Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae

Lee, Sae-Byuk; Tremaine, Mary; Place, Michael; Liu, Lisa; Pier, Austin; Krause, David J.; Xie, Dan; Zhang, Yaoping; Landick, Robert; Gasch, Audrey P.; Hittinger, Chris Todd; Sato, Trey K.

doi:10.1016/j.ymben.2021.09.008

Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae

Journal Article · Mon Sep 27 00:00:00 EDT 2021 · Metabolic Engineering

DOI:https://doi.org/10.1016/j.ymben.2021.09.008· OSTI ID:1827679

^[1]; Tremaine, Mary ^[2]; Place, Michael ^[2]; Liu, Lisa ^[2]; Pier, Austin ^[2]; Krause, David J. ^[2]; Xie, Dan ^[2]; Zhang, Yaoping ^[2]; ^[2]; Gasch, Audrey P. ^[2]; ^[2]; ^[2]

Univ. of Wisconsin, Madison, WI (United States); University of Wisconsin-Madison Great Lakes Bioenergy Research Center
Univ. of Wisconsin, Madison, WI (United States)

Bottlenecks in the efficient conversion of xylose into cost-effective biofuels have limited the widespread use of plant lignocellulose as a renewable feedstock. The yeast Saccharomyces cerevisiae ferments glucose into ethanol with such high metabolic flux that it ferments high concentrations of glucose aerobically, a trait called the Crabtree/Warburg Effect. In contrast to glucose, most engineered S. cerevisiae strains do not ferment xylose at economically viable rates and yields, and they require respiration to achieve sufficient xylose metabolic flux and energy return for growth aerobically. Here, we evolved respiration-deficient S. cerevisiae strains that can grow on and ferment xylose to ethanol aerobically, a trait analogous to the Crabtree/Warburg Effect for glucose. Through genome sequence comparisons and directed engineering, we determined that duplications of genes encoding engineered xylose metabolism enzymes, as well as TKL1, a gene encoding a transketolase in the pentose phosphate pathway, were the causative genetic changes for the evolved phenotype. Reengineered duplications of these enzymes, in combination with deletion mutations in HOG1, ISU1, GRE3, and IRA2, increased the rates of aerobic and anaerobic xylose fermentation. Importantly, we found that these genetic modifications function in another genetic background and increase the rate and yield of xylose-to-ethanol conversion in industrially relevant switchgrass hydrolysate, indicating that these specific genetic modifications may enable the sustainable production of industrial biofuels from yeast. We propose a model for how key regulatory mutations prime yeast for aerobic xylose fermentation by lowering the threshold for overflow metabolism, allowing mutations to increase xylose flux and to redirect it into fermentation products.

View Accepted Manuscript (DOE)

Research Organization:: Great Lakes Bioenergy Research Center, Madison, WI (United States)

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

Grant/Contract Number:: FC02-07ER64494; SC0018409

OSTI ID:: 1827679

Journal Information:: Metabolic Engineering, Journal Name: Metabolic Engineering Vol. 68; ISSN 1096-7176

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (64)

