Plant Editosome Database
a curated database of RNA editosome in plants

RARE1 - Plant Editosome Database - BIG Data Center
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Summary

Editing Factor: RARE1
Synonym: REQUIRED FOR ACCD RNA EDITING 1
Description: Encodes RARE1 (Required for accD RNA Editing 1), a trans-factor essential for C-to-U editing of the chloroplast accD transcript. RARE1 carries 15 PPR (pentatricopeptide repeat) motifs, an E/E+ and a DYW domain (C-terminal tripeptide).
Protein Family: PPR
Subclass: DYW
Construct Structure: PLS-E-E+-DYW
Gene ID & Species: AT5G13270 (Arabidopsis thaliana)
Edited Gene(s): accD
Editing Type(s): C-to-U (20)
Publication(s): [1] The Analysis of the Editing Defects in the dyw2 Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins, Plants (Basel), 2020. [PMID=32098170]
[2] Expected and unexpected evolution of plant RNA editing factors CLB19, CRR28 and RARE1: retention of CLB19 despite a phylogenetically deep loss of its two known editing targets in Poaceae, BMC Evol Biol, 2018. [PMID=29879897]
[3] Multiple PPR Protein Interactions Are Involved in the RNA Editing System in Arabidopsis Mitochondria and Plastids, Proc Natl Acad Sci U S A, 2017. [PMID=28761003]
[4] A comparative genomics approach identifies a PPR-DYW protein that is essential for C-to-U editing of the Arabidopsis chloroplast accD transcript, RNA, 2009. [PMID=19395655]

Editing Details

Species Gene ID Organelle Edited Gene Position Region Editing Type Codon Amino Acid Molecular Effect Experiment Details
Arabidopsis thaliana AT5G13270 Chloroplast
Plastid		 accD 794 CDS C-to-U UCG=>UUG
NA=>NA		 S=>L
NA=>NA		 Recoding
NA
Experiment Details
Genotype (Ecotype) Allele Treatment Treatment Detail Mutant Type Phenotype Tissue Development Stage Detection Method Editing Frequency Editing Extent Mutant Effect PMID
WS-4, FLAG_424E06FLAG_424E06T-DNA InsertionT-DNA is inserted in the promoter (-78)Homozygous; Transcripts of AT5G13270 were observedNormal appearanceLeafNAPoisoned Primer Extension (PPE) AssayNANADecreased19395655
WS-4, FLAG_424E06FLAG_424E06T-DNA InsertionT-DNA is inserted in the promoter (-78)Heterozygous; Transcripts of AT5G13270 were observedNormal appearanceLeafNAPoisoned Primer Extension (PPE) AssayNANASimilar19395655
WS-4FLAG_424E06No treatmentNo treatmentNo treatmentNo treatmentLeafNAPoisoned Primer Extension (PPE) AssayNANANone19395655
GABI_167A04GABI_167A04T-DNA InsertionT-DNA is inserted at 269 base pairs (bp) downstream from the start codonHomozygousNormal appearanceLeafNAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent19395655
GABI_167A04GABI_167A04T-DNA InsertionT-DNA is inserted at 269 base pairs (bp) downstream from the start codonHeterozygousNormal appearanceLeafNAPoisoned Primer Extension (PPE) Assay100.00%CompleteRestored19395655
GABI_167A04GABI_167A04No treatmentNo treatmentNo treatmentNo treatmentLeafNAPoisoned Primer Extension (PPE) Assay100.00%CompleteNone19395655
WiscDsLox33H10WiscDsLox33H10T-DNA InsertionT-DNA is inserted within the region encoding the DYW domain (2160)Homozygous; Transcripts of AT5G13270 were detectedNormal appearanceRootNAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent19395655
WiscDsLox33H10WiscDsLox33H10T-DNA InsertionT-DNA is inserted within the region encoding the DYW domain (2160)Heterozygous; Transcripts of AT5G13270 were detectedNormal appearanceLeafNAPoisoned Primer Extension (PPE) Assay100.00%CompleteRestored19395655
WiscDsLox33H10WiscDsLox33H10T-DNA InsertionT-DNA is inserted within the region encoding the DYW domain (2160)Homozygous; Transcripts of AT5G13270 were detectedNormal appearanceLeafNAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent19395655
WiscDsLox33H10WiscDsLox33H10T-DNA InsertionT-DNA is inserted within the region encoding the DYW domain (2160)Homozygous; Transcripts of At5G13270 were detectedNormal appearanceLeafNAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent19395655
WiscDsLox33H10WiscDsLox33H10T-DNA InsertionT-DNA is inserted within the region encoding the DYW domain (2160)Homozygous; Transcripts of At5G13270 were detectedNormal appearanceFlowerNAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent19395655
Col-0WiscDsLox33H10No treatmentNo treatmentNo treatmentNo treatmentRootNAPoisoned Primer Extension (PPE) Assay100.00%CompleteRestored19395655
Col-0WiscDsLox33H10No treatmentNo treatmentNo treatmentNo treatmentLeafNAPoisoned Primer Extension (PPE) Assay100.00%CompleteRestored19395655
Col-0WiscDsLox33H10No treatmentNo treatmentNo treatmentNo treatmentLeafNAPoisoned Primer Extension (PPE) Assay100.00%CompleteRestored19395655
Col-0WiscDsLox33H10No treatmentNo treatmentNo treatmentNo treatmentFlowerNAPoisoned Primer Extension (PPE) Assay100.00%CompleteRestored19395655
NANANo treatmentNo treatmentNo treatmentNANANANANANANone29879897
Col-0WTNo treatmentNo treatmentNo treatmentNANANARNA-seq94.82%HighNone32098170
Col-0WTNo treatmentNo treatmentNo treatmentNormalRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract94.00%HighNone28761003
Col-0DYW2-GFP-OE1Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 geneCol-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independenNASlow growthRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract100.00%CompleteSimilar28761003
Col-0DYW2-GFP-OE2Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 geneCol-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independenNASlow growthRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract100.00%CompleteSimilar28761003
Last update: Jul 2021 (version 1.0)