Multiplex Navigation of Global Regulatory Networks (MINR) in yeast for Improved Ethanol Tolerance and Production
Abstract
Multiplex navigation of global regulatory networks (MINR) is an approach for combinatorially reprogramming gene expression to manipulate complex phenotypes. We designed, constructed, and mapped MINR libraries containing 43,020 specific mutations in 25 regulatory genes expected to perturb the yeast regulatory network. We selected growth competition experiments for library mutants conferring increased ethanol and/or glucose tolerance. We identified specific mutants that not only possessed improved ethanol and/or glucose tolerance but also produced ethanol at concentrations up to 2-fold higher than those produced by the wild-type strain. We further determined that mutations increasing ethanol tolerance were transferable to a diploid industrial yeast strain. The facile construction and mapping of 43,020 designer regulatory mutations provide a roadmap for how to access and engineer complex phenotypes in future synthetic biology and broader efforts.
- Authors:
-
- Univ. of Colorado, Boulder, CO (United States)
- Univ. of Colorado, Boulder, CO (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)
- Publication Date:
- Research Org.:
- National Renewable Energy Laboratory (NREL), Golden, CO (United States)
- Sponsoring Org.:
- USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office
- OSTI Identifier:
- 1465647
- Report Number(s):
- NREL/JA-2700-72224
Journal ID: ISSN 1096-7176
- Grant/Contract Number:
- AC36-08GO28308
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Metabolic Engineering
- Additional Journal Information:
- Journal Volume: 51; Journal ID: ISSN 1096-7176
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 09 BIOMASS FUELS; multiplex navigation; global regulatory networks; combinatorial programming; gene expression
Citation Formats
Liu, Rongming, Liang, Liya, Choudhury, Alaksh, Garst, Andrew D., Eckert, Carrie A., Oh, Eun Joong, Winkler, James, and Gill, Ryan T. Multiplex Navigation of Global Regulatory Networks (MINR) in yeast for Improved Ethanol Tolerance and Production. United States: N. p., 2018.
Web. doi:10.1016/j.ymben.2018.07.007.
Liu, Rongming, Liang, Liya, Choudhury, Alaksh, Garst, Andrew D., Eckert, Carrie A., Oh, Eun Joong, Winkler, James, & Gill, Ryan T. Multiplex Navigation of Global Regulatory Networks (MINR) in yeast for Improved Ethanol Tolerance and Production. United States. https://doi.org/10.1016/j.ymben.2018.07.007
Liu, Rongming, Liang, Liya, Choudhury, Alaksh, Garst, Andrew D., Eckert, Carrie A., Oh, Eun Joong, Winkler, James, and Gill, Ryan T. Tue .
"Multiplex Navigation of Global Regulatory Networks (MINR) in yeast for Improved Ethanol Tolerance and Production". United States. https://doi.org/10.1016/j.ymben.2018.07.007. https://www.osti.gov/servlets/purl/1465647.
@article{osti_1465647,
title = {Multiplex Navigation of Global Regulatory Networks (MINR) in yeast for Improved Ethanol Tolerance and Production},
author = {Liu, Rongming and Liang, Liya and Choudhury, Alaksh and Garst, Andrew D. and Eckert, Carrie A. and Oh, Eun Joong and Winkler, James and Gill, Ryan T.},
abstractNote = {Multiplex navigation of global regulatory networks (MINR) is an approach for combinatorially reprogramming gene expression to manipulate complex phenotypes. We designed, constructed, and mapped MINR libraries containing 43,020 specific mutations in 25 regulatory genes expected to perturb the yeast regulatory network. We selected growth competition experiments for library mutants conferring increased ethanol and/or glucose tolerance. We identified specific mutants that not only possessed improved ethanol and/or glucose tolerance but also produced ethanol at concentrations up to 2-fold higher than those produced by the wild-type strain. We further determined that mutations increasing ethanol tolerance were transferable to a diploid industrial yeast strain. The facile construction and mapping of 43,020 designer regulatory mutations provide a roadmap for how to access and engineer complex phenotypes in future synthetic biology and broader efforts.},
doi = {10.1016/j.ymben.2018.07.007},
journal = {Metabolic Engineering},
number = ,
volume = 51,
place = {United States},
year = {2018},
month = {7}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 20 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
journal, June 2008
- Nagalakshmi, U.; Wang, Z.; Waern, K.
- Science, Vol. 320, Issue 5881
Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae
journal, February 2007
- Vemuri, G. N.; Eiteman, M. A.; McEwen, J. E.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 7
Analysis of gene network regulating yeast multidrug resistance by artificial activation of transcription factors: involvement of Pdr3 in salt tolerance
journal, May 2004
- Onda, Miyuki; Ota, Kazuhisa; Chiba, Tomoko
- Gene, Vol. 332
Repressors Nrg1 and Nrg2 Regulate a Set of Stress-Responsive Genes in Saccharomyces cerevisiae
journal, November 2005
- Vyas, Valmik K.; Berkey, Cristin D.; Miyao, Takenori
- Eukaryotic Cell, Vol. 4, Issue 11
Nutritional Control of Growth and Development in Yeast
journal, September 2012
- Broach, James R.
