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 ICEValE0601 and ICEValHN492. ICEValE0601 and ICEValHN492 were treated as the same ICE. ICEValA056-1, ICEValE0601 and ICEValHN492 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. ICEValE0601 or ICEValHN492 contain 50 of 52 conserved core genes in the SXT/R391 ICEs (not s025 or s026). ICEValA056-2, ICEValHN396 and ICEValHN437 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 ICEValA056-1 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: ICEValA056-1, ICEValE0601 and ICEValHN492 are typical members of the SXT/R391 family. ICEValA056-2, ICEValHN396 and ICEValHN437 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.

Keywords: Comparative genomics; Integrative Conjugative Elements (ICEs); Transposable genetic Elements (TEs); Vibrio alginolyticus.

Fig. 1

Structural comparison between SXT and six ICEs from V. alginolyticus. a Schematic representation of the 52 core genes of SXT/R391 ICEs. Left lower part is the normal int/xis module of SXT/R391 ICEs, and the upper left part shows the alternative int/xis modules of ICEValA056-2, ICEValHN396 and ICEValHN437. Atypical insertions of ORFs of these ICEs and an extra copy of exo gene (pale green) of ICEValA056-2 are indicated with fold-down arrows. The absences of s025 and s026 in ICEValE0601/ICEValHN492 are shown with red crosses. b Variable ICE regions are shown with colors according to the elements in which they were originally described: SXT (blue), ICEValA056-1 (dark red), ICEValA056-2 (pale green), ICEValE0601/ICEValHN492 (red), ICEValHN396 (dark green) and ICEValHN437 (pink). Thin arrows indicate the sites of insertion for each VR region (I, II and III) and HS1–HS5 represent hotspots 1–5. Some notable genes in these regions are marked. Tm, trimethoprim cassette; Cm, chloramphenicol cassette; Sm, streptomycin cassette; Su, sulfamethoxazole cassette; mosAT, toxin-antitoxin system; prrABCD, an novel operon including a RM system and anticodon nuclease gene. Variable region III is shown at the top of the backbone of SXT/R391 ICEs for saving space

Fig. 2

Alignment generated using WebACT for ICEValA056-2, SXT, ICEVchMex1 and ICEVchBan8. Comparisons between the regions < 80 bp are filtered. Numbers show the identity values of the compared regions. Red areas indicate homologous regions; blue areas indicate inversions

Fig. 3

Phylogenetic trees of int (a), xis (b) and traI (c) genes from six ICEs, some randomly selected SXT/R391 ICEs and ICEVchBan8. The trees were constructed using the neighbor-joining method. Bootstrap values were obtained after 1000 repetitions