Synergistic action of the Arabidopsis spliceosome components PRP39a and SmD1 in promoting post-transcriptional transgene silencing

Abstract

Besides regulating splicing, the conserved spliceosome component SmD1 was shown to promote posttranscriptional silencing of sense transgenes (S-PTGS). Here, we show that the conserved spliceosome component PRP39a also plays a role in S-PTGS. However, PRP39a and SmD1 actions appear distinct in both splicing and S-PTGS. Indeed, RNA-seq analysis of prp39a and smd1 mutants identified different sets of deregulated mRNAs and non-coding RNAs, both at expression level and alternative splicing genome-wide. Moreover, double mutant analyses involving prp39a or smd1 and RNA quality control (RQC) mutants revealed genetic interactions of SmD1 and PRP39a with distinct nuclear RQC machineries, suggesting synergistic rather than redundant roles in the RQC/PTGS interplay. Supporting this hypothesis, a prp39a smd1 double mutant exhibited enhanced suppression of S-PTGS compared with single mutants. Because no major changes in the expression of PTGS or RQC components or in small RNA production were identified in prp39a and smd1 mutants, and because prp39a and smd1 mutations do not alter PTGS triggered by inverted-repeat transgenes directly producing dsRNA (IR-PTGS), PRP39a and SmD1 seem to synergistically promote a step specific to S-PTGS. We propose that, independent of their specific roles in splicing, PRP39a and SmD1 limit 3-to-5 and 5-to-3 degradation of transgene aberrant RNAs, respectively, thus favoring the export of aberrant RNAs to the cytoplasm where their transformation into dsRNA initiates S-PTGS.