following duplex strand separation, DRB1 directs the selective loading of miRNA guide strands onto AGO1 to form miRNA-loaded RISC (miRISC) [9]. In plants, miRISC can repress the expression of highly complementary target transcripts via directing either a transcript cleavage or translation inhibition, and the selection of either mechanism is determined by DCL1 partnering proteins, DRB1 (cleavage) and DRB2 (translation inhibition) [10] (Figure 1). …”

Regulation of Plant miRNA Biogenesis

“…It has been shown that DRBs might have similar functions in plant miRNA loading to AGOs (Eamens et al, 2009). It is also been reported that the outcome of miRNA targeting i.e., either target cleavage or translational inhibition is governed by dsRNA binding partners of DCL1 (Reis et al, 2015a). HYL1 mediates target cleavage while DRB2 mediates translational inhibition.…”