ECB2 - Plant Editosome Database

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:	NA
Construct Structure:	PLS-E-E+-DYW
Gene ID & Species:	BraA06g011520.3.5C (Brassica rapa)
Edited Gene(s):	accD ndhF
Editing Type(s):	C-to-U (12)
Publication(s):	NA

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

Brassica rapa

BraA06g011520.3.5C

Plastid

accD

1391

CDS

Brassica genome V3.5

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
136	136	Control; Self-crossing of the inbred line	No treatment	No mutant	Normal	Leaf	20-day-old	Unpurified PCR products were used for Sanger sequencing	86.00%	High	None	NONE
136	M136	A SNP	A T-to-C single nucleotide polymorphism (SNP) in the 4th PPR motif of BrECB2 caused a threonine-to-isoleucine amino acid substitution	Recessive	The young true leaves of ‘M136’ were yellow and gradually turned green with maturation; Chloroplast development, pigment contents, and photosynthetic parameters were impaired and gradually recovered with growth in ‘M136’, and chlorophyll fluorescence parameters were also impaired in ‘M136’	Leaf	20-day-old	Unpurified PCR products were used for Sanger sequencing	51.00%	Medium	Decreased	NONE
136	COM	Functional complementation of ‘M136’	The BrECB2 coding sequence (CDS) was PCR-amplified and subcloned into the pRI101 vector; The construct was transformed into GV3101 and the bacterial solution was cultured until OD600=0.8; The bacteria	Recessive	A green phenotype similar to that of ‘136’	Leaf	20-day-old	Unpurified PCR products were used for Sanger sequencing	67.00%	High	Decreased	NONE
136	T136	A SNP	A T-to-C single nucleotide polymorphism (SNP) in the 4th PPR motif of BrECB2 caused a threonine-to-isoleucine amino acid substitution	Recessive	‘M136’ after the leaves turned green	Leaf	45-day-old	Unpurified PCR products were used for Sanger sequencing	83.00%	High	Restored	NONE

Brassica rapa

BraA06g011520.3.5C

Plastid

accD

782

CDS

Brassica genome V3.5

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
136	136	Control; Self-crossing of the inbred line	No treatment	No mutant	Normal	Leaf	20-day-old	Unpurified PCR products were used for Sanger sequencing	81.00%	High	None	NONE
136	M136	A SNP	A T-to-C single nucleotide polymorphism (SNP) in the 4th PPR motif of BrECB2 caused a threonine-to-isoleucine amino acid substitution	Recessive	The young true leaves of ‘M136’ were yellow and gradually turned green with maturation; Chloroplast development, pigment contents, and photosynthetic parameters were impaired and gradually recovered with growth in ‘M136’, and chlorophyll fluorescence parameters were also impaired in ‘M136’	Leaf	20-day-old	Unpurified PCR products were used for Sanger sequencing	51.00%	Medium	Decreased	NONE
136	COM	Functional complementation of ‘M136’	The BrECB2 coding sequence (CDS) was PCR-amplified and subcloned into the pRI101 vector; The construct was transformed into GV3101 and the bacterial solution was cultured until OD600=0.8; The bacteria	Recessive	A green phenotype similar to that of ‘136’	Leaf	20-day-old	Unpurified PCR products were used for Sanger sequencing	66.00%	High	Decreased	NONE
136	T136	A SNP	A T-to-C single nucleotide polymorphism (SNP) in the 4th PPR motif of BrECB2 caused a threonine-to-isoleucine amino acid substitution	Recessive	‘M136’ after the leaves turned green	Leaf	45-day-old	Unpurified PCR products were used for Sanger sequencing	83.00%	High	Restored	NONE

Brassica rapa

BraA06g011520.3.5C

Plastid

ndhF

290

CDS

Brassica genome V3.5

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
136	136	Control; Self-crossing of the inbred line	No treatment	No mutant	Normal	Leaf	20-day-old	Unpurified PCR products were used for Sanger sequencing	93.00%	High	None	NONE
136	M136	A SNP	A T-to-C single nucleotide polymorphism (SNP) in the 4th PPR motif of BrECB2 caused a threonine-to-isoleucine amino acid substitution	Recessive	The young true leaves of ‘M136’ were yellow and gradually turned green with maturation; Chloroplast development, pigment contents, and photosynthetic parameters were impaired and gradually recovered with growth in ‘M136’, and chlorophyll fluorescence parameters were also impaired in ‘M136’	Leaf	20-day-old	Unpurified PCR products were used for Sanger sequencing	33.00%	Low	Decreased	NONE
136	COM	Functional complementation of ‘M136’	The BrECB2 coding sequence (CDS) was PCR-amplified and subcloned into the pRI101 vector; The construct was transformed into GV3101 and the bacterial solution was cultured until OD600=0.8; The bacteria	Recessive	A green phenotype similar to that of ‘136’	Leaf	20-day-old	Unpurified PCR products were used for Sanger sequencing	50.00%	Medium	Decreased	NONE
136	T136	A SNP	A T-to-C single nucleotide polymorphism (SNP) in the 4th PPR motif of BrECB2 caused a threonine-to-isoleucine amino acid substitution	Recessive	‘M136’ after the leaves turned green	Leaf	45-day-old	Unpurified PCR products were used for Sanger sequencing	91.00%	High	Restored	NONE