The ICE St1 element of Streptococcus thermophilus belongs to a large family of integrative and conjugative elements that exchange modules and change their specificity of integration

Abstract

The 34,734-bp element ICE St1 from Streptococcus thermophilus CNRZ368 is site-specifically integrated into the 3 ′ end of the gene fda. ICE St1 encodes integrative functions and putative transfer functions. Six proteins of the putative conjugative system of ICE St1 are related to those encoded by the conjugative transposon Tn 916 from Enterococcus faecalis. A comparison of these proteins with those encoded by the complete or partial genome sequences of various low G + C bacteria including Bacillus subtilis, Clostridium difficile, E. faecalis, Listeria monocytogenes, Staphylococcus aureus, and Streptococcus mutans revealed the presence of numerous putative site-specific integrative conjugative elements and/or conjugative transposons within these genomes. Sequence comparisons revealed that these elements possess a modular structure and that exchanges of unrelated or distantly related modules and genes have occurred between these elements, and also plasmids and prophages. These exchanges have probably led to modifications in the site specificity of integration of these elements. Therefore, a distinction between low specificity integrative conjugative elements (i.e., conjugative transposons) and site-specific integrative conjugative elements does not appear to be relevant. We propose to call all the conjugative elements that excise by site-specific recombination and integrate by recombination between a specific site of a circular intermediate and another site, “Integrative and Conjugative Elements” (ICEs), irrespective of the integration specificity.