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Sun ML, Gao X, Lin L, Yang J, Ledesma-Amaro R, Ji XJ. Building Yarrowia lipolytica Cell Factories for Advanced Biomanufacturing: Challenges and Solutions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:94-107. [PMID: 38126236 DOI: 10.1021/acs.jafc.3c07889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Microbial cell factories have shown great potential for industrial production with the benefit of being environmentally friendly and sustainable. Yarrowia lipolytica is a promising and superior non-model host for biomanufacturing due to its cumulated advantages compared to model microorganisms, such as high fluxes of metabolic precursors (acetyl-CoA and malonyl-CoA) and its naturally hydrophobic microenvironment. However, although diverse compounds have been synthesized in Y. lipolytica cell factories, most of the relevant studies have not reached the level of industrialization and commercialization due to a number of remaining challenges, including unbalanced metabolic flux, conflict between cell growth and product synthesis, and cytotoxic effects. Here, various metabolic engineering strategies for solving the challenges are summarized, which is developing fast and extremely conducive to rational design and reconstruction of robust Y. lipolytica cell factories for advanced biomanufacturing. Finally, future engineering efforts for enhancing the production efficiency of this platform strain are highlighted.
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Affiliation(s)
- Mei-Li Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Xiaoxia Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Jing Yang
- 2011 College, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
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2
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Li Z, Deng Y, Yang GY. Growth-coupled high throughput selection for directed enzyme evolution. Biotechnol Adv 2023; 68:108238. [PMID: 37619825 DOI: 10.1016/j.biotechadv.2023.108238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/03/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Directed enzyme evolution has revolutionized the rapid development of enzymes with desired properties. However, the lack of a high-throughput method to identify the most suitable variants from a large pool of genetic diversity poses a major bottleneck. To overcome this challenge, growth-coupled in vivo high-throughput selection approaches (GCHTS) have emerged as a novel selection system for enzyme evolution. GCHTS links the survival of the host cell with the properties of the target protein, resulting in a screening system that is easily measurable and has a high throughput-scale limited only by transformation efficiency. This allows for the rapid identification of desired variants from a pool of >109 variants in each experiment. In recent years, GCHTS approaches have been extensively utilized in the directed evolution of multiple enzymes, demonstrating success in catalyzing non-native substrates, enhancing catalytic activity, and acquiring novel functions. This review introduces three main strategies employed to achieve GCHTS: the elimination of toxic compounds via desired variants, enabling host cells to thrive in hazardous conditions; the complementation of an auxotroph with desired variants, where essential genes for cell growth have been eliminated; and the control of the transcription or expression of a reporter gene related to host cell growth, regulated by the desired variants. Additionally, we highlighted the recent developments in the in vivo continuous evolution of enzyme technology, including phage-assisted continuous evolution (PACE) and orthogonal DNA Replication (OrthoRep). Furthermore, this review discusses the challenges and future prospects in the field of growth-coupled selection for protein engineering.
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Affiliation(s)
- Zhengqun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuting Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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3
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Liu J, Yang J, Yuan L, Wu C, Jiang Y, Zhuang W, Ying H, Yang S. Modulated Arabinose Uptake and cAMP Signaling Synergistically Improve Glucose and Arabinose Consumption in Recombinant Yeast. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12797-12806. [PMID: 37592391 DOI: 10.1021/acs.jafc.3c04386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
During the production of ethanol from lignocellulose-derived sugars, recombinant yeasts tend to utilize xylose and arabinose after glucose exhaustion. So far, many glucose-insensitive pentose transporters have been reported to counteract this phenomenon, but few studies have described intracellular factors. In this study, the combination of adaptive evolution, comparative genomics, and genetic complementation revealed that the hexokinase-deficient (Hxk0) arabinose-fermenting Saccharomyces cerevisiae requires the arabinose transporter variant Gal2-N376T and the mutations of guanine nucleotide exchange factor Cdc25 to overcome glucose restriction during arabinose assimilation. The results showed that the Hxk0 recombinant yeasts could lower the metabolic/physiological threshold of cell proliferation by downregulating the intracellular cAMP levels, resulting in smaller cells and increased arabinose assimilation under glucose restriction. In the medium containing 80 g/L glucose and 20 g/L arabinose, the evolved strain restoring the hexokinase activity completed fermentation at 22 h, compared to 24 h for the parental strain. Overall, the experimental results provide new insights into glucose repression of biorefinery yeasts.
