Rice PALE GREEN LEAVES, encoding a DYW-type pentatricopeptide repeat protein, is involved in chloroplast RNA editing and splicing, and regulate chloroplast development

Abstract The chloroplast serves as the primary site of photosynthesis, and its development plays a crucial role in regulating plant growth and morphogenesis. The PentatricopeptideRepeat Sequence (PPR) proteins constitute a vast protein family that function in the post modification of RNA within plant organelles. In this study, we characterized a rice pale green leaves ( pgl3 ) mutant. The chlorophyll content of pgl3 at the seedling stage was significantly reduced compared to the wild type (WT). Transmission electron microscopy (TEM) and quantitative PCR analysis revealed that the pgl3 exhibited aberrant chloroplast development compared to the wild type (WT), accompanied by significant alterations in gene expression levels associated with chloroplast development and photosynthesis. The Mutmap analysis revealed that single base deletion occurred in the coding region of Os03g0136700 in pgl3 . By employing CRISPR/Cas9 mediated gene editing, two homozygous cr- pgl3 mutant were generated and exhibited similar phenotype to pgl3 , thereby confirming that Os03g0136700 was responsible for pgl3 and subsequently designating it as PGL3 . PGL3 belong to the DYW-type PPR protein family and is localized in chloroplasts. Moreover, we showed that RNA editing efficiency of rps8-182 and rpoC2-4106 , and splicing of ycf3-1 are significantly decreased in pgl3 mutants compared to WT. Collectively, these result indicate that PGL3 plays a crucial role in the process of chloroplast development via regulating the editing and splicing of chloroplast genes in rice.