Insertional editing in mitochondria of Physarum

RNA editing of 10 Didymium iridis mitochondrial genes and comparison with the homologous genes in Physarum polycephalum

“…Single C insertions predominated and were partially shared Single C insertions comprised the majority of insertional events (90%), which is identical to that observed in P. polycephalum (Miller et al 1993;Gott and Rhee 2008). The average interval between single C insertion events was 27.2 6 5.9 bp for the 10 genes (Supplemental Table 2).…”

“…The average interval between single C insertion events was 27.2 6 5.9 bp for the 10 genes (Supplemental Table 2). This is comparable to C insertions occurring on an average of every 25 bp in P. polycephalum mRNA (Miller et al 1993). …”

“…Extensive C nucleotide insertions were reported in the atp1 mitochondrial gene of the myxomycete Physarum polycephalum (Mahendran et al 1991). Further studies revealed that U insertions and mixed dinucleotide insertion editing events also occur in the mitochondrial protein-coding genes and ribosomal RNAs of this organism (Miller et al 1993;Mahendran et al 1994). In addition to base insertions, C-to-U changes occur in the cox1 gene of several Myxomycetes (Gott et al 1993;Horton and Landweber 2000).…”

Cotranscriptional editing of Physarum mitochondrial RNA requires local features of the native template

“…Gott downstream sites+ Indeed, the localized nucleic acid requirements for editing are not surprising given that nontemplated nucleotides are added to mRNAs every 25 nt on average, and frequently occur within 12-14 nucleotides of each other (Miller et al+, 1993)+…”

“…Many organisms, including humans, express RNAs with specific sequence differences relative to the genes from which they are transcribed+ These alterations, which include base substitutions and insertion or deletion of nucleotides, are needed to generate functional RNAs, and, in some cases, are used to produce alternative gene products and/or regulate expression of proteins (Gott & Emeson, 2000)+ Editing mechanisms are diverse, and can occur at the transcriptional or posttranscriptional level+ Cotranscriptional editing events are particularly interesting, as they may have parallels to processes regulating transcriptional elongation+ A majority of the RNAs transcribed from the mitochondrial genome of Physarum polycephalum are extensively edited by the precise insertion of mono-(C, U) and dinucleotides (CU, GU, UA, AA, GC, UU) in a process that is closely linked to transcription )+ Insertions occur, on average, once every 25 nt in mRNAs, and once every 40 nt in rRNAs and tRNAs (Miller et al+, 1993)+ These alterations are predicted to create open reading frames in mRNAs and conserved motifs in structural RNAs+ Four specific C-to-U changes have also been observed in Physarum mitochondrial RNAs (Gott et al+, 1993), but these appear to arise via a distinct mechanism )+ Two systems have been developed to study Physarum insertional RNA editing in vitro: isolated mitochondria and partially purified mitochondrial transcription elongation complexes (mtTEC)+ Both involve analysis of nascent RNAs that are initiated in vivo and extended in vitro+ Run-on transcripts synthesized in isolated mitochondria are generally fully edited (Visomirski-Robic & Gott, 1995), whereas there is only partial editing at each site in RNAs synthesized by mtTECs (Cheng & Gott, 2000)+ The extent of editing in both systems can be systematically varied, however, by altering the reaction conditions (Cheng et al+, 2001)+ Studies using these systems led to the conclusion that insertional editing in Physarum mitochondria is a cotranscriptional process, whereby nonencoded nucleotides are added to the 39 ends of nascent transcripts (Cheng et al+, 2001)+…”