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Affiliation(s)
- Jinle Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Junjie Yang
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lihua Yuan
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chunhua Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Sheng Yang
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
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4
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Zhang P, Wei W, Shang Y, Ye BC. Metabolic engineering of Yarrowia lipolytica for high-level production of scutellarin. BIORESOURCE TECHNOLOGY 2023:129421. [PMID: 37392967 DOI: 10.1016/j.biortech.2023.129421] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
Scutellarin drugs have been recognized as a key item in the national development of essential clinical emergency drugs for treating cardiovascular and cerebrovascular diseases; therefore, the market demand for scutellarin is growing rapidly. Microbial synthesis based on synthetic biology is a promising method for industrial production of scutellarin. In this study, the highest reported scutellarin titer in the shake flask of 703.01 ± 4.83 mg/L was achieved in Yarrowia lipolytica through the systematic metabolic engineering modifications, including screening for the optimal flavone-6-hydroxylase-cytochrome P450 reductase combination SbF6H-ATR2 to enhance P450 enzyme activity, increasing the copy numbers of rate-limiting enzyme genes, overexpressing ZWF1 and GND1 to increase NADPH supply, enhancing the supply of p-coumaric acid and uridine diphosphate glucose, and introducing the heterologous gene VHb to enhance oxygen supply. This study has significant implications for the industrial production of scutellarin and other valuable flavonoids in green economies.
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Affiliation(s)
- Ping Zhang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wenping Wei
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Yanzhe Shang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
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Han Z, Maruwan J, Tang Y, Su WW. Conditional protein degradation in Yarrowia lipolytica using the auxin-inducible degron. Front Bioeng Biotechnol 2023; 11:1188119. [PMID: 37324427 PMCID: PMC10264656 DOI: 10.3389/fbioe.2023.1188119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Conditional protein degradation is a powerful tool for controlled protein knockdown. The auxin-inducible degron (AID) technology uses a plant auxin to induce depletion of degron-tagged proteins, and it has been shown to be functional in several non-plant eukaryotes. In this study, we demonstrated AID-based protein knockdown in an industrially important oleaginous yeast Yarrowia lipolytica. Using the mini-IAA7 (mIAA7) degron derived from Arabidopsis IAA7, coupled with an Oryza sativa TIR1 (OsTIR1) plant auxin receptor F-box protein (expressed from the copper-inducible MT2 promoter), C-terminal degron-tagged superfolder GFP could be degraded in Yarrowia lipolytica upon addition of copper and the synthetic auxin 1-Naphthaleneacetic acid (NAA). However, leaky degradation of the degron-tagged GFP in the absence of NAA was also noted. This NAA-independent degradation was largely eliminated by replacing the wild-type OsTIR1 and NAA with the OsTIR1F74A variant and the auxin derivative 5-Ad-IAA, respectively. Degradation of the degron-tagged GFP was rapid and efficient. However, Western blot analysis revealed cellular proteolytic cleavage within the mIAA7 degron sequence, leading to the production of a GFP sub-population lacking an intact degron. The utility of the mIAA7/OsTIR1F74A system was further explored in controlled degradation of a metabolic enzyme, β-carotene ketolase, which converts β-carotene to canthaxanthin via echinenone. This enzyme was tagged with the mIAA7 degron and expressed in a β-carotene producing Y. lipolytica strain that also expressed OsTIR1F74A controlled by the MT2 promoter. By adding copper and 5-Ad-IAA at the time of culture inoculation, canthaxanthin production was found to be reduced by about 50% on day five compared to the control culture without adding 5-Ad-IAA. This is the first report that demonstrates the efficacy of the AID system in Y. lipolytica. Further improvement of AID-based protein knockdown in Y. lipolytica may be achieved by preventing proteolytic removal of the mIAA7 degron tag.
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Affiliation(s)
- Zhenlin Han
- Department of Molecular Biosciences and Bioengineering, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Jessica Maruwan
- Department of Molecular Biosciences and Bioengineering, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Yinjie Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, Saint Louis, MO, United States
| | - Wei Wen Su
- Department of Molecular Biosciences and Bioengineering, University of Hawai’i at Manoa, Honolulu, HI, United States
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Cao L, Li J, Yang Z, Hu X, Wang P. A review of synthetic biology tools in Yarrowia lipolytica. World J Microbiol Biotechnol 2023; 39:129. [PMID: 36944859 DOI: 10.1007/s11274-023-03557-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/24/2023] [Indexed: 03/23/2023]
Abstract
Yarrowia lipolytica is a non-conventional oleaginous yeast with great potential for industrial production. Y. lipolytica has a high propensity for flux through tricarboxylic acid cycle intermediates. Therefore, this host is currently being developed as a workhorse, and is rapidly emerging in biotechnology fields, especially for industrial chemical production, whole-cell bioconversion, and the treatment and recycling of industrial waste. In recent studies, Y. lipolytica has been rewritten and introduced with non-native metabolites of certain compounds of interest owing to the advancement in synthetic biology tools. In this review, we collate recent progress to present a detailed and insightful summary of the major developments in synthetic biology tools and techniques for Y. lipolytica, including promoters, terminators, selection markers, autonomously replicating sequences, DNA assembly techniques, genome editing techniques, and subcellular organelle engineering. This comprehensive overview would be a useful resource for future genetic engineering studies to improve the yield of desired metabolic products in Y. lipolytica.
