OTP84 - Plant Editosome Database

Editing Details

Species

Gene ID

Organelle

Edited Gene

Position

Region

Nuclear Genome

Organelle Genome

Other Position Region

Other Position

Editing Type

Codon

Amino Acid

Molecular Effect

Experiment Details

Arabidopsis thaliana

AT3G57430

Chloroplast
Plastid

ndhB

1481

CDS

NA
EnsemblGenomes (release 39)

NA
BK010421

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-0	WT	Control	Control	Control	Normal	Leaf	NA	Bulk Sequencing	NA	High	None	25739442
Col-0	OTP84trcDYW	Transformation	The truncated variants (OTP84 truncated DYW domain) are introduced into an OTP84 knock-out background	NA	NA	Leaf	NA	Bulk Sequencing	NA	High	Similar	25739442
Col-0	OTP84trcPG	Transformation	The truncated variants (OTP84 truncated PG box and DYW domain) are introduced into an OTP84 knock-out background	NA	NA	Leaf	NA	Bulk Sequencing	NA	Low	Decreased	25739442
SALK_142061C	otp84-3	T-DNA Insertion	T-DNA is inserted in the PLS repeat region	Knockout	NA	Leaf	NA	Bulk Sequencing	NA	Poor	Decreased	25739442
Col-0	WT + OTP84	Transformation	Wild type plants with OTP84 transgene	NA	NA	Leaf	NA	Bulk Sequencing	100.00%	Complete	Similar	25739442
Col-0	WT + OTP84-E824A	Transformation	The HXE motif of OTP84 is mutagenized to HXA to produce OTP84-E824A, which is introduced into the wild type Col-0 background	NA	NA	Leaf	NA	Bulk Sequencing	NA	High	Similar	25739442
SALK_142061C	KO + OTP84-E824A	Transformation	The HXE motif of OTP84 is mutagenized to HXA to produce OTP84-E824A, which is introduced into OTP84 knock-out line (otp84-3)	NA	NA	Leaf	NA	Bulk Sequencing	NA	Low	Decreased	25739442
Col-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	92.55%	High	None	32098170
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	88.00%	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	100.00%	Complete	Increased	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	Increased	28761003

Arabidopsis thaliana

AT3G57430

Chloroplast

ndhB

CDS

Arabidopsis Genome Initiative

AP000423

Genomic position

94,999

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-0	Col-0	Control	Control	Control	Normal growth	NA	NA	RT-PCR products are sequenced	NA	NA	None	19934379
SAIL_568_C04	otp84-1	T-DNA insertion	The T-DNA insertion is at +932 in CDS	Homozygous	Normal growth	NA	NA	RT-PCR products are sequenced	0.00%	Unedited	Absent	19934379
SALK_120902	otp84-2	T-DNA insertion	The T-DNA insertion is at +642 in CDS	Homozygous	Normal growth	NA	NA	RT-PCR products are sequenced	0.00%	Unedited	Absent	19934379
NA	Complement	Complement	The 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 Agroba	Homozygous	NA	NA	NA	RT-PCR products are sequenced	NA	NA	Restored	19934379

Arabidopsis thaliana

AT3G57430

Chloroplast
Plastid

ndhF

290

CDS

NA
EnsemblGenomes (release 39)

NA
BK010421

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-0	WT	Control	Control	Control	Normal	Leaf	NA	Bulk Sequencing	100.00%	Complete	None	25739442
Col-0	OTP84trcDYW	Transformation	The truncated variants (OTP84 truncated DYW domain) are introduced into an OTP84 knock-out background	NA	NA	Leaf	NA	Bulk Sequencing	NA	Low	Decreased	25739442
Col-0	OTP84trcPG	Transformation	The truncated variants (OTP84 truncated PG box and DYW domain) are introduced into an OTP84 knock-out background	NA	NA	Leaf	NA	Bulk Sequencing	NA	Low	Decreased	25739442
SALK_142061C	otp84-3	T-DNA Insertion	T-DNA is inserted in the PLS repeat region	Knockout	NA	Leaf	NA	Bulk Sequencing	NA	Poor	Decreased	25739442
Col-0	WT + OTP84	Transformation	Wild type plants with OTP84 transgene	NA	NA	Leaf	NA	Bulk Sequencing	NA	High	Similar	25739442
Col-0	WT + OTP84-E824A	Transformation	The HXE motif of OTP84 is mutagenized to HXA to produce OTP84-E824A, which is introduced into the wild type Col-0 background	NA	NA	Leaf	NA	Bulk Sequencing	NA	High	Similar	25739442
SALK_142061C	KO + OTP84-E824A	Transformation	The HXE motif of OTP84 is mutagenized to HXA to produce OTP84-E824A, which is introduced into OTP84 knock-out line (otp84-3)	NA	NA	Leaf	NA	Bulk Sequencing	NA	Poor	Decreased	25739442
Col-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	93.13%	High	None	32098170
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	48.00%	Medium	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	78.00%	High	Increased	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	61.00%	High	Increased	28761003

