ArticleRNA biology2013
A survey of PPR proteins identifies DYW domains like those of land plant RNA editing factors in diverse eukaryotes.
Article in RNA biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 50 citations in OpenAlex.
- Kingdom-wide evolutionary characterization of RNA editing factors in Archaeplastida.Molecular biology and evolution · 2026Article
- RNA-Binding Proteins in Dinoflagellates.International journal of molecular sciences · 2026Review
- A Generalized AI View of Tricopeptide Repeats: What's in a Name.International journal of molecular sciences · 2025Review
- Emerging clinical applications of ADAR based RNA editing.Stem cells translational medicine · 2025Review
- Pentatricopeptide repeat proteins in plants: Cellular functions, action mechanisms, and potential applications.Plant communications · 2025Review
- Massive RNA Editing in Ascetosporean Mitochondria.Microbes and environments · 2025Article
- Chloroplast gene expression: Recent advances and perspectives.Plant communications · 2023Review
- Mitochondrial RNA editing sites affect the phylogenetic reconstruction of gymnosperms.Plant diversity · 2023Article
- DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis.Nature catalysis · 2021Article
- Article
- Gene fragmentation and RNA editing without borders: eccentric mitochondrial genomes of diplonemids.Nucleic acids research · 2020Article
- A plant pentatricopeptide repeat protein with a DYW-deaminase domain is sufficient for catalyzing C-to-U RNA editingThe Journal of biological chemistry · 2020Article
- Article
- The Nature and Arrangement of Pentatricopeptide Domains and the Linker Sequences Between Them.Bioinformatics and biology insights · 2020Article
- The dual-targeted RNA editing factor AEF1 is universally conserved among angiosperms and reveals only minor adaptations upon loss of its chloroplast or its mitochondrial target.Plant molecular biology · 2020Article
- The Amount of RNA Editing Sites in Liverwort Organellar Genes Is Correlated with GC Content and Nuclear PPR Protein Diversity.Genome biology and evolution · 2019Article
- Plant-type pentatricopeptide repeat proteins with a DYW domain drive C-to-U RNA editing inCommunications biology · 2019Article
- Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0.BMC bioinformatics · 2018Article
- In Silico Identification of Candidate Genes for Fertility Restoration in Cytoplasmic Male Sterile Perennial Ryegrass (Lolium perenne L.).Genome biology and evolution · 2017Article
- Unveiling Chloroplast RNA Editing Events Using Next Generation Small RNA Sequencing Data.Frontiers in plant science · 2017Article
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Authors and funding
5 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The pentatricopeptide repeat modules of PPR proteins are key to their sequence-specific binding to RNAs. Gene families encoding PPR proteins are greatly expanded in land plants where hundreds of them participate in RNA maturation, mainly in mitochondria and chloroplasts. Many plant PPR proteins contain additional carboxyterminal domains and have been identified as essential factors for specific events of C-to-U RNA editing, which is abundant in the two endosymbiotic plant organelles. Among those carboxyterminal domain additions to plant PPR proteins, the so-called DYW domain is particularly interesting given its similarity to cytidine deaminases. The frequency of organelle C-to-U RNA editing and the diversity of DYW-type PPR proteins correlate well in plants and both were recently identified outside of land plants, in the protist Naegleria gruberi. Here we present a systematic survey of PPR protein genes and report on the identification of additional DYW-type PPR proteins in the protists Acanthamoeba castellanii, Malawimonas jakobiformis, and Physarum polycephalum. Moreover, DYW domains were also found in basal branches of multi-cellular lineages outside of land plants, including the alga Nitella flexilis and the rotifers Adineta ricciae and Philodina roseola. Intriguingly, the well-characterized and curious patterns of mitochondrial RNA editing in the slime mold Physarum also include examples of C-to-U changes. Finally, we identify candidate sites for mitochondrial RNA editing in Malawimonas, further supporting a link between DYW-type PPR proteins and C-to-U editing, which may have remained hitherto unnoticed in additional eukaryote lineages.
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