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Affiliation(s)
- Linshan Cao
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Jiajie Li
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Zihan Yang
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Xiao Hu
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Pengchao Wang
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China.
- Northeast Forestry University, No. 26 Hexing Road, Harbin, 150000, People's Republic of China.
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Park JH, Bassalo MC, Lin GM, Chen Y, Doosthosseini H, Schmitz J, Roubos JA, Voigt CA. Design of Four Small-Molecule-Inducible Systems in the Yeast Chromosome, Applied to Optimize Terpene Biosynthesis. ACS Synth Biol 2023; 12:1119-1132. [PMID: 36943773 PMCID: PMC10127285 DOI: 10.1021/acssynbio.2c00607] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The optimization of cellular functions often requires the balancing of gene expression, but the physical construction and screening of alternative designs are costly and time-consuming. Here, we construct a strain of Saccharomyces cerevisiae that contains a "sensor array" containing bacterial regulators that respond to four small-molecule inducers (vanillic acid, xylose, aTc, IPTG). Four promoters can be independently controlled with low background and a 40- to 5000-fold dynamic range. These systems can be used to study the impact of changing the level and timing of gene expression without requiring the construction of multiple strains. We apply this approach to the optimization of a four-gene heterologous pathway to the terpene linalool, which is a flavor and precursor to energetic materials. Using this approach, we identify bottlenecks in the metabolic pathway. This work can aid the rapid automated strain development of yeasts for the bio-manufacturing of diverse products, including chemicals, materials, fuels, and food ingredients.
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Affiliation(s)
- Jong Hyun Park
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Marcelo C Bassalo
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Geng-Min Lin
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Ye Chen
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Hamid Doosthosseini
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Joep Schmitz
- DSM Science & Innovation, Biodata & Translational Sciences, P.O. Box 1, 2600 MA Delft, The Netherlands
| | - Johannes A Roubos
- DSM Science & Innovation, Biodata & Translational Sciences, P.O. Box 1, 2600 MA Delft, The Netherlands
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, Massachusetts 02139, United States
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Madzak C, Poiret S, Salomé Desnoulez S, Foligné B, Lafont F, Daniel C. Study of the persistence and dynamics of recombinant mCherry-producing Yarrowia lipolytica strains in the mouse intestine using fluorescence imaging. Microb Biotechnol 2023; 16:618-631. [PMID: 36541039 PMCID: PMC9948224 DOI: 10.1111/1751-7915.14178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022] Open
Abstract
Yarrowia lipolytica is a dimorphic oleaginous non-conventional yeast widely used as a powerful host for expressing heterologous proteins, as well as a promising source of engineered cell factories for various applications. This microorganism has a documented use in Feed and Food and a GRAS (generally recognized as safe) status. Moreover, in vivo studies demonstrated a beneficial effect of this yeast on animal health. However, despite the focus on Y. lipolytica for the industrial manufacturing of heterologous proteins and for probiotic effects, its potential for oral delivery of recombinant therapeutic proteins has seldom been evaluated in mammals. As the first steps towards this aim, we engineered two Y. lipolytica strains, a dairy strain and a laboratory strain, to produce the model fluorescent protein mCherry. We demonstrated that both Y. lipolytica strains transiently persisted for at least 1 week after four daily oral administrations and they maintained the active expression of mCherry in the mouse intestine. We used confocal microscopy to image individual Y. lipolytica cells of freshly collected intestinal tissues. They were found essentially in the lumen and they were rarely in contact with epithelial cells while transiting through the ileum, caecum and colon of mice. Taken as a whole, our results have shown that fluorescent Y. lipolytica strains constitute novel tools to study the persistence and dynamics of orally administered yeasts which could be used in the future as oral delivery vectors for the secretion of active therapeutic proteins in the gut.
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Affiliation(s)
- Catherine Madzak
- INRAE, AgroParisTech, Paris-Saclay University, UMR 782 SayFood, Thiverval-Grignon, France
| | - Sabine Poiret
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, Lille, France
| | - Sophie Salomé Desnoulez
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France
| | - Benoit Foligné
- Univ. Lille, INSERM, CHU Lille, U1286 - Infinite - Institute for Translational Research in Inflammation, Lille, France
| | - Frank Lafont
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, Lille, France.,Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France
| | - Catherine Daniel
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, Lille, France
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He S, Zhang Z, Lu W. Natural promoters and promoter engineering strategies for metabolic regulation in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2023; 50:6986260. [PMID: 36633543 PMCID: PMC9936215 DOI: 10.1093/jimb/kuac029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Sharomyces cerevisiae is currently one of the most important foreign gene expression systems. S. cerevisiae is an excellent host for high-value metabolite cell factories due to its advantages of simplicity, safety, and nontoxicity. A promoter, as one of the basic elements of gene transcription, plays an important role in regulating gene expression and optimizing metabolic pathways. Promoters control the direction and intensity of transcription, and the application of promoters with different intensities and performances will largely determine the effect of gene expression and ultimately affect the experimental results. Due to its significant role, there have been many studies on promoters for decades. While some studies have explored and analyzed new promoters with different functions, more studies have focused on artificially modifying promoters to meet their own scientific needs. Thus, this article reviews current research on promoter engineering techniques and related natural promoters in S. cerevisiae. First, we introduce the basic structure of promoters and the classification of natural promoters. Then, the classification of various promoter strategies is reviewed. Finally, by grouping related articles together using various strategies, this review anticipates the future development direction of promoter engineering.
