Pentatricopeptide Repeat Proteins in Trypanosoma brucei Function in Mitochondrial Ribosomes

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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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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Identification of pentatricopeptide repeat proteins in Trypanosoma brucei

Molecular and Biochemical Parasitology ◽

10.1016/j.molbiopara.2006.06.006 ◽

2006 ◽

Vol 150 (1) ◽

pp. 37-45 ◽

Cited By ~ 32

Author(s):

Melissa K. Mingler ◽

Andrea M. Hingst ◽

Sandra L. Clement ◽

Laura E. Yu ◽

Larissa Reifur ◽

...

Keyword(s):

Trypanosoma Brucei ◽

Pentatricopeptide Repeat ◽

Repeat Proteins ◽

Pentatricopeptide Repeat Proteins

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The Analysis of the Editing Defects in the dyw2 Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins

Plants ◽

10.3390/plants9020280 ◽

2020 ◽

Vol 9 (2) ◽

pp. 280 ◽

Cited By ~ 3

Author(s):

Bastien Malbert ◽

Matthias Burger ◽

Mauricio Lopez-Obando ◽

Kevin Baudry ◽

Alexandra Launay-Avon ◽

...

Keyword(s):

Mitochondrial Genes ◽

Pentatricopeptide Repeat ◽

Repeat Proteins ◽

Rna Targets ◽

Ppr Proteins ◽

Almost All ◽

Pentatricopeptide Repeat Proteins

C to U editing is one of the post-transcriptional steps which are required for the proper expression of chloroplast and mitochondrial genes in plants. It depends on several proteins acting together which include the PLS-class pentatricopeptide repeat proteins (PPR). DYW2 was recently shown to be required for the editing of many sites in both organelles. In particular almost all the sites associated with the E+ subfamily of PPR proteins are depending on DYW2, suggesting that DYW2 is required for the function of E+-type PPR proteins. Here we strengthened this link by identifying 16 major editing sites controlled by 3 PPR proteins: OTP90, a DYW-type PPR and PGN and MEF37, 2 E+-type PPR proteins. A re-analysis of the DYW2 editotype showed that the 49 sites known to be associated with the 18 characterized E+-type PPR proteins all depend on DYW2. Considering only the 288 DYW2-dependent editing sites as potential E+-type PPR sites, instead of the 795 known editing sites, improves the performances of binding predictions systems based on the PPR code for E+-type PPR proteins. However, it does not compensate for poor binding predictions.

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P-class pentatricopeptide repeat proteins are required for efficient 5′ end formation of plant mitochondrial transcripts

RNA Biology ◽

10.4161/rna.26129 ◽

2013 ◽

Vol 10 (9) ◽

pp. 1511-1519 ◽

Cited By ~ 15

Author(s):

Stefan Binder ◽

Katrin Stoll ◽

Birgit Stoll

Keyword(s):

Pentatricopeptide Repeat ◽

Repeat Proteins ◽

Mitochondrial Transcripts ◽

Pentatricopeptide Repeat Proteins

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In Arabidopsis thaliana mitochondria 5′ end polymorphisms of nad4L-atp4 and nad3-rps12 transcripts are linked to RNA PROCESSING FACTORs 1 and 8

Plant Molecular Biology ◽

10.1007/s11103-021-01153-9 ◽

2021 ◽

Author(s):

Sarah Schleicher ◽

Stefan Binder

Keyword(s):

Arabidopsis Thaliana ◽

Rna Processing ◽

Degradation Products ◽

Underlying Mechanism ◽

Transcriptional Level ◽

Pentatricopeptide Repeat ◽

Repeat Proteins ◽

P Type ◽

Pentatricopeptide Repeat Proteins ◽

Processing Factors

Abstract Key message RNA PROCESSING FACTORs 1 AND 8 (RPF1 and RPF8), both restorer of fertility like pentatricopeptide repeat proteins, are required for processing of dicistronic nad4L-atp4 and nad3-rps12 transcripts in Arabidopsis mitochondria. Abstract In mitochondria of Arabidopsis thaliana (Arabidopsis), the 5′ termini of many RNAs are generated on the post-transcriptional level. This process is still poorly understood in terms of both the underlying mechanism as well as proteins required. Our studies now link the generation of polymorphic 5′ extremities of the dicistronic nad3-rps12 and nad4L-atp4 transcripts to the function of the P-type pentatricopeptide repeat proteins RNA PROCESSING FACTORs 8 (RPF8) and 1 (RPF1). RPF8 is required to generate the nad3-rps12 -141 5′ end in ecotype Van-0 whereas the RPF8 allele in Col has no function in the generation of any 5′ terminus of this transcript. This observation strongly suggests the involvement of an additional factor in the generation of the -229 5′ end of nad3-rps12 transcripts in Col. RPF1, previously found to be necessary for the generation of the -228 5′ end of the major 1538 nucleotide-long nad4 mRNAs, is also important for the formation of nad4L-atp4 transcripts with a 5′ end at position -318 in Col. Many Arabidopsis ecotypes contain inactive RPF1 alleles resulting in the accumulation of various low abundant nad4L-atp4 RNAs which might represent precursor and/or degradation products. Some of these ecotypes accumulate major, but slightly smaller RNA species. The introduction of RPF1 into these lines not only establishes the formation of the major nad4L-atp4 dicistronic mRNA with the -318 5′ terminus, the presence of this gene also suppresses the accumulation of most alternative nad4L-atp4 RNAs. Beside RPF1, several other factors contribute to nad4L-atp4 transcript formation.

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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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