Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision

Bao, Zehua; HamediRad, Mohammad; Xue, Pu; Xiao, Han; Tasan, Ipek; Chao, Ran; Liang, Jing; Zhao, Huimin

doi:10.1038/nbt.4132

Title: Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision

Abstract

Here, we developed a CRISPR/Cas9 and homology-directed-repair assisted genome-scale engineering method named CHAnGE that can rapidly output tens of thousands of specific genetic variants in yeast. More than 98% of target sequences were efficiently edited with an average frequency of 82%. We validate the single-nucleotide resolution genome-editing capability of this technology by creating a genome-wide gene disruption collection and apply our method to improve tolerance to growth inhibitors.

Authors:

^[1];

^[1]; Xiao, Han ^[2]; Tasan, Ipek ^[1]; Chao, Ran ^[1]; Liang, Jing ^[3];

^[4]

Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States); Shanghai Jiao Tong Univ., Shanghai (China)
Metabolic Engineering Research Lab. (Singapore)
Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States); Metabolic Engineering Research Lab. (Singapore)

Publication Date:: Mon May 07 00:00:00 EDT 2018

Research Org.:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

OSTI Identifier:: 1489638

Grant/Contract Number:: SC0018260

Resource Type:: Accepted Manuscript

Journal Name:: Nature Biotechnology

Additional Journal Information:: Journal Volume: 36; Journal Issue: 6; Journal ID: ISSN 1087-0156

Publisher:: Springer Nature

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Bao, Zehua, HamediRad, Mohammad, Xue, Pu, Xiao, Han, Tasan, Ipek, Chao, Ran, Liang, Jing, and Zhao, Huimin. Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision.  United States: N. p., 2018. 
Web.  doi:10.1038/nbt.4132.

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                    Bao, Zehua, HamediRad, Mohammad, Xue, Pu, Xiao, Han, Tasan, Ipek, Chao, Ran, Liang, Jing, & Zhao, Huimin. Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision.  United States.  https://doi.org/10.1038/nbt.4132

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                    Bao, Zehua, HamediRad, Mohammad, Xue, Pu, Xiao, Han, Tasan, Ipek, Chao, Ran, Liang, Jing, and Zhao, Huimin. Mon .  
"Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision".  United States.  https://doi.org/10.1038/nbt.4132.  https://www.osti.gov/servlets/purl/1489638.

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@article{osti_1489638,

  title        = {Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision},

  author       = {Bao, Zehua and HamediRad, Mohammad and Xue, Pu and Xiao, Han and Tasan, Ipek and Chao, Ran and Liang, Jing and Zhao, Huimin},

  abstractNote = {Here, we developed a CRISPR/Cas9 and homology-directed-repair assisted genome-scale engineering method named CHAnGE that can rapidly output tens of thousands of specific genetic variants in yeast. More than 98% of target sequences were efficiently edited with an average frequency of 82%. We validate the single-nucleotide resolution genome-editing capability of this technology by creating a genome-wide gene disruption collection and apply our method to improve tolerance to growth inhibitors.},

  doi          = {10.1038/nbt.4132},

  journal      = {Nature Biotechnology},

  number       = 6,

  volume       = 36,

  place        = {United States},

  year         = {Mon May 07 00:00:00 EDT 2018},

  month        = {Mon May 07 00:00:00 EDT 2018}

}

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https://doi.org/10.1038/nbt.4132

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Works referenced in this record:

Capturing a substrate in an activated RING E3/E2–SUMO complex
journal, August 2016

Streich Jr, Frederick C.; Lima, Christopher D.
Nature, Vol. 536, Issue 7616
DOI: 10.1038/nature19071

Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes
journal, November 2017

Barbieri, Edward M.; Muir, Paul; Akhuetie-Oni, Benjamin O.
Cell, Vol. 171, Issue 6
DOI: 10.1016/j.cell.2017.10.034

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites
journal, December 2014

Naito, Yuki; Hino, Kimihiro; Bono, Hidemasa
Bioinformatics, Vol. 31, Issue 7
DOI: 10.1093/bioinformatics/btu743

Multiplex Genome Engineering Using CRISPR/Cas Systems
journal, January 2013

Cong, L.; Ran, F. A.; Cox, D.
Science, Vol. 339, Issue 6121, p. 819-823
DOI: 10.1126/science.1231143

Structure of the Siz/PIAS SUMO E3 Ligase Siz1 and Determinants Required for SUMO Modification of PCNA
journal, September 2009

Yunus, Ali A.; Lima, Christopher D.
Molecular Cell, Vol. 35, Issue 5
DOI: 10.1016/j.molcel.2009.07.013

Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides
journal, July 2010

Warner, Joseph R.; Reeder, Philippa J.; Karimpour-Fard, Anis
Nature Biotechnology, Vol. 28, Issue 8, p. 856-862
DOI: 10.1038/nbt.1653

Homology-Integrated CRISPR–Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae
journal, September 2014

Bao, Zehua; Xiao, Han; Liang, Jing
ACS Synthetic Biology, Vol. 4, Issue 5
DOI: 10.1021/sb500255k

A guide to genome engineering with programmable nucleases
journal, April 2014

Kim, Hyongbum; Kim, Jin-Soo
Nature Reviews Genetics, Vol. 15, Issue 5, p. 321-334
DOI: 10.1038/nrg3686

Strategy for directing combinatorial genome engineering in Escherichia coli
journal, June 2012

Sandoval, N. R.; Kim, J. Y. H.; Glebes, T. Y.
Proceedings of the National Academy of Sciences, Vol. 109, Issue 26, p. 10540-10545
DOI: 10.1073/pnas.1206299109

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
journal, December 2016

Garst, Andrew D.; Bassalo, Marcelo C.; Pines, Gur
Nature Biotechnology, Vol. 35, Issue 1, p. 48-55
DOI: 10.1038/nbt.3718

Programming cells by multiplex genome engineering and accelerated evolution
journal, July 2009

Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A.
Nature, Vol. 460, Issue 7257, p. 894-898
DOI: 10.1038/nature08187

Genome-wide RNAi screen reveals the E3 SUMO-protein ligase gene SIZ1 as a novel determinant of furfural tolerance in Saccharomyces cerevisiae
journal, January 2014

Xiao, Han; Zhao, Huimin
Biotechnology for Biofuels, Vol. 7, Issue 1
DOI: 10.1186/1754-6834-7-78

High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method
journal, January 2007

Gietz, R. Daniel; Schiestl, Robert H.
Nature Protocols, Vol. 2, Issue 1
DOI: 10.1038/nprot.2007.13

Genetic Screens in Human Cells Using the CRISPR-Cas9 System
journal, December 2013

Wang, Tim; Wei, Jenny J.; Sabatini, David M.
Science, Vol. 343, Issue 6166
DOI: 10.1126/science.1246981

Production of genetically engineered mice with higher efficiency, lower mosaicism, and multiplexing capability using maternally expressed Cas9
journal, January 2020

Sakurai, Takayuki; Kamiyoshi, Akiko; Kawate, Hisaka
Scientific Reports, Vol. 10, Issue 1
DOI: 10.1038/s41598-020-57996-7

Engineering of Saccharomyces cerevisiae for anthranilate and methyl anthranilate production
journal, February 2021

Kuivanen, Joosu; Kannisto, Matti; Mojzita, Dominik
Microbial Cell Factories, Vol. 20, Issue 1
DOI: 10.1186/s12934-021-01532-3

Works referencing / citing this record:

Biosystems design by directed evolution
journal, July 2019

Wang, Yajie; Yu, Xiaowei; Zhao, Huimin
AIChE Journal
DOI: 10.1002/aic.16716

Efficient biosynthesis of antitumor ganoderic acid HLDOA using a dual tunable system for optimizing the expression of CYP5150L8 and a Ganoderma P450 reductase
journal, September 2019

Lan, Xiaoting; Yuan, Wei; Wang, Meng
Biotechnology and Bioengineering, Vol. 116, Issue 12
DOI: 10.1002/bit.27154

Whole‐Genome Regulation for Yeast Metabolic Engineering
journal, November 2019

Jiang, Shuangying; Si, Tong; Dai, Junbiao
Small Methods, Vol. 4, Issue 2
DOI: 10.1002/smtd.201900640

The renaissance of yeasts as microbial factories in the modern age of biomanufacturing
journal, September 2019

Payen, Celia; Thompson, Dawn
Yeast, Vol. 36, Issue 12
DOI: 10.1002/yea.3439

Recent advances in CRISPR/Cas9 mediated genome editing in Bacillus subtilis
journal, September 2018

Hong, Kun-Qiang; Liu, Ding-Yu; Chen, Tao
World Journal of Microbiology and Biotechnology, Vol. 34, Issue 10
DOI: 10.1007/s11274-018-2537-1

Regulation and metabolic engineering strategies for permeases of Saccharomyces cerevisiae
journal, July 2019

Zhang, Peng; Chen, Qian; Fu, Guiming
World Journal of Microbiology and Biotechnology, Vol. 35, Issue 7
DOI: 10.1007/s11274-019-2684-z

