Team:Tokyo Tech

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Revision as of 18:20, 29 October 2008

Main	Parts Submitted to the Registry	Our Team	Acknowledgements

1 1 Our project
2 2 Pressure induction
3 3 Touch display
4 4 Low pressure-inducible promoter
5 5 Write/Erase cycle
- 5.1 Genetic toggle switch
- 5.2 Mathematical model
6 Our Team
7 Acknowledgements

1 Our project

Our project is to create "Coli Touch"!!

What is "Coli touch"?

“Coli Touch” has a pressure sensitive display composed of an E. coli lawn. When you touch its display, touched section is colored.

Next I'll tell you about “Coli Touch” work system. Display of “Coli Touch” has many E. coli. When you touch this display, pressure input travel to E. coli in this display. And pressure applied E. coli expresses GFP.

Why pressure?

“Coli Touch” uses pressure as input. Then why we use pressure input? Past input way (small molecule, heat and light) are difficult to induce uniformly. Pressurize can induce uniformly. It's prospect of technological application in confirmatory experiment.

2 Pressure induction

Construction

figure2-1. We constructed Ptet-GFP and promoter less-GFP for confirmatory experiment

For confirming pressure-response ability of pressure-inducible promoter, we experimented under 0.1 MPa and 30 MPa pressure. We chose TetR promoter(Ptet) as pressure-inducible promoter and we constructed two plasmids - one is Ptet-GFP on pSB6, the other is promoter less-GFP on pSB6 as a negative control.

Result ~ activity of Ptet ~

figure2-2. Pressure response of Ptet.Ptet activity increased under 30 MPa

The result shows that Ptet activity under 30 MPa pressure is about 3 fold stronger than Ptet activity under 0.1 MPa pressure. Therefore, we confirmed that Ptet was induced under 30 MPa pressure.

3 Touch display

Touch display (plan)

figure 3-1. Plan to create touch display. We created basic display as the first step.

Basic touch display

figure 3-2.Basic touch display. The display has two kinds holes and two kinds covers.

We created a basic touch display made of acrylic glasses. This touch display has two kinds of holes. This device made of Acrylic glasses and has two holes (show figure). Each hole contains culture medium and E. coli is cultivated in those holes. One hole (A) can be pressurized, because the hole is covered with only a plastic tape, water pressure conducts into the hole. The other (B) is not pressurized, because the hole is covered with a block made of acrylic glass, water pressure doesn’t conduct into the hole.

figure 3-3.

How to press “touch display”

Dilute culture medium by 1% by adding fresh medium and suitable antibiotic (ampicillin; 50㎍/ml). Next, infuse this culture medium into holes of the display with oxygen-saturated Fluorinert (25% volume of medium). Put this tube into pressure vessel filled with water (1). Next cap the vessel (2). And then apply pressure to the vessel by pressure device (4). Finally, start incubation at 37℃ immediately at each the vessel for 16h (5).

figure 3-4.

Result ~ E. coli in the touch display ~

After pressurized the display, we observed the E. coli in the touch display by a fluorescence microscope.

figure 3-5.

The touch display successfully regulated GFP expression in E. coli!

4 Low pressure-inducible promoter

Figure 4-1. - Pressure response of Plac

It is known that lac promoter is induced under 30 MPa (T. Sato et al., 1995). However, 30 MPa is too high to use as input.

Therefore, we are trying to develop low pressure inducible promoter.

Method

Principle

LacI binds to LacI binding site and repress lac promoter. In addition, pressure of 30 MPa activated the lac promoter. We propose a hypothesis that 30 MPa induce a conformational change in LacI reprssure and change the affinity for lacI binding site weaker. Therefore, LacI can't repress lac promoter under 30 MPa.

Strategy

Figure 4-2 - PCR random mutagenesis

Figure 4-3 - Screening system with flow cytometer

We are trying to develop low pressure inducible promoter by PCR random mutagenesis to lac promoter in order to reduce affinity to LacI. And we are screening an E. coli library for promoters that are induced under low pressure using a fluorescence activated cell sorter (FACS). This scheme is based on the ability to separate bacteria with a FACS in response to expression, or lack of expression, of a fluorescent marker.

Step 1 - Fluorescent bacteria without repressor protein were collected by FACS. This sorted pool contains bacteria bearing both constitutive and low pressure-inducible promoter.

Step 2 - Constitutive promoter are removed with repressor protein and sorting all non-fluorescent bacteria.

Step 3 - A final passage through under pressure with repressor protein and sorting for fluorescent bacteria removes false negatives and enriches for bacteria bearing promoter that are low pressure inducible.

Results

We finished step 1. Fluorescent and non-fluorescent bacteria were sorted and we characterized their promoter.