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Affiliation(s)
| | - Zhanwei Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Wenyu Lu
- Correspondence should be addressed to: W. Y. Lu, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China. Phone: +86-22-853-56523. Fax: +86-22-274-00973. E-mail:
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10
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Global Cellular Metabolic Rewiring Adapts Corynebacterium glutamicum to Efficient Nonnatural Xylose Utilization. Appl Environ Microbiol 2022; 88:e0151822. [PMID: 36383019 PMCID: PMC9746319 DOI: 10.1128/aem.01518-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Xylose, the major component of lignocellulosic biomass, cannot be naturally or efficiently utilized by most microorganisms. Xylose (co)utilization is considered a cornerstone of efficient lignocellulose-based biomanufacturing. We evolved a rapidly xylose-utilizing strain, Cev2-18-5, which showed the highest reported specific growth rate (0.357 h-1) on xylose among plasmid-free Corynebacterium glutamicum strains. A genetically clear chassis strain, CGS15, was correspondingly reconstructed with an efficient glucose-xylose coutilization performance based on comparative genomic analysis and mutation reconstruction. With the introduction of a succinate-producing plasmid, the resulting strain, CGS15-SA1, can efficiently produce 97.1 g/L of succinate with an average productivity of 8.09 g/L/h by simultaneously utilizing glucose and xylose from corn stalk hydrolysate. We further revealed a novel xylose regulatory mechanism mediated by the endogenous transcription factor IpsA with global regulatory effects on C. glutamicum. A synergistic effect on carbon metabolism and energy supply, motivated by three genomic mutations (Psod(C131T)-xylAB, Ptuf(Δ21)-araE, and ipsAC331T), was found to endow C. glutamicum with the efficient xylose utilization and rapid growth phenotype. Overall, this work not only provides promising C. glutamicum chassis strains for a lignocellulosic biorefinery but also enriches the understanding of the xylose regulatory mechanism. IMPORTANCE A novel xylose regulatory mechanism mediated by the transcription factor IpsA was revealed. A synergistic effect on carbon metabolism and energy supply was found to endow C. glutamicum with the efficient xylose utilization and rapid growth phenotype. The new xylose regulatory mechanism enriches the understanding of nonnatural substrate metabolism and encourages exploration new engineering targets for rapid xylose utilization. This work also provides a paradigm to understand and engineer the metabolism of nonnatural renewable substrates for sustainable biomanufacturing.
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Chen S, Lu Y, Wang W, Hu Y, Wang J, Tang S, Lin CSK, Yang X. Efficient production of the β-ionone aroma compound from organic waste hydrolysates using an engineered Yarrowia lipolytica strain. Front Microbiol 2022; 13:960558. [PMID: 36212878 PMCID: PMC9532697 DOI: 10.3389/fmicb.2022.960558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
This study demonstrates the feasibility of establishing a natural compound supply chain in a biorefinery. The process starts with the biological or chemical hydrolysis of food and agricultural waste into simple and fermentative sugars, followed by their fermentation into more complex molecules. The yeast strain, Yarrowia lipolytica, was modified by introducing high membrane affinity variants of the carotenoid cleavage dioxygenase enzyme, PhCCD1, to increase the production of the aroma compound, β-ionone. The initial hydrolysis process converted food waste or sugarcane bagasse into nutrient-rich hydrolysates containing 78.4 g/L glucose and 8.3 g/L fructose, or 34.7 g/L glucose and 20.1 g/L xylose, respectively. During the next step, engineered Y. lipolytica strains were used to produce β-ionone from these feedstocks. The yeast strain YLBI3120, carrying a modified PhCCD1 gene was able to produce 4 g/L of β-ionone with a productivity of 13.9 mg/L/h from food waste hydrolysate. This is the highest yield reported for the fermentation of this compound to date. The integrated process described in this study could be scaled up to achieve economical large-scale conversion of inedible food and agricultural waste into valuable aroma compounds for a wide range of potential applications.
