Team:KULeuven/Modelling/Vanillin Production

From 2009.igem.org

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{| width=80% style="border: 1px solid #003E81; background-color: #EEFFFF;"
{| width=80% style="border: 1px solid #003E81; background-color: #EEFFFF;"
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|+ ''Parameter values (Memory)''
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|+ ''Parameter values (Vanillin Production)''
! width=15% | Name
! width=15% | Name
! width=15% | Value
! width=15% | Value
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|-
|-
| d<sub>mRNA</sub>
| d<sub>mRNA</sub>
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| 0.0023104906 s<sup>-1</sup>
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| 2.3105E-3 s<sup>-1</sup>
|
|
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [1<html>]</html>]
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [1<html>]</html>]
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| d<sub>Fcs</sub>  
| d<sub>Fcs</sub>  
| 1.9254E-5 s<sup>-1</sup>
| 1.9254E-5 s<sup>-1</sup>
-
| estimate: because this RNA isn't translated, it degrades faster
+
|  
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [2<html>]</html>]
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [2<html>]</html>]
|-
|-
-
| k<sub>Ech</sub>
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| d<sub>Ech</sub>
| 1.9254E-5 s<sup>-1</sup>
| 1.9254E-5 s<sup>-1</sup>
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|  
+
|
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [4<html>]</html>]
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [4<html>]</html>]
 +
|-
 +
| d<sub>Vanillin</sub>
 +
| 8.6643E-6 s<sup>-1</sup>
 +
| Equivalent degradation dilution rate of vanillin
 +
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [2<html>]</html>]
|-
|-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
|-
|-
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| k<sub>P22CII</sub>
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| k<sub>trans</sub>
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| 0.0125 s<sup>-1</sup>
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| 0.00848 s<sup>-1</sup>
| estimate
| estimate
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [4<html>]</html>]
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [4<html>]</html>]
|-
|-
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| k<sub>AntimRNA_LuxI</sub>
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Key Lock Parameters
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| 0.0094 s<sup>-1</sup>
+
-
| estimate
+
-
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [5<html>]</html>]
+
-
|-
+
-
! colspan="4" style="border-bottom: 1px solid #003E81;" | Dissociation Constants
+
|-
|-
-
| K<sub>P2ogr</sub>
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| k<sub>unlock</sub>
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| 4.2156
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| 0.00237 s<sup>-1</sup>
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| Used in two reactions for activator control at the transcription of P2ogr mRNA and CIIP22 mRNA
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| Rate of unlocking the RIBOLOCK through key
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [6<html>]</html>]
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [6<html>]</html>]
|-
|-
-
| K<sub>R0053_P22CII</sub>
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| k<sub>lock</sub>
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| 0.1099
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| 0.00416 s<sup>-1</sup>
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|  
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| Rate of locking of unlocked RIBOLOCK-Key complex.
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [3<html>]</html>]
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [3<html>]</html>]
|-
|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Hill Cooperativity
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| k<sub>open</sub>
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|-
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| 7.5 s<sup>-1</sup>
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| n<sub></sub>
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| Rate of unlocking RIBOLOCK when no key is present (LEAK).
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| 2
+
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [3<html>]</html>]
-
| Used for all reactions throughout the memory submodel using Hill kinetics
+
-
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [1<html>]</html>]
+
|-
|-
 +
| k<sub>close</sub>
 +
| 500 s<sup>-1</sup>
 +
| Rate of locking of leaked RIBOLOCK.
 +
| [https://2008.igem.org/Team:KULeuven/Model/Memory#References [3<html>]</html>]
|}
|}

Revision as of 08:17, 9 September 2009

Contents

Vanillin Production

overview

Vanillin production overview starting from Tyrosine.

The vanillin synthesis consists of a five step process starting from tyrosine. By locking both the transcription of the Sam 8 and COMT enzyme we prevent vanillin synthesis without the presence of RIBOKEY. E. coli controls its own tyrosine production which is an non essential amino acid. However,should this be insufficient, we can always add extra tyrosine. The production process will be tested in two steps. First, from tyrosine to ferulic acid; then from ferrulic acid to vanillin. Because we want the production of vanillin proportional to the amount of input key, it is essential that the regulated enzymes that catalyse the production of (intracellular) vanillin degrade as fast as possible. As proteins are normally very stable in the intracellular environment the SAM8 and COMT where labelled with a LVA-tag, which insures relatively fast half times.

Biologie vanillin synthesis.png
Biologie vanillin synthesis short.png
Biologie vanillin synthesis shortII.png

Models

Vanillin production.png
Parameter values (Vanillin Production)
Name Value Comments Reference
Degradation Rates
dmRNA 2.3105E-3 s-1 [1]
dSam8 2.8881E-4 s-1 Fast degradation through to LVA tag [2]
dSam5 1.9254E-5 s-1 [3]
dCOMT 2.8881E-4 s-1 Fast degradation through to LVA tag [2]
dFcs 1.9254E-5 s-1 [2]
dEch 1.9254E-5 s-1 [4]
dVanillin 8.6643E-6 s-1 Equivalent degradation dilution rate of vanillin [2]
Transcription Rates
ktrans 0.00848 s-1 estimate [4]
Key Lock Parameters
kunlock 0.00237 s-1 Rate of unlocking the RIBOLOCK through key [6]
klock 0.00416 s-1 Rate of locking of unlocked RIBOLOCK-Key complex. [3]
kopen 7.5 s-1 Rate of unlocking RIBOLOCK when no key is present (LEAK). [3]
kclose 500 s-1 Rate of locking of leaked RIBOLOCK. [3]

Simulation

Because COMT and SAM8 are regulated by the amount of mRNA key its worthy to investigate the change of COMT and SAM8 production in function of the input amount of mRNA key. Because Sam8 and COMT are located behind the same lock they are both translated at the same rate, therefore only the concentration of COMT is shown.

Concentration of COMT in function of time and input key
.

The following figure shows that the steady state level of vanillin concentration is (non linearly) regulated by the amount of mRNA input key.

Molecules of Vanillin in function of time and input key
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