scholarly journals The DYW-subgroup pentatricopeptide repeat protein PPR27 interacts with ZmMORF1 to facilitate mitochondrial RNA editing and seed development in maize

2020 ◽  
Vol 71 (18) ◽  
pp. 5495-5505 ◽  
Author(s):  
Rui Liu ◽  
Shi-Kai Cao ◽  
Aqib Sayyed ◽  
Huan-Huan Yang ◽  
Jiao Zhao ◽  
...  
Keyword(s):  
Rna Editing ◽  
Seed Development ◽  
Plant Mitochondria ◽  
Endosperm Development ◽  
Complex Iii ◽  
Mitochondrial Rna ◽  
Mitochondrial Complex ◽  
Pentatricopeptide Repeat ◽  
Ppr Protein ◽  
Ppr Proteins

Abstract C-to-U RNA editing in plant mitochondria requires the participation of many nucleus-encoded factors, most of which are pentatricopeptide repeat (PPR) proteins. There is a large number of PPR proteins and the functions many of them are unknown. Here, we report a mitochondrion-localized DYW-subgroup PPR protein, PPR27, which functions in the editing of multiple mitochondrial transcripts in maize. The ppr27 mutant is completely deficient in C-to-U editing at the ccmFN-1357 and rps3-707 sites, and editing at six other sites is substantially reduced. The lack of editing at ccmFN-1357 causes a deficiency of CcmFN protein. As CcmFN functions in the maturation pathway of cytochrome proteins that are subunits of mitochondrial complex III, its deficiency results in an absence of cytochrome c1 and cytochrome c proteins. Consequently, the assembly of mitochondrial complex III and super-complex I+III2 is decreased, which impairs the electron transport chain and respiration, leading to arrests in embryogenesis and endosperm development in ppr27. In addition, PPR27 was found to physically interact with ZmMORF1, which interacts with ZmMORF8, suggesting that these three proteins may facilitate C-to-U RNA editing via the formation of a complex in maize mitochondria. This RNA editing is essential for complex III assembly and seed development in maize.

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

2020 ◽  
Vol 71 (20) ◽  
pp. 6246-6261 ◽  
Author(s):  
Dawei Dai ◽  
Lifang Jin ◽  
Zhenzhen Huo ◽  
Shumei Yan ◽  
Zeyang Ma ◽  
...  
Keyword(s):  
Rna Editing ◽  
Protein Complexes ◽  
Plant Mitochondria ◽  
Mitochondrial Protein ◽  
Electron Microscopic Examination ◽  
Complex Iii ◽  
Mitochondrial Rna ◽  
Pentatricopeptide Repeat ◽  
Electron Microscopic ◽  
Ppr Protein

Abstract Pentatricopeptide repeat (PPR) proteins were identified as site-specific recognition factors for RNA editing in plant mitochondria and plastids. In this study, we characterized maize (Zea mays) kernel mutant defective kernel 53 (dek53), which has an embryo lethal and collapsed endosperm phenotype. Dek53 encodes an E-subgroup PPR protein, which possesses a short PLS repeat region of only seven repeats. Subcellular localization analysis indicated that DEK53 is localized in the mitochondrion. Strand- and transcript-specific RNA-seq analysis showed that the dek53 mutation affected C-to-U RNA editing at more than 60 mitochondrial C targets. Biochemical analysis of mitochondrial protein complexes revealed a significant reduction in the assembly of mitochondrial complex III in dek53. Transmission electron microscopic examination showed severe morphological defects of mitochondria in dek53 endosperm cells. In addition, yeast two-hybrid and luciferase complementation imaging assays indicated that DEK53 can interact with the mitochondrion-targeted non-PPR RNA editing factor ZmMORF1, suggesting that DEK53 might be a functional component of the organellar RNA editosome.

scholarly journals 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

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Ru Chang Ren ◽  
Xu Wei Yan ◽  
Ya Jie Zhao ◽  
Yi Ming Wei ◽  
Xiaoduo Lu ◽  
...  
Keyword(s):  
Rna Editing ◽  
Rna Processing ◽  
Mitochondrial Gene ◽  
Endosperm Development ◽  
Molecular Evidence ◽  
Pentatricopeptide Repeat ◽  
Reading Frame ◽  
Maize Kernel ◽  
Ppr Protein ◽  
Ppr Proteins

Abstract 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.

scholarly journals Non-canonical Features of Pentatricopeptide Repeat Protein-Facilitated RNA Editing in Arabidopsis Chloroplasts

2019 ◽  
Author(s):  
Yueming Kelly Sun ◽  
Bernard Gutmann ◽  
Ian Small
Keyword(s):  
Rna Editing ◽  
Plant Mitochondria ◽  
Pentatricopeptide Repeat ◽  
Site Specific ◽  
Ppr Protein ◽  
Sequence Variations ◽  
Ppr Proteins ◽  
Editing Activity ◽  
Chloroplast Rna ◽  
Plant Organelles

