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Team:Calgary/Notebook/Killswitch
From 2012.igem.org
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<p>We are continuing to look in to various other pathways. We discussed the possibility of a NOR-gated system to add a second layer of regulation to the kill gene. It would require the production of riboswitch ligands. Possible ligands include glucose, amino acids, and molybdenum cofactor.</p> | <p>We are continuing to look in to various other pathways. We discussed the possibility of a NOR-gated system to add a second layer of regulation to the kill gene. It would require the production of riboswitch ligands. Possible ligands include glucose, amino acids, and molybdenum cofactor.</p> | ||
| - | <p>We also looked into a co-dependent system where we would transform <i>E. coli</i> with two different plasmids and put them in the same bioreactor such that they produce ligands for each other that would repress the expression of the restriction enzyme and the nuclease. For this we explored riboswitches further and came up with the idea of using MOCO and SAM riboswitches as SAM is soluble in water and not found in the tailings ponds.</p> | + | <p>We also looked into a co-dependent system where we would transform <i>E. coli</i> with two different plasmids and put them in the same bioreactor such that they produce ligands for each other that would repress the expression of the restriction enzyme and the nuclease. For this we explored riboswitches further and came up with the idea of using MOCO and SAM riboswitches as SAM is soluble in water and not found in the tailings ponds.</p> |
| + | </html> [[File:Ucalgary_2012_Codependence_Mechanism_V2.png|400px|center]]<html> | ||
<p> We also found a glucose repressible promoter that we could have potentially used upstream of the kill switch. This promoter is found in <i>F. tularensis</i>. However we also found that this promoter is not found in <i>E. coli</i> and <i>F. tularensis</i> has a unique polymerase which used this promoter. Hence using this promoter does not seem feasible. | <p> We also found a glucose repressible promoter that we could have potentially used upstream of the kill switch. This promoter is found in <i>F. tularensis</i>. However we also found that this promoter is not found in <i>E. coli</i> and <i>F. tularensis</i> has a unique polymerase which used this promoter. Hence using this promoter does not seem feasible. | ||
Revision as of 20:36, 23 May 2012
Week 1 (May 1-4)
This was the first week where we met with other team members and summarized the primary subprojects the team will be tackling this coming summer.
Week 2 (May 7-11)
Members were assigned to the killswitch team. We spent a majority of this week performing literature searches and narrowing the killswitch to a few ideas.
The mechanism of death is still settled upon the micrococcal nuclease, but regulation of the death genes will be difficult. Existing repressible promoters in the registry still tend to be leaky in their expression, but we need to test this out. We may look into the TetR-repressible promoter (R0040) and also the clλ regulated promoter (R0051).
We also found a few riboswitches responsible to various metal ions such as Mg2+ and Mn2+. The mgtA riboswitch activates translation of the death gene when magnesium ions are not present in the solution. The mntA riboswitch deactivates translation of the death gene when manganese ions are not present. Considering this, we may be able to find a method of precipitating or otherwise sequestering Mn2+ ions out of the tailings water prior to entering the bioreactor. This way, our bacteria would not die when they come into contact with the manganese in the tailings water. Possible additives include carbonate (CO32-) or hydroxide (OH-), though this may alter the pH too greatly.
One other proposal would be to use promoters that activate when the bacteria detect the formation of a biofilm on, for example, glass beads. Engineering a monolayer of cells on a bead means that if a cell detaches, its death genes will activate. Further research into this is needed.
Week 3 (May 14-18)
We are continuing to look in to various other pathways. We discussed the possibility of a NOR-gated system to add a second layer of regulation to the kill gene. It would require the production of riboswitch ligands. Possible ligands include glucose, amino acids, and molybdenum cofactor.
We also looked into a co-dependent system where we would transform E. coli with two different plasmids and put them in the same bioreactor such that they produce ligands for each other that would repress the expression of the restriction enzyme and the nuclease. For this we explored riboswitches further and came up with the idea of using MOCO and SAM riboswitches as SAM is soluble in water and not found in the tailings ponds.
We also found a glucose repressible promoter that we could have potentially used upstream of the kill switch. This promoter is found in F. tularensis. However we also found that this promoter is not found in E. coli and F. tularensis has a unique polymerase which used this promoter. Hence using this promoter does not seem feasible. Next week we will be looking into further possibilities for the kill switch.
