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Team:UANL Mty-Mexico/Modelling/Parameters
From 2011.igem.org
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<p><b>Maximum transcription rates </b></p> | <p><b>Maximum transcription rates </b></p> | ||
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<p>Gene</p> | <p>Gene</p> | ||
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<p><b>Maximum Translation Rate</b></p> | <p><b>Maximum Translation Rate</b></p> | ||
Revision as of 21:00, 28 September 2011
Parameters
Maximum transcription rates
|
Gene |
Maximum Transcription Rate (molecules min.1) |
Source |
|
Red Photoreceptor |
1.879194631 |
A |
|
ompR |
5.857740586 |
A |
|
mnt |
14.58333333 |
A |
|
tetR |
6.363636364 |
A |
|
cI |
5.6 |
A |
|
lacI |
3.723404255 |
A |
|
cI434 |
6.278026906 |
A |
|
lasI |
1.20E-01 |
B |
|
lasR |
2.88E-01 |
B |
|
GFP |
5.533596838 |
A |
|
SBFP2 |
5.833333333 |
A |
|
CFP |
5.511811024 |
A |
|
YFP |
5.511811024 |
A |
|
RFP |
5.809128631 |
A |
Maximum Translation Rate
|
Protein |
Maximum Translation Rate (molecules min.1) |
Source |
|
Red Photoreceptor |
3.22147651 |
A |
|
OmpR |
10.041841 |
A |
|
Mnt |
25 |
A |
|
TetR |
10.90909091 |
A |
|
cI |
9.6 |
A |
|
LacI |
6.382978723 |
A |
|
cI434 |
10.76233184 |
A |
|
LasI |
9.60E-01 |
B |
|
LasR |
9.60E-01 |
B |
|
GFP |
9.486166008 |
A |
|
SBFP2 |
10 |
A |
|
CFP |
9.448818898 |
A |
|
YFP |
9.448818898 |
A |
|
RFP |
9.958506224 |
A |
Dissociation Constants and Phosphorylation Rates
|
Transcription factors/DNA-binding molecules |
||||||
|
Protein |
Dissociation constant (nM) |
Hill coefficient |
Source |
|||
|
CcaR-Phosphate |
N/A |
|
A |
|||
|
OmpR-pompC |
31.4 |
|
A |
|||
|
Mnt |
50 |
1 |
A |
|||
|
TetR |
0.179 |
3 |
A |
|||
|
LacI |
800 |
2 |
A |
|||
|
cI434 |
40 |
2 |
A |
|||
|
cI |
O2 Binding (No cooperativity) |
77.60592 |
O2 Binding (With cooperativity) |
1.7599E-08 |
2 |
A,D |
|
O3 Binding (No cooperativity) |
77.60592 |
O3 Binding (With cooperativity) |
2.3542E-07 |
A,D |
||
|
LasI-3-oxo-C12-HSL & LasR |
0.011 |
1 |
C |
|||
Light-induced systems:
The OmpR phosphorylation is expressed through the following expressions adapted from Srividhya and Krishnaswamy, (2006), reference E:
IMAGEN
OmpR-P dephosphorylation rate (from Qin, L, et al., 2001, reference F): 17 min when red light is present / 56 min when far-red light is present.
Quorum Sensing
For simplicity just the parameters of the LasI/LasR quorum sensing system are shown, because they are supposed to be equivalent according to the used general Quorum Sensing model.
|
Quorum sensing |
||
|
Parameter |
Constant |
Source |
|
Transcription of lasI |
1.20E-01 molecules min.1 |
C |
|
Translation of lasI |
9.60E-01 molecules min.1 |
C |
|
Degradation of lasI mRNA |
3.60E-01 min.1 |
C |
|
Degradation of LasI |
3.00E-03 min.1 |
C |
|
Transcription of lasR |
2.88E-01 molecules min.1 |
C |
|
Translation of lasR |
9.60E-01 molecules min.1 |
C |
|
Degradation of lasR mRNA |
3.60E-01 min.1 |
C |
|
Degradation of LasR |
1.20E-02 min.1 |
C |
|
Enzymatic activity LasI |
27 min.1 |
C |
|
Autoinductor diffusibility |
2.40E+01 min.1 |
C |
|
Binding between LasR/3-oxo-C12-HSL |
6.00E-03 molecules min.1 |
C |
|
Dissociation of LasR/3-oxo-C12-HSL |
1.80E-01 min.1 |
C |
|
Dimerization LasR/3-oxo-C12-HSL |
1.80E-03 molecules min.1 |
C |
|
Dissociation of the dimer |
6.00E-01 min.1 |
C |
Degradation rates
Following the recommendations of team Peking 2009, we set all mRNAs half-lives to 4.4 min and, supposing that all regulatory and reporter gene would have an LVG tag attached, all protein half-lives were set to 40 min, with the exception of phosphorylated OmpR, whose case is exposed on the last sections.
Considering a cell division rate of 30 min, then, the degradation rates for mRNA are: 1/4.4 + 1/30 min, and the protein degradation rates are: 1/40 + 1/30 min.
References:
- https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
- Schuster, M, et al., (2004), Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR, Proc. NatL Acad. Sci. USA, Vol. 101, pp. 15833–15839.
- Goryachev, AB, et al., (2005), Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants. Biosystems, pp. 178-87.
- Ackers, GK, et al., (1982), Quantitative model for gene regulation by A phage repressor, Proc. NatL Acad. Sci. USA, Vol. 79, pp. 1129-1133.
- Srividhya and Krishnaswamy, (2004), A simulation model of Escherichia coli osmoregulatory switch using E-CELL system, BMC Microbiology, 4:44
- Qin, L, et al., (2001), The critical role of DNA in the equilibrium betweenOmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli, PNAS, Vol. 98, No. 3, pp. 908-913.
