UNDER CONSTRUCTION

Biological switches

Many biological processes exist in mutually exclusive states. Cells or organisms exist in one of the distinct states depending on the level of stimulus input. A switch from one state to the other is triggered in response to fluctuations of a stimulus above or below threshold level, which is frequently mediated by a regulatory circuit with positive and/or negative feedback mechanisms.

Some biological switches enable cells to “remember” a state set by transient signals. Temperate bacteriophages are classic examples of such natural genetic switches as they can choose between two distinct life cycles, namely lytic and lysogenic. For more information please click here.

Bistable Switches

Now, taking an idea from the world of electronics, we define a bistable switch with a memory function and with two mutually exclusive steady states. Once stability in one state is reached; only stimulus above threshold level would switch the system towards reaching the other steady state. In bistable switches the threshold level of the stimulus input in forward reaction is different from the one in the reverse direction. Such behaviour is known as hysteresis.

However, bistable switches are not naturally occurring mechanisms. As in the example with bacteriophages, once the lytic cycle is induced, the lysogenic state cannot be reattained. This is also an example of a robust switch in which once the system is set to be in one state, reduction and in some cases even removal of the stimulus input does not trigger switching to the other state. Robust switches have biological importance because in mechanisms such as differentiation of cells during development, gene regulatory systems must hold the state set during development. This can be accomplished by a network of genes that regulate one another through repressor and activator proteins that they encode.

Design of our Bi[o]stable Switch

The simplest of such biological switches is one in which each of two repressor proteins represses the synthesis of the other. When both the repressor proteins are allowed to act, one of two stable states will be observed. In one steady state, the expression of repressor "one" is turned on and expression of repressor "two" is turned off. The repression of expression of repressor "two" is maintained by repressor "one", which means that the repressor "one" essentially acts as its own activator by inhibiting the expression of the repressor, repressor "two", that would repress its expression. In the other steady state, expression of repressor "two" is turned on and expression of repressor "one" is turned off.

In a system where the repressors can be controlled by outside input signals such as inducers or anti-repressor proteins, the system can be forced into its other stable state. This is illustrated in Figure 2.

Figure 2: Simple bistable switch.

We looked to nature for inspiration to design such a switch. The regulatory systems of the lambda phage as well as the Gifsy phages. The Gifsy phages are temperate phages found in Salmonella enterica that have an overall gene organisation typical of the lambdoid phage family (for more theory please see Regulatory Systems).

Step-wise Engineering of the Switch

The step-wise construction of our Bi[o]stable switch is demonstrated here, parts will be added to the switch as we build it up:

Step 1

The divergent promoters from both Gifsy1 and Gifsy2 phages are utilized in our system. The initial Gifsy1 and Gifsy2 constructs are illustrated below, Figure 3 and Figure 4, respectively.

Figure 3: The divergent promoters from the Gifsy 1 and Gifsy 2 phages have been highlighted. The divergent promoters from Gifsy 1 are pR1 and pRM1, whereas the Gifsy 2 divergent promoters are pR2 and pRM2.

Figure 4: Both sets of divergent promoters have been highlighted. As illustrated, GogR (Gifsy 1 phage repressor) will repress the pR1 promoter when it is expressed. Transcription of gtgR is still allowed to some degree due to the fact that GtgR does not also repress the pRM2 promoter.
Note:The strategy for the leakiness of pRM2 will be introduced later in Steps 3 and 4.

Figure 5: As similarly demonstrated in Figure 4, both sets of divergent promoters have been highlighted. GtgR (Gifsy 2 phage repressor) will repress the pR2 promoter when it is expressed. Transcription of gogR is still allowed to some degree due to fact that GtgR does not also repress the pRM1 promoter.
Note:The strategy for the leakiness of pRM1 will be introduced later in Steps 3 and 4.

Step 2

Figure 6: antO and antT are introduced in this image. antO codes for the anti-repressor protein responsible for preventing GogR from binding to and thereby repressing the pR1 promoter. antT codes for the anti-repressor protein responsible for preventing GtgR from binding to and thereby repressing the pR2 promoter.

Figure 7: The action of the anti-repressor protein, AntT from the Gifsy 2 phage is illustrated. AntT binds to repressor protein GtgR thereby preventing its repressor action. This means that GtgR is no longer able to bind to the pR2 promoter leaving the expressed GogR to bind to the pR1 promoter.
Note: The strategy for the leakiness of the pRM2 promoter will be introduced in Steps 3 and 4.

