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Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli

All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) wi...

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Autores principales: Maddamsetti, Rohan, Grant, Nkrumah A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7523724/
https://www.ncbi.nlm.nih.gov/pubmed/32853353
http://dx.doi.org/10.1093/gbe/evaa178
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author Maddamsetti, Rohan
Grant, Nkrumah A
author_facet Maddamsetti, Rohan
Grant, Nkrumah A
author_sort Maddamsetti, Rohan
collection PubMed
description All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM. 2017. The dynamics of molecular evolution over 60,000 generations. Nature 551(7678):45–50.), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic differences in their rates of point mutations, indels, and mobile element insertions, due to the fixation of various hypermutator and antimutator alleles. One LTEE population, called Ara+3, shows a strong, symmetric wave pattern in its density of point mutations, radiating from the origin of replication. This pattern is largely missing from the other LTEE populations, most of which evolved missense, indel, or structural mutations in topA, fis, and dusB—loci that all affect DNA topology. The distribution of mutations in those genes over time suggests epistasis and historical contingency in the evolution of DNA topology, which may have in turn affected local mutation rates. Overall, the replicate populations of the LTEE have largely diverged in their mutation rates and biases, even though they have adapted to identical abiotic conditions.
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spelling pubmed-75237242020-10-02 Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli Maddamsetti, Rohan Grant, Nkrumah A Genome Biol Evol Research Article All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM. 2017. The dynamics of molecular evolution over 60,000 generations. Nature 551(7678):45–50.), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic differences in their rates of point mutations, indels, and mobile element insertions, due to the fixation of various hypermutator and antimutator alleles. One LTEE population, called Ara+3, shows a strong, symmetric wave pattern in its density of point mutations, radiating from the origin of replication. This pattern is largely missing from the other LTEE populations, most of which evolved missense, indel, or structural mutations in topA, fis, and dusB—loci that all affect DNA topology. The distribution of mutations in those genes over time suggests epistasis and historical contingency in the evolution of DNA topology, which may have in turn affected local mutation rates. Overall, the replicate populations of the LTEE have largely diverged in their mutation rates and biases, even though they have adapted to identical abiotic conditions. Oxford University Press 2020-08-27 /pmc/articles/PMC7523724/ /pubmed/32853353 http://dx.doi.org/10.1093/gbe/evaa178 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Maddamsetti, Rohan
Grant, Nkrumah A
Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli
title Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli
title_full Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli
title_fullStr Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli
title_full_unstemmed Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli
title_short Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli
title_sort divergent evolution of mutation rates and biases in the long-term evolution experiment with escherichia coli
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7523724/
https://www.ncbi.nlm.nih.gov/pubmed/32853353
http://dx.doi.org/10.1093/gbe/evaa178
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