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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 » combination with our synthetic TF, has the potential to regulate numerous genes or pathways simultaneously, to multiple desired levels, in a single strain.« less

Authors:
 [1];  [1];  [1];  [2];  [3];  [4]; ORCiD logo [1]
  1. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division
  2. 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)
  3. 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)
  4. 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:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
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.
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. doi:10.1002/yea.3292.
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. doi:10.1002/yea.3292. https://www.osti.gov/servlets/purl/1433124.
@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 = {2017},
month = {10}
}

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Works referenced in this record:

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

  • Cuperus, Josh T.; Lo, Russell S.; Shumaker, Lucia
  • ACS Synthetic Biology, Vol. 4, Issue 7
  • DOI: 10.1021/sb500363y

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

  • Reider Apel, Amanda; Ouellet, Mario; Szmidt-Middleton, Heather
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep19512

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

  • Farzadfard, Fahim; Perli, Samuel D.; Lu, Timothy K.
  • ACS Synthetic Biology, Vol. 2, Issue 10
  • DOI: 10.1021/sb400081r

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


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


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

  • Bai Flagfeldt, Dongmei; Siewers, Verena; Huang, Le
  • Yeast, Vol. 26, Issue 10
  • DOI: 10.1002/yea.1705

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

  • Heins, Richard A.; Cheng, Xiaoliang; Nath, Sangeeta
  • ACS Chemical Biology, Vol. 9, Issue 9
  • DOI: 10.1021/cb500244v

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

  • Lubliner, Shai; Keren, Leeat; Segal, Eran
  • Nucleic Acids Research, Vol. 41, Issue 11
  • DOI: 10.1093/nar/gkt256

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

  • Oberortner, Ernst; Cheng, Jan-Fang; Hillson, Nathan J.
  • ACS Synthetic Biology, Vol. 6, Issue 3
  • DOI: 10.1021/acssynbio.6b00200

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

  • Richardson, Sarah M.; Nunley, Paul W.; Yarrington, Robert M.
  • Nucleic Acids Research, Vol. 38, Issue 8
  • DOI: 10.1093/nar/gkq143

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

  • Ottoz, Diana S. M.; Rudolf, Fabian; Stelling, Joerg
  • Nucleic Acids Research, Vol. 42, Issue 17
  • DOI: 10.1093/nar/gku616

j5 DNA Assembly Design Automation Software
journal, December 2011

  • Hillson, Nathan J.; Rosengarten, Rafael D.; Keasling, Jay D.
  • ACS Synthetic Biology, Vol. 1, Issue 1, p. 14-21
  • DOI: 10.1021/sb2000116

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

  • Blazeck, John; Garg, Rishi; Reed, Ben
  • Biotechnology and Bioengineering, Vol. 109, Issue 11
  • DOI: 10.1002/bit.24552

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


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

  • McIsaac, R. Scott; Silverman, Sanford J.; McClean, Megan N.
  • Molecular Biology of the Cell, Vol. 22, Issue 22
  • DOI: 10.1091/mbc.E11-05-0466

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

  • Lee, Michael E.; DeLoache, William C.; Cervantes, Bernardo
  • ACS Synthetic Biology, Vol. 4, Issue 9
  • DOI: 10.1021/sb500366v

Tuning genetic control through promoter engineering
journal, August 2005

  • Alper, H.; Fischer, C.; Nevoigt, E.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 36, p. 12678-12683
  • DOI: 10.1073/pnas.0504604102

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

  • Lubliner, Shai; Regev, Ifat; Lotan-Pompan, Maya
  • Genome Research, Vol. 25, Issue 7
  • DOI: 10.1101/gr.188193.114

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

  • McIsaac, R. Scott; Oakes, Benjamin L.; Wang, Xin
  • Nucleic Acids Research, Vol. 41, Issue 4
  • DOI: 10.1093/nar/gks1313

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

  • Reider Apel, Amanda; d'Espaux, Leo; Wehrs, Maren
  • Nucleic Acids Research, Vol. 45, Issue 1
  • DOI: 10.1093/nar/gkw1023

PaR-PaR Laboratory Automation Platform
journal, October 2012

  • Linshiz, Gregory; Stawski, Nina; Poust, Sean
  • ACS Synthetic Biology, Vol. 2, Issue 5
  • DOI: 10.1021/sb300075t

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

  • Peralta-Yahya, Pamela P.; Zhang, Fuzhong; del Cardayre, Stephen B.
  • Nature, Vol. 488, Issue 7411
  • DOI: 10.1038/nature11478

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

  • Buckingham, L. E.; Wang, H. T.; Elder, R. T.
  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 23
  • DOI: 10.1073/pnas.87.23.9406

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


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

  • Ikushima, Shigehito; Zhao, Yu; Boeke, Jef D.
  • G3: Genes|Genomes|Genetics, Vol. 5, Issue 10
  • DOI: 10.1534/g3.114.012765

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

  • McIsaac, R. Scott; Gibney, Patrick A.; Chandran, Sunil S.
  • Nucleic Acids Research, Vol. 42, Issue 6
  • DOI: 10.1093/nar/gkt1402

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

  • Ham, T. S.; Dmytriv, Z.; Plahar, H.
  • Nucleic Acids Research, Vol. 40, Issue 18
  • DOI: 10.1093/nar/gks531

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

  • Linshiz, Gregory; Stawski, Nina; Goyal, Garima
  • ACS Synthetic Biology, Vol. 3, Issue 8
  • DOI: 10.1021/sb4001728

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

  • Reisinger, Sarah J.; Patel, Kedar G.; Santi, Daniel V.
  • Nature Protocols, Vol. 1, Issue 6
  • DOI: 10.1038/nprot.2006.426