1
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Wang DN, Yu CX, Feng J, Wei LJ, Chen J, Liu Z, Ouyang L, Zhang L, Liu F, Hua Q. Comparative transcriptome analysis reveals the redirection of metabolic flux from cell growth to astaxanthin biosynthesis in Yarrowia lipolytica. Yeast 2024; 41:369-378. [PMID: 38613186 DOI: 10.1002/yea.3938] [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: 11/23/2022] [Revised: 03/09/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Engineering Yarrowia lipolytica to produce astaxanthin provides a promising route. Here, Y. lipolytica M2 producing a titer of 181 mg/L astaxanthin was isolated by iterative atmospheric and room-temperature plasma mutagenesis and diphenylamine-mediated screening. Interestingly, a negative correlation was observed between cell biomass and astaxanthin production. To reveal the underlying mechanism, RNA-seq analysis of transcriptional changes was performed in high producer M2 and reference strain M1, and a total of 1379 differentially expressed genes were obtained. Data analysis revealed that carbon flux was elevated through lipid metabolism, acetyl-CoA and mevalonate supply, but restrained through central carbon metabolism in strain M2. Moreover, upregulation of other pathways such as ATP-binding cassette transporter and thiamine pyrophosphate possibly provided more cofactors for carotenoid hydroxylase and relieved cell membrane stress caused by astaxanthin insertion. These results suggest that balancing cell growth and astaxanthin production may be important to promote efficient biosynthesis of astaxanthin in Y. lipolytica.
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Affiliation(s)
- Dan-Ni Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chen-Xi Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jie Feng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Liu-Jing Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jun Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhijie Liu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Liming Ouyang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
| | - Feng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
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2
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Qin Z, Liu M, Ren X, Zeng W, Luo Z, Zhou J. De Novo Biosynthesis of Lutein in Yarrowia lipolytica. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5348-5357. [PMID: 38412053 DOI: 10.1021/acs.jafc.3c09080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Lutein is a high-value tetraterpenoid carotenoid that is widely used in feed, cosmetics, food, and drugs. Microbial synthesis of lutein is an important method for green and sustainable production, serving as an alternative to plant extraction methods. However, an inadequate precursor supply and low catalytic efficiency of key pathway enzymes are the main reasons for the low efficacy of microbial synthesis of lutein. In this study, some strategies, such as enhancing the MVA pathway and localizing α-carotene synthase OluLCY within the subcellular organelles in Yarrowia lipolytica, were adopted to enhance the synthesis of precursor α-carotene, which resulted in a 10.50-fold increase in α-carotene titer, reaching 38.50 mg/L. Subsequently, by improving hydroxylase activity with truncated N-terminal transport peptide and locating hydroxylases to subcellular organelles, the final strain L9 producing 75.25 mg/L lutein was obtained. Eventually, a lutein titer of 675.40 mg/L (6.13 mg/g DCW) was achieved in a 5 L bioreactor by adding the antioxidant 2,6-ditert-butyl-4-methylphenol. This study realizes de novo synthesis of lutein in Y. lipolytica for the first time and achieves the highest lutein titer reported so far.
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Affiliation(s)
- Zhilei Qin
- 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
| | - Xuefeng Ren
- 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
| | - Weizhu Zeng
- 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
| | - Zhengshan Luo
- 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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3
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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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4
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Lewis AG, Carmichael L, Wang RY, Gibney PA. Characterizing a panel of amino acid auxotrophs under auxotrophic starvation conditions. Yeast 2024; 41:5-18. [PMID: 37997284 DOI: 10.1002/yea.3910] [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: 08/09/2023] [Revised: 10/20/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Auxotrophic strains starving for their cognate nutrient, termed auxotrophic starvation, are characterized by a shorter lifespan, higher glucose wasting phenotype, and inability to accomplish cell cycle arrest when compared to a "natural starvation," where a cell is starving for natural environmental growth-limiting nutrients such as phosphate. Since evidence of this physiological response is limited to only a subset of auxotrophs, we evaluated a panel of auxotrophic mutants to determine whether these responses are characteristic of a broader range of amino acid auxotrophs. Based on the starvation survival kinetics, the panel of strains was grouped into three categories-short-lived strains, strains with survival similar to a prototrophic wild type strain, and long-lived strains. Among the short-lived strains, we observed that the tyrosine, asparagine, threonine, and aspartic acid auxotrophs rapidly decline in viability, with all strains unable to arrest cell cycle progression. The three basic amino acid auxotrophs had a survival similar to a prototrophic strain starving in minimal media. The leucine, tryptophan, methionine, and cysteine auxotrophs displayed the longest lifespan. We also demonstrate how the phenomenon of glucose wasting is limited to only a subset of the tested auxotrophs, namely the asparagine, leucine, and lysine auxotrophs. Furthermore, we observed pleiotropic phenotypes associated with a subgroup of auxotrophs, highlighting the importance of considering unintended phenotypic effects when using auxotrophic strains especially in chronological aging experiments.
