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Xu W, Liu M, Li H, Chen J, Zhou J. De Novo Synthesis of Chrysin in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6481-6490. [PMID: 38481145 DOI: 10.1021/acs.jafc.3c09820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Chrysin, a flavonoid, has been found to have been widely used in the health food field. But at present, chrysin production is hindered by the low availability of precursors and the lack of catalytic enzymes with high activity. Therefore, ZmPAL was initially screened to synthesize trans-cinnamic acid with high catalytic activity and specificity. To enhance the supply of precursors, the shikimic acid and chorismic acid pathway genes were overexpressed. Besides, the expression of the intracellular and mitochondrial carbon metabolism genes CIT, MAC1/3, CTP1, YHM2, RtME, and MDH was enhanced to increase the intracellular acetyl-CoA content. Chrysin was synthesized through a novel gene combination of ScCPR-EbFNSI-1 and PcFNSI. Finally, de novo synthesis of chrysin was achieved, reaching 41.9 mg/L, which is the highest reported concentration to date. In summary, we identified efficient enzymes for chrysin production and increased it by regulating acetyl-CoA metabolism in mitochondria and the cytoplasm, laying a foundation for future large-scale production.
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Affiliation(s)
- Weiqi Xu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Mengsu Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Hongbiao Li
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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2
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Marx R, Liu H, Yoon S, Xie D. CFD evaluation of hydrophobic feedstock bench-scale fermenters for efficient high agitation volumetric mass transfer. Biotechnol J 2024; 19:e2300384. [PMID: 38403465 DOI: 10.1002/biot.202300384] [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: 08/01/2023] [Revised: 12/08/2023] [Accepted: 01/02/2024] [Indexed: 02/27/2024]
Abstract
A new biomanufacturing platform combining intracellular metabolic engineering of the oleaginous yeast Yarrowia lipolytica and extracellular bioreaction engineering provides efficient bioconversion of plant oils/animal fats into high-value products. However, predicting the hydrodynamics and mass transfer parameters is difficult due to the high agitation and sparging required to create dispersed oil droplets in an aqueous medium for efficient yeast fermentation. In the current study, commercial computational fluid dynamic (CFD) solver Ansys CFX coupled with the MUSIG model first predicts two-phase system (oil/water and air/water) mixing dynamics and their particle size distributions. Then, a three-phase model (oil, air, and water) utilizing dispersed air bubbles and a polydispersed oil phase was implemented to explore fermenter mixing, gas dispersion efficiency, and volumetric mass transfer coefficient estimations (kL a). The study analyzed the effect of the impeller type, agitation speed, and power input on the tank's flow field and revealed that upward-pumping pitched blade impellers (PBI) in the top two positions (compared to Rushton-type) provided advantageous oil phase homogeneity and similar estimated kL a values with reduced power. These results show good agreement with the experimental mixing and kL a data.
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Affiliation(s)
- Richard Marx
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Huolong Liu
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
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3
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Darvishi F, Rafatiyan S, Abbaspour Motlagh Moghaddam MH, Atkinson E, Ledesma-Amaro R. Applications of synthetic yeast consortia for the production of native and non-native chemicals. Crit Rev Biotechnol 2024; 44:15-30. [PMID: 36130800 DOI: 10.1080/07388551.2022.2118569] [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: 06/03/2022] [Revised: 08/03/2022] [Accepted: 08/19/2022] [Indexed: 11/03/2022]
Abstract
The application of microbial consortia is a new approach in synthetic biology. Synthetic yeast consortia, simple or complex synthetic mixed cultures, have been used for the production of various metabolites. Cooperation between the members of a consortium and cross-feeding can be applied to create stable microbial communication. These consortia can: consume a variety of substrates, perform more complex functions, produce metabolites in high titer, rate, and yield (TRY), and show higher stability during industrial fermentations. Due to the new research context of synthetic consortia, few yeasts were used to build these consortia, including Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica. Here, application of the yeasts for design of synthetic microbial consortia and their advantages and bottlenecks for effective and robust production of valuable metabolites from bioresource, including: cellulose, xylose, glycerol and so on, have been reviewed. Key trends and challenges are also discussed for the future development of synthetic yeast consortia.
