Analysis of mobile genetic elements in the genomes of Bacillus thuringiensis and Bacillus cereus

Bacillus cereus sensu lato is an ecologically diverse bacterial group that comprises nine phylogenetically close species. Its three most studied members are B. thuringiensis, the worldwide biopesticide, B. cereus sensu stricto, the potential human foodborne pathogen and B. anthracis, the causative agent of anthrax, a potential “biological weapon”. This group holds a collection of mobile genetic elements (MGE) that include toxin-carrying and conjugative plasmids, and transposable elements such as insertion sequences (IS) or class II transposons. Some of these elements are very well studied, whereas others remain uncharted, as is the case of IS982, a family that was reviewed within this manuscript. Globally, in the course of this work, the distribution of MGE as well as the mobile DNA-based genome plasticity of the B. cereus group were probed, with a particular focus on B. thuringiensis, its entomopathogenic member. In this scope, the first objective was to analyze four distinct types of mobile genetic elements including IS, Class II transposons of the Tn3 family, group II introns and B. cereus repeats (bcr), in 102 completely sequenced genomes of nine B. cereus s.l. species via a bioinformatics approach. Our study shows, not only the variable distribution of MGE between species, but also among strains of the same species. Moreover, our results reveal the existence of significant correlations between bcr pairs, whose variation between species could be used as an additional parameter to whole genome-based phylogenetic approaches. Furthermore, this work highlights the potential impact of these MGE elements on the plasmid pool, particularly the toxin-carrying plasmids of B. thuringiensis, key players in its entomopathogenic capacities. The focus was then set on B. thuringiensis with the characterization of novel mosquitocidal strains, isolated from Lebanese soil, by in-depth analysis of the strains’ genomes, toxin-carrying plasmids and parasporal crystal proteins content. Two strains, AR23 and H3, highly toxic and displaying unusual killing activities, and plasmid and crystal protein profiles, were probed for the toxin-coding genes they carry, their MGE repertoire and possible interconnection between virulence and genome plasticity. AR23 belongs to B. thuringiensis sv. israelensis, whose mobile DNA pool was extensively reviewed in the introduction of this thesis. However, AR23 is more toxic than the reference AM65-52 for three mosquito species, most likely thanks to an additional functional copy of cry4Ba gene and a simplified plasmid content. As for H3, it is a non-cytolytic B. thuringiensis strain, active against mosquito larvae but at higher doses than the reference strain AM65-52. Analysis of this strain uncovered the novel Cry toxins it produces, four of which have an unusual ORF1-gap-ORF2 organization. H3 toxin-coding genes are also located in a highly dynamic plasmid environment with three novel mega-plasmids and a wealth of transposable elements. In summary, his study highlighted the distribution and the importance of MGE within B. cereus group and particularly that of B. thuringiensis active against Dipteran larvae.