Functioning of PPR Proteins in Organelle RNA Metabolism and Chloroplast Biogenesis

Abstract

The pentatricopeptide repeat (PPR) proteins constitute one of the largest nuclear-encoded protein families in higher plants, with over 400 members in most sequenced plant species. The molecular functions of these proteins and their physiological roles during plant growth and development have been widely studied. Generally, there is mounting evidence that PPR proteins are involved in the post-transcriptional regulation of chloroplast and/or mitochondrial genes, including RNA maturation, editing, intron splicing, transcripts’ stabilization, and translation initiation. The cooperative action of RNA metabolism has profound effects on the biogenesis and functioning of both chloroplasts and mitochondria and, consequently, on the photosynthesis, respiration, and development of plants and their environmental responses. In this review, we summarize the latest research on PPR proteins, specifically how they might function in the chloroplast, by documenting their mechanism of molecular function, their corresponding RNA targets, and their specific effects upon chloroplast biogenesis and host organisms.

Organellar Introns in Fungi, Algae, and Plants

“…Among the plant mitochondria, one frequently encounters trans-spliced introns where two initially separate transcripts become covalently joined through the splicing process. The mechanism of mitochondrial intron splicing is complex involving many splicing factors, which facilitate the trans-splicing of Group II introns, including pentatricopeptide repeat (PPR) proteins, chloroplast RNA splicing and ribosome maturation (CRM) proteins, RNA DEAD-box helicases, plant organellar RNA recognition (PORR) domain proteins, regulator of chromosome condensation (RCC) proteins, and others [192][193][194][195]. Among them, PPR, PORR, and RCC may act as the factors that recognize the specific RNA-binding sites [69].…”

An Analytical Review of the Structural Features of Pentatricopeptide Repeats: Strategic Amino Acids, Repeat Arrangements and Superhelical Architecture

“…As stated earlier, PPR-containing proteins bind RNA in a sequence-specific manner [3][4][5][6][7][8]38]. The 3D structures of PPR-RNA complexes revealed that multiple contact points are required in these interactions [5][6][7]39].…”

Exploring patterns of cytonuclear incompatibility in Pelargonium section Ciconium

“…Genes or alleles identified as the basis of pCNI remain largely unidentified but nuclear encoded genes such as PPR, sigma factors and Whirly genes have been implicated (Wang et al 2021, Wei et al 2015, Isemer et al 2012. This makes sense, as these genes are all involved in expression and maintenance of the chloroplast.…”

“…A recent study of the numerous interactome proteins required for proper plastome expression found that nuclear encoded PPR genes assist in ribosome assembly (Westrich et al 2012). PPR genes play major roles in many steps of plastome and ribosome development, (reviewed by Wang et al 2021) and are often targeted specifically at organelles (Barkan 2014). PPR genes also play a role in compensating for changes in plastid genes via RNA editing (Ichinose 2017, Small et al 2020), but suppressing errors in 'micro-homology', which may occur in Pelargonium plastomes due to the rearrangements and repeats, is the domain of the nuclear encoded Whirly genes (Maréchal et al 2009, Isemer et al 2012).…”