1
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Cámara E, Mormino M, Siewers V, Nygård Y. Saccharomyces cerevisiae strains performing similarly during fermentation of lignocellulosic hydrolysates show pronounced differences in transcriptional stress responses. Appl Environ Microbiol 2024; 90:e0233023. [PMID: 38587374 PMCID: PMC11107148 DOI: 10.1128/aem.02330-23] [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: 12/22/2023] [Accepted: 03/14/2024] [Indexed: 04/09/2024] Open
Abstract
Improving our understanding of the transcriptional changes of Saccharomyces cerevisiae during fermentation of lignocellulosic hydrolysates is crucial for the creation of more efficient strains to be used in biorefineries. We performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. Many of the differently expressed genes identified among the strains have previously been reported to be important for tolerance to lignocellulosic hydrolysates or inhibitors therein. Our study demonstrates that stress responses typically identified during aerobic conditions such as glutathione metabolism, osmotolerance, and detoxification processes also are important for anaerobic processes. Overall, the transcriptomic responses were largely strain dependent, and we focused our study on similarities and differences in the transcriptomes of the LBCM strains. The expression of sugar transporter-encoding genes was higher in LBCM31 compared with LBCM109 that showed high expression of genes involved in iron metabolism and genes promoting the accumulation of sphingolipids, phospholipids, and ergosterol. These results highlight different evolutionary adaptations enabling S. cerevisiae to strive in lignocellulosic hydrolysates and suggest novel gene targets for improving fermentation performance and robustness. IMPORTANCE The need for sustainable alternatives to oil-based production of biochemicals and biofuels is undisputable. Saccharomyces cerevisiae is the most commonly used industrial fermentation workhorse. The fermentation of lignocellulosic hydrolysates, second-generation biomass unsuited for food and feed, is still hampered by lowered productivities as the raw material is inhibitory for the cells. In order to map the genetic responses of different S. cerevisiae strains, we performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. While the response to inhibitors of S. cerevisiae has been studied earlier, this has in previous studies been done in aerobic conditions. The transcriptomic analysis highlights different evolutionary adaptations among the different S. cerevisiae strains and suggests novel gene targets for improving fermentation performance and robustness.
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Affiliation(s)
- Elena Cámara
- Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Maurizio Mormino
- Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Yvonne Nygård
- Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- VTT Technical Research Centre of Finland, Espoo, Finland
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2
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Wang S, Zhao F, Yang M, Lin Y, Han S. Metabolic engineering of Saccharomyces cerevisiae for the synthesis of valuable chemicals. Crit Rev Biotechnol 2024; 44:163-190. [PMID: 36596577 DOI: 10.1080/07388551.2022.2153008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/11/2022] [Accepted: 10/29/2022] [Indexed: 01/05/2023]
Abstract
In the twenty first century, biotechnology offers great opportunities and solutions to climate change mitigation, energy and food security and resource efficiency. The use of metabolic engineering to modify microorganisms for producing industrially significant chemicals is developing and becoming a trend. As a famous, generally recognized as a safe (GRAS) model microorganism, Saccharomyces cerevisiae is widely used due to its excellent operational convenience and high fermentation efficiency. This review summarizes recent advancements in the field of using metabolic engineering strategies to construct engineered S. cerevisiae over the past ten years. Five different types of compounds are classified by their metabolites, and the modified metabolic pathways and strategies are summarized and discussed independently. This review may provide guidance for future metabolic engineering efforts toward such compounds and analogues. Additionally, the limitations of S. cerevisiae as a cell factory and its future trends are comprehensively discussed.
