Maize Empty Pericarp602 Encodes a P-Type PPR Protein That Is Essential for Seed Development

2019 ◽  
Vol 60 (8) ◽  
pp. 1734-1746 ◽  
Author(s):  
Zhenjing Ren ◽  
Kaijian Fan ◽  
Ting Fang ◽  
Jiaojiao Zhang ◽  
Li Yang ◽  
...  
Keyword(s):  
Seed Development ◽  
Rna Splicing ◽  
Complex I ◽  
Intron Splicing ◽  
Loss Of Function ◽  
Pentatricopeptide Repeat ◽  
Ppr Protein ◽  
Intron 1 ◽  
Ppr Proteins ◽  
P Type

Abstract Pentatricopeptide repeat (PPR) proteins play crucial roles in intron splicing, which is important for RNA maturation. Identification of novel PPR protein with the function of intron splicing would help to understand the RNA splicing mechanism. In this study, we identified the maize empty pericarp602 (emp602) mutants, the mature kernels of which showed empty pericarp phenotype. We cloned the Emp602 gene from emp602 mutants and revealed that Emp602 encodes a mitochondrial-localized P-type PPR protein. We further revealed that Emp602 is specific for the cis-splicing of mitochondrial Nad4 intron 1 and intron 3, and mutation of Emp602 led to the loss of mature Nad4 transcripts. The loss of function of Emp602 nearly damaged the assembly and accumulation of complex I and arrested mitochondria formation, which arrested the seed development. The failed assembly of complex I triggers significant upregulation of Aox expression in emp602 mutants. Transcriptome analysis showed that the expression of mitochondrial-related genes, e.g. the genes associated with mitochondrial inner membrane presequence translocase complex and electron carrier activity, were extensively upregulated in emp602 mutant. These results demonstrate that EMP602 functions in the splicing of Nad4 intron 1 and intron 3, and the loss of function of Emp602 arrested maize seed development by disrupting the mitochondria complex I assembly.

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 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 PPR20 Is Required for the cis-Splicing of Mitochondrial nad2 Intron 3 and Seed Development in Maize

2019 ◽  
Vol 61 (2) ◽  
pp. 370-380 ◽  
Author(s):  
Yan-Zhuo Yang ◽  
Shuo Ding ◽  
Yong Wang ◽  
Hong-Chun Wang ◽  
Xin-Yuan Liu ◽  
...  
Keyword(s):  
Seed Development ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Endosperm Development ◽  
Binding Activity ◽  
Pentatricopeptide Repeat ◽  
Ppr Protein ◽  
Exact Function ◽  
Ppr Proteins ◽  
P Type

Abstract Pentatricopeptide repeat (PPR) proteins are helical repeat RNA-binding proteins that function in RNA processing by conferring sequence-specific RNA-binding activity. Owing to the lethality of PPR mutants, functions of many PPR proteins remain obscure. In this study, we report the function of PPR20 in intron splicing in mitochondria and its role in maize seed development. PPR20 is a P-type PPR protein targeted to mitochondria. The ppr20 mutants display slow embryo and endosperm development. Null mutation of PPR20 severely reduces the cis-splicing of mitochondrial nad2 intron 3, resulting in reduction in the assembly and activity of mitochondrial complex I. The ppr20-35 allele with a Mu insertion in the N-terminal region shows a much weaker phenotype. Molecular analyses revealed that the mutant produces a truncated transcript, coding for PPR20ΔN120 lacking the N-terminal 120 amino acids. Subcellular localization revealed that PPR20ΔN120:GFP is able to target to mitochondria as well, suggesting the sequence diversity of the mitochondrial targeting peptides. Another mutant zm_mterf15 was also found to be impaired in the splicing of mitochondrial nad2 intron 3. Further analyses are required to identify the exact function of PPR20 and Zm_mTERF15 in the splicing of nad2 intron 3.

scholarly journals Empty Pericarp24 and Empty Pericarp25 Are Required for the Splicing of Mitochondrial Introns, Complex I Assembly, and Seed Development in Maize

