Mapping secondary metabolic pathways

The Plant physiology group currently runs a project in which metabolic pathways producing secondary metabolites are systemically mapped by genetic engineering of Nicotiana benthamiana. The goal is to produce perrilic acid, a precursor for the commodity chemical terephthalic acid, in planta [1]. To this end, a number of genes coding for enzymes are transiently expressed in N. benthamiana and tested for activity. As the factors influencing and regulating the pathway producing perrilic acid the availability of precursors, enzymatic activity, transport, sequestration are mostly unknown, this task is not straightforward.

In this project, the challenge will be to develop a simple model of the regulation of this pathway. Combining data found in literature (the BRENDA database on enzyme activities), pathway databases (Plant Reactome, KEGG) and available metabolomics data would provide an initial metabolic pathway layout. This model could help formulate hypothesis on pathway regulation; measurements resulting from directed genetic interventions in N. benthamiana could then be used to verify these hypotheses and extend the model.

[1] A. Aharoni et al. (2003). Terpenoid metabolism in wild-type and transgenic Arabidopsis plants. The Plant Cell 15:2866-84.

Used skills: Programming, modelling

Requirements: INF-22306 Programming in Python, SSB-30306Molecular systems biology, BRD-31806Parameter estimation and model structure ident. or SSB-30806Systems biology from gene to ecosystem