The P-type pentatricopeptide repeat protein YGS is essential for chloroplast development in rice

Pentatricopeptide repeat (PPR) proteins play crucial roles in the post-transcriptional regulation of gene expression, specifically RNA editing and RNA splicing, in plant organelles. Despite longstanding research on chloroplast biogenesis and development, the roles of most PPR genes in this process in rice (Oryza sativa) remain unclear. In this study, we identified a novel P-type PPR protein, YELLOW-GREEN LEAF AND SEEDLING LETHAL (YGS), that is targeted to rice chloroplasts. YGS is preferentially expressed in leaves. The ygs mutants were obtained by knocking out YGS gene using CRISPR/Cas9-mediated genome editing; these mutants exhibited yellow-green leaves and a seedling-lethal phenotype. Consistent with these phenotypes, the ygs mutants had lower levels of pigment contents and an abnormal chloroplast ultrastructure compared to the wild type. Moreover, the expression levels of genes related to chloroplast development and chlorophyll biosynthesis were significantly altered in the ygs mutants. In addition, loss of function of YGS impaired RNA editing of rpl2 and intron splicing of ycf3-1 in the plastid genome. Finally, YGS interacted with the chloroplast signal recognition particle protein OscpSRP54b in yeast two-hybrid and bimolecular fluorescence complementation assays. These findings suggest that YGS is involved in RNA editing and RNA splicing in chloroplasts, thereby playing a crucial role in chloroplast development in rice.