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Zhong Y, Shang C, Tao H, Hou J, Cui Z, Qi Q. Boosting succinic acid production of Yarrowia lipolytica at low pH through enhancing product tolerance and glucose metabolism. Microb Cell Fact 2024; 23:291. [PMID: 39443950 DOI: 10.1186/s12934-024-02565-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 10/11/2024] [Indexed: 10/25/2024] Open
Abstract
BACKGROUND Succinic acid (SA) is an important bio-based C4 platform chemical with versatile applications, including the production of 1,4-butanediol, tetrahydrofuran, and γ-butyrolactone. The non-conventional yeast Yarrowia lipolytica has garnered substantial interest as a robust cell factory for SA production at low pH. However, the high concentrations of SA, especially under acidic conditions, can impose significant stress on microbial cells, leading to reduced glucose metabolism viability and compromised production performance. Therefore, it is important to develop Y. lipolytica strains with enhanced SA tolerance for industrial-scale SA production. RESULTS An SA-tolerant Y. lipolytica strain E501 with improved SA production was obtained through adaptive laboratory evolution (ALE). In a 5-L bioreactor, the evolved strain E501 produced 89.62 g/L SA, representing a 7.2% increase over the starting strain Hi-SA2. Genome resequencing and transcriptome analysis identified a mutation in the 26S proteasome regulatory subunit Rpn1, as well as genes involved in transmembrane transport, which may be associated with enhanced SA tolerance. By further fine-tuning the glycolytic pathway flux, the highest SA titer of 112.54 g/L to date at low pH was achieved, with a yield of 0.67 g/g glucose and a productivity of 2.08 g/L/h. CONCLUSION This study provided a robust engineered Y. lipolytica strain capable of efficiently producing SA at low pH, thereby reducing the cost of industrial SA fermentation.
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Affiliation(s)
- Yutao Zhong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Changyu Shang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Huilin Tao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China.
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China.
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Rojo MC, Talia PM, Lerena MC, Ponsone ML, Gonzalez ML, Becerra LM, Mercado LA, Martín-Arranz V, Rodríguez-Gómez F, Arroyo-López FN, Combina M. Evaluation of different nitrogen sources on growth and fermentation performance for enhancing ethanol production by wine yeasts. Heliyon 2023; 9:e22608. [PMID: 38213578 PMCID: PMC10782155 DOI: 10.1016/j.heliyon.2023.e22608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/06/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
The utilization of grape juice from low oenological value grape varieties for bioethanol production represent an alternative for diversification and value addition in viticulture. Optimizing Very High Gravity (VHG) fermentation can significantly increase ethanol productivity while reducing water and energy consumption. In this study, the impact of different nitrogen sources on growth and fermentative performance of locally selected yeast strains was investigated. Five yeast strains of species Saccharomyces cerevisiae and Zygosaccharomyces rouxii were cultured in both synthetic culture media and natural grape juice supplemented with ammonium sulfate (NH), yeast extract (YE), Fermaid K (FERM), and urea (U) at varying concentrations. Due to the very low fermentation rate, the Z. rouxii strain was excluded from the selection. The results obtained in synthetic medium showed that nitrogen sources that promoted growth (NH and YE) had minimal effects on fermentative performance and were highly dependent on the specific yeast strain. However, the combination of urea and ammonium favored the rate of sugar consumption. When validated in natural grape juice, urea combined with ammonium (U + NH 300 + 75 mg/L) improved both growth parameters and ethanol yield. Doubling the concentration (U + NH 600 + 150 mg/L) further enhanced sugar consumption and ethanol production while reducing unwanted by-products. The combined use of urea and ammonium exhibited a synergistic effect, making it a cost-effective nitrogen supplement for VHG fermentations.
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Affiliation(s)
- María Cecilia Rojo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
| | - Paola Mónica Talia
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Cecilia Lerena
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
| | - María Lorena Ponsone
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (FCEN-UNCuyo) Padre Jorge Contreras 1300, Parque Gral San Martin (M5502JMA), Mendoza, Argentina
| | - Magalí Lucía Gonzalez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
| | - Lucía Maribel Becerra
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
| | - Laura Analía Mercado
- Wine Research Center, Estación Experimental Agropecuaria Mendoza, Instituto Nacional de Tecnología Agropecuaria (EEA Mza INTA), San Martín 3853, Luján de Cuyo, Mendoza 5507, Argentina
| | - Virginia Martín-Arranz
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Carretera de Utrera Km 1. Campus Universitario Pablo de Olavide, Building 46. 41013, Sevilla, Spain
| | - Francisco Rodríguez-Gómez
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Carretera de Utrera Km 1. Campus Universitario Pablo de Olavide, Building 46. 41013, Sevilla, Spain
| | - Francisco Noé Arroyo-López
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Carretera de Utrera Km 1. Campus Universitario Pablo de Olavide, Building 46. 41013, Sevilla, Spain
| | - Mariana Combina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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3
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Wu Z, Liang X, Li M, Ma M, Zheng Q, Li D, An T, Wang G. Advances in the optimization of central carbon metabolism in metabolic engineering. Microb Cell Fact 2023; 22:76. [PMID: 37085866 PMCID: PMC10122336 DOI: 10.1186/s12934-023-02090-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023] Open
Abstract
Central carbon metabolism (CCM), including glycolysis, tricarboxylic acid cycle and the pentose phosphate pathway, is the most fundamental metabolic process in the activities of living organisms that maintains normal cellular growth. CCM has been widely used in microbial metabolic engineering in recent years due to its unique regulatory role in cellular metabolism. Using yeast and Escherichia coli as the representative organisms, we summarized the metabolic engineering strategies on the optimization of CCM in eukaryotic and prokaryotic microbial chassis, such as the introduction of heterologous CCM metabolic pathways and the optimization of key enzymes or regulatory factors, to lay the groundwork for the future use of CCM optimization in metabolic engineering. Furthermore, the bottlenecks in the application of CCM optimization in metabolic engineering and future application prospects are summarized.
