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

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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]
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:

  1. Yield output of B-carotene ([B-carotene]/[All Caronoids]).
  2. 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.
Image:velocity of B-caro production.jpg

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:


[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


  • 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.


  • Device I: Anti Inflammatory Device


  • At last found all the paremeters needed for the IPP-->B-carotene model....(12:15p) Now trying to build up the model.


  • The rate/velocity of NO activating SoxR?

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