ECB2 - Plant Editosome Database

ECB2 - Plant Editosome Database - CNCB-NGDC

Summary

Editing Factor:	ECB2
Synonym:	EARLY CHLOROPLAST BIOGENESIS 2; VAC1; VANILLA CREAM 1; ATECB2
Description:	An investigation of the chloroplast gene expression profile indicated that PEP (plastid-encoded RNA polymerase) activity in ecb2-2 cotyledons was not obviously affected, whereas it was severely impaired in ecb2-1, suggesting that the PEP activities cause the different phenotypes of the ecb2-1 and ecb2-2 mutants; The editing efficiency of the three editing sites of accD (C794 and C1568) and ndhF (C290) in the mutant was dynamically altered, which was in agreement with the phenotype, indicating that the editing efficiency of accD and ndhF in the ecb2-2 mutant is associated with a delayed greening phenotype; AtECB2 is required for chloroplast transcript accD RNA editing and early chloroplast biogenesis in Arabidopsis thaliana; RNA immunoprecipitation analysis indicated that AtECB2 is associated with the transcripts of accD, ndhF, ndhG and petL; Co-immunoprecipitation and mass spectrometry experiments showed that multiple organelle RNA editing factor 2 (MORF2) and porphobilinogen deaminase HEMC are associated with AtECB2; Biochemical analysis showed that AtECB2 directly interacts with HEMC through its E domain, while HEMC interacts with MORF8/RIP1; Of the seven editing sites affected in atecb2, the editing of accD-794 and ndhF-290 was also reduced in hemc-1; RNA immunoprecipitation analysis suggested that HEMC is associated with the editing sites of ndhF transcripts; These results showed that both HEMC and multiple organellar RNA editing factor (MORF) proteins are associated with AtECB2 for RNA editing in plastids
Protein Family:	Pentatricopeptide repeat (PPR) protein
Subclass:	DYW
Physical Interaction:	HEMC
Construct Structure:	PLS-E1-E2-DYW
Gene ID & Species:	AT1G15510 (Arabidopsis thaliana)
Edited Gene(s):	accD ndhF ndhG petL rpoA rpoC1
Editing Type(s):	C-to-U (48)
Publication(s):	[1] A weak allele of AtECB2, a member of the pentatricopeptide repeat motif superfamily, causes leaf virescence in Arabidopsis, Plant Cell Rep, 2025. [doi:10.1007/s00299-024-03376-8] [2] Porphobilinogen deaminase HEMC interacts with the PPR-protein AtECB2 for chloroplast RNA editing, The Plant Journal, 2017. [doi:10.1111/tpj.13672] [3] A point mutation in the pentatricopeptide repeat motif of the AtECB2 protein causes delayed chloroplast development, Journal of Integrative Plant Biology, 2011. [doi:10.1111/j.1744-7909.2011.01030.x] [4] AtECB2, a pentatricopeptide repeat protein, is required for chloroplast transcript accD RNA editing and early chloroplast biogenesis in Arabidopsis thaliana, The Plant Journal, 2009. [doi:10.1111/j.1365-313X.2009.03930.x]

