Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer

Denby, Charles M.; Li, Rachel A.; Vu, Van T.; Costello, Zak; Lin, Weiyin; Chan, Leanne Jade G.; Williams, Joseph; Donaldson, Bryan; Bamforth, Charles W.; Petzold, Christopher J.; Scheller, Henrik V.; Martin, Hector Garcia; Keasling, Jay D.

doi:10.1038/s41467-018-03293-x

Title: Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer

Journal Article · Tue Mar 20 00:00:00 EDT 2018 · Nature Communications

DOI:https://doi.org/10.1038/s41467-018-03293-x· OSTI ID:1457017

Denby, Charles M. ^[1]; Li, Rachel A. ^[2]; Vu, Van T. ^[3]; Costello, Zak ^[4]; Lin, Weiyin ^[1]; Chan, Leanne Jade G. ^[5]; Williams, Joseph ^[6]; Donaldson, Bryan ^[7];

^[6]; Petzold, Christopher J. ^[5]; Scheller, Henrik V. ^[8];

^[4];

^[9]

Univ. of California, Berkeley, CA (United States). California Inst. of Quantitative Biosciences (QB3); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division; DOE 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, Davis, CA (United States). Dept. of Food Science and Technology
Lagunitas Brewing Company, Petaluma, CA (United States)
Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
Univ. of California, Berkeley, CA (United States). California Inst. of Quantitative Biosciences (QB3); 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 Bioengineering; Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engineering; Technical Univ. of Denmark, Hellerup (Denmark). Novo Nordisk Foundation Center for Sustainability

Flowers of the hop plant provide both bitterness and "hoppy" flavor to beer. Hops are, however, both a water and energy intensive crop and vary considerably in essential oil content, making it challenging to achieve a consistent hoppy taste in beer. Here, we report that brewer's yeast can be engineered to biosynthesize aromatic monoterpene molecules that impart hoppy flavor to beer by incorporating recombinant DNA derived from yeast, mint, and basil. Whereas metabolic engineering of biosynthetic pathways is commonly enlisted to maximize product titers, tuning expression of pathway enzymes to affect target production levels of multiple commercially important metabolites without major collateral metabolic changes represents a unique challenge. By applying state-of-the-art engineering techniques and a framework to guide iterative improvement, strains are generated with target performance characteristics. Finally, beers produced using these strains are perceived as hoppier than traditionally hopped beers by a sensory panel in a double-blind tasting.

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

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

Grant/Contract Number:: AC02-05CH11231; 1722376

OSTI ID:: 1457017

Journal Information:: Nature Communications, Vol. 9, Issue 1; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 122 works

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References (39)

