Team:Edinburgh

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Welcome to '''Edinburgh's''' 2011 iGEM effort, a.k.a. '''Team Synergy'''.
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==History==
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<center><big>'''Improved biorefineries using synergy'''</big></center>
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<center><big>'''An iGEM feasibility study by Edinburgh 2011'''</big></center>
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There exist situations where:
 
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* several enzymes are needed to produce the desired product
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A biorefinery is a special type of refinery in which biomass, such as plant <span class="hardword" id="cellulose">cellulose</span>, is converted by microorganisms into useful products. Edinburgh's [[Main Page | 2011 iGEM]] project is a feasibility study into the creation of biorefineries using <span class="hardword" id="ec">E. coli</span>, the workhorse of synthetic biology; and whether biorefineries can be improved by arranging for the different enzymes involved to be in close proximity to each other, so as to create <span class="hardword" id="synergy">synergy</span> between them. We investigated two methods of bringing the enzymes close together: [[Team:Edinburgh/Cell Display | cell surface display]] via Ice Nucleation Protein, and [[Team:Edinburgh/Phage Display | phage display]] via M13's major coat protein. We attempted a new DNA assembly protocol, provisionally named "[[Team:Edinburgh/BioSandwich |BioSandwich]]". We constructed [[Team:Edinburgh/Modelling | computer models]] of synergy to assess whether it is a feasible option. Finally, we  considered the broader [[Team:Edinburgh/Biorefinery | economic]] and [[Team:Edinburgh/Interviews | social]] questions surrounding the construction of a biorefinery: can it be done, and should it be done?
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* these enzymes work <span class="hardword" id="synergy">synergistically;</span> meaning they are best kept close together
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Last year, [https://2010.igem.org/Team:Slovenia Slovenia] found a way to achieve <span class="hardword" id="synergy">synergy</span> in the periplasm. This year, Edinburgh is focusing on achieving <span class="hardword" id="synergy">synergy</span> outside the cell.
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==Synergy==
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==Our project==
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In many applications, several enzymes are needed to produce the desired product. And it is often the case that these enzymes work synergistically; meaning their efficiency is increased if they are in close proximity.
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We will create microscopic <span class="hardword" id="bioreactor">bioreactors</span>, which we define as scaffolds holding various enzymes which carry out reactions in the extracellular environment. Our hope is that, by combining the activity of multiple enzymes in a small space, high efficiency will be achieved. At least 4 systems are being considered:
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Last year, [https://2010.igem.org/Team:Slovenia Slovenia] found a way to achieve synergy in the <span class="hardword" id="cytoplasm">cytoplasm</span>. This year, Edinburgh is investigating whether such synergy can be achieved outside the cell.
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We attempted to create microscopic reaction scaffolds holding various enzymes that carry out reactions in the extracellular environment. Our hope is that, by combining the activity of multiple enzymes in a small space, high efficiency will be achieved. Two different systems are being investigated.
===Cell surface display===
===Cell surface display===
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* The simplest system: use bacteria as the scaffold, and attach enzymes by cell surface display techniques.
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[[Image:Edinburgh-Surface-Display.png|thumb|300px|''E. coli'' displaying multiple enzymes.]]
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:* A modified version of the above: concentrate the enzymes on small parts of the bacterial surface, such as the <span class="hardword" id="flagellum">flagella</span>.
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[[Image:Edinburgh-Phage-Display.png|thumb|300px|M13 phage displaying multiple enzymes.]]
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The simplest system uses ''E. coli'' bacteria as the scaffold. Each bacterium generates several enzymes and displays them on its outer membrane. If sufficiently high numbers are present on each cell, the synergystic effect should be achieved.
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To achieve a high expression level, we will attempt to use <span class="hardword" id="inp">Ice Nucleation Protein</span> as a carrier for enzymes. See the [[Team:Edinburgh/Cell Display | cell surface display]] page for more details.
===Phage display===
===Phage display===
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* A radical proposal: use <span class="hardword" id="m13">M13</span> <span class="hardword" id="phage">phage</span> as the scaffold, and attach enzymes by phage-display techniques to the <span class="hardword" id="p8">pVIII</span> coat protein.
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A more radical proposal involves use <span class="hardword" id="m13">M13</span> <span class="hardword" id="phage">phage</span> as the scaffold, and attaching enzymes by phage-display techniques to the <span class="hardword" id="p8">pVIII</span> coat protein.
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These modified phage will be produced by modified ''E. coli''. If multiple copies of the enzymes could be attached to a single phage, then synergy should be achieved. See the [[Team:Edinburgh/Phage Display | phage display]] page for more details.
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===Modelling===
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Synergy can be assessed <span class="hardword" id="insilico">in silico</span>, using computer models. We created and compared multiple models of cellulase action and we showed that by just bringing enzymes close together we can increase their efficiency in our potential systems. See [[Team:Edinburgh/Modelling | our modelling page]] for more details.
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==DNA assembly==
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DNA assembly is a difficult problem, and some teams have almost abandoned the <span class="hardword" id="biobrick">BioBrick</span> approach in favour of <span class="hardword" id="homology">homology-based</span> methods like Gibson Assembly. During our project, we attempted to use a hybrid system, [[Team:Edinburgh/BioSandwich | BioSandwich]], which has some of the advantages of both approaches.
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:* A modified version of the above: attach multiple such phage to small beads via the <span class="hardword" id="p3">pIII</span> protein, making a larger "reactor".
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==Biorefineries in society==
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There are probably many uses for an extracellular reaction scaffold, so '''this technique is fairly general''' and could hopefully be used for many purposes, just by swapping in the correct BioBricks. As example systems, we will try to use <span class="hardword" id="cellulase">cellulases</span> as our enzymes of interest.
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We believe that it is insufficient to ask whether the low-level biological challenges can be overcome. There are also engineering and economic problems to consider, and so we have worked on an [[Team:Edinburgh/Biorefinery | actual design]] for a large-scale physical biorefinery.
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===Biorefinery===
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More than this, political and social implications of biorefineries demand our attention. We must ask not only whether we can do something, but also whether we should. Answering this question is one of the most important parts of our feasibility study, and so we conducted a number of [[Team:Edinburgh/Interviews | interviews]] with participants in the debate around synthetic biology.
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While we're at it, it makes sense to create something from the sugar we will generate. This would involve creation of a <span class="hardword" id="biorefinery">biorefinery</span>.
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==Questions==
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Our feasibility study therefore seeks to answer the following questions:
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* Would the efficiency of cellulases be increased by having different types close together?
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* Could this be done by displaying them on a cell outer membrane?
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* Could this be done by displaying them on a phage?
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* Does the BioSandwich DNA assembly method work properly?
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* How would a biorefinery involving either system actually be constructed?
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* Would such a biorefinery be economically viable?
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* What are the social implications of creating such a biorefinery?
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* What are people's thoughts and feelings regarding this project?
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* Should we (meaning society) actually build such a biorefinery?
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Our answers, or best attempts at answers, are found throughout this wiki.
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Latest revision as of 10:10, 27 October 2011

