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==Introduction== | ==Introduction== | ||
| - | ''[Slide: What it's all about]'' | + | :::''[Slide: What it's all about]'' |
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 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. | ||
| Line 21: | Line 21: | ||
The first question we asked is: what is this synergy phenomenon and how does it work? | The first question we asked is: what is this synergy phenomenon and how does it work? | ||
| - | ''[Slide: 3 enzyme actions]'' | + | :::''[Slide: 3 enzyme actions]'' |
Cellulose is a long chain of glucose sugars. It can be broken down by enzymes called "cellulases". Consider the following statements about cellulose degradation: | Cellulose is a long chain of glucose sugars. It can be broken down by enzymes called "cellulases". Consider the following statements about cellulose degradation: | ||
| Line 41: | Line 41: | ||
===C=== | ===C=== | ||
| - | ''[Slide: Play animation]'' | + | :::''[Slide: 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. | 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. | ||
| - | ''[Slide: Show graph]'' | + | :::''[Slide: Show graph]'' |
This model is very simplistic but does show that the synergy effect makes sense. | This model is very simplistic but does show that the synergy effect makes sense. | ||
| Line 55: | Line 55: | ||
The preliminary model was developed based on Kadam et al. 2004, and generates similar looking graphs: | The preliminary model was developed based on Kadam et al. 2004, and generates similar looking graphs: | ||
| - | ''[Slide: Normal Kappa graph]'' | + | :::''[Slide: Normal Kappa graph]'' |
The model is quite easily extended, so we aimed at creating a synergistic model to show whether synergy is at all a feasible option. | The model is quite easily extended, so we aimed at creating a synergistic model to show whether synergy is at all a feasible option. | ||
| Line 61: | Line 61: | ||
However, due to limitations of Kappa, we could not achieve it in Kappa alone. Therefore we used Spatial Kappa by Team Edinburgh 2010 (Donal Stewart). The added functionality means we could do that: | However, due to limitations of Kappa, we could not achieve it in Kappa alone. Therefore we used Spatial Kappa by Team Edinburgh 2010 (Donal Stewart). The added functionality means we could do that: | ||
| - | ''[Slide: Pacman animation]'' | + | :::''[Slide: Pacman animation]'' |
This model proved quite scalable - we can manipulate initial conditions, add more cellulose - emulating a biorefinery. | This model proved quite scalable - we can manipulate initial conditions, add more cellulose - emulating a biorefinery. | ||
| Line 67: | Line 67: | ||
Most importantly - it shows synergy (dependent mostly on diffusion rate). | Most importantly - it shows synergy (dependent mostly on diffusion rate). | ||
| - | ''[Slide: Spatial Kappa graph]'' | + | :::''[Slide: Spatial Kappa graph]'' |
===MATLAB=== | ===MATLAB=== | ||
| Line 75: | Line 75: | ||
==Biology== | ==Biology== | ||
| - | ''[Slide: Two options]'' | + | :::''[Slide: Two options]'' |
The fundamental biology problem we had to solve was how to actually get different types of cellulases close together. | The fundamental biology problem we had to solve was how to actually get different types of cellulases close together. | ||
| - | ''[Slide: Phage display]'' | + | :::''[Slide: Phage display]'' |
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. | 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. | ||
| Line 85: | Line 85: | ||
This approach has a number of difficulties, and has not advanced much beyond the theoretical. | This approach has a number of difficulties, and has not advanced much beyond the theoretical. | ||
| - | ''[Slide: Cell display]'' | + | :::''[Slide: Cell display]'' |
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. | 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. | ||
| Line 91: | Line 91: | ||
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. | 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. | ||
| - | ''[Slide: BioSandwich]'' | + | :::''[Slide: BioSandwich]'' |
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. | 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. | ||
| - | ''[Slide: INP-YFP]''' | + | :::''[Slide: INP-YFP]''' |
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. | 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. | ||
| - | ''[Slide: bglX]'' | + | :::''[Slide: bglX]'' |
Our project naturally requires working cellulases. We 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. | Our project naturally requires working cellulases. We 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. | ||
| - | ''[Slide: malS]'' | + | :::''[Slide: malS]'' |
Another BioBrick we created was the amylase ''malS'', the first amylase in the Registry. Amylases 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. | Another BioBrick we created was the amylase ''malS'', the first amylase in the Registry. Amylases 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. | ||
| Line 109: | Line 109: | ||
[Discuss any advances in attaching cellulases to INP since this was written.] | [Discuss any advances in attaching cellulases to INP since this was written.] | ||
| - | ''[Slide: genetic instability]'' | + | :::''[Slide: genetic instability]'' |
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. | 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. | ||
