GRASP: a modular toolkit for building synthetic pentatricopeptide repeat RNA-binding proteins

Pentatricopeptide repeat (PPR) proteins are eukaryotic RNA-binding proteins with multiple roles in mitochondrial and chloroplast transcript processing. PPR proteins are naturally modular and hold great potential for development into tools for RNA processing or controlling RNA folding or expression. However, construction of synthetic PPR (sPPR) proteins is challenging due to their highly repetitive sequences. Here, we present the GRASP kit for assembly of sPPR proteins. Utilizing the S-variant of PPR motifs, we designed a library of 42 plasmids which can be combined to assemble sPPR proteins with 9, 14, or 19 motifs to target any RNA sequence of the same length. The GRASP kit enables rapid design and construction of PPR proteins of any desired specificity and is compatible with the MoClo assembly standard. To demonstrate the capabilities of GRASP, we assembled a sPPR–RNA-editing protein and variants with altered sequence specificity. We tested the functionality of 31 sPPR protein variants against a set of 46 RNA targets and used RNA sequencing to determine levels of RNA editing. The variations in editing provide a wealth of insights into PPR–RNA interactions. The GRASP kit provides a foundation for further development of sPPR protein technologies.