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Affiliation(s)
- Farshad Darvishi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
- Research Center for Applied Microbiology and Microbial Biotechnology (CAMB), Alzahra University, Tehran, Iran
| | - Sajad Rafatiyan
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | | | - Eliza Atkinson
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
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4
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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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5
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Ramesh A, Lee S, Wheeldon I. Genome Editing, Transcriptional Regulation, and Forward Genetic Screening Using CRISPR-Cas12a Systems in Yarrowia lipolytica. Methods Mol Biol 2024; 2760:169-198. [PMID: 38468089 DOI: 10.1007/978-1-0716-3658-9_11] [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] [Indexed: 03/13/2024]
Abstract
Class II Type V endonucleases have increasingly been adapted to develop sophisticated and easily accessible synthetic biology tools for genome editing, transcriptional regulation, and functional genomic screening in a wide range of organisms. One such endonuclease, Cas12a, presents itself as an attractive alternative to Cas9-based systems. The ability to mature its own guide RNAs (gRNAs) from a single transcript has been leveraged for easy multiplexing, and its lack of requirement of a tracrRNA element, also allows for short gRNA expression cassettes. To extend these functionalities into the industrially relevant oleaginous yeast Yarrowia lipolytica, we developed a set of CRISPR-Cas12a vectors for easy multiplexed gene knockout, repression, and activation. We further extended the utility of this CRISPR-Cas12a system to functional genomic screening by constructing a genome-wide guide library targeting every gene with an eightfold coverage. Pooled CRISPR screens conducted with this library were used to profile Cas12a guide activities and develop a machine learning algorithm that could accurately predict highly efficient Cas12a gRNA. In this protocols chapter, we first present a method by which protein coding genes may be functionally disrupted via indel formation with CRISPR-Cas12a systems. Further, we describe how Cas12a fused to a transcriptional regulator can be used in conjunction with shortened gRNA to achieve transcriptional repression or activation. Finally, we describe the design, cloning, and validation of a genome-wide library as well as a protocol for the execution of a pooled CRISPR screen, to determine guide activity profiles in a genome-wide context in Y. lipolytica. The tools and strategies discussed here expand the list of available synthetic biology tools for facile genome engineering in this industrially important host.
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Affiliation(s)
- Adithya Ramesh
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Sangcheon Lee
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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Valle-Rodríguez JO, Siewers V, Nielsen J, Shi S. Directed evolution of a wax ester synthase for production of fatty acid ethyl esters in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2023; 107:2921-2932. [PMID: 36976306 DOI: 10.1007/s00253-023-12466-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023]
Abstract
Wax ester synthases (WSs) utilize a fatty alcohol and a fatty acyl-coenzyme A (activated fatty acid) to synthesize the corresponding wax ester. There is much interest in developing novel cell factories that can produce shorter esters, e.g., fatty acid ethyl esters (FAEEs), with properties similar to biodiesel in order to use these as transportation fuels. However, ethanol is a poor substrate for WSs, and this may limit the biosynthesis of FAEEs. Here, we implemented a random mutagenesis approach to enhance the catalytic efficiency of a WS from Marinobacter hydrocarbonoclasticus (MhWS2, encoded by the ws2 gene). Our selection system was based on FAEE formation serving as a detoxification mechanism for excessive oleate, where high WS activity was essential for a storage-lipid free yeast to survive. A random mutagenesis library of ws2 was used to transform the storage-lipid free yeast, and mutants could be selected by plating the transformants on oleate containing plates. The variants encoding WS with improved activity were sequenced, and an identified point mutation translated into the residue substitution at position A344 was discovered to substantially increase the selectivity of MhWS2 toward ethanol and other shorter alcohols. Structural modeling indicated that an A344T substitution might affect the alcohol selectivity due to change of both steric effects and polarity changes near the active site. This work not only provides a new WS variant with altered selectivity to shorter alcohols but also presents a new high-throughput selection system to isolate WSs with a desired selectivity. KEY POINTS: • The work provides WS variants with altered substrate preference for shorter alcohols • A novel method was developed for directed evolution of WS of desired selectivity.
