The Properties of the Standard Genetic Code and Its Selected Alternatives in Terms of the Optimal Graph Partition

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

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

Abstract

The standard genetic code (SGC) is a system of rules, which assigns 20 amino acids and stop translation signal to 64 codons, i.e triplets of nucleotides. The structure of the SGC shows some properties suggesting that this code evolved to minimize deleterious effects of mutations and translational errors. To analyse this issue, we presented the structure of the SGC and its natural alternative versions as a graph, in which vertices corresponded to codons and edges to point mutations between these codons. The mutations were weighted according to the mutation type, i.e. transitions and transversions. Under this representation, each genetic code is a partition of the set of vertices into 21 disjoint subsets, while its resistance to the mutation consequences can be reformulated into the optimal graph clustering task. In order to investigate this problem, we developed an appropriate clustering algorithm, which searched for the codes showing the minimum average calculated for the set conductance of codon groups. The algorithm found three best codes for various ranges of the weights for the mutations. The average weighted-conductance of the studied genetic codes 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 codes was not as perfect as the best codes and many alternative genetic codes performed better than the SGC. These results may suggest that the evolution of the SGC was driven not only by the selection for the robustness to mutations or mistranslations.

Original languageEnglish (US)
Title of host publicationBiomedical Engineering Systems and Technologies - 12th International Joint Conference, BIOSTEC 2019, Revised Selected Papers
EditorsAna Roque, Hugo Gamboa, Arkadiusz Tomczyk, Elisabetta De Maria, Felix Putze, Roman Moucek, Ana Fred
PublisherSpringer
Pages170-191
Number of pages22
ISBN (Print)9783030469696
DOIs
StatePublished - Jan 1 2020
Event12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019 - Prague, Czech Republic
Duration: Feb 22 2019Feb 24 2019

Publication series

NameCommunications in Computer and Information Science
Volume1211 CCIS
ISSN (Print)1865-0929
ISSN (Electronic)1865-0937

Conference

Conference12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019
CountryCzech Republic
CityPrague
Period2/22/192/24/19

Keywords

  • Code degeneracy
  • Graph theory
  • Mutation
  • Set conductance
  • Standard genetic code
  • Transition
  • Transversion

ASJC Scopus subject areas

  • Computer Science(all)
  • Mathematics(all)

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  • Cite this

    Aloqalaa, D. A., Kowalski, D. R., Błażej, P., Wnȩtrzak, M., Mackiewicz, D., & Mackiewicz, P. (2020). The Properties of the Standard Genetic Code and Its Selected Alternatives in Terms of the Optimal Graph Partition. In A. Roque, H. Gamboa, A. Tomczyk, E. De Maria, F. Putze, R. Moucek, & A. Fred (Eds.), Biomedical Engineering Systems and Technologies - 12th International Joint Conference, BIOSTEC 2019, Revised Selected Papers (pp. 170-191). (Communications in Computer and Information Science; Vol. 1211 CCIS). Springer. https://doi.org/10.1007/978-3-030-46970-2_9