MEF11 - 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

AT4G14850

Mitochondrion

ccmC

568

CDS

EnsemblGenomes (release 39)
NA

BK010421
NA

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	Control	NA	NA	NA	RNA-seq	96.47%	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	99.00%	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	97.00%	High	Similar	28761003

Arabidopsis thaliana

AT4G14850

Mitochondrion

ccmFn2

344

CDS

NA
EnsemblGenomes (release 39)

NA
BK010421

C-to-U

CCA=>CUA
NA=>NA

P=>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	mef11-1	Point Mutation	The single amino acid is exchanged in the second PPR repeat	NA	NA	NA	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	20436293
Salk_131734	mef11-2	T-DNA Insertion	T-DNA is inserted in the DYW-domain	Processing of the transcripts does not seem to be affected	NA	NA	NA	Direct Sequencing of PCR Products	60.00%	High	Decreased	20436293
Col	mef11-1	EMS Mutant	The EMS mutant causes a single amino acid alteration of Leu to Pheat residue 48 in the second PPR repeat	homozygous	The mef11-1 mutant shows slightly increased tolerance against lovastatin. In the presence of lovastatin, root elongation was inhibited more profoundly in the wild-type plants than in the mutant plants.	Leaf	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	19919573
SALK_131734	mef11-2	T-DNA Insertion	homozygous	NA	Normal growth under standard greenhouse conditions	Leaf	NA	Direct Sequencing of PCR Products	60.00%	High	Decreased	19919573
Col	MEF11	Complementation	The wild-type Col MEF11 gene is cloned under the control of the CaMV 35S promoter, and the plasmid DNA was transfected into mef11-1 mutant protoplasts	NA	NA	Leaf	NA	Direct Sequencing of PCR Products	NA	Low	Decreased	19919573
Col	mef11-3	The mutant sequences selected mef11-3 were transfected into mef11-1 protoplasts	Gene variant mef11-3 contains a single mutation in the fourth PPR repeat, which changes amino acid 125 from Val to Thr	NA	NA	Leaf	NA	Direct Sequencing of PCR Products	NA	Medium	Decreased	19919573
Col	mef11-4	The mutant sequences selecte mef11-4 were transfected into mef11-1 protoplasts	The mef11-4 gene variant with single nucleotide variations in PPR repeats 8 and 12 and in the E-like domain	NA	NA	Leaf	NA	Direct Sequencing of PCR Products	NA	Medium	Decreased	19919573
NA	mef11-2	T-DNA Insertion	T-DNA is located in the DYW domain	NA	Exhibited a wild-type phenotype	Seedling	NA	Direct Sequencing of PCR Products	NA	Medium	Decreased	25708384
SALK_061056	mef11-5	T-DNA Insertion	T-DNA is inserted in the first exon	NA	Hot leaf phenotype similar to mef11-6	Seedling	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25708384
Col-0	mef11-6	γ-Irradiation Induced Mutant	Three consecutive mutations (a G to C substitution, a 4-nucleotide deletion, and a 2-nucleotide insertion), which introduced a premature stop codon in the coding sequence	NA	mef11 plants are more resistant to progressive water stress and seed germination is more sensitive to paclobutrazol	Seedling	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25708384
NA	WT	Control	Control	Control	Normal	Seedling	NA	Direct Sequencing of PCR Products	NA	Medium	None	25708384
Col-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	93.41%	High	None	32098170
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	98.00%	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	97.00%	High	Similar	28761003

Arabidopsis thaliana

AT4G14850

Mitochondrion

cox3

422

CDS

NA
EnsemblGenomes (release 39)