AbstractCytosine (C) to uracil (U) RNA editing in plant mitochondria and chloroplasts is facilitated by site-specific pentatricopeptide repeat (PPR) editing factors. PPR editing factors contain multiple types of PPR motifs, and PPR motifs of the same type also show sequence variations. Therefore, no PPR motifs are invariant within a PPR protein or between different PPR proteins. This work evaluates the functional diversity of PPR motifs in CHLOROPLAST RNA EDITING FACTOR 3 (CREF3). The results indicate that previously overlooked features of PPR editing factors could also contribute to RNA editing activity. In particular, the N-terminal degenerated PPR motifs and the two L1-type PPR motifs in CREF3 are functionally indispensable. Furthermore, PPR motifs of the same type in CREF3 are not interchangeable. These non-canonical features of CREF3 have important implications on the understanding of PPR-facilitated RNA editing in plant organelles.

scholarly journals Maize Defective Kernel605 Encodes a Canonical DYW-Type PPR Protein that Edits a Conserved Site of nad1 and Is Essential for Seed Nutritional Quality

2020 ◽  
Vol 61 (11) ◽  
pp. 1954-1966 ◽  
Author(s):  
Kaijian Fan ◽  
Yixuan Peng ◽  
Zhenjing Ren ◽  
Delin Li ◽  
Sihan Zhen ◽  
...  
Keyword(s):  
Nutritional Quality ◽  
Complex I ◽  
Endosperm Development ◽  
Mitochondrial Rna ◽  
Loss Of Function ◽  
Pentatricopeptide Repeat ◽  
Respiratory Pathway ◽  
Ppr Protein ◽  
Normal Seed ◽  
Ppr Proteins

Abstract Pentatricopeptide repeat (PPR) proteins involved in mitochondrial RNA cytidine (C)-to-uridine (U) editing mostly result in stagnant embryo and endosperm development upon loss of function. However, less is known about PPRs that are involved in farinaceous endosperm formation and maize quality. Here, we cloned a maize DYW-type PPR Defective Kernel605 (Dek605). Mutation of Dek605 delayed seed and seedling development. Mitochondrial transcript analysis of dek605 revealed that loss of DEK605 impaired C-to-U editing at the nad1-608 site and fails to alter Ser203 to Phe203 in NAD1 (dehydrogenase complex I), disrupting complex I assembly and reducing NADH dehydrogenase activity. Meanwhile, complexes III and IV in the cytochrome pathway, as well as AOX2 in the alternative respiratory pathway, are dramatically increased. Interestingly, the dek605 mutation resulted in opaque endosperm and increased levels of the free amino acids alanine, aspartic acid and phenylalanine. The down- and upregulated genes mainly involved in stress response-related and seed dormancy-related pathways, respectively, were observed after transcriptome analysis of dek605 at 12 d after pollination. Collectively, these results indicate that Dek605 specifically affects the single nad1-608 site and is required for normal seed development and resulted in nutritional quality relevant amino acid accumulation.

scholarly journals A novel E-Subgroup Pentatricopeptide Repeat Protein DEK55 is Responsible for RNA Editing at 15 Sites and Splicing of nad1 and nad4 in Maize

2020 ◽  
Author(s):  
Ru Chang Ren ◽  
Xu Wei Yan ◽  
Ya Jie Zhao ◽  
Yi Ming Wei ◽  
Xiaoduo Lu ◽  
...  
Keyword(s):  
Rna Editing ◽  
Endosperm Development ◽  
Pentatricopeptide Repeat ◽  
Reading Frame ◽  
Maize Kernel ◽  
Ppr Protein ◽  
Ppr Proteins ◽  
Large Protein Family ◽  
Underlying Mechanisms ◽  
Mutant Phenotypes

Abstract Background Pentatricopeptide repeat (PPR) proteins is a large protein family, which participate in RNA processing in organelles and plant growth. Previous reports have generally considered E-subgroup PPR proteins as an editing factors for RNA editing. However, the underlying mechanisms and effects of E-subgroup PPR proteins remain to be investigated.Results In this study, we recognized and identified a new maize kernel mutant with arrested embryo and endosperm development, defective kernel 55 (dek55). Genetic and molecular evidences suggest that the defective kernels resulted from a mononucleotide alteration (C to T) at + 449 in the open reading frame (ORF) of Zm00001d014471 (hereafter referred to as DEK55). DEK55 encodes an E-subgroup PPR protein within mitochondria. Molecular analyses suggest that DEK55 plays crucial roles in RNA editing at multiple sites of ribosomal protein S13, ATP synthase subunit1, NADH dehydrogenase-6 (nad6), and nad9 transcripts as well as in splicing of nad1 and nad4. The mutation of DEK55 lead to the dysfunction of mitochondrial complex I.Conclusions Our results demonstrate that the DEK55 mutation is responsible for the dek55 mutant phenotypes, as it affects mitochondrial function that is essential for maize kernel development. This study also provides novel insight into the molecular function of E-subgroup PPR proteins in plant organellar RNA metabolism.

