CeBiTec Colloquium: 2009/02/16 Dr. Oliver Ebenhöh Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm

2009/02/16, 17:15

CeBiTec Laboratory Building, Room G2-104

Systems Biology approaches in plant science

Abstract:
In my talk I will present two different modeling approaches operating on different scales.
In the first, genome-scale metabolic networks are considered.  Such networks are usually constructed from the genome sequence of an organism by comparing gene or protein sequences to sequences of previously identified proteins found in databases.  Since homologies never guarantee identical functions and, moreover, for many enzymes no sequences are known, it is obvious that such networks are incomplete. I will present an approach which integrates experimental data of heterogeneous origin, such as metabolomics and genomics information, with modeling techniques to identify inconsistencies within the network and to suggest possible extensions of the network which are capable of resolving the inconsistencies.  This method allows to propose hypotheses on which reactions should additionally be present and which putative genes may code for the corresponding enzymes. I will present some results for the recently sequenced green alga Chlamydomonas reinhardtii.
The second model is concerned with a particular metabolic pathway which plays a central role in plant metabolism.  In plant leaves, energy is stored during the day in the form of starch. During the night, starch is degraded to provide required energy in the absence of light.  Since starch is insoluble, the process of starch degradation involves enzymatic steps at the interface of the starch granule and the bulk solution.  I outline how we incorporate models from surface physics with biochemical reaction models to simulate the initial enzymatic attack of the granule surface. Results are presented demonstrating that the model can realistically reproduce the synergistic effect of different enzymes that has been observed in in vitro experiments.