Pyruvate Metabolism inSaccharomyces cerevisiae Pronk, Jack T.; Yde Steensma, H.; Van Dijken, Johannes P. Yeast, Vol. 12, Issue 16 https://doi.org/10.1002/(SICI)1097-0061(199612)12:16<1607::AID-YEA70>3.0.CO;2-4	journal	December 1996
Xylose Assimilation for the Efficient Production of Biofuels and Chemicals by Engineered Saccharomyces cerevisiae Sun, Liang; Jin, Yong‐Su Biotechnology Journal, Vol. 16, Issue 4 https://doi.org/10.1002/biot.202000142	journal	November 2020
Xylose fermentation by Saccharomyces cerevisiae K�tter, Peter; Ciriacy, Michael Applied Microbiology and Biotechnology, Vol. 38, Issue 6 https://doi.org/10.1007/BF00167144	journal	March 1993
Towards industrial pentose-fermenting yeast strains Hahn-Hägerdal, Bärbel; Karhumaa, Kaisa; Fonseca, César Applied Microbiology and Biotechnology, Vol. 74, Issue 5 https://doi.org/10.1007/s00253-006-0827-2	journal	February 2007
Lactic acid production from xylose by engineered Saccharomyces cerevisiae without PDC or ADH deletion Turner, Timothy L.; Zhang, Guo-Chang; Kim, Soo Rin Applied Microbiology and Biotechnology, Vol. 99, Issue 19 https://doi.org/10.1007/s00253-015-6701-3	journal	June 2015
Comparative transcriptomes reveal novel evolutionary strategies adopted by Saccharomyces cerevisiae with improved xylose utilization capability Zeng, Wei-Yi; Tang, Yue-Qin; Gou, Min Applied Microbiology and Biotechnology, Vol. 101, Issue 4 https://doi.org/10.1007/s00253-016-8046-y	journal	December 2016
Inhibition of d-xylose isomerase by pentitols and d-lyxose Yamanaka, Kei Archives of Biochemistry and Biophysics, Vol. 131, Issue 2 https://doi.org/10.1016/0003-9861(69)90422-6	journal	May 1969
Multifunctional yeast high-copy-number shuttle vectors Christianson, Thomas W.; Sikorski, Robert S.; Dante, Michael Gene, Vol. 110, Issue 1 https://doi.org/10.1016/0378-1119(92)90454-W	journal	January 1992
Involvement of mitochondrial ferredoxin and Cox15p in hydroxylation of heme O Barros, Mario H.; Carlson, Christopher G.; Glerum, D. Moira FEBS Letters, Vol. 492, Issue 1-2 https://doi.org/10.1016/S0014-5793(01)02249-9	journal	March 2001
Getting started with yeast Sherman, Fred Guide to Yeast Genetics and Molecular and Cell Biology - Part B https://doi.org/10.1016/S0076-6879(02)50954-X	book	January 2002
Effect of auxotrophies on yeast performance in aerated fed-batch reactor Landi, Carmine; Paciello, Lucia; de Alteriis, Elisabetta Biochemical and Biophysical Research Communications, Vol. 414, Issue 3 https://doi.org/10.1016/j.bbrc.2011.09.129	journal	October 2011
Supercritical carbon dioxide pretreatment of corn stover and switchgrass for lignocellulosic ethanol production Narayanaswamy, Naveen; Faik, Ahmed; Goetz, Douglas J. Bioresource Technology, Vol. 102, Issue 13 https://doi.org/10.1016/j.biortech.2011.04.052	journal	July 2011
Strain engineering of Saccharomyces cerevisiae for enhanced xylose metabolism Kim, Soo Rin; Park, Yong-Cheol; Jin, Yong-Su Biotechnology Advances, Vol. 31, Issue 6 https://doi.org/10.1016/j.biotechadv.2013.03.004	journal	November 2013
Production of hydrolysates from unmilled AFEX-pretreated switchgrass and comparative fermentation with Zymomonas mobilis Zhang, Yaoping; Serate, Jose; Xie, Dan Bioresource Technology Reports, Vol. 11 https://doi.org/10.1016/j.biteb.2020.100517	journal	September 2020
Engineering xylose metabolism in yeasts to produce biofuels and chemicals Lee, Jae Won; Yook, Sangdo; Koh, Hyungi Current Opinion in Biotechnology, Vol. 67 https://doi.org/10.1016/j.copbio.2020.10.012	journal	February 2021
Metabolic engineering of a xylose-isomerase-expressing strain for rapid anaerobic xylose fermentation Kuyper, Marko; Hartog, Miranda; Toirkens, Maurice FEMS Yeast Research, Vol. 5, Issue 4-5, p. 399-409 https://doi.org/10.1016/j.femsyr.2004.09.010	journal	February 2005
