Department of Organismic Interactions

Molecular phytopathology [more]

Research concept:

Research in the department Organismic Interactions is focused on the mechanisms that enable biotrophic fungi to colonize plants successfully. Our prime model is the basidiomycete smut fungus Ustilago maydis, a pathogen infecting maize. For prioritizing virulence determinants we use comparative analyses relying on available genome sequences of the related smut fungi U. hordei, Sporisorium reilianum f. sp. zeae, S. reilianum f. sp. reilianum, U. scitaminea, U. bromivora and Melanopsichium pennsylvanicum. Some of these systems are genetically tractable and amenable to reverse genetics, either relying on homologous recombination or CRISPR-Cas9.

With respect to insights into how a fungus is able to colonize a plant and how the plant is reprogrammed to sustain fungal growth the U. maydis-maize system is by far the most advanced and most convenient to handle, because seedlings can be infected and symptoms develop on all above ground parts of the plant within a week after inoculation. Contrary is symptom development in the related pathosystems restricted to male and female flowers allowing to score virulence only several months after inoculation. U. maydis cells are recognized by the plant immune system through conserved molecular patterns already when the fungus makes contact with the leaf surface and this elicits strong defense responses. After plant penetration, these early defense responses are downregulated and U. maydis establishes a biotrophic relationship with its host in which the plant stays alive. To achieve this, U. maydis is shielded from direct contact with the plant cytoplasm by a newly formed plant plasma membrane that completely encases the invading hyphae. This creates an extended, tight interaction zone for the exchange of signals between fungus and host. The majority of fungal molecules that mediate this communication are secreted effectors. Their job is to suppress plant defense responses and to reprogram development and metabolism of the host to meet the needs of the pathogen. Effectors modulate the activity of host proteins either in the interaction zone or affect host processes inside plant cells after being taken up by plant cells. As most effectors are completely novel and rarely contain known motifs, the challenge is to determine their biochemical function and how this relates to accommodating the fungus in the host tissue.

The group of Regine Kahmann in November 2017.

Major achievements

• By comparative genomics using the genomes of five sequence smut fungi we have identified a set of core effectors that are present in all five species.
• By RNAseq profiling of U. maydis during all stages of infection we detected secreted proteins enriched in three distinct expression modules corresponding to stages on the plant surface, establishment of biotrophy and  induction of tumors. By measuring the intramodular connectivity of transcription factors, we identified the potential drivers for the virulence modules and demonstrated a crucial role for leaf tumor formation and effector  gene expression for one of these transcription factors.
• We have used the genomes of Sporisorium reilianum f. sp. zeae and S. reilianum f. sp. reilianum, two closely related formae speciales infecting maize and sorghum, respectively, together with the genomes three other smut fungi to identify effector genes which have signatures of positive selection. When assessed for their contribution to virulence in S. reilianum f. sp. one mutant was identified that had lost virulence. This suggests that effector genes under positive selection either do not play a role in virulence under the employed conditions or are selected for traits not directly linked to pathogenicity.
• We have successfully adapted the CRISPR-Cas9 system for multiplexing to be able to target gene families.

Other highlights

A second interdepartmental workshop on “Plant Fungus Interaction” was funded through the Université Franco-Allemande. Involved in writing the application and organizing the workshop were Pierre Grognet, Stefanie  Reissmann and Regine Kahmann from Marburg as well as Claire Veneault-Fourrey and Francis Martin from Nancy. The meeting took place at the MPIterMic between October 26-29, 2016 and was attended by 45 participants, mostly students and postdocs from the groups of Prof. Dr. Francis Martin from the Ecogenomics of Interactions group at INRA-Nancy, the groups of Prof. Dr. Gunther Doehlemann and Prof. Dr. Alga Zuccaro from the University of Cologne, the group of Prof. Dr. Eva Stukenbrock from the University in Kiel (all former group leaders in the department) and from the Department of Organismic Interactions at MPIterMic. The science was very much focused on ongoing, not yet published work, which provided an excellent basis for intense discussions – so much so that it was decided to organize another meeting of this kind in Cologne in 2018.

A second highlight was our retreat to the island of Usedom in the Baltic Sea in June 2017. 2 ½ days were spent with stimulating scientific discussions during which all graduate students and postdocs presented their work and gave an outlook on future perspectives. Additional time was set aside to discuss joint projects and main goals and how to achieve them until 2019.

National and international collaborations:

• with G. Bange (SYNMIKRO, Marburg, Germany) with respect to structure determination of U. maydis effectors.
• with H. Link (SYNMIKRO, Marburg) with respect to cAMP measurements.
• with S. Rensing (Philipps-Universität Marburg, Germany) with respect to the bioinformatic analysis of RNAseq data.
• with T. Glatter (MPIterMIC) with respect to mass spectroscopy.
• with M. Pauly (University of Düsseldorf, Germany) with respect to the analysis of polysaccharide matrix.
• with B. Zechmann (Baylor College, USA) with respect to effector localization by EM.
• with T. Heimerl at the EM-facility of SYNMIKRO (Marburg, Germany) with respect to microscopy of vesicles and fungal structures.
• with R. Roth and U. Paszkowski (Cambridge University, UK) with respect to EM- analyses of effectors after cryofixation.

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