Towards Genomes-to-Design: Building and Testing a Minimal Essential Chromosome

点击翻译按钮获取中文摘要

Synthetic biology follows engineering principles to build novel devices, pathways and circuits encoded by modular DNA parts, and more recently has turned to the engineering of entire genomes in living cells. The aim of much of the work of synthetic biology is to design and build cells to perform useful new functions they typically don't perform in nature. To further this field, it is important to engineer the workhorse living cell so that they perform their new tasks reliably and reproducibly. To this end there is significant interest in developing simplified cells built with minimal genomes. Through genome engineering and synthesis, it should be possible to create genomes that do not encode the many genes driving processes unnecessary for the cell to perform its main desired function. The work proposed here aims to accelerate the engineering and synthesis of such minimal genomes, by being the first project to build a working chromosome from just the elements deemed essential to support the cell for its function in the lab. Cells growing with this minimal genome should theoretically be more efficient at performing engineered tasks, such as the biosynthesis of a drug molecule at high yields. Our work will therefore be able to produce specialist strains valuable for use in biotechnology.To achieve this, we plan to use knowledge and tools gained from our work as part of the international Sc2.0 project, which is constructing an entirely synthetic genome for baker's yeast (Saccharomyces cerevisiae). We have just completed construction of one chromosome for this project, which now encodes all 334 genes normally found on its natural counterpart. In this project, we aim to replace this entire chromosome with a much smaller minimal version built-up from modules of DNA that each encode one of the genes from this chromosome deemed essential for cell growth in the lab. To do this we will use system called SCRaMbLE that is hard-coded into the DNA of our recently completed synthetic chromosome. Switching this system on leads to genes unnecessary for growth being automatically lost from the growing cells. Doing this at a large scale with our engineered yeast cells and then genome-sequencing whole populations, should provide us with a rich set of data that tells us which genes are required for growth of the yeast in the lab. With this important new dataset in hand, we will then proceed to building our minimal synthetic chromosome and assessing its ability to replace a full chromosome in growing yeast cells. We plan to measure how cells with the minimal chromosome perform in a variety of conditions and determine whether they can grow and express genes with greater efficiency than normal yeast, now that redundant DNA has been removed. This will generate important new insights for understanding how cells consume resources efficiently and have evolved to encode many non-essential genes on their genomes. It will also give us an opportunity to produce new specialist cells for use in biotechnology, and we plan to test our minimal chromosome yeast for their ability to produce a variety of drug molecules that are valuable for industry and particularly for UK industrial collaborators.