IGEM:Stanford/2009/Notebook/Marys iGEM Notebook/2009/08/05

Mary's SiGEM Project

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2 The IPP-->B-carotene-->RA Model Fig 2.1 A quick sketch of the IPP-->RA process Fig 2.1 A quick sketch of the IPP-->RA process Fig 2.2 The B-carotene production pathway [1] The process above can be devided into two procedures: IPP*8-->B-carotene B-carotene(+Blh)-->Retinal(+RalDH)-->Retinoic Acid 2.1 Modeling on the production of B-carotene The process of IPP producing B-carotene is quite complex, as shown in the Fig 2.2. In this process, we basically care about two main issues: Yield output of B-carotene ([B-carotene]/[All Caronoids]). Velocity of the whole process 2.1.1 Yield output of B-carotene We found the B-carotene distribution in yeast in [1]. Below is an important form as to the issue. Form 2.1 B-carotene distribution [1] Basically, using the cluster of "YB/I/E I", in the final product of caronoids, we get 68% of B-carotene, highest percentage in the paper. (Also 29% Phytoene, and 3% Neurosporene.) "YB/I/E tHMG1 I", producing 52% of B-carotene, might be another choice. 2.1.2 Production rate of B-carotene As this is a really long process....Basically, the velocity is mainly dependent on the most time-consuming reaction in the whole chain. Thus, Leon and I looked for the kcat values of different enzymes in the procedure, as shown in the cart below: Form 2.2 Paremeters in the IPP-->B-carotene model. (Source: mostly from Brenda) Apparently, cyclization of Lycopene is the slowest reaction, as the concentration of enzymes are approximately in the same level. 2.2 Modeling on the B-carotene-->RA process The production of RA is mainly based on a chain of two catalyzed reactions, as shown in the graph below: Fig 2.3 The production of RA Neither Retinal nor RA has any other degrading process in E.coli. Degrading rate of B-carotene is 9.769e-9 s^-1. Other paremeters we use in this model are shown in the form below: Form 2.3 Parameters used in the B-carotene-->RA model 2.3 Simulation and Analysis Equations for the IPP-->RA process: References [1] High-Level Production of Beta-Carotene in Saccharomyces cerevisiae by Successive Transformation with Carotenogenic Genes from Xanthophyllomyces dendrorhous. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, July 2007, p. 4342–4350 Daily Work Goals Find out the missing kcat values for the IPP-->B-carotene model. Calculate the approximate producation rate of B-carotene. If the velocity of NO activating SoxR is found, finish the NO-->SoxS-SoxR model. Project Device I: Anti Inflammatory Device Accomplishments At last found all the paremeters needed for the IPP-->B-carotene model....(12:15p) Now trying to build up the model. Problems The rate/velocity of NO activating SoxR? Alternative Solutions Comments Weekly Goals