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 under varying conditions. 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. We hence investigate the influence of regulatory systems on metabolism under different external conditions. One major goal is to employ this understanding for the targeted modification of metabolism and regulation in the construction of production strains.
Here is a list of current research topics:
- Zymomonas mobilis (ZIP project)
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. Genetic engineering for target modification of the Z. mobilis genome is possible but so far no efficient tools are available. We are aiming at developing a genetic toolbox for efficient genetic engineering of Z. mobilis. This toolbox shall contain plasmid-vectors for controlled expression of plasmid-based genes, different promoter elements and ribosome binding sites as well as tools for genome integration and knock-out of genes. Using the tools developed, we will engineer Z. mobilis for the production of other products than ethanol. Here, model-based analysis will predict promising modifications. Beside this, we are aiming to a better understanding of more general aspects of Z. mobilis physiology like the function and role of its respiratory chain, the mechanisms underlying the uncoupled growth phenotype and ATP metabolism.
2. 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 cheaper. Often the synthesis of the desired product is compromised by slow growth of the cells 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.
3. 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 under well defined conditions, 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.
4. Electrofermentations
E. coli can use different electron acceptors the most important being oxygen. By genetic engineering it is possible to construct E. coli cells that can use electrodes as electron acceptor. So far there are only proof of concept studies for this electrofermentations. We are investigating electroactive E.coli, focussing on two main objectives: i) the composition of the electron transport chain and its interplay with the regulators and ii) the exploitation of electrofermentations for the optimization of production strains and processes.