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RARE1 - Plant Editosome Database - CNCB-NGDC
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Summary

Editing Factor: RARE1
Synonym: REQUIRED FOR ACCD RNA EDITING 1
Description: Encoding 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); An Arabidopsis rare1 mutant with abolished accD-C794 editing and discovered that it exhibits a yellow and dwarf phenotype compared with the wild type under heat stress; Loss of accD-C794 editing results in a yellow and dwarf phenotype with decreased chloroplast gene expression under heat stress, and artificial improvement of C794-edited accD gene expression enhances heat tolerance in Arabidopsis; These observations indicate that defective accD-C794 editing may be intrinsic to reduced ACCase activity, thereby contributing to heat sensitivity; These results provide the first evidence that accD-C794 editing regulates FA biosynthesis for maintenance of membrane structural homeostasis under heat stress
Protein Family: PPR
Subclass: DYW
Physical Interaction: NA
Construct Structure: PLS-E-E+-DYW
Gene ID & Species: AT5G13270 (Arabidopsis thaliana)
Edited Gene(s): accD
Editing Type(s): C-to-U (24)
Publication(s): [1] The PPR protein RARE1-mediated editing of chloroplast accD transcripts is required for fatty acid biosynthesis and heat tolerance in Arabidopsis., Plant communications, 2023. [PMID=36221851]
[2] The Analysis of the Editing Defects in the Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins., Plants (Basel, Switzerland), 2020. [PMID=32098170]
[3] Multiple PPR protein interactions are involved in the RNA editing system in mitochondria and plastids., Proceedings of the National Academy of Sciences of the United States of America, 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 (New York, N.Y.), 2009. [PMID=19395655]

Editing Details

Species Gene ID Organelle Edited Gene Position Region Nuclear Genome Organelle Genome Other Position Region Other Position Editing Type Codon Amino Acid Molecular Effect Experiment Details
Arabidopsis thaliana AT5G13270 Chloroplast
Plastid		 accD 794 CDS NA
EnsemblGenomes (release 39)		 NA
BK010421		 NA NA 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_424E06ControlControlControlNormalLeafNAPoisoned 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_167A04ControlControlControlNormalLeafNAPoisoned 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-0WiscDsLox33H10ControlControlControlNormalRootNAPoisoned Primer Extension (PPE) Assay100.00%CompleteRestored19395655
Col-0WiscDsLox33H10ControlControlControlNormalLeafNAPoisoned Primer Extension (PPE) Assay100.00%CompleteRestored19395655
Col-0WiscDsLox33H10ControlControlControlNormalLeafNAPoisoned Primer Extension (PPE) Assay100.00%CompleteRestored19395655
Col-0WiscDsLox33H10ControlControlControlNormalFlowerNAPoisoned Primer Extension (PPE) Assay100.00%CompleteRestored19395655
Col-0WTControlControlControlNANANARNA-seq94.82%HighNone32098170
Col-0WTControlControlControlNormalLeafNART-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 growthLeafNART-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 growthLeafNART-PCR and calculated with the DNADynamo software (BlueTract100.00%CompleteSimilar28761003
NAWTControlControlNo mutantNormalLeaf7-day-oldSpecific cDNA fragments containing editing sites were amplif100.00%CompleteNone36221851
CS415940rare1-1A T-DNA insertionA T-DNA insertion is at +268 bp from ATG (+1)NAAt an elevated temperature of 28°C, all rare1 lines displayed yellow foliage and a slowed growth rate, whereas the more resilient wild-type plants retained typical green foliage. At an elevated temperature of 28°C, the contents of chlorophyll a, chlorophyll b, and total chlorophyll were significantly reduced in the rare1 lines compared with wild-type plants and the complemented lines. Heat stress is severely detrimental to chlorophyll synthesis in rare1 lines, which develop a yellow leaf phenotype.Leaf7-day-oldSpecific cDNA fragments containing editing sites were amplif0.00%UneditedAbsent36221851
CS851454rare1-2A T-DNA insertionA T-DNA insertion is at +2160 bp from ATG (+1)NAAt an elevated temperature of 28°C, all rare1 lines displayed yellow foliage and a slowed growth rate, whereas the more resilient wild-type plants retained typical green foliage. At an elevated temperature of 28°C, the contents of chlorophyll a, chlorophyll b, and total chlorophyll were significantly reduced in the rare1 lines compared with wild-type plants and the complemented lines. Heat stress is severely detrimental to chlorophyll synthesis in rare1 lines, which develop a yellow leaf phenotype.Leaf7-day-oldSpecific cDNA fragments containing editing sites were amplif0.00%UneditedAbsent36221851
NAComp #1ComplementationNANANormalLeaf7-day-oldSpecific cDNA fragments containing editing sites were amplif31.00%LowRestored36221851
NAComp #2ComplementationNANANormalLeaf7-day-oldSpecific cDNA fragments containing editing sites were amplif41.00%MediumRestored36221851
Last update: Feb 2026 (version 2.0)