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Affiliation(s)
- Zhenke Wu
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Xiqin Liang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Mingkai Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Mengyu Ma
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Qiusheng Zheng
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Defang Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
| | - Tianyue An
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
| | - Guoli Wang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
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Lane S, Turner TL, Jin YS. Glucose assimilation rate determines the partition of flux at pyruvate between lactic acid and ethanol in Saccharomyces cerevisiae. Biotechnol J 2023; 18:e2200535. [PMID: 36723451 DOI: 10.1002/biot.202200535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/16/2022] [Accepted: 01/19/2023] [Indexed: 02/02/2023]
Abstract
Engineered Saccharomyces cerevisiae expressing a lactic acid dehydrogenase can metabolize pyruvate into lactic acid. However, three pyruvate decarboxylase (PDC) isozymes drive most carbon flux toward ethanol rather than lactic acid. Deletion of endogenous PDCs will eliminate ethanol production, but the resulting strain suffers from C2 auxotrophy and struggles to complete a fermentation. Engineered yeast assimilating xylose or cellobiose produce lactic acid rather than ethanol as a major product without the deletion of any PDC genes. We report here that sugar flux, but not sensing, contributes to the partition of flux at the pyruvate branch point in S. cerevisiae expressing the Rhizopus oryzae lactic acid dehydrogenase (LdhA). While the membrane glucose sensors Snf3 and Rgt2 did not play any direct role in the option of predominant product, the sugar assimilation rate was strongly correlated to the partition of flux at pyruvate: fast sugar assimilation favors ethanol production while slow sugar assimilation favors lactic acid. Applying this knowledge, we created an engineered yeast capable of simultaneously converting glucose and xylose into lactic acid, increasing lactic acid production to approximately 17 g L-1 from the 12 g L-1 observed during sequential consumption of sugars. This work elucidates the carbon source-dependent effects on product selection in engineered yeast.
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Affiliation(s)
- Stephan Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Timothy L Turner
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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5
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Su C, Zhou X, Lu P, Dai X, Chen Z, Liang B, Tian Y, Chen M. Role of coke media strategy in an adsorption-biological coupling technology for wastewater treatment performance, microbial community, and metabolic pathways features. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:13469-13482. [PMID: 36131174 DOI: 10.1007/s11356-022-23090-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
With the increase of wastewater discharge, the requirement of wastewater treatment technology is gradually increased. How to treat wastewater economically, while making the treatment process short, easy to manage and low running cost, is the focus of attention. Adsorption-biological coupling technology could make adsorption and biodegradation complement each other, which has coupled accumulation effect. In this study, with coke as the adsorbent, the efficiency of the adsorption-biological coupling reactor on the treatment of total phosphorus (TP), chemical oxygen demand (COD), and ammonia nitrogen (NH3-N) in domestic wastewater under different influent modes was investigated. Meanwhile, microbial community and metabolic pathways analysis of the reactor were carried out. Results showed that when the influent modes of the coupling reactor was once a day and the daily sewage treatment capacity was 2 L, the treatment efficiency of TP, COD, and NH3-N was the best. The removal rate of TP and NH3-N was 87.96% and 96.14%, respectively. The dominant phylum was Proteobacteria (39.84-44.49%), and the dominant genus was Sphingomonas (4.27-7.16%), and Gemmatimonas (1.27-3.58%). According to the metagenomic analysis, carbon metabolism process was evenly distributed in U (upper), M (middle), and L (lower) layers of the coupling reactor. Phosphate metabolism was mainly in the U layer at first, then in the M and L layers gradually. Carbon metabolism and phosphate metabolism provided sufficient energy for microbial degradation of pollutants. Nitrogen removal in the reactor mainly happened in the S and Z layers by nitrification (M00528) and denitrification (M00529), respectively.
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Affiliation(s)
- Chengyuan Su
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, People's Republic of China.
- University Key Laboratory of Karst Ecology and Environmental Change of Guangxi Province (Guangxi Normal University), 15 Yucai Road, Guilin, 541004, People's Republic of China.
| | - Xibing Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Pingping Lu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Xiaoyun Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Zhuxin Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Bocai Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Yihao Tian
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Menglin Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, People's Republic of China
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6
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Gambacorta FV, Wagner ER, Jacobson TB, Tremaine M, Muehlbauer LK, McGee MA, Baerwald JJ, Wrobel RL, Wolters JF, Place M, Dietrich JJ, Xie D, Serate J, Gajbhiye S, Liu L, Vang-Smith M, Coon JJ, Zhang Y, Gasch AP, Amador-Noguez D, Hittinger CT, Sato TK, Pfleger BF. Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway. Synth Syst Biotechnol 2022; 7:738-749. [PMID: 35387233 PMCID: PMC8938195 DOI: 10.1016/j.synbio.2022.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/17/2021] [Accepted: 02/14/2022] [Indexed: 11/20/2022] Open
Abstract
Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol, a next-generation biofuel, in Saccharomyces cerevisiae. Here, we explore how two of these strategies, pathway re-localization and redox cofactor-balancing, affect the performance and physiology of isobutanol producing strains. We equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway and used either a redox-imbalanced (NADPH-dependent) or redox-balanced (NADH-dependent) ketol-acid reductoisomerase enzyme. We then conducted transcriptomic, proteomic and metabolomic analyses to elucidate molecular differences between the engineered strains. Pathway localization had a large effect on isobutanol production with the strain expressing the mitochondrial-localized enzymes producing 3.8-fold more isobutanol than strains expressing the cytosolic enzymes. Cofactor-balancing did not improve isobutanol titers and instead the strain with the redox-imbalanced pathway produced 1.5-fold more isobutanol than the balanced version, albeit at low overall pathway flux. Functional genomic analyses suggested that the poor performances of the cytosolic pathway strains were in part due to a shortage in cytosolic Fe-S clusters, which are required cofactors for the dihydroxyacid dehydratase enzyme. We then demonstrated that this cofactor limitation may be partially recovered by disrupting iron homeostasis with a fra2 mutation, thereby increasing cellular iron levels. The resulting isobutanol titer of the fra2 null strain harboring a cytosolic-localized isobutanol pathway outperformed the strain with the mitochondrial-localized pathway by 1.3-fold, demonstrating that both localizations can support flux to isobutanol.
