ISE2 - Plant Editosome Database

Summary

Editing Factor:	ISE2
Synonym:	115J-4A; EMB25; EMBRYO DEFECTIVE 25; INCREASED SIZE EXCLUSION LIMIT 2; PDE317; PIGMENT DEFECTIVE 317
Description:	Loss of ISE2 from Arabidopsis thaliana leaves resulted in defects in C-to-U RNA editing, altered accumulation of chloroplast transcripts and chloroplast-encoded proteins, and defective processing of chloroplast ribosomal RNAs; Potential ISE2 substrates were identified by RNA immunoprecipitation followed by next-generation sequencing (RIP-seq), and the diversity of RNA species identified supports ISE2's involvement in multiple aspects of chloroplast RNA metabolism; Comprehensive phylogenetic analyses revealed that ISE2 is a non-canonical Ski2-like RNA helicase that represents a separate sub-clade unique to green photosynthetic organisms, consistent with its function as an essential protein
Protein Family:	DEVH-box RNA helicase
Subclass:	NA
Physical Interaction:	IPI1
Construct Structure:	NA
Gene ID & Species:	AT1G70070 (Arabidopsis thaliana) NA (Nicotiana benthamiana)
Edited Gene(s):	clpP rps14 petL rpoA rpoB ndhD
Editing Type(s):	C-to-U (28)
Publication(s):	[1] The dicot homolog of maize PPR103 carries a C-terminal DYW domain and is required for C-to-U editing of chloroplast RNA transcripts, Research Square, 2023. [doi:10.21203/rs.3.rs-2574001/v1] [2] The chloroplast RNA helicase ISE2 is required for multiple chloroplast RNA processing steps in Arabidopsis thaliana, The Plant Journal, 2017. [doi:10.1111/tpj.13550]

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

AT1G70070

Chloroplast

clpP

559

CDS

TAIR (v10)

C-to-U

CAU=>UAU

H=>Y

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
ise2-2 homozygous	var2-2	NA	NA	NA	Variegation mutant	Leaf	12 days	Direct Sequencing of PCR Products	63.00%	High	Decreased	28346704
ise2-2 homozygous	ISE2-GFP (ISE2-OE)	Complementation	NA	NA	NA	Leaf	12 days	Direct Sequencing of PCR Products	77.30%	High	Restored	28346704
ise2-2 homozygous	ISE2-GFP transgene (ISE2-SUP)	Complementation	NA	NA	Leaves developed chlorosis	Leaf	12 days	Direct Sequencing of PCR Products	25.80%	Low	Decreased	28346704
NA	WT	Control	Control	No mutant	Normal	Leaf	12 days	Direct Sequencing of PCR Products	83.10%	High	None	28346704

Arabidopsis thaliana

AT1G70070

Chloroplast

petL

CDS

TAIR (v10)

C-to-U

CCU=>CUU

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
ise2-2 homozygous	var2-2	NA	NA	NA	Variegation mutant	Leaf	12 days	Direct Sequencing of PCR Products	64.00%	High	Decreased	28346704
ise2-2 homozygous	ISE2-GFP (ISE2-OE)	Complementation	NA	NA	NA	Leaf	12 days	Direct Sequencing of PCR Products	87.80%	High	Restored	28346704
ise2-2 homozygous	ISE2-GFP transgene (ISE2-SUP)	Complementation	NA	NA	Leaves developed chlorosis	Leaf	12 days	Direct Sequencing of PCR Products	48.50%	Medium	Decreased	28346704
NA	WT	Control	Control	No mutant	Normal	Leaf	12 days	Direct Sequencing of PCR Products	88.90%	High	None	28346704

Arabidopsis thaliana

AT1G70070

Chloroplast

rpoA

200

CDS

TAIR (v10)

C-to-U

UCU=>UUU

S=>F

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
ise2-2 homozygous	var2-2	NA	NA	NA	Variegation mutant	Leaf	12 days	Direct Sequencing of PCR Products	64.10%	High	Decreased	28346704
ise2-2 homozygous	ISE2-GFP (ISE2-OE)	Complementation	NA	NA	NA	Leaf	12 days	Direct Sequencing of PCR Products	90.50%	High	Restored	28346704
ise2-2 homozygous	ISE2-GFP transgene (ISE2-SUP)	Complementation	NA	NA	Leaves developed chlorosis	Leaf	12 days	Direct Sequencing of PCR Products	40.50%	Medium	Decreased	28346704
NA	WT	Control	Control	No mutant	Normal	Leaf	12 days	Direct Sequencing of PCR Products	88.20%	High	None	28346704