NA
BK010421

C-to-U

CCU=>CUU
NA=>NA

P=>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	mef11-1	Point Mutation	The single amino acid is exchanged in the second PPR repeat	NA	NA	NA	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	20436293
Salk_131734	mef11-2	T-DNA Insertion	T-DNA is inserted in the DYW-domain	Processing of the transcripts does not seem to be affected	NA	NA	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	20436293
Col	mef11-1	EMS Mutant	The EMS mutant causes a single amino acid alteration of Leu to Pheat residue 48 in the second PPR repeat	homozygous	The mef11-1 mutant shows slightly increased tolerance against lovastatin. In the presence of lovastatin, root elongation was inhibited more profoundly in the wild-type plants than in the mutant plants.	Leaf	NA	A multiplexed SNaPshot approach	0.00%	Unedited	Absent	19919573
SALK_131734	mef11-2	T-DNA Insertion	homozygous	NA	Normal growth under standard greenhouse conditions	Leaf	NA	A multiplexed SNaPshot approach	0.00%	Unedited	Absent	19919573
Col	WT	Control	Control	Control	Normal	Leaf	NA	A multiplexed SNaPshot approach	100.00%	Complete	None	19919573
Col	MEF11	Complementation	The wild-type Col MEF11 gene is cloned under the control of the CaMV 35S promoter, and the plasmid DNA was transfected into mef11-1 mutant protoplasts	NA	NA	Leaf	NA	Direct Sequencing of PCR Products	50.00%	Medium	Decreased	19919573
Col	mef11-3	The mutant sequences selected mef11-3 were transfected into mef11-1 protoplasts	Gene variant mef11-3 contains a single mutation in the fourth PPR repeat, which changes amino acid 125 from Val to Thr	NA	NA	Leaf	NA	Direct Sequencing of PCR Products	50.00%	Medium	Decreased	19919573
Col	mef11-4	The mutant sequences selecte mef11-4 were transfected into mef11-1 protoplasts	The mef11-4 gene variant with single nucleotide variations in PPR repeats 8 and 12 and in the E-like domain	NA	NA	Leaf	NA	Direct Sequencing of PCR Products	50.00%	Medium	Decreased	19919573
NA	mef11-2	T-DNA Insertion	T-DNA is located in the DYW domain	NA	Exhibited a wild-type phenotype	Seedling	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25708384
SALK_061056	mef11-5	T-DNA Insertion	T-DNA is inserted in the first exon	NA	Hot leaf phenotype similar to mef11-6	Seedling	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25708384
Col-0	mef11-6	γ-Irradiation Induced Mutant	Three consecutive mutations (a G to C substitution, a 4-nucleotide deletion, and a 2-nucleotide insertion), which introduced a premature stop codon in the coding sequence	NA	mef11 plants are more resistant to progressive water stress and seed germination is more sensitive to paclobutrazol	Seedling	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25708384
NA	WT	Control	Control	Control	Normal	Seedling	NA	Direct Sequencing of PCR Products	100.00%	Complete	None	25708384
Col-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	97.85%	High	None	32098170
Col-0	WT	Control	Control	Control	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	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

AT4G14850

Mitochondrion

matR

1730

CDS

EnsemblGenomes (release 39)
NA

BK010421
NA

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	Control	NA	NA	NA	RNA-seq	91.62%	High	None	32098170
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	87.00%	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	96.00%	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	74.00%	High	Decreased	28761003

Arabidopsis thaliana

AT4G14850

Mitochondrion

nad4

124

CDS

NA
EnsemblGenomes (release 39)

