The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons
There are two main forces that affect usage of synonymous codons: directional mutational pressure and selection. The effectiveness of protein translation is usually considered as the main selectional factor. However, biased codon usage can also be a byproduct of a general selection at the amino acid...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2017-03-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.116.038125 |
| _version_ | 1818431015301939200 |
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| author | Paweł Błażej Dorota Mackiewicz Małgorzata Wnętrzak Paweł Mackiewicz |
| author_facet | Paweł Błażej Dorota Mackiewicz Małgorzata Wnętrzak Paweł Mackiewicz |
| author_sort | Paweł Błażej |
| collection | DOAJ |
| description | There are two main forces that affect usage of synonymous codons: directional mutational pressure and selection. The effectiveness of protein translation is usually considered as the main selectional factor. However, biased codon usage can also be a byproduct of a general selection at the amino acid level interacting with nucleotide replacements. To evaluate the validity and strength of such an effect, we superimposed >3.5 billion unrestricted mutational processes on the selection of nonsynonymous substitutions based on the differences in physicochemical properties of the coded amino acids. Using a modified evolutionary optimization algorithm, we determined the conditions in which the effect on the relative codon usage is maximized. We found that the effect is enhanced by mutational processes generating more adenine and thymine than guanine and cytosine, as well as more purines than pyrimidines. Interestingly, this effect is observed only under an unrestricted model of nucleotide substitution, and disappears when the mutational process is time-reversible. Comparison of the simulation results with data for real protein coding sequences indicates that the impact of selection at the amino acid level on synonymous codon usage cannot be neglected. Furthermore, it can considerably interfere, especially in AT-rich genomes, with other selections on codon usage, e.g., translational efficiency. It may also lead to difficulties in the recognition of other effects influencing codon bias, and an overestimation of protein coding sequences whose codon usage is subjected to adaptational selection. |
| first_indexed | 2024-12-14T15:42:35Z |
| format | Article |
| id | doaj.art-5f6b8f36261d43fb95bd26a7e440e99d |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-14T15:42:35Z |
| publishDate | 2017-03-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-5f6b8f36261d43fb95bd26a7e440e99d2022-12-21T22:55:35ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362017-03-017396798110.1534/g3.116.03812520The Impact of Selection at the Amino Acid Level on the Usage of Synonymous CodonsPaweł BłażejDorota MackiewiczMałgorzata WnętrzakPaweł MackiewiczThere are two main forces that affect usage of synonymous codons: directional mutational pressure and selection. The effectiveness of protein translation is usually considered as the main selectional factor. However, biased codon usage can also be a byproduct of a general selection at the amino acid level interacting with nucleotide replacements. To evaluate the validity and strength of such an effect, we superimposed >3.5 billion unrestricted mutational processes on the selection of nonsynonymous substitutions based on the differences in physicochemical properties of the coded amino acids. Using a modified evolutionary optimization algorithm, we determined the conditions in which the effect on the relative codon usage is maximized. We found that the effect is enhanced by mutational processes generating more adenine and thymine than guanine and cytosine, as well as more purines than pyrimidines. Interestingly, this effect is observed only under an unrestricted model of nucleotide substitution, and disappears when the mutational process is time-reversible. Comparison of the simulation results with data for real protein coding sequences indicates that the impact of selection at the amino acid level on synonymous codon usage cannot be neglected. Furthermore, it can considerably interfere, especially in AT-rich genomes, with other selections on codon usage, e.g., translational efficiency. It may also lead to difficulties in the recognition of other effects influencing codon bias, and an overestimation of protein coding sequences whose codon usage is subjected to adaptational selection.http://g3journal.org/lookup/doi/10.1534/g3.116.038125amino acidcodon usagemutationselectionsynonymous codons |
| spellingShingle | Paweł Błażej Dorota Mackiewicz Małgorzata Wnętrzak Paweł Mackiewicz The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons G3: Genes, Genomes, Genetics amino acid codon usage mutation selection synonymous codons |
| title | The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons |
| title_full | The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons |
| title_fullStr | The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons |
| title_full_unstemmed | The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons |
| title_short | The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons |
| title_sort | impact of selection at the amino acid level on the usage of synonymous codons |
| topic | amino acid codon usage mutation selection synonymous codons |
| url | http://g3journal.org/lookup/doi/10.1534/g3.116.038125 |
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