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Affiliation(s)
- Francesca V. Gambacorta
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Ellen R. Wagner
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Tyler B. Jacobson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mary Tremaine
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Mick A. McGee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Justin J. Baerwald
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Russell L. Wrobel
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - John F. Wolters
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Mike Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J. Dietrich
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Dan Xie
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Jose Serate
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Shabda Gajbhiye
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Lisa Liu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Maikayeng Vang-Smith
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Audrey P. Gasch
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniel Amador-Noguez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian F. Pfleger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
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7
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Hoffman SM, Tang AY, Avalos JL. Optogenetics Illuminates Applications in Microbial Engineering. Annu Rev Chem Biomol Eng 2022; 13:373-403. [PMID: 35320696 DOI: 10.1146/annurev-chembioeng-092120-092340] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Optogenetics has been used in a variety of microbial engineering applications, such as chemical and protein production, studies of cell physiology, and engineered microbe-host interactions. These diverse applications benefit from the precise spatiotemporal control that light affords, as well as its tunability, reversibility, and orthogonality. This combination of unique capabilities has enabled a surge of studies in recent years investigating complex biological systems with completely new approaches. We briefly describe the optogenetic tools that have been developed for microbial engineering, emphasizing the scientific advancements that they have enabled. In particular, we focus on the unique benefits and applications of implementing optogenetic control, from bacterial therapeutics to cybergenetics. Finally, we discuss future research directions, with special attention given to the development of orthogonal multichromatic controls. With an abundance of advantages offered by optogenetics, the future is bright in microbial engineering. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Shannon M Hoffman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA; , ,
| | - Allison Y Tang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA; , ,
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA; , , .,The Andlinger Center for Energy and the Environment, Department of Molecular Biology, and High Meadows Environmental Institute, Princeton University, Princeton, New Jersey, USA
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8
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Ma Y, Liu N, Greisen P, Li J, Qiao K, Huang S, Stephanopoulos G. Removal of lycopene substrate inhibition enables high carotenoid productivity in Yarrowia lipolytica. Nat Commun 2022; 13:572. [PMID: 35102143 PMCID: PMC8803881 DOI: 10.1038/s41467-022-28277-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 01/11/2022] [Indexed: 01/28/2023] Open
Abstract
Substrate inhibition of enzymes can be a major obstacle to the production of valuable chemicals in engineered microorganisms. Here, we show substrate inhibition of lycopene cyclase as the main limitation in carotenoid biosynthesis in Yarrowia lipolytica. To overcome this bottleneck, we exploit two independent approaches. Structure-guided protein engineering yields a variant, Y27R, characterized by complete loss of substrate inhibition without reduction of enzymatic activity. Alternatively, establishing a geranylgeranyl pyrophosphate synthase-mediated flux flow restrictor also prevents the onset of substrate inhibition by diverting metabolic flux away from the inhibitory metabolite while maintaining sufficient flux towards product formation. Both approaches result in high levels of near-exclusive β-carotene production. Ultimately, we construct strains capable of producing 39.5 g/L β-carotene at a productivity of 0.165 g/L/h in bioreactor fermentations (a 1441-fold improvement over the initial strain). Our findings provide effective approaches for removing substrate inhibition in engineering pathways for efficient synthesis of natural products. Substrate inhibition has not been widely studied in the context of synthetic biology and metabolic engineering. Here, the authors report removal of lycopene substrate inhibition by two different strategies and enable high carotenoid productivity in Yarrowia lipolytica.
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9
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Liu Y, Huang Y, Lu R, Xin F, Liu G. Synthetic biology applications of the yeast mating signal pathway. Trends Biotechnol 2021; 40:620-631. [PMID: 34666896 DOI: 10.1016/j.tibtech.2021.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022]
Abstract
Cell fusion is a fundamental biological process that is involved in the development of most eukaryotic organisms. During the fusion process in Saccharomyces cerevisiae, cells respond to pheromones to trigger the MAPK (mitogen-activated protein kinase) cascade to initiate mating, followed by polarization, cell-wall remodeling, membrane fusion, and karyogamy. We highlight the applications of the yeast mating signal pathway in promoter engineering for tuning the expression of output genes, as well as in metabolic engineering for decoupling growth and metabolism, biosensors for sensitive detection and signal amplification, genetic circuits for programmable biological functionalities, and artificial consortia for cell-cell communication. Strategies such as exploiting rational engineering of modular circuits and optimizing the reproductive pathway to precisely maneuver physiological events have implications for scientific research and industrial development.
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Affiliation(s)
- Ying Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Yuxin Huang
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Ran Lu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Fengxue Xin
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Guannan Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China; Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Jiangsu Province, China.
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10
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Qiu X, Gu Y, Du G, Zhang J, Xu P, Li J. Conferring thermotolerant phenotype to wild-type Yarrowia lipolytica improves cell growth and erythritol production. Biotechnol Bioeng 2021; 118:3117-3127. [PMID: 34009652 DOI: 10.1002/bit.27835] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 04/22/2021] [Accepted: 05/09/2021] [Indexed: 12/19/2022]
Abstract
In microbial engineering, heat stress is an important environmental factor modulating cell growth, metabolic flux distribution and the synthesis of target products. Yarrowia lipolytica, as a GARS (generally recognized as safe) nonconventional yeast, has been widely used in the food industry, especially as the host of erythritol production. Biomanufacturing economics is limited by the high operational cost of cooling energy in large-scale fermentation. It is of great significance to select thermotolerant Y. lipolytica to reduce the cooling cost and elucidate the heat-resistant mechanism at molecular level. For this purpose, we performed adaptive evolution and obtained a thermotolerant strain named Y. lipolytica BBE-18. Transcriptome analysis allows us to identify four genes in thiamine metabolism pathway that are responsible for the complicated thermotolerant phenotype. The heat-resistant phenotype was validated with the model strain Y. lipolytica Po1f by overexpression of single and combined genes. Then, conferring the thermotolerant phenotype to the wild-type Y. lipolytica BBE-17 enable the strain to produce three-times more erythritol of the control strain with 3°C higher than optimal cultivation temperature. To our knowledge, this is the first report on engineering heat-resistant phenotype to improve the erythritol production in Y. lipolytica. However, due to the increase of culture temperature, a large amount of adenosine triphosphate is consumed to ensure the life activities of Y. lipolytica which limits the potential of cell synthetic products to a certain extent. Even so, this study provides a reference for Y. lipolytica to produce other products under high temperature.
