Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids

Abstract

Salmonella Genomic Island 1 (SGI1) and its variants are significant contributors to the spread of antibiotic resistance among Gammaproteobacteria . All known SGI1 variants integrate at the 3’ end of trmE , a gene coding for a tRNA modification enzyme. SGI1 variants are mobilized specifically by conjugative plasmids of the incompatibility groups A and C (IncA and IncC). Using a comparative genomics approach based on genes conserved among members of the SGI1 group, we identified diverse genomic islands (GIs) distantly related to SGI1 in several species of Vibrio , Aeromonas , Salmonella , Pokkaliibacter , and Escherichia . Unlike SGI1, these GIs target two alternative chromosomal loci, the 5’ end of dusA and the 3’ end of yicC . Although these elements share many features with SGI1, they lack antibiotic resistance genes and carry alternative integration/excision modules. Functional characterization of MGI Vch USA3, a dusA -specific GI, revealed promoters that respond to AcaCD, the master activator of IncC plasmid transfer genes. Quantitative PCR and mating assays confirmed that MGI Vch USA3 excises from the chromosome and is mobilized by an IncC helper plasmid from Vibrio cholerae to Escherichia coli . MGI Vch USA3 encodes the AcaC homolog SgaC that associates with AcaD to form a hybrid activator complex AcaD/SgaC essential for its excision and mobilization. We identified the dusA -specific recombination directionality factor RdfN required for the integrase-mediated excision of dusA -specific GIs from the chromosome. Like xis in SGI1, rdfN is under the control of an AcaCD-responsive promoter. Although the integration of MGI Vch USA3 disrupts dusA , the GI provides a new promoter sequence and restores the reading frame of dusA for proper expression of the tRNA-dihydrouridine synthase A. Phylogenetic analysis of the conserved proteins encoded by SGI1-like elements targeting dusA , yicC , and trmE gives a fresh perspective on the possible origin of SGI1 and its variants.