Requirement of Various Protein Combinations for Each C-to-U RNA Editosome in Plant Organelles

Takenaka, Mizuki; Jörg, Anja; Burger, Matthias; Haag, Sascha

doi:10.1007/978-3-319-78190-7_9

Cited by 3 publications

(3 citation statements)

References 128 publications

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“…PPR editing factors were first thought to be acting in a one PPR/one editing site fashion, without interacting with any other protein. Then, a more complex model for the editosome emerged (2, 3) in which the PPR tract of the PPR protein, helped by other proteins such as MORF/RIP proteins (47, 48), selectively binds the cis element surrounding the RNA editing site and the E+/DYW domain performs the cytidine-to-uracil editing reaction. Additionally, the E1/E2 domain is also involved in RNA binding (49), protein-protein interactions with other editosome components (50) and participates to the active site (23, 32).…”

Section: Discussionmentioning

confidence: 99%

“…In embryophyte organellar transcripts, RNA editing specifically deaminates hundreds of cytidines into uridines. It is catalyzed by a protein complex called "editosome" that contains several members of various nuclear encoded protein families such as Pentatrico Peptide Repeat (PPR), Multiple Organellar RNA editing Factor / RNA-editing factor Interacting Protein (MORF/RIP) or Organelle RNA Recognition Motif-containing (ORRM) proteins (1)(2)(3)(4). Among all these editing factors, the PPR proteins were shown to be the trans specificity factors that bind the RNA cis recognition elements, therefore allowing the specific targeting of the edited cytidines (5,6).…”

Section: Introductionmentioning

confidence: 99%

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Dissecting the molecular puzzle of the editosome core in Arabidopsis organelles

Baudry,

Monachello,

Castandet

et al. 2024

Preprint

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Over the last decade, the composition of the C-to-U RNA editing complex in embryophyte organelles has turned out to be much more complex than first expected. While PPR proteins were initially thought to act alone, significant evidences have clearly depicted a sophisticated mechanism with numerous protein-protein interaction involving PPR and non-PPR proteins. Moreover, the identification of specific functional partnership between PPRs also suggests that, in addition to the highly specific PPRs directly involved in the RNA target recognition, non-RNA-specific ones are required. Although some of them, such as DYW1 and DYW2, were shown to be the catalytic domains of the editing complex, the molecular function of others, such as NUWA, remains elusive. It was suggested that they might stabilize the complex by acting as a scaffold. We here performed functional complementation of thecrr28-2mutant with truncated CRR28 proteins mimicking PPR without the catalytic domain and show that they exhibit a specific dependency to one of the catalytic proteins DYW1 or DYW2. Moreover, we also characterized the role of the PPR NUWA in the editing reaction and show that it likely acts as a scaffolding factor. NUWA is no longer required for efficient editing of the CLB19 editing sites once this RNA specific PPR is fused to the DYW catalytic domain of its partner DYW2. Altogether, our results strongly support a flexible, evolutive and resilient editing complex in which RNA binding activity, editing activity and stabilization/scaffolding function can be provided by one or more PPRs.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Dissecting the molecular puzzle of the editosome core in Arabidopsis organelles

Baudry,

Monachello,

Castandet

et al. 2024

Preprint

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“…It is well known that PLS‐class PPR proteins are responsible for RNA editing (reviewed in Small et al., 2020). There are several ways to gain novel editing sites, for instance, proliferation of PLS‐class PPR proteins that target different RNA sequences and reassembly of E‐ and DYW‐subclass proteins to generate new editosome complexes that increase the number of accessible sites (Takenaka et al., 2018). PPR proteins in angiosperms typically comprise 400–600 members (Fujii & Small, 2011), fewer than in gymnosperms (509–2131).…”

Section: Discussionmentioning

confidence: 99%

Evolution of mitochondrial RNA editing in extant gymnosperms

Chaw

2022

The Plant Journal

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To unveil the evolution of mitochondrial RNA editing in gymnosperms, we characterized mitochondrial genomes (mitogenomes), plastid genomes, RNA editing sites, and pentatricopeptide repeat (PPR) proteins from 10 key taxa representing four of the five extant gymnosperm clades. The assembled mitogenomes vary in gene content due to massive gene losses in Gnetum and Conifer II clades. Mitochondrial gene expression levels also vary according to protein function, with the most highly expressed genes involved in the respiratory complex. We identified 9132 mitochondrial C-to-U editing sites, as well as 2846 P-class and 8530 PLS-class PPR proteins. Regains of editing sites were demonstrated in Conifer II rps3 transcripts whose corresponding mitogenomic sequences lack introns due to retroprocessing. Our analyses reveal that non-synonymous editing is efficient and results in more codons encoding hydrophobic amino acids. In contrast, synonymous editing, although performed with variable efficiency, can increase the number of U-ending codons that are preferentially utilized in gymnosperm mitochondria. The inferred loss-to-gain ratio of mitochondrial editing sites in gymnosperms is 2.1:1, of which losses of non-synonymous editing are mainly due to genomic C-to-T substitutions. However, such substitutions only explain a small fraction of synonymous editing site losses, indicating distinct evolutionary mechanisms. We show that gymnosperms have experienced multiple lineage-specific duplications in PLS-class PPR proteins. These duplications likely contribute to accumulated RNA editing sites, as a mechanistic correlation between RNA editing and PLS-class PPR proteins is statistically supported.

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