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Organellar RNA editing

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Abstract RNA editing is a term used for a number of mechanistically different processes that alter the nucleotide sequence of RNA molecules to differ from the gene sequence. RNA editing occurs in a wide variety of organisms and is particularly frequent in organelle transcripts of eukaryotes. The discontiguous phylogenetic distribution of mRNA editing, the mechanistic differences observed in different organisms, and the nonhomologous editing machinery described in different taxonomic groups all suggest that RNA editing has appeared independently several times. This raises questions about the selection pressures acting to maintain editing that are yet to be completely resolved. Editing tends to be frequent in organisms with atypical organelle genomes and acts to correct the effect of DNA mutations that would otherwise compromise the synthesis of functional proteins. Additional functions of editing in generating protein diversity or regulating gene expression have been proposed but so far lack widespread experimental evidence, at least in organelles. WIREs RNA 2011 2 493–506 DOI: 10.1002/wrna.72 This article is categorized under: RNA Processing > RNA Editing and Modification

Model for cytidine recognition and deamination in plant organelles. The C target of editing is specified by the presence of a cis‐element within the 20 nucleotides upstream. This sequence is recognized by a pentatricopeptide repeat (PPR) protein. PPR proteins involved in editing contain additional C‐terminal domains (the E and DYW domains). Mutant complementation assays with deleted PPR proteins showed that PPR motifs are involved in the recognition of the cis‐element and that the E domain is absolutely required for editing.90,91 Several models are plausible for the deamination reaction: the deamination could be catalyzed by the E domain (unlikely considering the lack of an obvious active site), by a yet‐to‐be‐discovered deaminase recruited by the E domain (top), or by the DYW domain (bottom) as proposed in Salone et al.92

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Eukaryote phylogeny and the distribution of organelle mRNA editing. The major eukaryote groups are shown, with groups where organellar mRNA editing has been reported in black.

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Cotranscriptional editing mechanism and machinery in Physarum polycephalum. Insertional editing in myxomycetes is cotranscriptional, and likely involves the mtRNAP (RNA polymerase). Myxomycetes MtRNAP normally incorporates nucleotides into the nascent RNA using the DNA sequence as template. Once an editing site is reached, templated transcription must be suspended to allow for the identification and insertion of a nontemplated nucleotide at the end of the nascent RNA. The nonpaired end of the RNA is then extended in a template‐dependent manner while accommodating the extra nucleotide within the transcription bubble. Editing site recognition requires ∼9 bp of the downstream template; it is not known how the identity of the added nucleotide is specified (Reprinted with permission from Ref 88. Copyright 2009 CSHL Press).

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RNA editing mechanism and editosome composition in Trypanosoma brucei. The sites of cleavage and the number of added or removed Us are specified in most cases by trans‐acting small RNAs (gRNAs).61 These gRNAs are partially complementary to the target pre‐edited sequence and fully complementary to the edited sequence. They interact with the target RNA to form a double‐stranded structure or ‘anchor’. An endonuclease cleaves at the first unpaired nucleotide upstream of the double‐stranded RNA structure. Then depending on the guide template, a U is added at the 3′ end of the cleaved RNA by a uridylyl‐transferase (TUTase) or a U is deleted by a U‐specific exonuclease. Recently the involvement of a 3'nucleotidyl phosphatase activity was shown.62 Ligation of the two mRNA fragments by a RNA ligase completes the process. RNA cleavage activity is carried out by RNase III‐type endonucleases KREN1‐3 (for Kinetoplastid RNA Editing 1‐3), U deletion by U specific 3' exonuclease KREX2, U insertion by 3' TUTase KRET2, and ligation by RNA ligase KREL1‐2. Additional proteins of the complex have been identified: KREPA 1‐6, also called MP (mitochondrial protein) 81, 63, 42, 24, 19, and 18 are proteins with a predicted oligonucleotide binding fold motif and zinc‐finger domains shown to be essential for the editosome integrity.63 Some editosome preparations also contain KREH1 or KREH2 RNA helicases involved in gRNA binding or in gRNA–mRNA hybrid unwinding.64 (Reprinted with permission from Ref 65. Copyright 2010 Elsevier).

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