Team:UANL Mty-Mexico/Project/The Code

The main idea consists of enabling a bacterial community to interpret a simple code. The code will be composed of just red and green lights. The genetic circuit on which the interpretation relies is not dependent on the nature of the stimuli though, whether light or chemical the information processing remains the same. We use light because it is an elegant non-invasive input.

The message sent to bacteria will depend on the pattern of light. The community should be able to interpret five messages and tell it did it right when expressing a reporter gene. As there will only be two lights, five patterns of them will be used. The five fluorescent proteins available in the registry (GFP,YFP,RFP,CFP,BFP) fit perfectly to this purpose. The next figure illustrates the five patterns of light that will result in the five different messages sent, each of them represented by the expression of a fluorescent protein.

Figure 1. The code. Short pulses of a single light will mean message one, while a long continuous pulse will mean a second message. That gives us two messages controlled by each light, summing up to four results. The fifth message will be sent with both lights present at the same time.

Constructing the necessary genetic circuitry inside one single cell may be possible but probably much harder to achieve. That being so, we decided to construct the genetic circuit divided in blocks on separate cells that overall interpret the code. We consider this an advantageous approach since compartmentalizing the circuit lowers the construction size and metabolic charge per cell.

There will be three kinds of cells with different genotypes, although initially all share the same E. coli strain. Two of them will have similar interpretation mechanisms, which will allow each one to take a single light as input and decide whether to express the first or the second reporter gene included in its genotype (decision that will depend on the code). The third kind of cell will be the one taking the input from both lights to express the last protein. Until now the community managed to control the expression of five fluorescent proteins, however we said each of them should be controlled independently. This is accomplished with cell to cell communication through quorum sensing. The following figure illustrates the way the cells within the community work together:

Figure 2. The community. Cells one and two control each the expression of two different fluorescent proteins. Cell three controls the expression of the fifth protein. Independent expression of each of the reporter genes is achieved through quorum sensing. Cells one and two have the capability to send and receive a different QS molecule each (QS1 and QS2 respectively), while cell three is only a receiver. When cell one or two receive an activating message, the production of a QS molecule is activated as well. These molecules will then diffuse through the medium and reach the rest of the cells. The effect of quorum sensing will depend on the receiver. QS2 molecules, when reaching cell one, will unleash the expression of a repressor that will block the production of any of cell's one reporter genes. QS1 molecules will have the same effect on cell two. On the other hand, cell three will be activated only when both QS molecules are present and therefore cells one and two are off.

Here we show an animated explanation for better understanding: