ArticleMolecular biology and evolution2017
Rapid Genetic Adaptation during the First Four Months of Survival under Resource Exhaustion.
Article in Molecular biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed.
- Host diets drive microbiome evolution and functional divergence.Genes & diseases · 2027Review
- Non-canonical gene amplifications facilitate adaptive evolution in bacteria.Nature microbiology · 2026Article
- Differentiation between regulated and disrupted growth arrests allows tailoring of effective treatments for antibiotic persistence.Science advances · 2026Article
- Structural dependence of ProQ-mRNA interactions in live bacterial cells.Communications biology · 2025Article
- Positive selection at core genes may underlie niche adaptation in Fusobacterium animalis.Gut pathogens · 2025Article
- Resource presentation dictates genetic and phenotypic adaptation in yeast.BMC ecology and evolution · 2025Article
- What Is the Impact of Antibiotic Resistance Determinants on the Bacterial Death Rate?Antibiotics (Basel, Switzerland) · 2025Article
- Genome and transcriptomic analysis of the adaptation ofComputational and structural biotechnology journal · 2024Review
- Survival dynamics of starving bacteria are determined by ion homeostasis that maintains plasmolysis.Nature physics · 2024Article
- Pseudomonas putida Dynamics of Adaptation under Prolonged Resource Exhaustion.Genome biology and evolution · 2024Article
- Escherichia coli adaptation under prolonged resource exhaustion is characterized by extreme parallelism and frequent historical contingency.PLoS genetics · 2024Article
- Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation during extreme cycles of feast and famine.Current biology : CB · 2024Article
- Biochemical and genetic dissection of the RNA-binding surface of the FinO domain ofRNA (New York, N.Y.) · 2023Article
- Mutation bias and adaptation in bacteria.Microbiology (Reading, England) · 2023Review
- Ribosome-binding antibiotics increase bacterial longevity and growth efficiency.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Metabolic adaptation to consume butyrate under prolonged resource exhaustion.PLoS genetics · 2023Article
- Biochemical and genetic dissection of the RNA-binding surface of the FinO domain ofbioRxiv : the preprint server for biology · 2023Article
- FinO/ProQ-family proteins: an evolutionary perspective.Bioscience reports · 2023Review
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4 authors.
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Abstract
Many bacteria, including the model bacterium Escherichia coli can survive for years within spent media, following resource exhaustion. We carried out evolutionary experiments, followed by whole genome sequencing of hundreds of evolved clones to study the dynamics by which E. coli adapts during the first 4 months of survival under resource exhaustion. Our results reveal that bacteria evolving under resource exhaustion are subject to intense selection, manifesting in rapid mutation accumulation, enrichment in functional mutation categories and extremely convergent adaptation. In the most striking example of convergent adaptation, we found that across five independent populations adaptation to conditions of resource exhaustion occurs through mutations to the three same specific positions of the RNA polymerase core enzyme. Mutations to these three sites are strongly antagonistically pleiotropic, in that they sharply reduce exponential growth rates in fresh media. Such antagonistically pleiotropic mutations, combined with the accumulation of additional mutations, severely reduce the ability of bacteria surviving under resource exhaustion to grow exponentially in fresh media. We further demonstrate that the three positions at which these resource exhaustion mutations occur are conserved for the ancestral E. coli allele, across bacterial phyla, with the exception of nonculturable bacteria that carry the resource exhaustion allele at one of these positions, at very high frequencies. Finally, our results demonstrate that adaptation to resource exhaustion is not limited by mutational input and that bacteria are able to rapidly adapt under resource exhaustion in a temporally precise manner through allele frequency fluctuations.
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