The growing global problem of antibiotic resistance was the challenge taken on by the Michigan Synthetic Biology Team (MSBT) over the last year for an international competition called International Genetically Engineered Machine (iGEM) .
A student-led club in the biological sciences, the MSBT draws on talents of students from all across campus. They work together to design a novel synthetic organism and carry out lab experiments to construct it, and also throughout the year address the social and ethical issues around the creation and use of synthetic organisms.
The World Health Organization has called the antibiotic resistance crisis “one of the top 10 global public health threats facing humanity.” The CDC reports that in the U.S., more than 2.8 million antimicrobial-resistant infections occur each year and 35,000 people die as a result.
AMPs are key to the team's approach
To protect our communities from such diseases, the MSBT embraced a new approach to fighting these pathogens. MSBT searched for ways to turn the naturally occurring defenses that organisms use to fend off bacterial infections—antimicrobial peptides (AMPs)—into an alternative to penicillin and such drugs.“AMPs are short, naturally occurring proteins derived from various organisms, including bacteria, viruses, snakes, chickens, cattle, moths, and so many more. Organisms naturally produce these peptides in response to the presence of bacteria in their environments as a defense mechanism against infection,” explained the team.
The usual approach to mass producing quantities of peptides, such as insulin, is to insert the genetic code for that protein into bacteria, which then create the protein. But because AMPS are lethal to the bacteria that produce them, the team needed to find a way to protect the AMPs while still producing enough product to be usual.
The team outlined their approach: “Our team used encapsulins to address the challenge of synthesizing a toxic product in the bacteria it naturally destructs. Encapsulins are protein compartments used in nature to sequester toxic reactions and materials within cells.”
“Research at the University of Michigan has demonstrated that the use of a targeting peptide can customize encapsulin cargo by signaling to the encapsulin what it should surround. We used this targeting peptide to selectively sequester antimicrobial peptides within encapsulins to prevent their toxicity in host E. coli, allowing protein based antibiotics to be produced in the same way as insulin and other protein therapeutics.”
The MSBT project built on existing research in numerous ways, including:
- Using an encapsulin-targeting peptide system engineered to disassemble under mildly acidic conditions
- Increasing ease-of-use through an easily separable targeting-peptide-based encapsulin-AMP attachment system
- Working toward stringing AMPs together on the same targeting peptide for maximized yields
Work began in November 2021 when the executive board settled on the project for the October 2022 competition. The MSBT added new members in January, and then wet lab work commenced in April. The work culminated with a trip to Paris, France for the iGEM competition, where teams from all over the world come to showcase their work. The Michigan team took home a gold medal for exemplary work.
Team members learned both hard and soft skills through the project—experience working in the lab, fundraising and managing finances, doing community outreach, helping with organization and leadership, and studying and communicating synthetic biology research. The team is a platform for budding scientists, communicators, and fascinated biologists to be introduced into the field and to the academic research process, according to the club’s website.
This year’s team of 30 students included majors in biomedical engineering; biochemistry; cellular and molecular biomedical science; mathematical biology; and molecular, cellular and developmental biology.
We asked the MSBT about their iGEM experience:
How was Paris?
It was amazing! At the conference we were able to meet teams from all over the world, and we not only talked about our projects but also about our experiences attending university in different countries. We met teams from Korea, Greece, Mexico, and so many other places and it was such a unique experience to have so many perspectives present in one place. We were also able to go out to dinner and sightsee with some of our new friends as well. We were super excited to get to see the city as well as attend the conference.
How was your project and trip funded?
We fundraised through university departments and external sources. Beckman Coulter, the University of Michigan departments of Biomedical Engineering; Molecular, Cellular, and Developmental Biology; and Chemistry, as well as the Program in Biology, student philanthropy, U-M Central Student Government, and U-M Engineering Student Government all generously contributed to our project. Giving Blueday is also a big day of fundraising for us.
Fundraising does tend to be difficult for us because the competition fees and international travel are very expensive, so we were very grateful to have the money to send several students from our team.
What was the most exciting part of the project?
The most exciting part of our project was when our DNA sequencing results showed that we had successfully used Gibson assembly to clone our plasmid constructs into E. coli. We really struggled with cloning last year and it took us multiple attempts at transformation and sequencing this year to successfully work. This was a huge step in the right direction because it meant that we could move forward with all of our other experiments and that we would have wet lab results to present at the competition.
What was the most frustrating?
The most frustrating part of our project was running growth assays to test the effects of adding our encapsulin construct into bacteria. The encapsulin is very large and adds significant metabolic burden to the bacteria expressing it. In some of our initial experiments, it appeared as though the bacteria with the AMP and encapsulin are growing worse than the one with the AMP alone, which is the opposite of the results we were expecting to see, as we were expecting the encapsulin to mitigate AMP toxicity and improve bacterial growth. After a couple of different interactions of this experiment, we were eventually able to optimize the conditions and eliminate the variability by using a plate reader for the assay to obtain our expected results. The assay is quite a long experiment though, so the initial failed experiments were definitely frustrating!
Rebuilding the team Additionally, the iGEM team at the University of Michigan has been present for many years, but when almost the entire team graduated during COVID-19 [restrictions on in-person activities], we lost the vast majority of our institutional knowledge and the team had to rebuild from scratch.
We have made great progress on our project, were very diligent in devising a well-thought out research plan, and are still working daily to produce significant scientific results with all new team members, for some of whom this is their first lab experience. This was a big rebuilding year for our team, which came with many challenges, however we are very proud of the accomplishments that came out of all of our hard work!
How has it shaped your future plans for education or career?
Being a part of the Michigan Synthetic Biology Team has been hands down one of our favorite parts of being in college. Developing a research project—especially as a student team lacking the funding and equipment of a professional lab, can be challenging but makes our successes even more rewarding. We were able to develop strong leadership skills through this experience which will be valuable in our careers as physicians and PIs.
Attending iGEM has opened our eyes to many areas of research that we may not have otherwise come across, and our team is not only using this as inspiration for next year but also as motivation for our future research careers. We were able to make many connections with people around the world as well, which will be helpful in our future careers.
You can learn more about the Michigan Synthetic Biology Team, their AMPLIFY project, and view their video explaining it, on the website they created for iGEM.
Find it at: https://2022.igem.wiki/michigan/index.html