Plants possess a unique C-to-U RNA editing mechanism mediated by PPR-DYW proteins, wherein the PPR domain recognizes specific RNA sequences while the DYW deaminase domain precisely edits the target C base—a process essential for functional protein expression in plant chloroplasts and mitochondria. The coordination of these two domains is considered crucial for precise RNA editing. In nature, this site-specific and precise base editing by PPR-DYW proteins distinguishes them from other base-editing deaminases. However, the absence of structures containing both PPR and DYW domains has limited our understanding of the precise RNA-editing mechanism of PPR-DYW proteins. Here, we present crystal structures of the consensus PPR-DYW (consPPR-DYW) protein, a representative of the PPR-DYW proteins, in both RNA-free and target RNA-bound states. Comparison between these states demonstrates domain movements upon target RNA binding, whereby the PPR domain accommodates the upstream sequence of the target C base in the proper conformation for editing while the DYW domain is optimally positioned for precise C-to-U conversion. These results, combined with comprehensive biochemical analyses, provide the foundation for a mechanistic model that explains the coordinated action of the PPR and DYW domains in achieving precise C-to-U editing. Plant organellar RNA editing requires PPR-DYW proteins to mediate cytidine-to-uridine conversions essential for gene expression. Here, the authors determine crystal structures of a consensus PPR-DYW protein in RNA-free and RNA-bound states, and combined with biochemical analyses, reveal the molecular mechanisms underlying how PPR-DYW proteins achieve precise C-to-U RNA editing.
Teramoto et al. (Mon,) studied this question.