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Projets de thèse ouverts au concours

Projets de thèse ouverts au concours
BIOGER propose 4 sujets de thèse au concours de l'école doctorale Sciences du Végétal - 4 new PhD projects are offered in BIOGER.

Les sujets de thèse sont les suivants:

- Caractérisation moléculaire du réseau de régulation MDR (résistance multi-drogues) chez le champignon phytopathogène Zymoseptoria tritici
sous la direction de Sabine FILLINGER (sabine.fillinger@inra.fr)
La résistance multi-drogue (MDR) affecte de nombreux traitements dans le secteur clinique (anticancereux, antibiotiques, antifongiques), mais également en agriculture. Dans le cas des champignons phytopathogènes elle diminue l'efficacité des traitements fongicides, nécessitant l'utilisation de doses plus fortes. La MDR est due à la surexpression de transporteurs membranaires qui expulsent les molécules toxiques des cellules. Chez le champignon responsable de la septoriose du blé, Zymoseptoria tritici, trois types d'insert dans le promoteur du gène MFS1 codant un transporteur de la famille des MFS, sont à l'origine du phénotype MDR chez des isolats du champ. L'objectif de cette thèse est d'identifier les éléments de régulation de la transcription de MFS1 chez la souche sensible et les souches MDR, puis de rechercher l'ensemble des gènes co-régulés (régulon MDR). Il s'agira notamment de caractériser les éléments de régulation des différents allèles MFS1 (éléments en cis) et de rechercher les facteurs de transcription impliqués (éléments en trans), puis de les analyser par génétique fonctionnelle. L'étude transcriptomique des mutants des facteurs de transcription générés permettra de décrire le premier réseau de régulation MDR chez un champignon phytopathogène.

- Manipulation microbienne des réponses de défense des plantes et des voies de signalisation
sous la direction de Richard O’CONNELL (richard.oconnell@inra.fr)
Pour faciliter l'infection de leur plantes hôtes, de nombreux microorganismes pathogènes et symbiotiques sécrètent des protéines de type effecteur pour supprimer les réponses immunitaires des plantes. En plus des effecteurs, les agents pathogènes fongiques sécrètent également une gamme variée de métabolites secondaires spécifiquement pendant l'infection des plantes. Cependant, on ne sait pas si ces molécules servent à supprimer les défenses des plantes. Nous avons précédemment identifié un terpène, EA27, produit par le champignon Colletotrichum higginsianum, l'agent de l'anthracnose des crucifères. Ce métabolite bloque la voie de défense de la plante médiée par l'acide jasmonique (JA) en empêchant la dégradation des protéines répresseurs JAZ par le protéasome. Un des objectifs est d'utiliser la génétique inverse pour identifier les gènes fongiques nécessaires à la synthèse d'EA27 et ainsi déterminer le rôle de cette molécule dans le pouvoir pathogène du champignon. Un deuxième objectif est d'évaluer le rôle des défenses médiées par JA dans la résistance des plantes à C. higginsianum en utilisant des mutants d'Arabidopsis et des lignées transgéniques de gènes rapporteurs. Enfin, une approche de génétique chimique sera utilisée pour rechercher d'autres métabolites fongiques ciblant l'immunité des plantes.

- Role of cryptic secondary metabolites in the development of the polyphagous and necrotrophic fungus Botrytis cinerea
sous la direction de Muriel VIAUD (viaud@inra.fr)
Phytopathogenic fungi produce a wide variety of secondary metabolites (SMs), most of which remain unknown because they are produced specifically during interaction with host plants. Deregulation of the synthesis of these SMs has recently made it possible to produce them in vitro, and the identification of their structure is underway. The objective of the PhD project is to characterize the role of these new SMs (called "cryptic SMs") in the grey mould agent Botrytis cinerea, and to understand their role in the lifestyle of this necrotrophic and polyphagous fungus. Biosynthetic gene clusters will be identified by transcriptomic approaches and validated by gene inactivation. The distribution of these clusters in fungal species, their expression profile in B. cinerea as well as the construction of null mutants and cytology approaches will make it possible to evaluate the role of these cryptic SMs in the infection process. Altogether this project should provide a better understanding of the role of fungal SMs as possible effectors of necrotrophy.
https://www6.versailles-grignon.inra.fr/bioger/Equipes/BOTRYTIS-MetabolismeSecondaire-et-Necrotrophie-Botrytis-cinerea
https://www6.inra.fr/herbifun/

- Analyse des déterminants de l’adaptation de Leptosphaeria maculans ‘brassicae’ à différentes espèces hôtes
sous la direction de Jessica SOYER (jessica.soyer@inra.fr)
Les champignons phytopathogènes présentent des capacités adaptatives exceptionnelles leur permettant de contourner les méthodes de lutte. Leptosphaeria maculans 'brassicae' (Lmb), champignon Dothideomycete causant la nécrose du collet des crucifères, présente un cycle de vie extrêmement complexe, de type hémibiotrophe. La méthode de lutte la plus efficace pour contrôler l'infection de Lmb sur le colza (Brassica napus) consiste à utiliser des cultivars de colza naturellement résistants. Ces résistances spécifiques monogéniques, cultivars-dépendantes, sont rapidement contournées par les agents pathogènes. Au contraire de la résistance hôte, la résistance non-hôte confère une résistance de tous les génotypes de plante contre tous les génotypes d'un agent pathogène donné. Les agents pathogènes peuvent également s'adapter à un nouvel hôte, on parle d'expansion de la gamme d'hôte ou de « saut d'hôte » lorsqu'il y a perte de la capacité à infecter l'hôte ancestral. Récemment, un seul isolat de Lmb a été identifié comme partiellement adapté à Brassica carinata, une espèce décrite comme non-hôte de Lmb ; cet isolat ne peut pas infecter B. napus. L'objectif de cette thèse est d'identifier les bases de l'adaptation de Lmb à différents hôtes, ainsi que les mécanismes de résistance de la plante lors de l'interaction non-hôte.
https://www6.versailles-grignon.inra.fr/bioger/Equipes/EPLM-Effecteurs-et-pathogenese-chez-Leptosphaeria-maculans

Les sujets sont mis à concours dans le cadre du concours de l'école doctorale Sciences du Végétal (Université Paris-Saclay).
Dans tous les cas, les postulants doivent contacter le directeur de thèse avant le 30 mai 2018.

