Four genes essential for recombination define GInts, a new type of mobile genomic island widespread in bacteria

Abstract

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 identified 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 fitness, 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-specifically, generating two flanking 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 specificity.

Deletion of genomic islands in the Pseudomonas putida KT2440 genome can create an optimal chassis for synthetic biology applications

“…The metabolic islands may consume energy and compete with basal metabolism and the production process of secondary metabolites. In addition, metabolic regulation related genes have been found in certain GIs from bacteria [30]. The GIs deleted in this study may also contain non-essential and high energy-consuming metabolic pathways and certain negative regulatory factors related to PHA biosynthesis.…”

Genetic diversity ofPseudomonas syringaepv.actinidiae, pathogen of kiwifruit bacterial canker

“…In addition, it is feared that because Psa has a high degree of genome plasticity, adaptive mutations may occur in destination countries, which may make the damage more severe. The many mobile genetic elements, such as genomic islands including IME and ICE, prophages, transposons and plasmids, which are present on the genomes of Psa could bring new features to Psa, leading to the introduction of environmental adaptability, such as drug resistance, and the acceleration of changes in pathogenicity/virulence (Sawada et al, 2002(Sawada et al, , 2014bGenka et al, 2006;Butler et al, 2013;McCann et al, 2013McCann et al, , 2017Fujikawa & Sawada, 2016Bardaji et al, 2017;Colombi et al, 2017;Vanneste, 2017). Each biovar has high homogeneity within the core genome, but when the information from the accessory genome is included in the phylogenomic analysis, a large diversity appears in each biovar, suggesting that Psa has been continuously accumulating insertion/ deletion and mutation events.…”

“…Recently, it was experimentally confirmed that the ginABCD operon (Fig. c) containing three tyrosine recombinase genes is actually involved in the excision and insertion of the tox island (Bardaji et al ., ). It has already been revealed that genomic island‐like structures containing similar operons to the ginABCD operon are widely distributed in diverse bacteria (Genka et al ., ).…”

“…Thus, Bardaji et al . () proposes to generically refer to these genomic island‐like structures as GInts (genomic island with three integrases).…”

“…It has already been revealed that genomic island-like structures containing similar operons to the ginABCD operon are widely distributed in diverse bacteria (Genka et al, 2006). Thus, Bardaji et al (2017) proposes to generically refer to these genomic island-like structures as GInts (genomic island with three integrases).…”