Team:Tokyo Tech/Modeling/Urea-cooler/urea-cooler
From 2011.igem.org
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compounds has similer effect on urea production.<br /><br /> | compounds has similer effect on urea production.<br /><br /> | ||
</p> | </p> | ||
- | <img src="https://static.igem.org/mediawiki/2011/5/50/TokyoTech_urea_fig7.png" alt="Fig7" width="400px" /> | + | <table align="center"> |
- | <img src="https://static.igem.org/mediawiki/2011/8/89/Urea-fig11.png" alt="fig9" width="400px" /> | + | <tr> |
- | + | <td><img src="https://static.igem.org/mediawiki/2011/5/50/TokyoTech_urea_fig7.png" alt="Fig7" width="400px" /></td> | |
- | <div class="graph_title"> | + | <td><img src="https://static.igem.org/mediawiki/2011/8/89/Urea-fig11.png" alt="fig9" width="400px" /></td></tr> |
+ | <tr> | ||
+ | <td><div class="graph_title"> | ||
<br />Fig.7 One of the urea producing cycles without supplying the intermediates | <br />Fig.7 One of the urea producing cycles without supplying the intermediates | ||
- | </div> | + | </div></td> |
- | <div class="graph_title"> | + | <td><div class="graph_title"> |
<br />Fig.9 One of the ornithine producing pathways from and intermediates of TCA cycle | <br />Fig.9 One of the ornithine producing pathways from and intermediates of TCA cycle | ||
- | </div> | + | </div></td> |
+ | </tr> | ||
+ | <table> | ||
<span style="font-style:italic, bold;"> <br /><big><b>What is elementary flux mode</b></big></span> | <span style="font-style:italic, bold;"> <br /><big><b>What is elementary flux mode</b></big></span> |
Revision as of 18:00, 4 October 2011
Flux analysis for providing more urea
Fig.5 The reactions related with the urea cycle
1. Introduction
In metabolic engineering, mathematical modeling is the effective way to increase the products.
Flux analysis, based on the hypothesis that the system is in steady state,
is the effective way to find expect how to increase the products. In this work,
we firstly focused on the concept of 'elementary flux modes' (Schuster et al, 2000),
which provides metabolic routes both stoichiometrically and thermodynamically feasible.
One elementary mode shows that the carbon atom of urea derives from HCO3- which abounds
in bacterial cytoplasm. Furthermore, in spite of L-glutamine consumption to transfer
the side-chain ammonium group for production of carbamoyl phosphate which transfers
the ammonium group to the urea cycle, ammonium ion can restore L-glutamine from
L-glutamate which is a byproduct of the carbamoyl phosphate production.
These findings suggest that there was little difference in the condition of
containing NH3 or L-glutamine in the culture to obtain more urea. This finding is
proven in previous report's experiment. (Mendel et al, 1996) We also confirmed that
the urea cycle in E.coli is well designed in a stoichiometrically point of view.
To provide more urea, there are two strategies. First one is to increase the
amount of carbamoyl phosphate which is the reactant of the rate-limiting step of
the urea cycle. The second one is to increase the amount of components of the
urea cycle. We focused on the second one. We identified the elementary flux
modes which produce these compounds from L-glutamine or compounds in TCA cycle.
In all modes, ornithine was intermediate or final product to produce the
components of the urea cycle. We also confirmed that E. coli have no feasible route for
production of the four compounds other than those indicated in Fig.5. Ornithine
production, which requires ATP, NADPH, Acetyl-CoA, and L-glutamine, is thus
the necessary step in this strategy.
Considering that L-arginine, L-glutamate, and L-aspartate are consumed in protein
biosynthesis, these compounds should be supplied from medium or produced by
E. coli itself not only for increase but for maintenance of the cycle. Positions of
L-arginine and L-aspartate in the reaction network show supplement of these
compounds has similer effect on urea production.
Fig.7 One of the urea producing cycles without supplying the intermediates |
Fig.9 One of the ornithine producing pathways from and intermediates of TCA cycle |