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  • Genetics of Prokaryotes

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Research

We are characterizing global gene regulation in Corynebacterium glutamicum and Escherichia coli with a particular focus on the central carbon metabolism and on amino acid biosynthesis. Especially, using the DNA microarray technology established in our group since several years made it possible to unravel regulatory mechanisms governing the adaptation of these bacteria to a changing environment. An additional focus is on the genetic and biochemical characterization of the involved enzymes and metabolic pathways.

Applied research aims at rational strain development based on the functional genomics results in the form of a genome-based biotechnology. We are constructing high-performance strains for the production of amino acids and primary metabolites under the framework of White Biotechnology.

Basic research work centers around the identification of the components and the logic of the gene regulatory network of C. glutamicum, which appears to have a modular and hierarchical structure. Finally, our work shall contribute to establishing a systems-level understanding of the bacterial cell with the biotechnologically important C. glutamicum as an example.

Methods

In our group, we are preparing whole-genome DNA microarrays for Escherichia coli and Corynebacterium glutamicum using a DNA microarray roboting system as developed at the Stanford University.

TheTranscriptome comprises all RNA levels of a cell under a defined condition. Using DNA microarrays global gene expression patterns can be compared. RNA isoloated from the culture are labelled fluorescently by reverse transcription into cDNA, which subsequently is hybridzied to a DNA microarray. Hybridization signals are quantified using a DNA microarray laser scanner.

DNA microarrays are also suitable to identify certain genome aberrations, e.g. deletions and amplifications.

The so-called ChIP-to-chip analyses allow identifying those regions on the genomic DNA, that are bound in vivo by DNA bindng proteins such as transcriptional repressors. The DNA-protein complexes can be islated by chromatin immunoprecipitation (ChIP) or similar affinity methods. After separation from the protein, the genomic DNA fragments bound by the transcriptional regulator can be identified by hybridization to a DNA microarray (thus, ChIP-to-chip).

Metabolic Engineering has been defined as ‘…the improvement of enzymatic, transport, and regulatory functions of the cell by the application of recombinant DNA technologies.’ Bailey (1991) Science, 252: 1668-1677. We are using Metabolic Engineering to optimize E. coli and C. glutamicum strains with respect to the production of amino acids and with respect to carbon source utilization.

Systems biology has been defined as '... endeavors to quantify all of the molecular elements of a biological system to assess their interactions and to integrate that information into [predictive] models.‘ Hood et al. (2004) Science, 306: 640-43. Our research on global regulation and an Metabolic Engineering of C. glutamicum are part of a multi-disciplinary approach to systems-level understanding of this bacterium. The prospect of applying systems biology to biotechnology promises great opportunities: novel biotechnological products, more efficient processes, rationally optimized producing strains.

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