TY - JOUR
T1 - Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing
AU - Jee, Justin
AU - Rasouly, Aviram
AU - Shamovsky, Ilya
AU - Akivis, Yonatan
AU - Steinman, Susan R.
AU - Mishra, Bud
AU - Nudler, Evgeny
N1 - Funding Information:
Acknowledgements We thank A. Heguy and the NYU Genome Technology Center, which is partially supported by the Cancer Center Support Grant, P30CA016087, at the Laura and Isaac Perlmutter Cancer Center. This work used computing resources at the High Performance Computing Facility of the Center for Health Informatics and Bioinformatics at the NYU Langone Medical Center. We thank D. Dwyer and K. Shankarling for materials, and T. Artemyev for his contribution. This work was supported by NIH grant R01GM107329 and HHMI (E.N.) and NCI PSOC grant U54 CA193313 (B.M.). J.J. was supported by the NYU Medical Scientist Training Program and a National Defense Science and Engineering Graduate Fellowship.
Publisher Copyright:
© 2016 Macmillan Publishers Limited. All rights reserved.
PY - 2016
Y1 - 2016
N2 - In 1943, Luria and Delbrack used a phage-resistance assay to establish spontaneous mutation as a driving force of microbial diversity1. Mutation rates are still studied using such assays, but these can only be used to examine the small minority of mutations conferring survival in a particular condition. Newer approaches, such as long-term evolution followed by whole-genome sequencing2, 3, may be skewed by mutational 'hot' or 'cold' spots3, 4. Both approaches are affected by numerous caveats5-7. Here 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 Escherichia 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 104-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.
AB - In 1943, Luria and Delbrack used a phage-resistance assay to establish spontaneous mutation as a driving force of microbial diversity1. Mutation rates are still studied using such assays, but these can only be used to examine the small minority of mutations conferring survival in a particular condition. Newer approaches, such as long-term evolution followed by whole-genome sequencing2, 3, may be skewed by mutational 'hot' or 'cold' spots3, 4. Both approaches are affected by numerous caveats5-7. Here 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 Escherichia 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 104-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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U2 - 10.1038/nature18313
DO - 10.1038/nature18313
M3 - Article
C2 - 27338792
AN - SCOPUS:84991784371
SN - 1465-7392
VL - 534
SP - 693
EP - 696
JO - Nature Cell Biology
JF - Nature Cell Biology
IS - 7609
ER -