This year's iGEM Giant Jamboree brought a real-life science fairy tale to the senior category's grand prize-winning team, Team Marburg, a team of 15 German master's students studying traditional biology, molecular and cellular biology science, chemistry, physics, and computer science. The idea, first hatched at a conference in 2017 and made possible in large part by lab automation leader Opentrons' OT-2 pipetting robot, ended up with a grand prize and a new biological tool that could transform The way synthetic biologists create new products. Metabolic pathways, genetic circuits, and other DNA structures.

The winning project? VibriGens, based on a new bacterial chassis organism: Vibrio natrigeni, the world's fastest growing bacterium with a doubling time of 10 minutes or less (compared to the gold standard chassis organism E. coli every half hours doubled). The team worked to establish protocols for cloning, protein expression, and protein interaction studies with V. natriegens and established a set of strains optimized for each application (any researcher can request one by emailing the team). They also created the "Marburg Collection," a Golden Gate-based cloning toolbox that enables researchers to combine any plasmid origin of replication, antibiotic resistance, and their desired target gene, eliminating the need to rely on vectors. Although the cloning toolbox was originally created for V. natriegens, the team ultimately designed it to be universally applicable to many different host organisms. Like their optimized strains, the Marburg strain will also be made available to researchers.

A long time ago...an idea was born

The choice of V. natriegens was no accident. The team first heard about the organism at a 2017 meeting of the German Society for Synthetic Biology in Marburg. One of the speakers was introducingV. natriegensand when the team learned not only how fast it grew, but also that no one was really using this organism, they started thinking about using it. Helping the synthetic biology community. , it's an organism that's never been used in an iGEM competition, so we can implement something new - and it could really help a lot of people. Because in every field of synthetic biology, you need an organism to build your structure. So we're going to have a project that affects everyone, so we thought it might be a good thing for us to build that up. ” explains team member Daniel Marchal. Because it lives in salt water, V. natriegens can also tolerate higher levels of salt than E. coli , making it It is more suitable for some environmental applications that require higher salt levels (for example, optimizing the bacterial degradation of plastics in the ocean). Since most organisms cannot tolerate high salt levels,V. natriegens is used, says team member Rene Inckemann. Theprotocols are also less likely to be contaminated, which is crucial when designing products for market with high purity of DNA or proteins, something Inkerman likes to do with antimalarial drugs. Take mycobacteria as an example.

"The development of antimycin took about seven years. Imagine if you usedVibriocould we speed up these processes, the development time?" he asked. He also sees Vibrio as a useful tool for synthetic biologists studying protein evolution, engineering proteins and enzymes, or designing genetic circuits. Basically, using the world's fastest-growing organisms increases the speed at which various parts can be developed, which is a good thing for synthetic biology. As more research groups, companies, and other organizations work to accelerate various aspects of synthetic biology, the synthetic biology stack (a layered integration of biological reagents, process execution tools, and biological CAD/CAM tools) continues to evolve. , to facilitate rapid product design and development) is constantly evolving. The Marburg team has essentially created a new tool at the biology layer of the synthetic biology stack that is well on its way to making it faster and easier for synthetic biologists around the world to do science. Automation plays a key role in helping them achieve this goal.

Make projects possible through automation

"When you think about cloning in a day or 12 hours - what we're proposing, a lot of people would say that's too much to implement in their daily workflow. We got this response early on in the project, "Inkerman said. “So we thought about lab automation and how to make this happen as early as possible.” The team submitted proposals to several lab automation companies to get automation support for their project. Opentrons is one of those companies. "We received 77 proposals in two weeks," said Kristin Ellis, director of scientific development at Opentrons, who found it difficult to select just ten teams from all the excellent submissions it received. . But choosing the Marlborough team was a "no brainer". "I'm shocked by what they're proposing," Ellis said. She was particularly drawn to their vision of reducing bacterial transformation time from days to 12 hours—the same vision that many others were skeptical of.

Ellis also appreciates the iGEM interlaboratory study proposed by the Marburg team, through which they plan to share V. natriegens and its protocols with other iGEM teams to understand how the bacteria behave in other laboratories Way. This is a particularly important component of Opentrons, which emphasizes and supports open source, collaboration, and reproducible science. Because OT-2 hadn't even been released when the proposal was due (it was announced in March and released in June), the Marburg team and the nine other iGEM teams that received OT-2 were the first in the world to use the robot ( Guinea pigs, so to speak) to produce brand new products. Experience in lab automation — some of us had taken a few college courses but had no real experience," Inkerman said. "But it turned out to be very easy to use the OT-2.

"In fact, their first protocol (replicating strains in 96-well plates) was up and running on the OT-2 in just one day. Crucially, with the OT-2, the team could spend their time Design and conceptualize the project while the robots run the experiments for them, saving months of human time and allowing the team to complete the project over the summer. The team even had time to build its own tool - Opentrons - on top of the OT-2 software. All users are encouraged to do this. The Marburg team built an easy-to-use interface that allows users to choose from 8 components or "tools" provided in the Marburg Toolbox. Once they make their selection, the robot knows what to do with each one. components to build the user's custom plasmid without any further input.