Integrative Mobile genetics Elements hijacking the bacterial Chromosome dimer resolution machinery: contribution to the emergence of new pathogenic strains. – IMEX

Our search starts with genetic screens to find the different factors that allow mobile elements to hi-jack the Xer machinery. Then, each of these factors is studied by biochemistry and cellular biology methods to determine its cellular localisation, its structure and its exact role in the integration of the mobile elements.

Revues à comité de lectures
Das B, Martinez E, Midonet C, & Barre FX (2012) Integrative mobile elements exploiting Xer recombination. Trends Microbiol 21(1):23-30.
Bischerour J, Spangenberg C, & Barre FX (2012) Holliday junction affinity of the base excision repair factor Endo III contributes to cholera toxin phage integration. EMBO J 31(18):3757-3767.
Conférences
- présentations orales
2012 13th Site-Specific Recombination, Transposition and DNA Dynamics workshop, Wood Hole, USA. IMEXs: Integrative Mobile Elements exploting Xer. Bischerour J, Das B, Martinez E, Midonet C, & Barre FX.
- posters
2012 Site-Specific Recombination, Transposition and DNA Dynamics workshop. Woods Hole, USA. Mechanism of replication of the cholera toxin phage genome. Martinez, E. and Barre F.-X.
2013 Colloque des 3Rs. Giens, France. Integration mechanism of TLC. Midonnet C., Das, B. and Barre F.-X.

A clear understanding of the molecular mechanisms by which Integrative Mobile genetic Elements can hijack the Xer dimer resolution system of their host is necessary if we want to be prepared against the potential emergence of new human, animal or plant bacterial pathogens in the environment, which might threaten human health, bring considerable socio-economic disruptions and/or threaten the equilibrium of ecological systems.

Revues à comité de lectures
Das B, Martinez E, Midonet C, & Barre FX (2012) Integrative mobile elements exploiting Xer recombination. Trends Microbiol 21(1):23-30.
Bischerour J, Spangenberg C, & Barre FX (2012) Holliday junction affinity of the base excision repair factor Endo III contributes to cholera toxin phage integration. EMBO J 31(18):3757-3767.
Conférences
- présentations orales
2012 13th Site-Specific Recombination, Transposition and DNA Dynamics workshop, Wood Hole, USA. IMEXs: Integrative Mobile Elements exploting Xer. Bischerour J, Das B, Martinez E, Midonet C, & Barre FX.
- posters
2012 Site-Specific Recombination, Transposition and DNA Dynamics workshop. Woods Hole, USA. Mechanism of replication of the cholera toxin phage genome. Martinez, E. and Barre F.-X.
2013 Colloque des 3Rs. Giens, France. Integration mechanism of TLC. Midonnet C., Das, B. and Barre F.-X.

Microbial genomes are dynamic mosaic structures. The fluidity of genome components and their relative arrangements allow bacteria to respond rapidly to changing environmental conditions and to new environmental challenges. This raised a considerable interest for integrative mobile genetic elements since they directly contribute to the dynamic nature of microbial genomes. Such elements generally encode their own dedicated transposition and/or site-specific recombination machineries. CTXf, a ?lamentous bacteriophage that harbors the genes encoding cholera toxin, the principal virulence factor of the diarrhoea-causing Gram-negative bacterium Vibrio cholerae, provides a notable exception to this rule. It hijacks XerC and XerD, two chromosome-encoded tyrosine recombinases that ordinarily function to resolve chromosome dimers at the specific dif recombination site, to mediate the integration of its 6.9 kb genome.
With the advent of highthroughput sequencing, numerous other Integrative Mobile DNA Elements making use of the Xer machinery of their host (IMEX) have been discovered in bacterial genomes. Intriguingly, their presence often correlates with the evolution towards pathogenicity of bacteria. Indeed, the emergence of the 7th pandemic clone of V. cholerae probably involved molecular interactions between 3 different IMEXs in addition to CTXf : a helper filamentous phages, such as VGJf, and two satellite filamentous phages, TLCf and RS1f. IMEXs have also been associated to the pathogenicity of Yersinia pestis, the agent of the plague, of Escherichia coli, of Neisseria meningitidis and Neisseria gonorrhea, and of 2 other Vibrios, V. parahaemolyticus and V. vulnificus. Indeed, IMEXs have been reported in almost all Vibrionacea, many species of which are marine animal pathogens. Finally, IMEXs have been found in several Xanthomonadales species that cause plant diseases. This suggests that a clear understanding of the mechanisms driving the acquisition and dissemination of IMEXs is necessary if we want to be prepared against the potential emergence of new human, animal or plant bacterial pathogens in the environment.
Several IMEXs, such as RS1f, are clearly related to CTXf and the mechanism of integration of CTXf that we previously described can probably serve as a paradigm for them. However, the attachment site of others is clearly different from the CTXf attachment site. A second category of IMEXs comprises most of the filamentous phages that have been described in Vibrios to date, such as VGJf. We recently showed that the mechanism of integration of VGJf differs from the one of CTXf, providing a second IMEX paradigm. In the third family of IMEXs are found genetic islands of Neisseriales, Xanthomondales filamentous phages and TLCf-derived elements.
The aim of the present project is to futher our understanding of the diverse mechanisms by which Integrative Mobile genetic Elements hijack the Xer recombination machninery of their host (IMEX). Two lines of studies will be pursued. On one hand, we want to explore the diversity of IMEXs. To this end, we will investigate the integration and excision mechanism of the TLC-related satellite phages of Vibrio cholerae, a representative member of the third type of IMEXs for which we still lack any biochemical data. A related task will be to understand in which circumstances and how TLCf itself can promote the integration of CTXf in V. cholerae. On the other hand, we want to explore the life-cycle of the different IMEXs. To this end, we will investigate the existence of additional host and IMEX factors that should be involved in integration. We will focus on these participating in the integration of CTXf and VGJf until we have obtained more data on the TLC-integration pathway. Finally, we will explore the balance between integration, excision and production of free copies of the genome of IMEXs.