Functional genomics of fungal morphogenesis

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 different 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:
Histone chaperones are proteins that are involved in nucleosome assembly and disassembly and can therefore influence all DNA-dependent processes including transcription, DNA replication and repair. ASF1 is a histone chaperone that is conserved throughout eukaryotes. In contrast to most other multicellular organisms, a deletion mutant of asf1 in the fungus Sordaria macrospora is viable; however, the mutant is sterile. In a recent study, we could show that the histone binding ability of ASF1 is required for fertility in Sordaria macrospora, whereas the function of ASF1 in maintenance of genome stability does not require histone binding. We also showed that the histone modifications H3K27me3 and H3K56ac are misregulated in the asf1 deletion mutant. Furthermore, we identified a large duplication on chromosome 2 of the mutant strain that is genetically linked to the delta-asf1 allele present on chromosome 6, suggesting that viability of the mutant might depend on the presence of the duplicated region. In a second project, we have analyzed two additional genes encoding chromatin-associated proteins. rtt109 encodes a histone acetyltransferase, and deletion of the gene in Sordaria macrospora results in a phenotype similar to that of a delta-asf1 mutant, whereas chk2 is involved in different aspects of the DNA damage response, but not in development.

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.
In a collaboration with the laboratory of Dominik Begerow (Universität Hamburg), and as part of the 1000 Fungal Genomes Project, we have recently sequenced the genomes of two strains of the basidiomycete yeast Filobasidium floriforme. This species belongs to the little-studied order Filobasidiales, which branches basally to the Tremellales, Trichosporonales and Holtermanniales. The genomes of strains CBS6241 and CBS6242 are approximately 27 Mb in size, and were analyzed with respect to genes that are part of mating type (MAT) loci as well as CAZyme-encoding genes.

Publications:

Breuer J, Ferreira DEA, Kramer M, Bollerman J, Nowrousian M (2024) Functional analysis of chromatin-associated proteins in Sordaria macrospora reveals similar roles for RTT109 and ASF1 in development and DNA damage response. G3 (Bethesda) 14: jkae019 Paper at G3

Breuer J, Busche T, Kalinowski J, Nowrousian M (2024) Histone binding of ASF1 is required for fruiting body development but not for genome stability in the filamentous fungus Sordaria macrospora. mBio 15: e0289623 Paper at mBio

Guerreiro MA, Ahrendt S, Pangilinan J, Chen C, Yan M, Lipzen A, Barry K, Grigoriev IV, Begerow D, Nowrousian M (2022) Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme. G3 (Bethesda) 12: jkab398, doi: 10.1093/g3journal/jkab398 Paper at G3

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