Plant Editosome Database
a curated database of RNA editosome in plants

QED1 - Plant Editosome Database - BIG Data Center
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Summary

Editing Factor: QED1
Synonym: ORGANELLE TRANSCRIPT PROCESSING 81, OTP81_ Quintuple Editing Factor 1
Description: Encodes a PPR-DYW editing factor which affects five different chloroplast C targets.
Protein Family: PPR
Subclass: DYW
Construct Structure: PLS-E-E+-DYW
Gene ID & Species: AT2G29760 (Arabidopsis thaliana)
Edited Gene(s): accD    matK    ndhB    rpoB    rps12
Editing Type(s): C-to-U (32)
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] 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]
[3] Cytidine Deaminase Motifs within the DYW Domain of Two Pentatricopeptide Repeat-containing Proteins Are Required for Site-specific Chloroplast RNA Editing, The Journal of Biological Chemistry, 2015. [PMID=25512379]

Editing Details

Species Gene ID Organelle Edited Gene Position Region Editing Type Codon Amino Acid Molecular Effect Experiment Details
Arabidopsis thaliana AT2G29760 Chloroplast
Plastid		 accD 1568 3'UTR
CDS		 C-to-U NA=>NA NA=>NA NA
Experiment Details
Genotype (Ecotype) Allele Treatment Treatment Detail Mutant Type Phenotype Tissue Development Stage Detection Method Editing Frequency Editing Extent Mutant Effect PMID
NAWTNo treatmentNo treatmentNo treatmentNo treatmentNANAPoisoned Primer Extension (PPE) AssayNAMediumNone25512379
SALK_092402Cqed1-1T-DNA InsertionT-DNA is located -15 nt from the start codonHomozygousMorphologically normal growing in soil in growth chambersNANAPoisoned Primer Extension (PPE) AssayNAPoorDecreased25512379
CSHL GT13864qed1-2T-DNA InsertionT-DNA is located in the E motif 1852 nt into the coding regionHomozygousThe CSHL line grows more slowly than wild type and accumulates yellow regions in the leaves after 5 weeks of growth.NANAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent25512379
Col-0WTNo treatmentNo treatmentNo treatmentNANANARNA-seq74.98%HighNone32098170
Col-0WTNo treatmentNo treatmentNo treatmentNormalRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract85.00%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 (BlueTract94.00%HighSimilar28761003
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 (BlueTract89.00%HighSimilar28761003
Arabidopsis thaliana AT2G29760 Plastid
Chloroplast		 matK 640 CDS C-to-U NA=>NA NA=>NA NA
Experiment Details
Genotype (Ecotype) Allele Treatment Treatment Detail Mutant Type Phenotype Tissue Development Stage Detection Method Editing Frequency Editing Extent Mutant Effect PMID
Col-0WTNo treatmentNo treatmentNo treatmentNANANARNA-seq79.42%HighNone32098170
Col-0WTNo treatmentNo treatmentNo treatmentNormalRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract83.00%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 (BlueTract84.00%HighSimilar28761003
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 (BlueTract90.00%HighSimilar28761003
Arabidopsis thaliana AT2G29760 Chloroplast matK 706 CDS C-to-U CAU=>UAU H=>Y Recoding
Experiment Details
Genotype (Ecotype) Allele Treatment Treatment Detail Mutant Type Phenotype Tissue Development Stage Detection Method Editing Frequency Editing Extent Mutant Effect PMID
NAWTNo treatmentNo treatmentNo treatmentNo treatmentNANAPoisoned Primer Extension (PPE) AssayNAHighNone25512379
SALK_092402Cqed1-1T-DNA InsertionT-DNA is located -15 nt from the start codonHomozygousMorphologically normal growing in soil in growth chambersNANAPoisoned Primer Extension (PPE) AssayNALowDecreased25512379
CSHL GT13864qed1-2T-DNA InsertionT-DNA is located in the E motif 1852 nt into the coding regionHomozygousThe CSHL line grows more slowly than wild type and accumulates yellow regions in the leaves after 5 weeks of growth.NANAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent25512379
Arabidopsis thaliana AT2G29760 Chloroplast
Plastid		 ndhB 872 CDS C-to-U UCA=>UUA
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
NAWTNo treatmentNo treatmentNo treatmentNo treatmentNANAPoisoned Primer Extension (PPE) AssayNAHighNone25512379
SALK_092402Cqed1-1T-DNA InsertionT-DNA is located -15 nt from the start codonHomozygousMorphologically normal growing in soil in growth chambersNANAPoisoned Primer Extension (PPE) AssayNALowDecreased25512379
CSHL GT13864qed1-2T-DNA InsertionT-DNA is located in the E motif 1852 nt into the coding regionHomozygousThe CSHL line grows more slowly than wild type and accumulates yellow regions in the leaves after 5 weeks of growth.NANAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent25512379
Col-0WTNo treatmentNo treatmentNo treatmentNANANARNA-seq84.33%HighNone32098170
Col-0WTNo treatmentNo treatmentNo treatmentNormalRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract88.00%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%CompleteIncreased28761003
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%CompleteIncreased28761003
Arabidopsis thaliana AT2G29760 Chloroplast
Plastid		 rpoB 2432 CDS C-to-U UCA=>UUA
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
NAWTNo treatmentNo treatmentNo treatmentNo treatmentNANAPoisoned Primer Extension (PPE) AssayNAHighNone25512379
SALK_092402Cqed1-1T-DNA InsertionT-DNA is located -15 nt from the start codonHomozygousMorphologically normal growing in soil in growth chambersNANAPoisoned Primer Extension (PPE) AssayNALowDecreased25512379
CSHL GT13864qed1-2T-DNA InsertionT-DNA is located in the E motif 1852 nt into the coding regionHomozygousThe CSHL line grows more slowly than wild type and accumulates yellow regions in the leaves after 5 weeks of growth.NANAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent25512379
Col-0WTNo treatmentNo treatmentNo treatmentNANANARNA-seq81.89%HighNone32098170
Col-0WTNo treatmentNo treatmentNo treatmentNormalRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract93.00%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 (BlueTract94.00%HighSimilar28761003
Arabidopsis thaliana AT2G29760 Plastid rps12 -69553 Intronic C-to-U NA=>NA NA=>NA NA
Experiment Details
Genotype (Ecotype) Allele Treatment Treatment Detail Mutant Type Phenotype Tissue Development Stage Detection Method Editing Frequency Editing Extent Mutant Effect PMID
Col-0WTNo treatmentNo treatmentNo treatmentNANANARNA-seq25.74%LowNone32098170
Arabidopsis thaliana AT2G29760 Chloroplast rps12 58 Intronic C-to-U NA=>NA NA=>NA NA
Experiment Details
Genotype (Ecotype) Allele Treatment Treatment Detail Mutant Type Phenotype Tissue Development Stage Detection Method Editing Frequency Editing Extent Mutant Effect PMID
NAWTNo treatmentNo treatmentNo treatmentNo treatmentNANAPoisoned Primer Extension (PPE) AssayNALowNone25512379
SALK_092402Cqed1-1T-DNA InsertionT-DNA is located -15 nt from the start codonHomozygousMorphologically normal growing in soil in growth chambersNANAPoisoned Primer Extension (PPE) AssayNAPoorDecreased25512379
CSHL GT13864qed1-2T-DNA InsertionT-DNA is located in the E motif 1852 nt into the coding regionHomozygousThe CSHL line grows more slowly than wild type and accumulates yellow regions in the leaves after 5 weeks of growth.NANAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent25512379
Last update: Jul 2021 (version 1.0)