Team:UANL Mty-Mexico/Modelling/Parameters

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Team: UANL_Mty-Mexico Team: UANL_Mty-Mexico

Modelling

Parameters

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
cI	O3 Binding (No cooperativity)	77.60592	O3 Binding (With cooperativity)	2.3542E-07	2	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.

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