Multiplex Navigation of Global Regulatory Networks (MINR) in yeast for Improved Ethanol Tolerance and Production

Liu, Rongming; Liang, Liya; Choudhury, Alaksh; Garst, Andrew D.; Eckert, Carrie A.; Oh, Eun Joong; Winkler, James; Gill, Ryan T.

doi:10.1016/j.ymben.2018.07.007

Title: Multiplex Navigation of Global Regulatory Networks (MINR) in yeast for Improved Ethanol Tolerance and Production

Journal Article · Tue Jul 17 00:00:00 EDT 2018 · Metabolic Engineering

DOI:https://doi.org/10.1016/j.ymben.2018.07.007· OSTI ID:1465647

Liu, Rongming ^[1]; Liang, Liya ^[1]; Choudhury, Alaksh ^[1]; Garst, Andrew D. ^[1]; Eckert, Carrie A. ^[2]; Oh, Eun Joong ^[1]; Winkler, James ^[1]; Gill, Ryan T. ^[1]

Univ. of Colorado, Boulder, CO (United States)
Univ. of Colorado, Boulder, CO (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)

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.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office

Grant/Contract Number:: AC36-08GO28308

OSTI ID:: 1465647

Report Number(s):: NREL/JA-2700-72224

Journal Information:: Metabolic Engineering, Vol. 51; ISSN 1096-7176

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 20 works

Citation information provided by
Web of Science

References (44)