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

3'UTR

TAIR10

C-to-U

NA=>NA

Synonymous

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Columbia (Col-0)	Col-0 leaf	Control	Control	No mutant	Normal	Leaf	21-day-old	PCR and Sanger sequencing; Image J software	99.58%	High	None	39579257
Columbia (Col-0)	ecb2-3 green patches	Mutant	A leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds library	Recessive	The chlorophyll content and photosystem II maximum photochemical efficiency of ecb2-3 are obviously lower than that of Col-0 and its complementation lines, respectively; The chloroplast development of ecb2-3 is also inferior to that of Col-0 and its complementation line at the observed time points using the transmission electron microscope	Patch	21-day-old	PCR and Sanger sequencing; Image J software	97.71%	High	Similar	39579257
Columbia (Col-0)	ecb2-3 yellow patches	Mutant	A leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds library	Recessive	The chlorophyll content and photosystem II maximum photochemical efficiency of ecb2-3 are obviously lower than that of Col-0 and its complementation lines, respectively; The chloroplast development of ecb2-3 is also inferior to that of Col-0 and its complementation line at the observed time points using the transmission electron microscope	Patch	21-day-old	PCR and Sanger sequencing; Image J software	46.90%	Medium	Decreased	39579257
Columbia (Col-0)	Comp leaf	Complementation	For complementation, the 1936 bp promotor and 2601 bp AtECB2 gene were amplified using AtECB2-P-1936-KpnI-F/AtECB2-DNA-403-MluI-R, AtECB2-DNA-398-MluI-F/AtECB2-DNA-2601-PstI-R, and constructed into pP	Recessive	Normal	Leaf	21-day-old	PCR and Sanger sequencing; Image J software	99.58%	High	Restored	39579257
Columbia (Col-0)	Col-0 cotyledon	Control	Control	No mutant	Normal	Cotyledon	7-day-old	PCR and Sanger sequencing; Image J software	99.42%	High	None	39579257
Columbia (Col-0)	ecb2-3 cotyledon	Mutant	A leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds library	Recessive	The chlorophyll content and photosystem II maximum photochemical efficiency of ecb2-3 are obviously lower than that of Col-0 and its complementation lines, respectively; The chloroplast development of ecb2-3 is also inferior to that of Col-0 and its complementation line at the observed time points using the transmission electron microscope	Cotyledon	7-day-old	PCR and Sanger sequencing; Image J software	93.17%	High	Similar	39579257

