By linking cell survival to the production of their target compound, the team was able to make the microbe able to produce xanthomatin. To do this, they started with a genetically engineered “sick” cell that could only survive if it produced both the desired pigment as well as a second chemical called formic acid. For every molecule of pigment produced, the cell also produced one molecule of formic acid. Formic acid, in turn, provides fuel for cell growth, forming a self-sustaining loop that drives pigment production.
Bushin said, “We have made it so that activity through this pathway, making the compound of interest, is absolutely essential for life. If the organism does not make xanthomatin, it will not evolve.”
To further enhance the cells’ ability to produce pigments, the team used robots to grow and adapt the engineered microbes through two high-throughput adaptive laboratory evolution campaigns, which were developed by the lab of study co-author Adam Feist, professor in the Shu Chien-Jean Le Department of Bioengineering at the UC San Diego Jacobs School of Engineering and senior scientist at the Novo Nordisk Foundation Center for Biosustainability. The team also applied custom bioinformatics tools from the Fist lab to identify key genetic mutations that increased efficiency and enabled the bacteria to produce pigments directly from a single nutrient source.
“This project offers a glimpse of a future where biology enables the sustainable production of valuable compounds and materials through advanced automation, data integration and computationally driven design,” Feist said. “Here, we show how we can accelerate innovation in biomanufacturing by bringing together engineers, biologists and chemists using some of the most advanced strain-engineering techniques to develop and optimize a new product in a relatively short time.”