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Affiliation(s)
- Shuyi Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Yanping Lu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
- Technology Research Center, Wuliangye Yibin Company Limited, Yibin, Sichuan, China
- Postdoctoral Research Workstation, Sichuan Yibin Wuliangye Group Company Limited, Yibin, Sichuan, China
| | - Wen Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences (CAS), Guangzhou, Guangdong, China
| | - Yunzi Hu
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences (CAS), Guangzhou, Guangdong, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Shixing Tang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
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12
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Fang TT, Zou ZP, Zhou Y, Ye BC. Prebiotics-Controlled Disposable Engineered Bacteria for Intestinal Diseases. ACS Synth Biol 2022; 11:3004-3014. [PMID: 36037444 DOI: 10.1021/acssynbio.2c00182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
As a new method of diagnosis and treatment for intestinal diseases, intelligent engineered bacteria based on synthetic biology have been developed vigorously in recent years. However, how to deal with the engineered bacteria in vivo after completing the tasks is an urgent problem to be resolved. In this study, we constructed a thiosulfate (a biomarker of inflammatory bowel disease)-responsive engineered bacteria to generate two signals, sfGFP (monitoring) and gain-of-function (translation activation) mutation (ACG to ATG), in the initiation codon of lysisE (recording) via the CRISPR/Cas9-mediated base editing system. Once these two signals were detected, xylose could be added to induce lysis E expression, resulting in the destruction of the edited bacteria and the release of AvCystain simultaneously. Overall, our innovative engineered bacteria can record instant and historical information of the disease, and especially, the edited bacteria can be artificially attenuated and release drug in situ when needed, ultimately serving as a disposable and recyclable candidate for more types of diseases.
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Affiliation(s)
- Ting-Ting Fang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhen-Ping Zou
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ying Zhou
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
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13
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Pham C, Stogios PJ, Savchenko A, Mahadevan R. Advances in engineering and optimization of transcription factor-based biosensors for plug-and-play small molecule detection. Curr Opin Biotechnol 2022; 76:102753. [PMID: 35872379 DOI: 10.1016/j.copbio.2022.102753] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022]
Abstract
Transcription factor (TF)-based biosensors have been applied in biotechnology for a variety of functions, including protein engineering, dynamic control, environmental detection, and point-of-care diagnostics. Such biosensors are promising analytical tools due to their wide range of detectable ligands and modular nature. However, designing biosensors tailored for applications of interest with the desired performance parameters, including ligand specificity, remains challenging. Biosensors often require significant engineering and tuning to meet desired specificity, sensitivity, dynamic range, and operating range parameters. Another limitation is the orthogonality of biosensors across hosts, given the role of the cellular context. Here, we describe recent advances and examples in the engineering and optimization of TF-based biosensors for plug-and-play small molecule detection. We highlight novel developments in TF discovery and biosensor design, TF specificity engineering, and biosensor tuning, with emphasis on emerging computational methods.
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Affiliation(s)
- Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada; Department of Microbiology, Immunology and Infectious Disease, University of Calgary, AB, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada; The Institute of Biomedical Engineering, University of Toronto, ON, Canada.
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14
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Wang Z, Yan Y, Zhang H. A Single-Component Blue Light-Induced System Based on EL222 in Yarrowia lipolytica. Int J Mol Sci 2022; 23:ijms23116344. [PMID: 35683022 PMCID: PMC9181742 DOI: 10.3390/ijms23116344] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/20/2022] [Accepted: 06/02/2022] [Indexed: 01/27/2023] Open
Abstract
Optogenetics has the advantages of a fast response time, reversibility, and high spatial and temporal resolution, which make it desirable in the metabolic engineering of chassis cells. In this study, a light-induced expression system of Yarrowia lipolytica was constructed, which successfully achieved the synthesis and functional verification of Bleomycin resistance protein (BleoR). The core of the blue light-induced system, the light-responsive element (TF), is constructed based on the blue photosensitive protein EL222 and the transcription activator VP16. The results show that the light-induced sensor based on TF, upstream activation sequence (C120)5, and minimal promoter CYC102 can respond to blue light and initiate the expression of GFPMut3 report gene. With four copies of the responsive promoter and reporter gene assembled, they can produce a 128.5-fold higher fluorescent signal than that under dark conditions after 8 h of induction. The effects of light dose and periodicity on this system were investigated, which proved that the system has good spatial and temporal controllability. On this basis, the light-controlled system was used for the synthesis of BleoR to realize the expression and verification of functional protein. These results demonstrated that this system has the potential for the transcriptional regulation of target genes, construction of large-scale synthetic networks, and overproduction of the desired product.
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15
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Analysis of Xylose Operon from Paenibacillus polymyxa ATCC842 and Development of Tools for Gene Expression. Int J Mol Sci 2022; 23:ijms23095024. [PMID: 35563415 PMCID: PMC9104551 DOI: 10.3390/ijms23095024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 01/27/2023] Open
Abstract
With numerous industrial applications, Paenibacillus polymyxa has been accepted as the candidate of the cell factory for many secondary metabolites. However, as the regulatory expression elements in P. polymyxa have not been systematically investigated, genetic modification on account of a specific metabolism pathway for the strain is limited. In this study, a xylose-inducible operon in the xylan-utilizing bacterium ATCC842 was identified, and the relative operon transcription was increased to 186-fold in the presence of xylose, while the relative enhanced green fluorescent protein (eGFP) fluorescence intensity was promoted by over four-fold. By contrast, glucose downregulated the operon to 0.5-fold that of the control. The binding site of the operon was “ACTTAGTTTAAGCAATAGACAAAGT”, and this can be degenerated to “ACTTWGTTTAWSSNATAVACAAAGT” in Paenibacillus spp., which differs from that in the Bacillus spp. xylose operon. The xylose operon binding site was transplanted to the constitutive promoter Pshuttle-09. The eGFP fluorescence intensity assay indicated that both the modified and original Pshuttle-09 had similar expression levels after induction, and the expression level of the modified promoter was decreased to 19.8% without induction. This research indicates that the operon has great potential as an ideal synthetic biology tool in Paenibacillus spp. that can dynamically regulate its gene circuit strength through xylose.
