Plant Editosome Database
a curated database of RNA editosome in plants

PpPPR_65 - Plant Editosome Database - BIG Data Center
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Summary

Editing Factor: PpPPR_65
Synonym: Phypa_175641
Description: Encodes DYW subclass PPR protein as RNA editing factor for atp9 site. Knockout of DYW-PPR_65 in Physcomitrella patens causes a severe developmental phenotype in the moss and specifically affects two editing sites located 18 nucleotides apart on the mitochondrial ccmFC mRNA.
Protein Family: PPR
Subclass: DYW
Construct Structure: PLS-E/E+-DYW
Gene ID & Species: PP1S13_264V6 (Physcomitrella patens)
Edited Gene(s): ccmFC
Editing Type(s): C-to-U (17)
Publication(s): [1] Two DYW Subclass PPR Proteins are Involved in RNA Editing of ccmFc and atp9 Transcripts in the Moss Physcomitrella patens: First Complete Set of PPR Editing Factors in Plant Mitochondria, Plant Cell Physiology, 2013. [PMID=24058147]
[2] A DYW-protein knockout in Physcomitrella affects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype, The Plant Journal, 2013. [PMID=23909746]

Editing Details

Species Gene ID Organelle Edited Gene Position Region Editing Type Codon Amino Acid Molecular Effect Experiment Details
Physcomitrella patens PP1S13_264V6 Mitochondrion ccmFC 103 CDS C-to-U CCC=>UCC P=>S Recoding
Experiment Details
Genotype (Ecotype) Allele Treatment Treatment Detail Mutant Type Phenotype Tissue Development Stage Detection Method Editing Frequency Editing Extent Mutant Effect PMID
NAWTNo treatmentNo treatmentNo treatmentNo treatmentProtonema4 daysDirect Sequencing of PCR Products90.00%HighNone24058147
NAΔ65-1Gene cassetteGene cassette deletes the cognate gene by replacing the coding region with the gfp and hptKnockoutSevere growth retardation of the moss protonemataProtonema4 daysDirect Sequencing of PCR Products0.00%UneditedAbsent24058147
GFP–tubulin/histone H2B–RFP expression lineGH line (-) (control to RNAi line)without β-estradiolNo treatmentNo treatmentNAProtonema4 daysDirect Sequencing of PCR Products90.00%HighNone24058147
GFP–tubulin/histone H2B–RFP expression lineGH line (+) (control to RNAi line)with β-estradiolProtonemata are cultured for 4 d in the presence of 1 mM β-estradiolNo treatmentNAProtonema4 daysDirect Sequencing of PCR Products90.00%HighNone24058147
GFP–tubulin/histone H2B–RFP expression line65RNAi#5 (-)RNAi without β-estradiolpMI-65RNAi is introduced into protonemata of GH line by particle bombardmentKnockdownNAProtonema4 daysDirect Sequencing of PCR Products70.00%HighDecreased24058147
GFP–tubulin/histone H2B–RFP expression line65RNAi#16 (-)RNAi without β-estradiolpMI-65RNAi is introduced into protonemata of GH line by particle bombardmentKnockdownNAProtonema4 daysDirect Sequencing of PCR Products70.00%HighDecreased24058147
NAWTNo treatmentNo treatmentNo treatmentNo treatmentNANADirect Sequencing of PCR ProductsNAHighNone23909746
NAKO_PPR_65Gene cassetteHomologous recombination is used to insert the selectable nptII marker cassette into PPR_65 upon protoplast transformationKnockoutSevere growth retardationNANADirect Sequencing of PCR Products0.00%UneditedAbsent23909746
Physcomitrella patens PP1S13_264V6 Mitochondrion ccmFC 122 CDS 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
NAWTNo treatmentNo treatmentNo treatmentNo treatmentProtonema4 daysDirect Sequencing of PCR Products80.00%HighNone24058147
NAΔ65-1Gene cassetteGene cassette deletes the cognate gene by replacing the coding region with the gfp and hptKnockoutSevere growth retardation of the moss protonemataProtonema4 daysDirect Sequencing of PCR Products0.00%UneditedAbsent24058147
GFP–tubulin/histone H2B–RFP expression lineGH line (+) (control to RNAi line)with β-estradiolProtonemata are cultured for 4 d in the presence of 1 mM β-estradiolNo treatmentNAProtonema4 daysDirect Sequencing of PCR Products80.00%HighNone24058147
GFP–tubulin/histone H2B–RFP expression line65RNAi#5 (-)RNAi without β-estradiolpMI-65RNAi is introduced into protonemata of GH line by particle bombardmentKnockdownNAProtonema4 daysDirect Sequencing of PCR Products70.00%HighDecreased24058147
GFP–tubulin/histone H2B–RFP expression line65RNAi#16 (-)RNAi without β-estradiolpMI-65RNAi is introduced into protonemata of GH line by particle bombardmentKnockdownNAProtonema4 daysDirect Sequencing of PCR Products70.00%HighDecreased24058147
NAWTNo treatmentNo treatmentNo treatmentNo treatmentNANADirect Sequencing of PCR Products100.00%CompleteNone23909746
NAKO_PPR_65Gene cassetteHomologous recombination is used to insert the selectable nptII marker cassette into PPR_65 upon protoplast transformationKnockoutSevere growth retardationNANADirect Sequencing of PCR Products0.00%UneditedAbsent23909746
NAKO_PPR_65Gene cassetteHomologous recombination is used to insert the selectable nptII marker cassette into PPR_65 upon protoplast transformationKnockoutSevere growth retardationNANAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent23909746
NAKO_PPR_65Gene cassetteHomologous recombination is used to insert the selectable nptII marker cassette into PPR_65 upon protoplast transformationKnockoutSevere growth retardationNANAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent23909746
Last update: Jul 2021 (version 1.0)