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Team:Imperial College London/Project Gene Modelling
From 2011.igem.org
Module 3: Gene Guard
Containment is a serious issue concerning the release of genetically modified organisms (GMOs) into the environment. To prevent horizontal gene transfer of the genes we are expressing in our chassis, we have developed a system based on the genes encoding holin, anti-holin and endolysin. We are engineering anti-holin into the genome of our chassis, where it acts as an anti-toxin, and holin and endolysin on plasmid DNA. In the event of horizontal gene transfer with a soil bacterium, holin and endolysin will be transferred without anti-holin, rendering the recipient cell non-viable and effectively containing the Auxin Xpress and Phyto-Route genes in our chassis.
Modelling
The Gene Guard device involves three proteins:
1) Holin is a protein that forms pore complexes in the inner membrane and these pores allow endolysin to move into the periplasmic space.
2) Endolysin is an enzyme that can break down the cell wall and causes cell lysis.
3) Anti-holin binds to holin and prevents it from forming pores.
Our system will have the holin and endolysin genes together with the Phyto-Route and the Auxin Xpress genes on the plasmid, and the anti-holin gene on the genome under control of strong promoter. The production of anti-holin will prevent cell lysis of the genetically modified (GM) bacteria by deactivating holin. If the plasmid is transferred to a different cell without anti-holin on its genome (e.g. any wild type soil bacteria), the expression of holin and endolysin will induce cell lysis. This will prevent the spread of the AuxIn plasmid to other cells.
The key to the success of this device is the correct ratio of holin and anti-holin production such that the anti-holin can deactivate all the holin produced in our GM bacteria, and the holin expression level in wild type bacteria is high enough to induce cell lysis. As gene expression is controlled by promoter strength and ribosome binding site (RBS) strength, modelling of the Gene Guard is important for helping us choose an appropriate promoter and RBS.
The modelling of the Gene Guard consists two parts, one is the holin production in wild type bacteria and the other part is the deactivation of holin by anti-holin in GM bacteria. Since all the genes in our system are constitutively expressed we only consider the steady state.
Holin production in wild type soil bacteria
This part of the modelling focused on deriving the relationships between promoter strength and RBS strength of holin on single plasmid. In order to model this, the following assumptions were made:
1) After horizontal plasmid transfer and duplication, the number of plasmids in one bacterium is 50.
2) The literature indicates that cell lysis happens at a holin concentration equal to 1000/cell[1], therefore we used 1000 holin/cell as the threshold concentration for cell lysis in our project.
Based on these assumptions, the kinetics of cell lysis in wild type bacteria was modelled using ordinary differential equations (ODEs) for the holin mRNA and holin protein (Equation 1). At steady state (i.e. d[ ] /dt = 0), rearranging Equation 1 with [holin] = 1000, we obtained an expression for Pholin Kholin as shown in Equation 2.
Holin inhibition in GM bacteria
In GM bacteria the strength of the promoter and RBS controlling expression of anti-holin on the genome should be higher than the promoter and RBS strength of holin on a single plasmid such that all the holin produced by 300 plasmid copies is be inhibited, where 300 is the maximum number of plasmids in a single bacterium. In this system, the anti-holin can bind to holin to form a dimer, which is defined as the deactivated holin. The mechanism in the GM bacteria is described by Equation 3.
By varying the ratio m in equation 4, we found that the holin concentration in GM bacteria decreased to zero at ratio m ≥ 300 (see Figure 1). Then, we tested m = 400 with the anti-holin promoter we have with strength 13.1 pg RNA/min/μg substrate DNA, the result is displayed in Figure 2.
Fig.1: The holin concentration in GM bacteria vs. ratio m (m = (Panti-holinKanti-holin)/(PholinKholin)). This graph shows that the intracellular concentration of holin remains at zero if m>300 .
Fig.2: The evolution of different protein species vs. time at m = 400. This graph shows that all the holin in the GM cell are inhibited as the holin concentration remains at 0 all the time, while the holin concentration in wild type bacteria reaches 1000 per cell after 5000 seconds.
[1] Christos G. Savva, Jill S. Dewey, John Deaton, Rebecca L. White, Douglas K. Struck, Andreas Holzenburg and Ry Young. The holin of bacteriophage lambda forms rings with large diameter. Molecular Microbiology 69(4), 784–793. 2008.
[2] http://ctb.pku.edu.cn/main/2011course/Network%20motifs/Sneppen%202010/pdf
[3] A. G. ndling., M. D. Manson, R. Young (2001)‘Holins kill without warning’ 9348–9352 PNAS July 31, 2001 vol. 98 u no. 16
