Plant Editosome Database
a curated database of RNA editosome in plants

OTP84 - Plant Editosome Database - BIG Data Center
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Summary

Editing Factor: OTP84
Synonym: ORGANELLE TRANSCRIPT PROCESSING 84
Description: Encodes a protein with intact DYW deaminase domain and is required for editing three chloroplast sites.
Protein Family: PPR
Subclass: DYW
Construct Structure: PLS-DYW, PLS-E-DYW, NA
Gene ID & Species: AT3G57430 (Arabidopsis thaliana)
Edited Gene(s): ndhF    psbZ    ndhB
Editing Type(s): C-to-U (45)
Publication(s): [1] The Analysis of the Editing Defects in the dyw2 Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins, Plants (Basel), 2020. [PMID=32098170]
[2] Multiple PPR Protein Interactions Are Involved in the RNA Editing System in Arabidopsis Mitochondria and Plastids, Proc Natl Acad Sci U S A, 2017. [PMID=28761003]
[3] A Conserved Glutamate Residue in the C-terminal Deaminase Domain of Pentatricopeptide Repeat Proteins Is Required for RNA Editing Activity, The Journal of Biological Chemistry, 2015. [PMID=25739442]
[4] A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites, Plant Cell, 2009. [PMID=19934379]

Editing Details

Species Gene ID Organelle Edited Gene Position Region Editing Type Codon Amino Acid Molecular Effect Experiment Details
Arabidopsis thaliana AT3G57430 Chloroplast ndhB null CDS C-to-U NA=>NA 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
Col-0Col-0No treatment No treatmentNo treatmentNormal growthNANART-PCR and poisoned primer extension of RT-PCR products is sNANANone19934379
SAIL_568_C04otp84-1T-DNA insertionThe T-DNA insertion is at +932 in CDSHomozygousNormal growthNANART-PCR and poisoned primer extension of RT-PCR products is s0.00%UneditedAbsent19934379
SALK_120902otp84-2T-DNA insertionThe T-DNA insertion is at +642 in CDSHomozygousNormal growthNANART-PCR and poisoned primer extension of RT-PCR products is s0.00%UneditedAbsent19934379
NAComplementComplementThe 2673 bp fragments containing the coding sequence of OTP80 was amplified by PCR on total cellular DNA. The construct were cloned into pGWB2 binary vectors and introduced into otp mutants via AgrobaHomozygousNANANART-PCR and poisoned primer extension of RT-PCR products is sNANARestored19934379
Arabidopsis thaliana AT3G57430 Chloroplast
Plastid		 ndhB 1481 CDS C-to-U CCA=>CUA
NA=>NA		 P=>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
Col-0WTNo treatmentNo treatmentNo treatmentNo treatmentLeafNABulk SequencingNAHighNone25739442
Col-0OTP84trcDYWTransformationThe truncated variants (OTP84 truncated DYW domain) are introduced into an OTP84 knock-out backgroundNANALeafNABulk SequencingNAHighSimilar25739442
Col-0OTP84trcPGTransformationThe truncated variants (OTP84 truncated PG box and DYW domain) are introduced into an OTP84 knock-out backgroundNANALeafNABulk SequencingNALowDecreased25739442
SALK_142061Cotp84-3T-DNA InsertionT-DNA is inserted in the PLS repeat regionKnockoutNALeafNABulk SequencingNAPoorDecreased25739442
Col-0WT + OTP84TransformationWild type plants with OTP84 transgeneNANALeafNABulk Sequencing100.00%CompleteSimilar25739442
Col-0WT + OTP84-E824ATransformationThe HXE motif of OTP84 is mutagenized to HXA to produce OTP84-E824A, which is introduced into the wild type Col-0 backgroundNANALeafNABulk SequencingNAHighSimilar25739442
SALK_142061CKO + OTP84-E824ATransformationThe HXE motif of OTP84 is mutagenized to HXA to produce OTP84-E824A, which is introduced into OTP84 knock-out line (otp84-3)NANALeafNABulk SequencingNALowDecreased25739442
Col-0WTNo treatmentNo treatmentNo treatmentNANANARNA-seq92.55%HighNone32098170
Col-0WTNo treatmentNo treatmentNo treatmentNormalRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract88.00%HighNone28761003
Col-0DYW2-GFP-OE1Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 geneCol-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 independenNASlow growthRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract100.00%CompleteIncreased28761003
Col-0DYW2-GFP-OE2Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 geneCol-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 independenNASlow growthRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract100.00%CompleteIncreased28761003
Arabidopsis thaliana AT3G57430 Chloroplast ndhF null CDS 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
Col-0Col-0No treatment No treatmentNo treatmentNormal growthNANART-PCR and poisoned primer extension of RT-PCR products is sNANANone19934379
SAIL_568_C04otp84-1T-DNA insertionThe T-DNA insertion is at +932 in CDSHomozygousNormal growthNANART-PCR and poisoned primer extension of RT-PCR products is s0.00%UneditedAbsent19934379
SALK_120902otp84-2T-DNA insertionThe T-DNA insertion is at +642 in CDSHomozygousNormal growthNANART-PCR and poisoned primer extension of RT-PCR products is s0.00%UneditedAbsent19934379
