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: OTP84 is required for editing three chloroplast sites, and transgenes expressing OTP84 with C-terminal truncations were capable of editing only one of the three cognate sites at high efficiency; These results suggest that the deaminase domain of OTP84 is required for editing two of the sites, but another deaminase is able to supply the deamination activity for the third site; OTP84 and CREF7 transgenes were mutagenized to replace the glutamate residue of the HXE motif, and transgenic plants expressing OTP84-E824A and CREF7-E554A were unable to efficiently edit the cognate editing sites for these genes;
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 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] 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., The 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
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-0WTControlControlControlNormalLeafNABulk 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-0WTControlControlControlNANANARNA-seq92.55%HighNone32098170
Col-0WTControlControlControlNormalLeafNART-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 growthLeafNART-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 growthLeafNART-PCR and calculated with the DNADynamo software (BlueTract100.00%CompleteIncreased28761003
Arabidopsis thaliana AT3G57430 Chloroplast ndhB NA 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-0ControlControlControlNormal growthNANART-PCR products are sequencedNANANone19934379
SAIL_568_C04otp84-1T-DNA insertionThe T-DNA insertion is at +932 in CDSHomozygousNormal growthNANART-PCR products are sequenced0.00%UneditedAbsent19934379
SALK_120902otp84-2T-DNA insertionThe T-DNA insertion is at +642 in CDSHomozygousNormal growthNANART-PCR products are sequenced0.00%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 products are sequencedNANARestored19934379
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-0WTControlControlControlNormalLeafNABulk 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-0WTControlControlControlNANANARNA-seq93.13%HighNone32098170
Col-0WTControlControlControlNormalLeafNART-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 growthLeafNART-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 growthLeafNART-PCR and calculated with the DNADynamo software (BlueTract61.00%HighIncreased28761003
Arabidopsis thaliana AT3G57430 Chloroplast ndhF NA 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-0ControlControlControlNormal growthNANART-PCR products are sequencedNANANone19934379
SAIL_568_C04otp84-1T-DNA insertionThe T-DNA insertion is at +932 in CDSHomozygousNormal growthNANART-PCR products are sequenced0.00%UneditedAbsent19934379
SALK_120902otp84-2T-DNA insertionThe T-DNA insertion is at +642 in CDSHomozygousNormal growthNANART-PCR products are sequenced0.00%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 products are sequencedNANARestored19934379
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-0WTControlControlControlNormalLeafNABulk 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-0WTControlControlControlNANANARNA-seq90.44%HighNone32098170
Col-0WTControlControlControlNormalLeafNART-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 growthLeafNART-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 growthLeafNART-PCR and calculated with the DNADynamo software (BlueTract92.00%HighSimilar28761003
Arabidopsis thaliana AT3G57430 Chloroplast psbZ NA 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-0ControlControlControlNormal growthNANART-PCR products are sequencedNANANone19934379
SAIL_568_C04otp84-1T-DNA insertionThe T-DNA insertion is at +932 in CDSHomozygousNormal growthNANART-PCR products are sequenced0.00%UneditedAbsent19934379
SALK_120902otp84-2T-DNA insertionThe T-DNA insertion is at +642 in CDSHomozygousNormal growthNANART-PCR products are sequenced0.00%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 products are sequencedNANARestored19934379
Last update: Jul 2021 (version 1.0)