RARE1 - Plant Editosome Database

Summary

Editing Factor:	RARE1
Synonym:	REQUIRED FOR ACCD RNA EDITING 1
Description:	RARE1 that is required for editing of the chloroplast accD transcript; The accD gene encodes the beta carboxyltransferase subunit of acetyl coA carboxylase, which catalyzes the first step in fatty acid biosynthesis in chloroplasts; Despite a lack of accD C794 editing and lack of restoration of an evolutionarily conserved leucine residue in the beta carboxyltransferase protein, rare1 mutants are unexpectedly robust and reproduce under growth room conditions; An Arabidopsis rare1 mutant with abolished accD-C794 editing and discovered that it exhibits a yellow and dwarf phenotype compared with the wild type under heat stress; Loss of accD-C794 editing results in a yellow and dwarf phenotype with decreased chloroplast gene expression under heat stress, and artificial improvement of C794-edited accD gene expression enhances heat tolerance in Arabidopsis; These observations indicate that defective accD-C794 editing may be intrinsic to reduced ACCase activity, thereby contributing to heat sensitivity; These results provide the first evidence that accD-C794 editing regulates FA biosynthesis for maintenance of membrane structural homeostasis under heat stress
Protein Family:	Pentatricopeptide repeat (PPR) protein
Subclass:	DYW
Physical Interaction:	NA
Construct Structure:	PLS-E-E+-DYW
Gene ID & Species:	AT5G13270 (Arabidopsis thaliana)
Edited Gene(s):	accD
Editing Type(s):	C-to-U (23)
Publication(s):	[1] The PPR protein RARE1-mediated editing of chloroplast accD transcripts is required for fatty acid biosynthesis and heat tolerance in Arabidopsis, Plant Commun, 2023. [doi:10.1016/j.xplc.2022.100461] [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. [doi:10.1073/pnas.1705815114] [3] A comparative genomics approach identifies a PPR-DYW protein that is essential for C-to-U editing of the Arabidopsis chloroplast accD transcript, RNA, 2009. [doi:10.1261/rna.1533909]

