New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration

Abstract

Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus. In this study, we searched for ICEs in the completely sequenced genomes of 124 strains belonging to 27 streptococcal species. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements whose limits were assessed and whose insertion site was identified. These ICEs were grouped in seven distinct unrelated or distantly related families, according to their conjugation modules. Integration of these streptococcal ICEs is catalyzed either by a site-specific tyrosine integrase, a low-specificity tyrosine integrase, a site-specific single serine integrase, a triplet of site-specific serine integrases or a DDE transposase. Analysis of their integration site led to the detection of 18 target-genes for streptococcal ICE insertion including eight that had not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG, and ebfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host. This overall analysis of streptococcal ICEs emphasizes their prevalence and diversity and demonstrates that exchanges or acquisitions of conjugation and recombination modules are frequent.

Diversity of Integrative and Conjugative Elements of Streptococcus salivarius and Their Intra- and Interspecies Transfer

“…S2 in the supplemental material). This is in agreement with the previously reported exchanges of recombination modules in the ICESt3 subfamily (11,26).…”

“…Proteins of 27 ICEs were included in the analysis. These ICEs correspond to (i) the 19 ICEs of the ICESt3 subfamily with closely related conjugation modules and (ii) 8 additional ones previously reported to belong to the same ICE subfamily but showing more distantly related conjugation modules (11,26). The sequences of signature proteins were aligned using Clustal omega with default parameters (53).…”

“…The increase of bacterial genome sequencing projects in the last few years provides a remarkable opportunity to explore the pool of bacterial genetic mobile elements ("mobilome"). These in silico analyses revealed the high abundance of ICEs in bacteria (11)(12)(13). In addition to the genes involved in or controlling their mobility, ICEs also carry cargo genes, which can provide new properties (virulence and antibiotic resistance, for example) to the recipient cell (7).…”

A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins

“…Such replacements were previously observed in streptococcal ICEs (Ambroset et al, 2016). The phylogenetic analysis of integrase families ( Figure 1 and Supplementary Figure S1 ) clearly shows that replacement of integration/excision modules can occur not only between IMEs or between ICEs but also between ICEs and IMEs.…”

“…MobT was previously identified in a few predicted IMEs (Bellanger et al, 2014) and in ICEs belonging to the Tn 916 superfamily (Ambroset et al, 2016). The four other superfamilies of putative relaxases are unrelated to any known relaxase of mobilizable or conjugative elements.…”