The conserved domain in MORF proteins has distinct affinities to the PPR and E elements in PPR RNA editing factors

Bayer-Császár, Eszter; Haag, Sascha; Jörg, Anja; Glass, Franziska; Härtel, Barbara; Obata, Toshihiro; Meyer, Etienne H.; Brennicke, Axel; Takenaka, Mizuki

doi:10.1016/j.bbagrm.2017.05.004

Cited by 46 publications

(36 citation statements)

References 60 publications

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“…Disruption of single-polypeptide RNA editing factors like in the moss Physcomitrella (Schallenberg-R€ udinger & may have occurred independently or may be yet another synapomorphy of the HT clade. We found no evidence in A. agrestis, however, for additional, non-PPR 'helper' components identified in angiosperms, such as MORFs/RIPs indicative of more complex editosomes (Bentolila et al, 2012;Takenaka et al, 2012;Zehrmann et al, 2015;Bayer-Cs asz ar et al, 2017;Haag et al, 2017).…”

Section: New Phytologistcontrasting

confidence: 79%

“…However, the setup of organelle RNA editing is evidently more complex in flowering plants, where truncated proteins require interactions with DYW domains supplied in trans, frequently mediated by extra helper proteins (e.g. NUWA and multiple organellar RNA editing factor (MORF)/RNA-editing factor interacting protein (RIP) proteins) in much more complex editosomes (Takenaka et al, 2012;Bentolila et al, 2012;Boussardon et al, 2012;Sun et al, 2013Sun et al, , 2015Sun et al, , 2016Zehrmann et al, 2015;Diaz et al, 2017;Bayer-Cs asz ar et al, 2017;Andr es-Col as et al, 2017;Guillaumot et al, 2017;Sandoval et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis

et al. 2019

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Summary Hornworts are crucial to understand the phylogeny of early land plants. The emergence of ‘reverse’ U‐to‐C RNA editing accompanying the widespread C‐to‐U RNA editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornwort–tracheophyte clade. C‐to‐U RNA editing is well understood after identification of many editing factors in models like Arabidopsis thaliana and Physcomitrella patens, but there is no plant model yet to investigate U‐to‐C RNA editing. The hornwort Anthoceros agrestis is now emerging as such a model system. We report on the assembly and analyses of the A. agrestis chloroplast and mitochondrial genomes, their transcriptomes and editomes, and a large nuclear gene family encoding pentatricopeptide repeat (PPR) proteins likely acting as RNA editing factors. Both organelles in A. agrestis feature high amounts of RNA editing, with altogether > 1100 sites of C‐to‐U and 1300 sites of U‐to‐C editing. The nuclear genome reveals > 1400 genes for PPR proteins with variable carboxyterminal DYW domains. We observe significant variants of the ‘classic’ DYW domain, in the meantime confirmed as the cytidine deaminase for C‐to‐U editing, and discuss the first attractive candidates for reverse editing factors given their excellent matches to U‐to‐C editing targets according to the PPR‐RNA binding code.

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Section: New Phytologistcontrasting

confidence: 79%

Section: Introductionmentioning

confidence: 99%

Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis

et al. 2019

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“…Bimolecular fluorescence complementation analyses suggested that NUWA enhances the interaction between SLO2, a mitochondrial E+ subclass PPR, and DYW2 in mitochondria (Andrés‐Colás et al , ; Guillaumot et al , ). The NUWA proteins were co‐immunoprecipitated with MORF1 or MORF2 proteins, suggesting that this protein is also associated with MORF proteins in vivo (Bayer‐Csaszar et al , ). It is unclear whether the 12 PPR motifs in NUWA contribute to specific RNA binding for target recognition.…”

Section: Insights Into the Plant Editosome: Towards The Identificatiomentioning

confidence: 99%

Plant organellar RNA editing: what 30 years of research has revealed

Small

Schallenberg‐Rüdinger

et al. 2019

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Summary The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C‐U base transitions) is highly prevalent within organelles (that is, mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA‐binding proteins are at the heart of post‐transcriptional RNA expression. The C‐to‐U RNA editing process in plant mitochondria involves numerous nuclear‐encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence‐specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.

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“…in the editing of organelle transcripts (2). In Arabidopsis, nine Multiple Organellar RNA editing Factors (MORF/RIPs) were described as required for many editing sites of plant organelles (19)(20)(21). Members of the ORRM family and the CP31 protein, containing RNA Recognition Motifs (RRMs), were also found to influence RNA editing in plant organelles (22,23).…”

Section: Significancementioning

confidence: 99%

Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria

Guillaumot

López-Obando

Baudry

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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RNA editing is converting hundreds of cytosines into uridines during organelle gene expression of land plants. The pentatricopeptide repeat (PPR) proteins are at the core of this posttranscriptional RNA modification. Even if a PPR protein defines the editing site, a DYW domain of the same or another PPR protein is believed to catalyze the deamination. To give insight into the organelle RNA editosome, we performed tandem affinity purification of the plastidial CHLOROPLAST BIOGENESIS 19 (CLB19) PPR editing factor. Two PPR proteins, dually targeted to mitochondria and chloroplasts, were identified as potential partners of CLB19. These two proteins, a P-type PPR and a member of a small PPR-DYW subfamily, were shown to interact in yeast. Insertional mutations resulted in embryo lethality that could be rescued by embryo-specific complementation. A transcriptome analysis of these complemented plants showed major editing defects in both organelles with a very high PPR type specificity, indicating that the two proteins are core members of E+-type PPR editosomes.

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The conserved domain in MORF proteins has distinct affinities to the PPR and E elements in PPR RNA editing factors

Cited by 46 publications

References 60 publications

Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis

Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis

Plant organellar RNA editing: what 30 years of research has revealed

Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria

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