ECB2 - Plant Editosome Database - BIG Data Center

Summary

Editing Factor: ECB2
Synonym: ARABIDOPSIS EARLY CHLOROPLAST BIOGENESIS2, ATECB2, EARLY CHLOROPLAST BIOGENESIS2, VAC1, VANILLA CREAM 1, AtECB2
Description: Encodes a pentatricopeptide repeat protein required for chloroplast transcript accD RNA editing and early chloroplast biogenesis.
Protein Family: PPR
Subclass: DYW
Construct Structure: PLS-E-DYW, 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 reports, 2024. [PMID=39579257]
[2] Porphobilinogen deaminase HEMC interacts with the PPR-protein AtECB2 for chloroplast RNA editing., The Plant journal : for cell and molecular biology, 2017. [PMID=28850756]
[3] A point mutation in the pentatricopeptide repeat motif of the AtECB2 protein causes delayed chloroplast development., Journal of integrative plant biology, 2011. [PMID=21294841]
[4] AtECB2, a pentatricopeptide repeat protein, is required for chloroplast transcript accD RNA editing and early chloroplast biogenesis in Arabidopsis thaliana., The Plant journal : for cell and molecular biology, 2009. [PMID=19500301]

Editing Details

Species Gene ID Organelle Edited Gene Position Region Editing Type Codon Amino Acid Molecular Effect Experiment Details
Arabidopsis thaliana At1g15510 Chloroplast accD 1568 3'UTR C-to-U NA=>NA 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 leafControlControlNo mutantNormalLeaf21-day-oldPCR and Sanger sequencing; Image J software99.58%HighNone39579257
Columbia (Col-0)ecb2-3 green patchesMutantA leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds libraryRecessiveThe 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 microscopePatch21-day-oldPCR and Sanger sequencing; Image J software97.71%HighSimilar39579257
Columbia (Col-0)ecb2-3 yellow patchesMutantA leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds libraryRecessiveThe 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 microscopePatch21-day-oldPCR and Sanger sequencing; Image J software46.90%MediumDecreased39579257
Columbia (Col-0)Comp leafComplementationFor 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 pPRecessiveNormalLeaf21-day-oldPCR and Sanger sequencing; Image J software99.58%HighRestored39579257
Columbia (Col-0)Col-0 cotyledonControlControlNo mutantNormalCotyledon7-day-oldPCR and Sanger sequencing; Image J software99.42%HighNone39579257
Columbia (Col-0)ecb2-3 cotyledonMutantA leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds libraryRecessiveThe 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 microscopeCotyledon7-day-oldPCR and Sanger sequencing; Image J software93.17%HighSimilar39579257
Arabidopsis thaliana AT1G15510 Chloroplast accD 794 CDS 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
Lerecb2-2Point mutationThe Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 proteinA weak allelic mutantDelayed greeningLeaf21 daysDirect Sequencing of PCR Products29.60%LowDecreased21294841
Lerecb2-2Point mutationThe Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 proteinA weak allelic mutantDelayed greeningLeaf21 daysDirect Sequencing of PCR Products39.90%LowDecreased21294841
Lerecb2-2Point mutationThe Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 proteinA weak allelic mutantDelayed greeningCotyledon5 daysDirect Sequencing of PCR Products57.30%MediumDecreased21294841
Lerecb2-2Point mutationThe Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 proteinA weak allelic mutantDelayed greeningLeaf21 daysDirect Sequencing of PCR Products60.00%HighDecreased21294841
Lerecb2-2Point mutationThe Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 proteinA weak allelic mutantDelayed greeningCotyledon14 daysDirect Sequencing of PCR Products87.10%HighRestored21294841
LerWTControlControlControlNormalLeaf21 daysDirect Sequencing of PCR Products95.40%HighNone21294841
LerWTControlControlControlNormalLeaf21 daysDirect Sequencing of PCR Products95.40%HighNone21294841
LerWTControlControlControlNormalLeaf21 daysDirect Sequencing of PCR Products95.40%HighNone21294841
LerWTControlControlControlNormalCotyledon14 daysDirect Sequencing of PCR Products96.50%HighNone21294841
LerWTControlControlControlNormalCotyledon5 daysDirect Sequencing of PCR Products98.50%HighNone21294841
SALK_112251atecb2T-DNA InsertionNAKnockoutMutant atecb2 displays albino cotyledons and is seedling lethalSeedling14 daysDirect Sequencing of PCR Products0.00%UneditedAbsent19500301
SALK_112251TCComplementationNANANASeedling14 daysDirect Sequencing of PCR Products86.20%HighRestored19500301
Col-0WTControlControlControlNormalSeedling14 daysDirect Sequencing of PCR Products89.50%HighNone19500301
NANARNA immunoprecipitation analysisNANANANANANANANANone28850756
Col-0AtECB2△E/E+ComplementationThe genomic sequence of AtECB2 lacking the E/E+ domain (AtECB2△E/E+) is introduced into atecb2/+ heterozygous plantsNAThese lines display seedling albino phenotypes similar to that of atecb2NANADirect Sequencing of PCR Products30.00%LowDecreased28850756
Col-0WTControlControlControlNormalNANADirect Sequencing of PCR Products100.00%CompleteNone28850756
