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Rates and Mechanisms of Bacterial Mutagenesis from Maximum-Depth Sequencing

In 1943, Luria and Delbrück used a phage resistance assay to establish spontaneous mutation as a driving force of microbial diversity(1). Mutation rates are still studied using such assays, but these can only examine the small minority of mutations conferring survival in a particular condition. Newe...

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Autores principales: Jee, Justin, Rasouly, Aviram, Shamovsky, Ilya, Akivis, Yonatan, Steinman, Susan, Mishra, Bud, Nudler, Evgeny
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940094/
https://www.ncbi.nlm.nih.gov/pubmed/27338792
http://dx.doi.org/10.1038/nature18313
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author Jee, Justin
Rasouly, Aviram
Shamovsky, Ilya
Akivis, Yonatan
Steinman, Susan
Mishra, Bud
Nudler, Evgeny
author_facet Jee, Justin
Rasouly, Aviram
Shamovsky, Ilya
Akivis, Yonatan
Steinman, Susan
Mishra, Bud
Nudler, Evgeny
author_sort Jee, Justin
collection PubMed
description In 1943, Luria and Delbrück used a phage resistance assay to establish spontaneous mutation as a driving force of microbial diversity(1). Mutation rates are still studied using such assays, but these can only examine the small minority of mutations conferring survival in a particular condition. Newer approaches, such as long-term evolution followed by whole-genome sequencing (2, 3), may be skewed by mutational “hot” or “cold” spots (3, 4). Both approaches are affected by numerous caveats (5, 6, 7) (see Supplemental Information). We devise a method, Maximum-Depth Sequencing (MDS), to detect extremely rare variants in a population of cells through error-corrected, high-throughput sequencing. We directly measure locus-specific mutation rates in E. coli and show that they vary across the genome by at least an order of magnitude. Our data suggest that certain types of nucleotide misincorporation occur 10(4)-fold more frequently than the basal rate of mutations, but are repaired in vivo. Our data also suggest specific mechanisms of antibiotic-induced mutagenesis, including downregulation of mismatch repair via oxidative stress; transcription-replication conflicts; and in the case of fluoroquinolones, direct damage to DNA.
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spelling pubmed-49400942016-12-30 Rates and Mechanisms of Bacterial Mutagenesis from Maximum-Depth Sequencing Jee, Justin Rasouly, Aviram Shamovsky, Ilya Akivis, Yonatan Steinman, Susan Mishra, Bud Nudler, Evgeny Nature Article In 1943, Luria and Delbrück used a phage resistance assay to establish spontaneous mutation as a driving force of microbial diversity(1). Mutation rates are still studied using such assays, but these can only examine the small minority of mutations conferring survival in a particular condition. Newer approaches, such as long-term evolution followed by whole-genome sequencing (2, 3), may be skewed by mutational “hot” or “cold” spots (3, 4). Both approaches are affected by numerous caveats (5, 6, 7) (see Supplemental Information). We devise a method, Maximum-Depth Sequencing (MDS), to detect extremely rare variants in a population of cells through error-corrected, high-throughput sequencing. We directly measure locus-specific mutation rates in E. coli and show that they vary across the genome by at least an order of magnitude. Our data suggest that certain types of nucleotide misincorporation occur 10(4)-fold more frequently than the basal rate of mutations, but are repaired in vivo. Our data also suggest specific mechanisms of antibiotic-induced mutagenesis, including downregulation of mismatch repair via oxidative stress; transcription-replication conflicts; and in the case of fluoroquinolones, direct damage to DNA. 2016-06-30 /pmc/articles/PMC4940094/ /pubmed/27338792 http://dx.doi.org/10.1038/nature18313 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Jee, Justin
Rasouly, Aviram
Shamovsky, Ilya
Akivis, Yonatan
Steinman, Susan
Mishra, Bud
Nudler, Evgeny
Rates and Mechanisms of Bacterial Mutagenesis from Maximum-Depth Sequencing
title Rates and Mechanisms of Bacterial Mutagenesis from Maximum-Depth Sequencing
title_full Rates and Mechanisms of Bacterial Mutagenesis from Maximum-Depth Sequencing
title_fullStr Rates and Mechanisms of Bacterial Mutagenesis from Maximum-Depth Sequencing
title_full_unstemmed Rates and Mechanisms of Bacterial Mutagenesis from Maximum-Depth Sequencing
title_short Rates and Mechanisms of Bacterial Mutagenesis from Maximum-Depth Sequencing
title_sort rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940094/
https://www.ncbi.nlm.nih.gov/pubmed/27338792
http://dx.doi.org/10.1038/nature18313
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