JCJC SVSE 6 - JCJC - SVSE 6 - Génomique, génétique, bioinformatique et biologie systémique

Genomic analysis of a new family of translocated oomycete effectors: role in adaptation to the host and pathogenicity in the legume root pathogen Aphanomyces euteiches – APHANO-Effect

How the fungus-like organisms Oomycetes, are able to interact with plants and animals ?

The aim of the APHAN-Effect project, by combining in silico and molecular analysis, is to gain a better insight into the function of a class of protein called effectors using species of the oomycetal genus Aphanomyces. An improved knowledge of effector biology is central for understanding and ultimately controlling diseases caused by Aphanomyces and other oomycete pathogens.

What can we learn on oomycetes pathogenicity by decrypting their genomes?

Oomycetes form a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms that are closely related to photosynthetic organisms such as brown algae and diatoms. Oomycetes cause severe damages on important crop species (potato, legumes, soybean), as well as in natural ecosystem. A variety of biochemical differences mean that oomycetes are not inhibited by many of the chemicals used to control fungi. Regarding the impact of diseases caused by oomycetes, a better understanding of mechanisms that underlie pathogenicity is required. <br />The Aphanomyces genus occurs within the Saprolegniales lineage which groups together both animal pathogens (crayfish, fish…) and plant pathogens infecting various plant families (Fabaceae, Chenopodiaceae). Thus studying Aphanomyces pathogens offers the opportunity to identify key factors involved in host adaptation (i,e effectors) by using comparative genomic approaches. The main objectives of the APHAN-Effect project are to characterize the repertoire and the evolution of effectors in Aphanomyces species infecting various animal and plant hosts to evaluate the role of these proteins in the adaption of the pathogens to their hosts. In the APHAN-Effect project we focus on the functional analysis of the Crinklers (CRN) family of oomycetal effectors.

In the first step of the project, a comparative genomic survey of the CRN repertoire in Aphanomyces sp. will be develop to identify key factors of host specificity. Using new sequencing technologies different species of Aphanomyces, including plant and animal parasite, will be sequenced and through comparative studies effectors (i,e CRNs) which could be involved in host specificity will be identify. Then the effect of selected candidates on plant-Aphanomyces interactions will be tested by molecular analysis.

During the first months of the APHAN-Effect project, the selected species of Aphanomyces harboring different life style (zoo, phyto or non pathogens) have been sequenced by Illumina technology. In silico analysis will be perform in the next months to identify candidates explaining host adaptation.

APHAN-Effect will provide a genomic survey of Crinklers (CRN) an intracellular effector family from the oomycete Aphanomyces genus, an important group of poorly studied but fascinating animal and plant pathogens. The rationale of the project is that CRN effectors are not identical amongst Aphanomyces species, and that they reprogram the host to favor pathogen colonization. Thus the expected results are: i) to provide an overview of the CRN repertoire of the Aphanomyces genus, ii) to identify CRN effectors acting as key factors in relation to host specificity, iii) to functionally characterize the plant targets of CRNs. Furthermore, the molecular elucidation of the events that determine the outcome of a microbial-plant interaction (symbiotic / pathogenic) will be critical to engineer crops for durable resistance against root pathogens.

This project is expected to provide results of academic interest in the field of plant-microbe interactions, including the roles of oomycete effectors. All genomic resources will be publicly available through an webinterface (APHANo-DB). therefore benefit undergraduate and graduate students through lectures and practical courses. Key research results, along with the novel strategies that will be developed in this project will be published in high-ranked journals. This information will also be disseminated through various scientific congresses. Any work that could lead to commercial exploitation will be examined and patented

Oomycetes form a phylogenetic lineage of fungus-like eukaryotic microorganisms related to photosynthetic organisms such as brown algae and diatoms. Oomycetes cause severe damages on important crops (potato, legumes) and in natural ecosystems. A variety of physiological differences mean that oomycetes are not inhibited by many of the chemicals used to control fungi. Regarding the impact of diseases caused by oomycetes, a better understanding of mechanisms that underlie pathogenicity is required. The recent completion of the genome sequence of several oomycete species (i.e Phytophthora infestans), has led to the discovery of two large and rapidly diverging superfamily of proteins translocated inside host cells. These proteins, also named effectors, possess a conserved N-terminal motif RXLR or LXLFLAK in the case of CRN (Crinkle and Necrosis) effectors and a highly divergent C-terminal part involved in effectors function. Once inside cells, effectors are presumed to interact with molecular targets to modify cellular functions, such as the suppression of host immune responses. CRN genes, and not RXLR genes, have been detected in all the plant pathogen oomycetes analyzed so far, suggesting that CRN are ancestral effectors in the oomycete lineage preceding the apparition of RXLR proteins. We are studying effectors and pathogenicity mechanisms in Aphanomyces euteiches, a root pathogen of legumes which is phylogenetically distant from Phytophthora and considered as an ancestral oomycete. We have recently identified A. euteiches CRN genes and showed that these proteins are translocated to host nuclei similarly to their Phytophthora orthologs. Within the phylum Oomycota, the genus Phytophthora is included in the Peronosporales lineage which includes most plant pathogens, whereas the Aphanomyces genus, which occurs within the Saprolegniales lineage, groups together both animal pathogens (crayfish, fish) and plant pathogens infecting various plant families (sugar beet, pea). Thus studying Aphanomyces pathogens offers the opportunity to identify key factors involved in host adaptation. The development in our research team of a powerful pathosystem involving A. euteiches and the legume model Medicago truncatula allows us to provide clues regarding the consequence of oomycete effectors production on interactions of plant roots with various type of microorganisms (pathogenic and symbiotic) occurring in the rhizosphere. By exploiting the advantages and originality of our biological system (host diversity of Aphanomyces sp., model plant able to interact with pathogenic and symbiotic microorganisms) the main objectives of the APHANO-Effect project are i) to evaluate the role of CRN effectors in the adaption of the pathogens by characterizing the repertoire and the evolution of CRN effectors in Aphanomyces species infecting animal and plant hosts, ii) to identify cellular targets of CRNs and iii) to study the impact of CRN expression on the perception of pathogenic and symbiotic signals and on their interaction with pathogenic and symbiotic microorganisms. To reach the objective 1, a comparative genomic approach based on transcriptomic analyses (RNAseq) will be conducted on Aphanomyces strains infecting various hosts (plants or animals) and by using the first genome draft of a Saprolegniale (A. euteiches, 69Mb) generated in the team in collaboration with the Genoscope.Molecular CRN targets (objectives 2) will be identified following a yeast 2-hybrid strategy as well as pull-down experiments upon in planta expression of tagged CRNs. Finally, M. truncatula roots expressing CRNs (composite plants) will be used to study the impact of CRN on pathogenic and symbiotic interactions. The project should impact appreciation about the diversity and conservation in functional evolutionary strategies used by pathogens, nevertheless genomic data obtained will be a valuable resource to identify keys actors implicated in host-specificity and pathogenicity of Aphanomyces sp.

Project coordinator

Madame Elodie Gaulin (Université Paul Sabatier Toulouse 3 - Laboratoire de Recherche en Sciences Végétales) – gaulin@lrsv.ups-tlse.fr

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

LRSV Université Paul Sabatier Toulouse 3 - Laboratoire de Recherche en Sciences Végétales

Help of the ANR 228,000 euros
Beginning and duration of the scientific project: October 2012 - 36 Months

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