1. Abstract

2. Reasons for the choice of modification

2.1 Modifiable parameters in the system

2.2 Modifications

2.3 Prhl or Plux should be changed

3. Further analysis

1. Abstract

2. Reasons for the choice of modification

2.1. Modifiable parameters in the system

Since the system has the fewest components to achieve the mutualism, what we can change is the values of parameters. In the parameters of the equations, modifiable parameters are listed in Table 4-2-2-1.

Table 4-2-2-1 Modifiable parameters

Leak is not listed above because Company and Customer will be independent if the leak increase.

2.2. Modifications

Since there was no time to modify two or more components in the system, we should be able to achieve the goal with just one modification of the components. In the following we will examine which one to be concerned one by one.

2.2.2. C4HSL, 3OC12HSL production rate by RhlI, LasI (corresponds to k in (3) and (4))

Signaling molecule production rate by RhlI, LasI can be changed by modifying RhlI , LasI protein to make more signaling molecule. We set these values to be 0.1 originally. The following graph shows how the final populations of Company and Customer change depending on the value of signaling molecule production rate. In this simulation the value of k in equation (4) is varied.

As shown in Fig. 4-2-2-3, if the value is over 0.1, then the final populations of Company and Customer get higher. Thus this value should be concerned when we want to make this system robust.

2.2.3. Degradation rate of C4HSL and 3OC12HSL

Changing pH of the medium can change degradation rates of C4HSL and 3OC12HSL. Degradation rates d of equation (3) and (4) are varied simultaneously because the variation of pH affects not only d of one signaling molecule, but both of them. In the simulation shown in Fig. 4-2-2-4., the degradation rates are varied from 10^-4 to 10^0.

2.2.4 Maximum expression rate of proteins following Prhl and Plux promoters (corresponds to alpha in equation (5) and (6))

Mutating promoter can result improving the maximum production rate of the following proteins. Thus the dependency of the final populations of Company and Customer was examined by varying the value of maximum expression rate alpha. The result is shown in Fig. 4-2-2-5.

The parameter alpha was originally set to 10. From the graph, if the parameter value increase, the populations of Company and Customer also increase. This means improving promoter can result in increasing populations. Thus this value should be concerned.

2.2.5. Degradation rates of RhlI, LasI, chloramphenicol resistance (corresponds to d in equation (5), (6), (7), (8))

The final populations are simulated with varying the parameter values. First degradation rate of RhlI was changed. The original value was 0.01. The graph in Fig. 4-2-2-6. is the result of the simulation.

The graph tells population of Company and Customer can be higher if the degradation rate of RhlI is made to be lower. But we have no way to make the degradation rate higher, we cannot make the system robust in this way.

About degradation rate of chloramphenicol resistance, there’s no meaning in changing values. What we can do is only increase the degradation rate, but that results in reducing the internal chloramphenicol resistance concentration. This means the cells become easy to be killed. This is not an expected outcome.

2.3. Prhl or Plux promoter should be changed

From the examination above, components which should be concerned are C4HSL, 3OC12HSL production rate by RhlI, LasI and Maximum expression rate of proteins following Prhl and Plux promoters.

Since it is difficult to change the protein’s properties, we decided to change the strength levels of Prhl and Plux promoters.

3. Further analysis

Finally, since we can change both of the promoters in the system, we simulated many combinations of promoter strengths. The following shows the result of our examination.

The above diagram shows the intensity of the two promoters should be in the red region in the figure. The figure shows not only we have to make the intensity stronger, but also have to make the intensity equal. Thus we made Prhl_RL(BBa_K1529300) which has approximately same intensity to the Plux promoter.