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Team:Newcastle/Project
From 2013.igem.org
Contents |
Project Overview
Planning
In the process of deciding on a project for iGEM 2013 we considered a multitude of ideas, including bacterial consortia against desertification, genomic encryption, anti-algal bacterial paint, and bacterial nano wires. Each of these were found to have their own strengths and weaknesses. For example bacterial consortia to tackle desertification had the potential to transform deserts into agriculturally usable soil, and it also has a strong foundation of research to support its implementation. However, due to the novelty of the subject and the time constraints imposed by iGEM, it was decided that we would be unable to make a significant contribution to this subject area.
The ideas genomic encryption and nano wires were not fully developed due concerns raised at team meetings around the lack of comprehensive information on these subjects. While researching modern synthetic biology techniques we have found that a cell wall, one of the standard components of the bacterial cell, often causes difficulties in these techniques. These included transformation efficiency, secretion of recombinant proteins, adaption to the environment etc. So we thought to ourselves: is there any way to remove the cell wall and still have a viable cell? As a result we have developed a revolutionary new chassis which will revolutionise how synthetic biology is performed.
As a result of this we have found a project we believe to be destined to revolutionise the approach to synthetic biology by introducing a BioBrick which would act as a switch for production and loss of bacterial cell wall in the model Gram positive bacteria Bacillus subtilis on our demand, while still allowing it to grow and divide. B. subtilis without a cell wall is better in many different ways and should be used as a new chassis for use in Synthetic Biology.
Bacteria which have lost their cell wall which are still able to grow and propagate are called L-forms, or as we prefer to call them, naked bacteria. There are loads of things that you can do with naked bacteria, we explored a few of them:
Fusion of bacteria is made significantly easier without a cell wall. This forces the fusants to reproduce sexually, where their genomes recombine, and this can be used in directed evolution.
L-forms have been shown to form symbiosis in plants. Plants with naked bacteria show increased resistance to fungus and they could be used to deliver useful compounds to the plant. This could give better crop yields, more nutritious harvest and reduce the need for spraying of fertiliser, pesticides or other compounds.
The loss of the cell wall leaves L-forms protected by only a cell membrane. The plasma membrane of l-forms is quite fluid. The advantage of this is that these cells would be able to adapt to shapes of various cracks and cavities, or will be able to "squeeze through" tiny channels and deliver cargo to hard-to reach targets.
[http://www.youtube.com/watch?v=b0Kk6bKKOQ0 Click here to view a short video which explains or project.]
This isn’t a finite list of what can be done with naked bacteria, there’s loads more! L-forms are currently used to discover novel antibiotics which don’t act on the cell wall. L-forms can teach us a great deal about how bacterial life has evolved, through acting as a model for a cell wall-less bacterial progenitor, and through being able to test the ease of induction of endosymbiosis in cell wall-less organisms (Mercier et al. 2013).
L-form bacteria can be used in any process which protoplasts are currently used for. Protoplasts are bacteria which have been chemically induced to lose their cell wall. They cannot however grow or divide (as L-forms can) and are not classified as being alive. L-forms can be used to transform bacteria which are recalcitrant to transformation (Chang and Cohen 1979).
And a very important bonus, which comes with our naked bacteria is that they are osmotically sensitive, meaning that they will lyse if they escape into the environment. Therefore they can be used in non-contained environments (e.g agriculture).
Analysis
Each of our chosen research themes has had a set of specific requirements, i.e. BioBricks, equipment and,of course, a research strategy.
Genome Shuffling
To explore the possibilities of using L-forms of B. subtilis for inducing the exchange of DNA fragments between related bacteria we have had to design two BioBricks for fluorescently tagged histone binding proteins (one GFP and one RFP) to be able to witness the fusion events and reliably analyse the collected data. The BioBricks were designed without a promoter, so they could be cloned into any plasmid under the control of the desired promoter and be used in various bacterial species. For our research we have used a pMutin4 plasmid. However before deciding to use this particular plamid we have tested a plasmid designed by the Groningen 2012 iGEM team. Although we were unable to use the plasmid we have managed to [http://parts.igem.org/Part:BBa_K818000:Experience characterise it.]
Introduction and Detection of Naked Bacteria in Plants
Shape Shifting
The loss of the cell wall leaves L-forms protected by only a cell membrane. The plasma membrane of l-forms is quite fluid. The advantage of this is that these cells would be able to adapt to shapes of various cracks and cavities, or will be able to "squeeze through" tiny channels and deliver cargo to hard-to reach targets.
We have planned to test this hypothesis by injecting the naked bacteria into specially designed microfluidics chambers and observing their behaviour under the microscope. Membrane would have been visualised with a commonly used membrane stain F.595
Modelling
The next step on the diagram is modelling. This step is an essential part of a successful synthetic biology project. Although it requires a lot of time and effort, and therefore is often neglected. We believe that in the long run modelling can save a lot of time, effort and resources to those who take their time in the beginning, simulating all the possible outcomes of the system and refining it at an early stage, before any in vitro and in vivo experiments have been planned and conducted. Another positive side to modelling prior to the "wet lab" sessions is the fact that a model behaves according to the known facts and principles, and if in real life the outcome drastically differs from the simulation, there's a good chance of finding out what may be causing the difference through adjusting the model and repeating the experiments.
For every research theme we have constructed a model to help us understand the systems we engineered. Click on the links to view each model or visit our modelling page:
Implementation
What we've done for each project (brief summary). Assuming the same format as Analysis.
Testing
This is the section where the summary of our results goes.
We have shown the recombination of the L-forms' genomes as a result of fusion.
We’ve shown that the naked bacteria that we created using our switch BioBrick also form these associations.
All you need to start using an L-form chassis is a culture of Bacillus subtilis, our L-form switch BioBrick and a set of instructions from us.
References
[http://www.ncbi.nlm.nih.gov/pubmed/11849491 Walker R, Ferguson CMJ, Booth NA and Allan EJ (2002) The symbiosis of Bacillus subtilis L-forms with Chinese cabbage seedlings inhibits conidial germination of ‘Botrytis cinerea. Letters in Applied Microbiology, 34, 42-45.]
[http://www.ncbi.nlm.nih.gov/pubmed/107388 Chang S and Cohen SN (1979)High frequency transformation of Bacillus subtilis protoplasts by plasmid DNA. Molecular Genetics & Genomics, 168, 111–115.]
[http://www.cell.com/abstract/S0092-8674(13)00135-9 Mercier R, Kawai Y and Errington J. (2013) Excess Membrane Synthesis Drives a Primitive Mode of Cell Proliferation, Cell, 152, 997–1007.]
