Research Progress in the Molecular Mechanism of PPR Protein-regulated Chloroplast RNA Editing

doi:10.13560/j.cnki.biotech.bull.1985.2025-0506

Abstract

Abstract:

As semi-autonomous organelles, chloroplasts possess their own genomes, and some of their transcribed RNAs require C-to-U base changes to ensure correct gene expression. PPR (pentatricopeptide repeat protein) proteins are the core regulatory factors controlling chloroplast RNA editing. This family is large and is divided into two subfamilies, P-type and PLS-type, based on their different C-terminal domains. The PLS-type subfamily can be further classified into PLS-E, PLS-E+, and PLS-DYW. Among them, the DYW domain in the PLS-DYW type has deaminase activity and directly participates in RNA editing. The PPR motif, which is unique to PPR proteins, recognizes the RNA sequence upstream of the editing site in the 5′-3′ direction based on the combination of the 6th and 1st amino acids from the N-terminal to the C-terminal. This modular recognition mechanism enables PPR proteins to screen editing sites in a one-PPR-motif-to-one-nucleotide manner, recruit and assemble the editing complex, and carry out the editing process. Defects in RNA editing regulated by related PPR proteins can lead to abnormal chloroplast development, causing plant wilting or death. This article reviews the current research progress, focusing on the molecular mechanisms by which PPR proteins regulate RNA editing of chloroplast genes in different plants, and prospects to the dynamic assembly process of the RNA editing complex, providing references for future in-depth exploration of the targeting mechanism of PPR proteins and their applications in agriculture.

Key words: chloroplast, PPR proteins, RNA editing, photosynthesis

LI Xin-ying, SUN Jing, LYU Ruo-tong, REN Ya-juan, LUO Lei, AI Peng-fei, WANG Yan-wei. Research Progress in the Molecular Mechanism of PPR Protein-regulated Chloroplast RNA Editing[J]. Biotechnology Bulletin, 2025, 41(10): 32-42.

Figures/Tables 3

Fig. 1 RNA editing of cytosine nucleoside (C) to uracil nucleoside (U)

Fig. 2 Structure of PPR proteins

Fig. 3 PPR recognition code for RNA bindingKey amino acid positions 6 and 1′ of each PPR motif are indicated as yellow and green colored square boxes, respectively. T, N, D, and S denote amino acids tyrosine, asparagine, aspartic acid, and serine, respectively. Combinations of amino acids at positions 6 and 1′ specify binding to specific bases as proposed in Barkan et al[45]. (T, N) (T at 6, N at 1′) specify binding to adenine (A), (T, D) to guanine (G), (N, S) to cytosine (C), (N, D) to uracil (U), and (N, N) to C or U

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