Precise control of SCRaMbLE in synthetic haploid and diploid yeast

Bin Jia; Yi Wu; Bing Zhi Li; Leslie A. Mitchell; Hong Liu; Shuo Pan; Juan Wang; Hao Ran Zhang; Nan Jia; Bo Li; Michael Shen; Ze Xiong Xie; Duo Liu; Ying Xiu Cao; Xia Li; Xiao Zhou; Hao Qi; Jef D. Boeke; Ying Jin Yuan

doi:10.1038/s41467-018-03084-4

Precise control of SCRaMbLE in synthetic haploid and diploid yeast

Bin Jia, Yi Wu, Bing Zhi Li, Leslie A. Mitchell, Hong Liu, Shuo Pan, Juan Wang, Hao Ran Zhang, Nan Jia, Bo Li, Michael Shen, Ze Xiong Xie, Duo Liu, Ying Xiu Cao, Xia Li, Xiao Zhou, Hao Qi, Jef D. Boeke, Ying Jin Yuan

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

Abstract

Compatibility between host cells and heterologous pathways is a challenge for constructing organisms with high productivity or gain of function. Designer yeast cells incorporating the Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system provide a platform for generating genotype diversity. Here we construct a genetic AND gate to enable precise control of the SCRaMbLE method to generate synthetic haploid and diploid yeast with desired phenotypes. The yield of carotenoids is increased to 1.5-fold by SCRaMbLEing haploid strains and we determine that the deletion of YEL013W is responsible for the increase. Based on the SCRaMbLEing in diploid strains, we develop a strategy called Multiplex SCRaMbLE Iterative Cycling (MuSIC) to increase the production of carotenoids up to 38.8-fold through 5 iterative cycles of SCRaMbLE. This strategy is potentially a powerful tool for increasing the production of bio-based chemicals and for mining deep knowledge.

Original language	English (US)
Article number	1933
Journal	Nature communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-03084-4
State	Published - Dec 1 2018

ASJC Scopus subject areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)

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Precise control of SCRaMbLE in synthetic haploid and diploid yeast. / Jia, Bin; Wu, Yi; Li, Bing Zhi; Mitchell, Leslie A.; Liu, Hong; Pan, Shuo; Wang, Juan; Zhang, Hao Ran; Jia, Nan; Li, Bo; Shen, Michael; Xie, Ze Xiong; Liu, Duo; Cao, Ying Xiu; Li, Xia; Zhou, Xiao; Qi, Hao; Boeke, Jef D.; Yuan, Ying Jin.

In: Nature communications, Vol. 9, No. 1, 1933, 01.12.2018.

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

Jia, Bin ; Wu, Yi ; Li, Bing Zhi ; Mitchell, Leslie A. ; Liu, Hong ; Pan, Shuo ; Wang, Juan ; Zhang, Hao Ran ; Jia, Nan ; Li, Bo ; Shen, Michael ; Xie, Ze Xiong ; Liu, Duo ; Cao, Ying Xiu ; Li, Xia ; Zhou, Xiao ; Qi, Hao ; Boeke, Jef D. ; Yuan, Ying Jin. / Precise control of SCRaMbLE in synthetic haploid and diploid yeast. In: Nature communications. 2018 ; Vol. 9, No. 1.

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title = "Precise control of SCRaMbLE in synthetic haploid and diploid yeast",

abstract = "Compatibility between host cells and heterologous pathways is a challenge for constructing organisms with high productivity or gain of function. Designer yeast cells incorporating the Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system provide a platform for generating genotype diversity. Here we construct a genetic AND gate to enable precise control of the SCRaMbLE method to generate synthetic haploid and diploid yeast with desired phenotypes. The yield of carotenoids is increased to 1.5-fold by SCRaMbLEing haploid strains and we determine that the deletion of YEL013W is responsible for the increase. Based on the SCRaMbLEing in diploid strains, we develop a strategy called Multiplex SCRaMbLE Iterative Cycling (MuSIC) to increase the production of carotenoids up to 38.8-fold through 5 iterative cycles of SCRaMbLE. This strategy is potentially a powerful tool for increasing the production of bio-based chemicals and for mining deep knowledge.",

author = "Bin Jia and Yi Wu and Li, {Bing Zhi} and Mitchell, {Leslie A.} and Hong Liu and Shuo Pan and Juan Wang and Zhang, {Hao Ran} and Nan Jia and Bo Li and Michael Shen and Xie, {Ze Xiong} and Duo Liu and Cao, {Ying Xiu} and Xia Li and Xiao Zhou and Hao Qi and Boeke, {Jef D.} and Yuan, {Ying Jin}",