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Affiliation(s)
- Xueliang Qiu
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yang Gu
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, USA.,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Juan Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Peng Xu
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Jianghua Li
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
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11
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Zhao EM, Lalwani MA, Chen JM, Orillac P, Toettcher JE, Avalos JL. Optogenetic Amplification Circuits for Light-Induced Metabolic Control. ACS Synth Biol 2021; 10:1143-1154. [PMID: 33835777 DOI: 10.1021/acssynbio.0c00642] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Dynamic control of microbial metabolism is an effective strategy to improve chemical production in fermentations. While dynamic control is most often implemented using chemical inducers, optogenetics offers an attractive alternative due to the high tunability and reversibility afforded by light. However, a major concern of applying optogenetics in metabolic engineering is the risk of insufficient light penetration at high cell densities, especially in large bioreactors. Here, we present a new series of optogenetic circuits we call OptoAMP, which amplify the transcriptional response to blue light by as much as 23-fold compared to the basal circuit (OptoEXP). These circuits show as much as a 41-fold induction between dark and light conditions, efficient activation at light duty cycles as low as ∼1%, and strong homogeneous light-induction in bioreactors of at least 5 L, with limited illumination at cell densities above 40 OD600. We demonstrate the ability of OptoAMP circuits to control engineered metabolic pathways in novel three-phase fermentations using different light schedules to control enzyme expression and improve production of lactic acid, isobutanol, and naringenin. These circuits expand the applicability of optogenetics to metabolic engineering.
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Affiliation(s)
- Evan M. Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Makoto A. Lalwani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Jhong-Min Chen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Paulina Orillac
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Jared E. Toettcher
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - José L. Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- The Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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12
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Lovelett RJ, Zhao EM, Lalwani MA, Toettcher JE, Kevrekidis IG, L Avalos J. Dynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering Applications. ACS Synth Biol 2021; 10:219-227. [PMID: 33492138 PMCID: PMC10410538 DOI: 10.1021/acssynbio.0c00372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic control of engineered microbes using light via optogenetics has been demonstrated as an effective strategy for improving the yield of biofuels, chemicals, and other products. An advantage of using light to manipulate microbial metabolism is the relative simplicity of interfacing biological and computer systems, thereby enabling in silico control of the microbe. Using this strategy for control and optimization of product yield requires an understanding of how the microbe responds in real-time to the light inputs. Toward this end, we present mechanistic models of a set of yeast optogenetic circuits. We show how these models can predict short- and long-time response to varying light inputs and how they are amenable to use with model predictive control (the industry standard among advanced control algorithms). These models reveal dynamics characterized by time-scale separation of different circuit components that affect the steady and transient levels of the protein under control of the circuit. Ultimately, this work will help enable real-time control and optimization tools for improving yield and consistency in the production of biofuels and chemicals using microbial fermentations.
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Affiliation(s)
- Robert J Lovelett
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Evan M Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Makoto A Lalwani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton, New Jersey 08544, United States
| | - Ioannis G Kevrekidis
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- The Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States
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13
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Du Q, Liu Y, Song Y, Qin Y. Creation of a Low-Alcohol-Production Yeast by a Mutated SPT15 Transcription Regulator Triggers Transcriptional and Metabolic Changes During Wine Fermentation. Front Microbiol 2021; 11:597828. [PMID: 33381093 PMCID: PMC7768003 DOI: 10.3389/fmicb.2020.597828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/23/2020] [Indexed: 11/23/2022] Open
Abstract
There is significant interest in the wine industry to develop methods to reduce the ethanol content of wine. Here the global transcription machinery engineering (gTME) technology was used to engineer a yeast strain with decreased ethanol yield, based on the mutation of the SPT15 gene. We created a strain of Saccharomyces cerevisiae (YS59-409), which possessed ethanol yield reduced by 34.9%; this was accompanied by the increase in CO2, biomass, and glycerol formation. Five mutation sites were identified in the mutated SPT15 gene of YS59-409. RNA-Seq and metabolome analysis of YS59-409 were conducted compared with control strain, suggesting that ribosome biogenesis, nucleotide metabolism, glycolysis flux, Crabtree effect, NAD+/NADH homeostasis and energy metabolism might be regulated by the mutagenesis of SPT15 gene. Furthermore, two genes related to energy metabolism, RGI1 and RGI2, were found to be associated with the weakened ethanol production capacity, although the precise mechanisms involved need to be further elucidated. This study highlighted the importance of applying gTME technology when attempting to reduce ethanol production by yeast, possibly reprogramming yeast’s metabolism at the global level.
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Affiliation(s)
- Qing Du
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China.,National Forestry and Grassland Administration Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Yanlin Liu
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China.,National Forestry and Grassland Administration Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Yuyang Song
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China.,National Forestry and Grassland Administration Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Yi Qin
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China.,National Forestry and Grassland Administration Engineering Research Center for Viti-Viniculture, Yangling, China
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14
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Zhao EM, Lalwani MA, Lovelett RJ, García-Echauri SA, Hoffman SM, Gonzalez CL, Toettcher JE, Kevrekidis IG, Avalos JL. Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering. ACS Synth Biol 2020; 9:3254-3266. [PMID: 33232598 PMCID: PMC10399620 DOI: 10.1021/acssynbio.0c00305] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The use of optogenetics in metabolic engineering for light-controlled microbial chemical production raises the prospect of utilizing control and optimization techniques routinely deployed in traditional chemical manufacturing. However, such mechanisms require well-characterized, customizable tools that respond fast enough to be used as real-time inputs during fermentations. Here, we present OptoINVRT7, a new rapid optogenetic inverter circuit to control gene expression in Saccharomyces cerevisiae. The circuit induces gene expression in only 0.6 h after switching cells from light to darkness, which is at least 6 times faster than previous OptoINVRT optogenetic circuits used for chemical production. In addition, we introduce an engineered inducible GAL1 promoter (PGAL1-S), which is stronger than any constitutive or inducible promoter commonly used in yeast. Combining OptoINVRT7 with PGAL1-S achieves strong and light-tunable levels of gene expression with as much as 132.9 ± 22.6-fold induction in darkness. The high performance of this new optogenetic circuit in controlling metabolic enzymes boosts production of lactic acid and isobutanol by more than 50% and 15%, respectively. The strength and controllability of OptoINVRT7 and PGAL1-S open the door to applying process control tools to engineered metabolisms to improve robustness and yields in microbial fermentations for chemical production.
