Properties of the Standard Genetic Code and Its Alternatives Measured by Codon Usage from Corresponding Genomes

Małgorzata Wnetrzak, Paweł Błażej, Paweł Mackiewicz

2020

Abstract

The standard genetic code (SGC) and its modifications, i.e. alternative genetic codes (AGCs), are coding systems responsible for decoding genetic information from DNA into proteins. The SGC is thought to be universal for almost all organisms, whereas alternative genetic codes operate mainly in organelles and some specific microorganisms containing usually reduced genomes. Previous analyzes showed that the AGCs minimize the consequences of amino acid replacements due to point mutations better than the SGC. However, these studies did not take into account the potential differences in codon usage between the genomes on which given codes operate. The previous analyzes assumed a uniform distribution of codons, even though we can observe significant codon bias in genomes. Therefore, we developed a new measure involving codon usage as an additional parameter, which allowed us to assess the quality of a given genetic code. We tested our approach on the SGC and its 13 alternatives. For each AGC we applied an appropriate codon usage characteristic of a genome on which this code operates. This approach is more reliable for testing the impact of codon reassignments observed in the AGCs on their robustness to point mutations. The results indicate that the AGCs are generally more robust to point mutation than the SGC, especially when we consider the codon usages characteristic of their corresponding genomes. Moreover, we did not find a genetic code optimal for all considered codon usages, which indicates that the alternative variants of the SGC evolved in specific conditions.

Paper Citation

in Harvard Style

Wnetrzak M., Błażej P. and Mackiewicz P. (2020). Properties of the Standard Genetic Code and Its Alternatives Measured by Codon Usage from Corresponding Genomes. In Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - Volume 3: BIOINFORMATICS; ISBN 978-989-758-398-8, SciTePress, pages 44-51. DOI: 10.5220/0008981000440051

in Bibtex Style

@conference{bioinformatics20,
author={Małgorzata Wnetrzak and Paweł Błażej and Paweł Mackiewicz},
title={Properties of the Standard Genetic Code and Its Alternatives Measured by Codon Usage from Corresponding Genomes},
booktitle={Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - Volume 3: BIOINFORMATICS},
year={2020},
pages={44-51},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0008981000440051},
isbn={978-989-758-398-8},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - Volume 3: BIOINFORMATICS
TI - Properties of the Standard Genetic Code and Its Alternatives Measured by Codon Usage from Corresponding Genomes
SN - 978-989-758-398-8
AU - Wnetrzak M.
AU - Błażej P.
AU - Mackiewicz P.
PY - 2020
SP - 44
EP - 51
DO - 10.5220/0008981000440051
PB - SciTePress