ArticleBMC genomics2015
The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 13 citations in OpenAlex.
- Novel approach toward the understanding of genetic diversity based on the two types of amino acid repeats in Erwinia amylovora.Scientific reports · 2023Article
- The DNA Phosphorothioation Restriction-Modification System Influences the Antimicrobial Resistance of Pathogenic Bacteria.Microbiology spectrum · 2023Article
- DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome.Biomolecules · 2020Article
- Serratia liquefaciens FG3 isolated from a metallophyte plant sheds light on the evolution and mechanisms of adaptive traits in extreme environments.Scientific reports · 2019Article
- Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7.BMC genomics · 2019Article
- DNA phosphorothioate modification-a new multi-functional epigenetic system in bacteria.FEMS microbiology reviews · 2019Review
- Evolutionary Genomics of Defense Systems in Archaea and Bacteria.Annual review of microbiology · 2017Review
- Structural investigation into physiological DNA phosphorothioate modification.Scientific reports · 2016Article
- New Insights into the Genetic Diversity of Clostridium botulinum Group III through Extensive Genome Exploration.Frontiers in microbiology · 2016Article
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundStrains of Escherichia coli that are non-typeable by pulsed-field gel electrophoresis (PFGE) due to in-gel degradation can influence their molecular epidemiological data. The DNA degradation phenotype (Dnd(+)) is mediated by the dnd operon that encode enzymes catalyzing the phosphorothioation of DNA, rendering the modified DNA susceptible to oxidative cleavage during a PFGE run. In this study, a PCR assay was developed to detect the presence of the dnd operon in Dnd(+) E. coli strains and to improve their typeability. Investigations into the genetic environments of the dnd operon in various E. coli strains led to the discovery that the dnd operon is harboured in various diverse genomic islands.
resultsThe dndBCDE genes (dnd operon) were detected in all Dnd(+) E. coli strains by PCR. The addition of thiourea improved the typeability of Dnd(+) E. coli strains to 100% using PFGE and the Dnd(+) phenotype can be observed in both clonal and genetically diverse E. coli strains. Genomic analysis of 101 dnd operons from genome sequences of Enterobacteriaceae revealed that the dnd operons of the same bacterial species were generally clustered together in the phylogenetic tree. Further analysis of dnd operons of 52 E. coli genomes together with their respective immediate genetic environments revealed a total of 7 types of genetic organizations, all of which were found to be associated with genomic islands designated dnd-encoding GIs. The dnd-encoding GIs displayed mosaic structure and the genomic context of the 7 islands (with 1 representative genome from each type of genetic organization) were also highly variable, suggesting multiple recombination events. This is also the first report where two dnd operons were found within a strain although the biological implication is unknown. Surprisingly, dnd operons were frequently found in pathogenic E. coli although their link with virulence has not been explored.
conclusionGenomic islands likely play an important role in facilitating the horizontal gene transfer of the dnd operons in E. coli with 7 different types of islands discovered so far.
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