Race for carbon in microbial communities

In nature microbes are usually embedded in intimate interaction networks with other microorganisms. One prime example is the lichen symbiosis, a very ancient and tight association of algae and/or cyanobacteria with asco- and basidiomycete fungi. The current understanding of such a cross-kingdom community is poor. We aim to get deeper insights into the underlying molecular principles by employing synthetic communities of cyanobacteria and fungi. By targeted manipulation using synthetic biological tools we will modulate the interaction at the level of carbon metabolism and physical interaction and read-out the physiological consequences. Using this principle, we will gather information on the organisation of organismic interaction networks in order to assemble new associations from scratch in the future.

Exploring synthetic communities for biotechnological applications

Microbial communities have major advantages in comparison to pure cultures. For example, they follow the strategy of work sharing and complementary metabolism. This decreases the individual burden of the cells. In a biotechnological approach we aim to exploit lichen-like communities for the production of valuable molecules from sunlight. Here, engineered phototrophic cyanobacteria grow on light and CO₂ and produce sucrose to feed heterotrophic fungi like U. maydis or S. cerevisiae. Depending on the associated fungi, different valuable substances will be produced from sunlight. Currently, we are focussing on the product class sesquiterpenes, that have varius industrial applications. 

In the past years the classical view of conventional eukaryotic secretion based on protein export via the endomembrane system has been challenged. The observation that an increasing number of important extracellular proteins is exported through alternative pathways has led to the discovery of fascinating and diverse export routes collectively termed ‘unconventional secretion’. In our group, we are interested in the unconventional secretion of the chitinase Cts1 in Ustilago maydis. In concert with the second but conventionally secreted chitinase Cts2, Cts1 mediates cell separation during cytokinesis. A lack of the two proteins results prevents cell separation and thus leads to cellular aggregation. While the function of Cts1 has been demonstrated by our group, its recruitment to the fragmentation zone connecting mother and daughter cell remains unclear. Recently, we identified Jps1, a protein that plays an important role for Cts1 secretion and accordingly cell separation. Like Cts1, this protein localises to the fragmentation zone. It binds to phosphoinositol phosphates, in particular PI4,5P₂ and forms dimers. We currently aim at deciphering further molecular details of this unconventional secretion mechanism by tackling the individual proteins and their crosstalk.

This project is associated with the CRC1208. 

Export of pharma proteins via unconventional secretion 

Protein secretion is highly attractive for the production of recombinant proteins with biotechnological application as it significantly reduces downstream processing costs. However, proteins travelling via the endomembrane system are frequently modified by post-translational modifications like N-glycosylation which can be disruptive for their activity in heterologous hosts. To avoid these modifications, we employ unconventional secretion in U. maydis for the export of hydrolytic and pharmaceutical proteins like nanobodies, single-chain variable fragments or carbohydrate-active enzymes (CAZymes). Here, we employ the aforementioned Cts1 as a carrier. A unique feature of the system is that Cts1 binds to chitin which can be employed for purification. To establish the fungus as an expression host, we are currently tuning the yields of the system and optimize the system at different levels. In parallel we evaluate the option of surface immobilization via chitin interaction. Potential future applications of our platform are versatile virus detection systems based on inexpensive chitin surfaces or production of antibody formats for pharma.  

This project is part of the graduate cluster „AUFBRUCH – Die Transformation in eine nachhaltige regionale Bioökonomie gestalten“.

Platform for bioactive mushroom compounds

Mushrooms are a tremendously rich source of bioactive terpenes and terpenoids. Many of these are, however, not easily accessible. Microbial chassis are a good opportunity to produce these compounds for those cases, where the biosynthesis is known. However, due to metabolic incompatibilities and other issues, not every compound can be produced easily in the current microbial hosts. U. maydis is a promising alternative, as this Basidiomycete model fungus is related to mushrooms. Recently, as a proof-of-principle, we successfully produced different sesquiterpenes. 

New tools for biotech approaches

To enable complex genetic modifications or metabolic engineering approaches, we recently implemented the standardized, modular cloning system “UstiGate", as well as a set of novel promoters and novel efficient genome insertion sites. This toolbox, generated in the framework of the SFB1535, transfers genetic manipulation of U. maydis into the synthetic biology era.  

Microbial oil as a palm oil replacement? 

Palm oil is a crucial compound and used in various industrial applications. The tremendous dimensions of palm tree planataions however threaten our environment. We are investigating the production of a palm oil replacement in U. maydis. Distince mutants of this fungus produce high amounts of microbial oil (single cell oil) in lipid droplets with a composition that is already close to palm oil. Using a genetic approach, we aim to tailor the oil composition as well as to further increase the space-time yields. We further aim to engineer the fatty acids towards industrially relevant medium-chain length. The project is currently funded by the BioSC project FamoUs. 

Biomass valorisation

As a plant pathogen U. maydis harbours a small but potent set of hydrolytic enzymes for the degradation of biomass polymers. In the past years we successfully enhanced the capacity of the fungus for degradation of biomass components like cellulose or polygalacturonic acid. We used a combination of genetic activation of intrinsic enzymes and complementation with potent foreign enzymes via conventional and unconventional secretion. In addition, U. maydis is a natural producer of valuable molecules including glycolipids, polyols, organic acids and hydrolytic enzymes. We also engineered the fungus for production of foreign molecules like sesquiterpenes and pharmaceutical proteins via unconventional secretion. In the future we will combine both properties and produced valuable compounds from plant biomass waste and industrial side- and waste streams.

Several applied projects are associated with the BioSC. 

F. Mostafa, A. Krüger, T. Nies, J. Frunzke, K. Schipper, A. Matuszynska (2024) Microbial markets: socio-economic perspective in studying microbial communities. microLife. 5:uqae016

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D. Hasenklever^$, J. C. Pohlentz^$, T. Berwanger^$, E. J. Kokarakis, T. Hassan, K. Schipper, A. Matuszyńska, I. M. Axmann, D. C. Ducat (2024). Assembly and quantification of co-cultures combining heterotrophic yeast with phototrophic sugar-secreting cyanobacteria. J. Vis. Exp. 214:e67311

^$shared first authorship

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S. Dali, M. Schultz, M. Köster, M. Kamel, M. Busch, W. Steinchen, S. Hänsch, J. Reiners, S.H.S. Smits, A. Kedrov, F. Altegoer^*, K. Schipper^* (2025) Specific phosphoinositide interaction of Jps1 is a key feature during unconventional secretion in Ustilago maydis. J. Biol. Chem. 6:301

* shared corresponding authorship

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P. Richter, M. Maßjosthusmann, T. Seidel, L. Walter, K. Miebach, M. Mann, J. Büchs, K. Schipper, M. Feldbrügge, J. Goeke, D. M. Wieland, H. Hayen, J. B. Magnus (2025) Tailoring the fatty acid profile of microbial triglycerides in Ustilago maydis by adapting the cultivation conditions. Bioresource Technology Reports, 102119

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M. Philipp, L. Müller, M. Andrée, K.P. Hussnaetter, H. Schaal, M. Feldbrügge, K. Schipper (2022) Efficient SARS-CoV-2 detection utilizing chitin-immobilized nanobodies synthesized in Ustilago maydis. bioRxiv

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