ArticleNucleic acids research2016
Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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73 citing papers in PubMed, 98 citations in OpenAlex.
- Pervasive genome structure heterogeneity iniScience · 2026Article
- Article
- Characterizing the ecological niche of insertion sequences within prokaryotic genomes.The ISME journal · 2026Article
- Accelerated Genomic Evolution and Divergence ofMicroorganisms · 2026Article
- Investigating the Trans Effects of IS<italic>1</italic> Transposases on Intragenomic DNA Movements in <italic>Escherichia coli</italic>.Microbial physiology · 2026Article
- Large-scale plasmidome and carbapenem mobilome analysis reveals a mechanistic duality: high-power specialists and structural generalists mobile genetic elements.Frontiers in microbiology · 2026Article
- The nature of mutation: a legacy of bacterial genetics.Genetics · 2025Review
- Article
- A 69.9-kb long inverted repeat increases genome instability in a strain ofNAR genomics and bioinformatics · 2025Article
- Laboratory evolution of the bacterial genome structure through insertion sequence activation.Nucleic acids research · 2025Article
- Investigating How Genomic Contexts Impact IS5 Transposition Within theMicroorganisms · 2024Article
- Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems.Journal of microbiology (Seoul, Korea) · 2024Review
- Genomic Profile of a Multidrug-Resistant Klebsiella pneumoniae Strain Isolated from a Urine Specimen.Current microbiology · 2024Article
- Article
- Draft genome sequence of a Shiga toxin-producingMicrobiology resource announcements · 2024Article
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.Cell host & microbe · 2024Article
- Article
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.bioRxiv : the preprint server for biology · 2024Article
- Phage-plasmids promote recombination and emergence of phages and plasmids.Nature communications · 2024Article
- Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 × 10(-4) insertions per genome per generation and the rate of IS homologous recombination is 4.5 × 10(-5) recombinations per genome per generation. These events are mostly contributed by the IS elements IS1, IS2, IS5 and IS186 Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS186 target-sites, 5'-GGGG(N6/N7)CCCC-3'. We also detected 48 long deletions not involving IS elements.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.