Mitochondrial RNA editing PPR proteins can tolerate protein tags at E as well as at DYW domain termini

Brehme, Nadja; Zehrmann, Anja; Verbitskiy, Daniil; Härtel, Barbara; Takenaka, Mizuki

doi:10.3389/fpls.2014.00127

Cited by 10 publications

(6 citation statements)

References 29 publications

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“…7). These results are consistent with reports that several mitochondrial PPR-DYW editing factors cannot tolerate C-terminal fusions to GFP nor to a His tag (31,32). It is likely that C-terminal tags interfere with the function of the C-terminal DYW motif in some PPR-DYW proteins.…”

Section: Similar Sequences Are Present Upstream Of the Five Editing Tsupporting

confidence: 82%

Cytidine Deaminase Motifs within the DYW Domain of Two Pentatricopeptide Repeat-containing Proteins Are Required for Site-specific Chloroplast RNA Editing

Wagoner

Sun

Lin

et al. 2015

Journal of Biological Chemistry

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Background: Pentatricopeptide repeat (PPR) proteins are site-specific RNA editing factors; many have C-terminal motifs of unknown function. Results: Site-directed mutagenesis of two PPR-DYW domains significantly reduces editing efficiency. Conclusion: Residues conserved in cytidine deaminases in the DYW domains are important for editing activity. Significance: This study strengthens the evidence that the DYW domains of PPR proteins carry the deaminase activity necessary for C-to-U modification.

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Section: Similar Sequences Are Present Upstream Of the Five Editing Tsupporting

confidence: 82%

Cytidine Deaminase Motifs within the DYW Domain of Two Pentatricopeptide Repeat-containing Proteins Are Required for Site-specific Chloroplast RNA Editing

Wagoner

Sun

Lin

et al. 2015

Journal of Biological Chemistry

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“…These data were further supported by the analysis of PPR protein-RNA crystal structures [24,25,[34][35][36][37]. PPRs are classified into two main groups: P and PLS type proteins, which in addition to canonical 35-amino acid PPR motifs (P) include long (L) or short (S) repeat variants [22,38]. While PLS-type proteins are almost exclusively associated with RNA editing [9,39], P-type PPR factors facilitate a wide range of organellar RNA expression steps going from stabilization to translation [27,40].…”

Section: Introductionmentioning

confidence: 73%

MISF2 Encodes an Essential Mitochondrial Splicing Co-factor Required for nad2 mRNA Processing and Embryo Development in Arabidopsis thaliana

Nguyen¹,

Best²,

Shevtsov³

et al. 2022

Preprint

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Mitochondria play key roles in cellular energy metabolism in eukaryotes. Mitochondria of most organisms contain their own genome and specific transcription and translation machineries. The expression of angiosperm mtDNA involves extensive RNA-processing steps, such as RNA trimming, editing, and the splicing of numerous group II-type introns. Pentatricopeptide repeat (PPR) proteins are key players of plant organelle gene expression and RNA metabolism. In the present analysis, we reveal the function of the MITOCHONDRIAL SPLICING FACTOR 2 gene (MISF2, AT3G22670) and show that it encodes a mitochondria-localized PPR protein that is crucial for early embryo-development in Arabidopsis. Molecular characterization of embryo-rescued misf2 plantlets indicates that the splicing of nad2 intron 1 and thus respiratory complex I biogenesis are strongly compromised. Moreover, the molecular function seems conserved between MISF2 protein in Arabidopsis and its orthologous gene (EMP10) in maize, suggesting that the ancestor of MISF2/EMP10 was recruited to function in nad2 processing before the monocot-dicot divergence, ~200 million years ago. These data provide new insights into the function of nuclear-encoded factors in mitochondrial gene expression and respiratory chain biogenesis during plant embryo development.

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“…It was previously reported that MORF genes family have role in abiotic stress and involved in RNA editing ( Wang et al, 2019 ). Pentatricopeptide repeat proteins contains a C-terminal domain and interact with MORF genes ( Takenaka et al, 2012 ; Brehme et al, 2014 ). Latest research reported that MORF involved in plant growth, development, stress response such as survival of seedling rice, drought resistance in poplar, and pathogen resistance in tobacco ( Wang et al, 2019 ; Zhang et al, 2019 ; Yang et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress

Rehman

Uzair²,

Chao

et al. 2022

Front. Plant Sci.

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Ribonucleic acid editing (RE) is a post-transcriptional process that altered the genetics of RNA which provide the extra level of gene expression through insertion, deletions, and substitutions. In animals, it converts nucleotide residues C-U. Similarly in plants, the role of RNA editing sites (RES) in rice under alkaline stress is not fully studied. Rice is a staple food for most of the world population. Alkaline stress cause reduction in yield. Here, we explored the effect of alkaline stress on RES in the whole mRNA from rice chloroplast and mitochondria. Ribonucleic acid editing sites in both genomes (3336 RESs) including chloroplast (345 RESs) and mitochondria (2991 RESs) with average RES efficiency ∼55% were predicted. Our findings showed that majority of editing events found in non-synonymous codon changes and change trend in amino acids was hydrophobic. Four types of RNA editing A-G (A-I), C-T (C-U), G-A, and T-C were identified in treated and untreated samples. Overall, RNA editing efficiency was increased in the treated samples. Analysis of Gene Ontology revealed that mapped genes were engaged in many biological functions and molecular processes. We also checked the expression of pentatricopeptide repeat (PPR), organelle zinc-finger (OZI), and multiple organellar RNA editing factors/RNA editing factor interacting proteins genes in control and treatment, results revealed upregulation of PPR and OZ1 genes in treated samples. This induction showed the role of these genes in RNA editing. The current findings report that RNA editing increased under alkaline stress which may contribute in adaptation for rice by changing amino acids in edited genes (88 genes). These findings will provide basis for identification of RES in other crops and also will be useful in alkaline tolerance development in rice.

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Mitochondrial RNA editing PPR proteins can tolerate protein tags at E as well as at DYW domain termini

Cited by 10 publications

References 29 publications

Cytidine Deaminase Motifs within the DYW Domain of Two Pentatricopeptide Repeat-containing Proteins Are Required for Site-specific Chloroplast RNA Editing

Cytidine Deaminase Motifs within the DYW Domain of Two Pentatricopeptide Repeat-containing Proteins Are Required for Site-specific Chloroplast RNA Editing

MISF2 Encodes an Essential Mitochondrial Splicing Co-factor Required for nad2 mRNA Processing and Embryo Development in Arabidopsis thaliana

Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress

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