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 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 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.

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 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 In vivo stabilization of endogenous chloroplast RNAs by customized artificial pentatricopeptide repeat proteins

2020 ◽  
Author(s):  
Nikolay Manavski ◽  
Louis-Valentin Meteignier ◽  
Margarita Rojas ◽  
Andreas Brachmann ◽  
Alice Barkan ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Sequence Specificity ◽  
Pentatricopeptide Repeat ◽  
Functional Capabilities ◽  
Ppr Protein ◽  
Repeat Proteins ◽  
Ppr Proteins ◽  
Physical Barriers

ABSTRACTPentatricopeptide repeat (PPR) proteins are helical repeat-proteins that bind RNA in a modular fashion with a sequence-specificity that can be manipulated by the use of an amino acid code. As such, PPR repeats are promising scaffolds for the design of RNA binding proteins for synthetic biology applications. However, the in vivo functional capabilities of artificial PPR proteins built from consensus PPR motifs are just starting to be explored. Here, we report in vivo functions of an artificial PPR protein, dPPRrbcL, made of consensus PPR motifs that were designed to bind a sequence near the 5’ end of rbcL transcripts in Arabidopsis chloroplasts. We used a functional complementation assay to demonstrate that this protein bound its intended RNA target with specificity in vivo and that it substituted for a natural PPR protein by stabilizing processed rbcL mRNA. We targeted a second protein of analogous design to the petL 5’ UTR, where it substituted for the native stabilizing PPR protein PGR3, albeit inefficiently. These results showed that artificial PPRs can be engineered to functionally mimic the class of native PPR proteins that serve as physical barriers against exoribonucleases.

scholarly journals GENE EXPRESSION DURING INDIRECT SOMATIC EMBRYOGENESIS OF PLANTS

2004 ◽  
Vol 42 (2) ◽  
Author(s):  
Tammy Estabrooks ◽  
Zhongmin Dong
Keyword(s):  
Gene Expression ◽  
Somatic Embryogenesis ◽  
Embryo Development ◽  
Current Literature ◽  
Molecular Mechanisms ◽  
Indirect Somatic Embryogenesis ◽  
Experimental Tool ◽  
Plant Embryo ◽  
Plant Embryo Development

Somatic embryogenesis is the process by which somatic cells are induced into an embryogenic state, followed by differentiation into embryos. Somatic embryogenesis, in addition to being a method of propagation, can serve as an experimental tool for research into plant embryo development. This is a review of the current literature on in vitro plant somatic embryogenesis and the molecular advances made to identify genes expressed during the various stages of this process. Some factors hindering the elucidation of the molecular mechanisms underlying somatic embryogenesis are discussed.L’embryogenèse somatique est le processus par lequel les cellules somatiques passent à l’état embryogène et se différencient en embryons. En plus de constituer une méthode de propagation, elle peut servir d’outil expérimental de recherche pour développer des embryons de plantes. Le présent document est une revue de la documentation sur l’embryogenèse somatique végétale in vitro et sur les progrès réalisés à l’échelle moléculaire pour identifier les gènes exprimés au cours des divers stades du processus. On examine aussi certains facteurs qui rendent difficile l’élucidation des mécanismes moléculaires de l’embryogenèse somatique.

P–181 Morphine regulates BMP4 growth factor and is involved in in-vitro early embryo development and PGCs formation

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
I Muñoa ◽  
M Araolaza-Lasa ◽  
I Urizar-Arenaza ◽  
M Gianzo Citores ◽  
N Subiran Ciudad
Keyword(s):  
Gene Expression ◽  
Growth Factor ◽  
Environmental Factors ◽  
Embryo Development ◽  
Early Embryo ◽  
Epigenetic Changes ◽  
Morphine Treatment ◽  
Early Embryo Development

Abstract Study question To elucidate if morphine can alter embryo development. Summary answer Chronic morphine treatment regulates BMP4 growth factor, in terms of gene expression and H3K27me3 enrichment and promotes in-vitro blastocysts development and PGC formation. What is known already BMP4 is a member of the bone morphogenetic protein family, which acts mainly through SMAD dependent pathway, to play an important role in early embryo development. Indeed, BMP4 enhances pluripotency in mouse embryonic stem cells (mESCs) and, specifically, is involved in blastocysts formation and primordial germ cells (PGCs) generation. Although, external morphine influence has been previously reported on the early embryo development, focus on implantation and uterus function, there is a big concern in understanding how environmental factors can cause stable epigenetic changes, which could be maintained during development and lead to health problems. Study design, size, duration First, OCT4-reported mESCs were chronically treated with morphine during 24h, 10–5mM. After morphine removal, mESCs were collected for RNA-seq and H3K27me3 ChIP-seq study. To elucidate the role of morphine in early embryo development, two cell- embryos stage were chronically treated with morphine for 24h and in-vitro cultured up to the blastocyst stage in the absence of morphine. Furthermore, after morphine treatment mESCs were differentiated to PGCs, to elucidate the role of morphine in PGC differentiation. Participants/materials, setting, methods Transcriptomic analyses and H3K27me3 genome wide distribution were carried out by RNA-Sequencing and Chip-Sequencing respectively. Validations were performed by RNA-RT-qPCR and Chip-RT-qPCR. Main results and the role of chance Dynamic transcriptional analyses identified a total of 932 differentially expressed genes (DEGs) after morphine treatment on mESCs, providing strong evidence of a transcriptional epigenetic effect induced by morphine. High-throughput screening approaches showed up Bmp4 as one of the main morphine targets on mESCs. Morphine caused an up-regulation of Bmp4 gene expression together with a decrease of H3K27me3 enrichment at promoter level. However, no significant differences were observed on gene expression and H3K27me3 enrichment on BMP4 signaling pathway components (such as Smad1, Smad4, Smad5, Smad7, Prdm1 and Prmd14) after morphine treatment. On the other hand, the Bmp4 gene expression was also up-regulated in in-vitro morphine treated blastocyst and in-vitro morphine treated PGCs. These results were consistent with the increase in blastocyst rate and PGC transformation rate observed after morphine chronic treatment. Limitations, reasons for caution To perform the in-vitro analysis. Further studies are needed to describe the whole signaling pathways underlying BMP4 epigenetic regulation after morphine treatment. Wider implications of the findings: Our findings confirmed that mESCs and two-cell embryos are able to memorize morphine exposure and promote both blastocyst development and PGCs formation through potentially BMP4 epigenetic regulation. These results provide insights understanding how environmental factors can cause epigenetic changes during the embryo development, leading to alterations and producing health problems/diseases Trial registration number Not applicable

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.

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