Sequence and Characterization

Figure 4-4 - FACS

Figure 4-5 - Sequencing

We sorted fluorescent (A) and non-fluorescent bacteria (B) with a FACS. Then, we analyze these base sequences.

A have mutations in LacI binding site or non-functional DNA.
B have mutations in CAP binding site, -35 or non-functional DNA.

Conclusion

We have successfully demonstrated that it is possible to collect objective promoter by PCR random mutagenesis and screening with a FACS. So we clearly believe that we can screen low pressure inducible lac promoter mutant with this strategy.

5 Write/Erase cycle

figure5-1. Write/Erase cycle

While we can implement write-function, we want to implement additionally erase-function and memory-function. Erase-function enables us to erase the painted picture, and memory-function enables us to keep the picture when we stop induction. We call these functions "Write/Erase cycle". In order to implement Write/Erase cycle, we tried to construct genetic toggle switch.

Genetic toggle switch

figure 5-2. Genetic toggle switch

1. Write-function

30 MPa pressure activates P_lac.

P_lac expresses CI and GFP.

CI represses P_L and causes low LacI expression.

Low LacI expression increases P_lac activity. ⇒ Bright!!

2. Erase-function

The heat activates P_L.

P_L expresses LacI.

LacI represses Plac.

Therefore, GFP expression decreases.

Mathematical model

Why did we use mathematical model?

figure 5-3. Left If P_L is not activated or is a bit, write-function is available. Right If P_L is activated too much, write-function is not unavailable

As mentioned above, it is known that P_lac is activated 94.0-fold under 30 MPa while we don't know the increase of P_L strength under 30 MPa. If P_L is activated too much, P_lac activity may be weaker than P_L activity and we can't implement write-function. So, how much is the range of the increase of P_L activity under 30 MPa so as to become advantageous to P_lac? To know this range, we need to use mathematical model.

Classical toggle switch model

figure. 5-4 Classical toggle switch model

figure 5-5. Hill function

Our mathematical model under atmospheric pressure is equal to a classical toggle switch model shown in figure 5-4. Where n_CI and n_LacI are hill coefficients, and α_PL and α_Plac are strength of promoter-RBS which are adjustable. We need to identify value of n_CI and n_LacI respectively. But we fortunately know n_CI = 3.0 (T. Tian et al., 2006). So, we experimented IPTG assay aimed to identify n_LacI.

IPTG assay

By testing how LacI represses the lac promoter, Hill coefficient of lac promoter should be decided. In order to adjust effective concentration of LacI, IPTG was added.

GFP fluorescence intensity was enhanced in an IPTG-dose dependent manner. It indicates that the LacI repression was getting weaker by adding IPTG. We formulated Hill function fitting the data shown in figure 5-5, and the characteristics of the lac promoter expressed in Hill function was determined. Finally, we obtained n_LacI = 2.2.

Conditions for bistability

We simulated the range of α_PL in which a toggle switch model is bistability. Here, we set α_Plac = 3.0. The result is below.

Pressure model

figure 5-6. Pressure model

We proposed pressure model which has additional parameters to the classic toggle switch model. These parameters are the increase of activity by pressure (β_(p)Plac or β_(p)PL). Under atmospheric pressure (0.1 MPa), β_(0.1)Plac = 1.0 and β_(0.1)PL = 1.0. On the other hand, under 30 MPa, β_(30)Plac = 94 and β_(30)PL is not known.

In order to implement write-function, we need the transit of the system from bistability to monostable (P_lac is stronger than P_L) by 30 MPa pressure. Therefore, we calculated the range of β_(30)PL which satisfies the above condition.

The feasibility of implementation of Write/Erase cycle

figure 5-7. The domain of appropriate parameters if α_Plac = 3.0

According to the result of simulation, we found that we can implement Write/Erase function even if P_L is activated 7-fold when α_PL = 3.0.

figure 5-8. Pressure-response ability of P_L

We identified β_(30)PL = 1.4 by our experiment under 30MPa pressure(figure 5-6). Therefore, we can implement Write/Erase cycle if we choose an appropriate P_L - RBS strength.

@@ Line 293: / Line 293: @@
 [[Image:Desirable_condition.png|700px|thumb|left|figure 5-5. Desirable condition. left:under atmospheric pressure (nullclines of figure 5-2), right:under 30MPa pressure (nullclines of figure 5-4).]]-->
-==== Why did we use mathematical model ? ====
+==== Why did we use mathematical model? ====
 [[Image:Conditions_for_Write-function.png|thumb|500px|right| figure 5-3. Left If P<sub>L</sub> is not activated or is a bit, write-function is available. Right If P<sub>L</sub>  is activated too much, write-function is not unavailable]]