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Affiliation(s)
- Evan M. Zhao
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Makoto A. Lalwani
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Robert J. Lovelett
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, 221 Maryland
Hall, Johns Hopkins University, 2400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Sergio A. García-Echauri
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Shannon M. Hoffman
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Christopher L. Gonzalez
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Jared E. Toettcher
- Department of Molecular Biology, 140 Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Ioannis G. Kevrekidis
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, 221 Maryland
Hall, Johns Hopkins University, 2400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - José L. Avalos
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, 140 Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
- The Andlinger Center for Energy and the Environment, Princeton University, 86 Olden Street, Princeton, New Jersey 08544, United States
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15
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Tian J, Yang G, Gu Y, Sun X, Lu Y, Jiang W. Developing an endogenous quorum-sensing based CRISPRi circuit for autonomous and tunable dynamic regulation of multiple targets in Streptomyces. Nucleic Acids Res 2020; 48:8188-8202. [PMID: 32672817 PMCID: PMC7430639 DOI: 10.1093/nar/gkaa602] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/01/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
Quorum-sensing (QS) mediated dynamic regulation has emerged as an effective strategy for optimizing product titers in microbes. However, these QS-based circuits are often created on heterologous systems and require careful tuning via a tedious testing/optimization process. This hampers their application in industrial microbes. Here, we design a novel QS circuit by directly integrating an endogenous QS system with CRISPRi (named EQCi) in the industrial rapamycin-producing strain Streptomyces rapamycinicus. EQCi combines the advantages of both the QS system and CRISPRi to enable tunable, autonomous, and dynamic regulation of multiple targets simultaneously. Using EQCi, we separately downregulate three key nodes in essential pathways to divert metabolic flux towards rapamycin biosynthesis and significantly increase its titers. Further application of EQCi to simultaneously regulate these three key nodes with fine-tuned repression strength boosts the rapamycin titer by ∼660%, achieving the highest reported titer (1836 ± 191 mg/l). Notably, compared to static engineering strategies, which result in growth arrest and suboptimal rapamycin titers, EQCi-based regulation substantially promotes rapamycin titers without affecting cell growth, indicating that it can achieve a trade-off between essential pathways and product synthesis. Collectively, this study provides a convenient and effective strategy for strain improvement and shows potential for application in other industrial microorganisms.
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Affiliation(s)
- Jinzhong Tian
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Gaohua Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yang Gu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Xinqiang Sun
- XinChang Pharmaceutical Factory, Zhejiang medicine LTD, Xinchang 312500, Zhejiang Province, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China
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16
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Gambacorta FV, Dietrich JJ, Yan Q, Pfleger BF. Rewiring yeast metabolism to synthesize products beyond ethanol. Curr Opin Chem Biol 2020; 59:182-192. [PMID: 33032255 DOI: 10.1016/j.cbpa.2020.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 12/20/2022]
Abstract
Saccharomyces cerevisiae, Baker's yeast, is the industrial workhorse for producing ethanol and the subject of substantial metabolic engineering research in both industry and academia. S. cerevisiae has been used to demonstrate production of a wide range of chemical products from glucose. However, in many cases, the demonstrations report titers and yields that fall below thresholds for industrial feasibility. Ethanol synthesis is a central part of S. cerevisiae metabolism, and redirecting flux to other products remains a barrier to industrialize strains for producing other molecules. Removing ethanol producing pathways leads to poor fitness, such as impaired growth on glucose. Here, we review metabolic engineering efforts aimed at restoring growth in non-ethanol producing strains with emphasis on relieving glucose repression associated with the Crabtree effect and rewiring metabolism to provide access to critical cellular building blocks. Substantial progress has been made in the past decade, but many opportunities for improvement remain.
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Affiliation(s)
- Francesca V Gambacorta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA; DOE Great Lakes Bioenergy Research Center, Univ. of Wisconsin-Madison, USA
| | - Joshua J Dietrich
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA; DOE Great Lakes Bioenergy Research Center, Univ. of Wisconsin-Madison, USA
| | - Qiang Yan
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, Univ. of Wisconsin-Madison, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA; DOE Great Lakes Bioenergy Research Center, Univ. of Wisconsin-Madison, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, Univ. of Wisconsin-Madison, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
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17
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Dinh CV, Prather KLJ. Layered and multi-input autonomous dynamic control strategies for metabolic engineering. Curr Opin Biotechnol 2020; 65:156-162. [DOI: 10.1016/j.copbio.2020.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 10/24/2022]
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18
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Hill BD, Prabhu P, Rizvi SM, Wen F. Yeast Intracellular Staining (yICS): Enabling High-Throughput, Quantitative Detection of Intracellular Proteins via Flow Cytometry for Pathway Engineering. ACS Synth Biol 2020; 9:2119-2131. [PMID: 32603587 DOI: 10.1021/acssynbio.0c00199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complexities of pathway engineering necessitate screening libraries to discover phenotypes of interest. However, this approach is challenging when desirable phenotypes cannot be directly linked to growth advantages or fluorescence. In these cases, the ability to rapidly quantify intracellular proteins in the pathway of interest is critical to expedite the clonal selection process. While Saccharomyces cerevisiae remains a common host for pathway engineering, current approaches for intracellular protein detection in yeast either have low throughput, can interfere with protein function, or lack the ability to detect multiple proteins simultaneously. To fill this need, we developed yeast intracellular staining (yICS) that enables fluorescent antibodies to access intracellular compartments of yeast cells while maintaining their cellular integrity for analysis by flow cytometry. Using the housekeeping proteins β actin and glyceraldehyde 3-phophate dehydrogenase (GAPDH) as targets for yICS, we demonstrated for the first time successful antibody-based flow cytometric detection of yeast intracellular proteins with no modification. Further, yICS characterization of a recombinant d-xylose assimilation pathway showed 3-plexed, quantitative detection of the xylose reductase (XR), xylitol dehydrogenase (XDH), and xylulokinase (XK) enzymes each fused with a small (6-10 amino acids) tag, revealing distinct enzyme expression profiles between plasmid-based and genome-integrated expression approaches. As a result of its high-throughput and quantitative capability, yICS enabled rapid screening of a library created from CRISPR-mediated XDH integration into the yeast δ site, identifying rare (1%) clones that led to an 8.4-fold increase in XDH activity. These results demonstrate the utility of yICS for greatly accelerating pathway engineering efforts, as well as any application where the high-throughput and quantitative detection of intracellular proteins is desired.
