Emergence of Novel RNA-Editing Sites by Changes in the Binding Affinity of a Conserved PPR Protein.
PPR code
PPR protein
RNA editing
RNA-binding protein
chloroplast
co-evolution
Journal
Molecular biology and evolution
ISSN: 1537-1719
Titre abrégé: Mol Biol Evol
Pays: United States
ID NLM: 8501455
Informations de publication
Date de publication:
05 12 2022
05 12 2022
Historique:
pubmed:
14
10
2022
medline:
17
12
2022
entrez:
13
10
2022
Statut:
ppublish
Résumé
RNA editing converts cytidines to uridines in plant organellar transcripts. Editing typically restores codons for conserved amino acids. During evolution, specific C-to-U editing sites can be lost from some plant lineages by genomic C-to-T mutations. By contrast, the emergence of novel editing sites is less well documented. Editing sites are recognized by pentatricopeptide repeat (PPR) proteins with high specificity. RNA recognition by PPR proteins is partially predictable, but prediction is often inadequate for PPRs involved in RNA editing. Here we have characterized evolution and recognition of a recently gained editing site. We demonstrate that changes in the RNA recognition motifs that are not explainable with the current PPR code allow an ancient PPR protein, QED1, to uniquely target the ndhB-291 site in Brassicaceae. When expressed in tobacco, the Arabidopsis QED1 edits 33 high-confident off-target sites in chloroplasts and mitochondria causing a spectrum of mutant phenotypes. By manipulating the relative expression levels of QED1 and ndhB-291, we show that the target specificity of the PPR protein depends on the RNA:protein ratio. Finally, our data suggest that the low expression levels of PPR proteins are necessary to ensure the specificity of editing site selection and prevent deleterious off-target editing.
Identifiants
pubmed: 36227729
pii: 6760358
doi: 10.1093/molbev/msac222
pmc: PMC9750133
pii:
doi:
Substances chimiques
Arabidopsis Proteins
0
RNA
63231-63-0
Plant Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
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