RID4 - Plant Editosome Database

Summary

Editing Factor:	RID4
Synonym:	Root Initiation Defective 4
Description:	Through analysis of temperature-dependent fasciation (TDF) mutants of Arabidopsis, root redifferentiation defective 1 (rrd1), rrd2, and root initiation defective 4 (rid4), that mitochondrial RNA processing is required for limiting cell division during early lateral root (LR) organogenesis; Further analysis suggested that LR fasciation in the TDF mutants is triggered by reactive oxygen species generation caused by defective mitochondrial respiration; Defective protein composition of the mitochondrial electron transport chain was found in rrd2 and rid4; Phenocopying of the TDF mutants by mitochondrial respiratory inhibition and reactive oxygen species (ROS) induction, together with its reversal by ROS scavenging, suggested that ROS generation resulting from impaired RNA processing is the primary cause of the extra cell division observed during early LR development in the TDF mutants
Protein Family:	PPR
Subclass:	E+
Physical Interaction:	NA
Construct Structure:	PLS-E1-E2-E+
Gene ID & Species:	AT2G33680 (Arabidopsis thaliana)
Edited Gene(s):	atp4 rpl5 rps3 rps4
Editing Type(s):	C-to-U (10)
Publication(s):	[1] Temperature-dependent fasciation mutants provide a link between mitochondrial RNA processing and lateral root morphogenesis., eLife, 2021. [PMID=33443014]

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

AT2G33680

Mitochondrion

atp4

395

CDS

C-to-U

UCA=>UUA

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
Ler	WT	Under high-temperature conditions	Lateral roots (LRs) were induced at 28°C for 12 hr	No mutant	Normal	Root	NA	Sequencing PCR products	100.00%	Complete	None	33443014
Ler	rid4-1	Under high-temperature conditions; Temperature-dependent fasciation (TDF) mutants	Lateral roots (LRs) were induced at 28°C for 12 hr	NA	Lateral root (LR) fasciation as well as retarded seedling growth at high-temperature conditions	Root	NA	Sequencing PCR products	0.00%	Unedited	Absent	33443014

Arabidopsis thaliana

AT2G33680

Mitochondrion

rpl5

58, 59

CDS

C-to-U

CCG=>UUG

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
Ler	WT	Under high-temperature conditions	Lateral roots (LRs) were induced at 28°C for 12 hr	No mutant	Normal	Root	NA	Sequencing PCR products	50.00%, 76	Medium, Hi	None	33443014
Ler	rid4-1	Under high-temperature conditions; Temperature-dependent fasciation (TDF) mutants	Lateral roots (LRs) were induced at 28°C for 12 hr	NA	Lateral root (LR) fasciation as well as retarded seedling growth at high-temperature conditions	Root	NA	Sequencing PCR products	0.00%, 0.0	Unedited,	Absent, Ab	33443014

Arabidopsis thaliana

AT2G33680

Mitochondrion

rps3

1344

CDS

C-to-U

AGC=>AGU

S=>S

Synonymous

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Ler	WT	Under high-temperature conditions	Lateral roots (LRs) were induced at 28°C for 12 hr	No mutant	Normal	Root	NA	Sequencing PCR products	31.43%	Low	None	33443014
Ler	rid4-1	Under high-temperature conditions; Temperature-dependent fasciation (TDF) mutants	Lateral roots (LRs) were induced at 28°C for 12 hr	NA	Lateral root (LR) fasciation as well as retarded seedling growth at high-temperature conditions	Root	NA	Sequencing PCR products	0.00%	Unedited	Absent	33443014

Arabidopsis thaliana

AT2G33680

Mitochondrion

rps4

332

CDS

C-to-U

CCG=>CUG

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
Ler	WT	Under high-temperature conditions	Lateral roots (LRs) were induced at 28°C for 12 hr	No mutant	Normal	Root	NA	Sequencing PCR products	69.23%	High	None	33443014
Ler	rid4-1	Under high-temperature conditions; Temperature-dependent fasciation (TDF) mutants	Lateral roots (LRs) were induced at 28°C for 12 hr	NA	Lateral root (LR) fasciation as well as retarded seedling growth at high-temperature conditions	Root	NA	Sequencing PCR products	0.00%	Unedited	Absent	33443014

Arabidopsis thaliana

AT2G33680

Mitochondrion

rps4

CDS

C-to-U

UCA=>UUA

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
Ler	WT	Under high-temperature conditions	Lateral roots (LRs) were induced at 28°C for 12 hr	No mutant	Normal	Root	NA	Sequencing PCR products	68.57%	High	None	33443014
Ler	rid4-1	Under high-temperature conditions; Temperature-dependent fasciation (TDF) mutants	Lateral roots (LRs) were induced at 28°C for 12 hr	NA	Lateral root (LR) fasciation as well as retarded seedling growth at high-temperature conditions	Root	NA	Sequencing PCR products	0.00%	Unedited	Absent	33443014