Characterization and chimeric structure of a family of integrative and potentially conjugative elements from Streptococcus thermophilus

A 34.7-kb element, ICESt1, is integrated in the 3' end of fda locus from Streptococcus thermophilus CNRZ368. ICESt1 excises by a site-specific recombination between two 27-pb identical sequences flanking the element. It encodes an integrase required for excision. Furthermore, eleven putative proteins encoded by ICESt1 are related to proteins encoded by various conjugative elements from low G + C Gram positive bacteria. Therefore, ICESt1 could be a site-specific integrative conjugative element (ICE). Comparison of proteins encoded by ICESt1 and the sequenced genome of Bacillus subtilis 168 revealed a putative 20.5-kb ICE, ICEBs1. Sequence comparison of ICESt1, ICEBs1, Tn916 and Tn5252 revealed exchanges of modules between ICEs, conjugative transposons and prophages. Four types of elements related to ICESt1 (IEs) were found in seven other strains of S. thermophilus and are integrated in the same location as ICESt1. One of these elements, IE385, could be an ICE whereas the others do not seem to be integrative and conjugative. Comparison of the various elements and ICESt1 showed that all of them have a chimerical structure resulting from exchanges of regions from different origins. The left end of IE19258 is identical to an internal recombination site of ICESt1, attL', but shares only 57% identity with its left end, attL. The site-specific recombination between the cores of attL' and of the right end, attR, leads to the excision of a circular molecule corresponding to the region flanked by these sites. Therefore, this suggests that ICESt1 results from the integration of a 28.2-kb ICE, ICESt2, in the attR' site of an IE element and that ICESt2 have mobilized the IE.