Team:TU Delft/Modeling/MFA/additional pathways

From 2010.igem.org

(Difference between revisions)
(New page: == Pathways added to the ''E. coli'' metabolic network == blabla == Alkane degradation == slurp == PHB production == In previous situations the hydrocarbons were degraded only to for...)
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In previous situations the hydrocarbons were degraded only to form biomass and CO2. It is interesting to see how much product could be made from hydrocarbons. PHB is a polymer of polyhydroxybutyrate. The production pathway of PHB is well known. PHB is a solid product which is to recover in the down stream process.
In previous situations the hydrocarbons were degraded only to form biomass and CO2. It is interesting to see how much product could be made from hydrocarbons. PHB is a polymer of polyhydroxybutyrate. The production pathway of PHB is well known. PHB is a solid product which is to recover in the down stream process.
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The pathway is displayed here http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY1-3&detail-level=2&detail-level=1
The pathway is displayed here http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY1-3&detail-level=2&detail-level=1
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In oily environments oxygen diffuses more difficult into the water phase. The oxygen is used for the oxidative phosphorylation, regenerating NADH, and for the first step in the hydrocarbon degradation. To be more efficient with oxygen an additional electron acceptor was introduced.
In oily environments oxygen diffuses more difficult into the water phase. The oxygen is used for the oxidative phosphorylation, regenerating NADH, and for the first step in the hydrocarbon degradation. To be more efficient with oxygen an additional electron acceptor was introduced.
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*note: make link open up a new window
In this scenario the oxidative phosphorylation was disabled and a replacement was implemented;
In this scenario the oxidative phosphorylation was disabled and a replacement was implemented;
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In previous situations the hydrocarbons were degraded only to form biomass and CO2. It is interesting to see how much product could be made from hydrocarbons. Isoprene is a volatile product found in plants. ''E. coli'' will not be able to produce is in the near future, but it is an interesting product It is a very reduced product, with a similar amount of electron per carbon atom. Hydrocarbons have 6 - 6.3 electrons per carbon atom depending on the length and isoprene has 5.6 electron per carbon electron. ''If these values are close to each other, it has a positive influence on the maximal theoretical yield.'' Also the volatile nature of isoprene is very favorable for the downstream process
In previous situations the hydrocarbons were degraded only to form biomass and CO2. It is interesting to see how much product could be made from hydrocarbons. Isoprene is a volatile product found in plants. ''E. coli'' will not be able to produce is in the near future, but it is an interesting product It is a very reduced product, with a similar amount of electron per carbon atom. Hydrocarbons have 6 - 6.3 electrons per carbon atom depending on the length and isoprene has 5.6 electron per carbon electron. ''If these values are close to each other, it has a positive influence on the maximal theoretical yield.'' Also the volatile nature of isoprene is very favorable for the downstream process
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*note: make link open up a new window
The pathway is displayed here http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-6270&detail-level=2
The pathway is displayed here http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-6270&detail-level=2
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The pathway is displayed here http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=FHLMULTI-RXN
The pathway is displayed here http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=FHLMULTI-RXN

Revision as of 12:38, 8 October 2010

Contents

Pathways added to the E. coli metabolic network

blabla

Alkane degradation

slurp


PHB production

In previous situations the hydrocarbons were degraded only to form biomass and CO2. It is interesting to see how much product could be made from hydrocarbons. PHB is a polymer of polyhydroxybutyrate. The production pathway of PHB is well known. PHB is a solid product which is to recover in the down stream process.

  • note: make link open up a new window

The pathway is displayed here http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY1-3&detail-level=2&detail-level=1


In this scenario the lumped PHB production pathway was added to metabolic network;

2 acetyl-CoA + NADPH -> (R)-3-hydroxybutanoyl-CoA the polymerization reaction just consumes (R)-3-hydroxybutanoyl-CoA.


NO3 as electron acceptor

In oily environments oxygen diffuses more difficult into the water phase. The oxygen is used for the oxidative phosphorylation, regenerating NADH, and for the first step in the hydrocarbon degradation. To be more efficient with oxygen an additional electron acceptor was introduced.

  • note: make link open up a new window

In this scenario the oxidative phosphorylation was disabled and a replacement was implemented;

NO3- + NADH + 8 H+ -> NO2- + NAD+ + H+ + 4 Hex+ + H2O


This reaction uses NO3 as an electron acceptor to regenerate NADH and export protons to generate ATP. Less protons are exported per mol of NADH, so the ATP/NADH ratio will drop compared to oxygen. The goal of implementing this pathway however, is to see how much the oxygen requirement of E. coli can be reduced.

isoprene production

In previous situations the hydrocarbons were degraded only to form biomass and CO2. It is interesting to see how much product could be made from hydrocarbons. Isoprene is a volatile product found in plants. E. coli will not be able to produce is in the near future, but it is an interesting product It is a very reduced product, with a similar amount of electron per carbon atom. Hydrocarbons have 6 - 6.3 electrons per carbon atom depending on the length and isoprene has 5.6 electron per carbon electron. If these values are close to each other, it has a positive influence on the maximal theoretical yield. Also the volatile nature of isoprene is very favorable for the downstream process

  • note: make link open up a new window

The pathway is displayed here http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-6270&detail-level=2


In this scenario the lumped isoprene production pathway was added to metabolic network;


1 pyruvate + 1 D-glyceraldehyde-3-phosphate + 1 NADPH + 3 NADH + 3 ATP -> isoprene + CO2

isoprene export


hydrogen production

In previous situations the hydrocarbons were degraded only to form biomass and CO2. It is interesting to see how much product could be made from hydrocarbons. Hydrogen is considered a green fuel. Hydrogen is a volatile product and is easily separated from fermentation broth. It does however contain no carbon atoms, so hydrogen will result in production of CO2 and biomass.


  • note: make link open up a new window

The pathway is displayed here http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=FHLMULTI-RXN


In this scenario the hydrogen production pathway was added to metabolic network;


Formate + H+ -> H2 + CO2

hydrogen export


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