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing Nagalakshmi, U.; Wang, Z.; Waern, K. Science, Vol. 320, Issue 5881 https://doi.org/10.1126/science.1158441	journal	June 2008
Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae Vemuri, G. N.; Eiteman, M. A.; McEwen, J. E. Proceedings of the National Academy of Sciences, Vol. 104, Issue 7 https://doi.org/10.1073/pnas.0607469104	journal	February 2007
Analysis of gene network regulating yeast multidrug resistance by artificial activation of transcription factors: involvement of Pdr3 in salt tolerance Onda, Miyuki; Ota, Kazuhisa; Chiba, Tomoko Gene, Vol. 332 https://doi.org/10.1016/j.gene.2004.02.003	journal	May 2004
Repressors Nrg1 and Nrg2 Regulate a Set of Stress-Responsive Genes in Saccharomyces cerevisiae Vyas, Valmik K.; Berkey, Cristin D.; Miyao, Takenori Eukaryotic Cell, Vol. 4, Issue 11 https://doi.org/10.1128/EC.4.11.1882-1891.2005	journal	November 2005
Nutritional Control of Growth and Development in Yeast Broach, James R. Genetics, Vol. 192, Issue 1 https://doi.org/10.1534/genetics.111.135731	journal	September 2012
An improved protocol for the preparation of yeast cells for transformation by electroporation Thompson, J. R.; Register, E.; Curotto, J. Yeast, Vol. 14, Issue 6 https://doi.org/10.1002/(SICI)1097-0061(19980430)14:6<565::AID-YEA251>3.0.CO;2-B	journal	April 1998
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 Montañés, Fernando Martínez; Pascual-Ahuir, Amparo; Proft, Markus Molecular Microbiology, Vol. 79, Issue 4 https://doi.org/10.1111/j.1365-2958.2010.07502.x	journal	December 2010
Automated multiplex genome-scale engineering in yeast Si, Tong; Chao, Ran; Min, Yuhao Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15187	journal	May 2017
Genome-wide recruitment profiling of transcription factor Crz1 in response to high pH stress Roque, Alicia; Petrezsélyová, Silvia; Serra-Cardona, Albert BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-3006-6	journal	August 2016
Metabolic engineering of a Saccharomyces cerevisiae strain capable of simultaneously utilizing glucose and galactose to produce enantiopure (2R,3R)-butanediol Lian, Jiazhang; Chao, Ran; Zhao, Huimin Metabolic Engineering, Vol. 23 https://doi.org/10.1016/j.ymben.2014.02.003	journal	May 2014
Identification of Genes Required for Maximal Tolerance to High-Glucose Concentrations, as Those Present in Industrial Alcoholic Fermentation Media, Through a Chemogenomics Approach Teixeira, Miguel C.; Raposo, Luís R.; Palma, Margarida OMICS: A Journal of Integrative Biology, Vol. 14, Issue 2 https://doi.org/10.1089/omi.2009.0149	journal	April 2010
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems DiCarlo, James E.; Norville, Julie E.; Mali, Prashant Nucleic Acids Research, Vol. 41, Issue 7, p. 4336-4343 https://doi.org/10.1093/nar/gkt135	journal	March 2013
Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stress in Saccharomyces cerevisiae Yoshikawa, Katsunori; Tanaka, Tadamasa; Furusawa, Chikara FEMS Yeast Research, Vol. 9, Issue 1 https://doi.org/10.1111/j.1567-1364.2008.00456.x	journal	February 2009
Stb3 Binds to Ribosomal RNA Processing Element Motifs That Control Transcriptional Responses to Growth in Saccharomyces cerevisiae Liko, Dritan; Slattery, Matthew G.; Heideman, Warren Journal of Biological Chemistry, Vol. 282, Issue 36 https://doi.org/10.1074/jbc.M704762200	journal	July 2007
Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli Cooper, T. F.; Rozen, D. E.; Lenski, R. E. Proceedings of the National Academy of Sciences, Vol. 100, Issue 3 https://doi.org/10.1073/pnas.0334340100	journal	January 2003
Evolutionarily engineered ethanologenic yeast detoxifies lignocellulosic biomass conversion inhibitors by reprogrammed pathways Lewis Liu, Z.; Ma, Menggen; Song, Mingzhou Molecular Genetics and Genomics, Vol. 282, Issue 3 https://doi.org/10.1007/s00438-009-0461-7	journal	June 2009
Tempo and mode of genome evolution in a 50,000-generation experiment Tenaillon, Olivier; Barrick, Jeffrey E.; Ribeck, Noah Nature, Vol. 536, Issue 7615 https://doi.org/10.1038/nature18959	journal	August 2016
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media Conrad, T. M.; Frazier, M.; Joyce, A. R. Proceedings of the National Academy of Sciences, Vol. 107, Issue 47 https://doi.org/10.1073/pnas.0911253107	journal	November 2010
CrEdit: CRISPR mediated multi-loci gene integration in Saccharomyces cerevisiae Ronda, Carlotta; Maury, Jérôme; Jakočiu̅nas, Tadas Microbial Cell Factories, Vol. 14, Issue 1 https://doi.org/10.1186/s12934-015-0288-3	journal	July 2015
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 Yang, Jungwoo; Bae, Ju Yun; Lee, Young Mi Biotechnology and Bioengineering, Vol. 108, Issue 8 https://doi.org/10.1002/bit.23141	journal	April 2011
Targeting the MEF2-Like Transcription Factor Smp1 by the Stress-Activated Hog1 Mitogen-Activated Protein Kinase Nadal, Eulàlia de; Casadomé, Laura; Posas, Francesc Molecular and Cellular Biology, Vol. 23, Issue 1 https://doi.org/10.1128/MCB.23.1.229-237.2003	journal	January 2003
High-resolution chemical dissection of a model eukaryote reveals targets, pathways and gene functions Hoepfner, Dominic; Helliwell, Stephen B.; Sadlish, Heather Microbiological Research, Vol. 169, Issue 2-3 https://doi.org/10.1016/j.micres.2013.11.004	journal	February 2014
Improvement of oxidative stress tolerance in Saccharomyces cerevisiae through global transcription machinery engineering Zhao, Hongwei; Li, Jingyuan; Han, Beizhong Journal of Industrial Microbiology & Biotechnology, Vol. 41, Issue 5 https://doi.org/10.1007/s10295-014-1421-8	journal	March 2014
Long-Term Experimental Evolution in Escherichia coli. XII. DNA Topology as a Key Target of Selection Crozat, Estelle; Philippe, Nadège; Lenski, Richard E. Genetics, Vol. 169, Issue 2 https://doi.org/10.1534/genetics.104.035717	journal	February 2005
Design and construction of acetyl-CoA overproducing Saccharomyces cerevisiae strains Lian, Jiazhang; Si, Tong; Nair, Nikhil U. Metabolic Engineering, Vol. 24 https://doi.org/10.1016/j.ymben.2014.05.010	journal	July 2014
Saccharomyces cerevisiae Hsp31p, a stress response protein conferring protection against reactive oxygen species Skoneczna, A.; Micialkiewicz, A.; Skoneczny, M. Free Radical Biology and Medicine, Vol. 42, Issue 9 https://doi.org/10.1016/j.freeradbiomed.2007.01.042	journal	May 2007
Genome-Wide Identification of Saccharomyces cerevisiae Genes Required for Maximal Tolerance to Ethanol Teixeira, M. C.; Raposo, L. R.; Mira, N. P. Applied and Environmental Microbiology, Vol. 75, Issue 18 https://doi.org/10.1128/AEM.00845-09	journal	July 2009
Saturation editing of genomic regions by multiplex homology-directed repair Findlay, Gregory M.; Boyle, Evan A.; Hause, Ronald J. Nature, Vol. 513, Issue 7516, p. 120-123 https://doi.org/10.1038/nature13695	journal	September 2014
Using global transcription machinery engineering (gTME) to improve ethanol tolerance of Zymomonas mobilis Tan, Furong; Wu, Bo; Dai, Lichun Microbial Cell Factories, Vol. 15, Issue 1 https://doi.org/10.1186/s12934-015-0398-y	journal	January 2016
Protein tolerance to random amino acid change Guo, H. H.; Choe, J.; Loeb, L. A. Proceedings of the National Academy of Sciences, Vol. 101, Issue 25, p. 9205-9210 https://doi.org/10.1073/pnas.0403255101	journal	June 2004
Genome dynamics during experimental evolution Barrick, Jeffrey E.; Lenski, Richard E. Nature Reviews Genetics, Vol. 14, Issue 12 https://doi.org/10.1038/nrg3564	journal	October 2013
Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation Elena, Santiago F.; Lenski, Richard E. Nature Reviews Genetics, Vol. 4, Issue 6 https://doi.org/10.1038/nrg1088	journal	June 2003
Simultaneous generation of many RNA-seq libraries in a single reaction Shishkin, Alexander A.; Giannoukos, Georgia; Kucukural, Alper Nature Methods, Vol. 12, Issue 4 https://doi.org/10.1038/nmeth.3313	journal	March 2015
ROX1 and ERG Regulation in Saccharomyces cerevisiae : Implications for Antifungal Susceptibility Henry, Karl W.; Nickels, Joseph T.; Edlind, Thomas D. Eukaryotic Cell, Vol. 1, Issue 6 https://doi.org/10.1128/EC.1.6.1041-1044.2002	journal	December 2002
Exploring protein fitness landscapes by directed evolution Romero, Philip A.; Arnold, Frances H. Nature Reviews Molecular Cell Biology, Vol. 10, Issue 12 https://doi.org/10.1038/nrm2805	journal	December 2009
Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production Alper, H.; Moxley, J.; Nevoigt, E. Science, Vol. 314, Issue 5805, p. 1565-1568 https://doi.org/10.1126/science.1131969	journal	December 2006
Exploiting Natural Variation in Saccharomyces cerevisiae to Identify Genes for Increased Ethanol Resistance Lewis, Jeffrey A.; Elkon, Isaac M.; McGee, Mick A. Genetics, Vol. 186, Issue 4 https://doi.org/10.1534/genetics.110.121871	journal	September 2010
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 Ma, Menggen; Liu, Z. Lewis BMC Genomics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2164-11-660	journal	January 2010
Quick and easy yeast transformation using the LiAc/SS carrier DNA/PEG method Gietz, R. Daniel; Schiestl, Robert H. Nature Protocols, Vol. 2, Issue 1 https://doi.org/10.1038/nprot.2007.14	journal	January 2007
RNA-guided editing of bacterial genomes using CRISPR-Cas systems Jiang, Wenyan; Bikard, David; Cox, David Nature Biotechnology, Vol. 31, Issue 3, p. 233-239 https://doi.org/10.1038/nbt.2508	journal	January 2013
Natural Variation in the Yeast Glucose-Signaling Network Reveals a New Role for the Mig3p Transcription Factor Lewis, Jeffrey A.; Gasch, Audrey P. G3: Genes\|Genomes\|Genetics, Vol. 2, Issue 12 https://doi.org/10.1534/g3.112.004127	journal	December 2012
The Genomic Landscape and Evolutionary Resolution of Antagonistic Pleiotropy in Yeast Qian, Wenfeng; Ma, Di; Xiao, Che Cell Reports, Vol. 2, Issue 5 https://doi.org/10.1016/j.celrep.2012.09.017	journal	November 2012
Yap1 and Skn7 Control Two Specialized Oxidative Stress Response Regulons in Yeast Lee, Jaekwon; Godon, Christian; Lagniel, Gilles Journal of Biological Chemistry, Vol. 274, Issue 23 https://doi.org/10.1074/jbc.274.23.16040	journal	June 1999
The ethanol stress response and ethanol tolerance of Saccharomyces cerevisiae Stanley, D.; Bandara, A.; Fraser, S. Journal of Applied Microbiology https://doi.org/10.1111/j.1365-2672.2009.04657.x	journal	January 2010