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Affiliation(s)
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark.
| | - Shuobo Shi
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Using oils and fats to replace sugars as feedstocks for biomanufacturing: Challenges and opportunities for the yeast Yarrowia lipolytica. Biotechnol Adv 2023; 65:108128. [PMID: 36921878 DOI: 10.1016/j.biotechadv.2023.108128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023]
Abstract
More than 200 million tons of plant oils and animal fats are produced annually worldwide from oil, crops, and the rendered animal fat industry. Triacylglycerol, an abundant energy-dense compound, is the major form of lipid in oils and fats. While oils or fats are very important raw materials and functional ingredients for food or related products, a significant portion is currently diverted to or recovered as waste. To significantly increase the value of waste oils or fats and expand their applications with a minimal environmental footprint, microbial biomanufacturing is presented as an effective strategy for adding value. Though both bacteria and yeast can be engineered to use oils or fats as the biomanufacturing feedstocks, the yeast Yarrowia lipolytica is presented as one of the most attractive platforms. Y. lipolytica is oleaginous, generally regarded as safe, demonstrated as a promising industrial producer, and has unique capabilities for efficient catabolism and bioconversion of lipid substrates. This review summarizes the major challenges and opportunities for Y. lipolytica as a new biomanufacturing platform for the production of value-added products from oils and fats. This review also discusses relevant cellular and metabolic engineering strategies such as fatty acid transport, fatty acid catabolism and bioconversion, redox balances and energy yield, cell morphology and stress response, and bioreaction engineering. Finally, this review highlights specific product classes including long-chain diacids, wax esters, terpenes, and carotenoids with unique synthesis opportunities from oils and fats in Y. lipolytica.
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Ploessl D, Zhao Y, Shao Z. Engineering of non-model eukaryotes for bioenergy and biochemical production. Curr Opin Biotechnol 2023; 79:102869. [PMID: 36584447 DOI: 10.1016/j.copbio.2022.102869] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/14/2022] [Accepted: 11/23/2022] [Indexed: 12/29/2022]
Abstract
The prospect of leveraging naturally occurring phenotypes to overcome bottlenecks constraining the bioeconomy has marshalled increased exploration of nonconventional organisms. This review discusses the status of non-model eukaryotic species in bioproduction, the evaluation criteria for effectively matching a candidate host to a biosynthetic process, and the genetic engineering tools needed for host domestication. We present breakthroughs in genome editing and heterologous pathway design, delving into innovative spatiotemporal modulation strategies that potentiate more refined engineering capabilities. We cover current understanding of genetic instability and its ramifications for industrial scale-up, highlighting key factors and possible remedies. Finally, we propose future opportunities to expand the current collection of available hosts and provide guidance to benefit the broader bioeconomy.
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Affiliation(s)
- Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA; NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Yuxin Zhao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA; NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA; NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Interdepartmental Microbiology Program, Iowa State University, Ames, IA, USA; Bioeconomy Institute, Iowa State University, Ames, IA, USA; The Ames Laboratory, Ames, IA, USA.
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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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Guo Q, Peng QQ, Chen YY, Song P, Ji XJ, Huang H, Shi TQ. High-yield α-humulene production in Yarrowia lipolytica from waste cooking oil based on transcriptome analysis and metabolic engineering. Microb Cell Fact 2022; 21:271. [PMID: 36566177 DOI: 10.1186/s12934-022-01986-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/08/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND α-Humulene is an important biologically active sesquiterpene, whose heterologous production in microorganisms is a promising alternative biotechnological process to plant extraction and chemical synthesis. In addition, the reduction of production expenses is also an extremely critical factor in the sustainable and industrial production of α-humulene. In order to meet the requirements of industrialization, finding renewable substitute feedstocks such as low cost or waste substrates for terpenoids production remains an area of active research. RESULTS In this study, we investigated the feasibility of peroxisome-engineering strain to utilize waste cooking oil (WCO) for high production of α-humulene while reducing the cost. Subsequently, transcriptome analysis revealed differences in gene expression levels with different carbon sources. The results showed that single or combination regulations of target genes identified by transcriptome were effective to enhance the α-humulene titer. Finally, the engineered strain could produce 5.9 g/L α-humulene in a 5-L bioreactor. CONCLUSION To the best of our knowledge, this is the first report that converted WCO to α-humulene in peroxisome-engineering strain. These findings provide valuable insights into the high-level production of α-humulene in Y. lipolytica and its utilization in WCO bioconversion.
