Optimization of amino acid replacement costs by mutational pressure in bacterial genomes

Abstract Mutations are considered a spontaneous and random process, which is important component of evolution because it generates genetic variation. On the other hand, mutations are deleterious leading to non-functional genes and energetically costly repairs. Therefore, one can expect that the muta...

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Autores principales:	Paweł Błażej, Dorota Mackiewicz, Małgorzata Grabińska, Małgorzata Wnętrzak, Paweł Mackiewicz
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/649b5aa9f39e472ab3f78e6a9163408b
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spelling	oai:doaj.org-article:649b5aa9f39e472ab3f78e6a9163408b2021-12-02T11:40:32ZOptimization of amino acid replacement costs by mutational pressure in bacterial genomes10.1038/s41598-017-01130-72045-2322https://doaj.org/article/649b5aa9f39e472ab3f78e6a9163408b2017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-01130-7https://doaj.org/toc/2045-2322Abstract Mutations are considered a spontaneous and random process, which is important component of evolution because it generates genetic variation. On the other hand, mutations are deleterious leading to non-functional genes and energetically costly repairs. Therefore, one can expect that the mutational pressure is optimized to simultaneously generate genetic diversity and preserve genetic information. To check if empirical mutational pressures are optimized in these ways, we compared matrices of nucleotide mutation rates derived from bacterial genomes with their best possible alternatives that minimized or maximized costs of amino acid replacements associated with differences in their physicochemical properties (e.g. hydropathy and polarity). It should be noted that the studied empirical nucleotide substitution matrices and the costs of amino acid replacements are independent because these matrices were derived from sites free of selection on amino acid properties and the amino acid costs assumed only amino acid physicochemical properties without any information about mutation at the nucleotide level. Obtained results indicate that the empirical mutational matrices show a tendency to minimize costs of amino acid replacements. It implies that bacterial mutational pressures can evolve to decrease consequences of amino acid substitutions. However, the optimization is not full, which enables generation of some genetic variability.Paweł BłażejDorota MackiewiczMałgorzata GrabińskaMałgorzata WnętrzakPaweł MackiewiczNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-18 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Paweł Błażej Dorota Mackiewicz Małgorzata Grabińska Małgorzata Wnętrzak Paweł Mackiewicz Optimization of amino acid replacement costs by mutational pressure in bacterial genomes
description	Abstract Mutations are considered a spontaneous and random process, which is important component of evolution because it generates genetic variation. On the other hand, mutations are deleterious leading to non-functional genes and energetically costly repairs. Therefore, one can expect that the mutational pressure is optimized to simultaneously generate genetic diversity and preserve genetic information. To check if empirical mutational pressures are optimized in these ways, we compared matrices of nucleotide mutation rates derived from bacterial genomes with their best possible alternatives that minimized or maximized costs of amino acid replacements associated with differences in their physicochemical properties (e.g. hydropathy and polarity). It should be noted that the studied empirical nucleotide substitution matrices and the costs of amino acid replacements are independent because these matrices were derived from sites free of selection on amino acid properties and the amino acid costs assumed only amino acid physicochemical properties without any information about mutation at the nucleotide level. Obtained results indicate that the empirical mutational matrices show a tendency to minimize costs of amino acid replacements. It implies that bacterial mutational pressures can evolve to decrease consequences of amino acid substitutions. However, the optimization is not full, which enables generation of some genetic variability.
format	article
author	Paweł Błażej Dorota Mackiewicz Małgorzata Grabińska Małgorzata Wnętrzak Paweł Mackiewicz
author_facet	Paweł Błażej Dorota Mackiewicz Małgorzata Grabińska Małgorzata Wnętrzak Paweł Mackiewicz
author_sort	Paweł Błażej
title	Optimization of amino acid replacement costs by mutational pressure in bacterial genomes
title_short	Optimization of amino acid replacement costs by mutational pressure in bacterial genomes
title_full	Optimization of amino acid replacement costs by mutational pressure in bacterial genomes
title_fullStr	Optimization of amino acid replacement costs by mutational pressure in bacterial genomes
title_full_unstemmed	Optimization of amino acid replacement costs by mutational pressure in bacterial genomes
title_sort	optimization of amino acid replacement costs by mutational pressure in bacterial genomes
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/649b5aa9f39e472ab3f78e6a9163408b
work_keys_str_mv	AT pawełbłazej optimizationofaminoacidreplacementcostsbymutationalpressureinbacterialgenomes AT dorotamackiewicz optimizationofaminoacidreplacementcostsbymutationalpressureinbacterialgenomes AT małgorzatagrabinska optimizationofaminoacidreplacementcostsbymutationalpressureinbacterialgenomes AT małgorzatawnetrzak optimizationofaminoacidreplacementcostsbymutationalpressureinbacterialgenomes AT pawełmackiewicz optimizationofaminoacidreplacementcostsbymutationalpressureinbacterialgenomes
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Optimization of amino acid replacement costs by mutational pressure in bacterial genomes

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