Differential degradation of RNA species by autophagy-related pathways in Arabidopsis

Abstract

The plant vacuole recycles proteins and RNA delivered to it by autophagy. Here, we provide a comprehensive characterization of the plant vacuolar RNAome by isolating intact vacuoles from Arabidopsis plants, subsequent RNA purification and deep sequencing. In the vacuolar RNAomes, we detected ribosomal RNAs, and transfer RNAs, including those of chloroplast origin and small RNA types in addition. As autophagy is a main mechanism for the transport of RNA to the vacuole, atg5-1 mutants deficient in autophagy were included in our analysis. We observed severely reduced amounts of most chloroplast-derived RNA species in these mutants. By comparison with the cellular RNA composition, indications for the upregulation of alternative RNA breakdown pathways were obtained. By contrast, vacuolar RNA processing and composition in plants lacking vacuolar ribonuclease 2, involved in cellular RNA homeostasis, only showed minor alterations, possibly because of the presence of further so far unknown vacuolar RNase species. Among the small RNA types, we detected mature miRNAs in all vacuolar preparations but at much lower frequency in atg5-1, raising the possibility of a biological role for vacuolar miRNAs.