OTP82 - Plant Editosome Database

Editing Details

Species

Gene ID

Organelle

Edited Gene

Position

Region

Editing Type

Codon

Amino Acid

Molecular Effect

Experiment Details

Arabidopsis thaliana

AT1G08070

Chloroplast
Plastid

ndhB

836

CDS

C-to-U

UCA=>UUA
NA=>NA

S=>L
NA=>NA

Recoding
NA

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Nossen	otp82-1	Ds Insertion	Ds is inserted at site +465 bp	Homozygous	No obvious visible phenotypes	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	0.80%	Poor	Decreased	19845878
Nossen	otp82-1+OTP82	Complementation	Introduction of the wild-type genomic sequence of OTP82	NA	NA	Leaf	15 days	Direct Sequencing of PCR Products	NA	High	Restored	19845878
Nossen	otp82-1+OTP82△DYW	Complementation	A truncated version of OTP82 lacking its DYW motif was introduced into otp82-1	NA	NA	Leaf	15 days	Direct Sequencing of PCR Products	NA	High	Restored	19845878
Nossen	otp82-2	Ds Insertion	Ds is inserted site +793 bp	Homozygous	No obvious visible phenotypes	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	0.10%	Poor	Absent	19845878
SALK_027812	otp82-3	T-DNA Insertion	NA	Homozygous	No obvious visible phenotypes	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19845878
SAIL_851_G04	otp82-4	T-DNA Insertion	NA	Homozygous	No obvious visible phenotypes	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19845878
Nossen	WT	Control	Control	Control	Normal	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	71.10%	High	None	19845878
Col-0	WT	Control	Control	Control	Normal	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	86.30%	High	None	19845878
NA	NA	Gel mobility shift (GMS) assays	NA	NA	NA	NA	NA	NA	NA	NA	NA	22362750
Col-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	87.20%	High	None	32098170
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	96.00%	High	None	28761003
Col-0	DYW2-GFP-OE1	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	97.00%	High	Similar	28761003
Col-0	DYW2-GFP-OE2	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	100.00%	Complete	Similar	28761003

Arabidopsis thaliana

AT1G08070

Chloroplast
Plastid

ndhB

CDS
NA

C-to-U

NA=>NA

S=>L
NA=>NA

Recoding
NA

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
SAIL_851_G04	NA	T-DNA insertion	The T-DNA insertion is in CDS	Homozygous	NA	NA	NA	RT-PCR products are sequenced	NA	NA	None	19934379
Col-0	Col	Control	Control	Control	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	72.00%	High	None	25649437
SALK_027812	OTP82wt	Complemented	otp82 plants transformed with a construct that includes a wild-type copy of OTP82 driven by the same promoter as used to drive expression of the S3[TD] variant.	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	88.83%	High	Restored	25649437
SALK_027812	otp82	A T-DNA insertion	A T-DNA insertion (SALK_027812) in At1g08070	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	1.50%	Poor	Decreased	25649437
SALK_027812	S3[TD]	A T-DNA insertion	A T-DNA insertion (SALK_027812) in At1g08070	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	51.00%	Medium	Decreased	25649437

Arabidopsis thaliana

AT1G08070

Chloroplast
Plastid

ndhG

CDS

C-to-U

UCC=>UUC
NA=>NA

S=>F
NA=>NA

Recoding
NA

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Nossen	otp82-1	Ds Insertion	Ds is inserted at site +465 bp	Homozygous	No obvious visible phenotypes	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	2.40%	Poor	Decreased	19845878
Nossen	otp82-1+OTP82	Complementation	Introduction of the wild-type genomic sequence of OTP82	NA	NA	Leaf	15 days	Direct Sequencing of PCR Products	NA	High	Restored	19845878
Nossen	otp82-1+OTP82△DYW	Complementation	A truncated version of OTP82 lacking its DYW motif was introduced into otp82-1	NA	NA	Leaf	15 days	Direct Sequencing of PCR Products	NA	High	Restored	19845878
Nossen	otp82-2	Ds Insertion	Ds is inserted at site +793 bp	Homozygous	No obvious visible phenotypes	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19845878
SALK_027812	otp82-3	T-DNA Insertion	NA	Homozygous	No obvious visible phenotypes	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19845878
SAIL_851_G04	otp82-4	T-DNA Insertion	NA	Homozygous	No obvious visible phenotypes	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	0.10%	Poor	Absent	19845878
Nossen	WT	Control	Control	Control	Normal	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	67.20%	High	None	19845878
Col-0	WT	Control	Control	Control	Normal	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	78.90%	High	None	19845878
NA	NA	Gel mobility shift (GMS) assays	NA	NA	NA	NA	NA	NA	NA	NA	NA	22362750
Col-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	77.56%	High	None	32098170
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	64.00%	High	None	28761003
Col-0	DYW2-GFP-OE1	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	56.00%	Medium	Similar	28761003
Col-0	DYW2-GFP-OE2	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	81.00%	High	Increased	28761003

Arabidopsis thaliana

AT1G08070

Chloroplast
Plastid

ndhG

CDS
NA

C-to-U

NA=>NA

S=>F
NA=>NA

Recoding
NA

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
SAIL_851_G04	NA	T-DNA insertion	The T-DNA insertion is in CDS	Homozygous	NA	NA	NA	RT-PCR products are sequenced	NA	NA	None	19934379
Col-0	Col	Control	Control	Control	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	69.00%	High	None	25649437
SALK_027812	OTP82wt	Complemented	otp82 plants transformed with a construct that includes a wild-type copy of OTP82 driven by the same promoter as used to drive expression of the S3[TD] variant.	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	79.67%	High	Restored	25649437
SALK_027812	otp82	A T-DNA insertion	A T-DNA insertion (SALK_027812) in At1g08070	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	0.00%	Unedited	Absent	25649437
SALK_027812	S3[TD]	A T-DNA insertion	A T-DNA insertion (SALK_027812) in At1g08070	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	73.83%	High	Similar	25649437

Editing Factor:	OTP82
Synonym:	EMB3102, EMBRYO DEFECTIVE 3102, ORGANELLE TRANSCRIPT PROCESSING 82
Description:	Encoding a factor required for RNA editing of plastid ndhB and ndhG transcripts.
Protein Family:	PPR
Subclass:	DYW
Construct Structure:	PLS-E-DYW, NA
Gene ID & Species:	AT1G08070 (Arabidopsis thaliana)
Edited Gene(s):	ndhB ndhG
Editing Type(s):	C-to-U (36)
Publication(s):	[1] The Analysis of the Editing Defects in the Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins., Plants (Basel, Switzerland), 2020. [PMID=32098170] [2] Multiple PPR protein interactions are involved in the RNA editing system in mitochondria and plastids., Proceedings of the National Academy of Sciences of the United States of America, 2017. [PMID=28761003] [3] Predictable alteration of sequence recognition by RNA editing factors from Arabidopsis., The Plant cell, 2015. [PMID=25649437] [4] A pentatricopeptide repeat protein acts as a site-specificity factor at multiple RNA editing sites with unrelated cis-acting elements in plastids., Nucleic acids research, 2012. [PMID=22362750] [5] A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites., The Plant cell, 2009. [PMID=19934379] [6] The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts., The Plant journal : for cell and molecular biology, 2010. [PMID=19845878]

Plant Editosome Database
a curated database of RNA editosome in plants

Summary

Editing Details