Metabolic-flux dependent regulation of microbial physiology Litsios, Athanasios; Ortega, Álvaro D.; Wit, Ernst C. Current Opinion in Microbiology, Vol. 42 https://doi.org/10.1016/j.mib.2017.10.029	journal	April 2018
Improving carotenoids production in yeast via adaptive laboratory evolution Reyes, Luis H.; Gomez, Jose M.; Kao, Katy C. Metabolic Engineering, Vol. 21 https://doi.org/10.1016/j.ymben.2013.11.002	journal	January 2014
The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology Sandberg, Troy E.; Salazar, Michael J.; Weng, Liam L. Metabolic Engineering, Vol. 56 https://doi.org/10.1016/j.ymben.2019.08.004	journal	December 2019
Gene duplication and the adaptive evolution of a classic genetic switch Hittinger, Chris Todd; Carroll, Sean B. Nature, Vol. 449, Issue 7163 https://doi.org/10.1038/nature06151	journal	October 2007
High-efficiency 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.2007.13	journal	January 2007
An upper limit on Gibbs energy dissipation governs cellular metabolism Niebel, Bastian; Leupold, Simeon; Heinemann, Matthias Nature Metabolism, Vol. 1, Issue 1 https://doi.org/10.1038/s42255-018-0006-7	journal	January 2019
Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae Reider Apel, Amanda; Ouellet, Mario; Szmidt-Middleton, Heather Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep19512	journal	January 2016
Unraveling the genetic basis of xylose consumption in engineered Saccharomyces cerevisiae strains dos Santos, Leandro Vieira; Carazzolle, Marcelo Falsarella; Nagamatsu, Sheila Tiemi Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep38676	journal	December 2016
Mutations in PMR1 stimulate xylose isomerase activity and anaerobic growth on xylose of engineered Saccharomyces cerevisiae by influencing manganese homeostasis Verhoeven, Maarten D.; Lee, Misun; Kamoen, Lycka Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep46155	journal	April 2017
Glucose as a hormone: receptor-mediated glucose sensing in the yeast Saccharomyces cerevisiae Johnston, M.; Kim, J. -H. Biochemical Society Transactions, Vol. 33, Issue 1 https://doi.org/10.1042/BST0330247	journal	February 2005
Observations on the carbohydrate metabolism of tumours Crabtree, Herbert Grace Biochemical Journal, Vol. 23, Issue 3 https://doi.org/10.1042/bj0230536	journal	January 1929
COX15 Codes for a Mitochondrial Protein Essential for the Assembly of Yeast Cytochrome Oxidase Glerum, D. Moira; Muroff, Ivor; Jin, Can Journal of Biological Chemistry, Vol. 272, Issue 30 https://doi.org/10.1074/jbc.272.30.19088	journal	July 1997
The Metabolism of Tumors in the body Warburg, O. The Journal of General Physiology, Vol. 8, Issue 6 https://doi.org/10.1085/jgp.8.6.519	journal	March 1927
Glucose repression in Saccharomyces cerevisiae Kayikci, Ömur; Nielsen, Jens FEMS Yeast Research, Vol. 15, Issue 6 https://doi.org/10.1093/femsyr/fov068	journal	July 2015
Assessing the effect of d-xylose on the sugar signaling pathways of Saccharomyces cerevisiae in strains engineered for xylose transport and assimilation Osiro, Karen O.; Brink, Daniel P.; Borgström, Celina FEMS Yeast Research, Vol. 18, Issue 1 https://doi.org/10.1093/femsyr/fox096	journal	January 2018
Expansion of Hexose Transporter Genes Was Associated with the Evolution of Aerobic Fermentation in Yeasts Lin, Z.; Li, W. -H. Molecular Biology and Evolution, Vol. 28, Issue 1 https://doi.org/10.1093/molbev/msq184	journal	July 2010
A new efficient gene disruption cassette for repeated use in budding yeast Guldener, U. Nucleic Acids Research, Vol. 24, Issue 13 https://doi.org/10.1093/nar/24.13.2519	journal	July 1996
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data McKenna, A.; Hanna, M.; Banks, E. Genome Research, Vol. 20, Issue 9 https://doi.org/10.1101/gr.107524.110	journal	July 2010
Isobutanol production from d -xylose by recombinant Saccharomyces cerevisiae Brat, Dawid; Boles, Eckhard FEMS Yeast Research, Vol. 13, Issue 2 https://doi.org/10.1111/1567-1364.12028	journal	January 2013
