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 sensor and regulatory systems. A number of different global and specific regulatory systems influencing the cells behavior have been identified in the past. Many of them have been analyzed extensively and a lot of molecular details about these interactions are known. But in spite of this knowledge very little is known about the interplay of different regulatory systems and about the interplay of the different levels of biological regulations.
The interactions of the different levels of regulation are in the focus of the different projects investigated by this research team.
- Systems Understanding of Microbial Oxygen-Dependent and Independent Catabolism (SysMO SUMO2)
In this project E. coli MG1655 growing with defined oxygen supply is analyzed. By varying the oxygen input to glucose-limited chemostat cultures it is possible to set defined conditions also in the microaerobic range. In the frame of this project the wildtype strain MG1655 as well a set of isogenic mutants is characterized. Besides the glucose uptake rate and the production rates of fermentations 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 varying additional parameters. The influence of mutations in metabolic enzymes, in enzymes involved in glucose uptake and in components of the electron transport chain is analysed experimentally.
The data obtained are used in mathematical modelling by our collaborations partners from the University of Stuttgart.
2. Bet-hedging and Communication in E. coli? Investigations of Heterogeneous Gene Expression of Carbohydrate Uptake Systems
The E. coli lac operon is in the focus of this project. It has been known for a long time that, due to a positive feedback loop, this operon can display bistability if induced with the artificial inducers IPTG and TMG. So far, no bistability after induction with the natural substrate lactose was shown. We are analyzing the induction of the lac operon in a GFP reporter strain after induction with lactose and are investigating factors and conditions that favor bistable gene expression.
lac Operon expression is dependent on the presence of the cAMP.CRP complex. cAMP is known as a hunger signal in E. coli. It is present and active inside the cells but it is also exported into the growth medium. The effect of intra- and extracellular cAMP on lac Operon expression is therefore also a topic of our research.
3. Dynamic Process Optimization in Biotechnology
The application of biological processes in the production of building blocks is getting more and more interesting. But 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 proteins activity will be needed. In the project at hand different targets and strategies for the control of intracellular parameters are evaluated.
4. Analysis the E. coli PEP-dependent phopshotransferase system and central metabolism
This projects continues previous projects that dealt with the analysis of glucose-lactose diauxic growth and the control exerted by the PTS in E. coli. In addition the nitrogen-PTS, a system homologous to the carbon-PTS, is under investigation.