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Affiliation(s)
- Brett D. Hill
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ponnandy Prabhu
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Syed M. Rizvi
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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19
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Liu Y, Ghosh IN, Martien J, Zhang Y, Amador-Noguez D, Landick R. Regulated redirection of central carbon flux enhances anaerobic production of bioproducts in Zymomonas mobilis. Metab Eng 2020; 61:261-274. [PMID: 32590077 DOI: 10.1016/j.ymben.2020.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/06/2020] [Accepted: 06/07/2020] [Indexed: 01/25/2023]
Abstract
The microbial production of chemicals and fuels from plant biomass offers a sustainable alternative to fossilized carbon but requires high rates and yields of bioproduct synthesis. Z. mobilis is a promising chassis microbe due to its high glycolytic rate in anaerobic conditions that are favorable for large-scale production. However, diverting flux from its robust ethanol fermentation pathway to nonnative pathways remains a major engineering hurdle. To enable controlled, high-yield synthesis of bioproducts, we implemented a central-carbon metabolism control-valve strategy using regulated, ectopic expression of pyruvate decarboxylase (Pdc) and deletion of chromosomal pdc. Metabolomic and genetic analyses revealed that glycolytic intermediates and NADH accumulate when Pdc is depleted and that Pdc is essential for anaerobic growth of Z. mobilis. Aerobically, all flux can be redirected to a 2,3-butanediol pathway for which respiration maintains redox balance. Anaerobically, flux can be redirected to redox-balanced lactate or isobutanol pathways with ≥65% overall yield from glucose. This strategy provides a promising path for future metabolic engineering of Z. mobilis.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Indro Neil Ghosh
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Julia Martien
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States.
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20
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Critical Roles of the Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in Yeast. Cell Syst 2019; 9:534-547.e5. [DOI: 10.1016/j.cels.2019.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 08/23/2019] [Accepted: 10/18/2019] [Indexed: 02/01/2023]
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21
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Lane S, Zhang Y, Yun EJ, Ziolkowski L, Zhang G, Jin YS, Avalos JL. Xylose assimilation enhances the production of isobutanol in engineered Saccharomyces cerevisiae. Biotechnol Bioeng 2019; 117:372-381. [PMID: 31631318 DOI: 10.1002/bit.27202] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/17/2019] [Accepted: 10/14/2019] [Indexed: 12/30/2022]
Abstract
Bioconversion of xylose-the second most abundant sugar in nature-into high-value fuels and chemicals by engineered Saccharomyces cerevisiae has been a long-term goal of the metabolic engineering community. Although most efforts have heavily focused on the production of ethanol by engineered S. cerevisiae, yields and productivities of ethanol produced from xylose have remained inferior as compared with ethanol produced from glucose. However, this entrenched focus on ethanol has concealed the fact that many aspects of xylose metabolism favor the production of nonethanol products. Through reduced overall metabolic flux, a more respiratory nature of consumption, and evading glucose signaling pathways, the bioconversion of xylose can be more amenable to redirecting flux away from ethanol towards the desired target product. In this report, we show that coupling xylose consumption via the oxidoreductive pathway with a mitochondrially-targeted isobutanol biosynthesis pathway leads to enhanced product yields and titers as compared to cultures utilizing glucose or galactose as a carbon source. Through the optimization of culture conditions, we achieve 2.6 g/L of isobutanol in the fed-batch flask and bioreactor fermentations. These results suggest that there may be synergistic benefits of coupling xylose assimilation with the production of nonethanol value-added products.
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Affiliation(s)
- Stephan Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Yanfei Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Eun Ju Yun
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Leah Ziolkowski
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Guochang Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey.,Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey.,Department of Molecular Biology, Princeton University, Princeton, New Jersey
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22
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Lee SW, Lee BY, Oh MK. Combination of Three Methods to Reduce Glucose Metabolic Rate For Improving N-Acetylglucosamine Production in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:13191-13198. [PMID: 30463407 DOI: 10.1021/acs.jafc.8b04291] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Previously, the production of N-acetylglucosamine (GlcNAc) in Saccharomyces cerevisiae was improved by deletion of the genes encoding phosphofructokinase 2 (PFK-2) isoforms, which reduced the glycolytic flux by eliminating the pathway to produce fructose-2,6-bisphosphate, an allosteric activator of phosphofructokinase 1 (PFK-1). We further examined the effects of an additional reduction in glucose metabolic rate on N-acetylglucosamine production. Glucose uptake rate was lowered by expressing a gene encoding truncated glucose-sensing regulator ( MTH1-Δ T). In addition, catalytically dead Cas9 (dCas9) was introduced in order to down-regulate the expression levels of PFK-1 and pyruvate kinase-1 (Pyk1). Finally, the three strategies were introduced into S. cerevisiae strains in a combinatorial way; the strain containing all three modules resulted in the highest N-acetylglucosamine production yield. The results showed that the three modules cooperatively reduced the glucose metabolism and improved N-acetylglucosamine production up to 3.0 g/L in shake flask cultivation.
