Synthetic gene circuits – The Transcriptome

This blog was started as a collaboration between two iGEM teams (see post “What is iGEM”) with the goal of making biology as accessible and understandable as possible. Building on last week’s post, today we are going to introduce a relatively essential part of synthetic biology: synthetic gene circuits.

What is a synthetic gene circuit?

To understand what a synthetic gene circuit is, first we need to explore what a “natural” gene circuit is! According to Science Direct, a gene circuit “is an assembly of biological parts encoding RNA (the molecule that allows for the creation of proteins from DNA) or protein (molecules that are the workers of the cell) that enables individual cells to respond and interact with each other to perform some logical functions” [1]. A logical function tests whether a situation is true or false and emits a response according to the answer it gets.

When it comes to synthetic gene circuits, the only difference is that scientists have designed a circuit using the same biological building blocks (genes, RNA, proteins) to create a circuit that performs logical functions such as those found in electronic circuits.

Multiple different kinds of synthetic genetic circuits already exist and are being tested! They all have a different way of working and can be used for many different application. These include oscillators (such as the repressilator, which we use in our iGEM project) and bi-stable switches (like the toggle-switch), the most well-known and researched examples.

Figure 1: Examples of established synthetic circuits and how they behave. Taken from A Brief History of Synthetic Biology [2]

Why are they interesting?

So why are synthetic biologists so fascinated with the recreation of something that already exists, and works pretty well in nature? Well, as Richard Feynman once said, “what I cannot create, I do not understand”. Biology as a field has advanced a lot over the past decades, but there’s a lot that we still don’t know about networks between cells, and within cells, at a very basic molecular level. The idea of trying to create these networks from scratch is just another way of trying to understand why living organisms act and react the way that they do, as well as trying to find out the mechanisms they use. Once we figure out the details in these networks and pathways, we can target them for various reasons, such as therapies for various diseases [3 ].

A review published in 2018 covers precisely all the things we can use synthetic circuits for, notably in the diagnosis, prevention and elimination of various diseases [4]. The authors also mention how the circuits were created and establish an extensive list of diseases that could be tackled with this technology, including:

Infections
- By V. cholerae, the bacteria leading to cholera disease
- By HIV
- By Influenza viruses (such as the annual flu virus)
Parkinson’s disease
Epilepsy
Allergies
Immune disorders
Type 1 and 2 diabetes
Cancer

The idea is that we can not only diagnose patients using synthetic gene circuits, but we could also help cure them by using these as drug-delivery mechanisms. The end goal is to have a less invasive and more comfortable way of treating various diseases using these genetic circuits.

At a more fundamental level, the creation of these circuits allows us to understand how cells react to certain stimuli and why they react that way. They can also help us understand interactions such as the circadian cycle, the natural sleep-wake cycle found in all organisms. This cycle is attuned to the 24-hour days on Earth and is central to multiple processes, such as healing, brain activity, hormone production and cellular regeneration [5].

What are the dangers?

The dangers of using these circuits come down to the dangers of synthetic biology in general. At its core, this domain is only a tool and it really depends on the imagined applications if it can be more of a positive force than a negative one. The main dangers that concern both those in the field and those outside of it is the potential to mix-and-match different organisms, as well as the growing accessibility to biological tools as the techniques required for different experiments get cheaper and cheaper. Even though we all strive towards making science as accessible as possible, there is a real danger that comes with “DIY (do it yourself) biology” when living organisms are manipulated without adequate training or care (both for the experimenter and those around them) [6].

It can also sound troubling to think that synthetic biologists are messing about with living organisms like bacteria, and these kinds of manipulations are subjected to many kinds of regulations. However, there is a tremendous amount of research being done into cell-free circuits. These circuits, as their name suggests, can run independently of a “host cell”, so the dangers associated with using cells are removed [7] [8]. Whilst they have their own flaws and advantages, it’s only as research into them progresses that we will be able to know when and where to use which kind of circuit.

How and why are we using this for iGEM?

I don’t want to spoil a future post where we’ll go more into detail about our iGEM project at the University of Lausanne, but I’d like to give a brief overview of our project to explain why we wanted to introduce synthetic circuits. The central part of our project is actually a synthetic circuit: it’s the one called the repressilator that was detailed earlier on in the post. In short, we’ll be using this circuit to deliver an anti-cancer drug straight to tumours in the colon (in the case of colorectal cancer) at precise intervals. We wanted to do this as recent studies suggest that the application of anti-cancer drugs at a specific time of day can increase their toxicity to the malignant cells whilst decreasing the effects on the healthy cells, which leads to a decrease in side-effects felt by the patient [9] [10]. This however is the topic of a whole other post! In the meantime, you can check out our wiki page for more information.

Conclusion

Hopefully this post has given you, dear reader, a clear enough overview of one of the most prominent parts of synthetic biology, as well as explaining briefly why there is so much interest in them and why they can be useful and important!

References

Ilinca Dragan

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