An active RNA transport mechanism into plant vacuoles

RNA degradation inside the plant vacuole by the ribonuclease RNS2 is essential for maintaining nucleotide concentrations and cellular homeostasis via the nucleotide salvage pathway. However, the mechanisms by which RNA is transported into the vacuole are not well understood. While selective macroautophagy may contribute to this transport, macroautophagy-independent transport pathways also exist. Here, we demonstrate a mechanism for direct RNA transport into Arabidopsis vacuoles that is active in purified vacuoles and is ATP hydrolysis-dependent. We identify the RNA helicase SKI2 as a factor required for this transport pathway, as ski2 mutant vacuoles are defective in transport. ski2 mutants have an increased autophagy phenotype that can be rescued by exogenous addition of inosine, consistent with a function in nucleotide salvage. Moreover, ski2 mutants accumulate reduced levels of 3'-NMP in the vacuole, indicating defects in vacuolar RNA turnover. This newly described transport mechanism is therefore critical for RNA degradation, recycling and cytoplasmic nucleotide homeostasis.