The impact of the transversion/transition ratio on the optimal genetic code graph partition

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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.

Original languageEnglish (US)
Title of host publicationBIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019
EditorsElisabetta De Maria, Hugo Gamboa, Ana Fred
PublisherSciTePress
Pages55-65
Number of pages11
ISBN (Electronic)9789897583537
StatePublished - Jan 1 2019
Externally publishedYes
Event10th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2019 - Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019 - Prague, Czech Republic
Duration: Feb 22 2019Feb 24 2019

Publication series

NameBIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019

Conference

Conference10th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2019 - Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019
CountryCzech Republic
CityPrague
Period2/22/192/24/19

Fingerprint

Amino acids
Nucleotides
Clustering algorithms
Metabolic Networks and Pathways

Keywords

  • Code Degeneracy
  • Graph Theory
  • Mutation
  • Set Conductance
  • Standard Genetic Code
  • Transition
  • Transversion

ASJC Scopus subject areas

  • Biomedical Engineering
  • Electrical and Electronic Engineering

Cite this

Aloqalaa, D. A., Kowalski, D. R., Błazej, P., Wnetrzak, M., Mackiewicz, D., & Mackiewicz, P. (2019). The impact of the transversion/transition ratio on the optimal genetic code graph partition. In E. De Maria, H. Gamboa, & A. Fred (Eds.), BIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019 (pp. 55-65). (BIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019). SciTePress.

The impact of the transversion/transition ratio on the optimal genetic code graph partition. / Aloqalaa, Daniyah A.; Kowalski, Dariusz R.; Błazej, Paweł; Wnetrzak, Małgorzata; Mackiewicz, Dorota; Mackiewicz, Paweł.

BIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019. ed. / Elisabetta De Maria; Hugo Gamboa; Ana Fred. SciTePress, 2019. p. 55-65 (BIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Aloqalaa, DA, Kowalski, DR, Błazej, P, Wnetrzak, M, Mackiewicz, D & Mackiewicz, P 2019, The impact of the transversion/transition ratio on the optimal genetic code graph partition. in E De Maria, H Gamboa & A Fred (eds), BIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019. BIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019, SciTePress, pp. 55-65, 10th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2019 - Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019, Prague, Czech Republic, 2/22/19.
Aloqalaa DA, Kowalski DR, Błazej P, Wnetrzak M, Mackiewicz D, Mackiewicz P. The impact of the transversion/transition ratio on the optimal genetic code graph partition. In De Maria E, Gamboa H, Fred A, editors, BIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019. SciTePress. 2019. p. 55-65. (BIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019).
Aloqalaa, Daniyah A. ; Kowalski, Dariusz R. ; Błazej, Paweł ; Wnetrzak, Małgorzata ; Mackiewicz, Dorota ; Mackiewicz, Paweł. / The impact of the transversion/transition ratio on the optimal genetic code graph partition. BIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019. editor / Elisabetta De Maria ; Hugo Gamboa ; Ana Fred. SciTePress, 2019. pp. 55-65 (BIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019).
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