Discovering New Proteins in Plant Mitochondria by RNA Editing Simulation

Fabio Fassetti, Claudia Giallombardo, Ofelia Leone, Luigi Palopoli, Simona E. Rombo, Adolfo Saiardi

2016

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.

Paper Citation

in Harvard Style

Fassetti F., Giallombardo C., Leone O., Palopoli L., Rombo S. and Saiardi A. (2016). Discovering New Proteins in Plant Mitochondria by RNA Editing Simulation . In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2016) ISBN 978-989-758-170-0, pages 182-189. DOI: 10.5220/0005664901820189

in Bibtex Style

@conference{bioinformatics16,
author={Fabio Fassetti and Claudia Giallombardo and Ofelia Leone and Luigi Palopoli and Simona E. Rombo and Adolfo Saiardi},
title={Discovering New Proteins in Plant Mitochondria by RNA Editing Simulation},
booktitle={Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2016)},
year={2016},
pages={182-189},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005664901820189},
isbn={978-989-758-170-0},
}

in EndNote Style

TY - CONF
JO - Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2016)
TI - Discovering New Proteins in Plant Mitochondria by RNA Editing Simulation
SN - 978-989-758-170-0
AU - Fassetti F.
AU - Giallombardo C.
AU - Leone O.
AU - Palopoli L.
AU - Rombo S.
AU - Saiardi A.
PY - 2016
SP - 182
EP - 189
DO - 10.5220/0005664901820189