Why, when, and how did yeast evolve alcoholic fermentation? Dashko, Sofia; Zhou, Nerve; Compagno, Concetta FEMS Yeast Research, Vol. 14, Issue 6 https://doi.org/10.1111/1567-1364.12161	journal	June 2014
Cell-wall carbohydrates and their modification as a resource for biofuels Pauly, Markus; Keegstra, Kenneth The Plant Journal, Vol. 54, Issue 4, p. 559-568 https://doi.org/10.1111/j.1365-313X.2008.03463.x	journal	May 2008
A flux-sensing mechanism could regulate the switch between respiration and fermentation Huberts, Daphne H. E. W.; Niebel, Bastian; Heinemann, Matthias FEMS Yeast Research, Vol. 12, Issue 2 https://doi.org/10.1111/j.1567-1364.2011.00767.x	journal	December 2011
Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption Scalcinati, Gionata; Otero, José Manuel; Vleet, Jennifer R. H. FEMS Yeast Research, Vol. 12, Issue 5 https://doi.org/10.1111/j.1567-1364.2012.00808.x	journal	April 2012
Directed Evolution of Xylose Isomerase for Improved Xylose Catabolism and Fermentation in the Yeast Saccharomyces cerevisiae Lee, Sun-Mi; Jellison, Taylor; Alper, Hal S. Applied and Environmental Microbiology, Vol. 78, Issue 16 https://doi.org/10.1128/AEM.01419-12	journal	June 2012
Functional Expression of a Bacterial Xylose Isomerase in Saccharomyces cerevisiae Brat, D.; Boles, E.; Wiedemann, B. Applied and Environmental Microbiology, Vol. 75, Issue 8 https://doi.org/10.1128/AEM.02522-08	journal	February 2009
Complex Physiology and Compound Stress Responses during Fermentation of Alkali-Pretreated Corn Stover Hydrolysate by an Escherichia coli Ethanologen Schwalbach, Michael S.; Keating, David H.; Tremaine, Mary Applied and Environmental Microbiology, Vol. 78, Issue 9, p. 3442-3457 https://doi.org/10.1128/AEM.07329-11	journal	March 2012
Deletion of the GRE3 Aldose Reductase Gene and Its Influence on Xylose Metabolism in Recombinant Strains of Saccharomyces cerevisiae Expressing the xylA and XKS1 Genes Traff, K. L.; Otero Cordero, R. R.; van Zyl, W. H. Applied and Environmental Microbiology, Vol. 67, Issue 12 https://doi.org/10.1128/AEM.67.12.5668-5674.2001	journal	December 2001
Xylulokinase Overexpression in Two Strains of Saccharomyces cerevisiae Also Expressing Xylose Reductase and Xylitol Dehydrogenase and Its Effect on Fermentation of Xylose and Lignocellulosic Hydrolysate Johansson, B.; Christensson, C.; Hobley, T. Applied and Environmental Microbiology, Vol. 67, Issue 9 https://doi.org/10.1128/AEM.67.9.4249-4255.2001	journal	September 2001
Saccharomyces cerevisiae Engineered for Xylose Metabolism Exhibits a Respiratory Response Jin, Y.-S.; Laplaza, J. M.; Jeffries, T. W. Applied and Environmental Microbiology, Vol. 70, Issue 11, p. 6816-6825 https://doi.org/10.1128/AEM.70.11.6816-6825.2004	journal	November 2004
Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae Salusjärvi, Laura; Kankainen, Matti; Soliymani, Rabah Microbial Cell Factories, Vol. 7, Issue 1 https://doi.org/10.1186/1475-2859-7-18	journal	January 2008
Increased expression of the oxidative pentose phosphate pathway and gluconeogenesis in anaerobically growing xylose-utilizing Saccharomyces cerevisiae Runquist, David; Hahn-Hägerdal, Bärbel; Bettiga, Maurizio Microbial Cell Factories, Vol. 8, Issue 1 https://doi.org/10.1186/1475-2859-8-49	journal	January 2009
Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering Demeke, Mekonnen M.; Dietz, Heiko; Li, Yingying Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-89	journal	January 2013
Production of fuels and chemicals from xylose by engineered Saccharomyces cerevisiae: a review and perspective Kwak, Suryang; Jin, Yong-Su Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-017-0694-9	journal	May 2017