| Line 122: | Line 122: | ||
* Should we as a society proceed down this road? | * Should we as a society proceed down this road? | ||
| - | ''[Slide: Process flow diagram]'' | + | :::''[Slide: Process flow diagram]'' |
To answer the first question, we constructed a process flow diagram, which is an engineering design tool (point to the slides, the PFD comes up) illustrating how a biorefinery would be arranged in the real world. The PFD is not a definitive answer to what a biorefinery should look like but an articulation of what it can. It shows biomass raw materials subjected to pre-treatment via fractionation and depolymerisation of lignocellulose and hemilcellulose. After lignin is seperated it undergoes hydrous pyrolysis to convert it into phenols. Cellulose is separated and undergoes conversion into glucose. Finally glucose is converted here to sorbitol, but there is potential for conversion to other food and chemical products. | To answer the first question, we constructed a process flow diagram, which is an engineering design tool (point to the slides, the PFD comes up) illustrating how a biorefinery would be arranged in the real world. The PFD is not a definitive answer to what a biorefinery should look like but an articulation of what it can. It shows biomass raw materials subjected to pre-treatment via fractionation and depolymerisation of lignocellulose and hemilcellulose. After lignin is seperated it undergoes hydrous pyrolysis to convert it into phenols. Cellulose is separated and undergoes conversion into glucose. Finally glucose is converted here to sorbitol, but there is potential for conversion to other food and chemical products. | ||
Revision as of 16:22, 14 September 2011
Presentation
A version of the accompanying PowerPoint presentation is [http://www.nothinginbiology.com/iGEM-presentation.ppt available].
Contents |
Introduction
- [Slide: What it's all about]
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?
- [Slide: 3 enzyme actions]
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
- [Slide: 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.
- [Slide: Show graph]
This model is very simplistic but does show that the synergy effect makes sense.
Kappa
A more sophisticated model uses the Kappa modelling language. This includes two models - one preliminary model in Kappa, and another model in Spatial Kappa. Kappa is a language for running stochastic simulations of biochemical systems. It uses probabilistic kinetic rates to advance simulation. The preliminary model was developed based on Kadam et al. 2004, and generates similar looking graphs:
- [Slide: Normal Kappa graph]
The model is quite easily extended, so we aimed at creating a synergistic model to show whether synergy is at all a feasible option.
However, due to limitations of Kappa, we could not achieve it in Kappa alone. Therefore we used Spatial Kappa by Team Edinburgh 2010 (Donal Stewart). The added functionality means we could do that:
- [Slide: Pacman animation]
This model proved quite scalable - we can manipulate initial conditions, add more cellulose - emulating a biorefinery.
Most importantly - it shows synergy (dependent mostly on diffusion rate).
- [Slide: Spatial Kappa graph]
MATLAB
We also tried MATLAB modelling, but found we couldn't model synergy with it. Our MATLAB model uses ordinary differential equations to model the progress of the reaction over time. We found that it works best within certain limits; if allowed to run indefinitely, the results violate the laws of thermodynamics; for example the amount of cellobiose going negative.
Biology
- [Slide: Two options]
The fundamental biology problem we had to solve was how to actually get different types of cellulases close together.
- [Slide: Phage display]
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.
- [Slide: Cell display]
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.
- [Slide: BioSandwich]
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.
- [Slide: INP-YFP]'
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.
- [Slide: bglX]
Our project naturally requires working cellulases. We 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.
- [Slide: malS]
Another BioBrick we created was the amylase malS, the first amylase in the Registry. Amylases 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.]
- [Slide: genetic instability]
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.
We wrote a software tool to assist in this process.
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?
- [Slide: Process flow diagram]
To answer the first question, we constructed a process flow diagram, which is an engineering design tool (point to the slides, the PFD comes up) illustrating how a biorefinery would be arranged in the real world. The PFD is not a definitive answer to what a biorefinery should look like but an articulation of what it can. It shows biomass raw materials subjected to pre-treatment via fractionation and depolymerisation of lignocellulose and hemilcellulose. After lignin is seperated it undergoes hydrous pyrolysis to convert it into phenols. Cellulose is separated and undergoes conversion into glucose. Finally glucose is converted here to sorbitol, but there is potential for conversion to other food and chemical products.
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. We estimated $2.5 million dollars of investment is required plus $4.5 million in production costs.
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.
