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.

References

  1. Altschul, S. F. et al. (1997). Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17):3389- 3402.
  2. Boguski, M. S., Lowe, T. M., and Tolstoshev, C. M. (1993). dbEST-database for Expressed Sequence Tags. Nat Genet., pages 332-333.
  3. Brennicke, A., Marchfelder, A., and Binder, S. (1999). RNA editing. FEMS Microbiol. Rev., 23:297-316.
  4. Bundschuh, R. (2004). Computational prediction of rna editing sites. Bioinformatics, 20(17):3214-3220.
  5. Burger, G., Gray, M. W., and Lang, B. F. (2003). Mitochondrial genomes: anything goes. TRENDS in Genetics, 19(12):709-716.
  6. Gray, M. W., Hanic-Joyce, P. J., and Covello, P. S. (1992). Transcription, processing and editing in plant mitochondria. Annu. Rev. Plant Physiol. Plant Mol. Biol., 43:145-175.
  7. Gualberto, J. M., Lamattina, L., Bonnard, G., Weil, J. H., and Grienenberger, J. M. (1989). RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature, 341:660-662.
  8. Hoch, B., Maier, R. M., Appel, K., Igloi, G. L., and Kossel, H. (1991). Editing of a chloroplast mRNA by creation of an initiation codon. Nature, 353:178-180.
  9. Lenz, H. and Knoop, V. (2013). PREPACT 2.0: Predicting C-to-U and U-to-C RNA editing in organelle genome sequences with multiple references and curated RNA editing annotation. Bioinform Biol Insights, 7:1-19.
  10. Levenshtein, V. I. (1966). Binary codes capable of correcting deletions, insertions, and reversals. Soviet Physics Doklady, 10(8):707-710.
  11. Mower, J. P. (2005). PREP-Mt: predictive RNA editor for plant mitochondrial genes. BMC Bioinformatics, 6:96.
  12. Mulligan, R., Chang, K. L., and Chou, C. C. (2007). Computational analysis of rna editing sites in plant mitochondrial genomes reveals similar information content and a sporadic distribution of editing sites. Mol Biol Evol, 24(9):1971-1981.
  13. Notsu, Y. et al. (2002). The complete sequence of the rice (oryza sativa l.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol Genet Genomics, 268(4):434- 445.
  14. Palopoli, L., Rombo, S. E., Terracina, G., Tradigo, G., and Veltri, P. (2009). Improving protein secondary structure predictions by prediction fusion. Information Fusion, 10(3):217-232.
  15. Picardi, E. and Pesole, G. (2013). REDItools: highthroughput RNA editing detection made easy. Bioinformatics, 29(14):1813-1814.
  16. Picardi, E. and Quagliariello, C. (2005). EdiPy: a resource to simulate the evolution of plant mitochondrial genes under the RNA editing. Comput. Biol. Chem., 30(1):77-80.
  17. Picardi, E., Regina, T. M. R., Brennicke, A., and Quagliariello, C. (2007). Redidb:the rna editing database. Nucleic Acids Research, 35:D173-D177.
  18. Regina, T. M. R., Lopez, L., Picardi, E., and Quagliariello, C. (2002). Striking differences in RNA editing requirements to express the rps4 gene in magnolia and sunflower mitochondria. Gene, 286:33-41.
  19. Schuster, W., Unseld, M., Wissinger, B., and Brennicke, A. (1990). Ribosomal protein S14 transcripts are edited in Oenothera mitochondria. Nucleic Acids Res., 18:229-233.
  20. Takenaka, M., D., D. V., van der Merwe, J. A., Zehrmann, A., and Brennicke, A. (2008). The process of RNA editing in plant mitochondria. Mitochondrion, 8:35- 46.
  21. Wintz, H. and Hanson, M. R. (1991). A termination codon is created by RNA editing in the petunia mitochondrial atp9 gene transcript. Curr Genet, 19:61-64.
Download


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