Comparison of Insertional RNA Editing in Myxomycetes

Cai Chen, David Frankhouser and Ralf Bundschuh

PLOS Computational Biology, 2012, vol. 8, issue 2, 1-11

Abstract: RNA editing describes the process in which individual or short stretches of nucleotides in a messenger or structural RNA are inserted, deleted, or substituted. A high level of RNA editing has been observed in the mitochondrial genome of Physarum polycephalum. The most frequent editing type in Physarum is the insertion of individual Cs. RNA editing is extremely accurate in Physarum; however, little is known about its mechanism. Here, we demonstrate how analyzing two organisms from the Myxomycetes, namely Physarum polycephalum and Didymium iridis, allows us to test hypotheses about the editing mechanism that can not be tested from a single organism alone. First, we show that using the recently determined full transcriptome information of Physarum dramatically improves the accuracy of computational editing site prediction in Didymium. We use this approach to predict genes in the mitochondrial genome of Didymium and identify six new edited genes as well as one new gene that appears unedited. Next we investigate sequence conservation in the vicinity of editing sites between the two organisms in order to identify sites that harbor the information for the location of editing sites based on increased conservation. Our results imply that the information contained within only nine or ten nucleotides on either side of the editing site (a distance previously suggested through experiments) is not enough to locate the editing sites. Finally, we show that the codon position bias in C insertional RNA editing of these two organisms is correlated with the selection pressure on the respective genes thereby directly testing an evolutionary theory on the origin of this codon bias. Beyond revealing interesting properties of insertional RNA editing in Myxomycetes, our work suggests possible approaches to be used when finding sequence motifs for any biological process fails. Author Summary: RNA is an important biomolecule that is deeply involved in all aspects of molecular biology, such as protein production, gene regulation, and viral replication. However, many significant aspects such as the mechanism of RNA editing are not well understood. RNA editing is the process in which an organism's RNA is modified through the insertion, deletion, or substitution of single or short stretches of nucleotides. The slime mold Physarum polycephalum is a model organism for the study of RNA editing; however, hardly anything is known about its editing machinery. We show that the combination of two organisms (Physarum polycephalum and Didymium iridis) can provide a better understanding of insertional RNA editing than one organism alone. We predict several new edited genes in Didymium. By comparing the sequences of the two organisms in the vicinity of the editing sites we establish minimal requirements for the location of the information by which these editing sites are recognized. Lastly, we directly verify a theory for one of the most striking features of the editing sites, namely their codon bias.

Date: 2012
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1002400

DOI: 10.1371/journal.pcbi.1002400

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