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A role for circular code properties in translation
Circular codes represent a form of coding allowing detection/correction of frame-shift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to th...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8080828/ https://www.ncbi.nlm.nih.gov/pubmed/33911089 http://dx.doi.org/10.1038/s41598-021-87534-y |
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author | Giannerini, Simone Gonzalez, Diego Luis Goracci, Greta Danielli, Alberto |
author_facet | Giannerini, Simone Gonzalez, Diego Luis Goracci, Greta Danielli, Alberto |
author_sort | Giannerini, Simone |
collection | PubMed |
description | Circular codes represent a form of coding allowing detection/correction of frame-shift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino transformation of codon bases. These properties strongly correlate with translation speed, codon influence and protein synthesis levels. Strikingly, circular code marks are absent at the beginning of coding sequences, but stably occur 40 codons after the initiator codon, hinting at the translation elongation process. Finally, we use the lens of circular codes to show that codon influence on translation correlates with the strong-weak dichotomy of the first two bases of the codon. The results can lead to defining new universal tools for sequence indicators and sequence optimization for bioinformatics and biotechnological applications, and can shed light on the molecular mechanisms behind the decoding process. |
format | Online Article Text |
id | pubmed-8080828 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-80808282021-04-30 A role for circular code properties in translation Giannerini, Simone Gonzalez, Diego Luis Goracci, Greta Danielli, Alberto Sci Rep Article Circular codes represent a form of coding allowing detection/correction of frame-shift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino transformation of codon bases. These properties strongly correlate with translation speed, codon influence and protein synthesis levels. Strikingly, circular code marks are absent at the beginning of coding sequences, but stably occur 40 codons after the initiator codon, hinting at the translation elongation process. Finally, we use the lens of circular codes to show that codon influence on translation correlates with the strong-weak dichotomy of the first two bases of the codon. The results can lead to defining new universal tools for sequence indicators and sequence optimization for bioinformatics and biotechnological applications, and can shed light on the molecular mechanisms behind the decoding process. Nature Publishing Group UK 2021-04-28 /pmc/articles/PMC8080828/ /pubmed/33911089 http://dx.doi.org/10.1038/s41598-021-87534-y Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Giannerini, Simone Gonzalez, Diego Luis Goracci, Greta Danielli, Alberto A role for circular code properties in translation |
title | A role for circular code properties in translation |
title_full | A role for circular code properties in translation |
title_fullStr | A role for circular code properties in translation |
title_full_unstemmed | A role for circular code properties in translation |
title_short | A role for circular code properties in translation |
title_sort | role for circular code properties in translation |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8080828/ https://www.ncbi.nlm.nih.gov/pubmed/33911089 http://dx.doi.org/10.1038/s41598-021-87534-y |
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