Experimental Systems Biology (Team Bettenbrock)
Biological systems are inherently complex. Even a simple model organism like the bacterium Escherichia coli is composed of a great number of molecules ranging from simple metabolites to proteins, RNA and DNA. Complex interactions of these molecules take place in order to secure survival and replication. Systems Biology aims to a holistic and quantitative understanding of these interactions by combining experimental biological research with mathematical and computational methods.
Due to their small size and their way of life bacteria are subjected to fast and drastic changes in their environment. To cope with this, each cell has to monitor its environment and to react in a favorable way. This is achieved by a complex network of sensors and regulatory systems. The regulatory systems control gene expression and thereby tune metabolic pathways, in catabolism as well as in anabolism. In addition, metabolism is influenced by the control of enzyme activities by modification or by allosteric control. A deep understanding of bacterial metabolism and its regulation is vital for engineering bacteria for biotechnological applications. One major goal of our research hence lies in understanding and in targeted modification of bacterial metabolism and regulation. In addition, the interactions of different regulatory systems with metabolism is in the focus of this research team.
Here is a list of current research topics:
- Analysis of microaerobic growth and of the aerobic-anaerobic switch in E. coli
In this project E. coli growing with defined oxygen supply is analyzed. By varying the oxygen input to cultures growing in well controlled bioreactors, it is possible to set defined conditions also in the microaerobic range. In the frame of this project, the E. coli wildtype strain MG1655 as well as a set of isogenic mutants is characterized. Growth with the fermentable carbon source glucose as well as growth with the non-fermentable carbon source glycerol is investigated. Besides the carbon uptake rate and the production rates of fermentation products and CO2, we determine e.g. the expression of selected genes via RealTime RT PCR, the phosphorylation state of the regulator ArcA, the amounts of the different quinone-species present in E. coli and various additional parameters. The influence of mutations in metabolic enzymes and in components of the electron transport chain is analyzed experimentally.
The results from this project will be valuable for process design in biotechnological applications. The exploitation of microaerobic conditions will allow for an optimization of production processes.
The bacterium Zymomonas mobilis is characterized by a particularly high glucose uptake rate and high glycolytic flux compared to most other microorganisms. In addition, glucose taken up by Z. mobilis is converted almost completely to its main fermentation product ethanol. These characteristics make Z. mobilis a promising workhorse for biotechnology applications. In collaboration with international partners from Riga, Trondheim, Sheffield, Athens and Stuttgart we investigate the acetaldehyde and ethanol production of this organism. A set of mutant strains was constructed and is analyzed in order to maximize the production of acetaldehyde with Z. mobilis. Acetaldehyde is a promising precursor of biofuels. Beside this optimization, we are aiming to a better understanding of the function of the respiratory chain and of ATP metabolism of Z. mobilis.
3. Dynamic Process Optimization in Biotechnology
The application of biological processes in the production of building blocks is getting more and more important. In order to replace petrochemistry, the biological production processes have to become more efficient and also cheaper. Often the synthesis of the desired product is compromised by slow growth of the cell and/or by the use of the compounds as building blocks for the cells themselves. In order to overcome this obstacle, the application of dynamic process control strategies is promising. Besides simple control of external parameters, also the control of intracellular parameters like gene expression or protein activity will be needed. In the project at hand, different targets and strategies for the control of intracellular parameters are evaluated.
4. Analysis of the E. coli PEP-dependent phosphotransferase system and of central metabolism
This project continues previous projects that dealt with the analysis and modeling of glucose-lactose diauxic growth and the control exerted by the PTS in E. coli. The PTS represents the main carbohydrate uptake system in E. coli, but it is one of the most important regulation systems of E. coli, too. We hence analyze its function in controlling fluxes and search for approaches to control this system for bioprocess optimization.