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