ArticleProceedings of the National Academy of Sciences of the United States of America2015
Determinants of spontaneous mutation in the bacterium Escherichia coli as revealed by whole-genome sequencing.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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117 citing papers in PubMed.
- A reference genome without a virus: cDNA reconstruction reveals the provenance and function of the MS2 phage sequence.bioRxiv : the preprint server for biology · 2026Article
- Simple birth-death-mutation models predict some-but not all-aspects of the experimental evolution of antibiotic resistance.PLoS computational biology · 2026Article
- Translation accuracy in E. coli.Nucleic acids research · 2026Article
- Reciprocal cross-feeding between bacteria can limit the emergence of metabolic dependencies.Applied and environmental microbiology · 2026Article
- Mutation-biased adaptation is consequential even in large bacterial populations.Nature communications · 2026Article
- Extended sequence context shapes mutational bias inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Redox stress agents strongly enhance mutagenesis during horizontal gene transfer in bacteria and leave distinct mutational and metabolic footprints.bioRxiv : the preprint server for biology · 2026Article
- Disruption of bacteriophage integration site promotes rapid diversification of multicellular traits inMicrobiology spectrum · 2026Article
- Loss of DNA mismatch repair genes leads to acquisition of antibiotic resistance independent of secondary mutations.PLoS genetics · 2026Article
- Detection of mutations: from Ames test to duplex sequencing.Frontiers in molecular biosciences · 2026Review
- Elevated rates and biased spectra of mutations in anaerobically cultured lactic acid bacteria.mBio · 2025Article
- Bacterial gene 5' ends have unusual mutation rates that can mislead tests of selection.PLoS biology · 2025Article
- Conflicts between the DNA replication and repair machineries promote cell death in Gram-positive bacteria.Microbiology (Reading, England) · 2025Article
- Climate-driven co-evolution of antimicrobial resistance and virulence in Escherichia coli on dairy farms: unraveling adaptive genetic signatures with novel SSCP-PCR.World journal of microbiology & biotechnology · 2025Article
- Within-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult.Nature communications · 2025Article
- Antimutator and Mutational Spectrum Effects Can Combine to Reduce Evolutionary Potential in Escherichia coli ΔnudJ.Molecular biology and evolution · 2025Article
- Methylglyoxal is an antibacterial effector produced by macrophages during infection.Cell host & microbe · 2025Article
- Mutation bias alters the distribution of fitness effects of mutations.PLoS biology · 2025Article
- Reduced Genetic Heterogeneity for Stable Bioproduction by Harnessing the Bias and Mechanism of Mutation.Microbial biotechnology · 2025Article
- Self-authenticating genomic materials in Escherichia coli via advanced genome signatures.Communications biology · 2025Article
57 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
A complete understanding of evolutionary processes requires that factors determining spontaneous mutation rates and spectra be identified and characterized. Using mutation accumulation followed by whole-genome sequencing, we found that the mutation rates of three widely diverged commensal Escherichia coli strains differ only by about 50%, suggesting that a rate of 1-2 × 10(-3) mutations per generation per genome is common for this bacterium. Four major forces are postulated to contribute to spontaneous mutations: intrinsic DNA polymerase errors, endogenously induced DNA damage, DNA damage caused by exogenous agents, and the activities of error-prone polymerases. To determine the relative importance of these factors, we studied 11 strains, each defective for a major DNA repair pathway. The striking result was that only loss of the ability to prevent or repair oxidative DNA damage significantly impacted mutation rates or spectra. These results suggest that, with the exception of oxidative damage, endogenously induced DNA damage does not perturb the overall accuracy of DNA replication in normally growing cells and that repair pathways may exist primarily to defend against exogenously induced DNA damage. The thousands of mutations caused by oxidative damage recovered across the entire genome revealed strong local-sequence biases of these mutations. Specifically, we found that the identity of the 3' base can affect the mutability of a purine by oxidative damage by as much as eightfold.
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