Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods

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 () and Yizhi Cai ()
Additional contact information
Wei Liu: University of Edinburgh
Zhouqing Luo: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences
Yun Wang: BGI-Shenzhen, Beishan Industrial Zone
Nhan T. Pham: University of Edinburgh
Laura Tuck: University of Edinburgh
Irene Pérez-Pi: University of Edinburgh
Longying Liu: BGI-Shenzhen, Beishan Industrial Zone
Yue Shen: University of Edinburgh
Chris French: University of Edinburgh
Manfred Auer: University of Edinburgh
Jon Marles-Wright: Devonshire Building, Newcastle University
Junbiao Dai: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences
Yizhi Cai: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

Nature Communications, 2018, vol. 9, issue 1, 1-12

Abstract: Abstract Exogenous pathway optimization and chassis engineering are two crucial methods for heterologous pathway expression. The two methods are normally carried out step-wise and in a trial-and-error manner. Here we report a recombinase-based combinatorial method (termed “SCRaMbLE-in”) to tackle both challenges simultaneously. SCRaMbLE-in includes an in vitro recombinase toolkit to rapidly prototype and diversify gene expression at the pathway level and an in vivo genome reshuffling system to integrate assembled pathways into the synthetic yeast genome while combinatorially causing massive genome rearrangements in the host chassis. A set of loxP mutant pairs was identified to maximize the efficiency of the in vitro diversification. Exemplar pathways of β-carotene and violacein were successfully assembled, diversified, and integrated using this SCRaMbLE-in method. High-throughput sequencing was performed on selected engineered strains to reveal the resulting genotype-to-phenotype relationships. The SCRaMbLE-in method proves to be a rapid, efficient, and universal method to fast track the cycle of engineering biology.

Date: 2018
References: Add references at CitEc
Citations: View citations in EconPapers (1)

Downloads: (external link)
https://www.nature.com/articles/s41467-018-04254-0 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-04254-0

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-018-04254-0

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().