CRR28 - Plant Editosome Database

Summary

Editing Factor:	CRR28
Synonym:	CHLORORESPIRATORY REDUCTION28
Description:	Encodes a PPR-DYW protein with endonuclease activity required for editing of multiple plastid transcripts.
Protein Family:	PPR
Subclass:	DYW
Construct Structure:	PLS-E-DYW
Gene ID & Species:	AT1G59720 (Arabidopsis thaliana)
Edited Gene(s):	ndhB ndhD
Editing Type(s):	C-to-U (30)
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] Expected and unexpected evolution of plant RNA editing factors CLB19, CRR28 and RARE1: retention of CLB19 despite a phylogenetically deep loss of its two known editing targets in Poaceae, BMC Evol Biol, 2018. [PMID=29879897] [3] 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] [4] Quantitative analysis of motifs contributing to the interaction between PLS-subfamily members and their target RNA sequences in plastid RNA editing, Plant J, 2014. [PMID=25279799] [5] Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts, The Plant Cell, 2009. [PMID=19182104]

Editing Details

Species

Gene ID

Organelle

Edited Gene

Position

Region

Editing Type

Codon

Amino Acid

Molecular Effect

Experiment Details

Arabidopsis thaliana

AT1G59720

Plastid

ndhB

null

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	No treatment	NA	NA	NA	NA	NA	NA	NA	25279799

Arabidopsis thaliana

AT1G59720

Chloroplast
Plastid

ndhB

467

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-0	Col-0	No treatment	No treatment	No treatment	No treatment	Leaf	4 weeks	Poisoned Primer Extension (PPE) Assay	100.00%	Complete	None	19182104
Ler	crr28-1	Ds Insertion	NA	Recessive mutation	Impaired NDH activity	Leaf	4 weeks	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19182104
Ler	crr28-1+CRR28DYW2	Complementation	crr28-1 is transformed with CRR28, in which the DYW motif is replaced by that of CRR2	NA	NA	Leaf	4 weeks	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	19182104
Ler	crr28-1+CRR28DYW22	Complementation	crr28-1 is transformed with CRR28, in which the DYW motif is replaced by that of CRR22	NA	NA	Leaf	4 weeks	Direct Sequencing of PCR Products	100.00%	Complete	Restored	19182104
Ler	crr28-1+CRR28ΔDYW	Complementation	crr28-1 is transformed with CRR28 lacking the DYW motif	NA	NA	Leaf	4 weeks	Direct Sequencing of PCR Products	100.00%	Complete	Restored	19182104
Ler	crr28-1+CRR28ΔE/DYW	Complementation	crr28-1 is transformed with CRR28 lacking the E and DYW motifs	NA	NA	Leaf	4 weeks	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	19182104
SALK_115133	crr28-2	T-DNA Insertion	NA	NA	Impaired NDH activity	Leaf	4 weeks	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19182104
SALK_012455	crr28-3	T-DNA Insertion	NA	NA	Impaired NDH activity	Leaf	4 weeks	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19182104
Ler	Ler	No treatment	No treatment	No treatment	No treatment	Leaf	4 weeks	Poisoned Primer Extension (PPE) Assay	100.00%	Complete	None	19182104
NA	NA	No treatment	No treatment	No treatment	NA	NA	NA	NA	NA	NA	None	29879897
Col-0	WT	No treatment	No treatment	No treatment	NA	NA	NA	RNA-seq	87.52%	High	None	32098170
Col-0	WT	No treatment	No treatment	No treatment	Normal	Rosette leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	82.00%	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	Rosette leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	99.00%	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	Rosette leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	99.00%	High	Increased	28761003

Arabidopsis thaliana

AT1G59720

Plastid

ndhD

null

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	No treatment	NA	NA	NA	NA	NA	NA	NA	25279799

Arabidopsis thaliana

AT1G59720

Chloroplast
Plastid

ndhD

878

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-0	Col-0	No treatment	No treatment	No treatment	No treatment	Leaf	4 weeks	Poisoned Primer Extension (PPE) Assay	100.00%	Complete	None	19182104
Ler	crr28-1	Ds Insertion	NA	Recessive mutation	Impaired NDH activity	Leaf	4 weeks	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19182104
Ler	crr28-1+CRR28DYW2	Complementation	crr28-1 is transformed with CRR28, in which the DYW motif is replaced by that of CRR2	NA	NA	Leaf	4 weeks	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	19182104
Ler	crr28-1+CRR28DYW22	Complementation	crr28-1 is transformed with CRR28, in which the DYW motif is replaced by that of CRR22	NA	NA	Leaf	4 weeks	Direct Sequencing of PCR Products	100.00%	Complete	Restored	19182104
Ler	crr28-1+CRR28ΔDYW	Complementation	crr28-1 is transformed with CRR28 lacking the DYW motif	NA	NA	Leaf	4 weeks	Direct Sequencing of PCR Products	100.00%	Complete	Restored	19182104
Ler	crr28-1+CRR28ΔE/DYW	Complementation	crr28-1 is transformed with CRR28 lacking the E and DYW motifs	NA	NA	Leaf	4 weeks	Direct Sequencing of PCR Products	0.00%	Unedited	Absent	19182104
SALK_115133	crr28-2	T-DNA Insertion	NA	NA	Impaired NDH activity	Leaf	4 weeks	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19182104
SALK_012455	crr28-3	T-DNA Insertion	NA	NA	Impaired NDH activity	Leaf	4 weeks	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19182104
Ler	Ler	No treatment	No treatment	No treatment	No treatment	Leaf	4 weeks	Poisoned Primer Extension (PPE) Assay	100.00%	Complete	None	19182104
NA	NA	No treatment	No treatment	No treatment	NA	NA	NA	NA	NA	NA	None	29879897
Col-0	WT	No treatment	No treatment	No treatment	NA	NA	NA	RNA-seq	83.91%	High	None	32098170
Col-0	WT	No treatment	No treatment	No treatment	Normal	Rosette 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	Rosette 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	Rosette leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	100.00%	Complete	Increased	28761003