In vitro DNA SCRaMbLE

Yi Wu; Rui Ying Zhu; Leslie A. Mitchell; Lu Ma; Rui Liu; Meng Zhao; Bin Jia; Hui Xu; Yun Xiang Li; Zu Ming Yang; Yuan Ma; Xia Li; Hong Liu; Duo Liu; Wen Hai Xiao; Xiao Zhou; Bing Zhi Li; Ying Jin Yuan; Jef D. Boeke

doi:10.1038/s41467-018-03743-6

In vitro DNA SCRaMbLE

Yi Wu, Rui Ying Zhu, Leslie A. Mitchell, Lu Ma, Rui Liu, Meng Zhao, Bin Jia, Hui Xu, Yun Xiang Li, Zu Ming Yang, Yuan Ma, Xia Li, Hong Liu, Duo Liu, Wen Hai Xiao, Xiao Zhou, Bing Zhi Li, Ying Jin Yuan, Jef D. Boeke

Biomedical Engineering

Research output: Contribution to journal › Article › peer-review

Abstract

The power of synthetic biology has enabled the expression of heterologous pathways in cells, as well as genome-scale synthesis projects. The complexity of biological networks makes rational de novo design a grand challenge. Introducing features that confer genetic flexibility is a powerful strategy for downstream engineering. Here we develop an in vitro method of DNA library construction based on structural variation to accomplish this goal. The "in vitro SCRaMbLE system" uses Cre recombinase mixed in a test tube with purified DNA encoding multiple loxPsym sites. Using a β-carotene pathway designed for expression in yeast as an example, we demonstrate top-down and bottom-up in vitro SCRaMbLE, enabling optimization of biosynthetic pathway flux via the rearrangement of relevant transcription units. We show that our system provides a straightforward way to correlate phenotype and genotype and is potentially amenable to biochemical optimization in ways that the in vivo system cannot achieve.

Original language	English (US)
Article number	1935
Journal	Nature communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-03743-6
State	Published - Dec 1 2018

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

Access to Document

10.1038/s41467-018-03743-6

Cite this

@article{66d604789afd4caf8b1ac6b34a1540e0,

title = "In vitro DNA SCRaMbLE",

abstract = "The power of synthetic biology has enabled the expression of heterologous pathways in cells, as well as genome-scale synthesis projects. The complexity of biological networks makes rational de novo design a grand challenge. Introducing features that confer genetic flexibility is a powerful strategy for downstream engineering. Here we develop an in vitro method of DNA library construction based on structural variation to accomplish this goal. The {"}in vitro SCRaMbLE system{"} uses Cre recombinase mixed in a test tube with purified DNA encoding multiple loxPsym sites. Using a β-carotene pathway designed for expression in yeast as an example, we demonstrate top-down and bottom-up in vitro SCRaMbLE, enabling optimization of biosynthetic pathway flux via the rearrangement of relevant transcription units. We show that our system provides a straightforward way to correlate phenotype and genotype and is potentially amenable to biochemical optimization in ways that the in vivo system cannot achieve.",

author = "Yi Wu and Zhu, {Rui Ying} and Mitchell, {Leslie A.} and Lu Ma and Rui Liu and Meng Zhao and Bin Jia and Hui Xu and Li, {Yun Xiang} and Yang, {Zu Ming} and Yuan Ma and Xia Li and Hong Liu and Duo Liu and Xiao, {Wen Hai} and Xiao Zhou and Li, {Bing Zhi} and Yuan, {Ying Jin} and Boeke, {Jef D.}",

note = "Funding Information: This work was funded by the National Natural Science Foundation of China (21750001, 21621004, and 21676192), the Ministry of Science and Technology of China (“973” Program, 2014CB745100), and the International S&T Cooperation Program of China (2015DFA00960), and US research was funded by NSF grants MCB-1026068 and MCB-1158201. We thank Andrew Martin, Yu Zhao, Mingzhe Han, and Sijie Zhou for their technical support. Publisher Copyright: {\textcopyright} 2018 The Author(s).",

year = "2018",

month = dec,

day = "1",

doi = "10.1038/s41467-018-03743-6",

language = "English (US)",

volume = "9",

journal = "Nature communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

number = "1",

}

TY - JOUR

T1 - In vitro DNA SCRaMbLE

AU - Wu, Yi

AU - Zhu, Rui Ying

AU - Mitchell, Leslie A.

AU - Ma, Lu

AU - Liu, Rui

AU - Zhao, Meng

AU - Jia, Bin

AU - Xu, Hui

AU - Li, Yun Xiang

AU - Yang, Zu Ming

AU - Ma, Yuan

AU - Li, Xia

AU - Liu, Hong

AU - Liu, Duo

AU - Xiao, Wen Hai

AU - Zhou, Xiao

AU - Li, Bing Zhi

AU - Yuan, Ying Jin

AU - Boeke, Jef D.

N1 - Funding Information: This work was funded by the National Natural Science Foundation of China (21750001, 21621004, and 21676192), the Ministry of Science and Technology of China (“973” Program, 2014CB745100), and the International S&T Cooperation Program of China (2015DFA00960), and US research was funded by NSF grants MCB-1026068 and MCB-1158201. We thank Andrew Martin, Yu Zhao, Mingzhe Han, and Sijie Zhou for their technical support. Publisher Copyright: © 2018 The Author(s).

PY - 2018/12/1

Y1 - 2018/12/1

N2 - The power of synthetic biology has enabled the expression of heterologous pathways in cells, as well as genome-scale synthesis projects. The complexity of biological networks makes rational de novo design a grand challenge. Introducing features that confer genetic flexibility is a powerful strategy for downstream engineering. Here we develop an in vitro method of DNA library construction based on structural variation to accomplish this goal. The "in vitro SCRaMbLE system" uses Cre recombinase mixed in a test tube with purified DNA encoding multiple loxPsym sites. Using a β-carotene pathway designed for expression in yeast as an example, we demonstrate top-down and bottom-up in vitro SCRaMbLE, enabling optimization of biosynthetic pathway flux via the rearrangement of relevant transcription units. We show that our system provides a straightforward way to correlate phenotype and genotype and is potentially amenable to biochemical optimization in ways that the in vivo system cannot achieve.

AB - The power of synthetic biology has enabled the expression of heterologous pathways in cells, as well as genome-scale synthesis projects. The complexity of biological networks makes rational de novo design a grand challenge. Introducing features that confer genetic flexibility is a powerful strategy for downstream engineering. Here we develop an in vitro method of DNA library construction based on structural variation to accomplish this goal. The "in vitro SCRaMbLE system" uses Cre recombinase mixed in a test tube with purified DNA encoding multiple loxPsym sites. Using a β-carotene pathway designed for expression in yeast as an example, we demonstrate top-down and bottom-up in vitro SCRaMbLE, enabling optimization of biosynthetic pathway flux via the rearrangement of relevant transcription units. We show that our system provides a straightforward way to correlate phenotype and genotype and is potentially amenable to biochemical optimization in ways that the in vivo system cannot achieve.

UR - http://www.scopus.com/inward/record.url?scp=85047751666&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85047751666&partnerID=8YFLogxK

U2 - 10.1038/s41467-018-03743-6

DO - 10.1038/s41467-018-03743-6

M3 - Article

C2 - 29789594

AN - SCOPUS:85047751666

SN - 2041-1723

VL - 9

JO - Nature communications

JF - Nature communications

IS - 1

M1 - 1935

ER -

In vitro DNA SCRaMbLE

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this