Excision and transfer of an integrating and conjugative element in a bacterial species with high recombination efficiency

Evelyn Weiss,Carolin Spicher,Wolfgang Fischer,Rainer Haas

doi:10.1038/s41598-019-45429-z

Abstract

Horizontal transfer of mobile genetic elements, such as integrating and conjugative elements (ICEs), plays an important role in generating diversity and maintaining comprehensive pan-genomes in bacterial populations. The human gastric pathogen Helicobacter pylori, which is known for its extreme genetic diversity, possesses highly efficient transformation and recombination systems to achieve this diversity, but it is unclear to what extent these systems influence ICE physiology. In this study, we have examined the excision/integration and horizontal transfer characteristics of an ICE (termed ICEHptfs4) in these bacteria. We show that transfer of ICEHptfs4 DNA during mating between donor and recipient strains is independent of its conjugation genes, and that homologous recombination is much more efficient than site-specific integration into the recipient chromosome. Nevertheless, ICEHptfs4 excision by site-specific recombination occurs permanently in a subpopulation of cells and involves relocation of a circularization-dependent promoter. Selection experiments for excision indicate that the circular form of ICEHptfs4 is not replicative, but readily reintegrates by site-specific recombination. Thus, although ICEHptfs4 harbours all essential transfer genes, and typical ICE functions such as site-specific integration are active in H. pylori, canonical ICE transfer is subordinate to the more efficient general DNA uptake and homologous recombination machineries in these bacteria.

Highlights

Integrating and conjugative elements (ICEs) are mobile genetic elements carrying a wide range of cargo genes which confer upon their hosts traits such as additional metabolic or colonization abilities, or antibiotic or metal resistance[1]
We have previously reported that a resistance gene marker inserted into the ICEHptfs[4] element of H. pylori strain P12 could be transferred from donor to recipient bacteria co-cultivated in the presence of DNase I to prevent natural transformation, suggesting that conjugative transfer of the whole genome island takes place[13]
Individual double-resistant clones were analysed by sequencing the region surrounding the insertion site of the cat gene, and single-nucleotide polymorphisms between donor and recipient strains were used to identify recombination breakpoint regions. Such breakpoints were typically located 400–4,000 bp away from the cat insertion site (Fig. 1a). Since these import lengths are typical for DNA introduced by natural transformation and subsequent homologous recombination[21,22,23], this indicates that most transfer events under the applied conditions are mediated by homologous recombination into a pre-existing integrating and conjugative elements (ICEs), rather than by transfer and site-specific integration of the complete element

Summary

Introduction

Integrating and conjugative elements (ICEs) are mobile genetic elements carrying a wide range of cargo genes which confer upon their hosts traits such as additional metabolic or colonization abilities, or antibiotic or metal resistance[1]. We have previously reported that a resistance gene marker inserted into the ICEHptfs[4] element of H. pylori strain P12 could be transferred from donor to recipient bacteria co-cultivated in the presence of DNase I to prevent natural transformation, suggesting that conjugative transfer of the whole genome island takes place[13]. Such a transfer was only achieved when recipient strains harboring at least a part of a similar ICE element were used. Comparative genomic analysis strongly suggests a transfer activity of ICEHptfs[4] in a classical, ICE-like manner, this mechanism is superimposed in H. pylori by the much more efficient recombination machinery

Methods

Results

Conclusion