iGEM

iGEM is the world's largest synthetic biology competition, with hundreds of student teams competing from universities all over the world. The Imperial iGEM 2022 team worked on B. subtilis germination and its potential applications to combat plant diseases. I worked with the bioinformatics subgroup and spent the summer studying B. subtilis germinant receptor proteins, which gave me a good introduction to several protein analysis tools. We used these to design a combinatorial mutant library for a protein design experiment, drawing on AlphaFold structure prediction, sequence alignments, homology models, and comparison with the literature. The project placed in the top 10 of the competition overall.

It was a great learning experience, and completely undirected. We came up with the problem and the solution ourselves, and raised all the funding too — more than £30k overall.

Our ambitious goal was to perform directed evolution on the B. subtilis germinant receptor so that it would initiate germination in the presence of a molecule found in stem rust, a fungal disease that affects wheat, and trigger antifungal properties in response. We quickly realised this was unfeasible over a single summer, so we settled on one round of screening across a collection of protein mutants, chosen using computational tools and the literature. We narrowed the search space by identifying key binding pocket residues in the GerA receptor's B subunit — otherwise, the mutant library would have been astronomically too large to screen. We also consulted structural biologists and the authors of several of the B. subtilis germination papers to learn as much as we could about the pathway. Something that surprised me was that the more specific our questions became, the less was actually known — there were papers with conflicting conclusions, and real uncertainty about the nature of the germination pathway itself.