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Affiliation(s)
- Shuai Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Fengguang Zhao
- School of Light Industry and Engineering, South China University of Technology, Guangzhou, China
| | - Manli Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ying Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuangyan Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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3
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Ekim Kocabey A, Schneiter R. Human lipocalins bind and export fatty acids through the secretory pathway of yeast cells. Front Microbiol 2024; 14:1309024. [PMID: 38328584 PMCID: PMC10849133 DOI: 10.3389/fmicb.2023.1309024] [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: 10/07/2023] [Accepted: 12/12/2023] [Indexed: 02/09/2024] Open
Abstract
The activation of fatty acids to their acyl-CoA derivatives is a crucial step for their integration into more complex lipids or their degradation via beta-oxidation. Yeast cells employ five distinct acyl-CoA synthases to facilitate this ATP-dependent activation of acyl chains. Notably, mutant cells that are deficient in two of these fatty acid-activating (FAA) enzymes, namely, Faa1 and Faa4, do not take up free fatty acids but rather export them out of the cell. This unique fatty acid export pathway depends on small, secreted pathogenesis-related yeast proteins (Pry). In this study, we investigate whether the expression of human fatty acid-binding proteins, including Albumin, fatty acid-binding protein 4 (Fabp4), and three distinct lipocalins (ApoD, Lcn1, and Obp2a), could promote fatty acid secretion in yeast. To optimize the expression and secretion of these proteins, we systematically examined various signal sequences in both low-copy and high-copy number plasmids. Our findings reveal that directing these fatty-acid binding proteins into the secretory pathway effectively promotes fatty acid secretion from a sensitized quadruple mutant model strain (faa1∆ faa4∆ pry1∆ pry3∆). Furthermore, the level of fatty acid secretion exhibited a positive correlation with the efficiency of protein secretion. Importantly, the expression of all human lipid-binding proteins rescued Pry-dependent fatty acid secretion, resulting in the secretion of both long-chain saturated and unsaturated fatty acids. These results not only affirm the in vitro binding capabilities of lipocalins to fatty acids but also present a novel avenue for enhancing the secretion of valuable lipidic compounds. Given the growing interest in utilizing yeast as a cellular factory for producing poorly soluble compounds and the potential of lipocalins as platforms for engineering substrate-binding specificity, our model is considered as a powerful tool for promoting the secretion of high-value lipid-based molecules.
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Affiliation(s)
| | - Roger Schneiter
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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4
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Bai S, Qiao B, Hou ZJ, Gao GR, Cao CY, Cheng JS, Yuan YJ. Mutualistic microbial community of Bacillus amyloliquefaciens and recombinant Yarrowia lipolytica co-produced lipopeptides and fatty acids from food waste. CHEMOSPHERE 2023; 310:136864. [PMID: 36243085 DOI: 10.1016/j.chemosphere.2022.136864] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Bioconversion is an important method for transforming food waste (FW) into high value-added products, rendering it harmless, and recycling resources. An artificial microbial consortium (AMC) was constructed to produce FW-based lipopeptides in order to investigate the strategy of FW bioconversion into value-added products. Exogenous fatty acids as a precursor significantly improved the lipopeptide production of Bacillus amyloliquefaciens HM618. To enhance fatty acid synthesis and efflux in AMC, the recombinant Yarrowia lipolytica YL21 (strain YL21) was constructed by screening 12 target genes related to fatty acids to replace exogenous fatty acids in order to improve lipopeptide production. The levels of fengycin, surfactin, and iturin A in the AMC of strains HM618 and YL21 reached 76.19, 192.80, and 31.32 mg L-1, increasing 7.24-, 12.13-, and 3.23-fold compared to the results from the pure culture of strain HM618 in flask with Landy medium, respectively. Furthermore, free fatty acids were almost undetectable in the co-culture of strains HM618 and YL21, although its level was around 1.25 g L-1 in the pure culture of strain YL21 with Landy medium. Interestingly, 470.24 mg L-1 of lipopeptides and 18.11 g L-1 of fatty acids were co-produced in this AMC in a bioreactor with FW medium. To our knowledge, it is the first report of FW biotransformation into co-produce of lipopeptides and fatty acids in the AMC of B. amyloliquefaciens and Y. lipolytica. These results provide new insights into the biotransformation potential of FW for value-added co-products by AMC.
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Affiliation(s)
- Song Bai
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China; Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China
| | - Zheng-Jie Hou
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China; Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China
| | - Geng-Rong Gao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China; Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China
| | - Chun-Yang Cao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China; Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China
| | - Jing-Sheng Cheng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China; Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China.
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China; Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, PR China
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5
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Spatial-temporal regulation of fatty alcohol biosynthesis in yeast. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:141. [PMID: 36527110 PMCID: PMC9758912 DOI: 10.1186/s13068-022-02242-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Construction of efficient microbial cell factories is one of the core steps for establishing green bio-manufacturing processes. However, the complex metabolic regulation makes it challenging in driving the metabolic flux toward the product biosynthesis. Dynamically coupling the biosynthetic pathways with the cellular metabolism at spatial-temporal manner should be helpful for improving the production with alleviating the cellular stresses. RESULTS In this study, we observed the mismatch between fatty alcohol biosynthesis and cellular metabolism, which compromised the fatty alcohol production in Saccharomyces cerevisiae. To enhance the fatty alcohol production, we spatial-temporally regulated fatty alcohol biosynthetic pathway by peroxisomal compartmentalization (spatial) and dynamic regulation of gene expression (temporal). In particular, fatty acid/acyl-CoA responsive promoters were identified by comparative transcriptional analysis, which helped to dynamically regulate the expression of acyl-CoA reductase gene MaFAR1 and improved fatty alcohol biosynthesis by 1.62-fold. Furthermore, enhancing the peroxisomal supply of acyl-CoA and NADPH further improved fatty alcohol production to 282 mg/L, 2.52 times higher than the starting strain. CONCLUSIONS This spatial-temporal regulation strategy partially coordinated fatty alcohol biosynthesis with cellular metabolism including peroxisome biogenesis and precursor supply, which should be applied for production of other products in microbes.
