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

Leire Bardaji,Pedro M Martínez-García,Pablo Rodríguez-Palenzuela,Myriam Echeverría,Jesús Murillo

doi:10.1038/srep46254

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.

Highlights

Embedded into the 38 kb putative pathogenicity island Pht-PAI, whose 5′end is defined by three genes coding for products with similarities to Tyrosine-based site-specific recombinases (TRases)[13,17]
The Pht-cluster is included in a genomic island (Pht-PAI) that has been exchanged horizontally among Ps strains, and it is accompanied by three putative TRases that are associated to dissimilar DNA in different strains[13,14,19]
We found many examples among pseudomonads of genomic islands showing the same organization than the Pht-PAI, namely, a tripartite structure consisting of 1) the highly conserved ginABCD operon in the 5′end; 2) a variable amount of cargo DNA, starting immediately before or after the stop codon of ginD; and 3) a short and poorly conserved 3′end containing some well-conserved AT-rich sequence stretches (Fig. 1 and Table S1)

Summary

Introduction

Embedded into the 38 kb putative pathogenicity island Pht-PAI, whose 5′end is defined by three genes coding for products with similarities to TRases[13,17]. Phaseolicola CYL314, integrated into the same genomic location as the Pht-PAI but associated to dissimilar DNA13,17. These correlational data, together with the phylogeny of diverse genes from the Pht cluster, led to the hypothesis that this putative island was possibly first acquired from a Gram-positive bacterium by lateral gene transfer, and later exchanged among P. syringae pathovars[13,17,18]. We used comparative genomics and functional assays to study the functionality of the Pht-PAI and its potential mobility This showed that the Pht-PAI belongs to a new type of MGE, designated GInt, that is widely distributed in diverse bacterial phyla. GInts are characterized by the ginABCD operon, coding for three TRases and a fourth product that are essential for recombination, and can carry up to at least 70 kb of cargo DNA containing genes potentially increasing fitness and virulence

Methods

Results

Conclusion