Arabidopsis thaliana

AT1G15510

Chloroplast

accD

794

CDS

TAIR (http://www.arabidopsis.org)
NA
TAIR10

NA
TAIR10

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
Ler	ecb2-2	Point mutation	The Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 protein	Homozygous; Recessive	Delayed greening	Leaf	21 days	Direct Sequencing of PCR Products	29.60%	Low	Decreased	21294841
Ler	ecb2-2	Point mutation	The Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 protein	Homozygous; Recessive	Delayed greening	Leaf	21 days	Direct Sequencing of PCR Products	39.90%	Low	Decreased	21294841
Ler	ecb2-2	Point mutation	The Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 protein	Homozygous; Recessive	Delayed greening	Cotyledon	5 days	Direct Sequencing of PCR Products	57.30%	Medium	Decreased	21294841
Ler	ecb2-2	Point mutation	The Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 protein	Homozygous; Recessive	Delayed greening	Leaf	21 days	Direct Sequencing of PCR Products	60.00%	High	Decreased	21294841
Ler	ecb2-2	Point mutation	The Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 protein	Homozygous; Recessive	Delayed greening	Cotyledon	14 days	Direct Sequencing of PCR Products	87.10%	High	Restored	21294841
Ler	WT	Control	Control	No mutant	Normal	Leaf	21 days	Direct Sequencing of PCR Products	95.40%	High	None	21294841
Ler	WT	Control	Control	No mutant	Normal	Leaf	21 days	Direct Sequencing of PCR Products	95.40%	High	None	21294841
Ler	WT	Control	Control	No mutant	Normal	Leaf	21 days	Direct Sequencing of PCR Products	95.40%	High	None	21294841
Ler	WT	Control	Control	No mutant	Normal	Cotyledon	14 days	Direct Sequencing of PCR Products	96.50%	High	None	21294841
Ler	WT	Control	Control	No mutant	Normal	Cotyledon	5 days	Direct Sequencing of PCR Products	98.50%	High	None	21294841
SALK_112251	atecb2	T-DNA Insertion	NA	Knockout	Mutant atecb2 displays albino cotyledons and is seedling lethal	Seedling	14 days	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	19500301
SALK_112251	TC	Complementation	NA	NA	NA	Seedling	14 days	Direct Sequencing of PCR Products	86.20%	High	Restored	19500301
Col-0	WT	Control	Control	No mutant	Normal	Seedling	14 days	Direct Sequencing of PCR Products	89.50%	High	None	19500301
NA	NA	RNA immunoprecipitation analysis	NA	NA	NA	NA	NA	NA	NA	NA	None	28850756
Col-0	AtECB2△E/E+	Complementation	The genomic sequence of AtECB2 lacking the E/E+ domain (AtECB2△E/E+) is introduced into atecb2/+ heterozygous plants	NA	These lines display seedling albino phenotypes similar to that of atecb2	NA	NA	Direct Sequencing of PCR Products	30.00%	Low	Decreased	28850756
Col-0	WT	Control	Control	No mutant	Normal	NA	NA	Direct Sequencing of PCR Products	100.00%	Complete	None	28850756
Columbia (Col-0)	Col-0 leaf	Control	Control	No mutant	Normal	Leaf	21-day-old	PCR and Sanger sequencing; Image J software	99.48%	High	None	39579257
Columbia (Col-0)	ecb2-3 green patches	Mutant	A leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds library	Recessive	The chlorophyll content and photosystem II maximum photochemical efficiency of ecb2-3 are obviously lower than that of Col-0 and its complementation lines, respectively; The chloroplast development of ecb2-3 is also inferior to that of Col-0 and its complementation line at the observed time points using the transmission electron microscope	Patch	21-day-old	PCR and Sanger sequencing; Image J software	45.39%	Medium	Decreased	39579257
Columbia (Col-0)	ecb2-3 yellow patches	Mutant	A leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds library	Recessive	The chlorophyll content and photosystem II maximum photochemical efficiency of ecb2-3 are obviously lower than that of Col-0 and its complementation lines, respectively; The chloroplast development of ecb2-3 is also inferior to that of Col-0 and its complementation line at the observed time points using the transmission electron microscope	Patch	21-day-old	PCR and Sanger sequencing; Image J software	2.45%	Poor	Decreased	39579257
Columbia (Col-0)	Comp leaf	Complementation	For complementation, the 1936 bp promotor and 2601 bp AtECB2 gene were amplified using AtECB2-P-1936-KpnI-F/AtECB2-DNA-403-MluI-R, AtECB2-DNA-398-MluI-F/AtECB2-DNA-2601-PstI-R, and constructed into pP	Recessive	Normal	Leaf	21-day-old	PCR and Sanger sequencing; Image J software	99.48%	High	Restored	39579257
Columbia (Col-0)	Col-0 cotyledon	Control	Control	No mutant	Normal	Cotyledon	7-day-old	PCR and Sanger sequencing; Image J software	95.63%	High	None	39579257
Columbia (Col-0)	ecb2-3 cotyledon	Mutant	A leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds library	Recessive	The chlorophyll content and photosystem II maximum photochemical efficiency of ecb2-3 are obviously lower than that of Col-0 and its complementation lines, respectively; The chloroplast development of ecb2-3 is also inferior to that of Col-0 and its complementation line at the observed time points using the transmission electron microscope	Cotyledon	7-day-old	PCR and Sanger sequencing; Image J software	4.42%	Poor	Decreased	39579257

Arabidopsis thaliana

AT1G15510

Chloroplast

accD

3'UTR

TAIR (http://www.arabidopsis.org)
NA

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
Ler	ecb2-2	Point mutation	The Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 protein	Homozygous; Recessive	Delayed greening	Cotyledon	5 days	Direct Sequencing of PCR Products	NA	Low	Decreased	21294841
Ler	ecb2-2	Point mutation	The Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 protein	Homozygous; Recessive	Delayed greening	Cotyledon	14 days	Direct Sequencing of PCR Products	NA	Medium	Restored	21294841
NA	NA	RNA immunoprecipitation analysis	NA	NA	NA	NA	NA	NA	NA	NA	None	28850756
Col-0	AtECB2△E/E+	Complementation	The genomic sequence of AtECB2 lacking the E/E+ domain (AtECB2△E/E+) is introduced into atecb2/+ heterozygous plants	NA	These lines display seedling albino phenotypes similar to that of atecb2	NA	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	28850756
Col-0	WT	Control	Control	No mutant	Normal	NA	NA	Direct Sequencing of PCR Products	80.00%	High	None	28850756

