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Nucleic Acids Research 2005 33(16):5063-5072; doi:10.1093/nar/gki820
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Published online 7 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs

Jonatha M. Gott*, Neeta Parimi and Ralf Bundschuh1

Center for RNA Molecular Biology, Case Western Reserve University Cleveland, OH 44106, USA 1Department of Physics, The Ohio State University Columbus, OH 43210, USA

*To whom correspondence should be addressed. Tel: +1 216 368 3930; Fax: +1 216 368 2010; Email: jmg13{at}case.edu

Received June 13, 2005. Revised August 19, 2005. Accepted August 19, 2005.

Gene finding is complicated in organisms that exhibit insertional RNA editing. Here, we demonstrate how our new algorithm Predictor of Insertional Editing (PIE) can be used to locate genes whose mRNAs are subjected to multiple frameshifting events, and extend the algorithm to include probabilistic predictions for sites of nucleotide insertion; this feature is particularly useful when designing primers for sequencing edited RNAs. Applying this algorithm, we successfully identified the nad2, nad4L, nad6 and atp8 genes within the mitochondrial genome of Physarum polycephalum, which had gone undetected by existing programs. Characterization of their mRNA products led to the unanticipated discovery of nucleotide deletion editing in Physarum. The deletion event, which results in the removal of three adjacent A residues, was confirmed by primer extension sequencing of total RNA. This finding is remarkable in that it comprises the first known instance of nucleotide deletion in this organelle, to be contrasted with nearly 500 sites of single and dinucleotide addition in characterized mitochondrial RNAs. Statistical analysis of this larger pool of editing sites indicates that there are significant biases in the 2 nt immediately upstream of editing sites, including a reduced incidence of nucleotide repeats, in addition to the previously identified purine-U bias.

Correspondence may also be addressed to Ralf Bundschuh. Tel: +1 614 688 3978; Fax: +1 614 292 7557; Email: Bundschuh{at}mps.ohio-state.edu


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C. Beargie, T. Liu, M. Corriveau, H. Y. Lee, J. Gott, and R. Bundschuh
Genome annotation in the presence of insertional RNA editing
Bioinformatics, November 15, 2008; 24(22): 2571 - 2578.
[Abstract] [Full Text] [PDF]


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