Synthetic Pentatricopeptide Repeat Proteins: Building a Toolkit for Precise RNA Control

In plants, cytidine-to-uridine (C-to-U) and uridine-to-cytidine (U-to-C) editing events are directed by pentatricopeptide repeat (PPR) proteins, modular RNA-binding factors that recognize their RNA targets through a predictable amino acid-nucleotide recognition code. Deciphering this code has enabled the rational design of synthetic PPR (synPPR) proteins with programmable RNA-binding specificity and robust stability in heterologous systems. Recent advances have extended these synthetic scaffolds to active RNA editors by fusing them to catalytically competent DYW deaminase domains, generating customizable enzymes capable of precise base conversion in bacteria, plants, and even human cells. This review summarizes current understanding of the structural and mechanistic principles underlying PPR-mediated RNA editing and highlights recent progress in the design and application of synPPR proteins. We discuss how synthetic PPR proteins have been used as programmable RNA stabilizers, translational regulators, and targeted C-to-U or U-to-C editors, as well as their emerging therapeutic potential in RNA-mediated diseases. The development of compact, cofactor-independent editors derived from early-diverging plant lineages further expands the versatility of this platform. Together, these efforts establish synthetic PPR proteins as a powerful and flexible class of RNA engineering tools with applications spanning basic research, biotechnology, and biomedicine. Continued refinement of targeting specificity, catalytic efficiency, and effector modularity will propel PPR-based editors toward broader use in synthetic biology and therapeutic RNA modulation.