RNA editing in plant mitochondria —Connecting RNA target sequences and acting proteins

Takenaka, Mizuki; Verbitskiy, Daniil; Zehrmann, Anja; Härtel, Barbara; Bayer-Császár, Eszter; Glass, Franziska; Brennicke, Axel

doi:10.1016/j.mito.2014.04.005

Cited by 37 publications

(27 citation statements)

References 89 publications

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“…The data so far demonstrate that the interaction of CLB19 with its RNA targets depends primarily on the PPR repeats, whereas the E domain is essential for CLB19 function but does not have a direct participation in target recognition. Recent data support the hypothesis that E domains might be important for the interaction with other proteins of the editosome (Takenaka et al ., ). A prominent group of proteins shown to be essential in organelle RNA editing is the MORF/RIP family (Bentolila et al ., ; Takenaka et al ., ; Sun et al ., ).…”

Section: Resultsmentioning

confidence: 97%

“…We also corroborated the idea that the E domain is essential for the CLB19 editing function, because the CLB19 that is missing its E domain cannot complement the clb19 mutant phenotype. These results are consistent with the findings for other editing PPR proteins of the E‐ or the DYW‐classes and support an essential role of this domain in the editing process (Okuda et al ., , , ; Takenaka et al ., ). However, these findings stand in contrast with the DWY domain that has been shown to be dispensable for RNA editing in some PPR proteins but not in others (Okuda et al ., ; Wagoner et al ., ).…”

Section: Discussionmentioning

confidence: 97%

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Functional analysis of the Arabidopsis thaliana CHLOROPLAST BIOGENESIS 19 pentatricopeptide repeat editing protein

Ramos‐Vega¹,

Guevara-García²,

Llamas³

et al. 2015

New Phytologist

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SummaryThe Arabidopsis thaliana pentatricopeptide repeat (PPR) family of proteins contains several degenerate 35-aa motifs named PPR repeats. These proteins control diverse post-transcriptional regulatory mechanisms, including RNA editing. CLB19 belongs to the PLS subfamily of PPR proteins and is essential for the editing and functionality of the subunit A of plastidencoded RNA polymerase (RpoA) and the catalytic subunit of the Clp protease (ClpP1).We demonstrate in vitro that CLB19 has a specific interaction with these two targets, in spite of their modest sequence similarity. Using site-directed mutagenesis of the rpoA target, we analyzed the essential nucleotides required for CLB19-rpoA interactions.We verified that, similar to other editing proteins, the C-terminal E domain of CLB19 is essential for editing but not for RNA binding. Using biomolecular fluorescence complementation, we demonstrated that the E domain of CLB19 interacts with the RNA-interacting protein MORF2/RIP2 but not with MORF9/RIP9. An interesting finding from this analysis was that overexpression of a truncated CLB19 protein lacking the E domain interferes with cell fate during megasporogenesis and the subsequent establishment of a female gametophyte, supporting an important role of plastids in female gametogenesis.Together these analyses provide important clues about the particularities of the CLB19 editing protein.

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Section: Resultsmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 97%

Functional analysis of the Arabidopsis thaliana CHLOROPLAST BIOGENESIS 19 pentatricopeptide repeat editing protein

Ramos‐Vega¹,

Guevara-García²,

Llamas³

et al. 2015

New Phytologist

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“…An example of this is a chloroplast RRM (RNA recognition motif) protein, which supports, but is not essential for, the accumulation of a footprint in the 3′-UTR of chloroplast ndhF mRNA (30). Also, recent reports that PPRs involved in editing interact with RRM-proteins and other factors suggest that larger protein complexes that assemble around a PPR may increase footprint size (62,63). …”

Section: Resultsmentioning

confidence: 99%

Systematic analysis of plant mitochondrial and chloroplast small RNAs suggests organelle-specific mRNA stabilization mechanisms

