title: Identification and analysis of integrons and cassette arrays in bacterial genomes.
abstract: Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program - IntegronFinder - to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as α-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome.
authors.affiliation: Microbial Evolutionary Genomics, Institut Pasteur, 28, rue Dr Roux, Paris, 75015, France CNRS, UMR3525, 28, rue Dr Roux, Paris, 75015, France jean.cury@normalesup.org.
authors.forename: Jean
authors.identifier: 0000-0002-6462-8783
authors.initials: J
authors.lastname: Cury
authors.affiliation: Univ. Limoges, INSERM, CHU Limoges, UMR_S 1092, F-87000 Limoges, France.
authors.forename: Thomas
authors.identifier: 0000-0002-4638-325X
authors.initials: T
authors.lastname: Jové
authors.affiliation: Microbial Evolutionary Genomics, Institut Pasteur, 28, rue Dr Roux, Paris, 75015, France CNRS, UMR3525, 28, rue Dr Roux, Paris, 75015, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Touchon
authors.affiliation: Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, Paris, France.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Néron
authors.affiliation: Microbial Evolutionary Genomics, Institut Pasteur, 28, rue Dr Roux, Paris, 75015, France CNRS, UMR3525, 28, rue Dr Roux, Paris, 75015, France.
authors.forename: Eduardo Pc
authors.initials: EP
authors.lastname: Rocha
mesh_terms: D001287:Attachment Sites, Microbiological / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D032023:Integrons; D008957:Models, Genetic; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D011544:Pseudogenes; D012984:Software
chemical_list: D001426:Bacterial Proteins