NA
BK010421

C-to-U

CUG=>UUG
NA=>NA

L=>L
NA=>NA

Synonymous
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	mef11-1	Point Mutation	The single amino acid is exchanged in the second PPR repeat	NA	NA	NA	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	20436293
Salk_131734	mef11-2	T-DNA Insertion	T-DNA is inserted in the DYW-domain	Processing of the transcripts does not seem to be affected	NA	NA	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	20436293
Col	mef11-1	EMS Mutant	The EMS mutant causes a single amino acid alteration of Leu to Pheat residue 48 in the second PPR repeat	homozygous	The mef11-1 mutant shows slightly increased tolerance against lovastatin. In the presence of lovastatin, root elongation was inhibited more profoundly in the wild-type plants than in the mutant plants.	Leaf	NA	A multiplexed SNaPshot approach	0.00%	Unedited	Absent	19919573
SALK_131734	mef11-2	T-DNA Insertion	homozygous	NA	Normal growth under standard greenhouse conditions	Leaf	NA	A multiplexed SNaPshot approach	NA	Poor	Decreased	19919573
Col	WT	Control	Control	Control	Normal	Leaf	NA	A multiplexed SNaPshot approach	100.00%	Complete	None	19919573
Col	MEF11	Complementation	The wild-type Col MEF11 gene is cloned under the control of the CaMV 35S promoter, and the plasmid DNA was transfected into mef11-1 mutant protoplasts	NA	NA	Leaf	NA	Direct Sequencing of PCR Products	50.00%	Medium	Decreased	19919573
Col	mef11-3	The mutant sequences selected mef11-3 were transfected into mef11-1 protoplasts	Gene variant mef11-3 contains a single mutation in the fourth PPR repeat, which changes amino acid 125 from Val to Thr	NA	NA	Leaf	NA	Direct Sequencing of PCR Products	50.00%	Medium	Decreased	19919573
Col	mef11-4	The mutant sequences selecte mef11-4 were transfected into mef11-1 protoplasts	The mef11-4 gene variant with single nucleotide variations in PPR repeats 8 and 12 and in the E-like domain	NA	NA	Leaf	NA	Direct Sequencing of PCR Products	50.00%	Medium	Decreased	19919573
NA	mef11-2	T-DNA Insertion	T-DNA is located in the DYW domain	NA	Exhibited a wild-type phenotype	Seedling	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25708384
SALK_061056	mef11-5	T-DNA Insertion	T-DNA is inserted in the first exon	NA	Hot leaf phenotype similar to mef11-6	Seedling	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25708384
Col-0	mef11-6	γ-Irradiation Induced Mutant	Three consecutive mutations (a G to C substitution, a 4-nucleotide deletion, and a 2-nucleotide insertion), which introduced a premature stop codon in the coding sequence	NA	mef11 plants are more resistant to progressive water stress and seed germination is more sensitive to paclobutrazol	Seedling	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	25708384
NA	WT	Control	Control	Control	Normal	Seedling	NA	Direct Sequencing of PCR Products	NA	Low	None	25708384
Col-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	98.94%	High	None	32098170
Col-0	WT	Control	Control	Control	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	99.00%	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	100.00%	Complete	Similar	28761003

Editing Factor:	MEF11
Synonym:	LOI1; LOVASTATIN INSENSITIVE 1; MITOCHONDRIAL RNA EDITING FACTOR 11
Description:	Encoding a pentatricopeptide (PPR) protein that binds single-stranded RNA, the N-terminal portion of the protein can localize to the mitochondria; Mutations in this gene make plants less sensitive to inhibitors of the MEP and MVA pathways of isoprenoid biosynthesis and increase the activity of HMG CoA reductase
Protein Family:	PPR
Subclass:	DYW
Physical Interaction:	NA
Construct Structure:	PLS-E-DYW, PLS-E like-DYW
Gene ID & Species:	AT4G14850 (Arabidopsis thaliana)
Edited Gene(s):	cox3 nad4 ccmFn2 ccmC matR
Editing Type(s):	C-to-U (55)
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] The ABA-deficiency suppressor locus HAS2 encodes the PPR protein LOI1/MEF11 involved in mitochondrial RNA editing., Molecular plant, 2015. [PMID=25708384] [4] A truncated MEF11 protein shows site-specific effects on mitochondrial RNA editing., Plant signaling & behavior, 2010. [PMID=20436293] [5] The PPR protein encoded by the LOVASTATIN INSENSITIVE 1 gene is involved in RNA editing at three sites in mitochondria of Arabidopsis thaliana., The Plant journal : for cell and molecular biology, 2010. [PMID=19919573]

Summary

Editing Details