Synthetic biology is commonly defined as the application of engineering design principles to biology in order to develop valuable methods and tools that benefit society and the world.¹ Teams pursuing such endeavours engage in the systematic forward-engineering of biological systems to effectively design systems that take into consideration physical, commercial and technological feasibility.

The UNSW iGEM team strived to follow suit, utilising literature and advice to appropriately follow an engineering design procedure.² Given that design is the first stage of the “Design-Build-Test” paradigm it was important that we considered all aspects of the system to avoid running into problems with building and testing. We started this process by researching and defining the need in the market for our tool, to ensure that our design was purpose-orientated. We then developed a list of requirements that our system must adhere to, a process that involved abstracting away the layers of the identified problem. Following this we went through design iterations, learning from modelling data and experimental issues to arrive upon our finalised scaffold system design.

Defining a Need

In industry and research there has been a growing interest in the construction of novel metabolic pathways, as alternatives to synthetic chemistry, for the production of cheap and renewable products.³ Yet, as these biocatalytic pathways gain complexity, the ability to gain viable productivity is diminished due to undesirable side reactions and low turnover rates.

One way that this is being addressed is through the development of scaffolds that will co-localise enzymes from such a pathway. By spatially organising enzymes to generate high local concentrations, this strategy aims to enhance metabolic flux and reduce the diversion of pathway intermediates into competing pathways that lead to undesirable side reactions. Ultimately, the use of scaffolds to create enzyme agglomerates will allow for the acceleration of reaction intermediate processing leading to increases in product titre.

This approach mimics enzyme clustering that is frequently observed in nature.⁴ However, previous attempts to replicate this natural enzyme organisation have fallen short, with no commercially viable modular tool available to facilitate enzyme clustering for the production of valuable metabolites. As such, the UNSW iGEM team decided to reflect on these past solutions and compile a list of requirements that would enable us to develop a versatile, commercially viable tool that could be used in laboratories and industry worldwide.