Our lab focuses on elucidating the structure and function of microbial secondary metabolites. These natural products are important sources of structurally-diverse leads in the development of therapeutic agents. In particular, their applications as anti-infectives are well known. We tap into different ecological niches to mine for new natural products and to understand their ecological functions. Much of our research is centered on the social amoeba, Dictyostelium disocideum. This soil inhabitant is a voracious predator of bacteria on which it exerts a strong evolutionary pressure. In our lab, we apply a variety of methods and techniques ranging from state-of-the-art analytics and chemical synthesis to molecular biology and bioinformatics.
Natural Products from Prehistoric Microbiomes
The department Paleobiotechnology aims to access an untapped source of natural product diversity. We do not limit our search for new molecules solely to the microorganisms existing today but also intensively investigate the time dimension. We do so by analyzing the genetic information of prehistoric materials, e.g. microbial DNA from dental calculus or fecal remains. We can thus study the evolution of natural product biosyntheses and retrieve active compounds, which were lost in nature. For this purpose, we apply state-of-the art technologies for both genome analysis and for the identification and isolation of natural products. Yet not only fossils, also traditionally produced food from regions of the world that have not been influenced by modern industry provide promising starting points for the hunt for natural products. We closely collaborate with Prof. Dr. Christina Warinner from the Max Planck Institute for the Science of Human History in Jena/Harvard University, Cambridge, USA.
Bacterial Defense Mechanisms Against Predators
Bacteria are constantly exposed to a multitude of threats: bacteriophages can infect and kill bacteria; amoebae, nematodes, and insects can prey on prokaryotes, and competitor strains fight for the same resources. In order to survive in this battlefield, bacteria have evolved highly effective defense mechanisms. Because killing and deterring the antagonists are powerful ways to thrive in this environment, bacteria display a great diversity of toxins and antibiotics that selectively act on their enemies. Amoebae are voracious and ubiquitous predators to bacteria that cause constant depletion of huge bacterial reservoirs. This puts both organisms under strong evolutionary selection pressure: the bacteria have evolved mechanisms to prevent grazing and the amoebae must counteract or surmount these mechanisms in order to survive.
We focus on the interactions between the eukaryotic soil amoeba Dictyostelium disocideum and various soil bacteria. In particular, we are interested in bacterial secondary metabolites that kill the amoebal predator. We use modern spectroscopic techniques as well as chemical synthesis to determine the structures of these compounds. Additionally, we use whole genome sequencing of the producer strain as well as mutational analyses to investigate the biosynthesis and regulation of these metabolites.
The Role of Secondary Metabolites in Bacteria-Amoeba Symbioses
Recently, it was shown that some bacteria engage in symbiotic relationships with the social amoeba D. discoideum. We could show that bacterial secondary metabolites play a crucial role in this interaction. Little is however known about the molecular communication mechanisms between the eukaryote and its prokaryotic symbionts. We are aiming at deciphering this chemical language.
Structure and Function of Polyketides in Dictyostelium discoideum
The genome of the social amoeba D. discoideum contains over 40 putative polyketide synthase (pks) genes and their biosynthetic products as well as their functions are largely unknown. To identify and investigate these polyketides, we use a combination of molecular biology and analytical chemistry tools. Knockout mutants of selected pks genes are generated and the resulting secondary metabolome is compared with the wildtype strain. However, the pks genes of D. discoideum are a class of genes with high nucleotide sequence similarity. For this reason, well-established methods to edit the social amoeba’s genome show little success.
Targeted genome editing in D. discoideum using the clustered, regularly interspaced repeated short palindromic repeat (CRISPR) RNA-guided Cas9 nuclease is a valuable molecular tool to address these problems. This tool is very specific, even for genes with high similarity to others.
We are currently establishing this technology in D. discoideum, thus generating a mutant library of pks genes in D. discoideum to elucidate the structure and function of the so far unknown secondary metabolites.
Small Molecules in Amoeba-Amoeba Interactions
The social amoeba D. discoideum typically preys on bacteria, yet it can also serve as a food source for the related dictyostelid D. caveatum. This feature was first described 30 years ago and has since been subject to further investigations. Importantly, D. caveatum can only feed on D. discoideum if the latter is present in a pre-culminant state. Previous studies have shown that D. caveatum secretes a factor that effectively freezes D. discoideum in a pre-culminant state, inhibiting the formation of the multicellular fruiting body and allowing D. caveatum to phagocytose its prey. While preliminary experiments clearly show that a small diffusible molecule is the responsible morphogenesis inhibitor, its structure, biosynthesis, and mode of action remain elusive. We utilize bioassay-guided fractionation to attempt to isolate and elucidate the structure of the small molecule(s) responsible for the inhibition of multicellular development in D. discoideum.
Furthermore, we are interested in glorin, the acrasin (i.e. the metabolite that orchestrates the aggregation of the amoeba) of D. caveatum. Since little is known about the receptor of this signaling molecule, we are constructing chemical probes to address this question.
presence of D. caveatum extract.
Boehringer Ingelheim Foundation: Exploration Grant
Deutsche Forschungsgemeinschaft (DFG: STA1431/2-1, STA1431/3-1, SFB 1127 and EXC 2051)
Daimler and Benz Foundation
Dr. Illing Foundation
Jena School for Microbial Communication (JSMC)
Fonds der Chemischen Industrie
Europäischer Fonds für regionale Entwicklung (EFRE)
International Leibniz Research School for Microbial and Biomolecular Interactions Jena (ILRS)