The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes
Synonymous codon usage can be influenced by mutations and/or selection, e.g., for speed of protein translation and correct folding. However, this codon bias can also be affected by a general selection at the amino acid level due to differences in the acceptance of the loss and generation of these co...
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MDPI AG
2023-01-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/2/1185 |
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| author | Konrad Pawlak Paweł Błażej Dorota Mackiewicz Paweł Mackiewicz |
| author_facet | Konrad Pawlak Paweł Błażej Dorota Mackiewicz Paweł Mackiewicz |
| author_sort | Konrad Pawlak |
| collection | DOAJ |
| description | Synonymous codon usage can be influenced by mutations and/or selection, e.g., for speed of protein translation and correct folding. However, this codon bias can also be affected by a general selection at the amino acid level due to differences in the acceptance of the loss and generation of these codons. To assess the importance of this effect, we constructed a mutation–selection model model, in which we generated almost 90,000 stationary nucleotide distributions produced by mutational processes and applied a selection based on differences in physicochemical properties of amino acids. Under these conditions, we calculated the usage of fourfold degenerated (4FD) codons and compared it with the usage characteristic of the pure mutations. We considered both the standard genetic code (SGC) and alternative genetic codes (AGCs). The analyses showed that a majority of AGCs produced a greater 4FD codon bias than the SGC. The mutations producing more thymine or adenine than guanine and cytosine increased the differences in usage. On the other hand, the mutational pressures generating a lot of cytosine or guanine with a low content of adenine and thymine decreased this bias because the nucleotide content of most 4FD codons stayed in the compositional equilibrium with these pressures. The comparison of the theoretical results with those for real protein coding sequences showed that the influence of selection at the amino acid level on the synonymous codon usage cannot be neglected. The analyses indicate that the effect of amino acid selection cannot be disregarded and that it can interfere with other selection factors influencing codon usage, especially in AT-rich genomes, in which AGCs are usually used. |
| first_indexed | 2024-03-09T12:24:52Z |
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| id | doaj.art-737abec5ef6b4d03b388ef7e6cb164c9 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T12:24:52Z |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-737abec5ef6b4d03b388ef7e6cb164c92023-11-30T22:36:39ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-01-01242118510.3390/ijms24021185The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic CodesKonrad Pawlak0Paweł Błażej1Dorota Mackiewicz2Paweł Mackiewicz3Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383 Wroclaw, PolandDepartment of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383 Wroclaw, PolandDepartment of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383 Wroclaw, PolandDepartment of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383 Wroclaw, PolandSynonymous codon usage can be influenced by mutations and/or selection, e.g., for speed of protein translation and correct folding. However, this codon bias can also be affected by a general selection at the amino acid level due to differences in the acceptance of the loss and generation of these codons. To assess the importance of this effect, we constructed a mutation–selection model model, in which we generated almost 90,000 stationary nucleotide distributions produced by mutational processes and applied a selection based on differences in physicochemical properties of amino acids. Under these conditions, we calculated the usage of fourfold degenerated (4FD) codons and compared it with the usage characteristic of the pure mutations. We considered both the standard genetic code (SGC) and alternative genetic codes (AGCs). The analyses showed that a majority of AGCs produced a greater 4FD codon bias than the SGC. The mutations producing more thymine or adenine than guanine and cytosine increased the differences in usage. On the other hand, the mutational pressures generating a lot of cytosine or guanine with a low content of adenine and thymine decreased this bias because the nucleotide content of most 4FD codons stayed in the compositional equilibrium with these pressures. The comparison of the theoretical results with those for real protein coding sequences showed that the influence of selection at the amino acid level on the synonymous codon usage cannot be neglected. The analyses indicate that the effect of amino acid selection cannot be disregarded and that it can interfere with other selection factors influencing codon usage, especially in AT-rich genomes, in which AGCs are usually used.https://www.mdpi.com/1422-0067/24/2/1185amino acidcodoncodon usagegenetic codemutationsselection |
| spellingShingle | Konrad Pawlak Paweł Błażej Dorota Mackiewicz Paweł Mackiewicz The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes International Journal of Molecular Sciences amino acid codon codon usage genetic code mutations selection |
| title | The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes |
| title_full | The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes |
| title_fullStr | The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes |
| title_full_unstemmed | The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes |
| title_short | The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes |
| title_sort | influence of the selection at the amino acid level on synonymous codon usage from the viewpoint of alternative genetic codes |
| topic | amino acid codon codon usage genetic code mutations selection |
| url | https://www.mdpi.com/1422-0067/24/2/1185 |
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