OTP82 - Plant Editosome Database

Summary

Editing Factor:	OTP82
Synonym:	EMB3102; EMBRYO DEFECTIVE 3102; ORGANELLE TRANSCRIPT PROCESSING 82
Description:	PPR protein OTP82 is essential for RNA editing of the ndhB-9 and ndhG-1 sites within transcripts encoding subunits of chloroplast NAD(P)H dehydrogenase; Despite the defects in RNA editing, otp82 did not show any phenotypes in NDH activity, stability or interaction with photosystem I, suggesting that the RNA editing events mediated by OTP82 are functionally silent even though they induce amino acid alterations; Recombinant OTP82 specifically bound to the -15 to 0 regions of its target sites; OTP82 and CRR22 act as site-specificity factors at multiple sites in plastids; OTP80, OTP81, OTP85, and OTP86 target only one editing site each, OTP82 two sites, and OTP84 three sites in different transcripts; An analysis of the target sites requiring the five editing factors involved in editing of multiple sites (CRR22, CRR28, CLB19, OTP82, and OTP84) suggests that editing factors can generally distinguish pyrimidines from purines and, at some positions, must be able to recognize specific bases; Each motif recognizes one nucleotide in the RNA target with the protein aligned parallel to the RNA and contiguous motifs aligned with contiguous nucleotides such that the final PPR motif aligns four nucleotides upstream of the edited cytidine
Protein Family:	Pentatricopeptide repeat (PPR) protein
Subclass:	DYW
Physical Interaction:	NA
Construct Structure:	PLS-E-DYW
Gene ID & Species:	AT1G08070 (Arabidopsis thaliana)
Edited Gene(s):	ndhB ndhG
Editing Type(s):	C-to-U (34)
Publication(s):	[1] Multiple PPR Protein Interactions Are Involved in the RNA Editing System in Arabidopsis Mitochondria and Plastids, Proc Natl Acad Sci U S A, 2017. [doi:10.1073/pnas.1705815114] [2] Predictable alteration of sequence recognition by RNA editing factors from Arabidopsis, Plant Cell, 2015. [doi:10.1105/tpc.114.134189] [3] 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. [doi:10.1093/nar/gks164] [4] A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites, Plant Cell, 2009. [doi:10.1105/tpc.109.071472] [5] The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts, The Plant Journal, 2010. [doi:10.1111/j.1365-313X.2009.04059.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

AT1G08070

Chloroplast

ndhB

836

CDS

AP000423
NA

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	No mutant	Normal	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	71.10%	High	None	19845878
Col-0	WT	Control	Control	No mutant	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	No mutant	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

ndhB

CDS

Arabidopsis Genome Initiative

AP000423

Genomic position

95,644

C-to-U

NA=>NA

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
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

Arabidopsis thaliana

AT1G08070

Plastid

ndhB

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
Col-0	Col	Control	Control	No mutant	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

ndhG

CDS

AP000423
NA

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	No mutant	Normal	Leaf	15 days	Poisoned Primer Extension (PPE) Assay	67.20%	High	None	19845878
Col-0	WT	Control	Control	No mutant	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	No mutant	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

ndhG

CDS

Arabidopsis Genome Initiative

AP000423

Genomic position

118,858

C-to-U

NA=>NA

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
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

Arabidopsis thaliana

AT1G08070

Plastid

ndhG

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
Col-0	Col	Control	Control	No mutant	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