TRANSCRIPTOME 2002: From Functional Genomics to Systems
Multiple Determinants of RNA Editing in Physarum Mitochondria
Jonatha M. Gott, Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH
The term RNA editing is used to describe a number of mechanistically distinct processes which result in the production of an RNA whose sequence differs in specific ways from that of its template. Editing can involve alteration of either bases (substitution) or nucleotides (insertion/deletion). Substitutional editing involves changing one base into another at the RNA level, usually via deamination of cytosine to uridine (C to U) or adenosine to inosine (A to I). Other forms of editing entail the deletion of encoded nucleotides and/or the insertion of additional, non-encoded nucleotides, either post-transcriptionally or as the RNA is being synthesized. These changes lead to programmed alterations in gene expression, ranging from amino acid substitutions to the creation of entire open reading frames.
The organism that carries out the broadest range of editing events known to date is the myxomycete Physarum polycephalum. The majority of the RNAs encoded in the Physarum mitochondrial genome (including mRNAs, tRNAs, and rRNAs) are altered through the frequent insertion of non-encoded C, U, UA, CU, GU, UU, AA, or GC residues at specific sites and rare C to U changes. These sequence alterations occur co-transcriptionally through a process that is both precise and extremely efficient. We are currently investigating the mechanism by which the insertional editing machinery specifies both the sites of insertion and the identity of the added nucleotides. Using a series of hybrid templates that consist of editing-competent transcription elongation complexes (mtTEC) linked to other DNA fragments, we show that editing is not strictly sequence-dependent and that the site of nucleotide insertion and the identity of the added nucleotide are likely to be specified independently.
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