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Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution

Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary stru...

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Detalles Bibliográficos
Autores principales: Chursov, Andrey, Frishman, Dmitrij, Shneider, Alexander
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763529/
https://www.ncbi.nlm.nih.gov/pubmed/23783573
http://dx.doi.org/10.1093/nar/gkt507
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author Chursov, Andrey
Frishman, Dmitrij
Shneider, Alexander
author_facet Chursov, Andrey
Frishman, Dmitrij
Shneider, Alexander
author_sort Chursov, Andrey
collection PubMed
description Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary structures of mRNA coding regions, a previously unknown factor in bacterial evolution, by comparing the structural consequences of mutations in essential and nonessential Escherichia coli genes accumulated over 40 000 generations in the course of the ‘long-term evolution experiment’. We monitored the extent to which mutations influence minimum free energy (MFE) values, assuming that a substantial change in MFE is indicative of structural perturbation. Our principal finding is that purifying selection tends to eliminate those mutations in essential genes that lead to greater changes of MFE values and, therefore, may be more disruptive for the corresponding mRNA secondary structures. This effect implies that synonymous mutations disrupting mRNA secondary structures may directly affect the fitness of the organism. These results demonstrate that the need to maintain intact mRNA structures imposes additional evolutionary constraints on bacterial genomes, which go beyond preservation of structure and function of the encoded proteins.
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spelling pubmed-37635292013-09-10 Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution Chursov, Andrey Frishman, Dmitrij Shneider, Alexander Nucleic Acids Res RNA Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary structures of mRNA coding regions, a previously unknown factor in bacterial evolution, by comparing the structural consequences of mutations in essential and nonessential Escherichia coli genes accumulated over 40 000 generations in the course of the ‘long-term evolution experiment’. We monitored the extent to which mutations influence minimum free energy (MFE) values, assuming that a substantial change in MFE is indicative of structural perturbation. Our principal finding is that purifying selection tends to eliminate those mutations in essential genes that lead to greater changes of MFE values and, therefore, may be more disruptive for the corresponding mRNA secondary structures. This effect implies that synonymous mutations disrupting mRNA secondary structures may directly affect the fitness of the organism. These results demonstrate that the need to maintain intact mRNA structures imposes additional evolutionary constraints on bacterial genomes, which go beyond preservation of structure and function of the encoded proteins. Oxford University Press 2013-09 2013-06-19 /pmc/articles/PMC3763529/ /pubmed/23783573 http://dx.doi.org/10.1093/nar/gkt507 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA
Chursov, Andrey
Frishman, Dmitrij
Shneider, Alexander
Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution
title Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution
title_full Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution
title_fullStr Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution
title_full_unstemmed Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution
title_short Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution
title_sort conservation of mrna secondary structures may filter out mutations in escherichia coli evolution
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763529/
https://www.ncbi.nlm.nih.gov/pubmed/23783573
http://dx.doi.org/10.1093/nar/gkt507
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