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Codon usage bias as a function of generation time and life expectancy

It has recently been demonstrated that human natural codon usage bias is optimized towards a higher buffering capacity to mutations (measured as the tendency of single point mutations in a DNA sequence to yield the same or similar amino acids) compared to random sequences. In this work, we investiga...

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Detalles Bibliográficos
Autores principales: Mahdi, Rami N, Rouchka, Eric C
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3283889/
https://www.ncbi.nlm.nih.gov/pubmed/22368389
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author Mahdi, Rami N
Rouchka, Eric C
author_facet Mahdi, Rami N
Rouchka, Eric C
author_sort Mahdi, Rami N
collection PubMed
description It has recently been demonstrated that human natural codon usage bias is optimized towards a higher buffering capacity to mutations (measured as the tendency of single point mutations in a DNA sequence to yield the same or similar amino acids) compared to random sequences. In this work, we investigate this phenomenon further by analyzing the natural DNA of four different species (human, mouse, zebrafish and fruit fly) to determine whether such a tolerance to mutations is correlated with the life span and age of sexual maturation for the corresponding organisms. We also propose a new measure to quantify the buffering capacity of a DNA sequence to mutations that takes into account the observed mutation rates within every genome and the effect of the corresponding mutation. Our results suggest there is a propensity for tolerance to mutations that is positively correlated with the life expectancy of the considered organisms. Moreover, random sequences that are constrained to produce the same protein as the naturally occurring sequences are found to be more buffered than completely random sequences while being less buffered than the natural sequences. These results suggest that optimization toward protective mechanisms tolerant to mutations is correlated with both life expectancy and age to sexual maturity at both the levels of codon usage bias and the bias of the natural sequence of codons itself.
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spelling pubmed-32838892012-02-24 Codon usage bias as a function of generation time and life expectancy Mahdi, Rami N Rouchka, Eric C Bioinformation Hypothesis It has recently been demonstrated that human natural codon usage bias is optimized towards a higher buffering capacity to mutations (measured as the tendency of single point mutations in a DNA sequence to yield the same or similar amino acids) compared to random sequences. In this work, we investigate this phenomenon further by analyzing the natural DNA of four different species (human, mouse, zebrafish and fruit fly) to determine whether such a tolerance to mutations is correlated with the life span and age of sexual maturation for the corresponding organisms. We also propose a new measure to quantify the buffering capacity of a DNA sequence to mutations that takes into account the observed mutation rates within every genome and the effect of the corresponding mutation. Our results suggest there is a propensity for tolerance to mutations that is positively correlated with the life expectancy of the considered organisms. Moreover, random sequences that are constrained to produce the same protein as the naturally occurring sequences are found to be more buffered than completely random sequences while being less buffered than the natural sequences. These results suggest that optimization toward protective mechanisms tolerant to mutations is correlated with both life expectancy and age to sexual maturity at both the levels of codon usage bias and the bias of the natural sequence of codons itself. Biomedical Informatics 2012-02-03 /pmc/articles/PMC3283889/ /pubmed/22368389 Text en © 2012 Biomedical Informatics This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
spellingShingle Hypothesis
Mahdi, Rami N
Rouchka, Eric C
Codon usage bias as a function of generation time and life expectancy
title Codon usage bias as a function of generation time and life expectancy
title_full Codon usage bias as a function of generation time and life expectancy
title_fullStr Codon usage bias as a function of generation time and life expectancy
title_full_unstemmed Codon usage bias as a function of generation time and life expectancy
title_short Codon usage bias as a function of generation time and life expectancy
title_sort codon usage bias as a function of generation time and life expectancy
topic Hypothesis
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3283889/
https://www.ncbi.nlm.nih.gov/pubmed/22368389
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