Team:Edinburgh/Presentation

Presentation

Introduction

Edinburgh's 2011 iGEM project is all about synergy - the ability some enzymes have to work better when close together. In 2010, the Slovenian team found a way to arrange enzymes in the cytoplasm so as to achieve synergy. We wondered whether it would be possible to get extracellular enzymes close together.

Edinburgh's project is also about biorefineries, which are special types of refineries in which biomass, such as cellulose, is converted into useful products. Our project is a feasibility study into the creation of a biorefinery using cellulases arranged in a synergistic manner.

Modelling

The first question we asked is: what is this synergy phenomenon and how does it work?

Cellulose is a long chain of glucose sugars. It can be broken down by enzymes called "cellulases". Consider the following statements about cellulose degradation:

• One type of cellulase, exoglucanase, attacks the end of a chain, producing disaccharides called cellobiose.
• Another type, endoglucanase, cuts the chain in the middle.

We can immediately see that these two facts mean the enzymes work best together: the enzyme that cuts chains in the middle also produces new chain ends for the other enzyme to attack.

Now consider the following:

• Exoglucanase is inhibited by the presence of cellobiose.
• A third enzyme, β-glucosidase, cuts cellobiose into glucose.

Here then we have another case of enzymes working best together.

We constructed computer models to investigate the above phenomena.

C

[Play animation]

Our first model is an ad hoc model written in C. Here cellulose is placed on a two dimensional grid, and cellulases move over the grid. There are two simulations: in one, the enzymes move about freely. In the other, enzymes travel in triplets, each triplet containing one of each enzyme.

This model is very simplistic but does show that the synergy effect makes sense.

Kappa

A more sophisticated model uses the Kappa modelling language. FIXME

Biology

The fundamental biology problem we had to solve was how to actually get different types of cellulases close together.

Our first thought was to use phage display technology to place several enzymes on an M13 phage. This works by creating fusion proteins containing both a cellulase and a phage protein, and allowing this fusion to integrate into the phage. The phage would then be excreted from the cell.

This approach has a number of difficulties, and has not advanced much beyond the theoretical.

A different approach is to place the various enzymes on the cell surface. If they can be placed there at a high enough density, the synergistic effect should appear. Enzymes can be placed on the cell surface using Ice Nucleation Protein (or INP), which seems to automagically transport itself to the outer membrane. We used a synthetic INP gene created by the 2009 UC Davis team.

By creating a fusion of a cellulase to Ice Nucleation Protein, it should be possible to have that cellulase carried to the outer membrane. A fully working system would incorporate multiple cellulases, displaying at a number of up to 100,000 in total.

To create a protein fusion poses interesting assembly challenges, and we pioneered the use of a new protocol, BioSandwich, invented by our supervisor Chris French. This assembly method is based on RFC10-compliant parts, but assembles them in a homology-based way. The homology between parts is created by attaching oligonucleotides to the end of each part.

As a proof both that BioSandwich works, and that INP works, we successfully attached INP to Yellow Fluorescent Protein. When we centrifuged the cells, we found that the fluorescence seemed to be localised to the membrane fraction.

We also successfully created a new β-glucosidase based on a cryptic E. coli gene, bglX. We showed that it is capable of degrading the cellobiose analog MUG.

Another BioBrick we created was the amylase malS, the first amylase in the Registry. Anylases degrade starch, not cellulose, but a fusion of INP to malS could be useful as a test system, since degradation of starch requires just this one enzyme.

[Discuss any advances in attaching cellulases to INP since this was written.]

It should be noted that the fully working system will require several copies of the INP gene in the construct, to fuse to the different cellulases. One worry is therefore the potential for genetic instability and recombination. However, we believe that in industry it will be possible to synthesise different versions of INP, which use synonymous codons to code for the same protein, while having different DNA sequences.

Human Practices

We set out to answer two different questions:

• Could a biorefinery plant using this technology be built and be economically viable?
• Should we as a society proceed down this road?

To answer the first question, we constructed a process flow diagram illustrating how a biorefinery would be arranged in the real world. Then we conducted an economic analysis of the biorefinery. While this analysis makes many assumptions, it shows that it is at least plausible that such a biorefinery could be economically viable.

To answer the question of whether we should build a biorefinery is more difficult. But we conducted interviews with a number of figures involved in the debate around synthetic biology: people from business, academia, philosophy, environmental groups, and the Church.

A number of key themes emerged.