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Affiliation(s)
- Alisha G Lewis
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Laurin Carmichael
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Rebecca Y Wang
- Calico Life Sciences LLC, South San Francisco, California, USA
| | - Patrick A Gibney
- Department of Food Science, Cornell University, Ithaca, New York, USA
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5
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Das S, Priyadarshani N, Basak P, Maitra P, Bhattacharya S, Bhattacharya SS. Capsaicin derived from endemic chili landraces combats Shigella pathogen: Insights on intracellular inhibition mechanism. Microb Pathog 2023; 181:106210. [PMID: 37343896 DOI: 10.1016/j.micpath.2023.106210] [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: 04/26/2023] [Revised: 06/16/2023] [Accepted: 06/18/2023] [Indexed: 06/23/2023]
Abstract
Ethnic tribals in northeast India have been growing and maintaining local chili landraces for ages. These chilies are known for their characteristic pungency and immense therapeutic properties. Capsaicin, a significant chili metabolite, is recognized as a natural drug for pain relief, diabetic neuropathy, psoriasis, arthritis, etc. In this study, we tried to observe the influence of locality factors on the pungency and bioactive features of Capsicum annuum L. landraces. We also checked the gastro-protective ability of these chilies, especially in the cure of shigellosis. Phytometabolite characterization and estimation were done through spectrophotometric methods. Preparative and analytical HPLC techniques were employed for extracting and purifying capsaicin-enriched fractions. Shigella flexneri growth retardation was determined through the broth dilution method. Gentamicin protection assay and ELISA were done to assess the intracellular invasion and IL-1β inflammasome production by S.flexneri. The correlation analyses postulated that phenols, flavonoids, chlorophylls, β-carotene, and capsaicin synthase upregulation strongly influenced capsaicin biosynthesis in chili cultivars. Correspondingly, the inhibitory efficacy of the HPLC-purified Balijuri-derived capsaicin was more effective than the Raja-derived capsaicin in inhibiting intracellular Shigella growth. Reduced levels of pro-inflammatory cytokine (IL1β) in capsaicin-treated Shigella-infected cells probably reduced inflammation-mediated intestinal damage, limiting bacterial spread. This investigation advocates the unique potential of local chilies in curing deadly 'shigellosis' with mechanistic evidence. Our observation justifies the traditional healing practices of the ethnic people of NE India.
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Affiliation(s)
- Subhasish Das
- Department of Environmental Science, Pachhunga University College, Mizoram University (A Central University), Aizawl, 796001, Mizoram, India.
| | - Nayana Priyadarshani
- Soil Agro Bio-engineering Laboratory, Department of Environmental Science, Tezpur University, Sonitpur, 784028, Assam, India
| | - Priyanka Basak
- Department of Biochemistry, ICMR-National Institute of Cholera and Enteric Diseases, Beleghata, Kolkata, 700010, India
| | - Priyanka Maitra
- Department of Biochemistry, ICMR-National Institute of Cholera and Enteric Diseases, Beleghata, Kolkata, 700010, India
| | - Sushmita Bhattacharya
- Department of Biochemistry, ICMR-National Institute of Cholera and Enteric Diseases, Beleghata, Kolkata, 700010, India
| | - Satya Sundar Bhattacharya
- Soil Agro Bio-engineering Laboratory, Department of Environmental Science, Tezpur University, Sonitpur, 784028, Assam, India.