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Affiliation(s)
- Qi Guo
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Qian-Qian Peng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210046, People's Republic of China
| | - Ying-Ying Chen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210046, People's Republic of China
| | - Ping Song
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210046, People's Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - He Huang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China. .,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210046, People's Republic of China. .,College of Pharmaceutical Sciences, 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, 2 Xuelin Road, Qixia District, Nanjing, 210046, People's Republic of China.
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11
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Xie D. Continuous biomanufacturing with microbes - upstream progresses and challenges. Curr Opin Biotechnol 2022; 78:102793. [PMID: 36088736 DOI: 10.1016/j.copbio.2022.102793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/15/2022] [Accepted: 08/07/2022] [Indexed: 12/14/2022]
Abstract
Current biomanufacturing facilities are mainly built for batch or fed-batch operations, which are subject to low productivities and do not achieve the great bioconversion potential of the rewired cells generated via modern biotechnology. Continuous biomanufacturing should be the future directions for high-yield and low-cost manufacturing of various fermentation products. This review discusses the major challenges and the strategies for continuous biomanufacturing with microbes, which include minimizing contamination risk, enhancing genetic stability over a long-term continuous operation, achieving high product titer, rate, and yield simultaneously by decoupling cell growth from product formation, and using modeling approach to accelerate research and development of continuous biomanufacturing. New strain designs and process engineering strategies, including integration with artificial intelligence, are also discussed for intelligent and the next generation of continuous biomanufacturing.
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Affiliation(s)
- Dongming Xie
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States.
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12
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New roles for Yarrowia lipolytica in molecules synthesis and biocontrol. Appl Microbiol Biotechnol 2022; 106:7397-7416. [PMID: 36241927 DOI: 10.1007/s00253-022-12227-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/02/2022]
Abstract
Reprogramming of host metabolism is a common strategy for improving desired compounds in host cells and is essential to generate overproducing strains in biotechnology. As a promising feedstock converter, Yarrowia lipolytica has been engineered to extend its bioproduction ability related to the synthesis of new value-added molecules relevant to human food and disease treatment. New synthetic tools have been reported and new enzymes with biotechnological importance are recovered. Additionally, metabolic events occurring during substrate utilization and recombinant protein production have been elucidated. Its contributions as feed and in controlling disease in the food industry have also been provided. Likewise, the recent abilities of Yarrowia lipolytica in the bioconversion of food waste into single-cell protein have been reported. These aforementioned events made the novelty of this review compared to the existing ones on this oleaginous yeast. KEY POINTS: • The production of biolipids by the heterotrophic yeast Yarrowia lipolytica is examined. • A Summary of information concerning new value-added molecules has been highlighted. • Special focus on the importance of Yarrowia lipolytica in regulating the immune system has been provided.
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Vollheyde K, Kühnel K, Lambrecht F, Kawelke S, Herrfurth C, Feussner I. Crystal Structure of the Bifunctional Wax Synthase 1 from Acinetobacter baylyi Suggests a Conformational Change upon Substrate Binding and Formation of Additional Substrate Binding Sites. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katharina Vollheyde
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077 Goettingen, Germany
| | - Karin Kühnel
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany
| | - Felix Lambrecht
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077 Goettingen, Germany
| | - Steffen Kawelke
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077 Goettingen, Germany
| | - Cornelia Herrfurth
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077 Goettingen, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, D-37077 Goettingen, Germany
| | - Ivo Feussner
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077 Goettingen, Germany
- Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, D-37077 Goettingen, Germany
- International Center for Advanced Studies of Energy Conversion (ICASEC), University of Goettingen, D-37077 Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, D-37077 Goettingen, Germany
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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15
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Demski K, Ding BJ, Wang HL, Tran TNT, Durrett TP, Lager I, Löfstedt C, Hofvander P. Manufacturing specialized wax esters in plants. Metab Eng 2022; 72:391-402. [PMID: 35598886 DOI: 10.1016/j.ymben.2022.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/07/2022] [Accepted: 05/15/2022] [Indexed: 01/11/2023]
Abstract
Biologically produced wax esters can fulfil different industrial purposes. These functionalities almost drove the sperm whale to extinction from hunting. After the ban on hunting, there is a niche in the global market for biolubricants with properties similar to spermaceti. Wax esters can also serve as a mechanism for producing insect sex pheromone fatty alcohols. Pheromone-based mating disruption strategies are in high demand to replace the toxic pesticides in agriculture and manage insect plagues threatening our food and fiber reserves. In this study we set out to investigate the possibilities of in planta assembly of wax esters, for specific applications, through transient expression of various mix-and-match combinations of genes in Nicotiana benthamiana leaves. Our synthetic biology designs were outlined in order to pivot plant lipid metabolism into producing wax esters with targeted fatty acyl and fatty alcohols moieties. Through this approach we managed to obtain industrially important spermaceti-like wax esters enriched in medium-chain fatty acyl and/or fatty alcohol moieties of wax esters. Via employment of plant codon-optimized moth acyl-CoA desaturases we also managed to capture unusual, unsaturated fatty alcohol and fatty acyl moieties, structurally similar to moth pheromone compounds, in plant-accumulated wax esters. Comparison between outcomes of different experimental designs identified targets for stable transformation to accumulate specialized wax esters and helped us to recognize possible bottlenecks of such accumulation.
