From genetic parts to neochromosome in yeast

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This project aims to develop tools which can be used for the rapid generation and testing of engineered yeast strains which can be applied to many different industrial and healthcare needs, using the tools of synthetic biology. Synthetic biology, also known as biological engineering, is a rapidly developing discipline which aims to apply the techniques of engineering to the creation of new and useful biological systems. One of the most useful organisms for such projects is ordinary baker's yeast, Saccharomyces cerevisiae. Yeast has been used in human food and beverage technology for thousands of years, and is currently used on an enormous scale worldwide for the production of bread, alcoholic beverages, and biofuels, among other products. Because of its long history of safe use, the availability of very large scale production technologies, and its widespread use in laboratories to study the basic processes of life, yeast is an ideal starting point for many biological engineering projects. Some recent examples include the manufacture of the anti-malarial drug artemisinin in yeast, as an alternative to plant sources, as well as the manufacture of the hydrocarbon fuel farnesene, and the recent demonstration that important pain-killers such as hydrocodone can be produced in modified yeast.Because engineering of biology is still as much an art as a science, it can be very useful to assemble and test many different variants of a system, to see which variants work best, as a starting point for further engineering. To do this kind of 'rapid prototyping' on a large scale requires the use of automated systems, which use robots to perform all of the necessary operations, from DNA assembly through strain construction to final testing. One major manufacturer of such automation is Thermo-Fisher, the industrial partner in this project. Thermo-Fisher automation systems constitute a platform which can assemble and test DNA constructs on a very large scale, to facilitate the rapid creation of new strains which can be applied to solve industrial and healthcare problems. To aid in this process, many different technologies are used. For example, a library of yeast DNA 'parts' is available in a format called 'YeastFab', which allows rapid automated assembly to join parts together in different combinations. Software tools are also required to aid in the design process and to keep track of parts and their properties. Thermo-Fisher's automation is controlled by software called 'Momentum'.In this project, we aim to develop a suite of tools which can be used to join all of these processes together, to enable users to take full advantage of the speed and flexibility of automated assembly and testing platforms. Specifically, we will develop and test software tools which link biological design tools and DNA library curation software to the Momentum software which controls the automated systems, enabling a seamless transition from design to construction and testing. We will use these tools to increase the usefulness of the system by expanding our YeastFab library of natural yeast promoters (DNA 'control' sequences, essential for building genetic machines) and generating new synthetic promoters which can be used to control engineered systems. We will also develop and test 'neochromosome' technology which allows the construction of entire new chromosomes in yeast, allowing the assembly of the very large metabolic pathways required for the production of many biological products such as antibiotics and anti-cancer drugs. Finally, we will demonstrate the effectiveness of these technologies by assembling a number of demonstration pathways. All of the software tools developed will be made available on an open source basis for the benefit of the user community.