Arabidopsis thaliana

AT1G15510

Chloroplast

ndhF

290

CDS

TAIR (http://www.arabidopsis.org)
NA
TAIR10

NA
TAIR10

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
Ler	ecb2-2	Point mutation	The Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 protein	Homozygous; Recessive	Delayed greening	Cotyledon	5 days	Direct Sequencing of PCR Products	NA	NA	Decreased	21294841
Ler	ecb2-2	Point mutation	The Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 protein	Homozygous; Recessive	Delayed greening	Cotyledon	14 days	Direct Sequencing of PCR Products	NA	NA	Restored	21294841
NA	NA	RNA immunoprecipitation analysis	NA	NA	NA	NA	NA	NA	NA	NA	None	28850756
Col-0	AtECB2△E/E+	Complementation	The genomic sequence of AtECB2 lacking the E/E+ domain (AtECB2△E/E+) is introduced into atecb2/+ heterozygous plants	NA	These lines display seedling albino phenotypes similar to that of atecb2	NA	NA	Direct Sequencing of PCR Products	30.00%	Low	Decreased	28850756
Col-0	WT	Control	Control	No mutant	Normal	NA	NA	Direct Sequencing of PCR Products	95.00%	High	None	28850756
Columbia (Col-0)	Col-0 leaf	Control	Control	No mutant	Normal	Leaf	21-day-old	PCR and Sanger sequencing; Image J software	95.26%	High	None	39579257
Columbia (Col-0)	ecb2-3 green patches	Mutant	A leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds library	Recessive	The chlorophyll content and photosystem II maximum photochemical efficiency of ecb2-3 are obviously lower than that of Col-0 and its complementation lines, respectively; The chloroplast development of ecb2-3 is also inferior to that of Col-0 and its complementation line at the observed time points using the transmission electron microscope	Patch	21-day-old	PCR and Sanger sequencing; Image J software	74.92%	High	Decreased	39579257
Columbia (Col-0)	ecb2-3 yellow patches	Mutant	A leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds library	Recessive	The chlorophyll content and photosystem II maximum photochemical efficiency of ecb2-3 are obviously lower than that of Col-0 and its complementation lines, respectively; The chloroplast development of ecb2-3 is also inferior to that of Col-0 and its complementation line at the observed time points using the transmission electron microscope	Patch	21-day-old	PCR and Sanger sequencing; Image J software	26.04%	Low	Decreased	39579257
Columbia (Col-0)	Comp leaf	Complementation	For complementation, the 1936 bp promotor and 2601 bp AtECB2 gene were amplified using AtECB2-P-1936-KpnI-F/AtECB2-DNA-403-MluI-R, AtECB2-DNA-398-MluI-F/AtECB2-DNA-2601-PstI-R, and constructed into pP	Recessive	Normal	Leaf	21-day-old	PCR and Sanger sequencing; Image J software	87.00%	High	Restored	39579257
Columbia (Col-0)	Col-0 cotyledon	Control	Control	No mutant	Normal	Cotyledon	7-day-old	PCR and Sanger sequencing; Image J software	85.50%	High	None	39579257
Columbia (Col-0)	ecb2-3 cotyledon	Mutant	A leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds library	Recessive	The chlorophyll content and photosystem II maximum photochemical efficiency of ecb2-3 are obviously lower than that of Col-0 and its complementation lines, respectively; The chloroplast development of ecb2-3 is also inferior to that of Col-0 and its complementation line at the observed time points using the transmission electron microscope	Cotyledon	7-day-old	PCR and Sanger sequencing; Image J software	31.25%	Low	Decreased	39579257

Arabidopsis thaliana

AT1G15510

Chloroplast

ndhG

CDS

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
NA	NA	RNA immunoprecipitation analysis	NA	NA	NA	NA	NA	NA	NA	NA	None	28850756

Arabidopsis thaliana

AT1G15510

Chloroplast

petL

CDS

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
NA	NA	RNA immunoprecipitation analysis	NA	NA	NA	NA	NA	NA	NA	NA	None	28850756

Arabidopsis thaliana

AT1G15510

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
NA	NA	RNA immunoprecipitation analysis	NA	NA	NA	NA	NA	NA	NA	NA	None	28850756

Arabidopsis thaliana

AT1G15510

Chloroplast

rpoC1

488

CDS

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
NA	NA	RNA immunoprecipitation analysis	NA	NA	NA	NA	NA	NA	NA	NA	None	28850756

Last update: Sep 2026 (version 2.0)