Intronic miRNA–directed regulation of mitochondrial RNA editing enhances plant stress tolerance in Arabidopsis

MicroRNAs (miRNAs) have emerged as key regulators in plant development and stress responses. Increasing evidence points to the crucial role of intronic miRNA that derived from the introns of other genes in animals, whereas few reports have explored this topic in plants. We report here an RNA splicing–mediated mechanism involved in stress responses, whereby intronic miR400 modulates mitochondrial RNA editing by targeting the PPR1 mRNA. An intronic miR400 splicing–dependent luciferase transgenic line was generated to monitor the intron splicing events. We determined that luciferase activity decreases upon cadmium (Cd) treatment due to the retention of the intron containing miR400, which inhibits the production of mature miR400. Overexpression of MIR400 rendered plants more sensitive to Cd stress, whereas impaired miR400 expression enhanced their tolerance. Genetic and molecular experiments identified the PENTATRICOPEPTIDE REPEAT PROTEIN 1 (PPR1) as the miR400 target responsible for the plant Cd response. In addition, we demonstrate that PPR1 affects RNA editing of the mitochondrial gene ccb206 to control reactive oxygen species accumulation and improve plant tolerance. Our study illustrates intron splicing as a key step in intronic miR400 regulation and highlights the function of intronic miRNA as a “signal transducer” to enhance plant stress tolerance. Overall design: Comparative gene expression profiling analysis of RNA-seq data for wild–type, OXmiR400 lines and OXrPPR1 lines.