scholarly journals Two DYW Subclass PPR Proteins are Involved in RNA Editing of ccmFc and atp9 Transcripts in the Moss Physcomitrella patens: First Complete Set of PPR Editing Factors in Plant Mitochondria

2013 ◽  
Vol 54 (11) ◽  
pp. 1907-1916 ◽  
Author(s):  
Mizuho Ichinose ◽  
Chieko Sugita ◽  
Yusuke Yagi ◽  
Takahiro Nakamura ◽  
Mamoru Sugita
Keyword(s):  
Rna Editing ◽  
Physcomitrella Patens ◽  
Plant Mitochondria ◽  
Ppr Proteins ◽  
Complete Set

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 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 Assigning DYW-type PPR proteins to RNA editing sites in the funariid mosses Physcomitrella patens and Funaria hygrometrica

2011 ◽  
Vol 67 (2) ◽  
pp. 370-380 ◽  
Author(s):  
Mareike Rüdinger ◽  
Péter Szövényi ◽  
Stefan A. Rensing ◽  
Volker Knoop
Keyword(s):  
Rna Editing ◽  
Physcomitrella Patens ◽  
Funaria Hygrometrica ◽  
Ppr Proteins

scholarly journals A plant pentatricopeptide repeat protein with a DYW-deaminase domain is sufficient for catalyzing C-to-U RNA editing in vitro

2020 ◽  
Vol 295 (11) ◽  
pp. 3497-3505 ◽  
Author(s):  
Michael L. Hayes ◽  
Paola I. Santibanez
Keyword(s):  
Rna Editing ◽  
Inductively Coupled Plasma ◽  
Electrostatic Interactions ◽  
Physcomitrella Patens ◽  
Cytidine Deaminase ◽  
Pentatricopeptide Repeat ◽  
Transition State Analogs ◽  
Ppr Proteins ◽  
Editing Activity

Pentatricopeptide repeat (PPR) proteins with C-terminal DYW domains are present in organisms that undergo C-to-U editing of organelle RNA transcripts. PPR domains act as specificity factors through electrostatic interactions between a pair of polar residues and the nitrogenous bases of an RNA target. DYW-deaminase domains act as the editing enzyme. Two moss (Physcomitrella patens) PPR proteins containing DYW-deaminase domains, PPR65 and PPR56, can convert Cs to Us in cognate, exogenous RNA targets co-expressed in Escherichia coli. We show here that purified, recombinant PPR65 exhibits robust editase activity on synthetic RNAs containing cognate, mitochondrial PpccmFC sequences in vitro, indicating that a PPR protein with a DYW domain is solely sufficient for catalyzing C-to-U RNA editing in vitro. Monomeric fractions possessed the highest conversion efficiency, and oligomeric fractions had reduced activity. Inductively coupled plasma (ICP)–MS analysis indicated a stoichiometry of two zinc ions per highly active PPR65 monomer. Editing activity was sensitive to addition of zinc acetate or the zinc chelators 1,10-o-phenanthroline and EDTA. Addition of ATP or nonhydrolyzable nucleotide analogs stimulated PPR65-catalyzed RNA-editing activity on PpccmFC substrates, indicating potential allosteric regulation of PPR65 by ATP. Unlike for bacterial cytidine deaminase, addition of two putative transition-state analogs, zebularine and tetrahydrouridine, failed to disrupt RNA-editing activity. RNA oligonucleotides with a single incorporated zebularine also did not disrupt editing in vitro, suggesting that PPR65 cannot bind modified bases due to differences in the structure of the active site compared with other zinc-dependent nucleotide deaminases.

scholarly journals Organelle Genetics in Plants

2021 ◽  
Vol 22 (4) ◽  
pp. 2104
Author(s):  
Pedro Robles ◽  
Víctor Quesada
Keyword(s):  
Rna Editing ◽  
Posttranscriptional Regulation ◽  
Genome Engineering ◽  
Plant Mitochondria ◽  
Plastid Dna ◽  
Chloroplast Genomes ◽  
Wide Range ◽  
Organelle Genetics ◽  
Selection Of

