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Team:Austin Texas/Project
From 2012.igem.org
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| + | == '''Abstract''' == | ||
| - | + | UT’s ZombiE.coli aims to a develop a tightly regulated genetic switch that is triggered by bacterial quorum signaling and leads to feed-forward propagation of the genetic output in the form of red or green fluorescence as well as amplification of quorum signaling. The switch relies on simple one-way Cre/loxP recombination combined with native quorum signaling to provide us with a system that models transmissible disease spread between populations. We have likened this to an airborne zombie epidemic, in which a an “infected” zombie cell is capable of restructuring the genes of a normal cell, turning it into a flesh-hungry counterpart. This system will be useful not only as a simple disease outbreak model for intermediate-level biology education, but also, could provide new insights to how bacterial populations communicate in three dimensions and under different genetic backgrounds. | |
| - | |||
| + | =='''Project Details'''== | ||
| + | ===Distinguishing Between ''E.coli'' populations=== | ||
| - | + | Features of a circuit modeling transmissible disease must include certain E.coli behaviors, one which allows for a zombie cell to infect normal cells, and one for a normal cell to irreversibly switch into a zombie cell. In order to easily distinguish between phenotypes of normal and zombie cells, different fluorescent proteins will be expressed in each cell population. A green fluorescent protein (GFP) will be expressed in normal cells, and a red fluorescent protein (RFP) expressed in zombie cells. The phenotypic switch will be controlled by an irreversible promoter flip accomplished through mutant CRE-Recombination LoxP sites. (Zhang 2002) This restructuring will result in a permanent change in genes being expressed upon infection. | |
| + | https://static.igem.org/mediawiki/2012/0/0f/ZMode.png | ||
| + | In the above figure, the left cell depicts a Z-Mode or zombie cell. The main features of this are its expression of RFP and the expression of LasI, an enzyme that produces quorum signaling molecule acyl-homoserine lactone (AHL). The quorum molecule diffuses out of the zombie cell and into the normal cell. Upon AHL reaching high enough concentration, LasR will activate the expression of CRE and the genetic restructuring event may occur. | ||
| - | === | + | ===Mechanism of Infection=== |
| - | + | The mechanism of infection that the zombie cells use is based on a quorum sensing (QS) molecule produced by the LasI protein encoded for by the gene LasI from ''Pseudomonas aeruginosa''. The QS molecule, acyl-homoserine lactone (AHL), permeates into the extracellular environment and is absorbed by the recipient normal cell. When AHL is in high enough concentration, the LasR enzyme from the gene LasR from Pseudomonas aeruginosa will convert AHL into a transcription factor to drive the LasR promoter, with the CRE-Recombinase protein under its control. CRE dictates the next behavior we want of our normal cells, to irreversibly switch into zombie cells, which can then infect other normal cells. | |
| - | === | + | https://static.igem.org/mediawiki/2012/archive/0/0f/20120711160917!ZMode.png |
| + | |||
| + | Features of the converter plasmid include a scheme for detecting the AHL quorum sensing molecule (from the LasR enhancer protein) and transduce the quorum molecule into the production of CRE recombinase. The expression of the LasR protein is under control of the endogenous Lac operator by the LacIm1 protein. This feature will serve to limit the expression of this molecule during the cloning and testing of this parental plasmid sequence and allow swift induction of expression after adding IPTG. The LacIm1 is a codon isomer of the LacI gene, meaning that it has large codon deviation from the wild-type LacI gene. This will prevent recombination between the Converter and Reporter plasmids in the experiments (Basu 2005). Upon the expression of the LasR protein and in the presence of a sufficient local concentration of AHL the CRE expression will be turned on. | ||
| + | |||
| + | ===Genetic Switch=== | ||
| + | |||
| + | Expression of CRE-Recombinase will then act as a genetic switch and trigger a restructuring in the Reporter plasmid. The genetic switch relies on a variant of the Cre/loxP recombination system. The protein CRE-Recombinase (causes recombination) catalyzes crossover events at specific DNA sequences termed loxP sites. Two variants, lox66 and lox71 can be combined to create the irreversible crossover event we want. CRE recombinase will trigger a one way recombination event of a LacUV5 promoter (Zhang 2002) causing it to switch and express the proteins it was previously facing away from. The LacUV5 flip is the essential difference between our normal and zombie cells. In a normal cell, IPTG induction will cause GFP expression, but if a cell has received the QS molecule AHL and expressed CRE-Recombinase, then the promoter will express the opposite set of genes. This results in a zombie cell expressing a RFP and the gene LasI, upon which it can now make the quorum molecule acyl-homoserine lactone, making it capable of further infecting proximal cells. | ||
| + | |||
| + | https://static.igem.org/mediawiki/2012/9/9c/Preporter.png | ||
| + | |||
| + | == '''Additional Project Ideas''' == | ||
| + | |||
| + | === E. Coli Decaffeination Circuit === | ||
| + | More info coming soon. | ||
| + | |||
| + | === Spinach-mCherry Dual Fluoresence Reporter === | ||
| + | More info coming soon. | ||
| + | |||
| + | === Adding zombie smell (cadaverine) === | ||
Background | Background | ||
| Line 39: | Line 61: | ||
== Results == | == Results == | ||
| + | |||
| + | ==References== | ||
| + | #Zhang and Lutz, “Cre recombinase-mediated inversion using lox66 and lox71: method to introduce conditional point mutations into the CREB-binding protein” Nucleic Acids Research, vol 30, issue 17, p. e90, 2002 | ||
| + | #Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R. A synthetic multicelluar system for programmed pattern formation. Nature, 2005 Apr 28;434(7037):1130-4. | ||
Revision as of 16:23, 11 July 2012
Contents |
Abstract
UT’s ZombiE.coli aims to a develop a tightly regulated genetic switch that is triggered by bacterial quorum signaling and leads to feed-forward propagation of the genetic output in the form of red or green fluorescence as well as amplification of quorum signaling. The switch relies on simple one-way Cre/loxP recombination combined with native quorum signaling to provide us with a system that models transmissible disease spread between populations. We have likened this to an airborne zombie epidemic, in which a an “infected” zombie cell is capable of restructuring the genes of a normal cell, turning it into a flesh-hungry counterpart. This system will be useful not only as a simple disease outbreak model for intermediate-level biology education, but also, could provide new insights to how bacterial populations communicate in three dimensions and under different genetic backgrounds.
