1) Molecular functions of type 3 effectors
R. solanacearum possesses an abundant repertoire of Type 3 effectors (T3Es) (https://iant.toulouse.inra.fr//bacteria/annotation/site/prj/T3Ev2/). Since these effectors are injected by the bacterium into plant cells, the elucidation of Type 3 effector functions require the identification and characterization of their plant targets in order to understand their mode of action in the host cell.
Through comparative genomic approaches on the many available genomes, we defined a group of 'core' T3Es whose presence is conserved in the strains representative of the biodiversity of the species. Systematic searches of protein interactors of these effectors in tomato are currently being carried out using yeast-two-hybrid. Using this knowledge we are performing reverse genetics (mainly on Solanaceae) to identify key players involved in the control of this bacterial disease. The objectives are to identify either (i) susceptibility genes and/or (ii) alleles able to escape the recognition by T3Es, in order to propose new means to improve plant tolerance/resistance to this bacterial pest.
The search for resistance or susceptibility genes by screening natural plant diversity (GWA approach) is also underway (Arabidopsis, tomato).
Several of these effectors have been functionally characterized such as the RipG effector family, which have LRR and F-box domains and which probably mimic the action of some plant components with E3 ubiquitin ligase activity. Another way of investigation concerns the regulation of the translocation process of Type 3 effectors into plant cells. We identified Type 3 chaperones controlling secretion of effectors and some observations suggest that alteration of the secretion process can be detrimental on specific hosts.
Our group also characterized several effector proteins that specify host range of R. solanacearum GMI1000 towards several plants, such as, for example, the AvrA and PopP1 avirulence proteins which are recognized by the tobacco immune system and trigger a defensive hypersensitive response.
Project members: Stéphane Genin, Nemo Peeters, Fabienne Vailleau, Patrick Barberis, Fabien Lonjon, Alice Morel, Cyrus Sabbagh, Manuel Gonzalez-Fuente.
2) Adaptation of R. solanacearum to its environment
Based on the still expanding host range described in the literature, it is known that R. solanacearum has a great adaptive potential that allows it to infect multiple hosts from distant botanical families. This offers a unique opportunity to study the molecular mechanisms governing this trait. Consequently, we initiated in 2008 a project on the experimental evolution of R. solanacearum by serial passage experiments on a variety of plants. We performed a complete genome re-sequencing of individuals with evolved beneficial adaptive traits. This approach has unraveled genetic alterations targeting essential regulatory genes impacting bacterial fitness in planta. The functional characterization of these genes is currently being carried out. More recently, we developed experiments aimed at determining the importance of epigenetic alterations in adaptation to the host.
In order to explore the metabolic adaptation of the pathogen to physiological host conditions in a global context, we developed a system’s biology approach aiming at reconstructing the bacterial metabolic and virulence regulatory networks. All the metabolic reactions identified through the genome annotation were manually curated to generate a high-quality genome-scale metabolic reconstruction. Predictive model-based approaches with these reconstructed networks will be used in the future to study how environmental variables constraint pathogenic fitness.
Project members: Stéphane Genin, Alice Guidot, Caroline Baroukh, Xavier Barlet, Anthony Perrier, Rekha Gopalan Nair