Diagnostic DNA and protein chips
The techniques of functional genomics enable a comprehensive monitoring of microbial bioprocesses such as for the production of biopharmaceuticals or technical enzymes. Our work focuses on the bacterial protein production hosts Bacillus subtilis and Bacillus licheniformis. The use of transcriptome and/or proteome analysis techniques allows for the characterization of the physiological constitution of these industrial strains during fermentation processes.
However, the application of the established techniques for DNA or protein analysis has one crucial disadvantage: The whole process from sampling to the data analysis of DNA arrays (these are chips, which visualize the mRNA profile of the cells) or the analysis of 2D-protein gels (which show the protein spectrum of the cells) takes at least 24 hours. Therefore, we have developed protocols based on an electronic chip, with which the expression of process relevant genes can be measured at-line in a reasonably short time.
A prerequisite for the application of the electrical chip technique in bioprocess monitoring was the identification of process critical marker genes in the production cells. By means of proteomics and DNA array techniques such marker genes could be determined. The knowledge about these process relevant genes or proteins is being used in our lab for the configuration of electric DNA and protein chips.
The electric chip system is developed in close collaboration with the group of Dr. Rainer Hintsche from the Fraunhofer Institut für Siliziumtechnologie and the companies eBiochipSystems (Itzehoe) and Henkel KGaA (Düsseldorf). The detection principle is based on an electrical readout of a Red/Ox-electrode. On this electrode a sandwich-hybridization is performed, which allows a direct detection of specific mRNAs or proteins during fermentation processes (Fig. 1).
This new analysis technique does not only allow for a productivity control of the cells during the process but also enables us to control the quality of the product. This is of particular importance in the pharmaceutical industry. There are considerable requirements as to quality and monitoring of industrial biopharmaceutical production processes.
Beside the application in bioprocess control the electrical DNA and protein chips are also suitable for medical and pharmacological diagnostic purposes.
Responsible staff members:
Dr. Norma Welsch
Literature:
Pioch D, Jürgen B, Evers S, Maurer KH, Hecker M, Schweder T. 2008. Improved sandwich-hybridization assay for an electrical DNA-chip-based monitoring of bioprocess-relevant marker genes. Appl Microbiol Biotechnol. 78(4):719-28.
Pioch D, Schweder T, Jürgen B. 2008. Novel developments for improved detection of specific mRNAs by DNA chips. Appl Microbiol Biotechnol. 80(6):953-63.
Voigt B, Hoi LT, Jürgen B, Albrecht D, Ehrenreich A, Veith B, Evers S, Maurer KH, Hecker M, Schweder T. 2007. The glucose and nitrogen starvation response of Bacillus licheniformis. Proteomics. 7(3):413-23.
Pioch D, Jürgen B, Evers S, Maurer KH, Hecker M, Schweder T. 2007. At-line Monitoring of Bioprocess-Relevant Marker Genes. Eng Li Sci. 7(4):373-379.
Hoi LT, Voigt B, Jürgen B, Ehrenreich A, Gottschalk G, Evers S, Feesche J, Maurer KH, Hecker M, Schweder T. 2006. The phosphate-starvation response of Bacillus licheniformis. Proteomics. 6(12):3582-601.
Elsholz B, Wörl R, Blohm L, Albers J, Feucht H, Grunwald T, Jürgen B, Schweder T, Hintsche R. 2006. Automated detection and quantitation of bacterial RNA by using electrical microarrays. Anal Chem. 78(14):4794-802.
Jürgen B, Tobisch S, Wümpelmann M, Gördes D, Koch A, Thurow K, Albrecht D, Hecker M, Schweder T. 2005. Global expression profiling of Bacillus subtilis cells during industrial-close fed-batch fermentations with different nitrogen sources. Biotechnol Bioeng. 92(3):277-98.
Jürgen B, Barken KB, Tobisch S, Pioch D, Wümpelmann M, Hecker M, Schweder T. 2005. Application of an electric DNA-chip for the expression analysis of bioprocess-relevant marker genes of Bacillus subtilis. Biotechnol Bioeng. 92(3):299-307.
Gabig-Ciminska M, Holmgren A, Andresen H, Bundvig Barken K, Wümpelmann M, Albers J, Hintsche R, Breitenstein A, Neubauer P, Los M, Czyz A, Wegrzyn G, Silfversparre G, Jürgen B, Schweder T, Enfors SO. 2004. Electric chips for rapid detection and quantification of nucleic acids. Biosens Bioelectron. 19(6):537-46.
Schweder T, Hecker M, Jürgen B, Voigt B, Feesche J, Brewes R, Maurer KH. 2003. DNA chips used for bioprocess control. PCT/EP2003/009979