Enzymes are the machines of biological engineering, performing the chemical transformations of the living world. Biodiversity holds an incredible array of evolved enzyme sequences with crucial functions. We use DNA synthesis and the foundry to discover the best enzyme for each job, whether to produce a cultured ingredient or to make a better cheese.
There are hundreds of thousands of enzymes that are relevant to the the sorts of products we are building at Ginkgo, encoded by an estimated 65 billion base pairs of DNA sequence. We use custom built software tools to search through that vast evolutionary space and design DNA sequences for rapid and large scale enzyme discovery.
Writing the DNA sequences and engineering them into yeast cells brings these enzymes to life. Leveraging the foundries and our DNA synthesis partnerships, we have synthesized, built, and tested thousands of variants from dozens of enzyme classes important for our products, identifying the sequences that deliver. For one key enzyme important in producing a large number of cultured fragrances, we have synthesized and screened over 8,000 variants, identifying key enzymes, new pathways, and new insights for future designs.
When designing a new genetic pathway made up of several enzymes, we test hundreds of combinatorial possibilities to find the optimal combination of variants. Sometimes the best combinations come from unexpected places—for one cultured ingredient we used enzymes from a yeast, a fruit, and a mustard plant. Only by testing these variants with the foundry could we identify the optimal combination.
Enzyme discovery and synthetic metagenomics enable organism engineers to identify powerful variants and optimize enzyme pathways. Identifying new enzymes is crucial to building new pathways to cultured ingredients and finding enzymes that can function in other applications, from brewing and baking to pharmaceuticals.