The Project

What we did

Our project was twofold; the incorporation of a new signalling mechanism in order to create more complicated systems, and to investigate the costs and considerations of designing a system.

Our signalling system was invented by Rafel Silva-Rocha and Victor de Lorenzo. Based on the usage of intermediary metabolites of metabolic pathways as a source for intercellular signalling, the system was aptly dubbed Metabolic Wiring. RewirED aimed to expand the number of designed and characterized Metabolic Wires and add them to the iGEM registry to allow complex, intercommunicating microbial consortia to be possible.

However, we knew that communication was not enough to allow the creation of such systems and wished to create a foundation for designing systems based on explorations into our work in the lab and with other iGEM teams. The topic we focussed on was the division of labour, both mental and physical, and the varying costs and considerations that would be required when designing a system based on achieving that. We came up with 5 themes found within a system, which we used as a design motif; Specialization, Communication, Supervision, Hierarchy, and Robustness.

For our three way system we considered all five themes to varying degrees during its design. The Specialization of each cell in the system came from its signalling method. Communication had been considered in the Metabolic Wire that had been used. Supervision of the system was improved with an enhanced characterization of degrons. Hierarchy had been made horizontal via allowing all strains to control each others populations due to the simplicity of the system. Robustness was not incorporated due to lacking time and sufficient metabolic wires.

The Sub-projects

PaperClip

This year the team was lucky enough to be working alongside Dr. Maryia Trubitsyna, a Research Fellow here at Edinburgh working in the same lab as us. As well as acting as a constant supply of lab expertise and tips, she also allowed us to try out her new method of DNA part assembly – PaperClip.

PaperClip assembly doesn’t require restriction enzymes, and allows parts to be assembled in any order using short linker sequences called ‘clips.’ Specially designed PaperClip primers are used to make ‘half-clips’ for any given part, an upstream and downstream one, and the upstream half-clip from one part can be ligated to the downstream half-clip of another to give a linking full-clip. The advantages should be obvious here – once half-clips are made for a part, it can be assembled as part of any assembly, next to any other part.

Once we picked up this technique, we were able to carry out several successful assemblies, which were transformed with equal success – PaperClip served us well. As it turned out though, we never really did assemblies with more than three parts and so we never got to fully appreciate the full power of PaperClip (its true strength lies in large assemblies). Nevertheless, it was a valuable experience which suited our needs just fine, and we are grateful to Dr. Trubitsyna for all her help and (considerable) patience.