Simulation of a Petri net-based model of the terpenoid biosynthesis pathway.
BACKGROUND
The development and simulation of dynamic models of terpenoid biosynthesis has yielded a systems perspective that provides new insights into how the structure of this biochemical pathway affects compound synthesis. These insights may eventually help identify reactions that could be experimentally manipulated to amplify terpenoid production. In this study, a dynamic model of the terpenoid biosynthesis pathway was constructed based on the Hybrid Functional Petri Net (HFPN) technique. This technique is a fusion of three other extended Petri net techniques, namely Hybrid Petri Net (HPN), Dynamic Petri Net (HDN) and Functional Petri Net (FPN).


RESULTS
The biological data needed to construct the terpenoid metabolic model were gathered from the literature and from biological databases. These data were used as building blocks to create an HFPNe model and to generate parameters that govern the global behaviour of the model. The dynamic model was simulated and validated against known experimental data obtained from extensive literature searches. The model successfully simulated metabolite concentration changes over time (pt) and the observations correlated with known data. Interactions between the intermediates that affect the production of terpenes could be observed through the introduction of inhibitors that established feedback loops within and crosstalk between the pathways.


CONCLUSIONS
Although this metabolic model is only preliminary, it will provide a platform for analysing various high-throughput data, and it should lead to a more holistic understanding of terpenoid biosynthesis.
Hawari
Aliah Hazmah
AH
School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia 43600 UKM Bangi, Selangor, Malaysia.
Mohamed-Hussein
Zeti-Azura
ZA
D019295:Computational Biology / Q000379:methods*; D020543:Proteome / Q000032:analysis; D015398:Signal Transduction; D013729:Terpenes / Q000378:metabolism*
D020543:Proteome; D013729:Terpenes