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EFFECTOMICS- elucidating the toolbox of
biotrophic pathogens

Final Report Summary - EFFECTOMICS (EFFECTOMICS- elucidating the toolbox of biotrophic pathogens)

The Effectomics project aims to elucidate secreted proteins of the fungal maize pathogen Ustilago maydis and to develop a systematic pipeline for effector research. These so-called effectors are the toolbox which the pathogen employs during its biotrophic life stage to manipulate and control its host plant. One major challenge in effector research is the very low degree of sequence conservation due to a continuous evolutionary pressure of effector recognition by the host immune system. The Effectomics approach allowed a comprehensive view on about 300 putative effectors of Ustilago maydis and promoted the field of effector biology and plant research at various levels. Systematic screening for effectors with the ability to suppress Pathogen-Associated Molecular Pattern (PAMP)-induced Reactive Oxygene Species (ROS) bursts led to the identification of more than 30 effectors with such a function. Among them we identified a set of nine effector genes co-regulated in a functional cluster in the genome with such redundant activity. We could identify a whole group of effector proteins that induce plant growth-hormone signaling in the plant – a feature that might be relevant for the gall-formation capability of this model pathogen. Our effector research revealed with the Nkd1 effector a direct antagonistic link between PAMP-triggered ROS burst and Auxin Signaling in plants and the Jsi1 effector function revealed the importance of the C-terminal part of Topless, a highly conserved negative co-regulator in all plants, to suppress ethylene signaling in plants.
Systematic interaction screens among the effector candidates of U. maydis indicate the existence of many effector- effector interactions and Interaction screens between the effector candidates and maize transcription factors revealed novel host-targets involved in meristem maintenance in the plant.
On the technical side, the effectomics approach allowed the establishment of a complete toolbox for the model pathosystem Ustilago bromivora and Brachypodium spec. including a high-quality genome, transcriptomic information, a transformation protocol for both, the smut fungus and the grass. The development of a half-automatized phenotyping and a software integration allows now the prediction of the infection outcome weeks before qualitative smut symptoms develop.
A novel sequencing-based method to identify insertion flanks called ipool-Seq allows now highly efficient negative selection screens in U. maydis and led so far to the identification of 23 novel virulence factors in this fungal system. The development of various reporters in plants including Unfolded protein response reporter will allow also in future many more functional screens to reveal effector functions and to widen our understanding in plant biology. The Effectomics project had a strong impact on the careers of the researcher involved in and more importantly moved the effector research in smut fungi to a new level.