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). We thank Hui-Min Liu and Zi-Xi Chen for help on mating type switching of synX yeast and flow cytometer experiments. We thank Wen-Hai Xiao and Ming-Zhu Ding for help on transcriptome analysis and helpful discussion. 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). We thank Hui-Min Liu and Zi-Xi Chen for help on mating type switching of synX yeast and flow cytometer experiments. We thank Wen-Hai Xiao and Ming-Zhu Ding for help on transcriptome analysis and helpful discussion. Publisher Copyright: {\textcopyright} 2018 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",

year = "2018",

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day = "1",

doi = "10.1038/s41467-018-03084-4",

language = "English (US)",

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T1 - Precise control of SCRaMbLE in synthetic haploid and diploid yeast

AU - Jia, Bin

AU - Wu, Yi

AU - Li, Bing Zhi

AU - Mitchell, Leslie A.

AU - Liu, Hong

AU - Pan, Shuo

AU - Wang, Juan

AU - Zhang, Hao Ran

AU - Jia, Nan

AU - Li, Bo

AU - Shen, Michael

AU - Xie, Ze Xiong

AU - Liu, Duo

AU - Cao, Ying Xiu

AU - Li, Xia

AU - Zhou, Xiao

AU - Qi, Hao

AU - Boeke, Jef D.

AU - Yuan, Ying Jin

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). We thank Hui-Min Liu and Zi-Xi Chen for help on mating type switching of synX yeast and flow cytometer experiments. We thank Wen-Hai Xiao and Ming-Zhu Ding for help on transcriptome analysis and helpful discussion. 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). We thank Hui-Min Liu and Zi-Xi Chen for help on mating type switching of synX yeast and flow cytometer experiments. We thank Wen-Hai Xiao and Ming-Zhu Ding for help on transcriptome analysis and helpful discussion. Publisher Copyright: © 2018 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2018/12/1

Y1 - 2018/12/1

N2 - Compatibility between host cells and heterologous pathways is a challenge for constructing organisms with high productivity or gain of function. Designer yeast cells incorporating the Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system provide a platform for generating genotype diversity. Here we construct a genetic AND gate to enable precise control of the SCRaMbLE method to generate synthetic haploid and diploid yeast with desired phenotypes. The yield of carotenoids is increased to 1.5-fold by SCRaMbLEing haploid strains and we determine that the deletion of YEL013W is responsible for the increase. Based on the SCRaMbLEing in diploid strains, we develop a strategy called Multiplex SCRaMbLE Iterative Cycling (MuSIC) to increase the production of carotenoids up to 38.8-fold through 5 iterative cycles of SCRaMbLE. This strategy is potentially a powerful tool for increasing the production of bio-based chemicals and for mining deep knowledge.

AB - Compatibility between host cells and heterologous pathways is a challenge for constructing organisms with high productivity or gain of function. Designer yeast cells incorporating the Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system provide a platform for generating genotype diversity. Here we construct a genetic AND gate to enable precise control of the SCRaMbLE method to generate synthetic haploid and diploid yeast with desired phenotypes. The yield of carotenoids is increased to 1.5-fold by SCRaMbLEing haploid strains and we determine that the deletion of YEL013W is responsible for the increase. Based on the SCRaMbLEing in diploid strains, we develop a strategy called Multiplex SCRaMbLE Iterative Cycling (MuSIC) to increase the production of carotenoids up to 38.8-fold through 5 iterative cycles of SCRaMbLE. This strategy is potentially a powerful tool for increasing the production of bio-based chemicals and for mining deep knowledge.

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DO - 10.1038/s41467-018-03084-4

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VL - 9

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 1933

ER -

Precise control of SCRaMbLE in synthetic haploid and diploid yeast

Abstract

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