Integrative Xer recombination complex Stabilization – InXS

Bacteria have evolved a highly conserved chromosomally encoded recombination machinery, Xer, to resolve chromosome dimers. With the exception of a few species, Xer is composed of two tyrosine recombinases, XerC and XerD, which act on a specific chromosome site, dif. Diverse mobile elements harness XerC and XerD for their own benefit. Indeed, Xer was initially discovered because of its role in multicopy plasmid dimer resolution. Since then, numerous Integrative Mobile Elements exploiting Xer (IMEX) have been described. Phages and genetic islands harness Xer recombination to integrate into the dif site of one of their host chromosomes, while small genetic cassettes flanked by pseudo dif (pdif) sites harness Xer to disseminate on plasmids.
IMEXs are generally associated with the evolution of pathogenic bacteria, including (in)famous human pathogens (Vibrio cholerae, Yersinia pestis, Neisseria meningitidis and gonorrhea, Acinetobacter baumannii), animal pathogens (a large panel of Vibrios) and plant pathogens (Xanthomonas campestris, Xylella fastidiosa). In particular, cholera toxin, which is responsible for the deadly pandemic diarrhea associated with the disease of the same name, is harbored in the genome of a V. cholerae IMEX, phage CTXF. Ecological interactions of CTXF with at least two other families of V. cholerae IMEX phage, VGJF and TLCF, are responsible for the constant rapid emergence of V. cholerae strains harboring new forms of the cholera toxin. The recent appearance of multidrug resistant strains of A. baumannii, a human opportunist pathogen that is responsible for nosocomial diseases, is linked the dissemination of carbapenem resistance genes by a fourth category of IMEXs, the pdif-modules. Thus, understanding how IMEXs exploit Xer recombination for their own benefit and unravelling their ecological interactions is crucial to prepare against new or re-emerging infectious diseases. Nevertheless, reports on IMEXs rarely go beyond the stage of the description of their genetic content and genomic context, due to the methodological challenges involved in probing the system from both a molecular-genetic and mechanistic viewpoint.
XerC and XerD proteins cluster in two narrow closely-related phylogenetic groups and act on highly conserved dif sites, which denotes high evolutionary constraints. Remarkably, the core dimer resolution sites of multicopy plasmids exploiting Xer and the attachment sites of IMEXs significantly deviate from the target host dif site. Our preliminary data suggest that IMEXs rely on Integrative Xer recombination complex Stabilization (InXS) factors. The aim of this research program is to search for InXS factors and unravel the complex Xer recombination reactions that they promote. To this end, four teams combining a deep expertise in Xer recombination, bioinformatics, molecular-genetics, genomics, single-molecule biophysics, and structural biology join their forces to study the Xer exploitation strategies of the V. cholerae CTXF, VGJF and TLCF IMEXs and the A. baumannii pdif-modules, which represent the four categories of IMEXs so far described.
The results of the InXS project will interest academic research scientists studying protein-DNA transactions and the microbiologist community in general. In addition, the results will be made available in an online database, thereby providing a new tool for the surveillance of pathogenic bacteria. The acquired knowledge could provide opportunities to take advantage and/or control of these 'natural genetic engineers'. In particular, we foresee the development of methodologies to enforce the excision of IMEXs that encode antibiotic resistance elements and/or toxins, which could serve as the basis of new prophylactic medical treatments.