Maize pentatricopeptide repeat protein DEK53 is required for mitochondrial RNA editing at multiple sites and seed development

Dai, Dawei; Jin, Lifang; Huo, Zhenzhen; Yan, Shumei; Ma, Zeyang; Qi, Weiwei; Song, Rentao

doi:10.1093/jxb/eraa348

Cited by 19 publications

(33 citation statements)

References 112 publications

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“…DEK55 is necessary for C-to-U editing of multiple sites in the mitochondrial transcripts of maize PPR proteins, including DYW2, EMP21, NUWA, MEF8, and DEK53, are involved in C-to-U editing at multiple sites [48][49][50][51][52]. In this study, we demonstrated that DEK55 participated in RNA editing at 31 sites, while the editing ratio of 24 editing sites was reduced and that of seven editing sites was increased in dek55, suggesting that DEK55 is also necessary for RNA editing at multiple sites.…”

Section: Discussionmentioning

confidence: 99%

“…EMP21 contains 11 PPR-motifs in addition to E and DYW domains and belongs to PPR-DYW proteins [51]. DEK53 is an E-subgroup PPR protein with seven PPR repeats [52]. DEK55 is considered as an E-subgroup PPR protein that contains the canonical E domain.…”

Section: Discussionmentioning

confidence: 99%

“…ZmMORF8 (GRMZM2G169384), an ortholog of MORF8 in maize, directly interacts with EMP21 and EMP5, suggesting that EMP21 and EMP5 participate in the editing of some sites by interacting with ZmMORF8 [51]. DEK53 is an E-subgroup PPR protein that interacts with ZmMORF1 to form an RNA editing complex, and which is responsible for more than 60 RNA editing in the maize mitochondrion [52]. In our study, DEK55 participated in C-to-U editing of 14 mitochondrial transcripts at 31 editing sites, while the editing ratios of 24 sites were decreased in dek55 (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Although the Zmmorf8 mutant has not been identi ed in maize yet, our ndings might provide evidence that the DEK55 might interact with ZmMORF8 to function at these RNA editing sites in maize. In dek53, over 60 RNA editing sites were affected [52], and three of them (nad3-146, nad6-146, and atp8-123) were also affected in dek55. DEK53 and DEK55 interact with ZmMORF1 [52, this study].…”

Section: Discussionmentioning

confidence: 99%

“…The sequenced data was ltered for the lower quality reads, the adaptor reads, and the unknown base reads. The clean reads were mapped to the 35 mitochondrial gene transcripts and nad4 intron 1 using 'Bowtie 2', and the allele frequency count was performed as described previously [52]. The editing e ciencies of 482 RNA editing sites were calculated, and the affected editing site in the dek55 mutant was de ned as described by previously reported [51].…”

Section: Rna Editing E Ciency Analysismentioning

confidence: 99%

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

Ren

Zhao

et al. 2020

Preprint

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Background: Pentatricopeptide repeat (PPR) proteins form a large protein family that participates in RNA processing in organelles and plant growth. Previous reports regard E-subgroup PPR proteins as editing factors for RNA editing. However, additional functions and roles of the E-subgroup PPR proteins remain to be investigated.Results: In this study, we developed and identified a new maize kernel mutant with arrested embryo and endosperm development, i.e., defective kernel 55 (dek55). Genetic and molecular evidence suggested that the defective kernels was a result of a mononucleotide alteration (C to T) at +449 bp in the open reading frame (ORF) of Zm00001d014471 (hereafter referred to as DEK55). DEK55 encodes an E-subgroup PPR protein within mitochondria. Molecular analyses showed that the editing ratio of 24 RNA editing sites was decreased and that of seven RNA editing sites was increased in dek55 mutant kernels, which were distributed in 14 mitochondrial gene transcripts. Meanwhile, the splicing efficiency of the nad1 introns 1 and 4 and nad4 intron 1 was significantly decreased in dek55 compared with that of 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. Yeast two-hybrid assays showed that the DEK55 interacts with two multiple organellar RNA editing factors (MORFs), i.e., ZmMORF1 (Zm00001d049043) and ZmMORF8 (Zm00001d048291), respectively.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 the E-subgroup PPR proteins in plant organellar RNA processing.

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