Plant BioMEMs is a new field of cellular manipulation. The idea is to integrate plant cells into a Lab-on-Chip device to administer gradients or to combine different cell types by a microfluidic flow to simulate the interaction of cells in a real tissue. A promising application of this strategy is metabolic engineering. Metabolic engineering means that a metabolic pathway is diverted at branching points, either by blocking a branch (downregulation of a gene) or by activating a branch (upregulation of a key enzyme). Plants are extremely proficient with respect to secondary metabolism. Many of these metabolites are of medical interest. To produce them in cell culture (so called plant cell fermentation) would be promising. There is a drawback, however: plant cell cultures are reluctant to unfold their metabolic potency, because they consist of only one cell type - in real tissues, several cell types work together and produce different steps of the pathway, similar to the division of labour in a factory.
To find some background on the principles and applications of Plant BioMEMs refer to Ilias: Fakultät für Chemie und Biowissenschaften - current semester - BIO_MA_FOR_1201_Plant_Cell_Biology
Your task is now to work out a strategy, for one of our current projects (cephalotaxines in Cephalotaxus), a metabolic strategy based on the chip. As a first step, you must infer the metabolic pathways. There are no good reconstructions for conifers, but for the heterosporic fern Selaginella moellendorffii, a close relative to the gymnosperm ancestor, the metabolism is represented in the KEGG database. (to find the reconstructed phenylpropanoid pathway, you can click here). Using this pathway as a template, you have now to locate the positions of the cloned enzymes from Cephalotaxus (ask Nasim Reshadinejad for the peptide sequences) into the KEGG map (when you click on the boxes with the numbers in the map, you will get the information of the respective Selaginella homologue including their annotation). You will find that some of these enzymes can do different jobs. Now, design three set-ups using three chips in a microfluidic flow, where each chip harbours a different transgenic line overexpressing one of these enzymes and predict, what might come out of that. Into the appendix of your solution, please list the peptide sequence of the Cephalotaxus enzyme and the corresponding Selaginella homologue recovered from the KEGG database.