Taking Automated Strain Engineering to new heights

Engineering microbes to produce fuels and chemicals economically requires iterative design-build-test cycles of genome engineering. The Amyris pipeline for executing these cycles is called Automated Strain Engineering (ASE). Hundreds of DNA constructs are built every 3 weeks, integrated into yeast strains, and the strains tested in high throughput for desired phenotypes, such as increased yield and productivity of the desired product. Extremely important to the overall success of this pipeline is rapid, cost-effective, and accurate assembly of large DNA constructs. Current DNA assembly methods are limited in the number of parts that can be assembled efficiently or are slow and labor-intensive. To address this deficiency Amyris has developed an assembly method called the Ligase Chain Reaction (LCR), which can efficiently assemble large numbers of DNA parts relatively rapidly. To ensure that each DNA construct built has the intended sequence, quality control (QC) is also essential. Until now full sequence QC methods have been too expensive, but we have developed methods to obtain the full sequence of thousands of plasmids in a single MiSeq run, dramatically reducing costs. We will discuss the development of both these tools in detail and present data on their performance within our ASE pipeline. These tools will significantly benefit the entire synthetic biology community, allowing sustainable biological solutions to be applied to many new products.