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6
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Homayoonfar M, Roosta Azad R, Sardari S. Analytical methods in fatty acid analysis for microbial applications: the recent trends. Prep Biochem Biotechnol 2021; 51:937-952. [PMID: 34506247 DOI: 10.1080/10826068.2021.1881910] [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: 10/20/2022]
Abstract
Fatty acids are among the most important components of many biological systems and have been highlighted in many research fields in recent decades. In the food industry, it is important to check the amount and types of fatty acids in edible oils, beverages and other foods products, and checking the fatty acids parameters are among the quality control parameters for those products. In medical applications, investigation of fatty acids in biological samples and comparing imbalances in them can help to diagnose some diseases. On the other hand, the development of cell factories for the production of biofuels and other valuable chemicals requires the accurate analysis of fatty acids, which serve as precursors in development of those products. As a result, given all these different applications of fatty acids, rapid and accurate methods for characterization and quantification of fatty acids are essential. In recent years, various methods for the analysis of fatty acids have been proposed, which according to the specific purpose of the analysis, some of them can be used with consideration of speed, accuracy and cost. In this article, the available methods for the analysis of fatty acids are reviewed with a special emphasis on the analysis of microbial samples to pave the way for more widespread metabolic engineering research.
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Affiliation(s)
- Mohammad Homayoonfar
- Chemical and Petroleum Engineering Department, Sharif University of Technology, Tahran, Iran.,Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Reza Roosta Azad
- Chemical and Petroleum Engineering Department, Sharif University of Technology, Tahran, Iran
| | - Soroush Sardari
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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7
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Agnoletti BZ, Folli GS, Pereira LL, Pinheiro PF, Guarçoni RC, da Silva Oliveira EC, Filgueiras PR. Multivariate calibration applied to study of volatile predictors of arabica coffee quality. Food Chem 2021; 367:130679. [PMID: 34352695 DOI: 10.1016/j.foodchem.2021.130679] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/09/2021] [Accepted: 07/20/2021] [Indexed: 01/29/2023]
Abstract
The chemical complexity of coffee influences the sensory evaluation of the beverage, the main method used to define the quality of the coffee. In view of the subjectivity that method offers, we propose the association of an instrumental method with multivariate calibration (PLS and GA-SVR) to predict the quality of arabica coffee as support for sensory analysis. Arabica coffee samples were submitted to sensory evaluation using the Specialty Coffee Association (SCA) protocol and HS-SPME-GC/MS analysis. The models presented RMSEp results from 0.20 to 0.25, within the evaluation range the quality levels of sensory attributes (0.25). For the fragrance/aroma attribute, a value of R2p equal to 0.8503 was reached. 15 volatile compounds were identified as responsible for predicting the quality of arabica coffee, among which, 1-nonadecene was first reported as an impact compound in the prediction of important sensory attributes.
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Affiliation(s)
- Bárbara Zani Agnoletti
- Federal University of Espirito Santo/UFES, Department of Chemistry, Campus Goiabeiras, Avenida Fernando Ferrari, 514, CEP 29075-910 Vitória, Espírito Santo, Brazil.
