Comparative genomic analysis of six new-found integrative conjugative elements (ICEs) in Vibrio alginolyticus

Abstract

Background

Vibrio alginolyticus is ubiquitous in marine and estuarine environments. In 2012–2013, SXT/R391-like integrative conjugative elements (ICEs) in environmental V. alginolyticus strains were discovered and found to occur in 8.9 % of 192  V. alginolyticus strains, which suggests that V. alginolyticus may be a natural pool possessing resourceful ICEs. However, complete ICE sequences originating from this bacterium have not been reported, which represents a significant barrier to characterizing the ICEs of this bacterium and exploring their relationships with other ICEs. In the present study, we acquired six ICE sequences from five V. alginolyticus strains and performed a comparative analysis of these ICE genomes.

Results

A sequence analysis showed that there were only 14 variable bases dispersed between ICE ValE0601 and ICE ValHN492. ICE ValE0601 and ICE ValHN492 were treated as the same ICE. ICE ValA056-1, ICE ValE0601 and ICE ValHN492 integrate into the 5′ end of the host’s prfC gene, and their Int and Xis share at least 97 % identity with their counterparts from SXT. ICE ValE0601 or ICE ValHN492 contain 50 of 52 conserved core genes in the SXT/R391 ICEs (not s025 or s026) . ICE ValA056-2, ICE ValHN396 and ICE ValHN437 have a different tRNA-ser integration site and a distinct int/xis module; however, the remaining backbone genes are highly similar to their counterparts in SXT/R391 ICEs. DNA sequences inserted into hotspot and variable regions of the ICEs are of various sizes. The variable genes of six ICEs encode a large array of functions to bestow various adaptive abilities upon their hosts, and only ICE ValA056-1 contains drug-resistant genes. Many variable genes have orthologous and functionally related genes to those found in SXT/R391 ICEs, such as genes coding for a toxin-antitoxin system, a restriction-modification system, helicases and endonucleases. Six ICEs also contain a large number of unique genes or gene clusters that were not found in other ICEs. Six ICEs harbor more abundant transposase genes compared with other parts of their host genomes. A phylogenetic analysis indicated that transposase genes in these ICEs are highly diverse.

Conclusions

ICE ValA056-1, ICE ValE0601 and ICE ValHN492 are typical members of the SXT/R391 family. ICE ValA056-2, ICE ValHN396 and ICE ValHN437 form a new atypical group belonging to the SXT/R391 family. In addition to the many genes found to be present in other ICEs, six ICEs contain a large number of unique genes or gene clusters that were not found in other ICEs. ICEs may serve as a carrier for transposable genetic elements (TEs) and largely facilitate the dissemination of TEs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0692-9) contains supplementary material, which is available to authorized users.