ArticlePLoS genetics2007
Identification of DNA motifs implicated in maintenance of bacterial core genomes by predictive modeling.
Article in PLoS genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 53 citations in OpenAlex.
- Rescuing the bacterial replisome at a nick requires recombinational repair and helicase reloading.Nature communications · 2025Article
- Review
- Cleavage of viral DNA by restriction endonucleases stimulates the type II CRISPR-Cas immune response.Molecular cell · 2022Article
- RecBCD enzyme and Chi recombination hotspots as determinants of self vs. non-self: Myths and mechanisms.Advances in genetics · 2022Article
- Evolution of Chi motifs in Proteobacteria.G3 (Bethesda, Md.) · 2021Article
- Ribosomal protein L4 of Lactobacillus rhamnosus LRB alters resistance to macrolides and other antibiotics.Molecular oral microbiology · 2020Article
- Genetics of Lactococci.Microbiology spectrum · 2019Review
- Genome Variation in the Model Halophilic BacteriumFrontiers in microbiology · 2018Article
- Biochemical characterization of RecBCD enzyme from an Antarctic Pseudomonas species and identification of its cognate Chi (χ) sequence.PloS one · 2018Article
- CRISPR-Cas systems exploit viral DNA injection to establish and maintain adaptive immunity.Nature · 2017Article
- Unexpected DNA context-dependence identifies a new determinant of Chi recombination hotspots.Nucleic acids research · 2016Article
- Coevolution of the Organization and Structure of Prokaryotic Genomes.Cold Spring Harbor perspectives in biology · 2016Review
- Ebolavirus Database: Gene and Protein Information Resource for Ebolaviruses.Advances in bioinformatics · 2016Article
- YOC, A new strategy for pairwise alignment of collinear genomes.BMC bioinformatics · 2015Article
- On the mechanism of recombination hotspot scanning during double-stranded DNA break resection.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Dialects of the DNA uptake sequence in Neisseriaceae.PLoS genetics · 2013Article
- Diverse functions of restriction-modification systems in addition to cellular defense.Microbiology and molecular biology reviews : MMBR · 2013Review
- Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability.PLoS genetics · 2013Article
- Google matrix analysis of DNA sequences.PloS one · 2013Article
- Bacterial DNA repair: recent insights into the mechanism of RecBCD, AddAB and AdnAB.Nature reviews. Microbiology · 2013Review
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial biodiversity at the species level, in terms of gene acquisition or loss, is so immense that it raises the question of how essential chromosomal regions are spared from uncontrolled rearrangements. Protection of the genome likely depends on specific DNA motifs that impose limits on the regions that undergo recombination. Although most such motifs remain unidentified, they are theoretically predictable based on their genomic distribution properties. We examined the distribution of the "crossover hotspot instigator," or Chi, in Escherichia coli, and found that its exceptional distribution is restricted to the core genome common to three strains. We then formulated a set of criteria that were incorporated in a statistical model to search core genomes for motifs potentially involved in genome stability in other species. Our strategy led us to identify and biologically validate two distinct heptamers that possess Chi properties, one in Staphylococcus aureus, and the other in several streptococci. This strategy paves the way for wide-scale discovery of other important functional noncoding motifs that distinguish core genomes from the strain-variable regions.
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Registered trials
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.