Computational Systems BiologyOpen OpportunitiesWe recently developed a platform in yeast (Evolverator) that can perform in vivo evolution of binding interactions and will expand this platform to evolve peptides and proteins that bind G-protein coupled receptors (GPCRs). These receptors are important drug targets, and this platform will aim to produce agonists and antagonists for these receptors, with the eventual goal of contributing to drug discovery.
One of the key components of the platform is targeted in vivo mutagenesis of the candidate binders. The more efficient this process, the more diversified the library of binders we can screen. In the first iteration of this platform, we used the MutaT7 system[1], [2] together with an adenine and a cytosine base editor. With this system, the DNA polymerase of phage T7 is fused to the base editors. We then place a T7 promoter in front of the gene we want to target. As the gene is transcribed by the T7 polymerase, the base editors introduce mutations. While this system is quite efficient, recent publications have shown that both the type of mutations and its efficiency can be further improved[3].
The challenge is to find the most efficient set up for our specific context. There are many factors to be tested, including the placement and number of T7 promoters, new and improved base editors, as well as additional proteins that have been shown to increase mutation efficiency. The goal of this master project will be to optimize the MutaT7 system for the context of the Evolverator, with which we will first evolve ligands for the mating pathway receptor STE2 as a proof of concept. You’ll be provided with direction and initial ideas, but you will be free (and expected) to bring your own ideas as you gain experience with the method.
- Genetic Technologies: Transformation, Site-directed Mutagenesis, etc.
- ETH Zurich (ETHZ), Master Thesis
| Our lab developed transcriptional control systems (Well Tempered Controllers) in yeast that allow us to control protein levels precisely within the yeast cell[1], [2]. To build WTC systems, we design new eukaryotic promoters that can be repressed by bacterial repressors (like TetR) and induce expression using small molecules (like anhydrotetracycline). These have wide ranging applications from investigating gene-gene interactions to building complex synthetic circuits within yeast.
Currently we are building one such complex circuit in yeast that will be able to evolve functional antibodies towards G-protein coupled receptors, which are important drug targets. Although we have already developed three orthogonal WTC systems that allow orthogonal control over three separate proteins within the cell, this complex circuit requires even more orthogonal systems to achieve control over different components. The aim of this project will be to design, test, and validate more orthogonal inducer-bacterial repressor pairs that can be used to build WTC systems.
- Genetic Engineering and Enzyme Technology
- ETH Zurich (ETHZ), Master Thesis
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