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6
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Zhang TL, Yu HW, Ye LD. Metabolic Engineering of Yarrowia lipolytica for Terpenoid Production: Tools and Strategies. ACS Synth Biol 2023; 12:639-656. [PMID: 36867718 DOI: 10.1021/acssynbio.2c00569] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Terpenoids are a diverse group of compounds with isoprene units as basic building blocks. They are widely used in the food, feed, pharmaceutical, and cosmetic industries due to their diverse biological functions such as antioxidant, anticancer, and immune enhancement. With an increase in understanding the biosynthetic pathways of terpenoids and advances in synthetic biology techniques, microbial cell factories have been built for the heterologous production of terpenoids, with the oleaginous yeast Yarrowia lipolytica emerging as an outstanding chassis. In this paper, recent progress in the development of Y. lipolytica cell factories for terpenoid production with a focus on the advances in novel synbio tools and metabolic engineering strategies toward enhanced terpenoid biosynthesis is reviewed.
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Affiliation(s)
- Tang-Lei Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, 310058 Hangzhou, China
| | - Hong-Wei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, 310058 Hangzhou, China.,Zhejiang Key Laboratory of Smart Biomaterials, 310058 Hangzhou, China
| | - Li-Dan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, 310058 Hangzhou, China.,Zhejiang Key Laboratory of Smart Biomaterials, 310058 Hangzhou, China
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7
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Watcharawipas A, Runguphan W. Red yeasts and their carotenogenic enzymes for microbial carotenoid production. FEMS Yeast Res 2023; 23:6895548. [PMID: 36513367 DOI: 10.1093/femsyr/foac063] [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: 06/24/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Carotenoids are C40 isoprene-based compounds with significant commercial interests that harbor diverse bioactivities. Prominent examples of carotenoids are beta-carotene, a precursor to vitamin A essential for proper eye health, and lycopene and astaxanthin, powerful antioxidants implicated in preventing cancers and atherosclerosis. Due to their benefits to human health, the market value for carotenoids is rapidly increasing and is projected to reach USD 1.7 billion by 2025. However, their production now relies on chemical synthesis and extraction from plants that pose risks to food management and numerous biological safety issues. Thus, carotenoid production from microbes is considered a promising strategy for achieving a healthy society with more sustainability. Red yeast is a heterogeneous group of basidiomycetous fungi capable of producing carotenoids. It is a critical source of microbial carotenoids from low-cost substrates. Carotenogenic enzymes from red yeasts have also been highly efficient, invaluable biological resources for biotechnological applications. In this minireview, we focus on red yeast as a promising source for microbial carotenoids, strain engineering strategies for improving carotenoid production in red yeasts, and potential applications of carotenogenic enzymes from red yeasts in conventional and nonconventional yeasts.
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Affiliation(s)
- Akaraphol Watcharawipas
- Department of Microbiology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
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8
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Integrated pathway engineering and transcriptome analysis for improved astaxanthin biosynthesis in Yarrowia lipolytica. Synth Syst Biotechnol 2022; 7:1133-1141. [PMID: 36092272 PMCID: PMC9428815 DOI: 10.1016/j.synbio.2022.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/14/2022] [Accepted: 08/05/2022] [Indexed: 11/24/2022] Open
Abstract
Astaxanthin is a high value carotenoid with a broad range of commercial applications due to its superior antioxidant properties. In this study, β-carotene-producing Yarrowia lipolytica XK17 constructed in the lab was employed for astaxanthin biosynthesis. The catalytic effects of β-carotene ketolase CrtW and β-carotene hydroxylase CrtZ from various species were investigated. The PspCrtW from Paracoccus sp. and HpCrtZ# from Haematococcus pluvialis were confirmed to be the best combination in converting β-carotene. Several key bottlenecks in biomass and astaxanthin biosynthesis were effectively eliminated by optimizing the expression of the above enzymes and restoring uracil/leucine biosynthesis. In addition, the effects of astaxanthin biosynthesis on cell metabolism were investigated by integrated analysis of pathway modification and transcriptome information. After further optimization, strain DN30 was able to synthesize up to 730.3 mg/L astaxanthin in laboratory 5-L fermenter. This study provides a good metabolic strategy and a sustainable development platform for high-value carotenoid production.
