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Energy efficiency trade-offs drive nucleotide usage in transcribed regions
Efficient nutrient usage is a trait under universal selection. A substantial part of cellular resources is spent on making nucleotides. We thus expect preferential use of cheaper nucleotides especially in transcribed sequences, which are often amplified thousand-fold compared with genomic sequences....
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844684/ https://www.ncbi.nlm.nih.gov/pubmed/27098217 http://dx.doi.org/10.1038/ncomms11334 |
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author | Chen, Wei-Hua Lu, Guanting Bork, Peer Hu, Songnian Lercher, Martin J. |
author_facet | Chen, Wei-Hua Lu, Guanting Bork, Peer Hu, Songnian Lercher, Martin J. |
author_sort | Chen, Wei-Hua |
collection | PubMed |
description | Efficient nutrient usage is a trait under universal selection. A substantial part of cellular resources is spent on making nucleotides. We thus expect preferential use of cheaper nucleotides especially in transcribed sequences, which are often amplified thousand-fold compared with genomic sequences. To test this hypothesis, we derive a mutation-selection-drift equilibrium model for nucleotide skews (strand-specific usage of ‘A' versus ‘T' and ‘G' versus ‘C'), which explains nucleotide skews across 1,550 prokaryotic genomes as a consequence of selection on efficient resource usage. Transcription-related selection generally favours the cheaper nucleotides ‘U' and ‘C' at synonymous sites. However, the information encoded in mRNA is further amplified through translation. Due to unexpected trade-offs in the codon table, cheaper nucleotides encode on average energetically more expensive amino acids. These trade-offs apply to both strand-specific nucleotide usage and GC content, causing a universal bias towards the more expensive nucleotides ‘A' and ‘G' at non-synonymous coding sites. |
format | Online Article Text |
id | pubmed-4844684 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-48446842016-04-27 Energy efficiency trade-offs drive nucleotide usage in transcribed regions Chen, Wei-Hua Lu, Guanting Bork, Peer Hu, Songnian Lercher, Martin J. Nat Commun Article Efficient nutrient usage is a trait under universal selection. A substantial part of cellular resources is spent on making nucleotides. We thus expect preferential use of cheaper nucleotides especially in transcribed sequences, which are often amplified thousand-fold compared with genomic sequences. To test this hypothesis, we derive a mutation-selection-drift equilibrium model for nucleotide skews (strand-specific usage of ‘A' versus ‘T' and ‘G' versus ‘C'), which explains nucleotide skews across 1,550 prokaryotic genomes as a consequence of selection on efficient resource usage. Transcription-related selection generally favours the cheaper nucleotides ‘U' and ‘C' at synonymous sites. However, the information encoded in mRNA is further amplified through translation. Due to unexpected trade-offs in the codon table, cheaper nucleotides encode on average energetically more expensive amino acids. These trade-offs apply to both strand-specific nucleotide usage and GC content, causing a universal bias towards the more expensive nucleotides ‘A' and ‘G' at non-synonymous coding sites. Nature Publishing Group 2016-04-21 /pmc/articles/PMC4844684/ /pubmed/27098217 http://dx.doi.org/10.1038/ncomms11334 Text en Copyright © 2016, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Chen, Wei-Hua Lu, Guanting Bork, Peer Hu, Songnian Lercher, Martin J. Energy efficiency trade-offs drive nucleotide usage in transcribed regions |
title | Energy efficiency trade-offs drive nucleotide usage in transcribed regions |
title_full | Energy efficiency trade-offs drive nucleotide usage in transcribed regions |
title_fullStr | Energy efficiency trade-offs drive nucleotide usage in transcribed regions |
title_full_unstemmed | Energy efficiency trade-offs drive nucleotide usage in transcribed regions |
title_short | Energy efficiency trade-offs drive nucleotide usage in transcribed regions |
title_sort | energy efficiency trade-offs drive nucleotide usage in transcribed regions |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844684/ https://www.ncbi.nlm.nih.gov/pubmed/27098217 http://dx.doi.org/10.1038/ncomms11334 |
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