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Team:Bielefeld-Germany/Project/Approach
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== The Approach == | == The Approach == | ||
| - | + | First we looked for a sensor system which is able to detect substances and we searched for a substances of interest. The system of interest has to be taken out of a different bacteria species than ''Escherichia coli'' , in order to avoid any background. Therefore we checked the literature for a well reviewed sensor system, which is not part of the ''E. coli'' genome. The system of choice was the phenolic sensing system ''virA'' of ''Agrobacterium tumefaciens''. It naturally detects acetosyringone, which is a secondary metabolite of plants that affects bacteria as an attractant. After repeated research to check for any other possible substances which could be detected by the system, we got a really long list of possibilities and picked 'capcaicin', which is responsible for the spiciness of edibles. | |
| - | First we looked for a sensor system which is able to detect substances | + | |
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| - | # | + | # extract the ''virA'' system out of ''A. tumefaciens'' |
# create new BioBricks out of the exciting environmental parts | # create new BioBricks out of the exciting environmental parts | ||
# transform the new BioBricks into ''E. coli'' | # transform the new BioBricks into ''E. coli'' | ||
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=== Preparing the system === | === Preparing the system === | ||
| - | We tried to work with the already existing | + | We tried to work with the already existing virA from the registry (<partinfo>K238008</partinfo>). Unfortunately this ''virA'' BioBrick did not work. The sequence data of the BioBrick did not fit to the published ''virA'' sequence. So we had to extract the ''virA'' gene via PCR out of the ''A. tumefaciens'' TI-plasmid by ourselves in order to create a new BioBrick. |
| - | VirA does not work without the help of the VirG protein. The existing ''virG'' gene in the iGEM registry contains illegal restriction sites. Moreover it needs the help of Chev Protein and sugars to work perfectly with VirA. We | + | VirA does not work without the help of the VirG protein. The existing ''virG'' gene in the iGEM registry contains illegal restriction sites. Moreover it needs the help of Chev Protein and sugars to work perfectly with VirA. We changed the sequence manually and had the gene synthesized by Mr. Gene. |
=== Starting point for biobricks -> Go cloning=== | === Starting point for biobricks -> Go cloning=== | ||
| - | + | The applied screening system in E. coli consists of two plasmids. After discussing the possibility of creating only one big plasmid, we unifed that one plasmid would minimize the transformation efficiency and would be difficult to modify via error prone PCR. So we had to change the origin of a pSB1X3 plasmid in order to avoid compatibility problems in the transformation. Therefore we cloned the R6K origin into the <partinfo>pSB1A3</partinfo>, <partinfo>pSB1C3</partinfo> and <partinfo>pSB1T3</partinfo> plasmids. For this purpose we used the R6K sequence <partinfo>J61001</partinfo> and the pSBXXX sequence to create primers for the PCR, followed by the ligation of the PCR products. | |
| - | The applied screening system in | + | |
=== The error prone PCR === | === The error prone PCR === | ||
| - | After cloning the new origin into the pSBXXX-backbones we | + | After cloning the new origin into the pSBXXX-backbones we were able to create the two constructs. The first one will be found inside the competent bacteria cells and contains the ''virG'' gene under the constitutive promotor <partinfo>J23110</partinfo>, a terminator (<partinfo>B0017</partinfo>), a ''vir'' promotor and a readout or selection gene (luciferase, mRFP and kanamycin resistance, respectively): |
[[Image:Screening_plasmid.jpg]] | [[Image:Screening_plasmid.jpg]] | ||
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| - | The error prone PCR is a PCR under malfunction conditions for the polymerase. It is possible to regulate the frequency of the mutagenesis by editing unbalanced concentrations of nucleotides and co-factors to the PCR. So we are going to create a new BioBrick and transform it into our target | + | The error prone PCR is a PCR under malfunction conditions for the polymerase. It is possible to regulate the frequency of the mutagenesis by editing unbalanced concentrations of nucleotides and co-factors to the PCR. So we are going to create a new BioBrick and transform it into our target in one step. Before we are able to do the error prone PCR we need to get the backbones done. |
=== Survival of the fittest === | === Survival of the fittest === | ||