Editing Details

Species

Gene ID

Organelle

Edited Gene

Position

Region

Nuclear Genome

Organelle Genome

Other Region

Other Position

Editing Type

Codon

Amino Acid

Molecular Effect

Experiment Details

Arabidopsis thaliana

AT5G13270

Chloroplast

accD

794

CDS

C-to-U

UCG=>UUG
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
WS-4, FLAG_424E06	FLAG_424E06	T-DNA Insertion	T-DNA is inserted in the promoter (-78)	Homozygous	Normal appearance	Leaf	NA	Poisoned Primer Extension (PPE) Assay	NA	NA	Decreased	19395655
WS-4, FLAG_424E06	FLAG_424E06	T-DNA Insertion	T-DNA is inserted in the promoter (-78)	Heterozygous	Normal appearance	Leaf	NA	Poisoned Primer Extension (PPE) Assay	NA	NA	Similar	19395655
WS-4	FLAG_424E06	Control	Control	No mutant	Normal	Leaf	NA	Poisoned Primer Extension (PPE) Assay	NA	NA	None	19395655
GABI_167A04	GABI_167A04	T-DNA Insertion	T-DNA is inserted at 269 base pairs (bp) downstream from the start codon	Homozygous	Normal appearance	Leaf	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19395655
GABI_167A04	GABI_167A04	T-DNA Insertion	T-DNA is inserted at 269 base pairs (bp) downstream from the start codon	Heterozygous	Normal appearance	Leaf	NA	Poisoned Primer Extension (PPE) Assay	100.00%	Complete	Restored	19395655
GABI_167A04	GABI_167A04	Control	Control	No mutant	Normal	Leaf	NA	Poisoned Primer Extension (PPE) Assay	100.00%	Complete	None	19395655
WiscDsLox33H10	WiscDsLox33H10	T-DNA Insertion	T-DNA is inserted within the region encoding the DYW domain (2160)	Homozygous	Normal appearance	Root	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19395655
WiscDsLox33H10	WiscDsLox33H10	T-DNA Insertion	T-DNA is inserted within the region encoding the DYW domain (2160)	Heterozygous	Normal appearance	Leaf	NA	Poisoned Primer Extension (PPE) Assay	100.00%	Complete	Restored	19395655
WiscDsLox33H10	WiscDsLox33H10	T-DNA Insertion	T-DNA is inserted within the region encoding the DYW domain (2160)	Homozygous	Normal appearance	Leaf	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19395655
WiscDsLox33H10	WiscDsLox33H10	T-DNA Insertion	T-DNA is inserted within the region encoding the DYW domain (2160)	Homozygous	Normal appearance	Leaf	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19395655
WiscDsLox33H10	WiscDsLox33H10	T-DNA Insertion	T-DNA is inserted within the region encoding the DYW domain (2160)	Homozygous	Normal appearance	Flower	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	19395655
Col-0	WiscDsLox33H10	Control	Control	No mutant	Normal	Root	NA	Poisoned Primer Extension (PPE) Assay	100.00%	Complete	Restored	19395655
Col-0	WiscDsLox33H10	Control	Control	No mutant	Normal	Leaf	NA	Poisoned Primer Extension (PPE) Assay	100.00%	Complete	Restored	19395655
Col-0	WiscDsLox33H10	Control	Control	No mutant	Normal	Leaf	NA	Poisoned Primer Extension (PPE) Assay	100.00%	Complete	Restored	19395655
Col-0	WiscDsLox33H10	Control	Control	No mutant	Normal	Flower	NA	Poisoned Primer Extension (PPE) Assay	100.00%	Complete	Restored	19395655
Col-0	WT	Control	Control	No mutant	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	94.00%	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	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	100.00%	Complete	Similar	28761003
NA	WT	Control	Control	No mutant	Normal	Leaf	7-day-old	Specific cDNA fragments containing editing sites were amplif	100.00%	Complete	None	36221851
CS415940	rare1-1	A T-DNA insertion	A T-DNA insertion is at +268 bp from ATG (+1)	NA	At an elevated temperature of 28°C, all rare1 lines displayed yellow foliage and a slowed growth rate, whereas the more resilient wild-type plants retained typical green foliage. At an elevated temperature of 28°C, the contents of chlorophyll a, chlorophyll b, and total chlorophyll were significantly reduced in the rare1 lines compared with wild-type plants and the complemented lines. Heat stress is severely detrimental to chlorophyll synthesis in rare1 lines, which develop a yellow leaf phenotype.	Leaf	7-day-old	Specific cDNA fragments containing editing sites were amplif	0.00%	Unedited	Absent	36221851
CS851454	rare1-2	A T-DNA insertion	A T-DNA insertion is at +2160 bp from ATG (+1)	NA	At an elevated temperature of 28°C, all rare1 lines displayed yellow foliage and a slowed growth rate, whereas the more resilient wild-type plants retained typical green foliage. At an elevated temperature of 28°C, the contents of chlorophyll a, chlorophyll b, and total chlorophyll were significantly reduced in the rare1 lines compared with wild-type plants and the complemented lines. Heat stress is severely detrimental to chlorophyll synthesis in rare1 lines, which develop a yellow leaf phenotype.	Leaf	7-day-old	Specific cDNA fragments containing editing sites were amplif	0.00%	Unedited	Absent	36221851
NA	Comp #1	Complementation	NA	NA	Normal	Leaf	7-day-old	Specific cDNA fragments containing editing sites were amplif	31.00%	Low	Restored	36221851
NA	Comp #2	Complementation	NA	NA	Normal	Leaf	7-day-old	Specific cDNA fragments containing editing sites were amplif	41.00%	Medium	Restored	36221851