Editing of Mitochondrial RNAs in Physarum polycephalum
The mitochondrial transcriptome of the true acellular slime mold Physarum polycephalum (Physarum) undergoes extensive RNA editing to produce precise, site-specific changes not encoded at the DNA level. RNA editing in Physarum is essential for proper mitochondrial gene expression by creating open reading frames in protein-coding RNAs and by altering the folding stability of structural RNAs. Physarum carries out one of the widest range of RNA editing events yet described. These changes to mitochondrial RNAs involve the site-specific insertion of over 1300 “extra” nucleotides, deletion of 3 encoded nucleotides, targeted base conversions, and the removal and replacement of nucleotides at the 5′ end of certain tRNAs. While these sequence alterations are absolutely required for the production of functional transcripts, it remains a mystery why they are not encoded in the mitochondrial genome. Although various examples of RNA editing have been described in several eukaryotic organisms, Physarum mitochondria achieve non-templated nucleotide insertion by a unique co-transcriptional mechanism. The cis-acting elements required for insertion editing have been localized to a relatively small region in the vicinity of editing sites, but the details as to how editing sites are recognized and the identity of the trans-acting editing factor(s) required for insertion of these extra nucleotides remain to be elucidated. Two other mechanistically distinct forms of editing, 5′ tRNA editing and C-to-U conversion, have also been described, which proceed via two independent, posttranscriptional pathways. The relatively recent availability of genome and transcriptome sequence data has facilitated the identification of potential candidates for each of these activities and experiments to determine which of these factors are involved in the various forms of editing are underway.
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