RNA Editing Mechanisms in Plant Organelles

RNA editing in plant mitochondria and chloroplasts is a post-transcriptional process that alters specific nucleotide residues, most commonly converting cytidine to uridine. This editing restores conserved codons, creates start and stop signals and ensures the proper assembly of respiratory and photosynthetic complexes. Central to this process are nucleus-encoded pentatricopeptide repeat (PPR) proteins, which recognise cis-elements upstream of editing sites and recruit editing factors to form multi-protein editosome assemblies. Many PPR proteins carry a C-terminal DYW domain thought to house the catalytic deaminase activity required for cytidine conversion, although auxiliary proteins from RIP/MORF and ORRM families also contribute to site specificity and complex stability. Beyond editing, the maturation of organellar transcripts involves precise endonucleolytic and exonucleolytic processing, RNA splicing, and turnover. Collectively, these mechanisms underpin organellar biogenesis, plant development and stress adaptation, with practical applications ranging from crop improvement to synthetic biology approaches for targeted RNA modification.

Research from Nature Portfolio

Recent studies have revealed how mitochondrial PPR proteins can influence both RNA editing and stress tolerance. In rice, a mitochondria-localised PPR factor was shown to modulate editing efficiency of key nad transcripts, thereby restoring complex I function, reducing reactive oxygen species and enhancing cold tolerance. Overexpression of compartment-specific superoxide dismutases further demonstrated the interplay between editing, redox homeostasis and organellar biogenesis in crop resilience. In parallel, work with moss DYW-type PPR proteins expressed in bacterial cells established that individual PPR factors can catalyse efficient C-to-U editing outside the plant context. This heterologous system confirmed the DYW domain’s role as a cytidine deaminase and uncovered nucleotide determinants for target recognition, paving the way for designer PPRs to edit transcripts in diverse organisms.

RNA Editing Mechanisms in Plant Organelles publication trend

The graph below shows the total number of articles in rna editing mechanisms in plant organelles across all publications each year (not limited to Nature Index journals).

Technical terms

Pentatricopeptide repeat (PPR) proteins: A large family of nucleus-encoded RNA-binding proteins characterised by tandem 35-amino-acid repeats that confer sequence-specific recognition of organellar transcripts.

DYW domain: A C-terminal extension in many PPR proteins containing conserved residues homologous to cytidine deaminases, implicated in catalysing C-to-U conversion.

Editosome: A multi-protein complex in plant organelles that carries out site-specific RNA editing, comprising PPR proteins and auxiliary factors such as RIP/MORF and ORRM families.

Cytidine deamination: The enzymatic removal of an amine group from cytidine, yielding uridine and effecting a C-to-U change in the RNA sequence.

References

1. RNA Editing and Its Molecular Mechanism in Plant Organelles. Genes (2016).
2. An overview of pentatricopeptide repeat proteins and their applications. Biochimie (2015).
3. A mitochondrial pentatricopeptide repeat protein enhances cold tolerance by modulating mitochondrial superoxide in rice. Nature Communications (2023).
4. Plant-type pentatricopeptide repeat proteins with a DYW domain drive C-to-U RNA editing in Escherichia coli. Communications Biology (2019).
5. Interplay of endonucleolytic and exonucleolytic processing in the 3′-end formation of a mitochondrial nad2 RNA precursor in Arabidopsis. Nucleic Acids Research (2023).
6. Plant organellar RNA maturation. The Plant Cell (2023).
7. Chloroplast C-to-U editing, regulated by a PPR protein BoYgl-2, is important for chlorophyll biosynthesis in cabbage. Horticulture Research (2024).