Improved biorefineries using synergy
An iGEM feasibility study by Edinburgh 2011


A biorefinery is a special type of refinery in which biomass, such as plant cellulose, is converted by microorganisms into useful products. Edinburgh's 2011 iGEM project is a feasibility study into the creation of biorefineries using E. coli, the workhorse of synthetic biology; and whether biorefineries can be improved by arranging for the different enzymes involved to be in close proximity to each other, so as to create synergy between them. We investigated two methods of bringing the enzymes close together: cell surface display via Ice Nucleation Protein, and phage display via M13's major coat protein. We attempted a new DNA assembly protocol, provisionally named "BioSandwich". We constructed computer models of synergy to assess whether it is a feasible option. Finally, we considered the broader economic and social questions surrounding the construction of a biorefinery: can it be done, and should it be done?

Synergy

In many applications, several enzymes are needed to produce the desired product. And it is often the case that these enzymes work synergistically; meaning their efficiency is increased if they are in close proximity.

Last year, Slovenia found a way to achieve synergy in the cytoplasm. This year, Edinburgh is investigating whether such synergy can be achieved outside the cell.

We attempted to create microscopic reaction scaffolds holding various enzymes that carry out reactions in the extracellular environment. Our hope is that, by combining the activity of multiple enzymes in a small space, high efficiency will be achieved. Two different systems are being investigated.

Cell surface display

E. coli displaying multiple enzymes.
M13 phage displaying multiple enzymes.

The simplest system uses E. coli bacteria as the scaffold. Each bacterium generates several enzymes and displays them on its outer membrane. If sufficiently high numbers are present on each cell, the synergystic effect should be achieved.

To achieve a high expression level, we will attempt to use Ice Nucleation Protein as a carrier for enzymes. See the cell surface display page for more details.

Phage display

A more radical proposal involves use M13 phage as the scaffold, and attaching enzymes by phage-display techniques to the pVIII coat protein.

These modified phage will be produced by modified E. coli. If multiple copies of the enzymes could be attached to a single phage, then synergy should be achieved. See the phage display page for more details.

Modelling

Synergy can be assessed in silico, using computer models. We created and compared multiple models of cellulase action and we showed that by just bringing enzymes close together we can increase their efficiency in our potential systems. See our modelling page for more details.

DNA assembly

DNA assembly is a difficult problem, and some teams have almost abandoned the BioBrick approach in favour of homology-based methods like Gibson Assembly. During our project, we attempted to use a hybrid system, BioSandwich, which has some of the advantages of both approaches.

Biorefineries in society

We believe that it is insufficient to ask whether the low-level biological challenges can be overcome. There are also engineering and economic problems to consider, and so we have worked on an actual design for a large-scale physical biorefinery.

More than this, political and social implications of biorefineries demand our attention. We must ask not only whether we can do something, but also whether we should. Answering this question is one of the most important parts of our feasibility study, and so we conducted a number of interviews with participants in the debate around synthetic biology.

Questions

Our feasibility study therefore seeks to answer the following questions:

  • Would the efficiency of cellulases be increased by having different types close together?
  • Could this be done by displaying them on a cell outer membrane?
  • Could this be done by displaying them on a phage?
  • Does the BioSandwich DNA assembly method work properly?
  • How would a biorefinery involving either system actually be constructed?
  • Would such a biorefinery be economically viable?
  • What are the social implications of creating such a biorefinery?
  • What are people's thoughts and feelings regarding this project?
  • Should we (meaning society) actually build such a biorefinery?

Our answers, or best attempts at answers, are found throughout this wiki.

Retrieved from "http://2011.igem.org/Team:Edinburgh"