ArticleBMC genomics2022
From a large-scale genomic analysis of insertion sequences to insights into their regulatory roles in prokaryotes.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 22 citations in OpenAlex.
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- Mobile Genetic Elements as Key Drivers of Bacterial Evolution and Adaptation in Agroecosystems.Microbial ecology · 2026Review
- Comprehensive profiling of insertion sequences and eukaryotic-like transposons across archaeal genomes.BMC genomics · 2026Article
- Characterizing the ecological niche of insertion sequences within prokaryotic genomes.The ISME journal · 2026Article
- PCR analysis of insertion sequences leads to the generation of artefact amplicons.Access microbiology · 2026Article
- Integrative and conjugative elements inFrontiers in veterinary science · 2026Article
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- Naturally competent bacteria and their genetic parasites-a battle for control over horizontal gene transfer?FEMS microbiology reviews · 2025Review
- Large-scale genomic analysis of Elizabethkingia anophelis.BMC genomics · 2024Article
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.Cell host & microbe · 2024Article
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.bioRxiv : the preprint server for biology · 2024Article
- First report of coexistence of blaKPC-2 and blaNDM-1 in carbapenem-resistant clinical isolates ofFrontiers in microbiology · 2024Article
- Influence of insertion sequences on population structure of phytopathogenic bacteria in theMicrobiology (Reading, England) · 2023Article
- Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus.BMC genomics · 2023Article
- Complete genome sequence and comparative analysis of aFrontiers in microbiology · 2023Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundInsertion sequences (ISs) are mobile repeat sequences and most of them can copy themselves to new host genome locations, leading to genome plasticity and gene regulation in prokaryotes. In this study, we present functional and evolutionary relationships between IS and neighboring genes in a large-scale comparative genomic analysis.
resultsIS families were located in all prokaryotic phyla, with preferential occurrence of IS3, IS4, IS481, and IS5 families in Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria and Firmicutes as well as in eukaryote host-associated organisms and autotrophic opportunistic pathogens. We defined the concept of the IS-Gene couple (IG), which allowed to highlight the functional and regulatory impacts of an IS on the closest gene. Genes involved in transcriptional regulation and transport activities were found overrepresented in IG. In particular, major facilitator superfamily (MFS) transporters, ATP-binding proteins and transposases raised as favorite neighboring gene functions of IS hotspots. Then, evolutionary conserved IS-Gene sets across taxonomic lineages enabled the classification of IS-gene couples into phylum, class-to-genus, and species syntenic IS-Gene couples. The IS5, IS21, IS4, IS607, IS91, ISL3 and IS200 families displayed two to four times more ISs in the phylum and/or class-to-genus syntenic IGs compared to other IS families. This indicates that those families were probably inserted earlier than others and then subjected to horizontal transfer, transposition and deletion events over time. In phylum syntenic IG category, Betaproteobacteria, Crenarchaeota, Calditrichae, Planctomycetes, Acidithiobacillia and Cyanobacteria phyla act as IS reservoirs for other phyla, and neighboring gene functions are mostly related to transcriptional regulators. Comparison of IS occurrences with predicted regulatory motifs led to ~ 26.5% of motif-containing ISs with 2 motifs per IS in average. These results, concomitantly with short IS-Gene distances, suggest that those ISs would interfere with the expression of neighboring genes and thus form strong candidates for an adaptive pairing.
conclusionsAll together, our large-scale study provide new insights into the IS genetic context and strongly suggest their regulatory roles.
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