2020 ◽  
Vol 11 ◽  
Author(s):  
Zhihui Xiu ◽  
Ling Peng ◽  
Yong Wang ◽  
Huanhuan Yang ◽  
Feng Sun ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Complex I ◽  
Plant Mitochondria ◽  
Mass Spectrometry Identification ◽  
Ppr Proteins ◽  
P Type ◽  
Complex I Assembly ◽  
Post Transcriptional Regulation ◽  
Empty Pericarp ◽  
Mitochondrial Introns

RNA splicing is an essential post-transcriptional regulation in plant mitochondria and chloroplasts. As the mechanism of RNA splicing remains obscure, identification and functional elucidation of new splicing factors are necessary. Through a characterization of two maize mutants, we cloned Empty pericarp 24 (Emp24) and Empty pericarp 25 (Emp25). Both Emp24 and Emp25 encode mitochondrion-targeted P-type PPR proteins. EMP24 is required for the splicing of nad4 introns 1 and 3, which was reported (Ren Z. et al., 2019), and EMP25 functions in the splicing of nad5 introns 1, 2, and 3. Absence of either Nad4 or Nad5 proteins blocks the assembly of mitochondrial complex I, resulting in the formation of a sub-sized complex I of similar size in both mutants. Mass spectrometry identification revealed that the subcomplexes in both mutants lack an identical set of proteins of complex I. These results indicate that EMP24 and EMP25 function in the splicing of nad4 and nad5 introns, respectively, and are essential to maize kernel development. The identification of the subcomplexes provides genetic and molecular insights into the modular complex I assembly pathway in maize.

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 Dek37 Encodes a P-type PPR Protein That Affects cis-Splicing of Mitochondrial nad2 Intron 1 and Seed Development

Genetics ◽  
2018 ◽  
Vol 208 (3) ◽  
pp. 1069-1082 ◽  
Author(s):  
Dawei Dai ◽  
Shengchao Luan ◽  
Xiuzu Chen ◽  
Qun Wang ◽  
Yang Feng ◽  
...  
Keyword(s):  
Seed Development ◽  
Ppr Protein ◽  
Intron 1 ◽  
P Type

scholarly journals Multiple PPR protein interactions are involved in the RNA editing system in Arabidopsis mitochondria and plastids

2017 ◽  
Vol 114 (33) ◽  
pp. 8883-8888 ◽  
Author(s):  
Nuria Andrés-Colás ◽  
Qiang Zhu ◽  
Mizuki Takenaka ◽  
Bert De Rybel ◽  
Dolf Weijers ◽  
...  
Keyword(s):  
Rna Editing ◽  
Protein Interactions ◽  
Cytidine Deaminase ◽  
Pentatricopeptide Repeat ◽  
Ppr Protein ◽  
Different Types ◽  
Ppr Proteins ◽  
P Type

Recent identification of several different types of RNA editing factors in plant organelles suggests complex RNA editosomes within which each factor has a different task. However, the precise protein interactions between the different editing factors are still poorly understood. In this paper, we show that the E+-type pentatricopeptide repeat (PPR) protein SLO2, which lacks a C-terminal cytidine deaminase-like DYW domain, interacts in vivo with the DYW-type PPR protein DYW2 and the P-type PPR protein NUWA in mitochondria, and that the latter enhances the interaction of the former ones. These results may reflect a protein scaffold or complex stabilization role of NUWA between E+-type PPR and DYW2 proteins. Interestingly, DYW2 and NUWA also interact in chloroplasts, and DYW2-GFP overexpressing lines show broad editing defects in both organelles, with predominant specificity for sites edited by E+-type PPR proteins. The latter suggests a coordinated regulation of organellar multiple site editing through DYW2, which probably provides the deaminase activity to E+ editosomes.

