Functional genomics of fungal morphogenesis

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fun with fungi

Project group "Functional genomics of fungal morphogenesis" (principal investigator: Minou Nowrousian) at the Department of Molecular and Cellular Botany at the Ruhr-Universität Bochum.

Filamentous fungi grow in form of hyphae (elongated, branched cell filaments). They can aggregate to form complex structures, e.g. fruiting bodies in which spores are formed. We are interested in the genetic basis of these differentiation processes. To analyze how fruiting body formation is regulated at the molecular level, we use mutant strains that are blocked at early stages of development and compare gene expression in the mutants to that of the wild type using a combination of laser microdissection and RNA-seq, and quantitative real time PCR. Additionally, we compare gene expression in several fungal species to identify expression patterns that are evolutionary conserved (comparative functional genomics). Genes with similar regulation will help to define a core group of genes involved in fungal fruiting body development.

In a second project, we are studying the evolution of mating type genes in the Tremellomycetes, a group of basidiomycetes that contains many species that grow as yeasts (unicellular fungi). The ancestral state of basidiomycete mating type organisation in thought to be tetrapolar, i.e. each strain contains two non-linked (independently segregating) mating type loci. However, in a number of basidiomycetes, the two mating type loci became physically linked on the same chromosome. This arrangement is predicted to facilitate inbreeding, which might be an advantage if mating partners are hard to find, e.g. for pathogenic species in a host environment. We are currently focusing on the order Trichosporonales, where all strains analyzed so far contain physically linked mating type loci in an evolutionary conserved genomic arrangement.

More details about these projects can be found on the projects page or in several publications.

Latest results from our projects:

Development of complex multicellular structures in ascomycetes: We have analyzed the functions of the two developmental genes asf1 and pro44 in Sordaria macrospora using RNA-seq, MNase-seq, BS-seq, fluorescence microscopy and protein-protein interaction techniques. Our results show that even though both genes are required at the same stage of fruiting body development, they regulate different aspects of sexual development. While asf1 acts as a suppressor of weakly expressed genes during morphogenesis, transcriptome analysis of gene expression in young fruiting bodies showed that pro44 is required for correct expression of genes involved in extracellular metabolism. Deletion of the putative transcription factor gene asm2, which is downregulated in young fruiting bodies of the pro44 mutant, results in defects during ascospore maturation.
In a parallel project, we have compared the genomes and development-dependent transcriptomes of the three ascomycetes Ascodesmis nigricans, Pyronema confluens, and Sordaria macrospora to identify genes with conserved expression patterns during multicellular development. The Ascodesmis nigricans genome, which was sequenced during this study, is part of the 1000 Fungal Genomes Project. We identified 83 genes that are upregulated only during fruiting body development in all three species. Genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes as well as genes with predicted roles in chromatin organization or the regulation of gene expression comprise 23 and 13 of the upregulated genes, respectively. Functional analysis of four of those genes revealed that three are involved in fruiting body formation, with two of them encoding predicted chromatin modifiers.

Evolution of mating type genes in basidiomycetes: In a collaboration with the laboratory of Joseph Heitman (Duke University, USA), we have analyzed the mating type loci of the Trichosporonales, a little-studied group of basidiomycetes. As it turned out, all analyzed Trichosporonales species have fused mating type loci; however, these mating type loci have different features compared to previously studied fused mating type loci in other basidiomycete groups. Both the gene sequences as well as the order of genes within the mating type loci are extremely conserved in the Trichosporonales, in contrast to fused mating type loci in other basidiomycetes, which often show degeneration.

Publications:

Lütkenhaus R, Traeger S, Breuer J, Carreté L, Kuo A, Lipzen A, Pangilinan J, Dilworth D, Sandor L, Pöggeler S, Gabaldón T, Barry K, Grigoriev IV, Nowrousian M (2019) Comparative genomics and transcriptomics to analyze fruiting body development in filamentous ascomycetes. Genetics (in press) Abstract Paper at Genetics

Schumacher DI, Lütkenhaus R, Altegoer F, Teichert I, Kück U, Nowrousian M (2018) The transcription factor PRO44 and the histone chaperone ASF1 regulate distinct aspects of multicellular development in the filamentous fungus Sordaria macrospora. BMC Genetics 19: 112 Paper at BMC Genetics

Sun S, Coelho MA, Heitman J, Nowrousian M (2019) Convergent evolution of linked mating-type loci in basidiomycete fungi. PLoS Genet 15: e1008365 Paper at PLoS Genetics