General Information/IS related to Integrative Conjugative Elements (ICEs)

Other structures which obscure the definition of an IS have been identified among various TEs. For example, ICE (Integrative Conjugative Elements), are found integrated into the host genome but can excise and transfer from cell to cell. Their insertion into and excision from their host chromosomes is generally using a tyrosine-based integrase related to phage integrases (Fig.7.1) while others possess a serine-recombinase (Fig.7.1 and Fig.11.1). Their transfer depends on a second set of proteins which includes a “relaxase”, often a single strand endonuclease of the HUH superfamily. However, ISSag10, a tIS member of the IS1595 family from Streptococcus agalactiae which includes an O-lincosamide nucleotidyltransferase gene, encodes a DDE transposase, nd undergoes cell-to-cell transfer when complemented with an autonomous ICE, Tn916. In this case, a cryptic origin of transfer is located within the 3’ end of the resistance gene. These non-autonomous ICE have been called IME (Integrative Mobilizable Elements) or CIME (CIs-Mobilizable Elements). More recent studies have identified a new ICE family, transposon of Group B Streptococcus (TnGBS), in which the enzyme catalyzing their integration and excision belongs to another DDE-group Tpase (Fig.11.1). This led to the identification of an entirely new family of classic IS carrying DDE Tpases, the ISLre2 family. Other ICE have been identified which include a DDE Tpase closely related to that of the IS30 family]. It is important to note that the IS with these associated DDE transposases transposes using a copy-paste mechanism which involves a double-strand transposon circle. ICE circles are presumably formed using this mechanism in contrast to those possessing tyrosine or serine recombinases. DDE-generated circular ICE would then undergo transfer using the specific relaxase system (Fig.11.2). It seems likely that examples of ICE with other IS family Tpases are awaiting identification. Moreover, in addition to a variety of transfer functions, certain ICE carries plasmid-related replication genes important in ensuring sufficient stability of the transposition intermediates to enable their subsequent integration . Early examples of ICE were initially thought to be resistance plasmids and assigned an incompatibility group, incJ. These are maintained as an integrated copy in the host chromosome but can nevertheless give rise to circular copies. This is yet another example of the increasingly indistinct frontiers between phage, plasmids, and transposons (http://db-mml.sjtu.edu.cn/ICEberg/).

Fig.11.1. Tip of ICEberg. Top panel. The figure shows two closely related ICE that share their conjugation genes, their origins of transfer (red vertical arrowhead), and the tetracycline resistance gene tetM (red arrow) but differs in the type of ‘transposase’ they encode. Tn916 (18032 bp) possesses a bacteriophage lambda-like system including a tyrosine site-specific recombinase (int) and a gene required with int for excision (xis). In Tn5397 (20658 bp) the int/xis system is replaced by a site-specific serine recombinase gene tndX. A group II intron insertion has occurred into one of the conjugation-like genes in Tn5397. Bottom panel. ICE with DDE transposases. The relationship between two ICE from Streptococcus agalactiae and a simple insertion sequence, ISLre2 is shown.

Fig.11.2. DDE ICE transfer using Copy out - Paste in the mechanism. The transposon is shown in green, the flanking donor, and target DNA in white. Transposon ends are shown as red. 1) Donor carrying the ICE. 2) Formation of a first synaptic complex SCA. 3) cleavage of the left or right inverted repeat (IR). 4) attack on the other end to form a single-strand bridge. 5) Circular double-strand DNA products of IS-specific replication (with the regeneration of the transposon donor) 6) activation of the transfer machinery. 7) ICE transfer into the recipient cell and re-circularisation. 8) Identification of a target. 9) Formation of a second synaptic complex SCB, engagement of the target DNA, and cleavage of the ICE circle. 10) attack of the target DNA by the two ICE 3' ends resulting in integration. 11) The newly integrated ICE.

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