Functional analysis of the Arabidopsis thaliana CHLOROPLAST BIOGENESIS 19 pentatricopeptide repeat editing protein

The Arabidopsis thaliana pentatricopeptide repeat (PPR) family of proteins contains several degenerate 35-aa motifs named PPR repeats. These proteins control diverse post-transcriptional regulatory mechanisms, including RNA editing. CLB19 belongs to the PLS subfamily of PPR proteins and is essential for the editing and functionality of the subunit A of plastid-encoded RNA polymerase (RpoA) and the catalytic subunit of the Clp protease (ClpP1). We demonstrate in vitro that CLB19 has a specific interaction with these two targets, in spite of their modest sequence similarity. Using site-directed mutagenesis of the rpoA target, we analyzed the essential nucleotides required for CLB19-rpoA interactions. We verified that, similar to other editing proteins, the C-terminal E domain of CLB19 is essential for editing but not for RNA binding. Using biomolecular fluorescence complementation, we demonstrated that the E domain of CLB19 interacts with the RNA-interacting protein MORF2/RIP2 but not with MORF9/RIP9. An interesting finding from this analysis was that overexpression of a truncated CLB19 protein lacking the E domain interferes with cell fate during megasporogenesis and the subsequent establishment of a female gametophyte, supporting an important role of plastids in female gametogenesis. Together these analyses provide important clues about the particularities of the CLB19 editing protein.