Team:UANL Mty-Mexico/Modelling/Parameters

From 2011.igem.org

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   <li>Goryachev AB,  Toh DJ, Lee T (2005) Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants. <i>Biosystems</i> <b>83</b>:178-87.</li>
   <li>Goryachev AB,  Toh DJ, Lee T (2005) Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants. <i>Biosystems</i> <b>83</b>:178-87.</li>
   <li>Ackers GK, Johnson AD, Shea MA (1982) Quantitative model for gene regulation by A phage repressor. <i>Proc Natl Acad Sci USA</i> <b>79</b>:1129-1133.</li>
   <li>Ackers GK, Johnson AD, Shea MA (1982) Quantitative model for gene regulation by A phage repressor. <i>Proc Natl Acad Sci USA</i> <b>79</b>:1129-1133.</li>
-
   <li>Srividhya, Krishnaswamy (2004) A simulation model of Escherichia coli osmoregulatory switch using E-CELL system. <i>BMC Microbiology</i> <b>4</b>:44</li>
+
   <li>Srividhya KV, Krishnaswamy S (2004) A simulation model of Escherichia coli osmoregulatory switch using E-CELL system. <i>BMC Microbiology</i> <b>4</b>:44.</li>
   <li>Qin L, Yoshida T, Inouye M (2001) The critical role of DNA in the equilibrium betweenOmpR and phosphorylated OmpR mediated by EnvZ in <i>Escherichia coli</i>.  <i>Proc Natl Acad Sci USA</i><b> 98</b>:908-913.</li>
   <li>Qin L, Yoshida T, Inouye M (2001) The critical role of DNA in the equilibrium betweenOmpR and phosphorylated OmpR mediated by EnvZ in <i>Escherichia coli</i>.  <i>Proc Natl Acad Sci USA</i><b> 98</b>:908-913.</li>
</ol>
</ol>

Revision as of 22:52, 28 September 2011

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Team: UANL_Mty-Mexico
Team: UANL_Mty-Mexico
Modelling
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
  1. https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
  2. Schuster M, Urbanowski L, Greenberg EP (2004) Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR. Proc Natl Acad Sci USA 101:15833–15839.
  3. Goryachev AB, Toh DJ, Lee T (2005) Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants. Biosystems 83:178-87.
  4. Ackers GK, Johnson AD, Shea MA (1982) Quantitative model for gene regulation by A phage repressor. Proc Natl Acad Sci USA 79:1129-1133.
  5. Srividhya KV, Krishnaswamy S (2004) A simulation model of Escherichia coli osmoregulatory switch using E-CELL system. BMC Microbiology 4:44.
  6. Qin L, Yoshida T, Inouye M (2001) The critical role of DNA in the equilibrium betweenOmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli. Proc Natl Acad Sci USA 98:908-913.


OurSymbol

Team: UANL_Mty-Mexico

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