Edinburgh Research Explorer

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

Research output: Contribution to journalArticle

Related Edinburgh Organisations

Open Access permissions



  • Download as Adobe PDF

    Rights statement: Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/ licenses/by/4.0/. © The Author(s) 2018

    Final published version, 2.84 MB, PDF document

    Licence: Creative Commons: Attribution (CC-BY)

Original languageEnglish
Article number1936
Number of pages12
JournalNature Communications
Issue number1
Publication statusPublished - 22 May 2018


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 rapid 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.

    Research areas

  • Genomic engineering, Metabolic engineering, Synthetic biology

Download statistics

No data available

ID: 59357877