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

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.

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

Plant and Cell Physiology ◽

10.1093/pcp/pcz083 ◽

2019 ◽

Vol 60 (8) ◽

pp. 1734-1746 ◽

Cited By ~ 12

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.

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Dek35 Encodes a PPR Protein that Affects cis -Splicing of Mitochondrial nad4 Intron 1 and Seed Development in Maize

Molecular Plant ◽

10.1016/j.molp.2016.08.008 ◽

2017 ◽

Vol 10 (3) ◽

pp. 427-441 ◽

Cited By ~ 55

Author(s):

Xinze Chen ◽

Fan Feng ◽

Weiwei Qi ◽

Liming Xu ◽

Dongsheng Yao ◽

...

Keyword(s):

Seed Development ◽

Ppr Protein ◽

Intron 1

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

Plant and Cell Physiology ◽

10.1093/pcp/pcz204 ◽

2019 ◽

Vol 61 (2) ◽

pp. 370-380 ◽

Cited By ~ 6

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.

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A PPR Protein ACM1 Is Involved in Chloroplast Gene Expression and Early Plastid Development in Arabidopsis

International Journal of Molecular Sciences ◽

10.3390/ijms22052512 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2512

Author(s):

Xinwei Wang ◽

Yaqi An ◽

Ye Li ◽

Jianwei Xiao

Keyword(s):

Fluorescent Protein ◽

Chloroplast Development ◽

Nuclear Gene ◽

Pentatricopeptide Repeat ◽

Plastid Development ◽

Chloroplast Gene Expression ◽

Knock Out ◽

Rnai Line ◽

Ppr Protein ◽

P Type

Chloroplasts cannot develop normally without the coordinated action of various proteins and signaling connections between the nucleus and the chloroplast genome. Many questions regarding these processes remain unanswered. Here, we report a novel P-type pentatricopeptide repeat (PPR) factor, named Albino Cotyledon Mutant1 (ACM1), which is encoded by a nuclear gene and involved in chloroplast development. Knock-down of ACM1 transgenic plants displayed albino cotyledons but normal true leaves, while knock-out of the ACM1 gene in seedlings was lethal. Fluorescent protein analysis showed that ACM1 was specifically localized within chloroplasts. PEP-dependent plastid transcript levels and splicing efficiency of several group II introns were seriously affected in cotyledons in the RNAi line. Furthermore, denaturing gel electrophoresis and Western blot experiments showed that the accumulation of chloroplast ribosomes was probably damaged. Collectively, our results indicate ACM1 is indispensable in early chloroplast development in Arabidopsis cotyledons.

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Comprehensive Transcriptome Analyses Reveal Candidate Genes for Variation in Seed Size/Weight During Peanut (Arachis hypogaea L.) Domestication

Frontiers in Plant Science ◽

10.3389/fpls.2021.666483 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhongfeng Li ◽

Xingguo Zhang ◽

Kunkun Zhao ◽

Kai Zhao ◽

Chengxin Qu ◽

...

Keyword(s):

Candidate Genes ◽

Seed Development ◽

Seed Size ◽

Snp Markers ◽

Pentatricopeptide Repeat ◽

Significant Differential Expression ◽

Ppr Protein ◽

Cultivated Peanut ◽

Transcriptome Analyses ◽

Wild Peanut

Seed size/weight, a key domestication trait, is also an important selection target during peanut breeding. However, the mechanisms that regulate peanut seed development are unknown. We re-sequenced 12 RNA samples from developing seeds of two cultivated peanut accessions (Lines 8106 and 8107) and wild Arachis monticola at 15, 30, 45, and 60 days past flowering (DPF). Transcriptome analyses showed that ∼36,000 gene loci were expressed in each of the 12 RNA samples, with nearly half exhibiting moderate (2 ≤ FPKM < 10) expression levels. Of these genes, 12.2% (4,523) were specifically expressed during seed development, mainly at 15 DPF. Also, ∼12,000 genes showed significant differential expression at 30, 45, and/or 60 DPF within each of the three peanut accessions, accounting for 31.8–34.1% of the total expressed genes. Using a method that combined comprehensive transcriptome analysis and previously mapped QTLs, we identified several candidate genes that encode transcription factor TGA7, topless-related protein 2, IAA-amino acid hydrolase ILR1-like 5, and putative pentatricopeptide repeat-containing (PPR) protein. Based on sequence variations identified in these genes, SNP markers were developed and used to genotype both 30 peanut landraces and a genetic segregated population, implying that EVM0025654 encoding a PPR protein may be associated with the increased seed size/weight of the cultivated accessions in comparison with the allotetraploid wild peanut. Our results provide additional knowledge for the identification and functional research into candidate genes responsible for the seed size/weight phenotype in peanut.

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

Journal of Experimental Botany ◽

10.1093/jxb/eraa273 ◽

2020 ◽

Vol 71 (18) ◽

pp. 5495-5505 ◽

Cited By ~ 1

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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