| - | We use high amounts of the antibiotic kanamycin in order to select the most specific system for our substances. By | + | We use high amounts of the antibiotic kanamycin in order to select the most specific system for our substances. By varying the amount of kanamycin we will be able to carefully select the best mutant out of our PCR-tests. The mutated ''virA'' system will be induced after the error prone PCR by a mix of possible targets for the system (like capcaicin, dopamin, homovanillic acid etc.). It is important to avoid any acetosyringone, so we will be able to search for systems with new targets. |
=== The final construct=== | === The final construct=== | ||
| - | If we | + | If we don’t have enough time, we are going to transform a sensitivity tuner into the BioBricks (compare Cambridge 2009). This will increase the sensitivity of our system. So our final system will work like this: |
[[Image:Bielefeld_Vorgehen.gif]] | [[Image:Bielefeld_Vorgehen.gif]] | ||
Revision as of 22:16, 19 September 2010
Contents |
The Approach
First we looked for a sensor system which is able to detect substances and we searched for a substances of interest. The system of interest has to be taken out of a different bacteria species than Escherichia coli , in order to avoid any background. Therefore we checked the literature for a well reviewed sensor system, which is not part of the E. coli genome. The system of choice was the phenolic sensing system virA of Agrobacterium tumefaciens. It naturally detects acetosyringone, which is a secondary metabolite of plants that affects bacteria as an attractant. After repeated research to check for any other possible substances which could be detected by the system, we got a really long list of possibilities and picked 'capcaicin', which is responsible for the spiciness of edibles.
The biological steps for creating a new sensor system are:
- extract the virA system out of A. tumefaciens
- create new BioBricks out of the exciting environmental parts
- transform the new BioBricks into E. coli
- modify the system for sensibility and specificity by error prone PCR
- find and select the most promising mutants
Preparing the system
We tried to work with the already existing virA from the registry (<partinfo>K238008</partinfo>). Unfortunately this virA BioBrick did not work. The sequence data of the BioBrick did not fit to the published virA sequence. So we had to extract the virA gene via PCR out of the A. tumefaciens TI-plasmid by ourselves in order to create a new BioBrick.
VirA does not work without the help of the VirG protein. The existing virG gene in the iGEM registry contains illegal restriction sites. Moreover it needs the help of Chev Protein and sugars to work perfectly with VirA. We changed the sequence manually and had the gene synthesized by Mr. Gene.
Starting point for biobricks -> Go cloning
The applied screening system in E. coli consists of two plasmids. After discussing the possibility of creating only one big plasmid, we unifed that one plasmid would minimize the transformation efficiency and would be difficult to modify via error prone PCR. So we had to change the origin of a pSB1X3 plasmid in order to avoid compatibility problems in the transformation. Therefore we cloned the R6K origin into the <partinfo>pSB1A3</partinfo>, <partinfo>pSB1C3</partinfo> and <partinfo>pSB1T3</partinfo> plasmids. For this purpose we used the R6K sequence <partinfo>J61001</partinfo> and the pSBXXX sequence to create primers for the PCR, followed by the ligation of the PCR products.
The error prone PCR
After cloning the new origin into the pSBXXX-backbones we were able to create the two constructs. The first one will be found inside the competent bacteria cells and contains the virG gene under the constitutive promotor <partinfo>J23110</partinfo>, a terminator (<partinfo>B0017</partinfo>), a vir promotor and a readout or selection gene (luciferase, mRFP and kanamycin resistance, respectively):
The second plasmid contains the virA gene under the control of the constitutive promotor <partinfo>J23110</partinfo> and will be transformed and modified in one step via error prone PCR.
The error prone PCR is a PCR under malfunction conditions for the polymerase. It is possible to regulate the frequency of the mutagenesis by editing unbalanced concentrations of nucleotides and co-factors to the PCR. So we are going to create a new BioBrick and transform it into our target in one step. Before we are able to do the error prone PCR we need to get the backbones done.
Survival of the fittest
We use high amounts of the antibiotic kanamycin in order to select the most specific system for our substances. By varying the amount of kanamycin we will be able to carefully select the best mutant out of our PCR-tests. The mutated virA system will be induced after the error prone PCR by a mix of possible targets for the system (like capcaicin, dopamin, homovanillic acid etc.). It is important to avoid any acetosyringone, so we will be able to search for systems with new targets.
The final construct
If we don’t have enough time, we are going to transform a sensitivity tuner into the BioBricks (compare Cambridge 2009). This will increase the sensitivity of our system. So our final system will work like this:
