1 Scientific RepoRts | 7:46254 | DOI: 10.1038/srep46254 www.nature.com/scientificreports Four genes essential for recombination defne GInts, a new type of mobile genomic island widespread in bacteria Leire Bardaji 1 , Myriam echeverría 1 , Pablo Rodríguez-Palenzuela 2 , Pedro M. Martínez-García 2,3 & Jesús Murillo 1 Integrases are a family of tyrosine recombinases that are highly abundant in bacterial genomes, actively disseminating adaptive characters such as pathogenicity determinants and antibiotics resistance. Using comparative genomics and functional assays, we identifed a novel type of mobile genetic element, the GInt, in many diverse bacterial groups but not in archaea. Integrated as genomic islands, GInts show a tripartite structure consisting of the ginABCD operon, a cargo DNA region from 2.5 to at least 70 kb, and a short AT-rich 3′ end. The gin operon is characteristic of GInts and codes for three putative integrases and a small putative helix-loop-helix protein, all of which are essential for integration and excision of the element. Genes in the cargo DNA are acquired mostly from phylogenetically related bacteria and often code for traits that might increase ftness, such as resistance to antimicrobials or virulence. GInts also tend to capture clusters of genes involved in complex processes, such as the biosynthesis of phaseolotoxin by Pseudomonas syringae. GInts integrate site-specifcally, generating two fanking direct imperfect repeats, and excise forming circular molecules. The excision process generates sequence variants at the element attachment site, which can increase frequency of integration and drive target specifcity. Tyrosine-based site-specifc recombinases (TRases) are exceedingly abundant in prokaryotic and eukaryotic genomes 1,2 , carrying out functions as diverse as ensuring proper chromosomal and plasmid segregation, reg- ulating gene expression or determining the life cycle of prophages towards dormancy or cell death 3 . Tey are also responsible for the movement of DNA through various types of mobile genetic elements (MGEs), such as integrons, phages, certain transposons, integrative conjugative elements, and genomic islands 1,4 . Tese elements have a signifcant impact in bacterial evolution by spurring lateral gene transfer, which favours the speciation of bacteria and their adaptation to new ecological niches, either by enhancing their ftness and/or enabling inter- actions with other organisms 4–6 . For instance, integrons are the major agents for the dissemination of antibiotic multiresistance in Gram-negative bacteria 7 , whereas integron-like elements are of signifcance to the transfer of ftness and virulence genes among environmental bacteria 8 . Likewise, genomic islands are key players in micro- bial evolution and adaptations that are of medical, agricultural and environmental interest 9,10 ; indeed, many plant and animal pathogenic bacteria carry diverse genomic islands that allow them to more efciently colonize their hosts and evade control measures, threatening the management of diseases in human settings 11 . Te bean plant pathogen Pseudomonas syringae (Ps) pv. phaseolicola contains a cluster of 23 genes, the Pht cluster, responsible for the biosynthesis of the wide-spectrum antimetabolite toxin phaseolotoxin 12–14 . Besides its relevance as a research model and potential biotechnological applications 15 , the Pht cluster is of practical sig- nifcance because it is generally used for the specifc detection of this important plant pathogen 16 . Te cluster is 1 Departamento de Producción Agraria, escuela técnica Superior de ingenieros Agrónomos, Universidad Pública de Navarra, 31006 Pamplona, Spain. 2 Centro de Biotecnología y Genómica de Plantas, E.T.S. Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, E-28223 Pozuelo de Alarcón, Madrid, Spain. 3 instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-consejo Superior de Investigaciones Científcas (IHSM-UMA-CSIC), Área de Genética, Facultad de Ciencias, Campus Teatinos s/n, 29010 Málaga, Spain. Correspondence and requests for materials should be addressed to J.M. (email: jesus.murillo@ unavarra.es) received: 15 December 2016 Accepted: 10 March 2017 Published: 10 April 2017 OPEN