Reconstruction And Prediction Of C₄₀ Carotenoids Biosynthesis Network And Constrait-Based Reconstruction And Analysis Of Lycopene In E.coli

Carotenoids usually refer to a class of compounds which consist of basic unitof isoprenoid molecules. They are widespread in nature and of specialphysiological functions and pharmacological features and closely related tohuman health. Although over700carotenoids have been isolated andidentified, the biosynthesis of only about30%carotenoids is currently known.Thus, the space of the entire carotenoids network remains largely unexplored.Lycopene is one of the most important industrial carotenoids and heterologoussynthesis is a new research direction. With the rapid development of systembiology, computational approach will be definitely helpful in the metabolicengineering design.In the first part of this thesis,170metabolic reactions of carotenoids werefound in literature and manually added to the BioPath.Database. Based on791carotenoids registered in the BioPath.Database and170currently knownbiochemical reactions, we limited the dataset under investigation tocarotenoids with a C₄₀ skeleton as this class has the most representatives. Thisdataset refers to541molecules and138reactions and a set of63transformation rules were generated after calculation. These transformationrules were then applied to541molecules and about over90%of the carotenoids can build a comprehensive network of the oxidativecarotenogenesis, which consists of1104reactions. Finally, the centrality ofnetwork, the prediction of intermediates and prediction of novel pathways, etal were performed based on the network.In the second part of this thesis, we introduced the MEP（2-C-methyl-D-erythritol-4-phosphate） pathway into the iAF1260model tobuild a genome-scale metabolic network of Escherichia coli which canproduce lycopene. An application of FBA （Flux Balance Analysis） on themodel predicted that glucose is the best substrate for the production oflycopene. In addition, using robustness and phenotypic phase plane analysis, itwas found that glucose is the limited factor in the production of lycopenethough oxygen plays an important role in the initial biosynthesis of lycopene.Simulations also revealed a direct invers relationship between the lycopeneyield and growth yield. We finally could not couple the lycopene yield withgrowth by using of OptKnock algorithm. We found that it might be the highnumber of carbons of the lycopene and not accurate biomass reaction lead tothe result.