QED1 - Plant Editosome Database

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

AT2G29760

Plastid
Chloroplast

accD

1568

CDS

EnsemblGenomes (release 39)
NA

BK010421
NA

C-to-U

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-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	74.98%	High	None	32098170
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	85.00%	High	None	28761003
Col-0	DYW2-GFP-OE1	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-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 independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	94.00%	High	Similar	28761003
Col-0	DYW2-GFP-OE2	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-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 independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	89.00%	High	Similar	28761003

Arabidopsis thaliana

AT2G29760

Chloroplast

accD

3'UTR

1568

C-to-U

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
NA	WT	Control	Control	Control	Normal	NA	NA	Poisoned Primer Extension (PPE) Assay	NA	Medium	None	25512379
SALK_092402C	qed1-1	T-DNA Insertion	T-DNA is located -15 nt from the start codon	Homozygous	Morphologically normal growing in soil in growth chambers	NA	NA	Poisoned Primer Extension (PPE) Assay	NA	Poor	Decreased	25512379
CSHL GT13864	qed1-2	T-DNA Insertion	T-DNA is located in the E motif 1852 nt into the coding region	Homozygous	The CSHL line grows more slowly than wild type and accumulates yellow regions in the leaves after 5 weeks of growth.	NA	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	25512379

Arabidopsis thaliana

AT2G29760

Plastid
Chloroplast

matK

640

CDS

EnsemblGenomes (release 39)
NA

BK010421
NA

C-to-U

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-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	79.42%	High	None	32098170
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	83.00%	High	None	28761003
Col-0	DYW2-GFP-OE1	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-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 independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	84.00%	High	Similar	28761003
Col-0	DYW2-GFP-OE2	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-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 independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	90.00%	High	Similar	28761003

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
NA	WT	Control	Control	Control	Normal	NA	NA	Poisoned Primer Extension (PPE) Assay	NA	High	None	25512379
SALK_092402C	qed1-1	T-DNA Insertion	T-DNA is located -15 nt from the start codon	Homozygous	Morphologically normal growing in soil in growth chambers	NA	NA	Poisoned Primer Extension (PPE) Assay	NA	Low	Decreased	25512379
CSHL GT13864	qed1-2	T-DNA Insertion	T-DNA is located in the E motif 1852 nt into the coding region	Homozygous	The CSHL line grows more slowly than wild type and accumulates yellow regions in the leaves after 5 weeks of growth.	NA	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	25512379

Arabidopsis thaliana

AT2G29760

Chloroplast
Plastid

ndhB

872

CDS

NA
EnsemblGenomes (release 39)

NA
BK010421

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
NA	WT	Control	Control	Control	Normal	NA	NA	Poisoned Primer Extension (PPE) Assay	NA	High	None	25512379
SALK_092402C	qed1-1	T-DNA Insertion	T-DNA is located -15 nt from the start codon	Homozygous	Morphologically normal growing in soil in growth chambers	NA	NA	Poisoned Primer Extension (PPE) Assay	NA	Low	Decreased	25512379
CSHL GT13864	qed1-2	T-DNA Insertion	T-DNA is located in the E motif 1852 nt into the coding region	Homozygous	The CSHL line grows more slowly than wild type and accumulates yellow regions in the leaves after 5 weeks of growth.	NA	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	25512379
Col-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	84.33%	High	None	32098170
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	88.00%	High	None	28761003
Col-0	DYW2-GFP-OE1	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-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 independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	100.00%	Complete	Increased	28761003
Col-0	DYW2-GFP-OE2	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-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 independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	100.00%	Complete	Increased	28761003

Arabidopsis thaliana

AT2G29760

Chloroplast
Plastid

rpoB

2432

CDS

NA
EnsemblGenomes (release 39)

NA
BK010421

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
NA	WT	Control	Control	Control	Normal	NA	NA	Poisoned Primer Extension (PPE) Assay	NA	High	None	25512379
SALK_092402C	qed1-1	T-DNA Insertion	T-DNA is located -15 nt from the start codon	Homozygous	Morphologically normal growing in soil in growth chambers	NA	NA	Poisoned Primer Extension (PPE) Assay	NA	Low	Decreased	25512379
CSHL GT13864	qed1-2	T-DNA Insertion	T-DNA is located in the E motif 1852 nt into the coding region	Homozygous	The CSHL line grows more slowly than wild type and accumulates yellow regions in the leaves after 5 weeks of growth.	NA	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	25512379
Col-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	81.89%	High	None	32098170
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	93.00%	High	None	28761003
Col-0	DYW2-GFP-OE1	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-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 independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	100.00%	Complete	Similar	28761003
Col-0	DYW2-GFP-OE2	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-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 independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	94.00%	High	Similar	28761003

Arabidopsis thaliana

AT2G29760

Chloroplast
Plastid

rps12

Intron

NA
EnsemblGenomes (release 39)

NA
BK010421

NA
Genomic position

58
69553

C-to-U

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
NA	WT	Control	Control	Control	Normal	NA	NA	Poisoned Primer Extension (PPE) Assay	NA	Low	None	25512379
SALK_092402C	qed1-1	T-DNA Insertion	T-DNA is located -15 nt from the start codon	Homozygous	Morphologically normal growing in soil in growth chambers	NA	NA	Poisoned Primer Extension (PPE) Assay	NA	Poor	Decreased	25512379
CSHL GT13864	qed1-2	T-DNA Insertion	T-DNA is located in the E motif 1852 nt into the coding region	Homozygous	The CSHL line grows more slowly than wild type and accumulates yellow regions in the leaves after 5 weeks of growth.	NA	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	25512379
Col-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	25.74%	Low	None	32098170

Editing Factor:	QED1
Synonym:	ORGANELLE TRANSCRIPT PROCESSING 81, OTP81_ Quintuple Editing Factor 1
Description:	Encoding a PPR-DYW editing factor which affects five different chloroplast C targets.
Protein Family:	PPR
Subclass:	DYW
Physical Interaction:	RIP1; RIP2; RIP3; RIP5; RIP9
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 Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins., Plants (Basel, Switzerland), 2020. [PMID=32098170] [2] 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] [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]

Summary

Editing Details