Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus

Laboratoire de Génétique et Microbiologie (UMR INRA-UHP no. 1128, IFR no. 110), Faculté des Sciences, Université Henri Poincaré (Nancy 1), BP239, 54506 Vand uvre-lès-Nancy, France Correspondence Gérard Guédon guedon{at}nancy.inra.fr The 34 734-bp integrative and potentially conjugative element (putative ICE) ICE St1 has been previously found to be site-specifically integrated in the 3' end of the fda locus of Streptococcus thermophilus CNRZ368. Four types of genomic islands related to ICE St1 are integrated in the same position in seven other strains of S. thermophilus . One of these elements, ICE St3 , harbours conjugation and recombination modules closely related to those of ICE St1 and excises by site-specific recombination. Two other types of elements, CIME19258 and CIME302, are flanked by site-specific attachment sites closely related to attL and attR of ICE St1 and ICE St3 , whereas CIME308 only possesses a putative attR site; none of these three elements carry complete conjugation and recombination modules. ICE St1 contains a functional internal recombination site, attL ', that is almost identical to attL of CIME19258. The recombination between attL ' and attR of ICE St1 leads to the excision of the expected circular molecule (putative ICE); a cis -mobilizable element (CIME) flanked by an attL site and an attB ' site remains integrated into the 3' end of fda . Furthermore, sequences that could be truncated att sites were found within ICE St1 , ICE St3 and CIME302. All together, these data suggest that these genomic islands evolved by deletion and tandem accretion of ICEs and CIMEs resulting from site-specific recombination. A model for this evolution is proposed and its application to other genomic islands is discussed. Abbreviations: CIME, cis -mobilizable element; ICE, integrative conjugative element; IS, insertion sequence; PAI, pathogenicity island The GenBank accession numbers for the sequences reported in this paper are AJ586568 , AJ586569 , AJ586570 and AJ586571 . Present address: Department of Molecular Biology and Microbiology, Howard Hughes Medical Institute/Tufts University, Boston, MA 02111, USA.