CRR4 - Plant Editosome Database

Editing Details

Species

Gene ID

Organelle

Edited Gene

Position

Region

Editing Type

Codon

Amino Acid

Molecular Effect

Experiment Details

Aethionema cordifolium

Chloroplast

ndhD

CDS

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
NA	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	50.00%	Medium	NA	22583633

Aethionema grandiflorum

JF521842

Chloroplast

ndhD

CDS

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
NA	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	50.00%	Medium	NA	22583633

Arabidopsis thaliana

AT2G45350

Chloroplast
Plastid

ndhD

CDS

C-to-U

ACG=>AUG
NA=>NA

T=>M
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	crr4-3	NA	NA	NA	NA	Leaf	4 weeks	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	18824480
Col-0	crr4-3+NsylCRR4	Heterogous Complementationation	NA	NA	NA	Leaf	4 weeks	Direct Sequencing of PCR Products	40.00%	Medium	Decreased	18824480
Col-0	crr4-3+NtomCRR4	Heterogous Complementationation	NA	NA	NA	Leaf	4 weeks	Direct Sequencing of PCR Products	21.00%	Low	Decreased	18824480
Col-0	WT	No treatment	No treatment	No treatment	No treatment	Leaf	4 weeks	Direct Sequencing of PCR Products	58.00%	Medium	None	18824480
NA	35S::CRR4 line	Overexpression	CRR4 is overexpressed under the control of the 35S promoter	Upregulation of CRR4 expression in the RNA level	NA	Root	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Restored	15662426
NA	35S::CRR4 line	Overexpression	CRR4 is overexpressed under the control of the 35S promoter	Upregulation of CRR4 expression in the RNA level	NA	Seedling	NA	Gel	NA	Low	Restored	15662426
NA	35S::CRR4 line	Overexpression	CRR4 is overexpressed under the control of the 35S promoter	Upregulation of CRR4 expression in the RNA level	NA	Leaf	NA	Gel	NA	Low	Restored	15662426
NA	crr4-1	NA	NA	NA	Impaired in NDH activity and lacking post-illumination increase in chlorophyll fluorescence	Leaf	NA	Direct Sequencing of PCR Products	0.90%	Poor	Decreased	15662426
NA	crr4-2	NA	NA	NA	NA	Leaf	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Decreased	15662426
NA	crr4-3	NA	NA	Knockout	NA	Leaf	NA	Direct Sequencing of PCR Products	0.00%	Unedited	Decreased	15662426
NA	crr4-4	NA	NA	NA	NA	Leaf	NA	Direct Sequencing of PCR Products	2.80%	Poor	Decreased	15662426
NA	WT	No treatment	No treatment	No treatment	No treatment	Root	NA	Direct Sequencing of PCR Products	0.00%	Unedited	None	15662426
NA	WT	No treatment	No treatment	No treatment	No treatment	Leaf	NA	Direct Sequencing of PCR Products	48.00%	Medium	None	15662426
NA	WT	No treatment	No treatment	No treatment	No treatment	Seedling	NA	Gel	NA	Low	None	15662426
Col-0	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	30.00%	Low	NA	22583633
Col-0	WT	No treatment	No treatment	No treatment	NA	NA	NA	RNA-seq	32.97%	Low	None	32098170
Col-0	WT	No treatment	No treatment	No treatment	Normal	Rosette leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	26.00%	Low	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	Rosette leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	37.00%	Low	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	Rosette leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	46.00%	Medium	Increased	28761003

Arabis hirsuta

JF521843

Chloroplast

ndhD

CDS

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
SJO02300	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	40.00%	Medium	NA	22583633

Barbarea verna

JF521844

Chloroplast

ndhD

CDS

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
NA	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	40.00%	Medium	NA	22583633

Brassica oleracea

JF521845

Chloroplast

ndhD

CDS

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
NA	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	60.00%	High	NA	22583633

Brassica rapa

JF521846

Chloroplast

ndhD

CDS

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
NA	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	30.00%	Low	NA	22583633

Capsella bursa-pastoris

JF521847

Chloroplast

ndhD

CDS

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
Serial # 0051714	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	80.00%	High	NA	22583633

Crucihimalaya wallichii

JF521848

Chloroplast

ndhD

CDS

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
SJS00500	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	60.00%	High	NA	22583633

