A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins

Abstract

Recent analyses of bacterial genomes have shown that integrated elements that transfer by conjugation play an essential role in horizontal gene transfer. Among these elements, the integrative and mobilizable elements (IMEs) are known to encode their own excision and integration machinery, and to carry all the sequences or genes necessary to hijack the mating pore of a conjugative element for their own transfer. However, knowledge of their prevalence and diversity is still severely lacking. In this work, an extensive analysis of 124 genomes from 27 species of Streptococcus reveals 144 IMEs. These IMEs encode either tyrosine or serine integrases. The identification of IME boundaries shows that 141 are specifically integrated in 17 target sites. The IME-encoded relaxases belong to nine superfamilies, among which four are previously unknown in any mobilizable or conjugative element. A total of 118 IMEs are found to encode a non-canonical relaxase related to rolling circle replication initiators (belonging to the four novel families or to MobT). Surprisingly, among these, 83 encode a TcpA protein (i.e., a non-canonical coupling protein (CP) that is more closely related to FtsK than VirD4) that was not previously known to be encoded by mobilizable elements. Phylogenetic analyses reveal not only many integration/excision module replacements but also losses, acquisitions or replacements of TcpA genes between IMEs. This glimpse into the still poorly known world of IMEs reveals that mobilizable elements have a very high prevalence. Their diversity is even greater than expected, with most encoding a CP and/or a non-canonical relaxase.

Multiple plasmid origin-of-transfer substrates enable the spread of natural antimicrobial resistance to human pathogens

“…Multiple oriT regions were identified in over 63% of both the relaxase-typed as well as untyped mobile plasmids, where on average, 2 orits from 2 different Mob groups were identified per plasmid ( Fig 2G). This supported the notion that, besides secondary and in trans oriTs, the untyped plasmids likely carried un-identified relaxases 15,[20][21][22][23][24] . Moreover, the number of Fig 2H).…”

“…The standard approach for characterization of plasmid mobility involves classification of conjugation and mobilization genes 14 , especially typing of relaxase enzymes into the respective mobility groups 15,19 . However, besides the possibility of yet unidentified enzymes and mobility groups 15,[20][21][22][23][24] , multiple new processes have recently been uncovered that might confer additional mobility to plasmids and involve the origin-of-transfer (oriT) DNA substrate. These include (i) broadened relaxase binding specificities to multiple different oriT sequence variants [25][26][27][28][29] , which, according to the evolutionary theory of such DNA regions 4,30,31 , indicates the possibility of plasmids carrying multiple functional secondary oriTs, and (ii) trans-mobilization of plasmids carrying oriTs triggered by relaxases from co-resident plasmids acting in trans on the non-cognate oriTs [32][33][34][35] .…”

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

“…It is difficult to define families for IMEs since a relaxase of a given family (defined according to phylogenetic analysis and 40% sequence identity clustering [22]) can be associated with different families of coupling proteins (for example, relaxase with a PF02486_6 domain can be associated with two different CPs in S. suis IMEs, Figure S1). In the same way, a coupling protein of a given family (for example, a TcpA_12 coupling protein) can be associated with different families of relaxases (2 different relaxases for the example of TcpA_12, Figure S1).…”

“…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.…”

“…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].…”