Identifying Plant Pentatricopeptide Repeat Proteins Using a Variable Selection Method

Motivation: Pentatricopeptide repeat (PPR), which is a triangular pentapeptide repeat domain, plays an important role in plant growth. Features extracted from sequences are applicable to PPR protein identification using certain classification methods. However, which components of a multidimensional feature (namely variables) are more effective for protein discrimination has never been discussed. Therefore, we seek to select variables from a multidimensional feature for identifying PPR proteins.Method: A framework of variable selection for identifying PPR proteins is proposed. Samples representing PPR positive proteins and negative ones are equally split into a training and a testing set. Variable importance is regarded as scores derived from an iteration of resampling, training, and scoring step on the training set. A model selection method based on Gaussian mixture model is applied to automatic choice of variables which are effective to identify PPR proteins. Measurements are used on the testing set to show the effectiveness of the selected variables.Results: Certain variables other than the multidimensional feature they belong to do work for discrimination between PPR positive proteins and those negative ones. In addition, the content of methionine may play an important role in predicting PPR proteins.

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

10.1101/2020.11.21.392746 ◽

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.

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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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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

BMC Plant Biology ◽

10.1186/s12870-020-02765-x ◽

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.

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Identification of Pentatricopeptide Repeat Proteins in the Model OrganismDictyostelium discoideum

International Journal of Genomics ◽

10.1155/2013/586498 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 2

Author(s):

Sam Manna ◽

Jessica Brewster ◽

Christian Barth

Keyword(s):

Dictyostelium Discoideum ◽

Rna Binding ◽

Rna Binding Proteins ◽

Gene Products ◽

Antisense Inhibition ◽

Pentatricopeptide Repeat ◽

Repeat Proteins ◽

Ppr Proteins ◽

Pentatricopeptide Repeat Proteins ◽

Encoding Genes

Pentatricopeptide repeat (PPR) proteins are RNA binding proteins with functions in organelle RNA metabolism. They are found in all eukaryotes but have been most extensively studied in plants. We report on the identification of 12 PPR-encoding genes in the genome of the protistDictyostelium discoideum, with potential homologs in other members of the same lineage and some predicted novel functions for the encoded gene products in protists. For one of the gene products, we show that it localizes to the mitochondria, and we also demonstrate that antisense inhibition of its expression leads to slower growth, a phenotype associated with mitochondrial dysfunction.

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Pentatricopeptide Repeat Proteins in Trypanosoma brucei Function in Mitochondrial Ribosomes

Molecular and Cellular Biology ◽

10.1128/mcb.00708-07 ◽

2007 ◽

Vol 27 (19) ◽

pp. 6876-6888 ◽

Cited By ~ 78

Author(s):

Mascha Pusnik ◽

Ian Small ◽

Laurie K. Read ◽

Thomas Fabbro ◽

André Schneider

Keyword(s):

Trypanosoma Brucei ◽

Large Subunit ◽

Direct Interaction ◽

Pentatricopeptide Repeat ◽

Amino Acid Motif ◽

Mitochondrial Ribosomes ◽

Repeat Proteins ◽

Ppr Proteins ◽

Pentatricopeptide Repeat Proteins ◽

Large Subunit Rrna

ABSTRACT The pentatricopeptide repeat (PPR), a degenerate 35-amino-acid motif, defines a novel eukaryotic protein family. Plants have 400 to 500 distinct PPR proteins, whereas other eukaryotes generally have fewer than 5. The few PPR proteins that have been studied have roles in organellar gene expression, probably via direct interaction with RNA. Here we show that the parasitic protozoan Trypanosoma brucei encodes 28 distinct PPR proteins, an extraordinarily high number for a nonplant organism. A comparative analysis shows that seven out of eight selected PPR proteins are mitochondrially localized and essential for oxidative phosphorylation. Six of these are required for the stabilization of mitochondrial rRNAs and, like ribosomes, are associated with the mitochondrial membranes. Furthermore, one of the PPR proteins copurifies with the large subunit rRNA. Finally, ablation of all of the PPR proteins that were tested induces degradation of the other PPR proteins, indicating that they function in concert. Our results show that a significant number of trypanosomal PPR proteins are individually essential for the maintenance and/or biogenesis of mitochondrial rRNAs.

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

10.1101/544486 ◽

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.

