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Team:EPF-Lausanne
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Our project goal was to set up a high-throughput method for generating and characterizing new transcription factors (TFs) that would recognize different promoter sequences. We mutated the TetR transcription factor and got about ten interesting mutants. For each of them, we individually characterized their affinity to the consensus sequence (the Ptet promoter) as well as their position-weight matrices. This characterization was done <i>in vitro</i> on a microfluidic chip, allowing to test a single mutant against hundreds of Ptet sequences. | Our project goal was to set up a high-throughput method for generating and characterizing new transcription factors (TFs) that would recognize different promoter sequences. We mutated the TetR transcription factor and got about ten interesting mutants. For each of them, we individually characterized their affinity to the consensus sequence (the Ptet promoter) as well as their position-weight matrices. This characterization was done <i>in vitro</i> on a microfluidic chip, allowing to test a single mutant against hundreds of Ptet sequences. | ||
| - | The next step of the characterization is an <i>in vivo</i> readout system; we created and tested 2 different reporter systems based on RFP expression, with either a positive or negative selection of the TetR-Ptet interaction. Wanting a high-throughput method, we decided also to use a lysis cassette as a reporter gene. The idea is to transform cells with one plasmid containing a TetR mutant and another plasmid containing a Ptet sequence(either the consensus or a mutated one), then to kill the cells in which the TetR mutant recognizes the Ptet sequence, in order to recover their DNA. This can then be coupled to microfluidics chemostat chambers, where hundreds of cell colonies can be grown at the same time. We also created T7 promoter variants, that can be coupled to the RFP or lysis genes, allowing modularity in the readout systems. Lysis ad DNA recovery experiments have been efficiently conducted, demonstrating the feasibility of our project design. | + | The next step of the characterization is an <i>in vivo</i> readout system; we therefore created and tested 2 different reporter systems based on RFP expression, with either a positive or negative selection of the TetR-Ptet interaction. Wanting a high-throughput method, we decided also to use a lysis cassette as a reporter gene. The idea is to transform cells with one plasmid containing a TetR mutant and another plasmid containing a Ptet sequence(either the consensus or a mutated one), then to kill the cells in which the TetR mutant recognizes the Ptet sequence, in order to recover their DNA. This can then be coupled to microfluidics chemostat chambers, where hundreds of cell colonies can be grown at the same time. We also created T7 promoter variants, that can be coupled to the RFP or lysis genes, allowing modularity in the readout systems. Lysis ad DNA recovery experiments have been efficiently conducted, demonstrating the feasibility of our project design. |
Revision as of 21:36, 18 September 2011
Welcome
It's on! After some warmup experiments during the semester, our team is now fully operational, and already having trouble getting away from the lab. Follow our adventures on twitter: IGEM_EPFL
Team, remember the Todo List
Project summary
Our project goal was to set up a high-throughput method for generating and characterizing new transcription factors (TFs) that would recognize different promoter sequences. We mutated the TetR transcription factor and got about ten interesting mutants. For each of them, we individually characterized their affinity to the consensus sequence (the Ptet promoter) as well as their position-weight matrices. This characterization was done in vitro on a microfluidic chip, allowing to test a single mutant against hundreds of Ptet sequences.
The next step of the characterization is an in vivo readout system; we therefore created and tested 2 different reporter systems based on RFP expression, with either a positive or negative selection of the TetR-Ptet interaction. Wanting a high-throughput method, we decided also to use a lysis cassette as a reporter gene. The idea is to transform cells with one plasmid containing a TetR mutant and another plasmid containing a Ptet sequence(either the consensus or a mutated one), then to kill the cells in which the TetR mutant recognizes the Ptet sequence, in order to recover their DNA. This can then be coupled to microfluidics chemostat chambers, where hundreds of cell colonies can be grown at the same time. We also created T7 promoter variants, that can be coupled to the RFP or lysis genes, allowing modularity in the readout systems. Lysis ad DNA recovery experiments have been efficiently conducted, demonstrating the feasibility of our project design.
Results for the TetR mutants, reporter systems, T7 promoter variants and DNA recovery experiments can be found on the data page.
For more details on the assembly and mutagenesis strategies, please refer to the following pages: TetR mutants, T7 promoter variants, Reporter plasmids.
