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Background  Pentatricopeptide repeat (PPR) proteins compose a large protein family whose members are involved in both RNA processing in organelles and plant growth. Previous reports have shown that E-subgroup PPR proteins are involved in RNA editing. However, the additional functions and roles of the E-subgroup PPR proteins are unknown.    Results  In this study, we developed and identified a new maize kernel mutant with arrested embryo and endosperm development, i.e.,  defective kernel  ( dek )  55  ( dek55 ). Genetic and molecular evidence suggested that the defective kernels resulted from a mononucleotide alteration (C to T) at + 449 bp within the open reading frame (ORF) of Zm00001d014471 (hereafter referred to as  DEK55 ).  DEK55  encodes an E-subgroup PPR protein within the mitochondria. Molecular analyses showed that the editing percentage of 24 RNA editing sites decreased and that of seven RNA editing sites increased in  dek55  kernels, the sites of which were distributed across 14 mitochondrial gene transcripts. Moreover, the splicing efficiency of  nad1  introns 1 and 4 and  nad4  intron 1 significantly decreased in  dek55  compared with the wild type (WT). These results indicate that DEK55 plays a crucial role in RNA editing at multiple sites as well as in the splicing of  nad1  and  nad4  introns. Mutation in the  DEK55  gene led to the dysfunction of mitochondrial complex I. Moreover, yeast two-hybrid assays showed that DEK55 interacts with two multiple organellar RNA-editing factors (MORFs), i.e., ZmMORF1 (Zm00001d049043) and ZmMORF8 (Zm00001d048291).    Conclusions  Our results demonstrated that a mutation in the  DEK55  gene affects the mitochondrial function essential for maize kernel development. Our results also provide novel insight into the molecular functions of E-subgroup PPR proteins involved in plant organellar RNA processing.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02765-x.

bmc plant biology

The novel E-subgroup pentatricopeptide repeat protein DEK55 is responsible for RNA editing at multiple sites and for the splicing of nad1 and nad4 in maize