RNA Binding Proteins Regulating Chloroplast RNA Metabolism

Nucleus-encoded RNA-binding proteins and ribonucleases have crucial roles in calibrating the transcriptional output of chloroplast genes. Primary chloroplast transcripts are processed through a series of regulated steps including polycistronic transcript processing, splicing to remove introns, cytidine-to-uridine (C-to-U) editing, and controlled mRNA turnover. Key players include pentatricopeptide repeat (PPR) proteins, which stabilize transcripts and guide their processing, RNA helicases, which unwind double-stranded RNA structures by utilizing the ATP hydrolysis energy, and a variety of RNases such as PNPase (a 3′ → 5′ exonuclease), RNase E (endoribonuclease), and RNase J (endoribonuclease and 5′ → 3′ exonuclease). These enzymes coordinate the maturation and degradation of RNA, ensuring the removal of defective or unnecessary transcripts and maintaining RNA stability. The intricate interplay between RNA-binding proteins and ribonucleases shapes the complex transcript patterns within chloroplasts and provides the precise regulation of gene expression. Given that chloroplasts play a pivotal role in cellular processes such as photosynthesis, plant defense, and primary and specialized metabolism, chloroplast RNA metabolism is therefore an essential component of plant development. This chapter discusses the roles of various nucleus-encoded, chloroplast-localized RBPs in chloroplast RNA metabolism and gene expression.