iGEM UChicago 2020 is tackling plastic pollution with synthetic biology
Inspired by the problem of plastic pollution, a group of students at the University of Chicago recently joined the iGEM program on Just One Giant Lab (JOGL). The iGEM UChicago 2020 team is developing a computational method to help save the planet from plastic waste.
PET is one of the most common plastics in the world and can linger in the environment for years. For the International Genetically Engineered Machine (iGEM) competition this year, the students decided to create a computational method to optimize PET degradation by engineered E. coli. To learn more about their project, we interviewed the team members by email:
How did your project get started? How did you become interested in this topic?
Jessica Oros: Our goal was to identify a prevalent issue that does not yet have an efficient solution. While researching plastic recycling, we realized that a majority of plastic products are ending up in landfills, which leads to breakdown into microplastics that contaminate water sources and devastating biomagnification. Focusing on polyethylene terephthalate (PET), we realized Ideonalla sakaiensis possesses a naturally occurring enzyme, PETase, that breaks down this plastic, and, using its byproducts, we assembled a pathway that leads to the production of catechol, used in pharmaceuticals but inefficiently produced.
Why is your research important? What are the possible real-world applications?
Avery Rosado: Our software tool offers a practical approach to refining the “behaviors” of systems of biosynthesis, biodegradation, and biocatalysis; these systems are essential to efforts ranging from sustainable production to environmental cleanup. Once refined via our novel algorithm, applicable systems are more likely to be viewed as viable on an industrial scale. Through our work on ‘Optizyme’, the name of our project and software tool, we aim to contribute to ongoing progress in making synthetic biology highly accessible and sought after by creating a tool that is capable of handling a diverse set of applications and can be easily integrated into scientists’ wet lab work.
Before work began on Optizyme, our team planned to develop a novel enzyme degradation pathway for converting PET microplastics to catechol compounds in a cell-free environment. When we are able to return to a wet lab setting and create our cell-free system, our usage of Optizyme to optimize the behavior (the turnover rate) of this pathway will ensure the efficient conversion of harmful waste into valuable products.
What is the coolest thing about your project?
Avery Rosado: Being a part of the iGEM community means looking for innovative ways to make positive impacts in the real world using synthetic biology. Often, diverse members of the iGEM community are drawn to similar issues, giving teams from around the world the opportunity to build upon and refine each other’s research. I think that the coolest thing about our project lies in its capacity for benefitting future iGEM efforts. With numerous teams working on systems of bioremediation, or in biosynthetic cell-free mediums, our tool has the capacity to positively contribute to future iGEM projects and to improve upon past projects.
What kinds of challenges are you facing?
Patrick Sun: Overall, I believe that our team was able to take the transition into a dry lab environment in stride. Still, Optizyme is intended to be used in conjunction with wet lab work, presenting a challenge to our attempts at putting its integrative capacities to the test during the quarantine. Additionally, our pathway for PET degradation is intended for development in a cell-free system, but a number of the teams that are working in similar areas of biosynthesis are working in-vitro. This poses a challenge to us, as the parameters that guide the outcomes of our algorithm are intended to be defined within a cell-free system, and certain assumptions must be made when modeling in-vitro systems in order to better align system behavior with the steady state assumption.
As we work to develop an accessible, appealing optimization tool based on rigorous mathematical modeling, we have been challenged to try to distill quantitative modeling down to its biological concepts. We aim for researchers to not have to write their own differential equations, for example.
What are your next steps? What do you want to achieve with your research?
Avery Rosado: Our work on Optizyme has been guided by our commitment to developing a highly accessible, useful tool. The package that our algorithm is available through will be readily available for anyone to download off of our team repository on Github; its design and layout maximize efficiency while providing the most straightforward possible structure for a beginner user who may not be well versed in coding in R or modeling enzyme kinetics. Moving forward, we intend to raise awareness of our project within target groups to ensure that our work is making positive contributions wherever possible. Our goal is for any biologist with applicable work to be able to easily model and optimize their system through Optizyme.
We have already begun and plan to continue raising awareness by meeting with researchers and industry professionals while developing our package as an open-source software, and while working to make Optizyme more intuitive and easier to use for end-users.
Additionally, because of our distance from campus over the spring and summer months, our work will extend into the summer of 2021, when we plan to produce our system — and put our tool to the test for our own purposes — in a wet-lab setting.
How can scientists harness synthetic biology to meet the 2030 UN Sustainable Development Goals?
Michelle Awh: To meet several of the 2030 UN Sustainable Development Goals, scientists ought to refer to the mechanisms by which nature solves its problems when creating novel solutions to some of the world’s biggest problems. The solutions to numerous SDGs, for example, can be designed by drawing inspiration from bacteria’s rapid rate of evolution in order to take steps to counter patterns in environmental contamination. Our own PET-degrading pathway is initiated by the enzyme PETase, which evolved within the vicinity of a PET recycling plant in Japan. Overall, scientists should make it their priority to discover, harness, and refine the preexistent, highly capable evolutionary mechanisms of model organisms when designing solutions to the world’s most pressing environmental issues.
What actions can other iGEM teams take this year in order to achieve some of the SDGs?
Patrick Sun: iGEM teams are well suited to address several SDGs by targeting pollutant compounds and using these compounds as inputs for a biological system to work toward environmental sustainability in an economically productive manner.
Note: learn more about how to join the iGEM program on JOGL, check out the video below.
