Spotlight on: Synthetic Biology
Synthetic biology has the power to revolutionise science. How is EI’s DNA Foundry going to help build life from its basic building blocks?
Twenty years ago, no-one had really heard of synthetic biology. Yet, since its foundations at the turn of the millennium, the field now promises to usher in a revolution in how we think about reconstructing the code of life.
Here, we interview Yaomin Cai of Nicola Patron’s DNA Foundry at Earlham Institute, on how he got into synthetic biology, how it can help us to tackle biological questions, and what the future has in store.
I was lucky enough to be doing my PhD while Dr. Yaomin Cai was working in the lab of Patrick Gallois at the University of Manchester. Yaomin helped me out on a lot of things, from qPCR to fluorescent tagging of proteins.
He has now joined Nicola Patron’s Synthetic Biology lab at Earlham Institute, where he will be helping to reconstruct life from its deconstructed biological building bricks.
So, Yaomin, what have you been up to since I left the University of Manchester in 2014, and what brought you to Earlham Institute?
I did my first-round postdoc at the University of Manchester which focused on plant programmed cell death. In my previous research, the lack of some techniques and methods, such as being able to quantitatively and precisely control genetic circuits, became the bottleneck preventing further progress.
So, in 2017, I moved to Earlham Institute to join the synthetic biology group led by Dr. Nicola Patron. Joining a synthetic biology group will deepen my insight on how to precisely control sophisticated genetic networks.
What interests you in synthetic biology?
Synthetic biology is an area where you can broaden your imagination. Many fancy tools, such as plant sensors, have been created based on the synthetic biology rationale. These are very interesting and useful for both industry and academia.
There are many definitions of synthetic biology, how would you describe the field?
This was also a question which I have been asked during my interview for this job. I wasn’t sure what was the best definition of synthetic biology. After several months of joining the synthetic biology group, I think synthetic biology is a field from decoding to designing.
We are gaining more and more knowledge about how an organism is established and we are now entering an era of designing novel biological machinery creatively; this is what I think synthetic biology is doing.
What will you be doing while you are at Earlham Institute?
My main project is to understand the rationale (e.g. features, architectures) behind plant constitutive promoters [turning genes on, all of the time].
Although several promoters from plant viruses and bacteria have been used to drive gene expression, we still lack the whole information for designing a novel constitutive promoter from scratch.
This will become a problem when people wants to design large scale sophisticated genetic networks, because repetitively using same promoter may result in inactivation due to promoter homology.
What is the difference between synthetic biology and genetic engineering?
Synthetic biology is a one step further from genetic engineering. Genetic engineering focused on modifying endogenous genes, while synthetic biology can bring a whole set of orthogonal genetic components into an organism, even create an organism de novo.
How will synthetic biology help us to tackle important biological questions?
Synthetic biology helps us to make novel, precisely controllable tools to generate important traits in an organism. For instance, we are now able to build sophisticated gene clusters and introduce them into bacteria and plants to produce pharmaceutical compounds.
What is your dream synthetic organism?
Something like a sea sheep (Costasiella kuroshimae).
It is an adorable species of sea slug which can incorporate chloroplasts after eating algae. If an organism can incorporate chloroplasts and living upon these chloroplasts, it may save much energy.
This is quite fun, because, during one of my biohacking workshops at WIRED: Next Generation, we challenged the kids to come up with their “dream” synthetic organism. One of the winning candidates was a slug-lettuce combination, which would provide food that feeds itself.
It just goes to show that kids are not too far off the mark when it comes to being creative with complex concepts. - Pete.
How small do you think we could slim down an animal, plant or fungal genome, while still being able to put it all back together again?
I am not sure, maybe as small as a virus genome?
How much of DNA, in your opinion, is junk? Is there any such thing as junk DNA?
This is a tricky question. As the research is progressing, more DNA fragments which were thought to be junk DNA are found to exhibit some extent of functionality. I would rather say DNA without known function than junk DNA.
After a workshop I gave in London about biohacking, one child suggested we should make a chicken-lizard-centipede. Is this technically possible?
I am not sure how possible it is now. But it may be in the future.
What are the limits of synthetic biology?
Maybe in evolution. Although synthetic biology can do many things, I am not sure whether synthetic biology can change anything on evolution (like the rate of evolution).
Where do you think the future of synthetic biology is heading? Is it in universities, or in the kitchens of amateur biologists?
Synthetic biology is trying to make it more standard and more accessible to public. So I tend to be open minded about where synthetic biology is heading.
It is very likely that when the tools and parts in synthetic biology are made available in a standard manner, people can assemble their own stuff in their garage (with health and safety approval), much like people developing personal computers.