Characterization of a Novel Integrative Element, ICE St1 , in the Lactic Acid Bacterium Streptococcus thermophilus

Abstract

The 35.5-kb ICESt1 element of Streptococcus thermophilus CNRZ368 is bordered by a 27-bp repeat and integrated into the 3 end of a gene encoding a putative fructose-1,6-biphosphate aldolase. This element encodes site-specific integrase and excisionase enzymes related to those of conjugative transposons Tn5276 and Tn5252. The integrase was found to be involved in a site-specific excision of a circular form. ICESt1 also encodes putative conjugative transfer proteins related to those of the conjugative transposon Tn916. Therefore, ICESt1 could be or could be derived from an integrative conjugative element.Cocultures of various lactic acid bacteria are used during the manufacture of dairy products. Sequence comparisons and hybridizations reveal that horizontal transfers between a large array of species of lactic acid bacteria have occurred, most likely during dairy cocultures (13,32). The most convincing evidence indicates that insertion sequences IS1191, IS981, ISS1, and IS1194 (4,5,14) and some open reading frames (ORFs) involved in exopolysaccharide synthesis (6) or in restriction-modification (24) were transferred between the lactic acid bacteria Streptococcus thermophilus and Lactococcus lactis in cocultures used during cheese manufacture. However, the mechanism of genetic exchange between these two species remains unknown, and no conjugative element has been previously characterized in S. thermophilus.Cloning of var1C and localization of its limits. The Sm4 fragment of the S. thermophilus CNRZ368 chromosome was previously found to contain the 35-kb variable region var1C, which was absent from the corresponding chromosomal fragments of strains A054 and NST2280 (28). A region containing an IS1191 copy inserted in a truncated IS981 element (14) was cloned and found to be included in var1C (28). Chromosome walking using a GEM11 genomic library of CNRZ368 (25) was performed to isolate recombinant bacteriophages overlapping the var1C region. Their inserts were subcloned in pBC KSϩ and used as hybridization probes on A054 and NST2280 DNAs. S35, ES27, I132.3, ES13, and SC02 fragments hybridized to A054 and NST2280 DNAs. On the contrary, all of the probes covering the 35.5-kb region (except IS1191 and IS981) and located between the HindIII sites H L and H R (Fig. 1) did not hybridize to A054 and NST2280 DNAs (data not shown). Furthermore, CNRZ368, A054, and NST2280 showed identical restriction maps in regions located to the left of the HindIII site H L and to the right of the HindIII site H R (Fig. 1). These data indicated that var1C limits are located near these HindIII sites. When ES27 including the left end and ES13 including the right end were hybridized to DNAs of the three strains digested by ClaI, EcoO109, EcoRI, PstI, or XbaI, they revealed the same fragment from A054 and NST2280, but two different fragments from CNRZ368. Thus, the flanking regions of var1C in CNRZ368 are adjacent to each other in strains A054 and NST2280 (Fig. 1).Because A054 and CNRZ368 are very closely related to each other, but distantly rel...

Biology of Three ICE Families: SXT/R391, ICE Bs1 , and ICE St1 /ICE St3

“…THE ICESt1/ICESt3 FAMILY ICESt1 was first described as a 35-kb polymorphic region in the chromosome of the lactic acid bacterium Streptococcus thermophilus CNRZ368 (100). Further investigations revealed that this region contains an ICE integrated in the 3′ end of fda, a gene coding for the 1,6-bisphosphate aldolase (101). fda is also the target for the integration of another closely related ICE named ICESt3, initially identified in S. thermophilus CNRZ385 (102).…”

“…They share a common organization in two main regions: a core region that encompasses the genes and sequences necessary for their intra-and intercellular mobility, and a highly variable region delimited by the attL site and the regulation module ( Fig. 6) (70,101,102). The core region of ICESt1 and ICESt3 is subdivided into three modules: the nearly identical conjugation and recombination modules that share 95% identity at the nucleotide level and a more variable regulation module (Fig.…”

The Dilemma of Phage Taxonomy Illustrated by Comparative Genomics of Sfi21-LikeSiphoviridaein Lactic Acid Bacteria

“…Interestingly, one of the rare S. thermophilus plasmids (30) showed sequence similarity to the origin of replication of S. thermophilus phages (25). However, in contrast to the situation for E. coli, where phages can replicate as extrachromosomal elements (phage P1), no good evidence for prophage-like plasmids exists for lactic acid bacteria (15). L. lactis phages are therefore under a much greater selection pressure to diversify within the species or to accept "foreign" phage modules from the environment than S. thermophilus phages.…”

Conjugative Transfer of the Integrative Conjugative Elements ICE St1 and ICE St3 from Streptococcus thermophilus

“…They carry sequences almost identical to L. lactis sequences, including insertion sequences (ISs), a restrictionmodification module, and a cadmium resistance module (19,20,54). Two of these elements, ICESt1 and ICESt3, harbor very closely related recombination modules that encode a tyrosine integrase and an excisionase.…”

“…Two of these elements, ICESt1 and ICESt3, harbor very closely related recombination modules that encode a tyrosine integrase and an excisionase. They excise by site-specific recombination between two 27-bp direct repeats included in their two attachment sites, attL and attR (20,54). A DNAdamaging agent, mitomycin C (MC), derepresses the site-specific excision of ICESt1 and ICESt3 (4).…”