CREF7 - Plant Editosome Database

Summary

Editing Factor:	CREF7
Synonym:	CHLOROPLAST RNA EDITING FACTOR 7
Description:	Encoding a pentatricopeptide repeat protein involved in chloroplast mRNA editing
Protein Family:	PPR
Subclass:	DYW
Physical Interaction:	NA
Construct Structure:	PLS-DYW
Gene ID & Species:	AT5G66520 (Arabidopsis thaliana)
Edited Gene(s):	ndhB rpoA
Editing Type(s):	C-to-U (15)
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] A conserved glutamate residue in the C-terminal deaminase domain of pentatricopeptide repeat proteins is required for RNA editing activity., The Journal of biological chemistry, 2015. [PMID=25739442] [4] Pentatricopeptide repeat proteins involved in plant organellar RNA editing., RNA biology, 2013. [PMID=23669716]

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

AT5G66520

Chloroplast
Plastid

ndhB

1255

CDS

NA
EnsemblGenomes (release 39)

NA
BK010421

C-to-U

CAU=>UAU
NA=>NA

H=>Y
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	WT	Control	Control	Control	Normal	Leaf	NA	Bulk Sequencing	100.00%	Complete	None	25739442
SALK_078415C	cref7-1	T-DNA Insertion	T-DNA is inserted in the PLS repeat region	Knockout	NA	Leaf	NA	Bulk Sequencing	0.00%	Unedited	Absent	25739442
Col-0	WT + CREF7	Transformation	Wild type plants with CREF7 transgene	NA	NA	Leaf	NA	Bulk Sequencing	100.00%	Complete	Similar	25739442
SALK_078415C	KO + CREF7-E554A	Transformation	Transgene for a mutant variant with the HXE motif changed to HXA (CREF7-E554A) is introduced into a CREF7 knock-out line (cref7-1)	NA	NA	Leaf	NA	Bulk Sequencing	NA	Low	Decreased	25739442
Col-0	WT + CREF7-E554A	Transformation	Transgene for a mutant variant with the HXE motif changed to HXA (CREF7-E554A) is introduced into a wild type line	NA	NA	Leaf	NA	Bulk Sequencing	100.00%	Complete	Similar	25739442
Col-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	98.44%	High	None	32098170
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	95.00%	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

AT5G66520

Chloroplast

ndhB

95225

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
Colombia	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and direct sequencing	83.33%	High	None	23669716
Salk_078415	Salk_078415	T-DNA insertion	An insertion of the T-DNA in the coding regions of the transgenic line	NA	No aberrant visible phenotype	Leaf	NA	RT-PCR and direct sequencing	0.00%	Unedited	Absent	23669716

Arabidopsis thaliana

AT5G66520

Chloroplast

rpoA

200

CDS

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
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	Bulk Sequencing	NA	High	None	25739442
SALK_078415C	cref7-1	T-DNA Insertion	T-DNA is inserted in the PLS repeat region	Knockout	NA	Leaf	NA	Bulk Sequencing	NA	High	Similar	25739442
SALK_078415C	KO + CREF7	Transformation	Transgene for wild type CREF7 is introduced into a CREF7 knock-out line (cref7-1)	NA	NA	Leaf	NA	Bulk Sequencing	NA	High	Similar	25739442
SALK_078415C	KO + CREF7-E554A	Transformation	Transgene for a mutant variant with the HXE motif changed to HXA (CREF7-E554A) is introduced into a CREF7 knock-out line (cref7-1)	NA	NA	Leaf	NA	Bulk Sequencing	NA	Low	Decreased	25739442