Identification and analysis of integrons and cassette arrays in bacterial genomes
| Autor: | Jean Cury, Thomas Jové, Marie Touchon, Eduardo P. C. Rocha, Bertrand Néron |
|---|---|
| Přispěvatelé: | Eduardo, Rocha, Evolution of gene mobility: how mobile elements shape the function and sociality of microbial communities - EVOMOBILOME - - EC:FP7:ERC2012-07-01 - 2017-06-30 - 281605 - VALID, Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Anti-infectieux : supports moléculaires des résistances et innovations thérapeutiques (RESINFIT), CHU Limoges-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), European Research Council [EVOMOBILOME, 281605 to E.P.C.R.]. Funding for open access charge: ERC EVOMOBILOME, European Project: 281605,EC:FP7:ERC,ERC-2011-StG_20101109,EVOMOBILOME(2012), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS) |
| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Pseudogene 030106 microbiology Genomics Bacterial genome size Computational biology Integron Genome Integrons 03 medical and health sciences Bacterial Proteins Phylogenetics Genetics Promoter Regions Genetic Gene Phylogeny 030304 developmental biology Comparative genomics 0303 health sciences [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] Models Genetic biology 030306 microbiology Phylum Computational Biology Integrases biochemical phenomena metabolism and nutrition bacterial infections and mycoses [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology 030104 developmental biology Evolutionary biology Horizontal gene transfer Attachment Sites Microbiological biology.protein [SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] bacteria [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology Genome Bacterial Pseudogenes Software |
| Zdroj: | Nucleic Acids Research Nucleic Acids Research, 2016, 44 (10), pp.4539-4550. ⟨10.1093/nar/gkw319⟩ Nucleic Acids Research, Oxford University Press, 2016, 44 (10), pp.4539-4550. ⟨10.1093/nar/gkw319⟩ |
| ISSN: | 0305-1048 1362-4962 |
| DOI: | 10.1093/nar/gkw319⟩ |
| Popis: | 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, attl 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|