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

Dennis, M. L.; Low, S. Y.; Viljoen, A.; Pullakhandam, A.; Colas des Francs-Small, C.; Campbell-Clause, L.; Bond, C. S.; Small, I.; Kwok van der Giezen, F. M.

doi:10.1101/2025.06.29.661641

bioRxiv · 10.1101/2025.06.29.661641

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

Dennis, M. L.·Low, S. Y.·Viljoen, A.·Pullakhandam, A.·Colas des Francs-Small, C.·Campbell-Clause, L.·Bond, C. S.·Small, I.·Kwok van der Giezen, F. M.

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Abstract

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 proteins is challenging due to their highly repetitive sequences. Here, we present the GRASP kit for assembly of synthetic PPR proteins. Utilising the S-variant of PPR motifs, we designed a library of 42 plasmids which can be combined to assemble synthetic PPR 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 synthetic PPR RNA editing protein and variants with altered sequence specificity. We tested the functionality of 31 synthetic PPR 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 synthetic PPR protein technologies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/661641v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@d8c1d2org.highwire.dtl.DTLVardef@9ccba8org.highwire.dtl.DTLVardef@1feadfeorg.highwire.dtl.DTLVardef@150ffb7_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Dennis, M. L., Low, S. Y., Viljoen, A., Pullakhandam, A., Colas des Francs-Small, C., Campbell-Clause, L., Bond, C. S., Small, I., Kwok van der Giezen, F. M.. 2025-06-30. GRASP: a modular toolkit for synthetic pentatricopeptide repeat RNA-binding proteins. https://doi.org/10.1101/2025.06.29.661641

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