| | - Gabriely Silveira Folli
- Federal University of Espirito Santo/UFES, Department of Chemistry, Campus Goiabeiras, Avenida Fernando Ferrari, 514, CEP 29075-910 Vitória, Espírito Santo, Brazil
| | - Lucas Louzada Pereira
- Federal Institute of Espírito Santo, Department of Food Science and Technology, Avenida Elizabeth Minete Perim, S/N, Bairro São Rafael, CEP 29375-000 Venda Nova do Imigrante, Espírito Santo, Brazil
| | - Patrícia Fontes Pinheiro
- Federal University of Viçosa, Department of Chemistry, Avenida Peter Henry Rolfs, S/N, CEP 36570-900 Viçosa, Minas Gerais, Brazil
| | - Rogério Carvalho Guarçoni
- Capixaba Institute of Technical Assistance, Research and Extension - INCAPER, Department of Statistics, Rua Afonso Sarlo, 160, Bento Ferreira, CEP 29052-010 Vitória, Espírito Santo, Brazil
| | - Emanuele Catarina da Silva Oliveira
- Federal Institute of Espírito Santo, Department of Food Science and Technology, Avenida Elizabeth Minete Perim, S/N, Bairro São Rafael, CEP 29375-000 Venda Nova do Imigrante, Espírito Santo, Brazil
| | - Paulo Roberto Filgueiras
- Federal University of Espirito Santo/UFES, Department of Chemistry, Campus Goiabeiras, Avenida Fernando Ferrari, 514, CEP 29075-910 Vitória, Espírito Santo, Brazil
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8
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Wong M, Badri A, Gasparis C, Belfort G, Koffas M. Modular optimization in metabolic engineering. Crit Rev Biochem Mol Biol 2021; 56:587-602. [PMID: 34180323 DOI: 10.1080/10409238.2021.1937928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
There is an increasing demand for bioproducts produced by metabolically engineered microbes, such as pharmaceuticals, biofuels, biochemicals and other high value compounds. In order to meet this demand, modular optimization, the optimizing of subsections instead of the whole system, has been adopted to engineer cells to overproduce products. Research into modularity has focused on traditional approaches such as DNA, RNA, and protein-level modularity of intercellular machinery, by optimizing metabolic pathways for enhanced production. While research into these traditional approaches continues, limitations such as scale-up and time cost hold them back from wider use, while at the same time there is a shift to more novel methods, such as moving from episomal expression to chromosomal integration. Recently, nontraditional approaches such as co-culture systems and cell-free metabolic engineering (CFME) are being investigated for modular optimization. Co-culture modularity looks to optimally divide the metabolic burden between different hosts. CFME seeks to modularly optimize metabolic pathways in vitro, both speeding up the design of such systems and eliminating the issues associated with live hosts. In this review we will examine both traditional and nontraditional approaches for modular optimization, examining recent developments and discussing issues and emerging solutions for future research in metabolic engineering.
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Affiliation(s)
- Matthew Wong
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Abinaya Badri
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Christopher Gasparis
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Mattheos Koffas
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
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9
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Krishnan A, McNeil BA, Stuart DT. Biosynthesis of Fatty Alcohols in Engineered Microbial Cell Factories: Advances and Limitations. Front Bioeng Biotechnol 2020; 8:610936. [PMID: 33344437 PMCID: PMC7744569 DOI: 10.3389/fbioe.2020.610936] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/10/2020] [Indexed: 11/19/2022] Open
Abstract
Concerns about climate change and environmental destruction have led to interest in technologies that can replace fossil fuels and petrochemicals with compounds derived from sustainable sources that have lower environmental impact. Fatty alcohols produced by chemical synthesis from ethylene or by chemical conversion of plant oils have a large range of industrial applications. These chemicals can be synthesized through biological routes but their free forms are produced in trace amounts naturally. This review focuses on how genetic engineering of endogenous fatty acid metabolism and heterologous expression of fatty alcohol producing enzymes have come together resulting in the current state of the field for production of fatty alcohols by microbial cell factories. We provide an overview of endogenous fatty acid synthesis, enzymatic methods of conversion to fatty alcohols and review the research to date on microbial fatty alcohol production. The primary focus is on work performed in the model microorganisms, Escherichia coli and Saccharomyces cerevisiae but advances made with cyanobacteria and oleaginous yeasts are also considered. The limitations to production of fatty alcohols by microbial cell factories are detailed along with consideration to potential research directions that may aid in achieving viable commercial scale production of fatty alcohols from renewable feedstock.
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Affiliation(s)
- Anagha Krishnan
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Bonnie A McNeil
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - David T Stuart
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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10
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Foo JL, Rasouliha BH, Susanto AV, Leong SSJ, Chang MW. Engineering an Alcohol-Forming Fatty Acyl-CoA Reductase for Aldehyde and Hydrocarbon Biosynthesis in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2020; 8:585935. [PMID: 33123518 PMCID: PMC7573125 DOI: 10.3389/fbioe.2020.585935] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/08/2020] [Indexed: 11/19/2022] Open
Abstract
Aldehydes are a class of highly versatile chemicals that can undergo a wide range of chemical reactions and are in high demand as starting materials for chemical manufacturing. Biologically, fatty aldehydes can be produced from fatty acyl-CoA by the action of fatty acyl-CoA reductases. The aldehydes produced can be further converted enzymatically to other valuable derivatives. Thus, metabolic engineering of microorganisms for biosynthesizing aldehydes and their derivatives could provide an economical and sustainable platform for key aldehyde precursor production and subsequent conversion to various value-added chemicals. Saccharomyces cerevisiae is an excellent host for this purpose because it is a robust organism that has been used extensively for industrial biochemical production. However, fatty acyl-CoA-dependent aldehyde-forming enzymes expressed in S. cerevisiae thus far have extremely low activities, hence limiting direct utilization of fatty acyl-CoA as substrate for aldehyde biosynthesis. Toward overcoming this challenge, we successfully engineered an alcohol-forming fatty acyl-CoA reductase for aldehyde production through rational design. We further improved aldehyde production through strain engineering by deleting competing pathways and increasing substrate availability. Subsequently, we demonstrated alkane and alkene production as one of the many possible applications of the aldehyde-producing strain. Overall, by protein engineering of a fatty acyl-CoA reductase to alter its activity and metabolic engineering of S. cerevisiae, we generated strains with the highest reported cytosolic aliphatic aldehyde and alkane/alkene production to date in S. cerevisiae from fatty acyl-CoA.