Exploring the xylose paradox in Saccharomyces cerevisiae through in vivo sugar signalomics of targeted deletants Osiro, Karen O.; Borgström, Celina; Brink, Daniel P. Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1141-x	journal	May 2019
Xylose fermentation efficiency of industrial Saccharomyces cerevisiae yeast with separate or combined xylose reductase/xylitol dehydrogenase and xylose isomerase pathways Cunha, Joana T.; Soares, Pedro O.; Romaní, Aloia Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1360-8	journal	January 2019
Structure-based directed evolution improves S. cerevisiae growth on xylose by influencing in vivo enzyme performance Lee, Misun; Rozeboom, Henriëtte J.; Keuning, Eline Biotechnology for Biofuels, Vol. 13, Issue 1 https://doi.org/10.1186/s13068-019-1643-0	journal	January 2020
Disruption of PHO13 improves ethanol production via the xylose isomerase pathway Bamba, Takahiro; Hasunuma, Tomohisa; Kondo, Akihiko AMB Express, Vol. 6, Issue 1 https://doi.org/10.1186/s13568-015-0175-7	journal	January 2016
Functional Partitioning of Yeast Co-Expression Networks after Genome Duplication Conant, Gavin C.; Wolfe, Kenneth H. PLoS Biology, Vol. 4, Issue 4 https://doi.org/10.1371/journal.pbio.0040109	journal	April 2006
Rapid Evolution of Recombinant Saccharomyces cerevisiae for Xylose Fermentation through Formation of Extra-chromosomal Circular DNA Demeke, Mekonnen M.; Foulquié-Moreno, María R.; Dumortier, Françoise PLOS Genetics, Vol. 11, Issue 3 https://doi.org/10.1371/journal.pgen.1005010	journal	March 2015
Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast Myers, Kevin S.; Riley, Nicholas M.; MacGilvray, Matthew E. PLOS Genetics, Vol. 15, Issue 3 https://doi.org/10.1371/journal.pgen.1008037	journal	March 2019
Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover Parreiras, Lucas S.; Breuer, Rebecca J.; Avanasi Narasimhan, Ragothaman PLoS ONE, Vol. 9, Issue 9 https://doi.org/10.1371/journal.pone.0107499	journal	September 2014
A Study on the Fundamental Mechanism and the Evolutionary Driving Forces behind Aerobic Fermentation in Yeast Hagman, Arne; Piškur, Jure PLOS ONE, Vol. 10, Issue 1 https://doi.org/10.1371/journal.pone.0116942	journal	January 2015
Signature pathway expression of xylose utilization in the genetically engineered industrial yeast Saccharomyces cerevisiae Feng, Quanzhou; Liu, Z. Lewis; Weber, Scott A. PLOS ONE, Vol. 13, Issue 4 https://doi.org/10.1371/journal.pone.0195633	journal	April 2018
PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production Wagner, Ellen R.; Myers, Kevin S.; Riley, Nicholas M. PLOS ONE, Vol. 14, Issue 5 https://doi.org/10.1371/journal.pone.0212389	journal	May 2019
Metabolic engineering considerations for the heterologous expression of xylose-catabolic pathways in Saccharomyces cerevisiae Jeong, Deokyeol; Oh, Eun Joong; Ko, Ja Kyong PLOS ONE, Vol. 15, Issue 7 https://doi.org/10.1371/journal.pone.0236294	journal	July 2020
Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast Higgins, Douglas A.; Young, Megan K. M.; Tremaine, Mary Genetics, Vol. 210, Issue 1 https://doi.org/10.1534/genetics.118.301161	journal	July 2018
Integration of Pretreatment With Simultaneous Counter-Current Extraction of Energy Sorghum for High-Titer Mixed Sugar Production Williams, Daniel L.; Ong, Rebecca G.; Mullet, John E. Frontiers in Energy Research, Vol. 6 https://doi.org/10.3389/fenrg.2018.00133	journal	January 2019
An evolutionary perspective on the Crabtree effect Pfeiffer, Thomas; Morley, Annabel Frontiers in Molecular Biosciences, Vol. 1 https://doi.org/10.3389/fmolb.2014.00017	journal	October 2014

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59 BASIC BIOLOGICAL SCIENCES
Adaptive laboratory evolution
Biofuels
Crabtree/Warburg effect
Metabolic engineering
Saccharomyces cerevisiae
Xylose fermentation

Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae

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