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 A Single-Target Mitochondrial RNA Editing Factor of Funaria hygrometrica Can Fully Reconstitute RNA Editing at Two Sites in Physcomitrella patens

2017 ◽  
Vol 58 (3) ◽  
pp. 496-507 ◽  
Author(s):  
Mareike Schallenberg-R�dinger ◽  
Bastian Oldenkott ◽  
Manuel Hiss ◽  
Phuong Le Trinh ◽  
Volker Knoop ◽  
...  
Keyword(s):  
Rna Editing ◽  
Physcomitrella Patens ◽  
Mitochondrial Rna ◽  
Funaria Hygrometrica ◽  
Single Target

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 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 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 Cofactor-Independent RNA Editing by a Synthetic S-Type PPR Protein

2021 ◽  
Author(s):  
Kalia Bernath-Levin ◽  
Jason Schmidberger ◽  
Suvi Honkanen ◽  
Bernard Gutmann ◽  
Yueming Kelly Sun ◽  
...  
Keyword(s):  
Rna Editing ◽  
Rna Processing ◽  
Tandem Repeats ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Screening Method ◽  
Pentatricopeptide Repeat ◽  
Wide Range ◽  
Ppr Proteins ◽  
P Type

ABSTRACT Pentatricopeptide repeat (PPR) proteins are RNA-binding proteins that are attractive tools for RNA processing in synthetic biology applications given their modular structure and ease of design. Several distinct types of motifs have been described from natural PPR proteins, but almost all work so far with synthetic PPR proteins has focused on the most widespread P-type motifs. We have investigated synthetic PPR proteins based on tandem repeats of the more compact S-type PPR motif found in plant organellar RNA editing factors, and particularly prevalent in the lycophyte Selaginella. With the aid of a novel plate-based screening method we show that synthetic S-type PPR proteins are easy to design, bind with high affinity and specificity, and are functional in a wide range of pH, salt and temperature conditions. We find that they outperform a synthetic P-type PPR scaffold in many situations. We designed an S-type editing factor to edit an RNA target in E. coli and demonstrate that it edits effectively without requiring any additional cofactors to be added to the system. These qualities make S-type PPR scaffolds ideal for developing new RNA processing tools.

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

2019 ◽  
Vol 11 (11) ◽  
pp. 3233-3239 ◽  
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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