COD1 - Plant Editosome Database

Summary

Editing Factor:	COD1
Synonym:	CYTOCHROME C OXIDASE DEFICIENT 1
Description:	cod1 mutants were defective in C-to-U editing events in cytochrome oxidase subunit2 and NADH dehydrogenase subunit4 transcripts, encoding subunits of respiratory complex IV and I, respectively, and consequently lacked cytochrome c oxidase activity; Respiratory oxygen consumption by cod1 plantlets is exclusively associated with alternative oxidase activity and that alternative NADH dehydrogenases are also up-regulated in these plants; The metabolomics pattern of cod1 mutants was also deeply altered, suggesting that alternative metabolic pathways compensated for the probable resulting restriction in NADH oxidation; Being the first complex IV-deficient mutants described in higher plants, cod1 lines should be instrumental to future studies on respiration homeostasis
Protein Family:	Pentatricopeptide repeat (PPR) protein
Subclass:	E+
Physical Interaction:	NA
Construct Structure:	PLS-E-E+
Gene ID & Species:	AT2G35030 (Arabidopsis thaliana)
Edited Gene(s):	cox2 nad4
Editing Type(s):	C-to-U (18)
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] Disruption of the CYTOCHROME C OXIDASE DEFICIENT1 gene leads to cytochrome c oxidase depletion and reorchestrated respiratory metabolism in Arabidopsis, Plant Physiol, 2014. [doi:10.1104/pp.114.248526]

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

AT2G35030

Mitochondrion

cox2

253

CDS

C-to-U

CGG=>UGG
NA=>NA

R=>W
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
Col-0	Col-0	Control	Control	No mutant	Normal	Seedling	3 to 4 weeks	Direct Sequencing of PCR Products	100.00%	Complete	None	25301889
SALK_000882	cod1-1	T-DNA insertion	A T-DNA insertion is mapped within the COD1 gene coding sequence, precisely 1,707(cod1-1) nucleotides downstream of the start codon	Heterozygous	Smaller size of the embryo; Retarded and very slow growth of the seed	Seedling	2 to 3 months	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25301889
SALK_615308	cod1-2	T-DNA insertion	A T-DNA insertion is mapped within the COD1 gene coding sequence, precisely 990(cod1-2) nucleotides downstream of the start codon	Heterozygous	Smaller size of the embryo; Retarded and very slow growth of the seed	Seedling	2 to 3 months	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25301889
Col-0	WT	Control	Control	No mutant	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	100.00%	Complete	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	57.00%	Medium	Decreased	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	53.00%	Medium	Decreased	28761003

Arabidopsis thaliana

AT2G35030

Mitochondrion

cox2

698

CDS

C-to-U

ACG=>AUG
NA=>NA

T=>M
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
Col-0	Col-0	Control	Control	No mutant	Normal	Seedling	3 to 4 weeks	Direct Sequencing of PCR Products	100.00%	Complete	None	25301889
SALK_000882	cod1-1	T-DNA insertion	A T-DNA insertion is mapped within the COD1 gene coding sequence, precisely 1,707(cod1-1) nucleotides downstream of the start codon	Heterozygous	Smaller size of the embryo; Retarded and very slow growth of the seed	Seedling	2 to 3 months	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25301889
SALK_615308	cod1-2	T-DNA insertion	A T-DNA insertion is mapped within the COD1 gene coding sequence, precisely 990(cod1-2) nucleotides downstream of the start codon	Heterozygous	Smaller size of the embryo; Retarded and very slow growth of the seed	Seedling	2 to 3 months	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25301889
Col-0	WT	Control	Control	No mutant	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	100.00%	Complete	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	88.00%	High	Decreased	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	93.00%	High	Similar	28761003

Arabidopsis thaliana

AT2G35030

Mitochondrion

nad4

1129

CDS

C-to-U

CUC=>UUC
NA=>NA

L=>F
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
Col-0	Col-0	Control	Control	No mutant	Normal	Seedling	3 to 4 weeks	Direct Sequencing of PCR Products	100.00%	Complete	None	25301889
SALK_000882	cod1-1	T-DNA insertion	A T-DNA insertion is mapped within the COD1 gene coding sequence, precisely 1,707(cod1-1) nucleotides downstream of the start codon	Heterozygous	Smaller size of the embryo; Retarded and very slow growth of the seed	Seedling	2 to 3 months	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25301889
SALK_615308	cod1-2	T-DNA insertion	A T-DNA insertion is mapped within the COD1 gene coding sequence, precisely 990(cod1-2) nucleotides downstream of the start codon	Heterozygous	Smaller size of the embryo; Retarded and very slow growth of the seed	Seedling	2 to 3 months	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25301889
Col-0	WT	Control	Control	No mutant	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	100.00%	Complete	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	83.00%	High	Decreased	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	86.00%	High	Decreased	28761003