The influence of different types of translational inaccuracies on the genetic code structure
Abstract Background The standard genetic code is a recipe for assigning unambiguously 21 labels, i.e. amino acids and stop translation signal, to 64 codons. However, at early stages of the translational machinery development, the codons did not have to be read unambiguously and the early genetic cod...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-03-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-019-2661-4 |
| _version_ | 1819278167030890496 |
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| author | Paweł BłaŻej Małgorzata Wnetrzak Dorota Mackiewicz Paweł Mackiewicz |
| author_facet | Paweł BłaŻej Małgorzata Wnetrzak Dorota Mackiewicz Paweł Mackiewicz |
| author_sort | Paweł BłaŻej |
| collection | DOAJ |
| description | Abstract Background The standard genetic code is a recipe for assigning unambiguously 21 labels, i.e. amino acids and stop translation signal, to 64 codons. However, at early stages of the translational machinery development, the codons did not have to be read unambiguously and the early genetic codes could have contained some ambiguous assignments of codons to amino acids. Therefore, the goal of this work was to obtain the genetic code structures which could have evolved assuming different types of inaccuracy of the translational machinery starting from unambiguous assignments of codons to amino acids. Results We developed a theoretical model assuming that the level of uncertainty of codon assignments can gradually decrease during the simulations. Since it is postulated that the standard code has evolved to be robust against point mutations and mistranslations, we developed three simulation scenarios assuming that such errors can influence one, two or three codon positions. The simulated codes were selected using the evolutionary algorithm methodology to decrease coding ambiguity and increase their robustness against mistranslation. Conclusions The results indicate that the typical codon block structure of the genetic code could have evolved to decrease the ambiguity of amino acid to codon assignments and to increase the fidelity of reading the genetic information. However, the robustness to errors was not the decisive factor that influenced the genetic code evolution because it is possible to find theoretical codes that minimize the reading errors better than the standard genetic code. |
| first_indexed | 2024-12-24T00:07:42Z |
| format | Article |
| id | doaj.art-2ac3a513ee344fd2839255a26d078ffe |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-24T00:07:42Z |
| publishDate | 2019-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-2ac3a513ee344fd2839255a26d078ffe2022-12-21T17:24:58ZengBMCBMC Bioinformatics1471-21052019-03-0120111410.1186/s12859-019-2661-4The influence of different types of translational inaccuracies on the genetic code structurePaweł BłaŻej0Małgorzata Wnetrzak1Dorota Mackiewicz2Paweł Mackiewicz3Department of Genomics, University of WrocławDepartment of Genomics, University of WrocławDepartment of Genomics, University of WrocławDepartment of Genomics, University of WrocławAbstract Background The standard genetic code is a recipe for assigning unambiguously 21 labels, i.e. amino acids and stop translation signal, to 64 codons. However, at early stages of the translational machinery development, the codons did not have to be read unambiguously and the early genetic codes could have contained some ambiguous assignments of codons to amino acids. Therefore, the goal of this work was to obtain the genetic code structures which could have evolved assuming different types of inaccuracy of the translational machinery starting from unambiguous assignments of codons to amino acids. Results We developed a theoretical model assuming that the level of uncertainty of codon assignments can gradually decrease during the simulations. Since it is postulated that the standard code has evolved to be robust against point mutations and mistranslations, we developed three simulation scenarios assuming that such errors can influence one, two or three codon positions. The simulated codes were selected using the evolutionary algorithm methodology to decrease coding ambiguity and increase their robustness against mistranslation. Conclusions The results indicate that the typical codon block structure of the genetic code could have evolved to decrease the ambiguity of amino acid to codon assignments and to increase the fidelity of reading the genetic information. However, the robustness to errors was not the decisive factor that influenced the genetic code evolution because it is possible to find theoretical codes that minimize the reading errors better than the standard genetic code.http://link.springer.com/article/10.1186/s12859-019-2661-4Amino acidCodonEvolutionEvolutionary algorithmGraph theoryOptimization |
| spellingShingle | Paweł BłaŻej Małgorzata Wnetrzak Dorota Mackiewicz Paweł Mackiewicz The influence of different types of translational inaccuracies on the genetic code structure BMC Bioinformatics Amino acid Codon Evolution Evolutionary algorithm Graph theory Optimization |
| title | The influence of different types of translational inaccuracies on the genetic code structure |
| title_full | The influence of different types of translational inaccuracies on the genetic code structure |
| title_fullStr | The influence of different types of translational inaccuracies on the genetic code structure |
| title_full_unstemmed | The influence of different types of translational inaccuracies on the genetic code structure |
| title_short | The influence of different types of translational inaccuracies on the genetic code structure |
| title_sort | influence of different types of translational inaccuracies on the genetic code structure |
| topic | Amino acid Codon Evolution Evolutionary algorithm Graph theory Optimization |
| url | http://link.springer.com/article/10.1186/s12859-019-2661-4 |
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