Figure 8: The action of the anti-repressor protein, AntO from the Gifsy 1 phage is illustrated. AntO binds to repressor protein GogR thereby preventing its repressor action. This means that GogR is no longer able to bind to the pR1 promoter leaving the expressed GtgR to bind to the pR2 promoter.
Note: The strategy for the leakiness of the pRM1 promoter will be introduced in Steps 3 and 4.

Step 3

Figure 9: The nut sites from p22 and lambda phages are introduced into the construct (for theory see Regulatory Systems). These nut sites will contribute to the robustness of the switch as described in Step 4.

Step 4

Figure 10: The anti-terminator proteins, Gp24 and GpN are introduced. In this image, Gp24 has been expressed and by binding to the p22 nut site, it enables RNA polymerase to bypass the terminator and continue transcription. This contributes to the robustness of the bistable switch as even though the pRM1 promoter allow transcription through them. Transcription through the terminator is prevented without the presence of the anti-terminator thereby not allowing spontaneous change of states.

Figure 11: In this image, GpN has been expressed and by binding to the lambda nut site, it enables RNA polymerase to bypass the terminator and continue transcription. Transcription through the terminator by GpN allows continuous expression of anti-terminator as well as anti-repressor, which will keep the cell in the induced state and thereby red. Even though transcription through pRM1 is permitted and GogR is expressed, it will be derepressed by the anti-repressor thus inactivating GogR. The state is maintained and the cell emits geen light.

In the switch design, each half switch contains a nut site followed by a terminator, as well as an antiterminator. The roles of these parts are to increase the stability of the current state of the switch. The pRM promoters are not very well repressed by the GogR/GtgR repressors and promotes transcription even in their presence. If transcription was allowed to continue to the antirepressor located on the inactive switch, the switch could change state spontaneously. The terminator ensures that this does not happen. The antiterminator of the active state is expressed, allowing continued transcription past the terminator.

Step 5

Now that we are able to keep the switch in each state stably, we also need a means to be able to switch the state of the switch at will. To do this we introduce two input plasmids illustrated in Figure 13. The plasmids contain the antiterminators and antirepressors of each state respectively, in front of two different inducible promoters.

Figure 13: Our final construct is illustrated.

When the plasmid corresponding to state 1 is induced, the switch is forced into state 1. This happens because the state’ s antiterminator and antirepressor are produced. The antirepressor inactivates state 2’ s repressor, resulting in increased transcription through state 1. At the same time, the antiterminator allows transcription to continue past state 1’ s terminator, where the genes for the same antirepressor and antiterminator are located. Thus, with a sufficient amount of induction, the switch will have switched states.

The Final Switch

Figure 13: Our final construct is illustrated.

Applications

If successfully engineered this new technological tool could advance methods used with in many different fields of biological science as environmental engineering, food applications and medico technology, a few suggestions are listed below. Further description of applications see the Switch section under applications.

• In manufacturing it could be applied as a cheap proof reading or control mechanism in production plants, if the product is exposed to the right or wrong treatment, or an un wanted biological infection or compound, it will change color.
• In manufacturing or environmental technology it could be used for error tracking or leakage tracking in process plants or in the environment. If the compound to be tracked cannot be measured, or measurements are difficult to obtain, if a biological sensor exists it is possible to track the organism or the reporter downstream of the inducer signal.
• In food control it could be used as a small piece of tape, containing the modified organism, on the package. It will then be possible to track if the product have been exposed to high temperatures, or unwanted compounds and the consumer can see it directly on the package.
• A medical application could be to ingest the modified organism. It can then be tested if the organism experience a certain drug, or condition on the way through the intestinal track.
• In molecular or medical science it could be used for investigations on chemotaxis and biofilm formation experiments, by exposing the biological matrix with, for an example, different light sources, there will be developed layers in the matrix and movements and development can be tracked, in relation to the two different exposures and the time between them.

Our original project idea was developed around the last example, where light (red light at 660nm and blue light at 470nm) would be used as input to induce switching between the two stable states. The initial ideas behind this was to use the bacteria to create artistic drawing or to track movement in biofilm.

Based on this idea, as well as research of biological switches and the regulatory mechanisms found in phages, we discovered untapped potential in designing a biological switch.