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16
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Zhou S, Alper HS, Zhou J, Deng Y. Intracellular biosensor-based dynamic regulation to manipulate gene expression at the spatiotemporal level. Crit Rev Biotechnol 2022; 43:646-663. [PMID: 35450502 DOI: 10.1080/07388551.2022.2040415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The use of intracellular, biosensor-based dynamic regulation strategies to regulate and improve the production of useful compounds have progressed significantly over previous decades. By employing such an approach, it is possible to simultaneously realize high productivity and optimum growth states. However, industrial fermentation conditions contain a mixture of high- and low-performance non-genetic variants, as well as young and aged cells at all growth phases. Such significant individual variations would hinder the precise controlling of metabolic flux at the single-cell level to achieve high productivity at the macroscopic population level. Intracellular biosensors, as the regulatory centers of metabolic networks, can real-time sense intra- and extracellular conditions and, thus, could be synthetically adapted to balance the biomass formation and overproduction of compounds by individual cells. Herein, we highlight advances in the designing and engineering approaches to intracellular biosensors. Then, the spatiotemporal properties of biosensors associated with the distribution of inducers are compared. Also discussed is the use of such biosensors to dynamically control the cellular metabolic flux. Such biosensors could achieve single-cell regulation or collective regulation goals, depending on whether or not the inducer distribution is only intracellular.
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Affiliation(s)
- Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.,McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
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17
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Engineering of Synthetic Transcriptional Switches in Yeast. Life (Basel) 2022; 12:life12040557. [PMID: 35455048 PMCID: PMC9030632 DOI: 10.3390/life12040557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 02/04/2023] Open
Abstract
Transcriptional switches can be utilized for many purposes in synthetic biology, including the assembly of complex genetic circuits to achieve sophisticated cellular systems and the construction of biosensors for real-time monitoring of intracellular metabolite concentrations. Although to date such switches have mainly been developed in prokaryotes, those for eukaryotes are increasingly being reported as both rational and random engineering technologies mature. In this review, we describe yeast transcriptional switches with different modes of action and how to alter their properties. We also discuss directed evolution technologies for the rapid and robust construction of yeast transcriptional switches.
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18
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Sun ML, Shi TQ, Lin L, Ledesma-Amaro R, Ji XJ. Advancing Yarrowia lipolytica as a superior biomanufacturing platform by tuning gene expression using promoter engineering. BIORESOURCE TECHNOLOGY 2022; 347:126717. [PMID: 35031438 DOI: 10.1016/j.biortech.2022.126717] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Yarrowia lipolytica is recognized as an excellent non-conventional yeast in the field of biomanufacturing, where it is used as a host to produce oleochemicals, terpenes, organic acids, polyols and recombinant proteins. Consequently, metabolic engineering of this yeast is becoming increasingly popular to advance it as a superior biomanufacturing platform, of which promoters are the most basic elements for tuning gene expression. Endogenous promoters of Yarrowia lipolytica were reviewed, which are the basis for promoter engineering. The engineering strategies, such as hybrid promoter engineering, intron enhancement promoter engineering, and transcription factor-based inducible promoter engineering are described. Additionally, the applications of Yarrowia lipolytica promoter engineering to rationally reconstruct biosynthetic gene clusters and improve the genome-editing efficiency of the CRISPR-Cas systems were reviewed. Finally, research needs and future directions for promoter engineering are also discussed in this review.
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Affiliation(s)
- Mei-Li Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210046, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China.
