ArticleNucleic acids research2020
New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 37 citations in OpenAlex.
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- Identification of a novel bacteriophage attachment site into ffs, the 4.5S non-coding RNA component of the signal recognition particle.Scientific reports · 2025Article
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- The TIGER/Islander resource for genomic islands.Microbiology resource announcements · 2025Article
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- Pipolins are bimodular platforms that maintain a reservoir of defense systems exchangeable with various bacterial genetic mobile elements.Nucleic acids research · 2024Article
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- Identification of mobile genetic elements with geNomad.Nature biotechnology · 2024Article
- Phylogenomics and genetic analysis of solvent-producing Clostridium species.Scientific data · 2024Article
- Speeding genomic island discovery through systematic design of reference database composition.PloS one · 2024Article
- Helper-embedded satellites from an integrase clade that repeatedly targets prophage late genes.NAR genomics and bioinformatics · 2023Article
- Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity.Science advances · 2023Article
- On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes.RNA biology · 2023Article
- BigDNA: Primer Design Software for Overlap-Based Assembly of Phage Genomes and Larger DNAs.PHAGE (New Rochelle, N.Y.) · 2022Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Integrative genetic elements (IGEs) are mobile multigene DNA units that integrate into and excise from host bacterial genomes. Each IGE usually targets a specific site within a conserved host gene, integrating in a manner that preserves target gene function. However, a small number of bacterial genes are known to be inactivated upon IGE integration and reactivated upon excision, regulating phenotypes of virulence, mutation rate, and terminal differentiation in multicellular bacteria. The list of regulated gene integrity (RGI) cases has been slow-growing because IGEs have been challenging to precisely and comprehensively locate in genomes. We present software (TIGER) that maps IGEs with unprecedented precision and without attB site bias. TIGER uses a comparative genomic, ping-pong BLAST approach, based on the principle that the IGE integration module (i.e. its int-attP region) is cohesive. The resultant IGEs from 2168 genomes, along with integrase phylogenetic analysis and gene inactivation tests, revealed 19 new cases of genes whose integrity is regulated by IGEs (including dut, eccCa1, gntT, hrpB, merA, ompN, prkA, tqsA, traG, yifB, yfaT and ynfE), as well as recovering previously known cases (in sigK, spsM, comK, mlrA and hlb genes). It also recovered known clades of site-promiscuous integrases and identified possible new ones.
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