We study the mechanisms responsible of the bacterial genome variability, with a special interest for those involved in exogenous gene acquisition the horizontal gene transfer. Our model system is the integron, a natural genetic engineering system involved in the development and dissemination of antibiotic resistance genes among Gram-negative species. We are also investigating other factors playing a role in the plasticity of the Vibrio species genomes, which are all constituted of two circular chromosomes with distinct dynamic characteristics.

Integrons. We study different aspects of this gene capture system: their distribution, their contribution to the adaptive capacity of their host and their recombination processes.

This natural genetic system is composed of two basic elements: a gene coding an integrase of the site-specific tyrosine recombinase family and a primary recombination site, attI. The integrase activity allows the insertion of open reading frames, in the form of a circular cassette, at the recombination site. All these cassettes are composed of a single gene associated to a recombination site, the attC site, indispensable for the integrase recognition and recombination with attI.

We have shown that the resistance integrons derived from sedentary super-integrons carried by environmental species, such as the different Vibrio.

We have shown that recombination in integrons, followed a novel model which only involved the attC bottom strand folded in a stem-and loop, based on its symmetrical structure, and a canonical double-strand (ds) attI site. We sustained this model with in vivo experiments, but also through the resolution of the 3D structure of integron integrase tetramer bound to single stranded substrates (collaboration with D. Gopaul). We have now shown that the integrase expression was controlled by the SOS response, and thus that antibiotics were triggering the capture of the genes allowing bacteria to resist to their antimicrobial activities.

Plasticity of the Vibrio species genomes. The second project is to investigate other factors involved in genome plasticity of the complex genome of Vibrio species. The Vibrio group includes a large number of pathogenic species whose hosts range from human to aquatic animals. The few species so far characterized have been found to carry two circular chromosomes showing a high variability. The selective advantage conferred by such an organization is unknown.

To increase our knowledge, we sequenced the genome of V. splendidus LGP 32, a strain which is only remotely related to the Vibrio species sequenced so far. Together with comparative analyses with the other sequenced Vibrio genome, we mapped the different hot spots of genetic variability. We are now modifying extensively the chromosome architecture of Vibrio cholerae, to test the different hypotheses made from the comparative genomics to better understand the rules governing the overall organization and the gene partition between the two chromosomes in Vibrio.

Keywords: Antibiotic resistance, bacterial genetics, genome plasticity, recombination, cholera

Le Roux F, Zouine M, Chakroun N, Binesse J, Saulnier D, Bouchier C, Zidane N, Ma L, Rusniok C, Lajus A, Buchrieser C, Médigue C, Polz MF and Mazel D (2009). Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity. Environmental Microbiology 11(8):1959-1970.

Guerin E*, Cambray G*, Sanchez-Alberola N*, Campoy S, Erill I, Da Re S, Gonzales-Zorn B, Barbé J, Ploy MC and Mazel D (2009). Recombination of integron cassettes is under control of the SOS response. Science 324(5930):1034 - (*, cofirst authors)

Baharoglu Z, Bikard D and Mazel D (2010). Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation. PLoS Genetics 6(10): e1001165.

Loot C, Bikard D, Rachlin A and Mazel D (2010). Cellular pathways controlling integron cassette site folding. EMBO J. 29(15): 262334

Bikard D, Loot C, Baharoglu Z and Mazel D (2010). Folded DNA in action: hairpin formation and biological functions in Prokaryotes. Microbiology and Molecular Biology Reviews 74:570-588.