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Affiliation(s)
- Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Bahareh Haji Rasouliha
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Adelia Vicanatalita Susanto
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Susanna Su Jan Leong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.,Singapore Institute of Technology, Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
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11
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Cho IJ, Choi KR, Lee SY. Microbial production of fatty acids and derivative chemicals. Curr Opin Biotechnol 2020; 65:129-141. [DOI: 10.1016/j.copbio.2020.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 12/11/2022]
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12
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Zhou S, Hao T, Xu S, Deng Y. Coenzyme A thioester-mediated carbon chain elongation as a paintbrush to draw colorful chemical compounds. Biotechnol Adv 2020; 43:107575. [PMID: 32512221 DOI: 10.1016/j.biotechadv.2020.107575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
The biosynthesis of various useful chemicals from simple substrates using industrial microorganisms is becoming increasingly crucial to address the challenge of dwindling non-renewable resources. As the most common intermediate substrates in organisms, Coenzyme A (CoA) thioesters play a central role in the carbon chain elongation process of their products. As a result, numerous of chemicals can be synthesized by the iterative addition of various CoA thioester extender units at a given CoA thioester primer backbone. However, these elongation reactions and the product yields are still restricted due to the low enzymatic performance and supply of CoA thioesters. This review highlights the current protein and metabolic engineering strategies used to enhance the diversity and product yield by coupling different primers, extender units, enzymes, and termination pathways, in an attempt to provide a road map for producing a more diverse range of industrial chemicals.
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Affiliation(s)
- Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Tingting Hao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shumin Xu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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13
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Ferreira R, Skrekas C, Hedin A, Sánchez BJ, Siewers V, Nielsen J, David F. Model-Assisted Fine-Tuning of Central Carbon Metabolism in Yeast through dCas9-Based Regulation. ACS Synth Biol 2019; 8:2457-2463. [PMID: 31577419 DOI: 10.1021/acssynbio.9b00258] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Engineering Saccharomyces cerevisiae for industrial-scale production of valuable chemicals involves extensive modulation of its metabolism. Here, we identified novel gene expression fine-tuning set-ups to enhance endogenous metabolic fluxes toward increasing levels of acetyl-CoA and malonyl-CoA. dCas9-based transcriptional regulation was combined together with a malonyl-CoA responsive intracellular biosensor to select for beneficial set-ups. The candidate genes for screening were predicted using a genome-scale metabolic model, and a gRNA library targeting a total of 168 selected genes was designed. After multiple rounds of fluorescence-activated cell sorting and library sequencing, the gRNAs that were functional and increased flux toward malonyl-CoA were assessed for their efficiency to enhance 3-hydroxypropionic acid (3-HP) production. 3-HP production was significantly improved upon fine-tuning genes involved in providing malonyl-CoA precursors, cofactor supply, as well as chromatin remodeling.
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Affiliation(s)
- Raphael Ferreira
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
- Novo Nordisk Foundation Center for Biosustainability , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
| | - Christos Skrekas
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
- Novo Nordisk Foundation Center for Biosustainability , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
| | - Alex Hedin
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
| | - Benjamín J Sánchez
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
- Novo Nordisk Foundation Center for Biosustainability , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
- Novo Nordisk Foundation Center for Biosustainability , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
- Novo Nordisk Foundation Center for Biosustainability , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
- Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , DK2800 Kgs . Lyngby , Denmark
| | - Florian David
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
- Novo Nordisk Foundation Center for Biosustainability , Chalmers University of Technology , SE412 96 Gothenburg , Sweden
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14
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Dabirian Y, Gonçalves Teixeira P, Nielsen J, Siewers V, David F. FadR-Based Biosensor-Assisted Screening for Genes Enhancing Fatty Acyl-CoA Pools in Saccharomyces cerevisiae. ACS Synth Biol 2019; 8:1788-1800. [PMID: 31314504 DOI: 10.1021/acssynbio.9b00118] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fatty acid-derived compounds have a range of industrial applications, from chemical building blocks to biofuels. Due to the highly dynamic nature of fatty acid metabolism, it is difficult to identify genes modulating fatty acyl-CoA levels using a rational approach. Metabolite biosensors can be used to screen genes from large-scale libraries in vivo in a high throughput manner. Here, a fatty acyl-CoA sensor based on the transcription factor FadR from Escherichia coli was established in Saccharomyces cerevisiae and combined with a gene overexpression library to screen for genes increasing the fatty acyl-CoA pool. Fluorescence-activated cell sorting, followed by data analysis, identified genes enhancing acyl-CoA levels. From these, overexpression of RTC3, GGA2, and LPP1 resulted in about 80% increased fatty alcohol levels. Changes in fatty acid saturation and chain length distribution could also be observed. These results indicate that the use of this acyl-CoA biosensor combined with a gene overexpression library allows for identification of gene targets improving production of fatty acids and derived products.
