EMP5 - Plant Editosome Database

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

Oryza sativa

LOC_Os01g72930

Mitochondrion

rpl16

458

CDS

C-to-U

CUA=>CCA

L=>P

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Nipponbare	OsEmp5-RNAi transgenic lines 19	RNAi	RNAi vector, pTCK303-OsEmp5, is introduced into the wild-type cultivar Nipponbare using Agrobacterium-mediated transformation	NA	The transgenic plants grew much slower than the wild type at seedling stage. But after the seedling stage, the plants gradually recovered and grew to normal adult plants	Leaf	NA	Direct Sequencing of PCR Products	NA	Low	Decreased	23463776
Nipponbare	OsEmp5-RNAi transgenic lines 23	RNAi	RNAi vector, pTCK303-OsEmp5, is introduced into the wild-type cultivar Nipponbare using Agrobacterium-mediated transformation	NA	The transgenic plants grew much slower than the wild type at seedling stage. But after the seedling stage, the plants gradually recovered and grew to normal adult plants	Leaf	NA	Direct Sequencing of PCR Products	NA	Medium	Decreased	23463776
Nipponbare	OsEmp5-RNAi transgenic lines 33	RNAi	RNAi vector, pTCK303-OsEmp5, is introduced into the wild-type cultivar Nipponbare using Agrobacterium-mediated transformation	NA	The transgenic plants grew much slower than the wild type at seedling stage. But after the seedling stage, the plants gradually recovered and grew to normal adult plants	Leaf	NA	Direct Sequencing of PCR Products	NA	Medium	Decreased	23463776
Nipponbare	WT	Control	Control	No mutant	Normal	Leaf	NA	Direct Sequencing of PCR Products	100.00%	Complete	None	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

atp6

953

CDS

AGPv2

C-to-U

UCA=>UUA

S=>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
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Medium	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	Increased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	NA	Similar	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

cob

1098

CDS

AGPv2

C-to-U

UUC=>UUU

F=>F

Synonymous

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Medium	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	Increased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	NA	Similar	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

cox3

245

CDS

AGPv2

C-to-U

CCU=>CUU

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
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	100.00%	Complete	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	Decreased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	NA	Similar	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

cox3

257

CDS

AGPv2

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
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	100.00%	Complete	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	Decreased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	NA	Similar	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

nad1

536

CDS

AGPv2

C-to-U

UUC=>UUU

F=>F

Synonymous

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Medium	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Medium	Increased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	NA	Similar	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

nad1

832

CDS

AGPv2

C-to-U

CUA=>UUA

L=>L

Synonymous

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Poor	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	Increased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	NA	Similar	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

nad9

190

CDS

AGPv2

C-to-U

CAU=>UAU

H=>Y

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	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Medium	Decreased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	High	Decreased	23463776
W22	WT	Control	Control	No mutant	Normal	Leaf	NA	Direct Sequencing of PCR Products	100.00%	Complete	None	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

nad9

356

CDS

AGPv2

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
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Low	Decreased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	NA	Similar	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

rpl16

444

CDS

AGPv2

C-to-U

UCC=>UCU

S=>S

Synonymous

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Medium	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	Increased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	High	Increased	23463776
W22	WT	Control	Control	No mutant	Normal	Leaf	NA	Direct Sequencing of PCR Products	NA	Medium	None	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

rpl16

458

CDS

AGPv2

C-to-U

CCA=>CUA

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
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	High	Decreased	23463776
W22	WT	Control	Control	No mutant	Normal	Leaf	NA	Direct Sequencing of PCR Products	100.00%	Complete	None	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

rps12

196

CDS

AGPv2

C-to-U

CAC=>UAC

H=>Y

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	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Low	Decreased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	NA	Similar	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

rps12

221

CDS

AGPv2

C-to-U

UCG=>UUG

S=>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
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Medium	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Medium	Decreased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	NA	Similar	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

rps12

269

CDS

AGPv2

C-to-U

UCG=>UUG

S=>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
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Low	Decreased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	NA	Similar	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

rps12

284

CDS

AGPv2

C-to-U

UCC=>UUC

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
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Low	Decreased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	NA	Similar	23463776

Zea mays

ZEAMMB73_Zm00001d042039

Mitochondrion

rps12

CDS

AGPv2

C-to-U

UCG=>UUG

S=>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
W22	WT	Control	Control	No mutant	Normal	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	High	None	23463776
W22	emp5-1	Mu2 insertion	A Mu2 is inserted in the first exon	Heterozygous	Kernels at maturity typically were small,containing a white pericarp that was often wrinkled	Kernel	13 DAP	Direct Sequencing of PCR Products	NA	Low	Decreased	23463776
TUSC population	emp5-4	Mu1 insertion	A 1.4-kb Mu1 element in the middle of the E+ motif disrupts the E+ and DYW domain	Homozygous	A normal embryo and endosperm	Leaf	NA	Direct Sequencing of PCR Products	NA	NA	Similar	23463776

Editing Factor:	EMP5
Synonym:	Empty Pericarp 5
Description:	Analysis of the mitochondrial transcripts revealed that loss of the EMP5 function abolishes the C-to-U editing of ribosomal protein L16 at the rpl16-458 site (100% edited in the wild type), decreases the editing at nine sites in NADH dehydrogenase9 (nad9), cytochrome c oxidase3 (cox3), and ribosomal protein S12 (rps12), and surprisingly increases the editing at five sites of ATP synthase F0 subunit a (atp6), apocytochrome b (cob), nad1, and rpl16; Mutant EMP5-4 lacking the E+ and DYW domains still retains the substrate specificity and editing function, only at reduced efficiency
Protein Family:	Pentatricopeptide repeat (PPR) protein
Subclass:	DYW
Physical Interaction:	NA
Construct Structure:	PLS-E-E+-DYW
Gene ID & Species:	LOC_Os01g72930 (Oryza sativa) ZEAMMB73_Zm00001d042039 (Zea mays)
Edited Gene(s):	rpl16 nad9 cox3 rps12 atp6 nad1 cob
Editing Type(s):	C-to-U (52)
Publication(s):	[1] Empty pericarp5 encodes a pentatricopeptide repeat protein that is required for mitochondrial RNA editing and seed development in maize, The Plant Cell, 2013. [doi:10.1105/tpc.112.106781]

Summary

Editing Details