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Affiliation(s)
- Kamil Demski
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden.
| | - Bao-Jian Ding
- Department of Biology, Lund University, 22362, Lund, Sweden
| | - Hong-Lei Wang
- Department of Biology, Lund University, 22362, Lund, Sweden
| | - Tam N T Tran
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Timothy P Durrett
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Ida Lager
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | | | - Per Hofvander
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden.
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Wang J, Singer SD, Souto BA, Asomaning J, Ullah A, Bressler DC, Chen G. Current progress in lipid-based biofuels: Feedstocks and production technologies. BIORESOURCE TECHNOLOGY 2022; 351:127020. [PMID: 35307524 DOI: 10.1016/j.biortech.2022.127020] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
The expanding use of fossil fuels has caused concern in terms of both energy security and environmental issues. Therefore, attempts have been made worldwide to promote the development of renewable energy sources, among which biofuel is especially attractive. Compared to other biofuels, lipid-derived biofuels have a higher energy density and better compatibility with existing infrastructure, and their performance can be readily improved by adjusting the chemical composition of lipid feedstocks. This review thus addresses the intrinsic interactions between lipid feedstocks and lipid-based biofuels, including biodiesel, and renewable equivalents to conventional gasoline, diesel, and jet fuel. Advancements in lipid-associated biofuel technology, as well as the properties and applicability of various lipid sources in terms of biofuel production, are also discussed. Furthermore, current progress in lipid production and profile optimization in the context of plant lipids, microbial lipids, and animal fats are presented to provide a wider context of lipid-based biofuel technology.
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Affiliation(s)
- Juli Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Stacy D Singer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Bernardo A Souto
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Justice Asomaning
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Aman Ullah
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - David C Bressler
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada.
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Zhang Y, Guo X, Yang H, Shi S. The Studies in Constructing Yeast Cell Factories for the Production of Fatty Acid Alkyl Esters. Front Bioeng Biotechnol 2022; 9:799032. [PMID: 35087801 PMCID: PMC8787340 DOI: 10.3389/fbioe.2021.799032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/19/2021] [Indexed: 12/25/2022] Open
Abstract
Fatty acid alkyl esters have broad applications in biofuels, lubricant formulas, paints, coatings, and cosmetics. Traditionally, these esters are mostly produced through unsustainable and energy-intensive processes. In contrast, microbial production of esters from renewable and sustainable feedstocks may provide a promising alternative and has attracted widespread attention in recent years. At present, yeasts are used as ideal hosts for producing such esters, due to their availability for high-density fermentation, resistance to phage infection, and tolerance against toxic inhibitors. Here, we summarize recent development on the biosynthesis of alkyl esters, including fatty acid ethyl esters (FAEEs), fatty acid short-branched chain alkyl esters (FASBEs), and wax esters (WEs) by various yeast cell factories. We focus mainly on the enzyme engineering strategies of critical wax ester synthases, and the pathway engineering strategies employed for the biosynthesis of various ester products. The bottlenecks that limit productivity and their potential solutions are also discussed in this review.
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Affiliation(s)
- Yang Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiao Guo
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huaiyi Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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