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Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production
Abstract
Global transcription machinery engineering (gTME) is an approach for reprogramming gene transcription to elicit cellular phenotypes important for technological applications. Here we show the application of gTME to Saccharomyces cerevisiae for improved glucose/ethanol tolerance, a key trait for many biofuels programs. Mutagenesis of the transcription factor Spt15p and selection led to dominant mutations that conferred increased tolerance and more efficient glucose conversion to ethanol. The desired phenotype results from the combined effect of three separate mutations in the SPT15 gene [serine substituted for phenylalanine (Phe 177 Ser) and, similarly, Tyr 195 His, and Lys 218 Arg]. Thus, gTME can provide a route to complex phenotypes that are not readily accessible by traditional methods.
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“For example, laboratory selection can lead to large-scale rewiring of gene regulatory networks, but an approach, that the authors called gTME, global transcription machinery engineering, can also yield similar results [2].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [2]
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Research works printed but not linked: 2
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“Examples include engineering of yeast for increased ethanol tolerance [43] or xylose consumption [44], as discussed below.”
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MethodStandard Flow Liquid Chromatography for Shotgun Proteomics in Bioenergy Research
Fernández‐Niño, S. M. G., Smith-moritz, A. M., Chan, L. J. G., Adams, P. D., Heazlewood, J. L., & Petzold, C. J. (2015) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2015.00044 · Cited by 49
“, 2014) as well as the genetic manipulation of microbes (Alper et al., 2006; Tyo et al., 2007; Keasling, 2008; Lee et al., 2008) have progressed significantly in the last few years.”
BackgroundAn ancient Chinese wisdom for metabolic engineering: Yin-Yang
Wu, S. G., He, L., Wang, Q., & Tang, Y. (2015) · Microbial Cell Factories · doi:10.1186/s12934-015-0219-3 · Cited by 52
“For example, engineering transcriptional machinery or up-regulation of the potassium/ proton pumps in Saccharomyces cerevisiae can improve both ethanol tolerance and the production titer (>100 g/L) [29,30].”
BackgroundHorinouchi, T., Sakai, A., Kotani, H., Tanabe, K., & Furusawa, C. (2017) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2017.06.408 · Cited by 50
“…and Liao, 2009; Minty et al., 2011), n-butanol (Reyes et al., 2012, 2011; Rutherford et al., 2010) on E. coli, the effect of alcohols on yeast (Alper et al., 2006; Ghiaci et al., 2013; Gonzalez-Ramos et al., 2013; Hirasawa et al., 2007), clostridia (Tomas et al., 2004) (Shi and Blaschek,…”
BackgroundLi, P., Fu, X., Zhang, L., Zhang, Z., Li, J., & Li, S. (2017) · Biotechnology for Biofuels · doi:10.1186/s13068-017-0984-9 · Cited by 49
“Since the exhibition of microbial complex phenotypes is largely dependent on transcription factors (TFs) that control the flow of genetic information from DNA to mRNA, TFs can be candidates to be engineered to improve complex phenotypes so that gene networks and cellular metabolism can be reprogramed [16, 17].”
BackgroundSystematic engineering of microorganisms to improve alcohol tolerance
Jia, K., Zhang, Y., & Li, Y. (2010) · Engineering in Life Sciences · doi:10.1002/elsc.201000076 · Cited by 48
Rapid prototyping of microbial cell factories via genome-scale engineering
Si, T., Xiao, H., & Zhao, H. (2014) · Biotechnology Advances · doi:10.1016/j.biotechadv.2014.11.007 · Cited by 48
“For example, differential expression of hundreds of genes caused by mutations in TFs can only be revealed by transcriptome analysis (Alper et al., 2006).”
InfluentialLi, P., Fu, X., Li, S., & Zhang, L. (2018) · Biotechnology for Biofuels · doi:10.1186/s13068-018-1206-9 · Cited by 48
Biosynthesis pathways and strategies for improving 3-hydroxypropionic acid production in bacteria
Zhao, P., & Tian, P. (2021) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-021-03091-6 · Cited by 55
Transcriptional changes associated with ethanol tolerance in Saccharomyces cerevisiae
Stanley, D., Chambers, P. J., Stanley, G. A., Borneman, A. R., & Fraser, S. (2010) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-010-2760-7 · Cited by 48
“The development of strategic approaches for improving yeast ethanol tolerance can be facilitated by extending transcriptional studies to include ethanol-tolerant mutants and their parental strains; only one previous study used this approach (Alper et al. 2006).”
BackgroundMethodChen, L., Lü, Y., Chen, J., Zhang, W., Shu, D., Qin, Z., Yang, S., & Jiang, W. (2008) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-008-1545-8 · Cited by 46
“It has been suggested recently that detection and modification of regulatory networks may represent an important strategy for further improving production of various industrial compounds (Alper et al. 2006; Nevoigt et al. 2007; Stephanopoulos 2007).”
