Function of PPR proteins in plastid gene expression

Abstract

PPR proteins form a huge family in flowering plants and are involved in RNA maturation in plastids and mitochondria. These proteins are sequence-specific RNA-binding proteins that recruit the machinery of RNA processing. We summarize progress in the research on the functional mechanisms of divergent RNA maturation and on the mechanism by which RNA sequences are recognized. We further focus on two topics. RNA editing is an enigmatic process of RNA maturation in organelles, in which members of the PLS subfamily contribute to target site recognition. As the first topic, we speculate on why the PLS subfamily was selected by the RNA editing machinery. Second, we discuss how the regulation of plastid gene expression contributes to efficient photosynthesis. Although the molecular functions of PPR proteins have been studied extensively, information on the physiological significance of regulation by these proteins remains very limited.

Keywords: PPR; RNA; RNA editing; chloroplast; photosynthesis.

Figure 1. Schematics of representative PPR protein structures.

Figure 2. Functions mediated by PGR3. The model is based on that of Cai et al. PGR3 binds the 5′UTR of petL operon RNA and protects RNA from 5′ → 3′ exonuclease (function 1). Simultaneously, PGR3 binding activates translation of petL, most likely modifying the secondary RNA structure of the region, including the SD element (function 2). PGR3 also activates translation of ndhA (function 3). All of the function of the pgr3-1 allele is affected. pgr3-2 is defective in functions 1 and 2, and pgr3-3 cannot translate petL and ndhA (functions 2 and 3).

Figure 3. The X-ray structure of two consecutive PPR motifs in human mitochondrial RNA polymerase (PDB 3SPA). Residues known to be involved in RNA binding are highlighted in color. Positions 1 (brown) and 6 (yellow) are the most important components of the PPR code.