ArticlePLoS computational biology2012
Nucleoid-associated proteins affect mutation dynamics in E. coli in a growth phase-specific manner.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Genome-wide mapping of spontaneous DNA replication error-hotspots using mismatch repair proteins in rapidly proliferating Escherichia coli.Nucleic acids research · 2025Article
- Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS.Nucleic acids research · 2024Article
- Modeling the mosaic structure of bacterial genomes to infer their evolutionary history.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Mutation bias and adaptation in bacteria.Microbiology (Reading, England) · 2023Review
- Special Issue: Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution.Microorganisms · 2021Article
- Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers.Molecular biology and evolution · 2021Review
- Mutation and Recombination Rates Vary Across Bacterial Chromosome.Microorganisms · 2019Review
- Periodic Variation of Mutation Rates in Bacterial Genomes Associated with Replication Timing.mBio · 2018Article
- A response regulator promotes Francisella tularensis intramacrophage growth by repressing an anti-virulence factor.Molecular microbiology · 2016Article
- H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes.PLoS genetics · 2016Article
- Regulation of Bacterial DNA Packaging in Early Stationary Phase by Competitive DNA Binding of Dps and IHF.Scientific reports · 2015Article
- Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in Starving Escherichia coli.Genetics · 2015Article
- Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment.Molecular biology and evolution · 2015Article
- Mutation bias, rather than binding preference, underlies the nucleosome-associated G+C% variation in eukaryotes.Genome biology and evolution · 2015Article
- Strong purifying selection at synonymous sites in D. melanogaster.PLoS genetics · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The binding of proteins can shield DNA from mutagenic processes but also interfere with efficient repair. How the presence of DNA-binding proteins shapes intra-genomic differences in mutability and, ultimately, sequence variation in natural populations, however, remains poorly understood. In this study, we examine sequence evolution in Escherichia coli in relation to the binding of four abundant nucleoid-associated proteins: Fis, H-NS, IhfA, and IhfB. We find that, for a subset of mutations, protein occupancy is associated with both increased and decreased mutability in the underlying sequence depending on when the protein is bound during the bacterial growth cycle. On average, protein-bound DNA exhibits reduced mutability compared to protein-free DNA. However, this net protective effect is weak and can be abolished or even reversed during stages of colony growth where binding coincides - and hence likely interferes with - DNA repair activity. We suggest that the four nucleoid-associated proteins analyzed here have played a minor but significant role in patterning extant sequence variation in E. coli.
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