Standard Flow Liquid Chromatography for Shotgun Proteomics in Bioenergy Research González Fernández-Niño, Susana M.; Smith-Moritz, A. Michelle; Chan, Leanne Jade G. Frontiers in Bioengineering and Biotechnology, Vol. 3 https://doi.org/10.3389/fbioe.2015.00044	journal	April 2015
Comparison of the Most Odor-Active Compounds in Fresh and Dried Hop Cones ( Humulus lupulus L. Variety Spalter Select) Based on GC−Olfactometry and Odor Dilution Techniques Steinhaus, Martin; Schieberle, Peter Journal of Agricultural and Food Chemistry, Vol. 48, Issue 5 https://doi.org/10.1021/jf990514l	journal	May 2000
ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites Emanuelsson, Olof; Nielsen, Henrik; Heijne, Gunnar Von Protein Science, Vol. 8, Issue 5 https://doi.org/10.1110/ps.8.5.978	journal	January 1999
Truncation of Limonene Synthase Preprotein Provides a Fully Active ‘Pseudomature' Form of This Monoterpene Cyclase and Reveals the Function of the Amino-Terminal Arginine Pair ^† Williams, David C.; McGarvey, Douglas J.; Katahira, Eva J. Biochemistry, Vol. 37, Issue 35 https://doi.org/10.1021/bi980854k	journal	September 1998
Molecular cloning and characterization of a new linalool synthase Crowell, Anastasia L.; Williams, David C.; Davis, Edward M. Archives of Biochemistry and Biophysics, Vol. 405, Issue 1 https://doi.org/10.1016/S0003-9861(02)00348-X	journal	September 2002
Floral hop aroma in beer Peacock, Val E.; Deinzer, Max L.; Likens, Sam T. Journal of Agricultural and Food Chemistry, Vol. 29, Issue 6 https://doi.org/10.1021/jf00108a041	journal	November 1981
Enhanced Levels of the Aroma and Flavor Compound S- Linalool by Metabolic Engineering of the Terpenoid Pathway in Tomato Fruits Lewinsohn, Efraim; Schalechet, Fernond; Wilkinson, Jack Plant Physiology, Vol. 127, Issue 3 https://doi.org/10.1104/pp.010293	journal	November 2001
j5 DNA Assembly Design Automation Software Hillson, Nathan J.; Rosengarten, Rafael D.; Keasling, Jay D. ACS Synthetic Biology, Vol. 1, Issue 1, p. 14-21 https://doi.org/10.1021/sb2000116	journal	December 2011
mProphet: automated data processing and statistical validation for large-scale SRM experiments Reiter, Lukas; Rinner, Oliver; Picotti, Paola Nature Methods, Vol. 8, Issue 5 https://doi.org/10.1038/nmeth.1584	journal	March 2011
Large-Scale Selection and Breeding To Generate Industrial Yeasts with Superior Aroma Production Steensels, Jan; Meersman, Esther; Snoek, Tim Applied and Environmental Microbiology, Vol. 80, Issue 22 https://doi.org/10.1128/AEM.02235-14	journal	September 2014
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments MacLean, Brendan; Tomazela, Daniela M.; Shulman, Nicholas Bioinformatics, Vol. 26, Issue 7 https://doi.org/10.1093/bioinformatics/btq054	journal	February 2010
A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly Lee, Michael E.; DeLoache, William C.; Cervantes, Bernardo ACS Synthetic Biology, Vol. 4, Issue 9 https://doi.org/10.1021/sb500366v	journal	April 2015
Terpene Biosynthesis in Glandular Trichomes of Hop Wang, Guodong; Tian, Li; Aziz, Naveed Plant Physiology, Vol. 148, Issue 3 https://doi.org/10.1104/pp.108.125187	journal	September 2008
Regulation of HMG-CoA reductase in mammals and yeast Burg, John S.; Espenshade, Peter J. Progress in Lipid Research, Vol. 50, Issue 4 https://doi.org/10.1016/j.plipres.2011.07.002	journal	October 2011
Production of the antimalarial drug precursor artemisinic acid in engineered yeast Ro, Dae-Kyun; Paradise, Eric M.; Ouellet, Mario Nature, Vol. 440, Issue 7086, p. 940-943 https://doi.org/10.1038/nature04640	journal	April 2006
Plant terpenoid synthases: Molecular biology and phylogenetic analysis Bohlmann, J.; Meyer-Gauen, G.; Croteau, R. Proceedings of the National Academy of Sciences, Vol. 95, Issue 8 https://doi.org/10.1073/pnas.95.8.4126	journal	April 1998
Overexpression of a cytosolic hydroxymethylglutaryl-CoA reductase leads to squalene accumulation in yeast Polakowski, T.; Stahl, U.; Lang, C. Applied Microbiology and Biotechnology, Vol. 49, Issue 1 https://doi.org/10.1007/s002530051138	journal	January 1998
Use of GC−Olfactometry to Identify the Hop Aromatic Compounds in Beer Lermusieau, Guillaume; Bulens, Marie; Collin, Sonia Journal of Agricultural and Food Chemistry, Vol. 49, Issue 8 https://doi.org/10.1021/jf0101509	journal	August 2001
Secreting Glandular Trichomes: More than Just Hairs Wagner, George J. Plant Physiology, Vol. 96, Issue 3 https://doi.org/10.1104/pp.96.3.675	journal	July 1991
Varietal Dependence of hop Flavour Volatiles in Lager Irwin, A. J. Journal of the Institute of Brewing, Vol. 95, Issue 3 https://doi.org/10.1002/j.2050-0416.1989.tb04625.x	journal	May 1989
Functional optimization of gene clusters by combinatorial design and assembly Smanski, Michael J.; Bhatia, Swapnil; Zhao, Dehua Nature Biotechnology, Vol. 32, Issue 12, p. 1241-1249 https://doi.org/10.1038/nbt.3063	journal	November 2014
