DG409 - 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

AT1G01970

Chloroplast

accD

1568

CDS

TAIR

C-to-U

UCA=>UUA

S=>L

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Columbia (Col-0)	Col-0-Y	Control	Control	No mutant	Normal	Leaf	4-wk-old	RNA-Seq	63.00%	High	None	37096684
Columbia (Col-0)	dg409-Y	Knockdown	NA	Knockdown	Compared with WT, the young central leaves of 1-, 2-, 3-, and 4-wk-old mutant plants were pale green, and the mature leaves gradually turned green. Other organs such as sepals and siliques also showed similar changes in phenotype. Under the same growth conditions, dg409 was much smaller than WT throughout its entire life cycle owing to developmental retardation. We also found that seeds of mutant plants were not as plump as WT, and the 1,000-grain weight of dg409 mutants was reduced 25% relative to WT.	Leaf	4-wk-old	RNA-Seq	35.00%	Low	Decreased	37096684
Columbia (Col-0)	dg409-CP-1Y	Complementation	The DG409 ORF sequence was cloned into the DX2181 vector under the control of the 35S promoter to construct the p35S::DG409 fusion vector. The fusion vector was transformed into dg409 mutant plants th	Knockdown	Similar to those of WT (Normal)	Leaf	4-wk-old	RNA-Seq	68.00%	High	Restored	37096684

Arabidopsis thaliana

AT1G01970

Chloroplast

clpP

559

CDS

TAIR

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
Columbia (Col-0)	Col-0-Y	Control	Control	No mutant	Normal	Leaf	4-wk-old	RNA-Seq	96.00%	High	None	37096684
Columbia (Col-0)	dg409-Y	Knockdown	NA	Knockdown	Compared with WT, the young central leaves of 1-, 2-, 3-, and 4-wk-old mutant plants were pale green, and the mature leaves gradually turned green. Other organs such as sepals and siliques also showed similar changes in phenotype. Under the same growth conditions, dg409 was much smaller than WT throughout its entire life cycle owing to developmental retardation. We also found that seeds of mutant plants were not as plump as WT, and the 1,000-grain weight of dg409 mutants was reduced 25% relative to WT.	Leaf	4-wk-old	RNA-Seq	60.00%	High	Decreased	37096684
Columbia (Col-0)	dg409-CP-1Y	Complementation	The DG409 ORF sequence was cloned into the DX2181 vector under the control of the 35S promoter to construct the p35S::DG409 fusion vector. The fusion vector was transformed into dg409 mutant plants th	Knockdown	Similar to those of WT (Normal)	Leaf	4-wk-old	RNA-Seq	92.00%	High	Restored	37096684

Arabidopsis thaliana

AT1G01970

Mitochondrion

nad7

1505

CDS

TAIR

C-to-U

UCU=>UUU

S=>F

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Columbia (Col-0)	Col-0-Y	Control	Control	No mutant	Normal	Leaf	4-wk-old	RNA-Seq	55.00%	Medium	None	37096684
Columbia (Col-0)	dg409-Y	Knockdown	NA	Knockdown	Compared with WT, the young central leaves of 1-, 2-, 3-, and 4-wk-old mutant plants were pale green, and the mature leaves gradually turned green. Other organs such as sepals and siliques also showed similar changes in phenotype. Under the same growth conditions, dg409 was much smaller than WT throughout its entire life cycle owing to developmental retardation. We also found that seeds of mutant plants were not as plump as WT, and the 1,000-grain weight of dg409 mutants was reduced 25% relative to WT.	Leaf	4-wk-old	RNA-Seq	23.00%	Low	Decreased	37096684
Columbia (Col-0)	dg409-CP-1Y	Complementation	The DG409 ORF sequence was cloned into the DX2181 vector under the control of the 35S promoter to construct the p35S::DG409 fusion vector. The fusion vector was transformed into dg409 mutant plants th	Knockdown	Similar to those of WT (Normal)	Leaf	4-wk-old	RNA-Seq	46.00%	Medium	Restored	37096684

Arabidopsis thaliana

AT1G01970

Mitochondrion

orf313

158

CDS

TAIR

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
Columbia (Col-0)	Col-0-Y	Control	Control	No mutant	Normal	Leaf	4-wk-old	RNA-Seq	NA	NA	None	37096684
Columbia (Col-0)	dg409-Y	Knockdown	NA	Knockdown	Compared with WT, the young central leaves of 1-, 2-, 3-, and 4-wk-old mutant plants were pale green, and the mature leaves gradually turned green. Other organs such as sepals and siliques also showed similar changes in phenotype. Under the same growth conditions, dg409 was much smaller than WT throughout its entire life cycle owing to developmental retardation. We also found that seeds of mutant plants were not as plump as WT, and the 1,000-grain weight of dg409 mutants was reduced 25% relative to WT.	Leaf	4-wk-old	RNA-Seq	NA	NA	Decreased	37096684

Arabidopsis thaliana

AT1G01970

Mitochondrion

orf313

220

CDS

TAIR

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
Columbia (Col-0)	Col-0-Y	Control	Control	No mutant	Normal	Leaf	4-wk-old	RNA-Seq	NA	NA	None	37096684
Columbia (Col-0)	dg409-Y	Knockdown	NA	Knockdown	Compared with WT, the young central leaves of 1-, 2-, 3-, and 4-wk-old mutant plants were pale green, and the mature leaves gradually turned green. Other organs such as sepals and siliques also showed similar changes in phenotype. Under the same growth conditions, dg409 was much smaller than WT throughout its entire life cycle owing to developmental retardation. We also found that seeds of mutant plants were not as plump as WT, and the 1,000-grain weight of dg409 mutants was reduced 25% relative to WT.	Leaf	4-wk-old	RNA-Seq	NA	NA	Decreased	37096684