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Affiliation(s)
- Yasaman Dabirian
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Paulo Gonçalves Teixeira
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Florian David
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Biopetrolia AB, Kemivägen 10, 41258 Gothenburg, Sweden
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15
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High production of fatty alcohols in Yarrowia lipolytica by coordination with glycolysis. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9456-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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Lian J, Mishra S, Zhao H. Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications. Metab Eng 2018; 50:85-108. [DOI: 10.1016/j.ymben.2018.04.011] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
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17
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Martins-Santana L, Nora LC, Sanches-Medeiros A, Lovate GL, Cassiano MHA, Silva-Rocha R. Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production. Front Bioeng Biotechnol 2018; 6:117. [PMID: 30338257 PMCID: PMC6178918 DOI: 10.3389/fbioe.2018.00117] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/02/2018] [Indexed: 01/16/2023] Open
Abstract
Since the advent of systems and synthetic biology, many studies have sought to harness microbes as cell factories through genetic and metabolic engineering approaches. Yeast and filamentous fungi have been successfully harnessed to produce fine and high value-added chemical products. In this review, we present some of the most promising advances from recent years in the use of fungi for this purpose, focusing on the manipulation of fungal strains using systems and synthetic biology tools to improve metabolic flow and the flow of secondary metabolites by pathway redesign. We also review the roles of bioinformatics analysis and predictions in synthetic circuits, highlighting in silico systemic approaches to improve the efficiency of synthetic modules.
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Affiliation(s)
- Leonardo Martins-Santana
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Luisa C Nora
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Ananda Sanches-Medeiros
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Gabriel L Lovate
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Murilo H A Cassiano
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
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18
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Santala S, Efimova E, Santala V. Dynamic decoupling of biomass and wax ester biosynthesis in Acinetobacter baylyi by an autonomously regulated switch. Metab Eng Commun 2018; 7:e00078. [PMID: 30271720 PMCID: PMC6158957 DOI: 10.1016/j.mec.2018.e00078] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/13/2018] [Accepted: 09/16/2018] [Indexed: 01/09/2023] Open
Abstract
For improving the microbial production of fuels and chemicals, gene knock-outs and overexpression are routinely applied to intensify the carbon flow from substrate to product. However, their possibilities in dynamic control of the flux between the biomass and product synthesis are limited, whereas dynamic metabolic switches can be used for optimizing the distribution of carbon and resources. The production of single cell oils is especially challenging, as the synthesis is strictly regulated, competes directly with biomass, and requires defined conditions, such as nitrogen limitation. Here, we engineered a metabolic switch for redirecting carbon flow from biomass to wax ester production in Acinetobacter baylyi ADP1 using acetate as a carbon source. Isocitrate lyase, an essential enzyme for growth on acetate, was expressed under an arabinose inducible promoter. The autonomous downregulation of the expression is based on the gradual oxidation of the arabinose inducer by a glucose dehydrogenase gcd. The depletion of the inducer, occurring simultaneously to acetate consumption, switches the cells from a biomass mode to a lipid synthesis mode, enabling the efficient channelling of carbon to wax esters in a simple batch culture. In the engineered strain, the yield and titer of wax esters were improved by 3.8 and 3.1 folds, respectively, over the control strain. In addition, the engineered strain accumulated wax esters 19% of cell dry weight, being the highest reported among microbes. The study provides important insights into the dynamic engineering of the biomass-dependent synthesis pathways for the improved production of biocompounds from low-cost and sustainable substrates. Efficient conversion of acetate to storage lipids (wax ester) is demonstrated. AraC-pBAD promoter coupled with glucose dehydrogenase was used as a dynamic switch. The autonomous switch allowed dynamic shift from biomass to lipid synthesis mode. Wax ester yield and titer were improved by 3–4 folds over the wild type strain. The highest amount of wax esters produced in microbes, 19% of CDW, was achieved.