DeviceEditor visual biological CAD canvas Chen, Joanna; Densmore, Douglas; Ham, Timothy S. Journal of Biological Engineering, Vol. 6, Issue 1 https://doi.org/10.1186/1754-1611-6-1	journal	December 2012
ggplot2: Elegant Graphics for Data Analysis by WICKHAM, H. Wilkinson, Leland Biometrics, Vol. 67, Issue 2 https://doi.org/10.1111/j.1541-0420.2011.01616.x	journal	June 2011
Engineering the Saccharomyces cerevisiae isoprenoid pathway for de novo production of aromatic monoterpenes in wine Herrero, Óscar; Ramón, Daniel; Orejas, Margarita Metabolic Engineering, Vol. 10, Issue 2 https://doi.org/10.1016/j.ymben.2007.11.001	journal	March 2008
Modern Applied Statistics with S Venables, W. N.; Ripley, B. D. Statistics and Computing https://doi.org/10.1007/978-0-387-21706-2	book	August 2002
De novo production of six key grape aroma monoterpenes by a geraniol synthase-engineered S. cerevisiae wine strain Pardo, Ester; Rico, Juan; Gil, José Vicente Microbial Cell Factories, Vol. 14, Issue 1 https://doi.org/10.1186/s12934-015-0306-5	journal	September 2015
Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools Ham, T. S.; Dmytriv, Z.; Plahar, H. Nucleic Acids Research, Vol. 40, Issue 18 https://doi.org/10.1093/nar/gks531	journal	June 2012
Reshaping Data with the reshape Package Wickham, Hadley Journal of Statistical Software, Vol. 21, Issue 12 https://doi.org/10.18637/jss.v021.i12	journal	January 2007
Quantitation of ( R )- and ( S )-Linalool in Beer Using Solid Phase Microextraction (SPME) in Combination with a Stable Isotope Dilution Assay (SIDA) Steinhaus, Martin; Fritsch, Helge T.; Schieberle, Peter Journal of Agricultural and Food Chemistry, Vol. 51, Issue 24 https://doi.org/10.1021/jf0347057	journal	November 2003
Expression Levels of the Yeast Alcohol Acetyltransferase Genes ATF1, Lg-ATF1, and ATF2 Control the Formation of a Broad Range of Volatile Esters Verstrepen, K. J.; Van Laere, S. D. M.; Vanderhaegen, B. M. P. Applied and Environmental Microbiology, Vol. 69, Issue 9 https://doi.org/10.1128/AEM.69.9.5228-5237.2003	journal	September 2003
A One Pot, One Step, Precision Cloning Method with High Throughput Capability Engler, Carola; Kandzia, Romy; Marillonnet, Sylvestre PLoS ONE, Vol. 3, Issue 11, Article No. e3647 https://doi.org/10.1371/journal.pone.0003647	journal	November 2008
Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli Ajikumar, P. K.; Xiao, W.-H.; Tyo, K. E. J. Science, Vol. 330, Issue 6000, p. 70-74 https://doi.org/10.1126/science.1191652	journal	September 2010
Enzymatic assembly of DNA molecules up to several hundred kilobases Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan Nature Methods, Vol. 6, Issue 5, p. 343-345 https://doi.org/10.1038/nmeth.1318	journal	April 2009
Improving industrial yeast strains: exploiting natural and artificial diversity Steensels, Jan; Snoek, Tim; Meersman, Esther FEMS Microbiology Reviews, Vol. 38, Issue 5 https://doi.org/10.1111/1574-6976.12073	journal	September 2014
Engineering Monoterpene Production in Yeast Using a Synthetic Dominant Negative Geranyl Diphosphate Synthase Ignea, Codruta; Pontini, Marianna; Maffei, Massimo E. ACS Synthetic Biology, Vol. 3, Issue 5 https://doi.org/10.1021/sb400115e	journal	January 2014
mProphet: automated data processing and statistical validation for large-scale SRM experiments Reiter, L.; Rinner, O.; Picotti, P. Nature Publishing Group https://doi.org/10.5167/uzh-47865	text	January 2011
Machine learning discovery of missing links that mediate alternative branches to plant alkaloids Vavricka, Christopher J.; Takahashi, Shunsuke; Watanabe, Naoki Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-28883-8	journal	March 2022
Estimating nitrogen and phosphorus concentrations in streams and rivers, within a machine learning framework Shen, Longzhu Q.; Amatulli, Giuseppe; Sethi, Tushar Scientific Data, Vol. 7, Issue 1 https://doi.org/10.1038/s41597-020-0478-7	journal	May 2020
Effect of design geometry, exposure energy, cytophilic molecules, cell type and load in fabrication of single-cell arrays using micro-contact printing Bhujbal, Swapnil Vilas; Dekov, Maren; Ottesen, Vegar Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-72080-w	journal	September 2020

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CRISPR/Cas9‐RNA interference system for combinatorial metabolic engineering of Saccharomyces cerevisiae Kildegaard, Kanchana Rueksomtawin; Tramontin, Larissa Ribeiro Ramos; Chekina, Ksenia Yeast, Vol. 36, Issue 5 https://doi.org/10.1002/yea.3390	journal	May 2019
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The molecular biology of fruity and floral aromas in beer and other alcoholic beverages Holt, Sylvester; Miks, Marta H.; de Carvalho, Bruna Trindade FEMS Microbiology Reviews, Vol. 43, Issue 3 https://doi.org/10.1093/femsre/fuy041	journal	November 2018
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