The Impact of the Transversion/Transition Ratio on the Optimal Genetic Code Graph Partition

Daniyah A. Aloqalaa, Dariusz R. Kowalski, Dariusz R. Kowalski, Paweł Błażej, Małgorzata Wnetrzak, Dorota Mackiewicz, Paweł Mackiewicz

2019

Abstract

The standard genetic code (SGC) is a system of rules ascribing 20 amino acids and stop translation signal to 64 codons, i.e triplets of nucleotides. It was proposed that the structure of the SGC evolved to minimize harmful consequences of mutations and translational errors. To study this problem, we described the SGC structure by a graph, in which codons are vertices and edges correspond to single nucleotide mutations occurring between the codons. We also introduced weights (W) for mutation types to distinguish transversions from transitions. Using this representation, the SGC is a partition of the set of vertices into 21 disjoint subsets. In this case, the question about the potential robustness of the genetic code to the mutations can be reformulated into the optimal graph clustering task. To investigate this problem, we applied an appropriate clustering algorithm, which searched for the codes characterized by the minimum average calculated from the set W-conductance of codon groups. Our algorithm found three best codes for various ranges of the applied weights. The average W-conductance of the SGC was the most similar to that of the best codes in the range of weights corresponding to the observed transversion/transition ratio in natural mutational pressures. However, it should be noted that the optimization of the SGC was not as perfect as the best codes. It implies that the evolution of the SGC was driven not only by the selection for the robustness against mutations or mistranslations but also other factors, e.g. subsequent addition of amino acids to the code according to the expansion of amino acid metabolic pathways.

Paper Citation

in Harvard Style

Aloqalaa D., Kowalski D., Błażej P., Wnetrzak M., Mackiewicz D. and Mackiewicz P. (2019). The Impact of the Transversion/Transition Ratio on the Optimal Genetic Code Graph Partition. In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS; ISBN 978-989-758-353-7, SciTePress, pages 55-65. DOI: 10.5220/0007381000550065

in Bibtex Style

@conference{bioinformatics19,
author={Daniyah A. Aloqalaa and Dariusz R. Kowalski and Paweł Błażej and Małgorzata Wnetrzak and Dorota Mackiewicz and Paweł Mackiewicz},
title={The Impact of the Transversion/Transition Ratio on the Optimal Genetic Code Graph Partition},
booktitle={Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS},
year={2019},
pages={55-65},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007381000550065},
isbn={978-989-758-353-7},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS
TI - The Impact of the Transversion/Transition Ratio on the Optimal Genetic Code Graph Partition
SN - 978-989-758-353-7
AU - Aloqalaa D.
AU - Kowalski D.
AU - Błażej P.
AU - Wnetrzak M.
AU - Mackiewicz D.
AU - Mackiewicz P.
PY - 2019
SP - 55
EP - 65
DO - 10.5220/0007381000550065
PB - SciTePress