ReviewBMC genomics2006
Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements.
Review in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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48 citing papers in PubMed, 110 citations in OpenAlex.
- Helicobacter pylori in Turkish Children with Dyspepsia: Diagnosis, Prevalence, Genotyping and Antibiotic Resistance.Indian journal of pediatrics · 2026Article
- The ISPpu9 insertion sequence of Pseudomonas putida KT2440 generates various circular intermediates enabling modular transposition.Nucleic acids research · 2025Article
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- Bridge RNAs direct modular and programmable recombination of target and donor DNA.bioRxiv : the preprint server for biology · 2024Article
- DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery.Genome biology · 2023Article
- Influence of insertion sequences on population structure of phytopathogenic bacteria in theMicrobiology (Reading, England) · 2023Article
- Identification and Characterization of Pseudomonas syringae pv. syringae, a Causative Bacterium of Apple Canker in Korea.The plant pathology journal · 2023Article
- Toxic/Bioactive Peptide Synthesis Genes Rearranged by Insertion Sequence Elements Among the Bloom-Forming CyanobacteriaFrontiers in microbiology · 2022Article
- Expression of the ISPpu9 transposase of Pseudomonas putida KT2440 is regulated by two small RNAs and the secondary structure of the mRNA 5'-untranslated region.Nucleic acids research · 2021Article
- Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes.Genome biology · 2021Article
- Deep learning for HGT insertion sites recognition.BMC genomics · 2020Article
- A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation.Cell host & microbe · 2020Article
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- Genetic Environment of cry1 Genes Indicates Their Common Origin.Genome biology and evolution · 2017Article
- Identification and Characterization of Domesticated Bacterial Transposases.Genome biology and evolution · 2017Article
- Dissection of genomic features and variations of three pathotypes of Puccinia striiformis through whole genome sequencing.Scientific reports · 2017Article
- Active and adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen.Cellular microbiology · 2016Article
- Emergence of nontoxic mutants as revealed by single filament analysis in bloom-forming cyanobacteria of the genus Planktothrix.BMC microbiology · 2016Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMobile elements are involved in genomic rearrangements and virulence acquisition, and hence, are important elements in bacterial genome evolution. The insertion of some specific Insertion Sequences had been associated with repetitive extragenic palindromic (REP) elements. Considering that there are a sufficient number of available genomes with described REPs, and exploiting the advantage of the traceability of transposition events in genomes, we decided to exhaustively analyze the relationship between REP sequences and mobile elements.
resultsThis global multigenome study highlights the importance of repetitive extragenic palindromic elements as target sequences for transposases. The study is based on the analysis of the DNA regions surrounding the 981 instances of Insertion Sequence elements with respect to the positioning of REP sequences in the 19 available annotated microbial genomes corresponding to species of bacteria with reported REP sequences. This analysis has allowed the detection of the specific insertion into REP sequences for ISPsy8 in Pseudomonas syringae DC3000, ISPa11 in P. aeruginosa PA01, ISPpu9 and ISPpu10 in P. putida KT2440, and ISRm22 and ISRm19 in Sinorhizobium meliloti 1021 genome. Preference for insertion in extragenic spaces with REP sequences has also been detected for ISPsy7 in P. syringae DC3000, ISRm5 in S. meliloti and ISNm1106 in Neisseria meningitidis MC58 and Z2491 genomes. Probably, the association with REP elements that we have detected analyzing genomes is only the tip of the iceberg, and this association could be even more frequent in natural isolates.
conclusionOur findings characterize REP elements as hot spots for transposition and reinforce the relationship between REP sequences and genomic plasticity mediated by mobile elements. In addition, this study defines a subset of REP-recognizer transposases with high target selectivity that can be useful in the development of new tools for genome manipulation.
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