The Thuronyi lab works to design, build, and test synthetic biology tools for directed evolution in the bacterium Vibrio natriegens ("Vnat").
Synthetic biology means engineering living things for human purposes. Synbio practitioners design and create custom DNA to reprogram organisms (especially, but not only, bacteria) to do useful things that they don't do in nature. As an engineering field, synbio relies on the design-build-test-learn cycle. Living things aren't "designed" to be engineerable, but working to make that more possible is teaching us both how to do biological engineering better and more about how life works. Synbio parts and devices can be improved by directed evolution...
Directed evolution uses the principles of natural evolution to create new biological function in the lab. It's like selective breeding (which gave us things like sweet corn and poodles) but much faster and usually with more molecular-level understanding. Dr. Frances Arnold won the Nobel Prize in Chemistry in 2018 for directed evolution of enzymes. Directed evolution works best when researchers can try out millions or billions of possible variations on a gene, pathway, or organism, to find the extremely rare ones that perform better than what they started with. Directed evolution can benefit from new hosts and tools...
Vnat is a bacterium (Vibrio natriegens, officially) that might be the fastest-growing organism discovered so far. It's been known for decades but only adopted by synthetic biologists in the mid 2010s. Vnat needs high salt to be comfortable but it can double every 10-15 minutes at 30 or 37 °C, which means growth in a few hours that would take E. coli all day. (The side-by-side comparison shown below is from Lee, H. H. et al. Nat. Microbiol. 4, 1105–1113 2019.) It's also naturally transformable, meaning that it can assimilate DNA from its environment and put it right into its genome, making it highly engineerable. Fast growth and easy genetic engineering make it a great host organism for synbio and directed evolution, once the necessary parts, tools, and methods are worked out. That's where we come in...
Our current research goals:
- Finishing the development of our collaborative DNA construction tool (a monster Google Sheet) and getting it ready to share with other labs
- Creating tools to improve the natural transformation of plasmids and testing their effectiveness
- Learning how best to work with Vnat and how to use it for synbio
Big picture goals:
- Implementing the tools directed evolution relies on, like:
- elevated mutation rates (for making diverse variations on its genome)
- selection tools (for allowing only improved variants to grow and pass on their genes)
- cultivation techniques (for continuous growth and selection, to create pools of variants in the billions)
- Aiming to set up genome shuffling in our favorite bug, a method that lets prokaryotes (like Vnat) exchange and recombine their genes just like eukaryotes do, by taking advantage of natural transformation