A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering

Dossani, Zain Y.; Reider Apel, Amanda; Szmidt-Middleton, Heather; Hillson, Nathan J.; Deutsch, Samuel; Keasling, Jay D.; Mukhopadhyay, Aindrila

doi:10.1002/yea.3292

Title: A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering

Abstract

Despite the need for inducible promoters in strain development efforts, the majority of engineering in Saccharomyces cerevisiae continues to rely on a few constitutively active or inducible promoters. Building on advances that use the modular nature of both transcription factors and promoter regions, we have built a library of hybrid promoters that are regulated by a synthetic transcription factor. The hybrid promoters consist of native S. cerevisiae promoters, in which the operator regions have been replaced with sequences that are recognized by the bacterial LexA DNA binding protein. Correspondingly, the synthetic transcription factor (TF) consists of the DNA binding domain of the LexA protein, fused with the human estrogen binding domain and the viral activator domain, VP16. The resulting system with a bacterial DNA binding domain avoids the transcription of native S. cerevisiae genes, and the hybrid promoters can be induced using estradiol, a compound with no detectable impact on S. cerevisiae physiology. Using combinations of one, two or three operator sequence repeats and a set of native S. cerevisiae promoters, we obtained a series of hybrid promoters that can be induced to different levels, using the same synthetic TF and a given estradiol. Finally, this set of promoters, inmore »« less

Authors:

Dossani, Zain Y. ^[1]; Reider Apel, Amanda ^[1]; Szmidt-Middleton, Heather ^[1]; Hillson, Nathan J. ^[2]; Deutsch, Samuel ^[3]; Keasling, Jay D. ^[4];

^[1]

Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division
Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); USDOE Agile BioFoundry, Emeryville, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); USDOE Agile BioFoundry, Emeryville, CA (United States)
Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engineering and Dept. of Bioengineering; Technical Univ. of Denmark, Lyngby (Denmark). Novo Nordisk Foundation Center forBiosustainability

Publication Date:: Mon Oct 30 00:00:00 EDT 2017

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

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

OSTI Identifier:: 1433124

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Yeast

Additional Journal Information:: Journal Volume: 35; Journal Issue: 3; Journal ID: ISSN 0749-503X

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; hybrid promoter; Saccharomyces; strain engineering; synthetic biology

Citation Formats


                    Dossani, Zain Y., Reider Apel, Amanda, Szmidt-Middleton, Heather, Hillson, Nathan J., Deutsch, Samuel, Keasling, Jay D., and Mukhopadhyay, Aindrila. A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering.  United States: N. p., 2017. 
Web.  doi:10.1002/yea.3292.

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                    Dossani, Zain Y., Reider Apel, Amanda, Szmidt-Middleton, Heather, Hillson, Nathan J., Deutsch, Samuel, Keasling, Jay D., & Mukhopadhyay, Aindrila. A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering.  United States.  https://doi.org/10.1002/yea.3292

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                    Dossani, Zain Y., Reider Apel, Amanda, Szmidt-Middleton, Heather, Hillson, Nathan J., Deutsch, Samuel, Keasling, Jay D., and Mukhopadhyay, Aindrila. Mon .  
"A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering".  United States.  https://doi.org/10.1002/yea.3292.  https://www.osti.gov/servlets/purl/1433124.

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@article{osti_1433124,

  title        = {A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering},

  author       = {Dossani, Zain Y. and Reider Apel, Amanda and Szmidt-Middleton, Heather and Hillson, Nathan J. and Deutsch, Samuel and Keasling, Jay D. and Mukhopadhyay, Aindrila},

  abstractNote = {Despite the need for inducible promoters in strain development efforts, the majority of engineering in Saccharomyces cerevisiae continues to rely on a few constitutively active or inducible promoters. Building on advances that use the modular nature of both transcription factors and promoter regions, we have built a library of hybrid promoters that are regulated by a synthetic transcription factor. The hybrid promoters consist of native S. cerevisiae promoters, in which the operator regions have been replaced with sequences that are recognized by the bacterial LexA DNA binding protein. Correspondingly, the synthetic transcription factor (TF) consists of the DNA binding domain of the LexA protein, fused with the human estrogen binding domain and the viral activator domain, VP16. The resulting system with a bacterial DNA binding domain avoids the transcription of native S. cerevisiae genes, and the hybrid promoters can be induced using estradiol, a compound with no detectable impact on S. cerevisiae physiology. Using combinations of one, two or three operator sequence repeats and a set of native S. cerevisiae promoters, we obtained a series of hybrid promoters that can be induced to different levels, using the same synthetic TF and a given estradiol. Finally, this set of promoters, in combination with our synthetic TF, has the potential to regulate numerous genes or pathways simultaneously, to multiple desired levels, in a single strain.},

  doi          = {10.1002/yea.3292},

  journal      = {Yeast},

  number       = 3,

  volume       = 35,

  place        = {United States},

  year         = {Mon Oct 30 00:00:00 EDT 2017},

  month        = {Mon Oct 30 00:00:00 EDT 2017}

}

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McIsaac, R. Scott; Oakes, Benjamin L.; Wang, Xin
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Sequence features of yeast and human core promoters that are predictive of maximal promoter activity
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Title: A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering

Abstract

Citation Formats

A tetO Toolkit To Alter Expression of Genes in Saccharomyces cerevisiae journal, March 2015

Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae journal, January 2016

Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas journal, June 2013

The RNA polymerase II core promoter: a key component in the regulation of gene expression journal, October 2002

Characterization of chromosomal integration sites for heterologous gene expression in Saccharomyces cerevisiae journal, October 2009

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes journal, July 2013

Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry journal, July 2014

Sequence features of yeast and human core promoters that are predictive of maximal promoter activity journal, April 2013

Streamlining the Design-to-Build Transition with Build-Optimization Software Tools journal, November 2016

GeneDesign 3.0 is an updated synthetic biology toolkit journal, March 2010

Inducible, tightly regulated and growth condition-independent transcription factor in Saccharomyces cerevisiae journal, July 2014

j5 DNA Assembly Design Automation Software journal, December 2011

Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters journal, May 2012

A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor journal, December 1985

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions journal, August 2012

A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly journal, April 2015

Tuning genetic control through promoter engineering journal, August 2005

Core promoter sequence in yeast is a major determinant of expression level journal, May 2015

Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast journal, December 2012

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data journal, July 2010

Two systems of glucose repression of the GAL1 promoter in Saccharomyces cerevisiae. journal, September 1990

Development of a Native Escherichia coli Induction System for Ionic Liquid Tolerance journal, July 2014

Tolerance engineering in bacteria for the production of advanced biofuels and chemicals journal, August 2015

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PaR-PaR Laboratory Automation Platform journal, October 2012

Microbial engineering for the production of advanced biofuels journal, August 2012

Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae journal, February 2016

Nucleotide sequence and promoter analysis of SPO13, a meiosis-specific gene of Saccharomyces cerevisiae. journal, December 1990

Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems journal, April 2011

Development of a Tightly Controlled Off Switch for Saccharomyces cerevisiae Regulated by Camphor, a Low-Cost Natural Product journal, July 2015

Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae journal, January 2014

Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools journal, June 2012

PR-PR: Cross-Platform Laboratory Automation System journal, January 2014

Total synthesis of multi-kilobase DNA sequences from oligonucleotides journal, December 2006

A Set of Vectors with a Tetracycline-Regulatable Promoter System for Modulated Gene Expression inSaccharomyces cerevisiae journal, July 1997

Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters journal, May 2012

Fusion of GAL4-VP16 to a steroid-binding domain provides a tool for gratuitous induction of galactose-responsive genes in yeast journal, September 1993

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions journal, August 2012

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes journal, July 2013

Two “what if” experiments journal, January 2004

Identification and Distinct Regulation of Yeast TATA Box-Containing Genes journal, March 2004

Streamlining the Design-to-Build Transition with Build-Optimization Software Tools journal, November 2016

Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry journal, July 2014

j5 DNA Assembly Design Automation Software journal, December 2011

Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas journal, June 2013

PR-PR: Cross-Platform Laboratory Automation System journal, January 2014

Microbial engineering for the production of advanced biofuels journal, August 2012

Tuning genetic control through promoter engineering journal, August 2005

Nucleotide sequence and promoter analysis of SPO13, a meiosis-specific gene of Saccharomyces cerevisiae. journal, December 1990

Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae journal, November 2011

GeneDesign 3.0 is an updated synthetic biology toolkit journal, March 2010

Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast journal, December 2012

Sequence features of yeast and human core promoters that are predictive of maximal promoter activity journal, April 2013

A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae journal, November 2016

The RNA polymerase II core promoter: a key component in the regulation of gene expression journal, October 2002

Two systems of glucose repression of the GAL1 promoter in Saccharomyces cerevisiae journal, September 1990

Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems journal, April 2011

Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae journal, February 2016

Development of a Tightly Controlled Off Switch for Saccharomyces cerevisiae Regulated by Camphor, a Low-Cost Natural Product journal, July 2015

