Dynamics of the SetCD-Regulated Integration and Excision of Genomic Islands Mobilized by Integrating Conjugative Elements of the SXT/R391 Family

Abstract

Mobilizable genomic islands (MGIs) are small genomic islands that are mobilizable by SXT/R391 integrating conjugative elements (ICEs) due to similar origins of transfer. Their site-specific integration and excision are catalyzed by the integrase that they encode, but their conjugative transfer entirely depends upon the conjugative machinery of SXT/R391 ICEs. In this study, we report the mechanisms that control the excision and integration processes of MGIs. We found that while the MGI-encoded integrase Int MGI is sufficient to promote MGI integration, efficient excision from the host chromosome requires the combined action of Int MGI and of a novel recombination directionality factor, RdfM. We determined that the genes encoding these proteins are activated by SetCD, the main transcriptional activators of SXT/R391 ICEs. Although they share the same regulators, we found that unlike rdfM, int MGI has a basal level of expression in the absence of SetCD. These findings explain how an MGI can integrate into the chromosome of a new host in the absence of a coresident ICE and shed new light on the cross talk that can occur between mobilizable and mobilizing elements that mobilize them, helping us to understand part of the rules that dictate horizontal transfer mechanisms.

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

“…Integration of MGIs into the chromosome of a naive host is independent of the co-transfer of an SXT/R391 ICE as int MGI is constitutively expressed at a low level, thereby favoring MGI dissemination regardless of the ability of the ICE to co-establish in the recipient cell (67). Int MGI also mediates the excision of MGIs, but only in the presence of the RDF RdfM (66,67). In a host devoid of an ICE of the SXT/R391 family, rdfM is not expressed and MGIs are unable to excise from the host's chromosome.…”

“…The gene int MGI codes for a tyrosine recombinase which mediates the integration of MGIs into the 3′ end of E. coli's yicC, a gene of unknown function, and its orthologs in all the known natural hosts of MGIs (66,69). Integration of MGIs into the chromosome of a naive host is independent of the co-transfer of an SXT/R391 ICE as int MGI is constitutively expressed at a low level, thereby favoring MGI dissemination regardless of the ability of the ICE to co-establish in the recipient cell (67). Int MGI also mediates the excision of MGIs, but only in the presence of the RDF RdfM (66,67).…”

“…In a host devoid of an ICE of the SXT/R391 family, rdfM is not expressed and MGIs are unable to excise from the host's chromosome. rdfM expression is triggered by the ICE-encoded transcriptional activator SetCD (67). Hence, MGI excision is responsive to DNA damage and occurs exclusively when an SXT/R391 ICE is present.…”

“…SetC and SetD are thought to assemble in a similar complex to activate the ASMscience.org/MicrobiolSpectrumexpression of various genes or groups of genes in SXT, including traLEKBVA and traFHG, the int and xis genes, the mosAT toxin-antitoxin system, and the bet/ exo RecA-independent homologous recombination system (47,56,58,63,64,65). Interestingly, the SetCD transcriptional activator also targets genes that are located outside of SXT/R391 ICEs; it stimulates the expression of int MGI and triggers the expression of rdfM, two genes encoded by mobilizable genomic islands (MGIs) (see below) (66,67).…”

Comparative Analysis of Mobilizable Genomic Islands

“…All three MGIs share the same integration site, i.e., the 3= end of a gene encoding a putative stressinduced protein named yicC in Escherichia coli (6). Besides the oriT SXT -like sequence, the three MGIs also share four conserved genes: int MGI , which encodes a tyrosine recombinase responsible for MGI excision and integration; rdfM, which encodes a recombination directionality factor necessary for excision; and two putative genes of unknown function (cds4 and cds8) (6,19). MGIVchUSA1 encodes two different putative toxin-antitoxin systems related to the HipA/B system of E. coli, a system that has been shown to promote bacterial multidrug tolerance (20).…”