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Affiliation(s)
- Sang-Woo Lee
- Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , 2800 Kongens Lyngby , Denmark
- Department of Chemical & Biological Engineering , Korea University , Anam-Ro 145, Seongbuk-Gu, Seoul 02841 , Republic of Korea
| | - Bo-Young Lee
- Department of Chemical & Biological Engineering , Korea University , Anam-Ro 145, Seongbuk-Gu, Seoul 02841 , Republic of Korea
| | - Min-Kyu Oh
- Department of Chemical & Biological Engineering , Korea University , Anam-Ro 145, Seongbuk-Gu, Seoul 02841 , Republic of Korea
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23
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Engineering Saccharomyces cerevisiae for co-utilization of D-galacturonic acid and D-glucose from citrus peel waste. Nat Commun 2018; 9:5059. [PMID: 30498222 PMCID: PMC6265301 DOI: 10.1038/s41467-018-07589-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/19/2018] [Indexed: 11/08/2022] Open
Abstract
Pectin-rich biomasses, such as citrus peel and sugar beet pulp, hold promise as inexpensive feedstocks for microbial fermentations as enzymatic hydrolysis of their component polysaccharides can be accomplished inexpensively to yield high concentrations of fermentable sugars and D-galacturonic acid (D-galUA). In this study, we tackle a number of challenges associated with engineering a microbial strain to convert pectin-rich hydrolysates into commodity and specialty chemicals. First, we engineer D-galUA utilization into yeast, Saccharomyces cerevisiae. Second, we identify that the mechanism of D-galUA uptake into yeast is mediated by hexose transporters and that consumption of D-galUA is inhibited by D-glucose. Third, we enable co-utilization of D-galUA and D-glucose by identifying and expressing a heterologous transporter, GatA, from Aspergillus niger. Last, we demonstrate the use of this transporter for production of the platform chemical, meso-galactaric acid, directly from industrial Navel orange peel waste.
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24
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Lalwani MA, Zhao EM, Avalos JL. Current and future modalities of dynamic control in metabolic engineering. Curr Opin Biotechnol 2018; 52:56-65. [DOI: 10.1016/j.copbio.2018.02.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 02/11/2018] [Indexed: 12/30/2022]
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25
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Li T, Chen X, Cai Y, Dai J. Artificial Protein Scaffold System (AProSS): An efficient method to optimize exogenous metabolic pathways in Saccharomyces cerevisiae. Metab Eng 2018; 49:13-20. [PMID: 30010058 DOI: 10.1016/j.ymben.2018.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 01/15/2023]
Abstract
Scaffold proteins influence cellular signaling by orchestrating multiple enzymes, receptors or ion channels, and could be tailored to enhance the efficiency of biochemical reactions by positioning related enzymes physically together. However, the number of applicable domains remains small, and the construction of scaffold proteins with optimal domain ratio could be tedious and time-consuming. In this study, we outlined a modular design to quickly assemble scaffold proteins using protein interaction domains, which have been constructed into a standardized vector. We generated multiple protein interaction domains and ligands for making artificial scaffold proteins. At the same time, we developed a robust Golden-Gate-based molecular toolkit for the construction of artificial scaffold proteins, allowing a variance of domain types, number, and positions. The synthesized domain-ligand interaction was verified by yeast two-hybrid and split-GFP assays. Using synthetic scaffolds, we demonstrated an increase in the yield of two target products by 29% and 63% respectively. Moreover, we demonstrated that the synthetic scaffold could be applied to rewire the metabolic flux. Our system could be a useful tool for metabolic engineering and beyond.
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Affiliation(s)
- Tianyi Li
- Key Laboratory of Industrial Biocatalysis (Ministry of Education) and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiuqi Chen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education) and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Department of Biology, Johns Hopkins University, 3400N. Charles Street, Baltimore, MD, USA
| | - Yizhi Cai
- Shenzhen Key Laboratory of Synthetic Genomics and Center for Synthetic Genomics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK.
| | - Junbiao Dai
- Key Laboratory of Industrial Biocatalysis (Ministry of Education) and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Shenzhen Key Laboratory of Synthetic Genomics and Center for Synthetic Genomics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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26
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Lane S, Dong J, Jin YS. Value-added biotransformation of cellulosic sugars by engineered Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2018; 260:380-394. [PMID: 29655899 DOI: 10.1016/j.biortech.2018.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 05/26/2023]
Abstract
The substantial research efforts into lignocellulosic biofuels have generated an abundance of valuable knowledge and technologies for metabolic engineering. In particular, these investments have led to a vast growth in proficiency of engineering the yeast Saccharomyces cerevisiae for consuming lignocellulosic sugars, enabling the simultaneous assimilation of multiple carbon sources, and producing a large variety of value-added products by introduction of heterologous metabolic pathways. While microbial conversion of cellulosic sugars into large-volume low-value biofuels is not currently economically feasible, there may still be opportunities to produce other value-added chemicals as regulation of cellulosic sugar metabolism is quite different from glucose metabolism. This review summarizes these recent advances with an emphasis on employing engineered yeast for the bioconversion of lignocellulosic sugars into a variety of non-ethanol value-added products.
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Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jia Dong
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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27
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Zhao EM, Zhang Y, Mehl J, Park H, Lalwani MA, Toettcher JE, Avalos JL. Optogenetic regulation of engineered cellular metabolism for microbial chemical production. Nature 2018; 555:683-687. [PMID: 29562237 PMCID: PMC5876151 DOI: 10.1038/nature26141] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 02/13/2018] [Indexed: 12/29/2022]
Abstract
The optimization of engineered metabolic pathways requires careful control over the levels and timing of metabolic enzyme expression1-4. Optogenetic tools are ideal for achieving such precise control, as light can be applied and removed instantly without complex media changes. Here we show that light-controlled transcription can be used to enhance the biosynthesis of valuable products in engineered Saccharomyces cerevisiae. We introduce new optogenetic circuits to shift cells from a light-induced growth phase to a darkness-induced production phase, which allows us to control fermentation purely with light. Furthermore, optogenetic control of engineered pathways enables a new mode of bioreactor operation using periodic light pulses to tune enzyme expression during the production phase of fermentation to increase yields. Using these advances, we control the mitochondrial isobutanol pathway to produce up to 8.49 ± 0.31 g/L of isobutanol and 2.38 ± 0.06 g/L of 2-methyl-1-butanol micro-aerobically from glucose. These results make a compelling case for the application of optogenetics to metabolic engineering for valuable products.