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Affiliation(s)
- Suvi Santala
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, FI-33720, Tampere, Finland
| | - Elena Efimova
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, FI-33720, Tampere, Finland
| | - Ville Santala
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, FI-33720, Tampere, Finland
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19
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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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20
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Zhang Y, Nielsen J, Liu Z. Metabolic engineering ofSaccharomyces cerevisiaefor production of fatty acid–derived hydrocarbons. Biotechnol Bioeng 2018; 115:2139-2147. [DOI: 10.1002/bit.26738] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/23/2018] [Accepted: 05/31/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Yiming Zhang
- Beijing Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Beijing China
| | - Jens Nielsen
- Beijing Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Beijing China
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburg Sweden
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Hørsholm Denmark
| | - Zihe Liu
- Beijing Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Beijing China
- College of Life Science and Technology, Beijing University of Chemical TechnologyBeijing China
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21
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Ferreira R, Teixeira PG, Siewers V, Nielsen J. Redirection of lipid flux toward phospholipids in yeast increases fatty acid turnover and secretion. Proc Natl Acad Sci U S A 2018; 115:1262-1267. [PMID: 29358378 PMCID: PMC5819412 DOI: 10.1073/pnas.1715282115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bio-based production of fatty acids and fatty acid-derived products can enable sustainable substitution of petroleum-derived fuels and chemicals. However, developing new microbial cell factories for producing high levels of fatty acids requires extensive engineering of lipid metabolism, a complex and tightly regulated metabolic network. Here we generated a Saccharomyces cerevisiae platform strain with a simplified lipid metabolism network with high-level production of free fatty acids (FFAs) due to redirected fatty acid metabolism and reduced feedback regulation. Deletion of the main fatty acid activation genes (the first step in β-oxidation), main storage lipid formation genes, and phosphatidate phosphatase genes resulted in a constrained lipid metabolic network in which fatty acid flux was directed to a large extent toward phospholipids. This resulted in simultaneous increases of phospholipids by up to 2.8-fold and of FFAs by up to 40-fold compared with wild-type levels. Further deletion of phospholipase genes PLB1 and PLB2 resulted in a 46% decrease in FFA levels and 105% increase in phospholipid levels, suggesting that phospholipid hydrolysis plays an important role in FFA production when phospholipid levels are increased. The multiple deletion mutant generated allowed for a study of fatty acid dynamics in lipid metabolism and represents a platform strain with interesting properties that provide insight into the future development of lipid-related cell factories.
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Affiliation(s)
- Raphael Ferreira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Paulo Gonçalves Teixeira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden;
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kongens Lyngby, Denmark
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22
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Ferreira R, Teixeira PG, Gossing M, David F, Siewers V, Nielsen J. Metabolic engineering of Saccharomyces cerevisiae for overproduction of triacylglycerols. Metab Eng Commun 2018; 6:22-27. [PMID: 29896445 PMCID: PMC5994799 DOI: 10.1016/j.meteno.2018.01.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/05/2018] [Accepted: 01/23/2018] [Indexed: 11/08/2022] Open
Abstract
Triacylglycerols (TAGs) are valuable versatile compounds that can be used as metabolites for nutrition and health, as well as feedstocks for biofuel production. Although Saccharomyces cerevisiae is the favored microbial cell factory for industrial production of biochemicals, it does not produce large amounts of lipids and TAGs comprise only ~1% of its cell dry weight. Here, we engineered S. cerevisiae to reorient its metabolism for overproduction of TAGs, by regulating lipid droplet associated-proteins involved in TAG synthesis and hydrolysis. We implemented a push-and-pull strategy by overexpressing genes encoding a deregulated acetyl-CoA carboxylase, ACC1S659A/S1157A(ACC1**), as well as the last two steps of TAG formation: phosphatidic phosphatase (PAH1) and diacylglycerol acyltransferase (DGA1), ultimately leading to 129 mg∙gCDW−1 of TAGs. Disruption of TAG lipase genes TGL3, TGL4, TGL5 and sterol acyltransferase gene ARE1 increased the TAG content to 218 mg∙gCDW−1. Further disruption of the beta-oxidation by deletion of POX1, as well as glycerol-3-phosphate utilization through deletion of GUT2, did not affect TAGs levels. Finally, disruption of the peroxisomal fatty acyl-CoA transporter PXA1 led to accumulation of 254 mg∙gCDW−1. The TAG levels achieved here are the highest titer reported in S. cerevisiae, reaching 27.4% of the maximum theoretical yield in minimal medium with 2% glucose. This work shows the potential of using an industrially established and robust yeast species for high level lipid production. Saccharomyces cerevisiae was engineered towards triacylglycerol (TAG) accumulation. Overexpression of TAG biosynthesis genes, and deletion of degradation pathways were targeted. Final strain reached 254 mg/gCDW TAG on 2% glucose media, achieving 27.4% of the maximum theoretical yield.
