Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing

Justin Jee, Aviram Rasouly, Ilya Shamovsky, Yonatan Akivis, Susan R. Steinman, Bud Mishra, Evgeny Nudler

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Pages (from-to)693-696
Number of pages4
JournalNature
Volume534
Issue number7609
DOIs
StatePublished - 2016

ASJC Scopus subject areas

  • General

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