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Affiliation(s)
- Evan M Zhao
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Yanfei Zhang
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Justin Mehl
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Helen Park
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Makoto A Lalwani
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, 140 Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey 08544, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA.,The Andlinger Center for Energy and the Environment, Princeton University, 86 Olden Street, Princeton, New Jersey 08544, USA
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28
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Layered dynamic regulation for improving metabolic pathway productivity in Escherichia coli. Proc Natl Acad Sci U S A 2018; 115:2964-2969. [PMID: 29507236 DOI: 10.1073/pnas.1716920115] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microbial production of value-added chemicals from biomass is a sustainable alternative to chemical synthesis. To improve product titer, yield, and selectivity, the pathways engineered into microbes must be optimized. One strategy for optimization is dynamic pathway regulation, which modulates expression of pathway-relevant enzymes over the course of fermentation. Metabolic engineers have used dynamic regulation to redirect endogenous flux toward product formation, balance the production and consumption rates of key intermediates, and suppress production of toxic intermediates until later in the fermentation. Most cases, however, have utilized a single strategy for dynamically regulating pathway fluxes. Here we layer two orthogonal, autonomous, and tunable dynamic regulation strategies to independently modulate expression of two different enzymes to improve production of D-glucaric acid from a heterologous pathway. The first strategy uses a previously described pathway-independent quorum sensing system to dynamically knock down glycolytic flux and redirect carbon into production of glucaric acid, thereby switching cells from "growth" to "production" mode. The second strategy, developed in this work, uses a biosensor for myo-inositol (MI), an intermediate in the glucaric acid production pathway, to induce expression of a downstream enzyme upon sufficient buildup of MI. The latter, pathway-dependent strategy leads to a 2.5-fold increase in titer when used in isolation and a fourfold increase when added to a strain employing the former, pathway-independent regulatory system. The dual-regulation strain produces nearly 2 g/L glucaric acid, representing the highest glucaric acid titer reported to date in Escherichia coli K-12 strains.
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29
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Brice C, Cubillos FA, Dequin S, Camarasa C, Martínez C. Adaptability of the Saccharomyces cerevisiae yeasts to wine fermentation conditions relies on their strong ability to consume nitrogen. PLoS One 2018; 13:e0192383. [PMID: 29432462 PMCID: PMC5809068 DOI: 10.1371/journal.pone.0192383] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/20/2018] [Indexed: 11/25/2022] Open
Abstract
Saccharomyces cerevisiae strains are genetically diverse, largely as a result of human efforts to develop strains specifically adapted to various fermentation processes. These adaptive pressures from various ecological niches have generated behavioral differences among these strains, particularly in terms of their nitrogen consumption capacities. In this work, we characterize this phenotype by the specific quantity of nitrogen consumed under oenological fermentation conditions using a new approach. Indeed, unlike previous studies, our experiments were conducted in an environment containing excess nitrogen, eliminating the nitrogen limitation/starvation factor that is generally observed in fermentation processes. Using these conditions, we evaluated differences in the nitrogen consumption capacities for a set of five strains from diverse origins. The strains presented extremely different phenotypes and variations in their capacities to take up nitrogen from a wine fermentation environment. These variations reflect the differences in the nitrogen uptake capacities between wine and non-wine strains. Finally, the strains differed in their ability to adapt to the nitrogen composition of the environment, leading to variations in the cellular stress states, fermentation performances and the activity of the nitrogen sensing signaling pathway.
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Affiliation(s)
- Claire Brice
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Francisco A. Cubillos
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
- Millennium Institute for Integrative Systems and Synthetic Biology (MII-SSB), Santiago, Chile
| | - Sylvie Dequin
- UMR SPO: INRA, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Carole Camarasa
- UMR SPO: INRA, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
- * E-mail:
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30
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Large-scale bioprocess competitiveness: the potential of dynamic metabolic control in two-stage fermentations. Curr Opin Chem Eng 2016. [DOI: 10.1016/j.coche.2016.09.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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31
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Porting the synthetic D‐glucaric acid pathway from
Escherichia coli
to
Saccharomyces cerevisiae. Biotechnol J 2016; 11:1201-8. [DOI: 10.1002/biot.201500563] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 06/05/2016] [Accepted: 06/07/2016] [Indexed: 01/14/2023]
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32
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Lee SW, Oh MK. Improved production ofN-acetylglucosamine inSaccharomyces cerevisiaeby reducing glycolytic flux. Biotechnol Bioeng 2016; 113:2524-8. [DOI: 10.1002/bit.26014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/13/2016] [Accepted: 05/15/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Sang-Woo Lee
- Department of Chemical and Biological Engineering; Korea University; Seongbuk-gu Seoul 136-713 Republic of Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering; Korea University; Seongbuk-gu Seoul 136-713 Republic of Korea
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33
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Liu Z, Liu P, Xiao D, Zhang X. Improving isobutanol production in metabolically engineered Escherichia coli by co-producing ethanol and modulation of pentose phosphate pathway. J Ind Microbiol Biotechnol 2016; 43:851-60. [PMID: 26946319 DOI: 10.1007/s10295-016-1751-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/16/2016] [Indexed: 11/29/2022]
Abstract
Redox imbalance has been regarded as the key limitation for anaerobic isobutanol production in metabolically engineered Escherichia coli strains. In this work, the ethanol synthetic pathway was recruited to solve the NADH redundant problem while the pentose phosphate pathway was modulated to solve the NADPH deficient problem for anaerobic isobutanol production. Recruiting the ethanol synthetic pathway in strain AS108 decreased isobutanol yield from 0.66 to 0.29 mol/mol glucose. It was found that there was a negative correlation between aldehyde/alcohol dehydrogenase (AdhE) activity and isobutanol production. Decreasing AdhE activity increased isobutanol yield from 0.29 to 0.6 mol/mol. On the other hand, modulation of the glucose 6-phosphate dehydrogenase gene of the pentose phosphate pathway increased isobutanol yield from 0.29 to 0.41 mol/mol. Combination of these two strategies had a synergistic effect on improving isobutanol production. Isobutanol titer and yield of the best strain ZL021 were 53 mM and 0.74 mol/mol, which were 51 % and 12 % higher than the starting strain AS108, respectively. The total alcohol yield of strain ZL021 was 0.81 mol/mol, which was 23 % higher than strain AS108.
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Affiliation(s)
- Zichun Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Pingping Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dongguang Xiao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
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34
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Ma CW, Zhou LB, Zeng AP. Engineering Biomolecular Switches for Dynamic Metabolic Control. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:45-76. [DOI: 10.1007/10_2016_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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35
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Kuroda K, Ueda M. Cellular and molecular engineering of yeastSaccharomyces cerevisiaefor advanced biobutanol production. FEMS Microbiol Lett 2015; 363:fnv247. [DOI: 10.1093/femsle/fnv247] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2015] [Indexed: 11/12/2022] Open
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