NAComplementComplementThe 2673 bp fragments containing the coding sequence of OTP80 was amplified by PCR on total cellular DNA. The construct were cloned into pGWB2 binary vectors and introduced into otp mutants via AgrobaHomozygousNANANART-PCR and poisoned primer extension of RT-PCR products is sNANARestored19934379
Arabidopsis thaliana AT3G57430 Chloroplast
Plastid		 ndhF 290 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
Col-0WTNo treatmentNo treatmentNo treatmentNo treatmentLeafNABulk Sequencing100.00%CompleteNone25739442
Col-0OTP84trcDYWTransformationThe truncated variants (OTP84 truncated DYW domain) are introduced into an OTP84 knock-out backgroundNANALeafNABulk SequencingNALowDecreased25739442
Col-0OTP84trcPGTransformationThe truncated variants (OTP84 truncated PG box and DYW domain) are introduced into an OTP84 knock-out backgroundNANALeafNABulk SequencingNALowDecreased25739442
SALK_142061Cotp84-3T-DNA InsertionT-DNA is inserted in the PLS repeat regionKnockoutNALeafNABulk SequencingNAPoorDecreased25739442
Col-0WT + OTP84TransformationWild type plants with OTP84 transgeneNANALeafNABulk SequencingNAHighSimilar25739442
Col-0WT + OTP84-E824ATransformationThe HXE motif of OTP84 is mutagenized to HXA to produce OTP84-E824A, which is introduced into the wild type Col-0 backgroundNANALeafNABulk SequencingNAHighSimilar25739442
SALK_142061CKO + OTP84-E824ATransformationThe HXE motif of OTP84 is mutagenized to HXA to produce OTP84-E824A, which is introduced into OTP84 knock-out line (otp84-3)NANALeafNABulk SequencingNAPoorDecreased25739442
Col-0WTNo treatmentNo treatmentNo treatmentNANANARNA-seq93.13%HighNone32098170
Col-0WTNo treatmentNo treatmentNo treatmentNormalRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract48.00%MediumNone28761003
Col-0DYW2-GFP-OE1Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 geneCol-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 independenNASlow growthRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract78.00%HighIncreased28761003
Col-0DYW2-GFP-OE2Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 geneCol-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 independenNASlow growthRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract61.00%HighIncreased28761003
Arabidopsis thaliana AT3G57430 Chloroplast psbZ null CDS 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
Col-0Col-0No treatment No treatmentNo treatmentNormal growthNANART-PCR and poisoned primer extension of RT-PCR products is sNANANone19934379
SAIL_568_C04otp84-1T-DNA insertionThe T-DNA insertion is at +932 in CDSHomozygousNormal growthNANART-PCR and poisoned primer extension of RT-PCR products is s0.00%UneditedAbsent19934379
SALK_120902otp84-2T-DNA insertionThe T-DNA insertion is at +642 in CDSHomozygousNormal growthNANART-PCR and poisoned primer extension of RT-PCR products is s0.00%UneditedAbsent19934379
NAComplementComplementThe 2673 bp fragments containing the coding sequence of OTP80 was amplified by PCR on total cellular DNA. The construct were cloned into pGWB2 binary vectors and introduced into otp mutants via AgrobaHomozygousNANANART-PCR and poisoned primer extension of RT-PCR products is sNANARestored19934379
Arabidopsis thaliana AT3G57430 Chloroplast
Plastid		 psbZ 50 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
Col-0WTNo treatmentNo treatmentNo treatmentNo treatmentLeafNABulk SequencingNAHighNone25739442
Col-0OTP84trcDYWTransformationThe truncated variants (OTP84 truncated DYW domain) are introduced into an OTP84 knock-out backgroundNANALeafNABulk SequencingNALowDecreased25739442
Col-0OTP84trcPGTransformationThe truncated variants (OTP84 truncated PG box and DYW domain) are introduced into an OTP84 knock-out backgroundNANALeafNABulk SequencingNALowDecreased25739442
SALK_142061Cotp84-3T-DNA InsertionT-DNA is inserted in the PLS repeat regionKnockoutNALeafNABulk SequencingNAPoorDecreased25739442
Col-0WT + OTP84TransformationWild type plants with OTP84 transgeneNANALeafNABulk SequencingNAHighSimilar25739442
Col-0WT + OTP84-E824ATransformationThe HXE motif of OTP84 is mutagenized to HXA to produce OTP84-E824A, which is introduced into the wild type Col-0 backgroundNANALeafNABulk SequencingNAHighSimilar25739442
SALK_142061CKO + OTP84-E824ATransformationThe HXE motif of OTP84 is mutagenized to HXA to produce OTP84-E824A, which is introduced into OTP84 knock-out line (otp84-3)NANALeafNABulk SequencingNAPoorDecreased25739442
Col-0WTNo treatmentNo treatmentNo treatmentNANANARNA-seq90.44%HighNone32098170
Col-0WTNo treatmentNo treatmentNo treatmentNormalRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract95.00%HighNone28761003
Col-0DYW2-GFP-OE1Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 geneCol-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 independenNASlow growthRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract92.00%HighSimilar28761003
Col-0DYW2-GFP-OE2Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 geneCol-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 independenNASlow growthRosette leafNART-PCR and calculated with the DNADynamo software (BlueTract92.00%HighSimilar28761003
Last update: Jul 2021 (version 1.0)