EMP9 - Plant Editosome Database

Editing Details

Species

Gene ID

Organelle

Edited Gene

Position

Region

Editing Type

Codon

Amino Acid

Molecular Effect

Experiment Details

Arabidopsis thaliana

AT4G32430

Mitochondrion

nad1

265

CDS

C-to-U

CGG=>UGG

R=>W

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
NA	grs1-1	T-DNA Insertion	T-DNA is located at 1325 bp downstream of the ATG start codon	Knockout	grs1-1 homozygotes are either lethal or exhibited growth retardation; cell division activity is reduced dramatically in the roots of grs1 plants	Seedling	20 days	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	27670716
NA	grs1-2	T-DNA Insertion	T-DNA is inserted at 850 bp downstream of the ATG start codon	Knockout	Homozygous grs1-2 plants are found to phenocopy grs1-1 homozygous plants	Seedling	20 days	Direct Sequencing of PCR Products	0.00%	Unedited	None	27670716
qrt 1	WT	No treatment	No treatment	No treatment	No treatment	Seedling	20 days	Direct Sequencing of PCR Products	100.00%	Complete	None	27670716
NA	grs1-1 complemented lines	Complementation	Genomic complemented lines	Homozygous	No obvious differences compared to the wild-type	Seedling	20 days	Direct Sequencing of PCR Products	100.00%	Complete	Restored	27670716

Arabidopsis thaliana

AT4G32430

Mitochondrion

nad4L

CDS

C-to-U

CGG=>UGG

R=>W

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
NA	grs1-1	T-DNA Insertion	T-DNA is located at 1325 bp downstream of the ATG start codon	Knockout	grs1-1 homozygotes are either lethal or exhibited growth retardation; cell division activity is reduced dramatically in the roots of grs1 plants	Seedling	20 days	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	27670716
NA	grs1-2	T-DNA Insertion	T-DNA is inserted at 850 bp downstream of the ATG start codon	Knockout	Homozygous grs1-2 plants are found to phenocopy grs1-1 homozygous plants	Seedling	20 days	Direct Sequencing of PCR Products	0.00%	Unedited	None	27670716
qrt 1	WT	No treatment	No treatment	No treatment	No treatment	Seedling	20 days	Direct Sequencing of PCR Products	100.00%	Complete	None	27670716
NA	grs1-1 complemented lines	Complementation	Genomic complemented lines	Homozygous	No obvious differences compared to the wild-type	Seedling	20 days	Direct Sequencing of PCR Products	100.00%	Complete	Restored	27670716

Arabidopsis thaliana

AT4G32430

Mitochondrion

nad6

103

CDS

C-to-U

CGC=>UGC

R=>C

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
NA	grs1-1	T-DNA Insertion	T-DNA is located at 1325 bp downstream of the ATG start codon	Knockout	grs1-1 homozygotes are either lethal or exhibited growth retardation; cell division activity is reduced dramatically in the roots of grs1 plants	Seedling	20 days	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	27670716
NA	grs1-2	T-DNA Insertion	T-DNA is inserted at 850 bp downstream of the ATG start codon	Knockout	Homozygous grs1-2 plants are found to phenocopy grs1-1 homozygous plants	Seedling	20 days	Direct Sequencing of PCR Products	0.00%	Unedited	None	27670716
qrt 1	WT	No treatment	No treatment	No treatment	No treatment	Seedling	20 days	Direct Sequencing of PCR Products	100.00%	Complete	None	27670716
NA	grs1-1 complemented lines	Complementation	Genomic complemented lines	Homozygous	No obvious differences compared to the wild-type	Seedling	20 days	Direct Sequencing of PCR Products	100.00%	Complete	Restored	27670716

Arabidopsis thaliana

AT4G32430

Mitochondrion

rps4

377

CDS

C-to-U

CCG=>CUG

P=>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
CS428796	atemp9	T-DNA Insertion	NA	Knockout	Seed and seedling lethal	NA	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	28121385
CS428796	atemp9:atemp9 AtEmp9-FL-OX-1 (FL, full-length; OX, overexpression)	Complementation	The atemp9 mutants are complemented with the full-length AtEMP9 coding region under the control of CaMV 35 promoter	NA	Seedling growth is restored to the WT level	NA	NA	Direct Sequencing of PCR Products	100.00%	Complete	Restored	28121385
CS428796	atemp9:atemp9 ZmEmp9-FL-OX-1 (FL, full-length; OX, overexpression)	Complementation	The full-length EMP9 coding region is expressed in the atemp9 plants under the control of the CaMV 35S promoter	NA	Grow well	NA	NA	Direct Sequencing of PCR Products	30.00%	Low	Restored	28121385
Col-0	WT	No treatment	No treatment	No treatment	No treatment	NA	NA	Direct Sequencing of PCR Products	100.00%	Complete	None	28121385
NA	grs1-1	T-DNA Insertion	T-DNA is located at 1325 bp downstream of the ATG start codon	Knockout	grs1-1 homozygotes are either lethal or exhibited growth retardation; cell division activity is reduced dramatically in the roots of grs1 plants	Seedling	20 days	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	27670716
NA	grs1-2	T-DNA Insertion	T-DNA is inserted at 850 bp downstream of the ATG start codon	Knockout	Homozygous grs1-2 plants are found to phenocopy grs1-1 homozygous plants	Seedling	20 days	Direct Sequencing of PCR Products	0.00%	Unedited	None	27670716
qrt 1	WT	No treatment	No treatment	No treatment	No treatment	Seedling	20 days	Direct Sequencing of PCR Products	100.00%	Complete	None	27670716
NA	grs1-1 complemented lines	Complementation	Genomic complemented lines	Homozygous	No obvious differences compared to the wild-type	Seedling	20 days	Direct Sequencing of PCR Products	100.00%	Complete	Restored	27670716