Columbia (Col-0)Col-0 leafControlControlNo mutantNormalLeaf21-day-oldPCR and Sanger sequencing; Image J software99.48%HighNone39579257
Columbia (Col-0)ecb2-3 green patchesMutantA leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds libraryRecessiveThe 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 microscopePatch21-day-oldPCR and Sanger sequencing; Image J software45.39%MediumDecreased39579257
Columbia (Col-0)ecb2-3 yellow patchesMutantA leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds libraryRecessiveThe 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 microscopePatch21-day-oldPCR and Sanger sequencing; Image J software2.45%PoorDecreased39579257
Columbia (Col-0)Comp leafComplementationFor 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 pPRecessiveNormalLeaf21-day-oldPCR and Sanger sequencing; Image J software99.48%HighRestored39579257
Columbia (Col-0)Col-0 cotyledonControlControlNo mutantNormalCotyledon7-day-oldPCR and Sanger sequencing; Image J software95.63%HighNone39579257
Columbia (Col-0)ecb2-3 cotyledonMutantA leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds libraryRecessiveThe 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 microscopeCotyledon7-day-oldPCR and Sanger sequencing; Image J software4.42%PoorDecreased39579257
Arabidopsis thaliana AT1G15510 Chloroplast accD NA 3'UTR C-to-U NA=>NA NA=>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
Lerecb2-2Point mutationThe Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 proteinA weak allelic mutantDelayed greeningCotyledon5 daysDirect Sequencing of PCR ProductsNALowDecreased21294841
Lerecb2-2Point mutationThe Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 proteinA weak allelic mutantDelayed greeningCotyledon14 daysDirect Sequencing of PCR ProductsNAMediumRestored21294841
NANARNA immunoprecipitation analysisNANANANANANANANANone28850756
Col-0AtECB2△E/E+ComplementationThe genomic sequence of AtECB2 lacking the E/E+ domain (AtECB2△E/E+) is introduced into atecb2/+ heterozygous plantsNAThese lines display seedling albino phenotypes similar to that of atecb2NANADirect Sequencing of PCR Products0.00%UneditedAbsent28850756
Col-0WTControlControlControlNormalNANADirect Sequencing of PCR Products80.00%HighNone28850756
Arabidopsis thaliana AT1G15510 Chloroplast ndhF 290 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
Lerecb2-2Point mutationThe Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 proteinA weak allelic mutantDelayed greeningCotyledon5 daysDirect Sequencing of PCR ProductsNANADecreased21294841
Lerecb2-2Point mutationThe Thr500 is converted to Ile500 in the 13th PPR motif of the atECB2 proteinA weak allelic mutantDelayed greeningCotyledon14 daysDirect Sequencing of PCR ProductsNANARestored21294841
NANARNA immunoprecipitation analysisNANANANANANANANANone28850756
Col-0AtECB2△E/E+ComplementationThe genomic sequence of AtECB2 lacking the E/E+ domain (AtECB2△E/E+) is introduced into atecb2/+ heterozygous plantsNAThese lines display seedling albino phenotypes similar to that of atecb2NANADirect Sequencing of PCR Products30.00%LowDecreased28850756
Col-0WTControlControlControlNormalNANADirect Sequencing of PCR Products95.00%HighNone28850756
Columbia (Col-0)Col-0 leafControlControlNo mutantNormalLeaf21-day-oldPCR and Sanger sequencing; Image J software95.26%HighNone39579257
Columbia (Col-0)ecb2-3 green patchesMutantA leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds libraryRecessiveThe 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 microscopePatch21-day-oldPCR and Sanger sequencing; Image J software74.92%HighDecreased39579257
Columbia (Col-0)ecb2-3 yellow patchesMutantA leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds libraryRecessiveThe 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 microscopePatch21-day-oldPCR and Sanger sequencing; Image J software26.04%LowDecreased39579257
Columbia (Col-0)Comp leafComplementationFor 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 pPRecessiveNormalLeaf21-day-oldPCR and Sanger sequencing; Image J software87.00%HighRestored39579257
Columbia (Col-0)Col-0 cotyledonControlControlNo mutantNormalCotyledon7-day-oldPCR and Sanger sequencing; Image J software85.50%HighNone39579257
Columbia (Col-0)ecb2-3 cotyledonMutantA leaf virescence mutant firstly named 27–27 was screened from EMS mutated Col-0 M2 seeds libraryRecessiveThe 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 microscopeCotyledon7-day-oldPCR and Sanger sequencing; Image J software31.25%LowDecreased39579257
Arabidopsis thaliana AT1G15510 Chloroplast ndhG 50 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
NANARNA immunoprecipitation analysisNANANANANANANANANone28850756
Arabidopsis thaliana AT1G15510 Chloroplast petL 5 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
NANARNA immunoprecipitation analysisNANANANANANANANANone28850756
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
NANARNA immunoprecipitation analysisNANANANANANANANANone28850756
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
NANARNA immunoprecipitation analysisNANANANANANANANANone28850756
Last update: Jul 2021 (version 1.0)