Arabidopsis thaliana

AT1G01970

Mitochondrion

ORFB

CDS

TAIR

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
Columbia (Col-0)	Col-0-Y	Control	Control	No mutant	Normal	Leaf	4-wk-old	RNA-Seq	NA	NA	None	37096684
Columbia (Col-0)	dg409-Y	Knockdown	NA	Knockdown	Compared with WT, the young central leaves of 1-, 2-, 3-, and 4-wk-old mutant plants were pale green, and the mature leaves gradually turned green. Other organs such as sepals and siliques also showed similar changes in phenotype. Under the same growth conditions, dg409 was much smaller than WT throughout its entire life cycle owing to developmental retardation. We also found that seeds of mutant plants were not as plump as WT, and the 1,000-grain weight of dg409 mutants was reduced 25% relative to WT.	Leaf	4-wk-old	RNA-Seq	NA	NA	Decreased	37096684

Arabidopsis thaliana

AT1G01970

Chloroplast

rpoA

200

CDS

TAIR

C-to-U

UCU=>UUU

S=>F

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Columbia (Col-0)	Col-0-Y	Control	Control	No mutant	Normal	Leaf	4-wk-old	RNA-Seq	65.00%	High	None	37096684
Columbia (Col-0)	dg409-Y	Knockdown	NA	Knockdown	Compared with WT, the young central leaves of 1-, 2-, 3-, and 4-wk-old mutant plants were pale green, and the mature leaves gradually turned green. Other organs such as sepals and siliques also showed similar changes in phenotype. Under the same growth conditions, dg409 was much smaller than WT throughout its entire life cycle owing to developmental retardation. We also found that seeds of mutant plants were not as plump as WT, and the 1,000-grain weight of dg409 mutants was reduced 25% relative to WT.	Leaf	4-wk-old	RNA-Seq	32.00%	Low	Decreased	37096684
Columbia (Col-0)	dg409-CP-1Y	Complementation	The DG409 ORF sequence was cloned into the DX2181 vector under the control of the 35S promoter to construct the p35S::DG409 fusion vector. The fusion vector was transformed into dg409 mutant plants th	Knockdown	Similar to those of WT (Normal)	Leaf	4-wk-old	RNA-Seq	58.00%	Medium	Restored	37096684

Arabidopsis thaliana

AT1G01970

Mitochondrion

rps3

1344

CDS

TAIR

C-to-U

AGC=>AGU

S=>S

Synonymous

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Columbia (Col-0)	Col-0-Y	Control	Control	No mutant	Normal	Leaf	4-wk-old	RNA-Seq	35.00%	Low	None	37096684
Columbia (Col-0)	dg409-Y	Knockdown	NA	Knockdown	Compared with WT, the young central leaves of 1-, 2-, 3-, and 4-wk-old mutant plants were pale green, and the mature leaves gradually turned green. Other organs such as sepals and siliques also showed similar changes in phenotype. Under the same growth conditions, dg409 was much smaller than WT throughout its entire life cycle owing to developmental retardation. We also found that seeds of mutant plants were not as plump as WT, and the 1,000-grain weight of dg409 mutants was reduced 25% relative to WT.	Leaf	4-wk-old	RNA-Seq	5.00%	Poor	Decreased	37096684
Columbia (Col-0)	dg409-CP-1Y	Complementation	The DG409 ORF sequence was cloned into the DX2181 vector under the control of the 35S promoter to construct the p35S::DG409 fusion vector. The fusion vector was transformed into dg409 mutant plants th	Knockdown	Similar to those of WT (Normal)	Leaf	4-wk-old	RNA-Seq	40.00%	Medium	Restored	37096684

Editing Factor:	DG409
Synonym:	DELAYED GREENING 409
Description:	Transcriptomic analysis of the dg409 knockdown plants showed some editing defects in genes from both organelles, including CASEINOLYTIC PROTEASE P (clpP)-559, RNA POLYMERASE SUBUNIT ALPHA (rpoA)-200, ACETYL-COA CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT BETA (accD)-1568, NADH DEHYDROGENASE SUBUNIT 7 (nad7)-1505, and RIBOSOMAL PROTEIN S3 (rps3)-1344; RNA immunoprecipitation showed that DG409 was associated with the targeted transcripts in vivo; Interaction assays revealed that DG409 directly interacted with 2 DYW-type PPR proteins (EARLY CHLOROPLAST BIOGENESIS2 [AtECB2] and DYW DOMAIN PROTEIN2 [DYW2]) and 3 multiple organellar RNA editing factors (MORF2, MORF8, and MORF9)
Protein Family:	PPR
Subclass:	PLS
Physical Interaction:	AtECB2; DYW2; MORF2; MORF8; MORF9
Construct Structure:	PLS
Gene ID & Species:	AT1G01970 (Arabidopsis thaliana)
Edited Gene(s):	clpP rpoA accD rps3 nad7 ORFB orf313
Editing Type(s):	C-to-U (21)
Publication(s):	[1] DELAYED GREENING 409 encodes a dual-localized pentatricopeptide repeat protein required for chloroplast and mitochondrial development., Plant physiology, 2023. [PMID=37096684]

Summary

Editing Details