Team:Edinburgh/Presentation
From 2011.igem.org
Presentation
Contents |
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.
Part One: 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. 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
Part Two: 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. FIXME
Part Three: 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. A different approach is to place the various enzymes on the cell surface. If they can be placed at a high enough density, the synergistic effect should appear. Enzymes can be placed on the cell surface using Ice Nucleation Protein, which seems to automagically transport itself to the outer membrane.
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.