A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae
journal, March 2019

Zhang, Yueping; Wang, Juan; Wang, Zibai
Nature Communications, Vol. 10, Issue 1
DOI: 10.1038/s41467-019-09005-3

Towards a fully automated algorithm driven platform for biosystems design
journal, November 2019

HamediRad, Mohammad; Chao, Ran; Weisberg, Scott
Nature Communications, Vol. 10, Issue 1
DOI: 10.1038/s41467-019-13189-z

Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping
journal, December 2019

Lian, Jiazhang; Schultz, Carl; Cao, Mingfeng
Nature Communications, Vol. 10, Issue 1
DOI: 10.1038/s41467-019-13621-4

Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors
journal, January 2020

Li, Chao; Zhang, Rui; Meng, Xiangbing
Nature Biotechnology
DOI: 10.1038/s41587-019-0393-7

Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production
journal, April 2019

Savitskaya, Judy; Protzko, Ryan J.; Li, Francesca-Zhoufan
Scientific Reports, Vol. 9, Issue 1
DOI: 10.1038/s41598-019-41759-0

Enhanced scale and scope of genome engineering and regulation using CRISPR/Cas in Saccharomyces cerevisiae
journal, October 2019

Deaner, Matthew; Alper, Hal S.
FEMS Yeast Research, Vol. 19, Issue 7
DOI: 10.1093/femsyr/foz076

Development and characterization of a CRISPR/Cas9n-based multiplex genome editing system for Bacillus subtilis
journal, September 2019

Liu, Dingyu; Huang, Can; Guo, Jiaxin
Biotechnology for Biofuels, Vol. 12, Issue 1
DOI: 10.1186/s13068-019-1537-1

DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories
journal, November 2019

Lutz, Sheila; Brion, Christian; Kliebhan, Margaret
PLOS Genetics, Vol. 15, Issue 11
DOI: 10.1371/journal.pgen.1008375

Deep scanning lysine metabolism in Escherichia coli
journal, November 2018

Bassalo, Marcelo C.; Garst, Andrew D.; Choudhury, Alaksh
Molecular Systems Biology, Vol. 14, Issue 11
DOI: 10.15252/msb.20188371

Double Selection Enhances the Efficiency of Target-AID and Cas9-Based Genome Editing in Yeast
journal, August 2018

Després, Philippe C.; Dubé, Alexandre K.; Nielly-Thibault, Lou
G3: Genes|Genomes|Genetics, Vol. 8, Issue 10
DOI: 10.1534/g3.118.200461

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases
journal, January 2014

Bae, S.; Park, J.; Kim, J. -S.
Bioinformatics, Vol. 30, Issue 10
DOI: 10.1093/bioinformatics/btu048

Perturbing proteomes at single residue resolution using base editing
journal, April 2020

Després, Philippe C.; Dubé, Alexandre K.; Seki, Motoaki
Nature Communications, Vol. 11, Issue 1
DOI: 10.1038/s41467-020-15796-7

Perturbing proteomes at single residue resolution using base editing
image, January 2020

Després, Philippe C.; Dubé, Alexandre K.; Seki, Motoaki
TAGC 2020
DOI: 10.6084/m9.figshare.12142344.v1

Towards a fully automated algorithm driven platform for biosystems design
journal, November 2019

HamediRad, Mohammad; Chao, Ran; Weisberg, Scott
Nature Communications, Vol. 10, Issue 1
DOI: 10.1038/s41467-019-13189-z

Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production
journal, April 2019

Savitskaya, Judy; Protzko, Ryan J.; Li, Francesca-Zhoufan
Scientific Reports, Vol. 9, Issue 1
DOI: 10.1038/s41598-019-41759-0

Double Selection Enhances the Efficiency of Target-AID and Cas9-Based Genome Editing in Yeast
journal, August 2018

Després, Philippe C.; Dubé, Alexandre K.; Nielly-Thibault, Lou
G3: Genes|Genomes|Genetics, Vol. 8, Issue 10
DOI: 10.1534/g3.118.200461

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Title: Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision

Abstract

Citation Formats

Capturing a substrate in an activated RING E3/E2–SUMO complex journal, August 2016

Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes journal, November 2017

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites journal, December 2014

Multiplex Genome Engineering Using CRISPR/Cas Systems journal, January 2013

Structure of the Siz/PIAS SUMO E3 Ligase Siz1 and Determinants Required for SUMO Modification of PCNA journal, September 2009

Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides journal, July 2010

Homology-Integrated CRISPR–Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae journal, September 2014

A guide to genome engineering with programmable nucleases journal, April 2014

Strategy for directing combinatorial genome engineering in Escherichia coli journal, June 2012

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering journal, December 2016