Draba nemorosa

JF521849

Chloroplast

ndhD

CDS

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
SJO02100	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	40.00%	Medium	NA	22583633

Hesperis matronalis

Chloroplast

ndhD

CDS

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
PI 586611	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	60.00%	High	NA	22583633

Iberis amara

Chloroplast

ndhD

CDS

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
PI 633243	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	70.00%	High	NA	22583633

Isatis tinctoria

Chloroplast

ndhD

CDS

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
NA	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	30.00%	Low	NA	22583633

Lepidium sativum

JF521850

Chloroplast

ndhD

CDS

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
NA	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	50.00%	Medium	NA	22583633

Lepidium virginicum

JF521851

Chloroplast

ndhD

CDS

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
SJO02600	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	50.00%	Medium	NA	22583633

Lobularia maritima

JF521852

Chloroplast

ndhD

CDS

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
NA	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	50.00%	Medium	NA	22583633

Matthiola incana

JF521853

Chloroplast

ndhD

CDS

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
NA	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	70.00%	High	NA	22583633

Nasturtium officinale

JF521854

Chloroplast

ndhD

CDS

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
Serial #0200327	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	10.00%	Poor	NA	22583633

Nicotiana sylvestris

Chloroplast

ndhD

CDS

C-to-U

ACG=>AUG

T=>M

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Nicotiana sylvestris	WT	No treatment	No treatment	No treatment	No treatment	Leaf	6 weeks	Direct Sequencing of PCR Products	37.00%	Low	None	18824480

Nicotiana tabacum

Chloroplast

ndhD

CDS

C-to-U

ACG=>AUG

T=>M

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Nicotiana tabacum	WT	No treatment	No treatment	No treatment	No treatment	Leaf	6 weeks	Direct Sequencing of PCR Products	42.00%	Medium	None	18824480

Nicotiana tomentosiformis

LOC104119586

Chloroplast

ndhD

CDS

C-to-U

ACG=>AUG

T=>M

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Nicotiana tabacum (L. var. Xanthi)	WT	No treatment	No treatment	No treatment	No treatment	Leaf	6 weeks	Direct Sequencing of PCR Products	15.00%	Poor	None	18824480

Olimarabidopsis pumila

JF521855

Chloroplast

ndhD

CDS

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
SJS00200	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	70.00%	High	NA	22583633

Raphanus sativus

JF521856

Chloroplast

ndhD

CDS

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
NA	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	50.00%	Medium	NA	22583633

Thlaspi arvense

Chloroplast

ndhD

CDS

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
Ames 29531	NA	NA	NA	NA	NA	Leaf	NA	PCR amplification and bulk sequencing	20.00%	Low	NA	22583633

Editing Factor:	CRR4
Synonym:	CHLORORESPIRATORY REDUCTION 4
Description:	Encodes a protein involved in RNA editing of ndhD in the chloroplast.
Protein Family:	PPR
Subclass:	E+
Construct Structure:	PLS-E-E+
Gene ID & Species:	NA (Aethionema cordifolium) JF521842 (Aethionema grandiflorum) AT2G45350 (Arabidopsis thaliana) JF521843 (Arabis hirsuta) JF521844 (Barbarea verna) JF521845 (Brassica oleracea) JF521846 (Brassica rapa) pastoris (Capsella bursa) JF521848 (Crucihimalaya wallichii) JF521849 (Draba nemorosa) NA (Hesperis matronalis) NA (Iberis amara) NA (Isatis tinctoria) JF521850 (Lepidium sativum) JF521851 (Lepidium virginicum) JF521852 (Lobularia maritima) JF521853 (Matthiola incana) JF521854 (Nasturtium officinale) NA (Nicotiana sylvestris) NA (Nicotiana tabacum) LOC104119586 (Nicotiana tomentosiformis) JF521855 (Olimarabidopsis pumila) JF521856 (Raphanus sativus) NA (Thlaspi arvense)
Edited Gene(s):	ndhD
Editing Type(s):	C-to-U (42)
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] Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures, BMC Evol Biol, 2012. [PMID=22583633] [4] Amino acid sequence variations in Nicotiana CRR4 orthologs determine the species-specific efficiency of RNA editing in plastids, Nucleic Acids Research, 2008. [PMID=18824480] [5] A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts, Nature, 2005. [PMID=15662426]

Plant Editosome Database
a curated database of RNA editosome in plants

Summary

Editing Details