scholarly journals 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

2020 ◽  
Author(s):  
Ru Chang Ren ◽  
Xu Wei Yan ◽  
Ya Jie Zhao ◽  
Yi Ming Wei ◽  
Xiaoduo Lu ◽  
...  
Keyword(s):  
Rna Editing ◽  
Rna Processing ◽  
Mitochondrial Gene ◽  
Endosperm Development ◽  
Molecular Evidence ◽  
Pentatricopeptide Repeat ◽  
Reading Frame ◽  
Maize Kernel ◽  
Ppr Protein ◽  
Ppr Proteins

Abstract 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.

scholarly journals The Mitochondrial Pentatricopeptide Repeat Protein PPR18 Is Required for the cis-Splicing of nad4 Intron 1 and Essential to Seed Development in Maize

2020 ◽  
Vol 21 (11) ◽  
pp. 4047 ◽  
Author(s):  
Rui Liu ◽  
Shi-Kai Cao ◽  
Aqib Sayyed ◽  
Chunhui Xu ◽  
Feng Sun ◽  
...  
Keyword(s):  
Seed Development ◽  
Complex I ◽  
Large Family ◽  
Endosperm Development ◽  
Pentatricopeptide Repeat ◽  
Ppr Protein ◽  
Intron 1 ◽  
Ppr Proteins ◽  
P Type ◽  
Complex I Assembly

Pentatricopeptide repeat (PPR) protein comprises a large family, participating in various aspects of organellar RNA metabolism in land plants. There are approximately 600 PPR proteins in maize, but the functions of many PPR proteins remain unknown. In this study, we defined the function of PPR18 in the cis-splicing of nad4 intron 1 in mitochondria and seed development in maize. Loss function of PPR18 seriously impairs embryo and endosperm development, resulting in the empty pericarp (emp) phenotype in maize. PPR18 encodes a mitochondrion-targeted P-type PPR protein with 18 PPR motifs. Transcripts analysis indicated that the splicing of nad4 intron 1 is impaired in the ppr18 mutant, resulting in the absence of nad4 transcript, leading to severely reduced assembly and activity of mitochondrial complex I and dramatically reduced respiration rate. These results demonstrate that PPR18 is required for the cis-splicing of nad4 intron 1 in mitochondria, and critical to complex I assembly and seed development in maize.

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

2020 ◽  
Author(s):  
Ru Chang Ren ◽  
Xu Wei Yan ◽  
Ya Jie Zhao ◽  
Yi Ming Wei ◽  
Xiaoduo Lu ◽  
...  
Keyword(s):  
Rna Editing ◽  
Rna Processing ◽  
Mitochondrial Gene ◽  
Endosperm Development ◽  
Molecular Evidence ◽  
Pentatricopeptide Repeat ◽  
Reading Frame ◽  
Maize Kernel ◽  
Ppr Protein ◽  
Ppr Proteins

Abstract 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.

scholarly journals PPR-DYW Protein EMP17 Is Required for Mitochondrial RNA Editing, Complex III Biogenesis, and Seed Development in Maize

2021 ◽  
Vol 12 ◽  
Author(s):  
Yong Wang ◽  
Xin-Yuan Liu ◽  
Zi-Qin Huang ◽  
Yan-Yan Li ◽  
Yan-Zhuo Yang ◽  
...  
Keyword(s):  
Seed Development ◽  
Complex I ◽  
Complex Iii ◽  
Mitochondrial Rna ◽  
Pentatricopeptide Repeat ◽  
Kernel Development ◽  
Maize Kernel ◽  
Ppr Proteins ◽  
Processing Event ◽  
Mitochondrial Transcripts

The conversion of cytidines to uridines (C-to-U) at specific sites in mitochondrial and plastid transcripts is a post-transcriptional processing event that is important to the expression of organellar genes. Pentatricopeptide repeat (PPR) proteins are involved in this process. In this study, we report the function of a previously uncharacterized PPR-DYW protein, Empty pericarp17 (EMP17), in the C-to-U editing and kernel development in maize. EMP17 is targeted to mitochondria. The loss-function of EMP17 arrests maize kernel development, abolishes the editing at ccmFC-799 and nad2-677 sites, and reduces the editing at ccmFC-906 and -966 sites. The absence of editing causes amino acid residue changes in CcmFC-267 (Ser to Pro) and Nad2-226 (Phe to Ser), respectively. As CcmFC functions in cytochrome c (Cytc) maturation, the amount of Cytc and Cytc1 protein is drastically reduced in emp17, suggesting that the CcmFC-267 (Ser to Pro) change impairs the CcmFC function. As a result, the assembly of complex III is strikingly decreased in emp17. In contrast, the assembly of complex I appears less affected, suggesting that the Nad2-226 (Phe to Ser) change may have less impact on Nad2 function. Together, these results indicate that EMP17 is required for the C-to-U editing at several sites in mitochondrial transcripts, complex III biogenesis, and seed development in maize.

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