Programming cells by multiplex genome engineering and accelerated evolution journal, July 2009

Genome-wide RNAi screen reveals the E3 SUMO-protein ligase gene SIZ1 as a novel determinant of furfural tolerance in Saccharomyces cerevisiae journal, January 2014

High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method journal, January 2007

Genetic Screens in Human Cells Using the CRISPR-Cas9 System journal, December 2013

Production of genetically engineered mice with higher efficiency, lower mosaicism, and multiplexing capability using maternally expressed Cas9 journal, January 2020

Engineering of Saccharomyces cerevisiae for anthranilate and methyl anthranilate production journal, February 2021

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Whole‐Genome Regulation for Yeast Metabolic Engineering journal, November 2019

The renaissance of yeasts as microbial factories in the modern age of biomanufacturing journal, September 2019

Recent advances in CRISPR/Cas9 mediated genome editing in Bacillus subtilis journal, September 2018

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A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae journal, March 2019

Towards a fully automated algorithm driven platform for biosystems design journal, November 2019

Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping journal, December 2019

Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors journal, January 2020

Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production journal, April 2019

Enhanced scale and scope of genome engineering and regulation using CRISPR/Cas in Saccharomyces cerevisiae journal, October 2019

Development and characterization of a CRISPR/Cas9n-based multiplex genome editing system for Bacillus subtilis journal, September 2019

DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories journal, November 2019

Deep scanning lysine metabolism in Escherichia coli journal, November 2018

Double Selection Enhances the Efficiency of Target-AID and Cas9-Based Genome Editing in Yeast journal, August 2018

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases journal, January 2014

Perturbing proteomes at single residue resolution using base editing journal, April 2020

Perturbing proteomes at single residue resolution using base editing image, January 2020

Towards a fully automated algorithm driven platform for biosystems design journal, November 2019

Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production journal, April 2019

Double Selection Enhances the Efficiency of Target-AID and Cas9-Based Genome Editing in Yeast journal, August 2018

Capturing a substrate in an activated RING E3/E2–SUMO complex
journal, August 2016

Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes
journal, November 2017

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites
journal, December 2014

Multiplex Genome Engineering Using CRISPR/Cas Systems
journal, January 2013

Structure of the Siz/PIAS SUMO E3 Ligase Siz1 and Determinants Required for SUMO Modification of PCNA
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Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides
journal, July 2010

Homology-Integrated CRISPR–Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae
journal, September 2014

A guide to genome engineering with programmable nucleases
journal, April 2014

Strategy for directing combinatorial genome engineering in Escherichia coli
journal, June 2012

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
journal, December 2016

Programming cells by multiplex genome engineering and accelerated evolution
journal, July 2009

Genome-wide RNAi screen reveals the E3 SUMO-protein ligase gene SIZ1 as a novel determinant of furfural tolerance in Saccharomyces cerevisiae
journal, January 2014

High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method
journal, January 2007

Genetic Screens in Human Cells Using the CRISPR-Cas9 System
journal, December 2013

Production of genetically engineered mice with higher efficiency, lower mosaicism, and multiplexing capability using maternally expressed Cas9
journal, January 2020

Engineering of Saccharomyces cerevisiae for anthranilate and methyl anthranilate production
journal, February 2021

Biosystems design by directed evolution
journal, July 2019

Efficient biosynthesis of antitumor ganoderic acid HLDOA using a dual tunable system for optimizing the expression of CYP5150L8 and a Ganoderma P450 reductase
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journal, September 2019

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journal, September 2018

Regulation and metabolic engineering strategies for permeases of Saccharomyces cerevisiae
journal, July 2019

A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae
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Towards a fully automated algorithm driven platform for biosystems design
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Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping
journal, December 2019

Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors
journal, January 2020

Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production
journal, April 2019

Enhanced scale and scope of genome engineering and regulation using CRISPR/Cas in Saccharomyces cerevisiae
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Development and characterization of a CRISPR/Cas9n-based multiplex genome editing system for Bacillus subtilis
journal, September 2019

DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories
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Deep scanning lysine metabolism in Escherichia coli
journal, November 2018

Double Selection Enhances the Efficiency of Target-AID and Cas9-Based Genome Editing in Yeast
journal, August 2018

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases
journal, January 2014

Perturbing proteomes at single residue resolution using base editing
journal, April 2020

Perturbing proteomes at single residue resolution using base editing
image, January 2020

Towards a fully automated algorithm driven platform for biosystems design
journal, November 2019

Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production
journal, April 2019

Double Selection Enhances the Efficiency of Target-AID and Cas9-Based Genome Editing in Yeast
journal, August 2018