The pentatricopeptide repeat protein EMBRYO DEFECTIVE 1417 is required for chloroplast RNA editing and intron splicing in Arabidopsis.

Abstract

Post-transcriptional RNA processing is essential for chloroplast biogenesis. The pentatricopeptide repeat (PPR) protein EMBRYO DEFECTIVE 1417 (EMB1417), which contains only two PPR motifs, was previously shown to be required for splicing of rpoC1 and ycf3.2 transcripts in chloroplasts. Here, we demonstrate that chemical-induced silencing of EMB1417 results in a yellow-leaf phenotype with markedly reduced chlorophyll content. RNA sequencing analyses revealed that EMB1417 is indispensable for efficient C-to-U editing at multiple sites, including rpoA-200, clpP-559, petL-5, psbZ-50, accD-1568, and ndhD-2. Protein-protein interaction assays demonstrated that EMB1417 physically interacts with multiple RNA editing cofactors, MORF2/8/9 and DG409, thereby facilitating RNA editing in chloroplasts. Strikingly, disruption of EMB1417 significantly also severely impairs the splicing of group II introns in ndhB, petB, and petD transcripts. We further identified a direct interaction between EMB1417 and the splicing factor CFM3A. These findings establish that EMB1417 participates in chloroplast RNA processing, providing critical insights into the mechanisms of RNA editing and splicing during chloroplast development.