 

These projects are:

-Molecular characterization of the MDR (multi-drug-resistance) network in the plant pathogenic fungus Zymoseptoria tritici
Supervisor: Sabine FILLINGER (sabine.fillinger@inra.fr)
Multidrug resistance (MDR) affects many treatments in the clinical sector (anticancer, antibiotics, antifungals), but also in agriculture. In the case of phytopathogenic fungi it reduces the efficacy of fungicide treatments, requiring higher doses. MDR is caused by the overexpression of membrane transporters that expel toxic molecules out of the cells. In the fungus Zymoseptoria tritici reponsible for septoria leaf blotch of wheat, three types of inserts in the MFS1 promoter (encoding a transporter of the MFS family), are responsible for the MDR phenotype in field isolates. The objective of this PhD project is to identify the regulatory elements of MFS1 transcription regulation in the susceptible strain and MDR strains, and to identify all co-regulated genes (MDR regulation). This includes characterizing the regulatory elements of the different MFS1 alleles (cis elements) and identifying the transcription factors involved (trans elements) their analysis through functional genetics. The transcriptomic study of generated transcription factor mutants will describe the first MDR regulation network in a phytopathogenic fungus.

-Microbial manipulation of plant defense responses and signalling pathways
Supervisor: Richard O'CONNELL (richard.oconnell@inra.fr)
To facilitate infection of their plant hosts, many pathogenic and symbiotic microbes secrete effector proteins to suppress plant immune responses. In addition to effectors, fungal pathogens also secrete a diverse array of secondary metabolites specifically during plant infection, but it is unknown if these molecules function to subvert plant defences. We previously identified a terpene metabolite, EA27, from the crucifer anthracnose fungus, Colletotrichum higginsianum, which blocks the plant jasmonic acid (JA) defense signalling pathway by preventing the proteasome-mediated degradation of JAZ repressor proteins. One objective is to use reverse genetics to identify the fungal genes required for EA27 synthesis and to determine the role of this molecule in fungal virulence. A second aim is to evaluate the role of JA-mediated defense in plant resistance to C. higginsianum using Arabidopsis mutants and transgenic reporter lines. Finally, a chemical genetics approach will be used to searchfor further fungal metabolites targeting plant immunity.

- Role of cryptic secondary metabolites in the development of the polyphagous and necrotrophic fungus Botrytis cinerea
Supervisor: Muriel VIAUD (Muriel.Viaud@inra.fr)
Phytopathogenic fungi produce a wide variety of secondary metabolites (SMs), most of which remain unknown because they are produced specifically during interaction with host plants. Deregulation of the synthesis of these SMs has recently made it possible to produce them in vitro, and the identification of their structure is underway. The objective of the PhD project is to characterize the role of these new SMs (called "cryptic SMs") in the grey mould agent Botrytis cinerea, and to understand their role in the lifestyle of this necrotrophic and polyphagous fungus. Biosynthetic gene clusters will be identified by transcriptomic approaches and validated by gene inactivation. The distribution of these clusters in fungal species, their expression profile in B. cinerea as well as the construction of null mutants and cytology approaches will make it possible to evaluate the role of these cryptic SMs in the infection process. Altogether this project should provide a better understanding of the role of fungal SMs as possible effectors of necrotrophy.
https://www6.versailles-grignon.inra.fr/bioger/Equipes/BOTRYTIS-MetabolismeSecondaire-et-Necrotrophie-Botrytis-cinerea
https://www6.inra.fr/herbifun

- Analysis of the determinants of adaptation of Leptosphaeria maculans 'brassicae' to different host species
Supervisor: Jessica SOYER (jessica.soyer@inra.fr)
Plant-pathogenic fungi present extreme adaptive abilities, allowing them to circumvent any new control methods. The Dothideomycete fungus Leptosphaeria maculans 'brassicae' (Lmb) causes stem canker of cruciferous species and exhibits a hemibiotrophic lifecycle on oilseed rape (Brassica napus). So far, the most effective control method against Lmb consists in breeding naturally resistant cultivar of B. napus. The disease resistance follows gene-for-generelationship:aproductofahost resistance gene(Rgene) interacts directlyor indirectly with the product of a matching avirulence gene (Avr) of the pathogen stimulating host immunity and resistance response. These monogenic, cultivar-dependant, resistant sources are rapidly overcome. Contrary to host resistance, nonhost resistance confers complete resistance of all genotypes of a plant species to all genotypes of a pathogen species. Plant pathogenic fungi can also adapt to a new host following a host range expansion or a host jump; in the latter case, the pathogen losses ability to infect the ancestral host. Recently, an isolate of Lmb was identified as partially adapted to Brassica carinata, a plant species considered as nonhost for Lmb so far; this isolate cannot infect B. napus. The objective of this project is to identify the molecular basis of the adaptation of Lmbto B. napus and B. carinata as well as themechanisms involved innonhostresistance.
https://www6.versailles-grignon.inra.fr/bioger/Equipes/EPLM-Effecteurs-et-pathogenese-chez-Leptosphaeria-maculans

Applicants should contact the project PIs by 30 May 2018.
More information regarding application and funding of the projects here.