Cited By (1)

Synthetic chimeric nucleases function for efficient genome editing Liu, R. M.; Liang, L. L.; Freed, E. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13500-y	journal	December 2019

Similar Records

Transcriptional Regulatory Networks Involved in C3–C4 Alcohol Stress Response and Tolerance in Yeast

Journal Article · Thu Dec 24 00:00:00 EST 2020 · ACS Synthetic Biology · OSTI ID:1465647

Liang, Liya; Liu, Rongming; Freed, Emily F.; +2 more

Engineering regulatory networks for complex phenotypes in E. coli

Journal Article · Thu Aug 13 00:00:00 EDT 2020 · Nature Communications · OSTI ID:1465647

Liu, Rongming; Liang, Liya; Freed, Emily F.; +3 more

Multiplex Evolution of Antibody Fragments Utilizing a Yeast Surface Display Platform

Journal Article · Thu Jun 18 00:00:00 EDT 2020 · ACS Synthetic Biology · OSTI ID:1465647

Oh, Eun Joong; Liu, Rongming; Liang, Liya; +3 more

Related Subjects

09 BIOMASS FUELS
multiplex navigation
global regulatory networks
combinatorial programming
gene expression

Title: Multiplex Navigation of Global Regulatory Networks (MINR) in yeast for Improved Ethanol Tolerance and Production

Citation Formats

References (44)

Cited By (1)

Similar Records

Related Subjects