et al. 2016

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Land plant organellar genomes encode a small number of genes, many of which are essential for respiration and photosynthesis. Organellar gene expression is characterized by a multitude of RNA processing events that lead to stable, translatable transcripts. RNA binding proteins (RBPs), have been shown to generate and protect transcript termini and eventually induce the accumulation of short RNA footprints. We applied knowledge of such RBP-derived footprints to develop software (sRNA miner) that enables identification of RBP footprints, or other clusters of small RNAs, in organelles. We used this tool to determine mitochondrial and chloroplast cosRNAs (clustered organellar sRNAs) in Arabidopsis. We found that in mitochondria, cosRNAs coincide with transcript 3′-ends, but are largely absent from 5′-ends. In chloroplasts this bias is absent, suggesting a different mode of 5′ processing, possibly owing to different sets of RNases. Furthermore, we identified a large number of cosRNAs that represent silenced insertions of mitochondrial DNA in the nuclear genome of Arabidopsis. Steady-state RNA analyses demonstrate that cosRNAs display differential accumulation during development. Finally, we demonstrate that the chloroplast RBP PPR10 associates in vivo with its cognate cosRNA. A hypothetical role of cosRNAs as competitors of mRNAs for PPR proteins is discussed.

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“…In plant organelles, RNA editing consists predominantly of a specific deamination of cytidine to uridine in RNA. RNA editing modifies genetic information (amino acid identity) or RNA structure (the stabilization of an intron structure for efficient splicing or processing) (Takenaka et al ., ). In Arabidopsis, a total of 46 editing sites have been identified in chloroplast transcripts and 619 editing sites have been identified in mitochondrial transcripts (Bentolila et al ., ; Ruwe et al ., ), including sites with low editing extent.…”

Section: Introductionmentioning

confidence: 97%

Empty pericarp7 encodes a mitochondrial E–subgroup pentatricopeptide repeat protein that is required for ccmF_N editing, mitochondrial function and seed development in maize

et al. 2015

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SUMMARYRNA editing, converting cytidines (C) to uridines (U) at specific sites in the transcripts of mitochondria and plastids, plays a critical role in organelle gene expression in land plants. Recently pentatricopeptide repeat (PPR) proteins were identified as site-specific recognition factors for RNA editing. In this study, we characterized an empty pericarp7 mutant (emp7) in Zea mays (maize), which confers an embryo-lethal phenotype. In emp7 mutants, mitochondrial functions are seriously perturbed, resulting in a strikingly reduced respiration rate. Emp7 encodes an E-subgroup PPR protein that is localized exclusively in the mitochondrion. Null mutation of Emp7 abolishes the C ? U editing of ccmF N transcript solely at position 1553. CcmF N is coding for a subunit of heme lyase complex in the cytochrome c maturation pathway. The resulting Phe ? Ser substitution in CcmF N leads to the loss of CcmF N protein and a strikingly reduced c-type cytochrome. Consequently, the mitochondrial cytochrome-linked respiratory chain is impaired as a result of the disassembly of complex III in the emp7 mutant. These results indicate that the PPR-E subgroup protein EMP7 is required for C ? U editing of ccmF N -1553 at a position essential for cytochrome c maturation and mitochondrial oxidative phosphorylation, and hence is essential to embryo and endosperm development in maize.

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RNA editing in plant mitochondria —Connecting RNA target sequences and acting proteins

Cited by 37 publications

References 89 publications

Functional analysis of the Arabidopsis thaliana CHLOROPLAST BIOGENESIS 19 pentatricopeptide repeat editing protein

Functional analysis of the Arabidopsis thaliana CHLOROPLAST BIOGENESIS 19 pentatricopeptide repeat editing protein

Systematic analysis of plant mitochondrial and chloroplast small RNAs suggests organelle-specific mRNA stabilization mechanisms

Empty pericarp7 encodes a mitochondrial E–subgroup pentatricopeptide repeat protein that is required for ccmF_N editing, mitochondrial function and seed development in maize

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RNA editing in plant mitochondria —Connecting RNA target sequences and acting proteins

Cited by 37 publications

References 89 publications

Functional analysis of the Arabidopsis thaliana CHLOROPLAST BIOGENESIS 19 pentatricopeptide repeat editing protein

Functional analysis of the Arabidopsis thaliana CHLOROPLAST BIOGENESIS 19 pentatricopeptide repeat editing protein

Systematic analysis of plant mitochondrial and chloroplast small RNAs suggests organelle-specific mRNA stabilization mechanisms

Empty pericarp7 encodes a mitochondrial E–subgroup pentatricopeptide repeat protein that is required for ccmFN editing, mitochondrial function and seed development in maize

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Empty pericarp7 encodes a mitochondrial E–subgroup pentatricopeptide repeat protein that is required for ccmF_N editing, mitochondrial function and seed development in maize