QED1 - Plant Editosome Database

Editing Details

Species

Gene ID

Organelle

Edited Gene

Position

Region

Nuclear Genome

Organelle Genome

Other Region

Other Position

Editing Type

Codon

Amino Acid

Molecular Effect

Experiment Details

Arabidopsis thaliana

AT2G29760

Chloroplast

accD

1568

CDS

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	No mutant	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	No mutant	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

Chloroplast

matK

640

CDS

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	No mutant	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	No mutant	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

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
NA	WT	Control	Control	No mutant	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	No mutant	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

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
NA	WT	Control	Control	No mutant	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	No mutant	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

rps12

Intron

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	No mutant	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

Editing Factor:	QED1
Synonym:	ORGANELLE TRANSCRIPT PROCESSING 81; OTP81
Description:	Adding a C-terminal protein tag to QED1 was found to severely inhibit editing function; QED1 and RARE1, another plastid PPR-DYW editing factor, were discovered to require their DYW motifs for efficient editing; To identify specific residues critical for editing, conserved deaminase residues in each PPR protein were mutagenized; The mutant PPR proteins, when expressed in qed1 or rare1 mutant protoplasts, could not complement the editing defect
Protein Family:	Pentatricopeptide repeat (PPR) protein
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 (27)
Publication(s):	[1] Multiple PPR Protein Interactions Are Involved in the RNA Editing System in Arabidopsis Mitochondria and Plastids, Proc Natl Acad Sci U S A, 2017. [doi:10.1073/pnas.1705815114] [2] 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. [doi:10.1074/jbc.M114.622084]

Summary

Editing Details