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Blount BA, Gowers GOF, Ho JCH, Ledesma-Amaro R, Jovicevic D, McKiernan RM, Xie ZX, Li BZ, Yuan YJ, Ellis T. Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome. Nat Commun 2018; 9:1932. [PMID: 29789540 PMCID: PMC5964169 DOI: 10.1038/s41467-018-03143-w] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/23/2018] [Indexed: 11/21/2022] Open
Abstract
Synthetic biology tools, such as modular parts and combinatorial DNA assembly, are routinely used to optimise the productivity of heterologous metabolic pathways for biosynthesis or substrate utilisation, yet it is well established that host strain background is just as important for determining productivity. Here we report that in vivo combinatorial genomic rearrangement of Saccharomyces cerevisiae yeast with a synthetic chromosome V can rapidly generate new, improved host strains with genetic backgrounds favourable to diverse heterologous pathways, including those for violacein and penicillin biosynthesis and for xylose utilisation. We show how the modular rearrangement of synthetic chromosomes by SCRaMbLE can be easily determined using long-read nanopore sequencing and we explore experimental conditions that optimise diversification and screening. This synthetic genome approach to metabolic engineering provides productivity improvements in a fast, simple and accessible way, making it a valuable addition to existing strain improvement techniques. The Sc2.0 project has built the Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system into their synthetic chromosomes. Here the authors use SCRaMbLE to rapidly develop, diversify and screen strains for diverse production and growth characteristics.
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Affiliation(s)
- B A Blount
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - G-O F Gowers
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - J C H Ho
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - R Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - D Jovicevic
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - R M McKiernan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Z X Xie
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, PR China
| | - B Z Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, PR China
| | - Y J Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, PR China
| | - T Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK. .,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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