Plastic degrading enzymes PhD project
Note: This project outline should be used as a starting point when writing the proposal on the dissertation project (max. 5 pages). Make sure to answer the questions in red font in the proposal.
“Discovery, characterisation and optimisation of plastic-degrading enzymes”
Plastic pollution has emerged as a pressing environmental issue in Austria, Europe and around the globe. Over 460 million metric tons (Mt) of plastic are currently produced worldwide per year, resulting in large amounts of plastic waste. Globally, recycling rates are low and of the 8,300 Mt of plastic produced until 2015, only about 600 Mt (9%) have been recycled, and just 10% of these 600 Mt have been recycled more than once. Among the main reason for the low recycling rates is the lack of suitable recycling approaches. However, a promising solution to fundamentally change the recycling process and to increase recycling efficiencies is now being offered by biorecycling (Peng et al. 2023). This emerging research field investigates the natural arsenal of microbial enzymes and explores their potential to break down synthetic plastic polymers.
The overall goal of the project is to characterise and optimise promising enzyme candidates for the degradation of Polyethylene terephthalate (PET), polystyrene, and polyethylene. The specific aims, objectives and challenges are:
Aim 1 – In silico enzyme characterisation
Objectives: Use our recently compiled sequence data catalogue of potential PET, polystyrene, and polyethylene degrading enzymes to find the most promising enzyme candidates. Propose computational methods for structural analysis, functional prediction, and mutagenesis studies, etc.
Challenges: Which challenges could you encounter, and how would you overcome them?
Aim 2 – In silico enzyme optimisation
Objective: Learn how to use machine learning to further improve enzymes candidates recovered in aim 1. Propose a conceptual workflow, the use of specific computational methods and software tools, such as Rosetta (https://www.rosettacommons.org/software), to produce improved enzyme designs.
Challenges: Which challenges could you come up in the enzyme optimisation process, and how would you overcome them?
Aim 3 – Heterologous expression and functional performance of optimised enzymes
Objective: Establish an enzyme expression platform to efficiently express and recover bacterial enzymes, and develop an assay to assess enzyme activities on plastic substrates. The latter could include measuring the release of specific breakdown products. Propose a workflow to achieve these objectives and include specific methods, such as colorimetric and fluorometric enzyme activity assays.
Challenges: Which challenges could arise in the protein expression and protein assay approach, and how would you overcome them?
Aim 4: Can you think of a 4th aim that could be added to this project?
Objectives: Which objectives should this aim have?
What potential applications in biotechnology could result from this project?
Peng, Yi, Apoorva Prabhu, Chris Rinke, Yi Peng, Apoorva Prabhu, and Chris Rinke. 2023. ‘Facing Our Plastic Waste Crisis: Biorecycling as a Promising Solution’. Microbiology Australia 44 (1): 52–56. https://doi.org/10.1071/MA23013.