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.

scholarly journals MISF2 Encodes an Essential Mitochondrial Splicing Co-factor Required for nad2 mRNA Processing and Embryo Development in Arabidopsis thaliana

2022 ◽  
Author(s):  
Tan-Trung Nguyen ◽  
Corinne Best ◽  
Sofia Shevtsov ◽  
Michal Zmudjak ◽  
Martine Quadrado ◽  
...  
Keyword(s):  
Gene Expression ◽  
Embryo Development ◽  
Mitochondrial Gene ◽  
Orthologous Gene ◽  
Early Embryo ◽  
Pentatricopeptide Repeat ◽  
Ppr Protein ◽  
Intron 1 ◽  
Ppr Proteins ◽  
Plant Embryo

Mitochondria play key roles in cellular energy metabolism in eukaryotes. Mitochondria of most organisms contain their own genome and specific transcription and translation machineries. The expression of angiosperm mtDNA involves extensive RNA-processing steps, such as RNA trimming, editing, and the splicing of numerous group II-type introns. Pentatricopeptide repeat (PPR) proteins are key players of plant organelle gene expression and RNA metabolism. In the present analysis, we reveal the function of the MITOCHONDRIAL SPLICING FACTOR 2 gene (MISF2, AT3G22670) and show that it encodes a mitochondria-localized PPR protein that is crucial for early embryo-development in Arabidopsis. Molecular characterization of embryo-rescued misf2 plantlets indicates that the splicing of nad2 intron 1 and thus respiratory complex I biogenesis are strongly compromised. Moreover, the molecular function seems conserved between MISF2 protein in Arabidopsis and its orthologous gene (EMP10) in maize, suggesting that the ancestor of MISF2/EMP10 was recruited to function in nad2 processing before the monocot-dicot divergence, ~200 million years ago. These data provide new insights into the function of nuclear-encoded factors in mitochondrial gene expression and respiratory chain biogenesis during plant embryo development.

scholarly journals The PPR-related splicing cofactor MSP1/EMB1025 protein, encoded by At4g20090, encode an essential protein that is required for the splicing of nad1 intron 1 and for the biogenesis of complex I in Arabidopsis mitochondria

2019 ◽  
Author(s):  
Corinne Best ◽  
Michal Zmudjak ◽  
Oren Ostersetzer-Biran
Keyword(s):  
Complex I ◽  
Rna Binding ◽  
Embryo Rescue ◽  
Plant Mitochondria ◽  
Rna Stability ◽  
Pentatricopeptide Repeat ◽  
Ppr Protein ◽  
Intron 1 ◽  
Rna Maturation ◽  
Embryonic Arrest

AbstractGroup II introns are particularly plentiful within plant mitochondrial genomes (mtDNAs), where they interrupt the coding-regions of many organellar genes, especialy within complex I (CI) subunits. Their splicing is essential for the biogenesis of the respiratory system and is facilitated by various protein-cofactors that belong to a diverse set of RNA-binding cofactors. These including maturases, which co-evolved with their host-introns, and various trans-acting factors, such as members of the pentatricopeptide-repeat (PPR) protein family. The genomes of angiosperms contain hundreds of PPR-related genes that are postulated to reside within the organelles and affect diverse posttranscriptional steps, such as editing, RNA-stability and processing or translation. Here, we report the characterization of MSP1 (Mitochondria Splicing PPR-factor 1; also denoted as EMB1025), which plays a key role in the processing of nad1 pre-RNAs in Arabidopsis mitochondria. Mutations in MSP1 gene-locus (At4g20090) result in early embryonic arrest. To analyze the putative roles of MSP1 in organellar RNA-metabolism we used a modified embryo-rescue method, which allowed us to obtain sufficient plant tissue for the analysis of the RNA and protein profiles associated with msp1 mutants. Our data indicate that MSP1 is essential for the trans-splicing of nad1 intron 1 in Arabidopsis mitochondria. Accordingly, msp1 mutants show CI biogenesis defects and reduced respiratory-mediated functions. These results provide with important insights into the roles of nuclear-encoded factors during early plant development, and contribute to our limited understanding of the importance of RNA-maturation and splicing in plant mitochondria during early embryogenesis.

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