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Affiliation(s)
- Raphael Ferreira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Paulo Gonçalves Teixeira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Michael Gossing
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Florian David
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kgs Lyngby, Denmark
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23
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Engineering microbial fatty acid metabolism for biofuels and biochemicals. Curr Opin Biotechnol 2017; 50:39-46. [PMID: 29101852 DOI: 10.1016/j.copbio.2017.10.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 11/22/2022]
Abstract
Traditional oleochemical industry chemically processes animal fats and plant oils to produce detergents, lubricants, biodiesel, plastics, coatings, and other products. Biotechnology offers an alternative process, where the same oleochemicals can be produced from abundant biomass feedstocks using microbial catalysis. This review summarizes the recent advances in the engineering of microbial metabolism for production of fatty acid-derived products. We highlight the efforts in engineering the central carbon metabolism, redox metabolism, controlling the chain length of the products, and obtaining metabolites with different functionalities. The prospects of commercializing microbial oleochemicals are also discussed.
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24
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Tan SZ, Prather KL. Dynamic pathway regulation: recent advances and methods of construction. Curr Opin Chem Biol 2017; 41:28-35. [PMID: 29059607 DOI: 10.1016/j.cbpa.2017.10.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 12/26/2022]
Abstract
Microbial cell factories are a renewable source for the production of biofuels and valuable chemicals. Dynamic pathway regulation has proved successful in improving production of molecules by balancing flux between growth of cells and production of metabolites. Systems for autonomous induction of pathway regulation are increasingly being developed, which include metabolite responsive promoters, biosensors, and quorum sensing systems. Since engineering such systems are dependent on the available methods for controlling protein abundance in the desired host, we review recent tools used for gene repression at the transcriptional, post-transcriptional and post-translational levels in Escherichia coli and Saccharomyces cerevisiae. These approaches may facilitate pathway engineering for biofuel and biochemical production.
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Affiliation(s)
- Sue Zanne Tan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kristala Lj Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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25
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Ferreira R, Gatto F, Nielsen J. Exploiting off-targeting in guide-RNAs for CRISPR systems for simultaneous editing of multiple genes. FEBS Lett 2017; 591:3288-3295. [PMID: 28884816 DOI: 10.1002/1873-3468.12835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/21/2017] [Accepted: 08/31/2017] [Indexed: 12/26/2022]
Abstract
Bioinformatics tools to design guide-RNAs (gRNAs) in Clustered Regularly Interspaced Short Palindromic Repeats systems mostly focused on minimizing off-targeting to enhance efficacy of genome editing. However, there are circumstances in which off-targeting might be desirable to target multiple genes simultaneously with a single gRNA. We termed these gRNAs as promiscuous gRNAs. Here, we present a computational workflow to identify promiscuous gRNAs that putatively bind to the region of interest for a defined list of genes in a genome. We experimentally validated two promiscuous gRNA for gene deletion, one targeting FAA1 and FAA4 and one targeting PLB1 and PLB2, thus demonstrating that multiplexed genome editing through design of promiscuous gRNA can be performed in a time and cost-effective manner.
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Affiliation(s)
- Raphael Ferreira
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Francesco Gatto
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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26
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Fernandez-Moya R, Da Silva NA. Engineering Saccharomyces cerevisiae for high-level synthesis of fatty acids and derived products. FEMS Yeast Res 2017; 17:4111148. [DOI: 10.1093/femsyr/fox071] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/10/2017] [Indexed: 01/16/2023] Open
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27
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Retooling microorganisms for the fermentative production of alcohols. Curr Opin Biotechnol 2017; 50:1-10. [PMID: 28888164 DOI: 10.1016/j.copbio.2017.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/31/2022]
Abstract
Bioengineering and synthetic biology approaches have revolutionised the field of biotechnology, enabling the introduction of non-native and de novo pathways for biofuels production. This 'retooling' of microorganisms is also applied to the utilisation of mixed carbon components derived from lignocellulosic biomass, a major technical barrier for the development of economically viable fermentations. This review will discuss recent advances in microorganism engineering for efficient production of alcohols from waste biomass. These advances span the introduction of new pathways to alcohols, host modifications for more cost-effective utilisation of lignocellulosic waste and modifications of existing pathways for generating new fuel additives.
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28
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Combinatorial Engineering of Yarrowia lipolytica as a Promising Cell Biorefinery Platform for the de novo Production of Multi-Purpose Long Chain Dicarboxylic Acids. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3030040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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