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The effect of tRNA levels on decoding times of mRNA codons
The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded s...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132755/ https://www.ncbi.nlm.nih.gov/pubmed/25056313 http://dx.doi.org/10.1093/nar/gku646 |
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author | Dana, Alexandra Tuller, Tamir |
author_facet | Dana, Alexandra Tuller, Tamir |
author_sort | Dana, Alexandra |
collection | PubMed |
description | The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded so far researchers in the field. In this study, we perform a novel analysis of the ribosome profiling data of four organisms which enables ranking the decoding times of different codons while filtering translational phenomena such as experimental biases, extreme ribosomal pauses and ribosome traffic jams. Based on this filtering, we show for the first time that there is a significant correlation between tRNA concentrations and the codons estimated decoding time both in prokaryotes and in eukaryotes in natural conditions (−0.38 to −0.66, all P values <0.006); in addition, we show that when considering tRNA concentrations, codons decoding times are not correlated with aminoacyl-tRNA levels. The reported results support the conjecture that translation efficiency is directly influenced by the tRNA levels in the cell. Thus, they should help to understand the evolution of synonymous aspects of coding sequences via the adaptation of their codons to the tRNA pool. |
format | Online Article Text |
id | pubmed-4132755 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-41327552014-12-01 The effect of tRNA levels on decoding times of mRNA codons Dana, Alexandra Tuller, Tamir Nucleic Acids Res Genomics The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded so far researchers in the field. In this study, we perform a novel analysis of the ribosome profiling data of four organisms which enables ranking the decoding times of different codons while filtering translational phenomena such as experimental biases, extreme ribosomal pauses and ribosome traffic jams. Based on this filtering, we show for the first time that there is a significant correlation between tRNA concentrations and the codons estimated decoding time both in prokaryotes and in eukaryotes in natural conditions (−0.38 to −0.66, all P values <0.006); in addition, we show that when considering tRNA concentrations, codons decoding times are not correlated with aminoacyl-tRNA levels. The reported results support the conjecture that translation efficiency is directly influenced by the tRNA levels in the cell. Thus, they should help to understand the evolution of synonymous aspects of coding sequences via the adaptation of their codons to the tRNA pool. Oxford University Press 2014-08-18 2014-07-23 /pmc/articles/PMC4132755/ /pubmed/25056313 http://dx.doi.org/10.1093/nar/gku646 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Genomics Dana, Alexandra Tuller, Tamir The effect of tRNA levels on decoding times of mRNA codons |
title | The effect of tRNA levels on decoding times of mRNA codons |
title_full | The effect of tRNA levels on decoding times of mRNA codons |
title_fullStr | The effect of tRNA levels on decoding times of mRNA codons |
title_full_unstemmed | The effect of tRNA levels on decoding times of mRNA codons |
title_short | The effect of tRNA levels on decoding times of mRNA codons |
title_sort | effect of trna levels on decoding times of mrna codons |
topic | Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132755/ https://www.ncbi.nlm.nih.gov/pubmed/25056313 http://dx.doi.org/10.1093/nar/gku646 |
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