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Localization of the Rf3 restorer-of-fertility gene for maize S-type cytoplasmic male sterility

10.32469/10355/41914 ◽

2012 ◽

Author(s):

◽

Tiffany Langewisch

Keyword(s):

Cytoplasmic Male Sterility ◽

Candidate Gene ◽

Male Sterility ◽

Pollen Grains ◽

Candidate Gene Approach ◽

Chromosome 2 ◽

Pentatricopeptide Repeat ◽

Restorer Of Fertility ◽

Ppr Proteins ◽

Pentatricopeptide Repeat Proteins

Maize S-type cytoplasmic male sterility (CMS-S) is a maternally inherited trait that prevents pollen grains from developing to maturity. CMS-S is associated with the high levels of a novel mitochondrial transcript, orf355/orf77. Cleavage of this RNA, mediated by the nuclear restorer Rf3, reverses the sterility. Rf3 was previously mapped on the long arm of chromosome 2. The goals of this research were to fine-map the locus and to identify Rf3 using a candidate gene approach. Genotyping of nearisogenic lines (NILs) mapped Rf3 to a 1.98 Mb region of 2L. Six candidate genes, all predicted to code for mitochondrially targeted pentatricopeptide repeat proteins (PPR), were PCR-amplified, sequenced, and compared from multiple Rf3-containing NILs and non-restoring rf3 inbreds. One PPR-Rf3 candidate gene had two consistent differences between multiple restoring and non-restoring lines. Gene expression in pre-emergent tassels from the fertility-restored and non-restored plants was compared. Within the 3 Mb region surrounding Rf3, 9 genes were differentially expressed between restoring and non-restoring lines, including genes that could code for an ATP-binding protein, an ATPase, and four PPR proteins. Although Rf3 has not yet been identified, this study has revealed five promising candidates.

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

Plant and Cell Physiology ◽

10.1093/pcp/pcaa110 ◽

2020 ◽

Vol 61 (11) ◽

pp. 1954-1966 ◽

Cited By ~ 1

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.

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The Amount of RNA Editing Sites in Liverwort Organellar Genes Is Correlated with GC Content and Nuclear PPR Protein Diversity

Genome Biology and Evolution ◽

10.1093/gbe/evz232 ◽

2019 ◽

Vol 11 (11) ◽

pp. 3233-3239 ◽

Cited By ~ 3

Author(s):

Shanshan Dong ◽

Chaoxian Zhao ◽

Shouzhou Zhang ◽

Hong Wu ◽

Weixue Mu ◽

...

Keyword(s):

Rna Editing ◽

Phylogenetic Diversity ◽

Gc Content ◽

Pentatricopeptide Repeat ◽

Protein Coding ◽

Protein Diversity ◽

Ppr Protein ◽

Ppr Proteins ◽

Codon Positions ◽

Positive Correlations

Abstract RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here, we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded pentatricopeptide repeat (PPR) proteins in the transcriptome assemblies of these taxa. We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059 PPR protein sequences. The abundance of organellar RNA editing sites varies greatly among liverwort lineages, genes, and codon positions, and shows strong positive correlations with the GC content of protein-coding genes, and the diversity of the PLS class of nuclear PPR proteins.

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The nuclear-localized PPR protein OsNPPR1 is important for mitochondrial function and endosperm development in rice

Journal of Experimental Botany ◽

10.1093/jxb/erz226 ◽

2019 ◽

Vol 70 (18) ◽

pp. 4705-4720 ◽

Cited By ~ 7

Author(s):

Yuanyuan Hao ◽

Yunlong Wang ◽

Mingming Wu ◽

Xiaopin Zhu ◽

Xuan Teng ◽

...

Keyword(s):

Mitochondrial Function ◽

Endosperm Development ◽

Pentatricopeptide Repeat ◽

Coding Region ◽

Rice Mutant ◽

Ppr Protein ◽

Isolation And Characterization ◽

Ppr Proteins

Abstract Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants. Recent studies revealed the functions of PPR proteins in organellar RNA metabolism and plant development, but the functions of most PPR proteins, especially PPRs localized in the nucleus, remain largely unknown. Here, we report the isolation and characterization of a rice mutant named floury and growth retardation1 (fgr1). fgr1 showed floury endosperm with loosely arranged starch grains, decreased starch and amylose contents, and retarded seedling growth. Map-based cloning showed that the mutant phenotype was caused by a single nucleotide substitution in the coding region of Os08g0290000. This gene encodes a nuclear-localized PPR protein, which we named OsNPPR1, that affected mitochondrial function. In vitro SELEX and RNA-EMSAs showed that OsNPPR1 was an RNA protein that bound to the CUCAC motif. Moreover, a number of retained intron (RI) events were detected in fgr1. Thus, OsNPPR1 was involved in regulation of mitochondrial development and/or functions that are important for endosperm development. Our results provide novel insights into coordinated interaction between nuclear-localized PPR proteins and mitochondrial function.

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