PED
Plant
Editosome
Database
DEK39 - Plant Editosome Database - CNCB-NGDC
  1. Home
  2. Editing Factors
  3. DEK39

Summary

Editing Factor: DEK39
Synonym: Defective Kernel 39
Description: Loss of Dek39 function leads to delayed embryogenesis and endosperm development, reduced kernel size, and seedling lethality; Dek39 encodes an E sub-class PPR protein that targets to both mitochondria and chloroplasts, and is involved in RNA editing in mitochondrial NADH dehydrogenase3 (nad3) at nad3-247 and nad3-275; C-to-U editing of nad3-275 is not conserved and even lost in Arabidopsis, consistent with the idea that no close DEK39 homologs are present in Arabidopsis; However, the amino acids generated by editing nad3-247 and nad3-275 are highly conserved in many other plant species, and the reductions of editing at these two sites decrease the activity of mitochondria NADH dehydrogenase complex I, indicating that the alteration of amino acid sequence is necessary for Nad3 function; Dek39 encodes an E sub-class PPR protein that is involved in RNA editing of multiple sites and is necessary for seed development of maize
Protein Family: Pentatricopeptide repeat (PPR) protein
Subclass: E
Physical Interaction: NA
Construct Structure: PLS-E1-E2
Gene ID & Species: GRMZM2G345128 (Zea mays)
Edited Gene(s): nad3
Editing Type(s): C-to-U (10)
Publication(s): [1] Defective Kernel 39 encodes a PPR protein required for seed development in maize, Journal of Integrative Plant Biology, 2017. [doi:10.1111/jipb.12602]

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
Zea mays GRMZM2G345128 Mitochondrion nad3 247 CDS MaizeGDB B73 RefGen_V4 NA NA C-to-U CCU=>UCU 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
B73dek39EMS MutationA G-to-A alteration results in Trp being converted to a stop codonHomozygousDelayed embryogenesis and endosperm development, reduced kernel size, and seedling lethalityEndosperm12 DAPRNA-Seq40.00%MediumDecreased28981206
siblings of the mutant or B73WTControlControlNo mutantNormalEndosperm12 DAPRNA-Seq80.00%HighNone28981206
B73dek39EMS MutationA G-to-A alteration results in Trp being converted to a stop codonHomozygousDelayed embryogenesis and endosperm development, reduced kernel size, and seedling lethalityEndosperm12 DAPDirect Sequencing of PCR Products50.70%MediumDecreased28981206
siblings of the mutant or B73WTControlControlNo mutantNormalEndosperm12 DAPDirect Sequencing of PCR Products68.40%HighNone28981206
B73comComplementationdek39 + ProDek39::Dek39-MYCNASimilar growth phenotype as wild-typeEndosperm12 DAPDirect Sequencing of PCR Products68.20%HighRestored28981206
Zea mays GRMZM2G345128 Mitochondrion nad3 275 CDS MaizeGDB B73 RefGen_V4 NA NA 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
B73dek39EMS MutationA G-to-A alteration results in Trp being converted to a stop codonHomozygousDelayed embryogenesis and endosperm development, reduced kernel size, and seedling lethalityEndosperm12 DAPRNA-Seq4.40%PoorDecreased28981206
siblings of the mutant or B73WTControlControlNo mutantNormalEndosperm12 DAPRNA-Seq64.00%HighNone28981206
B73dek39EMS MutationA G-to-A alteration results in Trp being converted to a stop codonHomozygousDelayed embryogenesis and endosperm development, reduced kernel size, and seedling lethalityEndosperm12 DAPDirect Sequencing of PCR Products0.00%UneditedAbsent28981206
siblings of the mutant or B73WTControlControlNo mutantNormalEndosperm12 DAPDirect Sequencing of PCR Products59.60%MediumNone28981206
B73comComplementationdek39 + ProDek39::Dek39-MYCNASimilar growth phenotype as wild-typeEndosperm12 DAPDirect Sequencing of PCR Products60.30%HighRestored28981206
Last update: Sep 2026 (version 2.0)