Project Details
Distinguishing Between E.coli populations
Features of a circuit modeling transmissible disease must include certain E.coli behaviors, one which allows for a zombie cell to infect normal cells, and one for a normal cell to irreversibly switch into a zombie cell. In order to easily distinguish between phenotypes of normal and zombie cells, different fluorescent proteins will be expressed in each cell population. A green fluorescent protein (GFP) will be expressed in normal cells, and a red fluorescent protein (RFP) expressed in zombie cells. The phenotypic switch will be controlled by an irreversible promoter flip accomplished through mutant CRE-Recombination LoxP sites. (Zhang 2002) This restructuring will result in a permanent change in genes being expressed upon infection.
In the above figure, the left cell depicts a Z-Mode or zombie cell. The main features of this are its expression of RFP and the expression of LasI, an enzyme that produces quorum signaling molecule acyl-homoserine lactone (AHL). The quorum molecule diffuses out of the zombie cell and into the normal cell. Upon AHL reaching high enough concentration, LasR will activate the expression of CRE and the genetic restructuring event may occur.
Mechanism of Infection
The mechanism of infection that the zombie cells use is based on a quorum sensing (QS) molecule produced by the LasI protein encoded for by the gene LasI from Pseudomonas aeruginosa. The QS molecule, acyl-homoserine lactone (AHL), permeates into the extracellular environment and is absorbed by the recipient normal cell. When AHL is in high enough concentration, the LasR enzyme from the gene LasR from Pseudomonas aeruginosa will convert AHL into a transcription factor to drive the LasR promoter, with the CRE-Recombinase protein under its control. CRE dictates the next behavior we want of our normal cells, to irreversibly switch into zombie cells, which can then infect other normal cells.
Features of the converter plasmid include a scheme for detecting the AHL quorum sensing molecule (from the LasR enhancer protein) and transduce the quorum molecule into the production of CRE recombinase. The expression of the LasR protein is under control of the endogenous Lac operator by the LacIm1 protein. This feature will serve to limit the expression of this molecule during the cloning and testing of this parental plasmid sequence and allow swift induction of expression after adding IPTG. The LacIm1 is a codon isomer of the LacI gene, meaning that it has large codon deviation from the wild-type LacI gene. This will prevent recombination between the Converter and Reporter plasmids in the experiments (Basu 2005). Upon the expression of the LasR protein and in the presence of a sufficient local concentration of AHL the CRE expression will be turned on.
Genetic Switch
Expression of CRE-Recombinase will then act as a genetic switch and trigger a restructuring in the Reporter plasmid. The genetic switch relies on a variant of the Cre/loxP recombination system. The protein CRE-Recombinase (causes recombination) catalyzes crossover events at specific DNA sequences termed loxP sites. Two variants, lox66 and lox71 can be combined to create the irreversible crossover event we want. CRE recombinase will trigger a one way recombination event of a LacUV5 promoter (Zhang 2002) causing it to switch and express the proteins it was previously facing away from. The LacUV5 flip is the essential difference between our normal and zombie cells. In a normal cell, IPTG induction will cause GFP expression, but if a cell has received the QS molecule AHL and expressed CRE-Recombinase, then the promoter will express the opposite set of genes. This results in a zombie cell expressing a RFP and the gene LasI, upon which it can now make the quorum molecule acyl-homoserine lactone, making it capable of further infecting proximal cells.
Additional Project Ideas
E. Coli Decaffeination Circuit
More info coming soon.
Spinach-mCherry Dual Fluoresence Reporter
More info coming soon.
Adding zombie smell (cadaverine)
Background
- [http://en.wikipedia.org/wiki/Cadaverine Cadaverine]
- [http://partsregistry.org/Part:BBa_J45999:Design Odor free chassis] has a tnaA mutation that prevents degradation of Tryptophan to indole.
- cadA and ldcC genes convert lysine to cadaverine. [http://www.ncbi.nlm.nih.gov/pubmed/21552989 Reference]
Results
References
- Zhang and Lutz, “Cre recombinase-mediated inversion using lox66 and lox71: method to introduce conditional point mutations into the CREB-binding protein” Nucleic Acids Research, vol 30, issue 17, p. e90, 2002
- Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R. A synthetic multicelluar system for programmed pattern formation. Nature, 2005 Apr 28;434(7037):1130-4.