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19
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Zhou P, Fang X, Xu N, Yao Z, Xie W, Ye L. Development of a Highly Efficient Copper-Inducible GAL Regulation System (CuIGR) in Saccharomyces cerevisiae. ACS Synth Biol 2021; 10:3435-3444. [PMID: 34874147 DOI: 10.1021/acssynbio.1c00378] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Dynamic regulation of gene expression to decouple growth and production has been proven to be effective for improving the biosynthetic efficiency of microbial cell factories. However, the number of efficient regulatory systems available for regulation of Saccharomyces cerevisiae is limited. In the present study, a novel copper-inducible gene expression system (CuIGR) composed of the copper-induced transcriptional activator Gal4 and the copper-inhibited repressor Gal80 was constructed in S. cerevisiae. When Gal80 was fused with a N-degron tag (K15), the resulting CuIGR4 system exhibited the most stringent regulation of gene expression driven by GAL1/2/7/10 promoters. As compared to the native Cu2+-inducible CUP1 promoter, the CuIGR4 system amplified the response to copper by as much as 2.7 folds, resulting in 72-fold induction of EGFP expression and a 33-fold change in lycopene production (3-100 mg/L) with addition of 20 μM copper. This newly developed copper-inducible system provides a powerful tool for gene expression control in S. cerevisiae, which is expected to be widely applicable in the regulation of yeast cell factories for enhanced biosynthesis of valuable products.
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Affiliation(s)
- Pingping Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Xin Fang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Nannan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Zhen Yao
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Wenping Xie
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
- Zhejiang NHU Company Limited, Shaoxing 312521, PR China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
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20
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Brink DP, Borgström C, Persson VC, Ofuji Osiro K, Gorwa-Grauslund MF. D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers. Int J Mol Sci 2021; 22:12410. [PMID: 34830296 PMCID: PMC8625115 DOI: 10.3390/ijms222212410] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
Extension of the substrate range is among one of the metabolic engineering goals for microorganisms used in biotechnological processes because it enables the use of a wide range of raw materials as substrates. One of the most prominent examples is the engineering of baker's yeast Saccharomyces cerevisiae for the utilization of d-xylose, a five-carbon sugar found in high abundance in lignocellulosic biomass and a key substrate to achieve good process economy in chemical production from renewable and non-edible plant feedstocks. Despite many excellent engineering strategies that have allowed recombinant S. cerevisiae to ferment d-xylose to ethanol at high yields, the consumption rate of d-xylose is still significantly lower than that of its preferred sugar d-glucose. In mixed d-glucose/d-xylose cultivations, d-xylose is only utilized after d-glucose depletion, which leads to prolonged process times and added costs. Due to this limitation, the response on d-xylose in the native sugar signaling pathways has emerged as a promising next-level engineering target. Here we review the current status of the knowledge of the response of S. cerevisiae signaling pathways to d-xylose. To do this, we first summarize the response of the native sensing and signaling pathways in S. cerevisiae to d-glucose (the preferred sugar of the yeast). Using the d-glucose case as a point of reference, we then proceed to discuss the known signaling response to d-xylose in S. cerevisiae and current attempts of improving the response by signaling engineering using native targets and synthetic (non-native) regulatory circuits.
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Affiliation(s)
- Daniel P. Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
| | - Celina Borgström
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St., Toronto, ON M5S 3E5, Canada
| | - Viktor C. Persson
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
| | - Karen Ofuji Osiro
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasília 70770-901, DF, Brazil
| | - Marie F. Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
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21
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Saccharomyces cerevisiae Promoter Engineering before and during the Synthetic Biology Era. BIOLOGY 2021; 10:biology10060504. [PMID: 34204069 PMCID: PMC8229000 DOI: 10.3390/biology10060504] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022]
Abstract
Simple Summary Promoters are DNA sequences where the process of transcription starts. They can work constitutively or be controlled by environmental signals of different types. The quantity of proteins and RNA present in yeast genetic circuits highly depends on promoter strength. Hence, they have been deeply studied and modified over, at least, the last forty years, especially since the year 2000 when Synthetic Biology was born. Here, we present how promoter engineering changed over these four decades and discuss its possible future directions due to novel computational methods and technology. Abstract Synthetic gene circuits are made of DNA sequences, referred to as transcription units, that communicate by exchanging proteins or RNA molecules. Proteins are, mostly, transcription factors that bind promoter sequences to modulate the expression of other molecules. Promoters are, therefore, key components in genetic circuits. In this review, we focus our attention on the construction of artificial promoters for the yeast S. cerevisiae, a popular chassis for gene circuits. We describe the initial techniques and achievements in promoter engineering that predated the start of the Synthetic Biology epoch of about 20 years. We present the main applications of synthetic promoters built via different methods and discuss the latest innovations in the wet-lab engineering of novel promoter sequences.
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22
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Cortés-Avalos D, Martínez-Pérez N, Ortiz-Moncada MA, Juárez-González A, Baños-Vargas AA, Estrada-de Los Santos P, Pérez-Rueda E, Ibarra JA. An update of the unceasingly growing and diverse AraC/XylS family of transcriptional activators. FEMS Microbiol Rev 2021; 45:6219864. [PMID: 33837749 DOI: 10.1093/femsre/fuab020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/31/2021] [Indexed: 01/09/2023] Open
Abstract
Transcriptional factors play an important role in gene regulation in all organisms, especially in Bacteria. Here special emphasis is placed in the AraC/XylS family of transcriptional regulators. This is one of the most abundant as many predicted members have been identified and more members are added because more bacterial genomes are sequenced. Given the way more experimental evidence has mounded in the past decades, we decided to update the information about this captivating family of proteins. Using bioinformatics tools on all the data available for experimentally characterized members of this family, we found that many members that display a similar functional classification can be clustered together and in some cases they have a similar regulatory scheme. A proposal for grouping these proteins is also discussed. Additionally, an analysis of surveyed proteins in bacterial genomes is presented. Altogether, the current review presents a panoramic view into this family and we hope it helps to stimulate future research in the field.
