Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods
Authors: Wei Liu, Zhouqing Luo, Yun Wang, Nhan T Pham, Laura Tuck, Irene Pérez-Pi, Longying Liu, Yue Shen, Chris French, Manfred Auer, Jon Marles-Wright, Junbiao Dai, Yizhi Cai
Journal: Nature Communications
Publication Date: 22 May, 2018
Department of: Chemistry
Faster genome evolution methods to transform yeast for industrial biotech
Researchers have created a toolkit to enable rapid metabolic engineering in yeast, termed SCRaMbLE-in. Metabolic engineering of an organism, to optimise genetic and regulatory processes within cells to produce a desired product, normally relies on time-consuming trial-and-error approaches to optimise both the production pathway for expression in a non-native host, and the host itself to support the expression of the pathway. SCRaMbLE-in aims to overcome this.
Researchers at the Universities of Manchester, Edinburgh and Newcastle, together with collaborators in China are collaborating in the ongoing ”Sc2.0” project to construct a synthetic yeast genome. This provides an artificial means of prompting evolution, called ”SCRaMbLE” (Synthetic Chromosome Rearrangement and Modification by loxP-mediated Evolution), to facilitate rapid rearrangement of the yeast genome. When carried out under selective conditions, this evolution can be directed to produce yeast strains with desired properties.
The SCRaMbLE-in toolkit presented here firstly rapidly prototypes and diversifies gene expression, and secondly uses SCRaMbLE to integrate the pathway into the synthetic genome, and optimise the host strain. The researchers demonstrate the use of SCRaMbLE-in to assemble, diversify and integrate exemplar yeast production pathways for the vitamin A precursor ß-carotene and the antibiotic violacein. They have shown that the SCRaMbLE-in method is a rapid, efficient and universal method to fast-track the engineering of biology. It is expected to expedite metabolic engineering to produce yeast strains for use in many fields of industrial biotechnology, including fine chemical and biofuel production.
- The Sc2.0 project is an international collaboration, to construct the first synthetic eukaryotic genome; that of the budding yeast S. cerevisiae.
- The Sc2.0 project introduces several design changes to the yeast genome, including the introduction of loxPsym sites.
- LoxPsym sites are symmetrical DNA sequences that can recombine upon induction, causing rearrangements of the synthetic DNA.
- Inclusion of loxPsym sites in the yeast genome allows the researcher to “SCRaMbLE” the genome, rearranging it in ways that may create a strain with preferential characteristics.
- Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences
- BGI-Shenzhen, Beishan Industrial Zone, 518083, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, 518120, Shenzhen, China
- University of Newcastle
- University of Edinburgh
- Manchester Institute of Biotechnology