Eleven published articles (4 reviews, 7 research papers) are collected in the Special Issue entitled “Organelle Genetics in Plants.” This selection of papers covers a wide range of topics related to chloroplasts and plant mitochondria research: (i) organellar gene expression (OGE) and, more specifically, chloroplast RNA editing in soybean, mitochondria RNA editing, and intron splicing in soybean during nodulation, as well as the study of the roles of transcriptional and posttranscriptional regulation of OGE in plant adaptation to environmental stress; (ii) analysis of the nuclear integrants of mitochondrial DNA (NUMTs) or plastid DNA (NUPTs); (iii) sequencing and characterization of mitochondrial and chloroplast genomes; (iv) recent advances in plastid genome engineering. Here we summarize the main findings of these works, which represent the latest research on the genetics, genomics, and biotechnology of chloroplasts and mitochondria.

Deepred-Mt: Deep representation learning for predicting C-to-U RNA editing in plant mitochondria

2021 ◽  
pp. 104682
Author(s):  
Alejandro A. Edera ◽  
Ian Small ◽  
Diego H. Milone ◽  
M. Virginia Sanchez-Puerta
Keyword(s):  
Rna Editing ◽  
Plant Mitochondria ◽  
Representation Learning

scholarly journals A Structural Perspective on the RNA Editing of Plant Respiratory Complexes

2022 ◽  
Vol 23 (2) ◽  
pp. 684
Author(s):  
Maria Maldonado ◽  
Kaitlyn Madison Abe ◽  
James Anthony Letts
Keyword(s):  
Rna Editing ◽  
Structural Information ◽  
Plant Mitochondria ◽  
Inner Mitochondrial Membrane ◽  
Respiratory Complexes ◽  
Core Energy ◽  
Harvesting Process ◽  
A Chain ◽  
The Impact ◽  
Structural Perspective

The last steps of respiration, a core energy-harvesting process, are carried out by a chain of multi-subunit complexes in the inner mitochondrial membrane. Several essential subunits of the respiratory complexes are RNA-edited in plants, frequently leading to changes in the encoded amino acids. While the impact of RNA editing is clear at the sequence and phenotypic levels, the underlying biochemical explanations for these effects have remained obscure. Here, we used the structures of plant respiratory complex I, complex III2 and complex IV to analyze the impact of the amino acid changes of RNA editing in terms of their location and biochemical features. Through specific examples, we demonstrate how the structural information can explain the phenotypes of RNA-editing mutants. This work shows how the structural perspective can bridge the gap between sequence and phenotype and provides a framework for the continued analysis of RNA-editing mutants in plant mitochondria and, by extension, in chloroplasts.

scholarly journals Functions of PPR Proteins in Plant Growth and Development

2021 ◽  
Vol 22 (20) ◽  
pp. 11274
Author(s):  
Xiulan Li ◽  
Mengdi Sun ◽  
Shijuan Liu ◽  
Qian Teng ◽  
Shihui Li ◽  
...  
Keyword(s):  
Plant Growth ◽  
Stress Responses ◽  
Rna Processing ◽  
Growth And Development ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Plant Mitochondria ◽  
Research Progress ◽  
Plant Growth And Development ◽  
Ppr Proteins

Pentatricopeptide repeat (PPR) proteins form a large protein family in land plants, with hundreds of different members in angiosperms. In the last decade, a number of studies have shown that PPR proteins are sequence-specific RNA-binding proteins involved in multiple aspects of plant organellar RNA processing, and perform numerous functions in plants throughout their life cycle. Recently, computational and structural studies have provided new insights into the working mechanisms of PPR proteins in RNA recognition and cytidine deamination. In this review, we summarized the research progress on the functions of PPR proteins in plant growth and development, with a particular focus on their effects on cytoplasmic male sterility, stress responses, and seed development. We also documented the molecular mechanisms of PPR proteins in mediating RNA processing in plant mitochondria and chloroplasts.

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