Locus specific engineering of tandem DNA repeats in the genome of Saccharomyces cerevisiae using CRISPR/Cas9 and overlapping oligonucleotides journal, May 2018

The Promoter Toolbox for Recombinant Gene Expression in Trichoderma reesei journal, October 2018

A tetO Toolkit To Alter Expression of Genes in Saccharomyces cerevisiae
journal, March 2015

Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae
journal, January 2016

Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas
journal, June 2013

The RNA polymerase II core promoter: a key component in the regulation of gene expression
journal, October 2002

Characterization of chromosomal integration sites for heterologous gene expression in Saccharomyces cerevisiae
journal, October 2009

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
journal, July 2013

Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry
journal, July 2014

Sequence features of yeast and human core promoters that are predictive of maximal promoter activity
journal, April 2013

Streamlining the Design-to-Build Transition with Build-Optimization Software Tools
journal, November 2016

GeneDesign 3.0 is an updated synthetic biology toolkit
journal, March 2010

Inducible, tightly regulated and growth condition-independent transcription factor in Saccharomyces cerevisiae
journal, July 2014

j5 DNA Assembly Design Automation Software
journal, December 2011

Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters
journal, May 2012

A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor
journal, December 1985

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions
journal, August 2012

A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly
journal, April 2015

Tuning genetic control through promoter engineering
journal, August 2005

Core promoter sequence in yeast is a major determinant of expression level
journal, May 2015

Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast
journal, December 2012

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
journal, July 2010

Two systems of glucose repression of the GAL1 promoter in Saccharomyces cerevisiae.
journal, September 1990

Development of a Native Escherichia coli Induction System for Ionic Liquid Tolerance
journal, July 2014

Tolerance engineering in bacteria for the production of advanced biofuels and chemicals
journal, August 2015

A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae
journal, November 2016

PaR-PaR Laboratory Automation Platform
journal, October 2012

Microbial engineering for the production of advanced biofuels
journal, August 2012

Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae
journal, February 2016

Nucleotide sequence and promoter analysis of SPO13, a meiosis-specific gene of Saccharomyces cerevisiae.
journal, December 1990

Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems
journal, April 2011

Development of a Tightly Controlled Off Switch for Saccharomyces cerevisiae Regulated by Camphor, a Low-Cost Natural Product
journal, July 2015

Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae
journal, January 2014

Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools
journal, June 2012

PR-PR: Cross-Platform Laboratory Automation System
journal, January 2014

Total synthesis of multi-kilobase DNA sequences from oligonucleotides
journal, December 2006

A Set of Vectors with a Tetracycline-Regulatable Promoter System for Modulated Gene Expression inSaccharomyces cerevisiae
journal, July 1997

Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters
journal, May 2012

Fusion of GAL4-VP16 to a steroid-binding domain provides a tool for gratuitous induction of galactose-responsive genes in yeast
journal, September 1993

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions
journal, August 2012

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
journal, July 2013

Two “what if” experiments
journal, January 2004

Identification and Distinct Regulation of Yeast TATA Box-Containing Genes
journal, March 2004

Streamlining the Design-to-Build Transition with Build-Optimization Software Tools
journal, November 2016

Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry
journal, July 2014

j5 DNA Assembly Design Automation Software
journal, December 2011

Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas
journal, June 2013

PR-PR: Cross-Platform Laboratory Automation System
journal, January 2014

Microbial engineering for the production of advanced biofuels
journal, August 2012

Tuning genetic control through promoter engineering
journal, August 2005

Nucleotide sequence and promoter analysis of SPO13, a meiosis-specific gene of Saccharomyces cerevisiae.
journal, December 1990

Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae
journal, November 2011

GeneDesign 3.0 is an updated synthetic biology toolkit
journal, March 2010

Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast
journal, December 2012

Sequence features of yeast and human core promoters that are predictive of maximal promoter activity
journal, April 2013

A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae
journal, November 2016

The RNA polymerase II core promoter: a key component in the regulation of gene expression
journal, October 2002

Two systems of glucose repression of the GAL1 promoter in Saccharomyces cerevisiae
journal, September 1990

Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems
journal, April 2011

Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae
journal, February 2016

Development of a Tightly Controlled Off Switch for Saccharomyces cerevisiae Regulated by Camphor, a Low-Cost Natural Product
journal, July 2015

Locus specific engineering of tandem DNA repeats in the genome of Saccharomyces cerevisiae using CRISPR/Cas9 and overlapping oligonucleotides
journal, May 2018

The Promoter Toolbox for Recombinant Gene Expression in Trichoderma reesei
journal, October 2018