A computer is any device that uses logic to solve a problem. Most modern computers are electronic and they solve problems using a system known as Boolean algebra based on two values, known as TRUE or FALSE or the binary digits 1 and 0. A Boolean logic gate takes one or two inputs - say 0 and 1, or 1 and 1, or just 0 - and converts them into a single output. For example:
- An AND gate has an output of 0 unless both inputs are 1.
- An OR gate outputs 1 as long as either (or both) of the inputs is 1.
- A NOT gate takes a single input and inverts it, so 0 becomes 1; 1 becomes 0.
Think of these gates like black boxes: inputs in, outputs out. In the case of electronics, the black boxes are electrical components like transistors and the inputs are voltages - for example, high voltage is 1 and low voltage is 0. But no matter what the black-box logic gates are, we can build circuits containing several logic gates to perform arbitrarily complex functions. This is essentially the basis of modern computers.
It turns out that logic gates can be built using DNA instead. Inducible promoters, which either activate or repress expression of a gene depending on presence of a transcription factor, are readily available as biological parts (BioBricks). The genes regulated by these promoters are the logical outputs.
Using standard genetic parts, we can build as many complicated logical gates as we like. Image two genes controlled by separate activate promoters, one activated by transcription factor A and the other activated by transcription factor B. But both these genes express transcription factors C and D, and a third gene is controlled by an activating promoter which needs both C and D to be switched on. Then the third gene will only be expressed if both A and B are present. We have designed an AND gate.
What can genetic circuits do?
Other groups have combined multiple logic gates to create even more complex biological circuits. In 2000, Elowitz et al. constructed a synthetic biological circuit called the repressilator. The name comes from the nature of the circuit, an oscillating system produced by the interaction of three repressive transcription factors. The circuit made use of three transcription factors called λ cI, LacI and TetR. By inserting specific promoter regions upstream of the genes encoding these proteins in E. coli, the researchers built a system in which λ cI repressed the expression of LacI, which repressed the expression of TetR, which in turn repressed the expression of λ cI, as shown above.
This leads to the oscillating expression of all three of these transcription factors in a sort of ongoing ‘rock-paper-scissors’ system. The expression of TetR was also linked to the expression of the protein GFP. GFP – green fluorescent protein – is a protein which fluoresces under specific wavelengths of light. This enables it to act as a reporter of expression and lets us see whether the system is behaving as simulations would predict it to.
The future of biological circuits
In the past decade, gene circuits have been significantly improved, making them:
- more robust to internal changes (such as the presence of other circuits or a change in metabolic load) and to external changes (such as temperature)
- more versatile in a variety of different host organisms (such as E. coli and Mycoplasma)
- more modular so that parts are more likely to keep their proper function when swapped between circuits
The applications of gene circuits have been very broad:
- Biosynthesis. Metabolic pathways can be modelled in computer simulations and then redesigned or modified using genetic circuits. For example, Jay Keasling redesigned existing biosynthetic circuits in yeast to make the anti-malarial drug artemisinin.
- Industrial control. Microbes used in diverse industrial processes can be engineered with genetic circuits to help them detect conditions and respond appropriately. For example, brewing yeast could contain a quorum sensing circuit so that they stop dividing when the population reaches a certain size.
- Therapy and drug delivery. Microbes can be engineered to find a target tissue within an organism (such as a tumour in the human body) and release drugs at the right time.
Translation between Genetic and Electric Logic Circuits
- E. Coli sees light
- Design Software and Circuit Database (iGem Team - Software Download)
- Cameron, E., Bashor, C., Collins, J., 2014. A brief history of synthetic biology. Nat Rev Microbiol 12, 381–390.
- Gardner, T., Cantor, C., Collins, J., 2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342.
- Elowitz, M., Leibler, S., 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338.