K. Niehaus: Proteome and Metabolome Research
Genes, transcripts, proteins and metabolites are the physical building blocks of the cell. The functional relations between these elements form a complex network of interactions that we call life. Our group intends to decode (tiny) parts of such networks to obtain a functional understanding of life processes.
Previous and Current Research
How do plants discriminate between beneficial and pathogenic microbes? To answer this question, the interaction of the legume Medicago truncatula with the symbiotic bacterium Sinorhizobium meliloti is analysed on a molecular level. The microbe seems able to suppress the plant defence in order to infect its host and thereby provide atmospheric nitrogen. On the other side, plant pathogenic microbes like Xanthomonas or the fungus Aphanomyces express extracellular proteins that damage the plant’s recognition system to facilitate their harmful infection. Plant cell cultures are used to analyse the very early recognition processes involving complex glyco-structures, calcium, GTP-binding proteins and the generation of reactive oxygen species (ROS).
Reconstructing bacterial metabolism based on genome data, and analysing the metabolite flux within bacteria allows the establishment of dynamic models of metabolism that are also relevant for industrial biotechnology.
Food metabolomics and food proteomics are emerging fields in safeguarding sustainable food supply by monitoring quality or optimising production processes. We contribute to this field by analysing the malting process of barley to identify biomarkers for beer brewing. In another project, we can differentiate between wheat from conventional and organic farming by metabolite fingerprinting.
Finally, automated microscopy was developed in collaboration with partners in bioinformatics to generate quantitative data for eukaryotic cells, their compartments, or infecting bacteria, permitting to monitor the behaviour of individual cells. In combination with reporter genes such as the green fluorescent protein (GFP) and smart dyes that give a read out on pH, respiratory activity or the production of ROS, this provides new insights into cellular function.
Future Projects and Aims
We aim at providing knowledge for biotechnology, screening or biomarker discovery. Thereby we focus on systems biology and plant-microbe interactions. In this field, more quantitative data is required on the levels of the transcriptome, proteome and metabolome in order to establish mathematical models that allow for predictions. Here, we analyse the regulation of the plant NADPH oxidase, the enzyme that generates ROS. As this enzyme is required for plant development, for beneficial and for pathogenic interactions, its activity has to be well balanced.
Likewise, by combining metabolic models with gene- and protein-based regulatory networks, global and mechanistic models can be obtained as a foundation for intricate systems biology approaches in industrial biotechnology. Such models can be used to redirect the bacterial metabolism for higher yields or different product qualities. The large-scale production of the biopolymer Xanthan by Xanthomonas campestris is our focus in this approach.