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On the efficiency of the genetic code after frameshift mutations

Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified th...

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Autores principales: Geyer, Regine, Madany Mamlouk, Amir
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967371/
https://www.ncbi.nlm.nih.gov/pubmed/29844977
http://dx.doi.org/10.7717/peerj.4825
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author Geyer, Regine
Madany Mamlouk, Amir
author_facet Geyer, Regine
Madany Mamlouk, Amir
author_sort Geyer, Regine
collection PubMed
description Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes. This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids. We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code—just as for the point mutations—appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other. For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features—just like the SGC does. We conclude that the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just “one in a million”.
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spelling pubmed-59673712018-05-29 On the efficiency of the genetic code after frameshift mutations Geyer, Regine Madany Mamlouk, Amir PeerJ Bioinformatics Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes. This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids. We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code—just as for the point mutations—appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other. For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features—just like the SGC does. We conclude that the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just “one in a million”. PeerJ Inc. 2018-05-21 /pmc/articles/PMC5967371/ /pubmed/29844977 http://dx.doi.org/10.7717/peerj.4825 Text en ©2018 Geyer and Madany Mamlouk http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Geyer, Regine
Madany Mamlouk, Amir
On the efficiency of the genetic code after frameshift mutations
title On the efficiency of the genetic code after frameshift mutations
title_full On the efficiency of the genetic code after frameshift mutations
title_fullStr On the efficiency of the genetic code after frameshift mutations
title_full_unstemmed On the efficiency of the genetic code after frameshift mutations
title_short On the efficiency of the genetic code after frameshift mutations
title_sort on the efficiency of the genetic code after frameshift mutations
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967371/
https://www.ncbi.nlm.nih.gov/pubmed/29844977
http://dx.doi.org/10.7717/peerj.4825
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