Quick Chat with David Stuart
By Emma Lindsay - 26th MAY 2024
Dr. David Stuart is a Professor and Graduate Coordinator at the University of Alberta in the Department of Biochemistry. His research focuses on the application of synthetic biology on the metabolic engineering of yeast and bacteria to produce biofuels.
Can you tell me about yourself and your research?
I did my PhD at the University of Alberta, and I did Postdoctoral work at The Scripps Research Institute, where I focused mostly on cell cycle control and yeast as a model. My PhD work I would say started my synthetic biology interest. I was building synthetic chromosomes for a pox virus to analyze its DNA replication and how its chromosomes were prepared for packaging. I got training in yeast genetics at Scripps Research Institute with Curt Wittenberg and Steve Reeds labs. I started my position here at University of Alberta initially working on cell cycle control and meiosis. Around 2010 there was a small group here that was interested in engineering yeast to generate biofuels. Not ethanol, but something more nonconventional. We got into the butanol space and started constructing strains to synthesize butanol and isobutanol. That required multi gene pseudo-operons to be constructed and introduced into yeast to synthesize the 4-carbon alcohol butanol. At that point, I got most interested in manipulating biology to create and solve problems and doing more applied research. A little bit less of the basic science side and more on the applied science side.
Was there anything specific that inspired you to go into biofuels?
I had some push from my children who recognized and had concern about environmental problems. Producing and burning petroleum liquid transport fuel at the scale that we currently do has a significant impact on our environment. I got intrigued with the potential benefits of a circular system that could use rapidly renewable carbohydrate feed-stock to be converted by yeast or bacteria into a viable transport fuel like butanol or isobutanol. Building a new metabolic pathway into cells and coaxing them to make a product that is not natural to them is a challenging but fun puzzle. Increasing the uptake of biofuels with a lower impact on the environment than petroleum products is not going to be the whole answer to our challenges, but it can be part of the answer. Another piece of this that I like is the idea that biofuel production can be a distributive thing rather than having all your fuel coming from one refinery. We can take the approach of having lots of little distributive hubs that can make whatever you want on smaller scales, but sufficient for the area. It’s economically beneficial and you don't have to move your feedstock from one end of the world to the other end to make something.
We progressed from engineering cells to produce short chain alcohols like butanol to making longer chain fatty alcohols. These are not used as fuel but are widely used in everything from food to shampoo, soaps, hair conditioners and cleaning agents. Most of the global supply of these chemicals is either synthesized from ethylene, a petroleum by product or from palm oil. Although palm oil is a renewable source expanding palm oil plantations have resulted in extensive deforestation and loss of biodiversity. It got me thinking that maybe we can engineer yeast to produce these products on demand in fermenters rather than displacing rain forest. Synthesizing the product with engineered yeast close to the end user industries also reduces the carbon footprint from shipping the raw material or products between continents.
What are some obstacles you’ve had to face in your Synbio career?
Technical issues, for some things there seems to be no way to get them work as well as you would like them to. Things like titres of final products, for example the fatty alcohols. We can engineer yeast to make and secrete them, but there are limits to productivity. So those are technical things that can be very difficult. Sometimes finding funding for projects is difficult too.
Do you have any sort of memorable achievements or experiences in your career so far?
Going back to the fatty alcohols project, I think the first time that we saw that the yeast we were working with, not only made the product, but secreted the product. One of the Postdocs, Bonnie McNeil, brought me this tube with all this gooey stuff floating on the top. The cells had made that, secreted it out, and it floated up to the top. And wow is that ever cool. So that was that was quite memorable, that was a big one for me.
What does a typical day look like for you?
Most days I swim with a master swim team in the morning, I feed my rabbits, and go to the lab. In the Biochemistry department at University of Alberta I wear several hats. My laboratory has three graduate students, four undergraduate students, and we have an intern from Peru here right now. I supervise people in the lab, and I occasionally do an experiment myself. Not that often anymore. My office is in the laboratory space, so I'm with the people in the lab a lot of the time. I'm also the graduate program director, so I deal with everything around graduate students and their programs, making sure people complete their theses and stuff like that. At different times of the of the year I have significant teaching loads. Right now, I teach a course on proteomics in the morning, and then a discussion group in the afternoon on molecular biology. I teach some classes, work with people in the lab and collaborators, have a few meetings around the graduate program, and that’s my day.
Are there any synthetic biology techniques or applications you’re excited about?
I'm very excited about the improved effectiveness and accuracy of Cas9-based prime editors for genome engineering. This just keeps getting better and has very wide-ranging potential. As far as applications, I think engineered probiotics are going to become a big thing. These have potential to identify and kill pathogens so can act as antimicrobials. They can also be used to secrete beneficial small molecules and metabolites or metabolize toxic or otherwise harmful metabolites and small molecules. There is potential for them to act as therapeutics for delivering cancer treatments or treat inborn errors of metabolism. I like the idea that these can act as little factories that can be set up to operate inside of us to deliver therapeutic molecules at the site of the infection or pathology. There’s a lot of possibilities that might not be immediately obvious, the lung microbiome for example. We could have engineered microbial cells that help support surfactants in the lung space or that degrade biofilms created by pathogens. In the colon, the bladder or on the skin engineered bacteria could specifically detect and kill pathogens, degrade toxic molecules or secrete beneficial ones. These could treat diseases as well as influence health or even your psychological state. I think that's a place that there's going to have a lot of impact. I'm also pretty excited about advances in cellular agriculture, although that is still pretty expensive as an application, and the potential to produce food protein and even milk with fungi or other microbial cells. Fungal protein is a lot easier in some respects and cheaper. It doesn't require a lot of the infrastructure that's necessary for lab grown meat. That could influence problems like food security, for example.
Where do you see your research going in the next five years?
I'm still working on bio-industrial problems related to production of fatty alcohols and lipid-based compounds to some extent, but it's moved a little bit more to the biomedical sector. My own research is heading more towards the engineered probiotics that can act as biosensors and provide specific benefits to humans and agricultural animals. I am currently very interested in appropriating enzymes from bacteriophages and using them to weaponize probiotic yeasts so that they can specifically identify and kill infectious pathogens. Related to this, I am investigating new ways to use nanobodies as antimicrobial agents.
What advice do you have for students interested in pursuing a career in synthetic biology?
I really like the broad definition of synthetic biology as engineering cells to make useful things or do cool stuff. There are a growing number of opportunities both academic and industrial for people who want to make this a career. This is a field that thrives on creativity, interdisciplinarity, and collaborative skills so those are characteristics that you should develop and nurture. Pay attention to the world around you and you will recognize that there are problems big and small, local and global that can be tackled. Synthetic biology has a big toolbox, it is more than just microbiology and molecular biology at the lab bench. Skills in software engineering, process engineering, bioinformatics, automation, business development, and more are involved so you can come to this from many different disciplines. A great place to get started is iGEM. I supervise an iGEM team here at the University of Alberta, it's a great place to get started because there's a lot of resources, and the competition aspect is highly motivating to get people thinking about problems that can be solved by engineering biology. In these groups, you can also see how an interdisciplinary team can be assembled with people who know how to manipulate DNA and microbial organisms, and integrate that with process engineering, bioinformatics, public outreach, even business development. The biggest thing is just having an open mind, being creative and being able to recognize needs. There are problems that we can solve, and it's not hard to find places to get involved.
Dr. David Stuart’s research spanning from yeast genetics and cell cycle control to biofuel production highlights the importance of synthetic biology applications in developing environmental crisis solutions. His work in addressing health and environmental challenges also inspires future scientists to pursue innovative solutions.