IGEM:Paris Bettencourt 2012/Notebooks/Semantic group: Difference between revisions
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=What we can use from others= | =What we can use from others= | ||
Church Lab already engineered a strain in order to remove the rarest stop codon in E coli MG1655, which is TAG (amber stop codon, 314 occurrences), and replace it with the most common stop codon which is TAA[2]. We should ask them for this strain. Moreover it already exists a tRNA amber suppressor gene, named supD | Church Lab already engineered a strain in order to remove the rarest stop codon in E coli MG1655, which is TAG (amber stop codon, 314 occurrences), and replace it with the most common stop codon which is TAA [2]. We should ask them for this strain. Moreover it already exists a tRNA amber suppressor gene, named supD, that replaces amber stop codon with a serine amino-acids [3]. This system used by Anderson et. al has already been used by different IGEM teams, including [http://2011.igem.org/Team:Paris_Bettencourt/tRNA_diffusion| Paris] and [http://2009.igem.org/Team:PKU_Beijing/Project/AND_Gate_1/Design| Pekin University]. | ||
=What we have to do= | =What we have to do= | ||
Revision as of 09:34, 25 June 2012
| Notebook | Design | Roadmap | Meetings and to-dos | Protocols | Bibliography | Previous Biosafety iGEM projects |
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The idea
We need to prevent our genetic construction from being used by other organism. Since horizontal gene transfer (HGT) can be perform either by conjugation, by transduction, or by transformation, and none of these system is only dependent of our organism, we cannot assume the fact that HGT is fully avoidable. Semantic containment [1] means that our bacteria won't be able to "speak" with other organism, since they don't speak the same language. The language being DNA. Here, it won't be all DNA that we are going to change, but just 1 stop codon that we are going to change in a normal aa codon, let say the aa 'X', for OUR GMO bacteria. So, in case of HGT, the gene transferred won't be able to be translate correctly, since it has many stop codon instead of the aa 'X'.
What we can use from others
Church Lab already engineered a strain in order to remove the rarest stop codon in E coli MG1655, which is TAG (amber stop codon, 314 occurrences), and replace it with the most common stop codon which is TAA [2]. We should ask them for this strain. Moreover it already exists a tRNA amber suppressor gene, named supD, that replaces amber stop codon with a serine amino-acids [3]. This system used by Anderson et. al has already been used by different IGEM teams, including Paris and Pekin University.
What we have to do
Get more information about the amino-acyl transferase of this tRNASerTAG
Proof of principle
We should design an experiment that will show that this system is efficient. For instance, we could imagine a conjugation test, in which the donor strains (which is supD +) code for a resistance gene with as much as TAG codon, and the recipient is obviously supD -. Here we would have the proof that this system prevent from HGT if we have no resistant colonies after conjugation. The reverse screen might be better.
Going farther
Every single synthetic gene we construct have to be coded with amber codon instead of any serine codon (TCN, N being A,T,C,G). Moreover, the aminoacyl-transferase, if it is specific to that tRNASerTAG, should also have TAG codon instead of normal serine codon. This would enhance massively the robustess of the system, if it's possible.
References
- Marliere, P. The farther, the safer : a manifesto for securely navigating synthetic species away from the old living world. System and Synthetic Biology 3, 77-84 (2009). [1]
- Isaacs, F.J. et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science (New York, N.Y.) 333, 348-53 (2011). [2]
- Anderson, J.C., Voigt, C. a & Arkin, A.P. Environmental signal integration by a modular AND gate. Molecular systems biology 3, 133 (2007).Paper
