VAC1 - Plant Editosome Database

Summary

Editing Factor:	VAC1
Synonym:	ARABIDOPSIS EARLY CHLOROPLAST BIOGENESIS 2; ATECB2; EARLY CHLOROPLAST BIOGENESIS 2; ECB2; VANILLA CREAM 1
Description:	The editing of accD and ndhF transcripts is partially affected in vac1; steady-state levels of chloroplast rRNAs are significantly decreased in vac1; The expression of plastid-encoded RNA polymerase transcribed genes is down-regulated, whereas the expression of nucleus-encoded RNA polymerase transcribed genes is up-regulated in vac1; Although the development and function of mutant chloroplasts are severely impaired, steady-state mRNA levels of nucleus-encoded photosynthetic genes are not affected or are only slightly decreased in vac1; VAC1 protein may be involved in plastid-to-nucleus retrograde signaling in addition to its role in chloroplast RNA editing and gene expression
Protein Family:	Pentatricopeptide repeat (PPR) protein
Subclass:	DYW
Physical Interaction:	NA
Construct Structure:	PLS-E1-E2-DYW
Gene ID & Species:	AT1G15510 (Arabidopsis thaliana)
Edited Gene(s):	accD ndhF
Editing Type(s):	C-to-U (15)
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] Editing of accD and ndhF chloroplast transcripts is partially affected in the Arabidopsis vanilla cream1 mutant, Plant Molecular Biology, 2010. [doi:10.1007/s11103-010-9616-5]

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

AT1G15510

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

AT1G15510

Chloroplast

accD

794

CDS

C-to-U

UCG=>UUG
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
ACR3p-GUS 73	heterozygous vac1	T-DNA Insertion	NA	Heterozygous	Albino to pale yellow phenotype	Seedling	2 weeks	Direct Sequencing of PCR Products	62.00%	High	Decreased	20143129
Col-0	WT	Control	Control	No mutant	Normal	Seedling	2 weeks	Direct Sequencing of PCR Products	100.00%	Complete	None	20143129
Col-0	WT	Control	Control	No mutant	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	94.00%	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	100.00%	Complete	Similar	28761003

Arabidopsis thaliana

AT1G15510

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
ACR3p-GUS 73	heterozygous vac1	T-DNA Insertion	NA	Heterozygous	Albino to pale yellow phenotype	Seedling	2 weeks	Direct Sequencing of PCR Products	8.00%	Poor	Decreased	20143129
Col-0	WT	Control	Control	No mutant	Normal	Seedling	2 weeks	Direct Sequencing of PCR Products	55.00%	Medium	None	20143129

Arabidopsis thaliana

AT1G15510

Chloroplast

ndhF

290

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
ACR3p-GUS 73	heterozygous vac1	T-DNA Insertion	NA	Heterozygous	Albino to pale yellow phenotype	Seedling	2 weeks	Direct Sequencing of PCR Products	49.00%	Medium	Decreased	20143129
Col-0	WT	Control	Control	No mutant	Normal	Seedling	2 weeks	Direct Sequencing of PCR Products	95.00%	High	None	20143129
Col-0	WT	Control	Control	No mutant	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	48.00%	Medium	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	78.00%	High	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	61.00%	High	Increased	28761003