New insights into the classification and integration specificity of streptococci integrative conjugative elements through extensive genome exploration

In this study, we searched for integrative conjugative elements (ICEs) in chromosomes of 124 strains of Streptococci. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements that were grouped in 7 distinct families. Comparison of the conjugation modules of ICEs belonging to each family allowed the identification of the conserved proteins. The phylogenetic analysis also revealed that exchanges or acquisition of conjugation and recombination modules are frequent. Integration of these streptococcal ICEs is catalyzed either by site-specific tyrosine integrases, low-specificity tyrosine integrases, site-specific single serine integrases, triplet of site-specific serine integrases or DDE transposases. Analysis of their integration sites led to the detection of 8 new target-genes for streptococcal ICE insertion that have not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG and ybaB/EbfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host.