Characterization and evolution of a family of integrative and potentially conjugative or mobilizable elements from Streptococcus thermophilus

The integrative and conjugative elements (ICEs) excise by site-specific recombination, self-transfer the resulting circular form by conjugation and integrate into the genome of the recipient bacterium. The 34.7-kb element from Streptococcus thermophilus CNRZ368, ICESt1, excises and integrates by site-specific recombination. This element also possesses a conjugation module distantly related to that of the conjugative transposon Tn9/6 from Enterococcus faecalis. Therefore, ICESt1 is probably an ICE. Four types of elements related to ICESt1 are integrated into the same location as ICESt1 in seven other strains of S. thermophilus. One of these elements, ICESt3, is probably an ICE whereas the three others (CIMEs) would have arisen from ICEs by deletion of the conjugation and recombination modules. These elements also encode functions that are not involved in element maintenance or transfer, such as restriction-modification systems. Each of these elements has a chimerical structure resulting from the acquisition of modules from different origins. Sequence analyses indicate that these elements are involved in horizontal transfers with various species of dairy or pathogenic lactic acid bacteria. δCIME308 has exchanged restriction-modification and cadmium resistance modules with plasmids. CIME19258 has acquired a cadmium resistance module by the integration of an ICE related to Tn9/6 within the CIME. The site-specific recombination between an internal attL-related site and attR of ICESt1 leads to the excision of a circular molecule which could be another ICE, ICESt2, suggesting that ICESt1 has arisen by accretion of a CIME and ICESt2. CIME302, ICESt2 and ICESt3 would also have arisen by site-specific accretion of CIMEs and ICEs and/or mobilization of CIMEs by ICEs. An ICE would integrate by site-specific recombination in the attR site of a CIME; then the CIME-ICE would excise by site-specific recombination and transfer by conjugation.