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

Abstract

Integrative and conjugative elements (ICEs) are widespread chromosomal mobile genetic elements which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICE<i>St3</i> of <i>Streptococcus thermophilus</i> were characterized in <i>Streptococcus salivarius</i> by whole-genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3' end of the <i>fda</i>, <i>rpsI</i>, or <i>rpmG</i> gene) with the conjugation module of the ICE<i>St3</i> subfamily. Sequence analyses also pointed out a recombination occurring at <i>oriT</i> (likely mediated by the relaxase) as a mechanism of ICE evolution. Despite a similar organization in two operons including three conserved genes, the regulation modules show a high diversity (about 50% amino acid sequence divergence for the encoded regulators and presence of unrelated additional genes) with a probable impact on the regulation of ICE activity. Concerning the accessory genes, ICEs of the ICE<i>St3</i> subfamily appear particularly rich in restriction-modification systems and orphan methyltransferase genes. Other cargo genes that could confer a selective advantage to the cell hosting the ICE were identified, in particular, genes for bacteriocin synthesis and cadmium resistance. The functionality of 2 ICEs of <i>S. salivarius</i> was investigated. Autonomous conjugative transfer to other <i>S. salivarius</i> strains, to <i>S. thermophilus</i>, and to <i>Enterococcus faecalis</i> was observed. The analysis of the ICE-<i>fda</i> border sequence in these transconjugants allowed the localization of the DNA cutting site of the ICE integrase.<b>IMPORTANCE</b> The ICE<i>St3</i> subfamily of ICEs appears to be widespread in streptococci and targets diverse chromosomal integration sites. These ICEs carry diverse cargo genes that can confer a selective advantage to the host strain. The maintenance of these mobile genetic elements likely relies in part on self-encoded restriction-modification systems. In this study, intra- and interspecies transfer was demonstrated for 2 ICEs of <i>S. salivarius</i> Closely related ICEs were also detected <i>in silico</i> in other <i>Streptococcus</i> species (<i>S. pneumoniae</i> and <i>S. parasanguinis</i>), thus indicating that diffusion of ICE<i>St3</i>-related elements probably plays a significant role in horizontal gene transfer (HGT) occurring in the oral cavity but also in the digestive tract, where <i>S. salivarius</i> is present.