Substitutional editing of Heterocapsa triquetra chloroplast transcripts and a folding model for its divergent chloroplast 16S rRNA

Substitutional editing increases genomic plasticity by changing or modifying bases at the RNA level. In this study we sequenced 10 mature chloroplast mRNAs, the chloroplast 16S rRNA and a partial chloroplast 23S rRNA from the dinoflagellate Heterocapsa triquetra, and found multiple types of substitutional editing, with A-to-G editing predominating. A-to-G editing of mRNAs converts two unusual AUA start codons into conventional AUG start codons, but three AUA start codons are not edited, showing that this dinoflagellate chloroplast has three possible start codons: AUG, AUA and UUG. To analyze the editing effects on rRNAs, we computationally predicted the secondary structure of the 16S rRNA based on the E. coli model. There are twenty editing sites in well-conserved regions of the secondary structure and eleven out of them restore conservation with other models. Moreover, A-to-G editing sites are frequently found in loop regions rather than double-stranded regions, suggesting that the A-to-G editing mechanism in dinoflagellate chloroplasts is different from that responsible for animal nuclear A-to-I(G) editing. The model of the edited 16S rRNA derived by the comparative method shares conserved secondary structural elements with other 16S rRNAs in spite of its very divergent primary sequence, supporting its role as a functional component of the chloroplast ribosome.