Eukaryotes harbor mitochondria obtained via ancient symbiosis events. The successful evolution of energy production in mitochondria has been dependent on the control of mitochondrial gene expression by the nucleus. In flowering plants, the nuclear-encoded pentatricopeptide repeat (PPR) superfamily proteins are widely involved in mitochondrial RNA metabolism. Here, we show that an Arabidopsis nuclear-encoded RNA-binding protein, Restorer-of-fertility-like PPR protein 2 (RFL2), is required for RNA degradation of the mitochondrialorf291transcript via endonucleolytic cleavage of the transcript in the middle of its reading frame. Bothin vivoandin vitro, this RNA cleavage requires the activity of mitochondrial proteinaceous RNase P, which is possibly recruited to the site by RFL2. The site of RNase P cleavage likely forms a tRNA-like structure in theorf291transcript. This study presents an example of functional collaboration between a PPR protein and an endonuclease in RNA cleavage. Furthermore, we show that the RFL2-binding region within theorf291gene is hypervariable in the family Brassicaceae, possibly correlated with the rapid evolution of the RNA-recognition interfaces of the RFL proteins.Significance Statement
Post-transcriptional modifications of mitochondrial RNA are often mediated by members of the nuclear-encoded pentatricopeptide repeat (PPR) protein superfamily, but little is known about how these proteins act because most PPR proteins lack enzymatic domains. Here we show that a PPR protein acts together with a RNase P to cleave a specific mitochondrial RNA.