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Novel and widespread RNA editing in dinoflagellates

RNA editing is a gene expression process in which some nucleotides in the mRNA sequence is "edited" during or immediately after transcription, and as a result the mRNA sequence differs from the transcribed copy of its coding DNA sequence (see Fig 1. RNA editing is particularly prominent in mitochondria, and is normally recognized by changes in an RNA sequence compared to that of its encoding DNA. Known RNA editing systems, which appear mechanistically and


evolutionarily unrelated, are of two general types: insertional/deletional, in which nucleotides are added to (and in some cases also removed from) a transcript, and substitutional, where one kind of nucleotide (nt) is replaced by another at a given location. Collaborating with Dr. Michael W. Gray's group from the Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada, we identified a novel type of substitutional mRNA editing that operates in dinoflagellate mitochondria and that appears to be widely distributed within this protist lineage. We found evidence of extensive substitutional editing of mitochondrial mRNAs in the dinoflagellate species Pfiesteria piscicida, Prorocentrum minimum and Crypthecodinium cohnii, based on a comparison of genomic and corresponding cDNA sequences determined for two mitochondrial DNA-encoded genes, cox1 (cytochrome oxidase subunit 1) and cob (apocytochrome b). In the cox1 mRNA, we identify 72 substitutions at 40 sites in 39 codons, whereas in cob mRNA, we infer 86 editing events at 51 sites in 48 codons. Editing, which takes place in distinct clusters, changes ~2% of the total sequence, occurs predominantly at first and second positions of codons, and involves mostly (but not exclusively) A-to-G (47%), U-to-C (23%) and C-to-U (17%) substitutions. In all but four of the 158 cases, editing changes the identity of the specified amino acid. At 21 (cox1) and 26 (cob) sites, the same nucleotide change is observed at the same position in at least two of the species investigated. At about one-third of the sites, editing results in an amino acid change that increases similarity between the dinoflagellate Cox1 and Cob sequences and their homologs in other organisms; presumably editing at these sites is of particular functional significance. Overall, about half of the editing events either maintain or increase similarity between the dinoflagellate protein sequences and their non-dinoflagellate homologs, while a further one-third of the alterations are "dinoflagellate-specific" (i.e., they involve a change to an amino acid residue selectively conserved in at least two of the dinoflagellate species at a given position). The nature, pattern and phylogenetic distribution of the inferred edits implies either that more than one type of previously described editing process operates on a given transcript in dinoflagellate mitochondria, or that a mechanistically unique type of mitochondrial mRNA editing has evolved within the dinoflagellate lineage. In addition, one conspicuous attribute of the extensive RNA editing in these dinoflagellates is that they tend to elevate G/C content of the genes which may as a result enhance translation by nucleus-coded tRNAs imported to the mitochondria.

J. Mol. Biol. 320:727-739