Team:ITB Indonesia/Modeling/Reporter kinetic

From 2013.igem.org

Reporter kinetic

After DNA damage occured, naturally cell will activate SOS promotor and SOS response. In our biosensor, SOS response will produce color (chromoprotein) as a response aid for user.
AFB-DNA adduct will affect replication process and leaves a single strand DNA (ssDNA). When ssDNA appears, therefore RecA* (activated RecA) increases:


Parameter

Definition

Value

Source

kreca_on

ssDNA binding with RecA

0,003 s-1

[1]

kreca_off

ssDNA unbinding with RecA

2 s-1

[1]

ssDNA

Amount of single stranded DNA

-

Calculated from previous step

Increasing amount of RecA* mediates LexA cleavage. LexA is repressor on SOS promotor to keep SOS response stay inactive.


Parameter

Definition

Value

Source

kclexa

lexA cleavage catalyzed by RecA*

7,5 x 10-6 s-1

[1]

How LexA and RecA interact to build SOS response in cell is showed in diagram below :



Image Source : [2]


LexA, when there is no ssDNA presence in cell, repressing 3 genes : lexA (gene to synthesize LexA), recA (gene to synthesize RecA), and GFP gene. LexA cleavage affects the GFP gene repressing strength and cell can start producing GFP as a result of ssDNA presence in cell.

How we did it in Simbiology?
In Simbiology, we build SOS response model as showed below :

To simplify this system, we neglect LexA and RecA synthesis and focusing just on the GFP synthesis.

LexA repressing system can be written in reaction form :


Parameters :

Parameter

Definition

Value

Source

klexabind

LexA binding to lexA gene

0,01 s-1

[2]

klexaunbind

LexA unbinding to lexA gene

0,01 s-1

[2]

krecabind

LexA binding to recA gene

0,02 s-1

[2]

krecaunbind

LexA unbinding to recA gene

0,04 s-1

[2]

kgfpbind

LexA binding to GFP gene

0,02 s-1

[2]

kgfpunbind

LexA unbinding to GFP gene

0,04 s-1

[2]

ktrcgfp

transcription rate of GFP gene

0,05 s-1

[2]

ktrlgfp

translation rate of mGFP

0,04 s-1

[2]

kdeggfp

degradation rate of mGFP

0,003 s-1

[2]

Reference
[1] Ming Ni, Si-Yuan Wang, Ji-Kun Li, and Qi Ouyang. Simulating the Temporal Modulation of Inducible DNA Damage Response in Escherichia coli
[2] Shimoni Y, Altuvia S, Margalit H, Biham O (2009) Stochastic Analysis of the SOS Response in Escherichia coli. PLoS ONE 4(5): e5363. doi:10.1371/journal.pone.0005363