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Affiliation(s)
- Daniel Cortés-Avalos
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Noemy Martínez-Pérez
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
| | - Mario A Ortiz-Moncada
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Aylin Juárez-González
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Arturo A Baños-Vargas
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Paulina Estrada-de Los Santos
- Laboratorio de Biotecnología Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México.,Facultad de Ciencias, Centro de Genómica y Bioinformática, Universidad Mayor, Santiago, Chile
| | - J Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
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23
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Zha J, Yuwen M, Qian W, Wu X. Yeast-Based Biosynthesis of Natural Products From Xylose. Front Bioeng Biotechnol 2021; 9:634919. [PMID: 33614617 PMCID: PMC7886706 DOI: 10.3389/fbioe.2021.634919] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/11/2021] [Indexed: 12/28/2022] Open
Abstract
Xylose is the second most abundant sugar in lignocellulosic hydrolysates. Transformation of xylose into valuable chemicals, such as plant natural products, is a feasible and sustainable route to industrializing biorefinery of biomass materials. Yeast strains, including Saccharomyces cerevisiae, Scheffersomyces stipitis, and Yarrowia lipolytica, display some paramount advantages in expressing heterologous enzymes and pathways from various sources and have been engineered extensively to produce natural products. In this review, we summarize the advances in the development of metabolically engineered yeasts to produce natural products from xylose, including aromatics, terpenoids, and flavonoids. The state-of-the-art metabolic engineering strategies and representative examples are reviewed. Future challenges and perspectives are also discussed on yeast engineering for commercial production of natural products using xylose as feedstocks.
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Affiliation(s)
- Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | | | | | - Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an, China
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24
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Tang RQ, Wagner JM, Alper HS, Zhao XQ, Bai FW. Design, Evolution, and Characterization of a Xylose Biosensor in Escherichia coli Using the XylR/ xylO System with an Expanded Operating Range. ACS Synth Biol 2020; 9:2714-2722. [PMID: 32886884 DOI: 10.1021/acssynbio.0c00225] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetically encoded biosensors are extensively utilized in synthetic biology and metabolic engineering. However, reported xylose biosensors are far too sensitive with a limited operating range to be useful for most sensing applications. In this study, we describe directed evolution of Escherichia coli XylR, and construction of biosensors based on XylR and the corresponding operator xylO. The operating range of biosensors containing the mutant XylR was increased by nearly 10-fold comparing with the control. Two individual amino acid mutations (either L73P or N220T) in XylR were sufficient to extend the linear response range to upward of 10 g/L xylose. The evolved biosensors described here are well suited for developing whole-cell biosensors for detecting varying xylose concentrations across an expanded range. As an alternative use of this system, we also demonstrate the utility of XylR and xylO as a xylose inducible system to enable graded gene expression through testing with β-galactosidase gene and the lycopene synthetic pathway. This evolution strategy identified a less-sensitive biosensor for real applications, thus providing new insights into strategies for expanding operating ranges of other biosensors for synthetic biology applications.
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Affiliation(s)
- Rui-Qi Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - James M. Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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25
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Wei W, Zhang P, Shang Y, Zhou Y, Ye BC. Metabolically engineering of Yarrowia lipolytica for the biosynthesis of naringenin from a mixture of glucose and xylose. BIORESOURCE TECHNOLOGY 2020; 314:123726. [PMID: 32622278 DOI: 10.1016/j.biortech.2020.123726] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
Xylose-inducible modules simultaneously expressing xylose utilization and naringenin biosynthesis pathways were developed in Yarrowia lipolytica to produce naringenin from a mixture of glucose and xylose. The naringenin synthetic pathway was constructed using a constitutive expression to yield 239.1 ± 5.1 mg/L naringenin. Furthermore, the introduction of an inducible pathway realized the dual function of xylose as a substrate and synthetic inducer, which coupled the xylose utilization with naringenin biosynthesis and increased production. Interestingly, the simultaneous enhancement of xylose reductase and xylose transporter expression along with that of xylitol dehydrogenase and xylulokinase can further improve the xylose utilization ability of Y. lipolytica. As expected, xylose-inducible synthesis of naringenin could achieved a titer of 715.3 ± 12.8 mg/L through the shake-flask cultivation level. Therefore, xylose-induced activation of both the xylose utilization and product biosynthesis pathway is considered to be an effective strategy for the biosynthesis of xylose-derived chemicals in yeast.
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Affiliation(s)
- Wenping Wei
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ping Zhang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yanzhe Shang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ying Zhou
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
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