- Genetics, Vol. 192, Issue 1
An improved protocol for the preparation of yeast cells for transformation by electroporation
journal, April 1998
- Thompson, J. R.; Register, E.; Curotto, J.
- Yeast, Vol. 14, Issue 6
Repression of ergosterol biosynthesis is essential for stress resistance and is mediated by the Hog1 MAP kinase and the Mot3 and Rox1 transcription factors: Stress-mediated repression of ergosterol biosynthesis
journal, December 2010
- Montañés, Fernando Martínez; Pascual-Ahuir, Amparo; Proft, Markus
- Molecular Microbiology, Vol. 79, Issue 4
Automated multiplex genome-scale engineering in yeast
journal, May 2017
- Si, Tong; Chao, Ran; Min, Yuhao
- Nature Communications, Vol. 8, Issue 1
Genome-wide recruitment profiling of transcription factor Crz1 in response to high pH stress
journal, August 2016
- Roque, Alicia; Petrezsélyová, Silvia; Serra-Cardona, Albert
- BMC Genomics, Vol. 17, Issue 1
Metabolic engineering of a Saccharomyces cerevisiae strain capable of simultaneously utilizing glucose and galactose to produce enantiopure (2R,3R)-butanediol
journal, May 2014
- Lian, Jiazhang; Chao, Ran; Zhao, Huimin
- Metabolic Engineering, Vol. 23
Identification of Genes Required for Maximal Tolerance to High-Glucose Concentrations, as Those Present in Industrial Alcoholic Fermentation Media, Through a Chemogenomics Approach
journal, April 2010
- Teixeira, Miguel C.; Raposo, Luís R.; Palma, Margarida
- OMICS: A Journal of Integrative Biology, Vol. 14, Issue 2
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems
journal, March 2013
- DiCarlo, James E.; Norville, Julie E.; Mali, Prashant
- Nucleic Acids Research, Vol. 41, Issue 7, p. 4336-4343
Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stress in Saccharomyces cerevisiae
journal, February 2009
- Yoshikawa, Katsunori; Tanaka, Tadamasa; Furusawa, Chikara
- FEMS Yeast Research, Vol. 9, Issue 1
Stb3 Binds to Ribosomal RNA Processing Element Motifs That Control Transcriptional Responses to Growth in Saccharomyces cerevisiae
journal, July 2007
- Liko, Dritan; Slattery, Matthew G.; Heideman, Warren
- Journal of Biological Chemistry, Vol. 282, Issue 36
Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli
journal, January 2003
- Cooper, T. F.; Rozen, D. E.; Lenski, R. E.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 3
Evolutionarily engineered ethanologenic yeast detoxifies lignocellulosic biomass conversion inhibitors by reprogrammed pathways
journal, June 2009
- Lewis Liu, Z.; Ma, Menggen; Song, Mingzhou
- Molecular Genetics and Genomics, Vol. 282, Issue 3
Tempo and mode of genome evolution in a 50,000-generation experiment
journal, August 2016
- Tenaillon, Olivier; Barrick, Jeffrey E.; Ribeck, Noah
- Nature, Vol. 536, Issue 7615
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media
journal, November 2010
- Conrad, T. M.; Frazier, M.; Joyce, A. R.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 47
CrEdit: CRISPR mediated multi-loci gene integration in Saccharomyces cerevisiae
journal, July 2015
- Ronda, Carlotta; Maury, Jérôme; Jakočiu̅nas, Tadas
- Microbial Cell Factories, Vol. 14, Issue 1
Construction of Saccharomyces cerevisiae strains with enhanced ethanol tolerance by mutagenesis of the TATA-binding protein gene and identification of novel genes associated with ethanol tolerance
journal, April 2011
- Yang, Jungwoo; Bae, Ju Yun; Lee, Young Mi
- Biotechnology and Bioengineering, Vol. 108, Issue 8
Targeting the MEF2-Like Transcription Factor Smp1 by the Stress-Activated Hog1 Mitogen-Activated Protein Kinase
journal, January 2003
- Nadal, Eulàlia de; Casadomé, Laura; Posas, Francesc
- Molecular and Cellular Biology, Vol. 23, Issue 1
High-resolution chemical dissection of a model eukaryote reveals targets, pathways and gene functions
journal, February 2014
- Hoepfner, Dominic; Helliwell, Stephen B.; Sadlish, Heather
- Microbiological Research, Vol. 169, Issue 2-3
Improvement of oxidative stress tolerance in Saccharomyces cerevisiae through global transcription machinery engineering
journal, March 2014
- Zhao, Hongwei; Li, Jingyuan; Han, Beizhong
- Journal of Industrial Microbiology & Biotechnology, Vol. 41, Issue 5
Long-Term Experimental Evolution in Escherichia coli. XII. DNA Topology as a Key Target of Selection
journal, February 2005
- Crozat, Estelle; Philippe, Nadège; Lenski, Richard E.
