Time series transcriptional profiling of Ustilago maydis infecting Zea mays

The basidiomycete fungus Ustilago maydis causes smut disease in maize and has become an important model for elucidating the strategies used for host colonization by biotrophic fungi. In this study, we performed an in-depth transcriptional profiling of the plant-associated development of a cross between U. maydis FB1 and FB2 wildtype strains. The analysis of eight different stages, including the development on the leaf surface, early colonization, tumor induction and spore maturation, offers an unprecedented view of the changes in the fungal transcriptome associated with the passage through the entirely biotrophic life cycle. In our analysis, we focus on fungal metabolism, nutritional strategies, secreted effectors and regulatory networks. Secreted proteins were enriched in three distinct expression modules corresponding to the plant surface, establishment of biotrophy and tumor formation, respectively. These modules are likely the key determinants for U. maydis virulence. With respect to nutrient utilization, we observed that expression of several nutrient transporters was tied to these virulence modules rather than being controlled by nutrient availability. We show that oligopeptide transporters likely involved in nitrogen supply during infection are important virulence determinants. By measuring the intramodular connectivity of transcription factors, we identified potential drivers for the virulence modules. While known components of the b-cascade served as inducers for the plant surface and biotrophy module, we identified a set of yet uncharacterized transcription factors as likely responsible for expression of the tumor module. We demonstrate a crucial role in effector gene expression and tumor formation for one of these transcription factors. Overall design: Crossings of the compatible U. maydis wild type strains FB1 and FB2 were injected into maize seedlings of the variety EGB. Infected leaf sections were collected at 12 and 24 hours, 2, 4, 6, 8, and 12 days post inoculation. Maize plants were also mock-infected (water) and samples collected at the same time points. Additionally, the U. maydis strains FB1 and FB2 were cultivated in axenic culture and samples collected during growth in mid-log phase (OD600=1.0). All samples were subjected to RNAseq analysis with mRNA as target molecule.

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Lanver D, Müller AN, Happel P, Schweizer G, Haas FB, Franitza M, Pellegrin C, Reissmann S, Altmüller J, Rensing SA, Kahmann R