Zea mays subsp. mays

AC212684.3_FG012

Mitochondrion

ccmB

CDS

C-to-U

CCC=>UCC

P=>S

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
W22	emp9-1	Mu Insertion	Mu is inserted in the middle of the PPR repeats	Recessive mutation; Heterozygous; Null alleles	Arrested in embryogenesis and endosperm development; The mutant kernels are white, small and defective	Kernel	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	28121385
NA	emp9-2	Mu Insertion	Mu is inserted in the E domain (at +2074 bp)	Null alleles	Severe emp phenotype	Kernel	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	28121385
NA	emp9-3	Mu Insertion	Mu is inserted in the putative N-terminal signal peptide (sp) region (at +19 bp)	NA	Slow growth (Slo) phenotype	Kernel	9 DAP	Direct Sequencing of PCR Products	25.00%	Low	Decreased	28121385
NA	emp9-3	Mu Insertion	Mu is inserted in the putative N-terminal signal peptide (sp) region (at +19 bp)	NA	Slow growth (Slo) phenotype	Kernel	11 DAP	Direct Sequencing of PCR Products	25.00%	Low	Decreased	28121385
NA	emp9-3	Mu Insertion	Mu is inserted in the putative N-terminal signal peptide (sp) region (at +19 bp)	NA	Slow growth (Slo) phenotype	Kernel	14 DAP	Direct Sequencing of PCR Products	25.00%	Low	Decreased	28121385
NA	emp9-3	Mu Insertion	Mu is inserted in the putative N-terminal signal peptide (sp) region (at +19 bp)	NA	Slow growth (Slo) phenotype	Leaf	NA	Direct Sequencing of PCR Products	25.00%	Low	Decreased	28121385
NA	emp9-4	Mu Insertion	Mu is inserted in the E+ domain (at +2190 bp)	NA	No visible seed and seedling phenotypes	Kernel	NA	Direct Sequencing of PCR Products	75.00%	High	Decreased	28121385
NA	Col-0	No treatment	No treatment	No treatment	No treatment	Kernel	NA	Direct Sequencing of PCR Products	90.00%	High	None	28121385

Zea mays subsp. mays

AC212684.3_FG012

Mitochondrion

rps4

335

CDS

C-to-U

CCG=>CUG

P=>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
NA	emp9-1	Mu Insertion	Mu is inserted in the middle of the PPR repeats	Recessive mutation; Heterozygous; Null alleles	Arrested in embryogenesis and endosperm development; The mutant kernels are white, small and defective	Kernel	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	28121385
NA	emp9-2	Mu Insertion	Mu is inserted in the E domain (at +2074 bp)	Null alleles	Severe emp phenotype	Kernel	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	28121385
NA	emp9-3	Mu Insertion	Mu is inserted in the putative N-terminal signal peptide (sp) region (at +19 bp)	NA	Slow growth (Slo) phenotype	Kernel	9 DAP	Direct Sequencing of PCR Products	20.00%	Low	Decreased	28121385
NA	emp9-3	Mu Insertion	Mu is inserted in the putative N-terminal signal peptide (sp) region (at +19 bp)	NA	Slow growth (Slo) phenotype	Kernel	11 DAP	Direct Sequencing of PCR Products	20.00%	Low	Decreased	28121385
NA	emp9-3	Mu Insertion	Mu is inserted in the putative N-terminal signal peptide (sp) region (at +19 bp)	NA	Slow growth (Slo) phenotype	Kernel	14 DAP	Direct Sequencing of PCR Products	20.00%	Low	Decreased	28121385
NA	emp9-3	Mu Insertion	Mu is inserted in the putative N-terminal signal peptide (sp) region (at +19 bp)	NA	Slow growth (Slo) phenotype	Leaf	NA	Direct Sequencing of PCR Products	20.00%	Low	Decreased	28121385
NA	emp9-4	Mu Insertion	Mu is inserted in the E+ domain (at +2190 bp)	NA	No visible seed and seedling phenotypes	Kernel	NA	Direct Sequencing of PCR Products	75.00%	High	Decreased	28121385
NA	Col-0	No treatment	No treatment	No treatment	No treatment	Kernel	NA	Direct Sequencing of PCR Products	90.00%	High	None	28121385

Editing Factor:	EMP9
Synonym:	AtEMP9, GROWING SLOWLY 1, GRS1
Description:	Encodes a protein required for mitochondrial editing, mitochondrial complex biogenesis and seed development.
Protein Family:	PPR
Subclass:	E+
Construct Structure:	PLS-E1/E2-E+
Gene ID & Species:	AT4G32430 (Arabidopsis thaliana) AC212684.3_FG012 (Zea mays subsp. mays)
Edited Gene(s):	rps4 ccmB nad1 nad4L nad6
Editing Type(s):	C-to-U (36)
Publication(s):	[1] The pentatricopeptide repeat protein EMP9 is required for mitochondrial ccmB and rps4 transcript editing, mitochondrial complex biogenesis and seed development in maize, New Phytologist, 2017. [PMID=28121385] [2] Growing Slowly 1 locus encodes a PLS-type PPR protein required for RNA editing and plant development in Arabidopsis, Journal of Experimental Botany, 2016. [PMID=27670716]

Plant Editosome Database
a curated database of RNA editosome in plants

Summary

Editing Details