BackgroundGeng, H., & Jiang, R. (2015) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-015-6587-0 · Cited by 46
Ethanol stress stimulates the Ca2+-mediated calcineurin/Crz1 pathway in Saccharomyces cerevisiae
Araki, Y., Wu, H., Kitagaki, H., Akao, T., Takagi, H., & Shimoi, H. (2009) · Journal of Bioscience and Bioengineering · doi:10.1016/j.jbiosc.2008.09.005 · Cited by 46
Moser, J. W., Prielhofer, R., Gerner, S. M., Graf, A. B., Wilson, I. B. H., Mattanovich, D., & Dragosits, M. (2017) · Microbial Cell Factories · doi:10.1186/s12934-017-0661-5 · Cited by 49
“improved ethanol tolerance [58]; therefore, judging from multiple mutational targets related to regulatory processes, we conclude that transcriptional rewiring may represent a preferred route towards improved growth on methanolbased growth media for P.”
BackgroundFundamental CRISPR-Cas9 tools and current applications in microbial systems
Tian, P., Wang, J., Shen, X., Rey, J. F., Yuan, Q., & Yan, Y. (2017) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2017.08.006 · Cited by 46
Improved acid tolerance of Lactobacillus pentosus by error-prone whole genome amplification
Ye, L., Zhao, H., Li, Z., & Wu, J. C. (2012) · Bioresource Technology · doi:10.1016/j.biortech.2012.10.042 · Cited by 45
“Changes in such complex traits always require the simultaneous alteration of the expression of several genes, something that cannot easily be achieved by sequential multi-gene modifications (Alper et al., 2006).”
BackgroundYin, N., Zhu, G., Luo, Q., Liu, J., Chen, X., & Liu, L. (2019) · Biotechnology and Bioengineering · doi:10.1002/bit.27244 · Cited by 45
Genetics and metabolic engineering of yeast strains for efficient ethanol production
Adebami, G. E., Kuila, A., Ajunwa, O. M., Fasiku, S. A., & Asemoloye, M. D. (2021) · Journal of Food Process Engineering · doi:10.1111/jfpe.13798 · Cited by 49
Development and optimization of a microbial co-culture system for heterologous indigo biosynthesis
Chen, T., Wang, X., Zhuang, L., Shao, A., Lu, Y., & Zhang, H. (2021) · Microbial Cell Factories · doi:10.1186/s12934-021-01636-w · Cited by 44
“gTME has been demonstrated to be an effective technique for introducing diverse changes into the global metabolic network [20, 33].”
MethodZabed, H. M., Akter, S., Rupani, P. F., Akor, J., Zhang, Y., Zhao, M., Zhang, C., Ragauskas, A. J., & Qi, X. (2022) · Biotechnology Advances · doi:10.1016/j.biotechadv.2022.108075 · Cited by 45
Re-engineering multicloning sites for function and convenience
Crook, N., Freeman, E. S., & Alper, H. S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr346 · Cited by 46
“Common improvements to vectors containing MCSs are focused at controlling transcript levels [via promoter replacement/engineering (2), transcription machinery engineering (3) or copy number manipulations (4)] or translation rate [e.”
BackgroundSelf-citationAvrahami-Moyal, L., Engelberg, D., Wenger, J. W., Sherlock, G., & Braun, S. (2012) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2012.00803.x · Cited by 43
“Alternatively, it has been claimed that a small number of ‘master’ genes (or, perhaps, even one) play a central role in ethanol tolerance (Alper et al., 2006), although these genes have not yet been identified with certainty (Baerends et al., 2009).”
BackgroundImproving furfural tolerance of Zymomonas mobilis by rewiring a sigma factor RpoD protein
Tan, F., Dai, L., Wu, B., Qin, H., Shui, Z.-X., Wang, J., Zhu, Q., Hu, Q.-C., Ruan, Z., & He, M. (2015) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-015-6577-2 · Cited by 43
Recek, N., Zhou, R., Zhou, R., Te’o, J., Speight, R. E., Mozetič, M., Vesel, A., Cvelbar, U., Bazaka, K., & Ostrikov, K. (2018) · Scientific Reports · doi:10.1038/s41598-018-26227-5 · Cited by 43
Metadata
- Authors
- Alper, H., Moxley, J., Nevoigt, E., Fink, G. R., & Stephanopoulos, G.
- Affiliations
- Whitehead Institute for Biomedical Research (US)
- Corresponding author
- Stephanopoulos, Gregory
- Venue
- Science
- Published
- 2006-12-08
- Volume
- 314
- Issue
- 5805
- Pages
- 1565-1568
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2080537888
- Cited by
- 823
- References
- 26
- Citations by year
- 2026: 10 · 2025: 23 · 2024: 31 · 2023: 18 · 2022: 28 · 2021: 39 · 2020: 43 · 2019: 37 · 2018: 39 · 2017: 44 · 2016: 49 · 2015: 61 · 2014: 55 · 2013: 57 · 2012: 68
- FWCI
- 14.67
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (GM035010)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Physical Sciences › Engineering › Biomedical Engineering › Biofuel production and bioconversion
- Keywords
- Saccharomyces cerevisiae, ethanol tolerance, glucose fermentation, transcription factor mutations, dominant mutations, biofuel production, yeast strain engineering
- MeSH terms
- Ethanol, Fermentation, Genetic Engineering, Glucose, Phenotype, Saccharomyces cerevisiae, Transcription Factors, Transcription, Genetic, Transformation, Genetic, Up-Regulation, Gene Expression Regulation, Fungal, Mutagenesis, Cell Cycle Proteins, Amino Acid Substitution, Gene Expression Profiling, Saccharomyces cerevisiae Proteins, TATA-Box Binding Protein, Transcription Factor TFIID, TATA-Binding Protein Associated Factors
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