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Cells with in-built logic circuits can act like computers
Different biological elements can be viewed as components of a circuit, in the same way that amplifiers, resistors and transistors are components of electrical circuits. Combining elements in different ways alters the output of the system, allowing specific goals to be achieved. At the simplest level for example, ‘reporters’ can be input into biological systems to test whether specific genes are being expressed. At more complex levels, biological circuits can be ‘programmed’ to be ‘on’ only under specific conditions, such as in response to light. This would be the biological equivalent of a light-sensitive resistor in an electrical circuit. Biological circuits can also be constructed to change their output over time.

Logic Gates

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.

Logic gates such as OR (top) and AND (bottom) can be encoded using genetic circuits. Next to each logic gate is its circuit symbol and a 'truth table' showing the possible inputs and outputs. © 2011 Wikipedia, MGJ
For example, the lac repressor protein is a negative transcription factor which binds to the lac promoter and switches off transcription of the lac operon. We can call the repressor the input: presence of repressor is equivalent to 1 and absence is equivalent to 0. Likewise, we can call transcription of the gene the output: successful transcription is 1 and minimal transcription is 0. Then an input of 1 (high repressor concentration) leads to repression and an output of zero (minimal transcription). By the same logic, an input of 0 leads to an output of 1. This is a genetic NOT gate!

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?

Inputs controlling GFP expression in the Toggle Switch
One of the earliest proofs of concept for genetic circuits was the toggle switch, designed and built in E. coli by James Collins at Boston University in 2000. The toggle switch contains two genes, each of which represses the promoter for the other. This is equivalent to placing two NOT gates in a loop. When one gene is highly expressed, the other is switched off; and vice-versa. The system is described as bistable because it always settles into one of two states: gene 1 on and gene 2 off, or gene 1 off and gene 2 on. Toggling the system between these two states requires chemical input to remove the product of the active gene, allowing the other gene to become active so the system can switch. 

The Repressilator


The repressilator circuit

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 cILacI 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.

A simulation showing how levels of the three repressors oscillate over time © 2012 Wikimedia - Belbojacopo

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

The equivalent of electronic logic circuits to the genetic process in cells.

  • 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.

 

 

 

What do you think?

4 Comments

  1. My feeling is that "Biological MIcroprocessors" should be in Applications of SynBio.

    Not sure that this belongs in DNA engineering....

  2. Good point, which actually reveals a deeper discussion about the structure of the wiki. For me, applications are the actual outcomes of SynBio that become marketed. I guess, it would rather fit into TechnologiesBioware, since that should become the place where you could categorize and structure technologies, that are used by the guys who make the applications. However, it's Engineering Biology at the same time. Should we focus Engineering Biology on the general concepts and put the technologies in the separate technology section?

    1. I think that circuit design is fundamental to synbio, so I would leave the article in '3. Engineering DNA'. Perhaps the parent article on biological microprocessors belongs more in Applications, so we could un-nest the circuits article and move the parent to Applications. We could copy/move the second half of the gene circuits article into applications and I can describe these in a bit more detail - but the toggle switch and repressilator are more proofs of concept than direct applications.

About the authors

View full profile Jérôme Lutz from Berlin & Munich, Germany

I like to share the great things I discover daily while researching and working in the field of Synthetic Biology.

When I talk to people about it, they often refer to Science Fiction. However, when I send them links to this wiki and they read through those pages, they start understanding that this is real and it's happening right now.

View full profile Jake Curtis from London

I am a student at Cambridge University who has just finished a BA in Natural Sciences, focusing on Genetics in my third year. I am now studying for an MSc in Systems Biology.

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