Automatic simulation of RNA editing in plants for the identification of novel putative Open Reading Frames

In plant mitochondria an essential mechanism for gene expression is RNA editing, often influencing the synthesis of functional proteins. RNA editing alters the linearity of genetic information transfer, intro- ducing differences between RNAs and their coding DNA sequences that hind both experimental and computational research of genes. Thus common software tools for gene search, successfully exploited to find canonic genes, often can fail in discovering genes encrypted in the genome of plants. In this work we propose a novel strategy useful to intercept candidate coding sequences resulting from some possible editing substitutions on the start and stop codons of a given input organism DNA. Our method is based on the simulation of the RNA editing mechanism, in order to generate candidate Open Reading Frame (ORF) sequences that could code for some, yet unknown, proteins. Results obtained on the mtDNA of Oryza sativa are promising, since we identified ORF sequences trascripted in Oriza, that do not cor- respond to already known proteins in this organism. Part of the corresponding amino acid sequences present high homologies with proteins already discovered in other organisms, the remaining ones could represent novel proteins not yet discovered in Oryza.