Authors:
Fabio Fassetti
1
;
Claudia Giallombardo
2
;
Ofelia Leone
1
;
Luigi Palopoli
1
;
Simona E. Rombo
2
and
Adolfo Saiardi
3
Affiliations:
1
Università della Calabria, Italy
;
2
Università degli Studi di Palermo, Italy
;
3
University College, United Kingdom
Keyword(s):
Sequence Analysis, Editing Simulation, ORF Sequences, Plant mtDNA, Protein Prediction.
Related
Ontology
Subjects/Areas/Topics:
Bioinformatics
;
Biomedical Engineering
;
Genomics and Proteomics
Abstract:
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. Indeed it causes
differences between RNAs and their coding DNA sequences that hinder both experimental and computational
research of genes. Therefore common software tools for gene search, successfully applied to find canonical
genes, often fail in discovering genes encrypted in the genome of plants.
Here we propose a novel strategy useful to identify candidate coding sequences resulting from possible editing
substitutions. In particular, we consider c!u substitutions leading to the creation of new start and stop codons
in the mitochondrial DNA of a given input organism. We try to mimic the natural RNA editing mechanism,
in order to generate candidate Open Reading Frame sequences that could code for novel, uncharacterized
proteins. Results obtained analyzing the mtDNA of Oryza sativa
are supportive of this approach, since we
identified thirteen Open Reading Frame sequences transcribed in Oryza, that do not correspond to already
known proteins. Five of the corresponding amino acid sequences present high homologies with proteins already
discovered in other organisms, whereas, for the remaining ones, no such homology was detected.
(More)