| Insertional RNA editing has been identified in the mitochondria, of the myxomycot, Physarum polycephalum. This editing is found in rRNAs, mRNAs and tRNAs. The predominant insertion is single cytidines, although uridines and dinucleotides are also inserted at some specific sites. The distribution and variation of editing sites in a conserved core region of the mitochondrial small subunit rRNA were studied (Chapter 2). Six different myxomycetes were analyzed for RNA editing—Didymium nigripes, Didymium iridis, Stemonitis flavogenita, Physarum didermoides, Physarum polycephalum, and Lycogala epidendrum. Analysis of editing sites in these organisms revealed that the predominantly inserted nucleotide is cytidine. A single uridine insertion site was also identified in this region. The two dinucleotide insertion sites (AA and CU) found in this region in Physarum polycephalum mitochondrial RNA are present in all of these organisms except Lycogala. There was not a single editing site that was present in all six organisms. A total of 23 different editing sites were identified among these organisms but no organism has more than 10 of these editing sites and no two editing sites were located closer than 9 nucleotides from one another. Phylogenetic trees based on the small subunit ribosomal RNA sequences revealed that Lycogala is the most anciently divergent of the six myxomycetes studied. Physarum, Stemonitis and Didymium genera are equally divergent from one another and from Lycogala. Alignment of the sequences from the mitochondrial and the nuclear small subunit rRNAs produced phylogenetic trees that are congruent but differ from the phylogenetic trees predicted by current classification. Furthermore, editing site variation does not correlate with the general sequence variation among these organisms. The most parsimonious explanation is that editing sites have been established and deleted at different sites since the divergences of these organisms.; Editing in the cytochrome b mRNA of Physarum polycephalum has been extensively studied. The RNA editing insertions include both mononucleotides and dinucleotides. The present investigation shows that cytochrome b mRNA of Didymium nigripes is edited with single cytidines, single uridines and dinucleotide insertions (Chapter 4). Comparison of the mitochondrial DNA of the cyt b gene of Didymium nigripes with the cytochrome b cDNA of Physarum polycephalum indicates that the cytochrome b mRNA of Didymium nigripes requires editing to be functional.; Recombination in the mitochondrial genome of Physarum polycephalum is known to occur in the presence of an exogenous mitochondrial fusion plasmid (pmF). The presence of the mitochondrial DNA with the integrated pmF can make the plasmodium immortal. A series of recombination events are required for the integration of the plasmid. In Chapter 3, I report the first example of endogenous recombination in Physarum mitochondria. Recombination between two 14 bp direct repeats results in the excision of a significant reading frame that could encode a protein in Physarum mitochondria. The excised portion of the mtDNA was not detected, presumably due to its failure to replicate or its rapid segregation from the major portion of the mitochondrial DNA. |