- Genetics, Vol. 169, Issue 2
Design and construction of acetyl-CoA overproducing Saccharomyces cerevisiae strains
journal, July 2014
- Lian, Jiazhang; Si, Tong; Nair, Nikhil U.
- Metabolic Engineering, Vol. 24
Saccharomyces cerevisiae Hsp31p, a stress response protein conferring protection against reactive oxygen species
journal, May 2007
- Skoneczna, A.; Micialkiewicz, A.; Skoneczny, M.
- Free Radical Biology and Medicine, Vol. 42, Issue 9
Genome-Wide Identification of Saccharomyces cerevisiae Genes Required for Maximal Tolerance to Ethanol
journal, July 2009
- Teixeira, M. C.; Raposo, L. R.; Mira, N. P.
- Applied and Environmental Microbiology, Vol. 75, Issue 18
Saturation editing of genomic regions by multiplex homology-directed repair
journal, September 2014
- Findlay, Gregory M.; Boyle, Evan A.; Hause, Ronald J.
- Nature, Vol. 513, Issue 7516, p. 120-123
Using global transcription machinery engineering (gTME) to improve ethanol tolerance of Zymomonas mobilis
journal, January 2016
- Tan, Furong; Wu, Bo; Dai, Lichun
- Microbial Cell Factories, Vol. 15, Issue 1
Protein tolerance to random amino acid change
journal, June 2004
- Guo, H. H.; Choe, J.; Loeb, L. A.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 25, p. 9205-9210
Genome dynamics during experimental evolution
journal, October 2013
- Barrick, Jeffrey E.; Lenski, Richard E.
- Nature Reviews Genetics, Vol. 14, Issue 12
Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation
journal, June 2003
- Elena, Santiago F.; Lenski, Richard E.
- Nature Reviews Genetics, Vol. 4, Issue 6
Simultaneous generation of many RNA-seq libraries in a single reaction
journal, March 2015
- Shishkin, Alexander A.; Giannoukos, Georgia; Kucukural, Alper
- Nature Methods, Vol. 12, Issue 4
ROX1 and ERG Regulation in Saccharomyces cerevisiae : Implications for Antifungal Susceptibility
journal, December 2002
- Henry, Karl W.; Nickels, Joseph T.; Edlind, Thomas D.
- Eukaryotic Cell, Vol. 1, Issue 6
Exploring protein fitness landscapes by directed evolution
journal, December 2009
- Romero, Philip A.; Arnold, Frances H.
- Nature Reviews Molecular Cell Biology, Vol. 10, Issue 12
Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production
journal, December 2006
- Alper, H.; Moxley, J.; Nevoigt, E.
- Science, Vol. 314, Issue 5805, p. 1565-1568
Exploiting Natural Variation in Saccharomyces cerevisiae to Identify Genes for Increased Ethanol Resistance
journal, September 2010
- Lewis, Jeffrey A.; Elkon, Isaac M.; McGee, Mick A.
- Genetics, Vol. 186, Issue 4
Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae
journal, January 2010
- Ma, Menggen; Liu, Z. Lewis
- BMC Genomics, Vol. 11, Issue 1
Quick and easy 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
RNA-guided editing of bacterial genomes using CRISPR-Cas systems
journal, January 2013
- Jiang, Wenyan; Bikard, David; Cox, David
- Nature Biotechnology, Vol. 31, Issue 3, p. 233-239
Natural Variation in the Yeast Glucose-Signaling Network Reveals a New Role for the Mig3p Transcription Factor
journal, December 2012
- Lewis, Jeffrey A.; Gasch, Audrey P.
- G3: Genes|Genomes|Genetics, Vol. 2, Issue 12
The Genomic Landscape and Evolutionary Resolution of Antagonistic Pleiotropy in Yeast
journal, November 2012
- Qian, Wenfeng; Ma, Di; Xiao, Che
- Cell Reports, Vol. 2, Issue 5
Yap1 and Skn7 Control Two Specialized Oxidative Stress Response Regulons in Yeast
journal, June 1999
- Lee, Jaekwon; Godon, Christian; Lagniel, Gilles
- Journal of Biological Chemistry, Vol. 274, Issue 23
The ethanol stress response and ethanol tolerance of Saccharomyces cerevisiae
journal, January 2010
- Stanley, D.; Bandara, A.; Fraser, S.
- Journal of Applied Microbiology
Works referencing / citing this record:
Synthetic chimeric nucleases function for efficient genome editing
journal, December 2019
- Liu, R. M.; Liang, L. L.; Freed, E.
- Nature Communications, Vol. 10, Issue 1
Synthetic chimeric nucleases function for efficient genome editing
journal, December 2019
- Liu, R. M.; Liang, L. L.; Freed, E.
- Nature Communications, Vol. 10, Issue 1