The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems

Abstract

Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. Recent findings indicated that the main actors of conjugative transfer are not the well-known conjugative or mobilizable plasmids but are the integrated elements. This paper reviews current knowledge on “integrative and mobilizable elements” (IMEs) that have recently been shown to be highly diverse and highly widespread but are still rarely described. IMEs encode their own excision and integration and use the conjugation machinery of unrelated co-resident conjugative element for their own transfer. Recent studies revealed a much more complex and much more diverse lifecycle than initially thought. Besides their main transmission as integrated elements, IMEs probably use plasmid-like strategies to ensure their maintenance after excision. Their interaction with conjugative elements reveals not only harmless hitchhikers but also hunters that use conjugative elements as target for their integration or harmful parasites that subvert the conjugative apparatus of incoming elements to invade cells that harbor them. IMEs carry genes conferring various functions, such as resistance to antibiotics, that can enhance the fitness of their hosts and that contribute to their maintenance in bacterial populations. Taken as a whole, IMEs are probably major contributors to bacterial evolution.

Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes

“…Some of these integration sites (PPI, three sites inside ICEs of the Tn1549 family and gene encoding a HTH-XRE regulator) are reported here for the first time. This further extends the repertoire of IMEs found in Streptococci [23]. Twenty-two different combinations of integrase-relaxase-(coupling protein) were observed.…”

“…More importantly, half of the IMEs harbor a putative non-canonical relaxase, i.e., related to RCR initiators (MOB T , PF01719, PF01719-helicase, PHA00330 or PF02407) and in most cases these IMEs also encode a coupling protein (always from the TcpA family). As proposed previously [23], IMEs encoding relaxases related to RCR initiators can likely only hijack conjugative elements that encode TcpA. The elements that encode a TcpA coupling protein could probably replace the CP from the T4SS of the helper conjugative element by their own CP to promote their transfer (likely at the expense of the helper element).…”

“…Elements were grouped according to the nature of their relaxase and the presence or absence of an associated coupling protein. * TnGBS1 is indicated in the elements with a MobP relaxase but it should be pointed out that its relaxase is only distantly related to MobP relaxases and does not possess the characteristic PF03432 domain of this family [23]. The sizes of the circles are at scale, except when zooming to provide further details.…”

“…IMEs were originally defined as excisable MGEs carrying their own oriT and encoding one or two mobilization proteins [21]. They can subvert the conjugation apparatus of unrelated conjugative elements to promote their own transfer [17,22,23]. According to their current definition, IMEs are not defective ICEs, i.e., elements deriving from these elements by deletion of parts of their conjugation modules.…”

“…According to their current definition, IMEs are not defective ICEs, i.e., elements deriving from these elements by deletion of parts of their conjugation modules. Furthermore, all known IMEs are unrelated or distantly related to ICEs [23]. So far, only one study examined the IME content of S. suis genomes (in 17 complete genomes), but cargo genes of these MGEs were not reported [22].…”