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Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction

Genome size is determined during evolution, but it can also be altered by genetic engineering in laboratories. The systematic characterization of reduced genomes provides valuable insights into the cellular properties that are quantitatively described by the global parameters related to the dynamics...

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Autores principales: Nishimura, Issei, Kurokawa, Masaomi, Liu, Liu, Ying, Bei-Wen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5573674/
https://www.ncbi.nlm.nih.gov/pubmed/28679744
http://dx.doi.org/10.1128/mBio.00676-17
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author Nishimura, Issei
Kurokawa, Masaomi
Liu, Liu
Ying, Bei-Wen
author_facet Nishimura, Issei
Kurokawa, Masaomi
Liu, Liu
Ying, Bei-Wen
author_sort Nishimura, Issei
collection PubMed
description Genome size is determined during evolution, but it can also be altered by genetic engineering in laboratories. The systematic characterization of reduced genomes provides valuable insights into the cellular properties that are quantitatively described by the global parameters related to the dynamics of growth and mutation. In the present study, we analyzed a small collection of W3110 Escherichia coli derivatives containing either the wild-type genome or reduced genomes of various lengths to examine whether the mutation rate, a global parameter representing genomic plasticity, was affected by genome reduction. We found that the mutation rates of these cells increased with genome reduction. The correlation between genome length and mutation rate, which has been reported for the evolution of bacteria, was also identified, intriguingly, for genome reduction. Gene function enrichment analysis indicated that the deletion of many of the genes encoding membrane and transport proteins play a role in the mutation rate changes mediated by genome reduction. Furthermore, the increase in the mutation rate with genome reduction was highly associated with a decrease in the growth rate in a nutrition-dependent manner; thus, poorer media showed a larger change that was of higher significance. This negative correlation was strongly supported by experimental evidence that the serial transfer of the reduced genome improved the growth rate and reduced the mutation rate to a large extent. Taken together, the global parameters corresponding to the genome, growth, and mutation showed a coordinated relationship, which might be an essential working principle for balancing the cellular dynamics appropriate to the environment.
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spelling pubmed-55736742017-08-30 Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction Nishimura, Issei Kurokawa, Masaomi Liu, Liu Ying, Bei-Wen mBio Research Article Genome size is determined during evolution, but it can also be altered by genetic engineering in laboratories. The systematic characterization of reduced genomes provides valuable insights into the cellular properties that are quantitatively described by the global parameters related to the dynamics of growth and mutation. In the present study, we analyzed a small collection of W3110 Escherichia coli derivatives containing either the wild-type genome or reduced genomes of various lengths to examine whether the mutation rate, a global parameter representing genomic plasticity, was affected by genome reduction. We found that the mutation rates of these cells increased with genome reduction. The correlation between genome length and mutation rate, which has been reported for the evolution of bacteria, was also identified, intriguingly, for genome reduction. Gene function enrichment analysis indicated that the deletion of many of the genes encoding membrane and transport proteins play a role in the mutation rate changes mediated by genome reduction. Furthermore, the increase in the mutation rate with genome reduction was highly associated with a decrease in the growth rate in a nutrition-dependent manner; thus, poorer media showed a larger change that was of higher significance. This negative correlation was strongly supported by experimental evidence that the serial transfer of the reduced genome improved the growth rate and reduced the mutation rate to a large extent. Taken together, the global parameters corresponding to the genome, growth, and mutation showed a coordinated relationship, which might be an essential working principle for balancing the cellular dynamics appropriate to the environment. American Society for Microbiology 2017-07-05 /pmc/articles/PMC5573674/ /pubmed/28679744 http://dx.doi.org/10.1128/mBio.00676-17 Text en Copyright © 2017 Nishimura et al. https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research Article
Nishimura, Issei
Kurokawa, Masaomi
Liu, Liu
Ying, Bei-Wen
Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction
title Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction
title_full Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction
title_fullStr Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction
title_full_unstemmed Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction
title_short Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction
title_sort coordinated changes in mutation and growth rates induced by genome reduction
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5573674/
https://www.ncbi.nlm.nih.gov/pubmed/28679744
http://dx.doi.org/10.1128/mBio.00676-17
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