Arabidopsis thaliana

AT1G70070

Chloroplast

rpoB

338

CDS

TAIR (v10)

C-to-U

UCU=>UUU

S=>F

Recoding

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
ise2-2 homozygous	var2-2	NA	NA	NA	Variegation mutant	Leaf	12 days	Direct Sequencing of PCR Products	93.80%	High	Similar	28346704
ise2-2 homozygous	ISE2-GFP (ISE2-OE)	Complementation	NA	NA	NA	Leaf	12 days	Direct Sequencing of PCR Products	97.60%	High	Restored	28346704
ise2-2 homozygous	ISE2-GFP transgene (ISE2-SUP)	Complementation	NA	NA	Leaves developed chlorosis	Leaf	12 days	Direct Sequencing of PCR Products	72.30%	High	Decreased	28346704
NA	WT	Control	Control	No mutant	Normal	Leaf	12 days	Direct Sequencing of PCR Products	94.10%	High	None	28346704

Arabidopsis thaliana

AT1G70070

Chloroplast

rpoB

551

CDS

TAIR (v10)

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
ise2-2 homozygous	var2-2	NA	NA	NA	Variegation mutant	Leaf	12 days	Direct Sequencing of PCR Products	98.80%	High	Similar	28346704
ise2-2 homozygous	ISE2-GFP (ISE2-OE)	Complementation	NA	NA	NA	Leaf	12 days	Direct Sequencing of PCR Products	97.70%	High	Restored	28346704
ise2-2 homozygous	ISE2-GFP transgene (ISE2-SUP)	Complementation	NA	NA	Leaves developed chlorosis	Leaf	12 days	Direct Sequencing of PCR Products	76.20%	High	Decreased	28346704
NA	WT	Control	Control	No mutant	Normal	Leaf	12 days	Direct Sequencing of PCR Products	95.70%	High	None	28346704

Arabidopsis thaliana

AT1G70070

Chloroplast

rps14

149

CDS

TAIR (v10)

C-to-U

CCA=>CUA

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
ise2-2 homozygous	var2-2	NA	NA	NA	Variegation mutant	Leaf	12 days	Direct Sequencing of PCR Products	66.20%	High	Similar	28346704
ise2-2 homozygous	ISE2-GFP (ISE2-OE)	Complementation	NA	NA	NA	Leaf	12 days	Direct Sequencing of PCR Products	86.10%	High	Restored	28346704
ise2-2 homozygous	ISE2-GFP transgene (ISE2-SUP)	Complementation	NA	NA	Leaves developed chlorosis	Leaf	12 days	Direct Sequencing of PCR Products	42.20%	Medium	Decreased	28346704
NA	WT	Control	Control	No mutant	Normal	Leaf	12 days	Direct Sequencing of PCR Products	69.10%	High	None	28346704

Nicotiana benthamiana

Chloroplast

ndhD

http://benthgenome.qut.edu.au

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	TRV-WT	TRV-infected and non-silenced controls	NA	No mutant	NA	Leaf	6 weeks	Sanger sequencing	NA	NA	None	36865278
NA	TRV-ISE2	Tobacco rattle virus (TRV)-mediated VIGS was used to knockdown NbISE2 expression in N. benthamiana leaves	NA	Knockdown	NA	Leaf	6 weeks	Sanger sequencing	NA	NA	Decreased	36865278

Nicotiana benthamiana

Chloroplast

rpoB

http://benthgenome.qut.edu.au

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	TRV-WT	TRV-infected and non-silenced controls	NA	No mutant	NA	Leaf	6 weeks	Sanger sequencing	NA	NA	None	36865278
NA	TRV-ISE2	Tobacco rattle virus (TRV)-mediated VIGS was used to knockdown NbISE2 expression in N. benthamiana leaves	NA	Knockdown	NA	Leaf	6 weeks	Sanger sequencing	NA	NA	Increased	36865278