Arabidopsis thaliana

AT3G57430

Chloroplast

ndhF

CDS

Arabidopsis Genome Initiative

AP000423

Genomic position

112,349

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-0	Col-0	Control	Control	Control	Normal growth	NA	NA	RT-PCR products are sequenced	NA	NA	None	19934379
SAIL_568_C04	otp84-1	T-DNA insertion	The T-DNA insertion is at +932 in CDS	Homozygous	Normal growth	NA	NA	RT-PCR products are sequenced	0.00%	Unedited	Absent	19934379
SALK_120902	otp84-2	T-DNA insertion	The T-DNA insertion is at +642 in CDS	Homozygous	Normal growth	NA	NA	RT-PCR products are sequenced	0.00%	Unedited	Absent	19934379
NA	Complement	Complement	The 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 Agroba	Homozygous	NA	NA	NA	RT-PCR products are sequenced	NA	NA	Restored	19934379

Arabidopsis thaliana

AT3G57430

Chloroplast
Plastid

psbZ

CDS

NA
EnsemblGenomes (release 39)

NA
BK010421

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-0	WT	Control	Control	Control	Normal	Leaf	NA	Bulk Sequencing	NA	High	None	25739442
Col-0	OTP84trcDYW	Transformation	The truncated variants (OTP84 truncated DYW domain) are introduced into an OTP84 knock-out background	NA	NA	Leaf	NA	Bulk Sequencing	NA	Low	Decreased	25739442
Col-0	OTP84trcPG	Transformation	The truncated variants (OTP84 truncated PG box and DYW domain) are introduced into an OTP84 knock-out background	NA	NA	Leaf	NA	Bulk Sequencing	NA	Low	Decreased	25739442
SALK_142061C	otp84-3	T-DNA Insertion	T-DNA is inserted in the PLS repeat region	Knockout	NA	Leaf	NA	Bulk Sequencing	NA	Poor	Decreased	25739442
Col-0	WT + OTP84	Transformation	Wild type plants with OTP84 transgene	NA	NA	Leaf	NA	Bulk Sequencing	NA	High	Similar	25739442
Col-0	WT + OTP84-E824A	Transformation	The HXE motif of OTP84 is mutagenized to HXA to produce OTP84-E824A, which is introduced into the wild type Col-0 background	NA	NA	Leaf	NA	Bulk Sequencing	NA	High	Similar	25739442
SALK_142061C	KO + OTP84-E824A	Transformation	The HXE motif of OTP84 is mutagenized to HXA to produce OTP84-E824A, which is introduced into OTP84 knock-out line (otp84-3)	NA	NA	Leaf	NA	Bulk Sequencing	NA	Poor	Decreased	25739442
Col-0	WT	Control	Control	Control	NA	NA	NA	RNA-seq	90.44%	High	None	32098170
Col-0	WT	Control	Control	Control	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	95.00%	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	92.00%	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	92.00%	High	Similar	28761003

Arabidopsis thaliana

AT3G57430

Chloroplast

psbZ

CDS

Arabidopsis Genome Initiative

AP000423

Genomic position

35,800

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-0	Col-0	Control	Control	Control	Normal growth	NA	NA	RT-PCR products are sequenced	NA	NA	None	19934379
SAIL_568_C04	otp84-1	T-DNA insertion	The T-DNA insertion is at +932 in CDS	Homozygous	Normal growth	NA	NA	RT-PCR products are sequenced	0.00%	Unedited	Absent	19934379
SALK_120902	otp84-2	T-DNA insertion	The T-DNA insertion is at +642 in CDS	Homozygous	Normal growth	NA	NA	RT-PCR products are sequenced	0.00%	Unedited	Absent	19934379
NA	Complement	Complement	The 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 Agroba	Homozygous	NA	NA	NA	RT-PCR products are sequenced	NA	NA	Restored	19934379

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
Physical Interaction:	NA
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]

Summary

Editing Details