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9
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Lupish B, Hall J, Schwartz C, Ramesh A, Morrison C, Wheeldon I. Genome-wide CRISPR-Cas9 screen reveals a persistent null-hyphal phenotype that maintains high carotenoid production in Yarrowia lipolytica. Biotechnol Bioeng 2022; 119:3623-3631. [PMID: 36042688 PMCID: PMC9825908 DOI: 10.1002/bit.28219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 01/11/2023]
Abstract
Yarrowia lipolytica is a metabolic engineering host of growing industrial interest due to its ability to metabolize hydrocarbons, fatty acids, glycerol, and other renewable carbon sources. This dimorphic yeast undergoes a stress-induced transition to a multicellular hyphal state, which can negatively impact biosynthetic activity, reduce oxygen and nutrient mass transfer in cell cultures, and increase culture viscosity. Identifying mutations that prevent the formation of hyphae would help alleviate the bioprocess challenges that they create. To this end, we conducted a genome-wide CRISPR screen to identify genetic knockouts that prevent the transition to hyphal morphology. The screen identified five mutants with a null-hyphal phenotype-ΔRAS2, ΔRHO5, ΔSFL1, ΔSNF2, and ΔPAXIP1. Of these hits, only ΔRAS2 suppressed hyphal formation in an engineered lycopene production strain over a multiday culture. The RAS2 knockout was also the only genetic disruption characterized that did not affect lycopene production, producing more than 5 mg L-1 OD-1 from a heterologous pathway with enhanced carbon flux through the mevalonate pathway. These data suggest that a ΔRAS2 mutant of Y. lipolytica could prove useful in engineering a metabolic engineering host of the production of carotenoids and other biochemicals.
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Affiliation(s)
- Brian Lupish
- Department of BioengineeringUniversity of CaliforniaRiversideCaliforniaUSA
| | - Jordan Hall
- Department of Chemical and Environmental EngineeringUniversity of CaliforniaRiversideCaliforniaUSA
| | - Cory Schwartz
- Department of Chemical and Environmental EngineeringUniversity of CaliforniaRiversideCaliforniaUSA,Present address:
iBio Inc.San DiegoCaliforniaUSA
| | - Adithya Ramesh
- Department of Chemical and Environmental EngineeringUniversity of CaliforniaRiversideCaliforniaUSA
| | - Clifford Morrison
- Department of Chemical and Environmental EngineeringUniversity of CaliforniaRiversideCaliforniaUSA
| | - Ian Wheeldon
- Department of Chemical and Environmental EngineeringUniversity of CaliforniaRiversideCaliforniaUSA,Center for Industrial BiotechnologyUniversity of CaliforniaRiversideCaliforniaUSA
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10
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Arnesen JA, Borodina I. Engineering of Yarrowia lipolytica for terpenoid production. Metab Eng Commun 2022; 15:e00213. [PMID: 36387772 PMCID: PMC9663531 DOI: 10.1016/j.mec.2022.e00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/31/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022] Open
Abstract
Terpenoids are a group of chemicals of great importance for human health and prosperity. Terpenoids can be used for human and animal nutrition, treating diseases, enhancing agricultural output, biofuels, fragrances, cosmetics, and flavouring. However, due to the rapid depletion of global natural resources and manufacturing practices relying on unsustainable petrochemical synthesis, there is a need for economic alternatives to supply the world's demand for these essential chemicals. Microbial biosynthesis offers the means to develop scalable and sustainable bioprocesses for terpenoid production. In particular, the non-conventional yeast Yarrowia lipolytica demonstrates excellent potential as a chassis for terpenoid production due to its amenability to industrial production scale-up, genetic engineering, and high accumulation of terpenoid precursors. This review aims to illustrate the scientific progress in developing Y. lipolytica terpenoid cell factories, focusing on metabolic engineering approaches for strain improvement and cultivation optimization.
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Affiliation(s)
- Jonathan Asmund Arnesen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
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11
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Advances in engineering the production of the natural red pigment lycopene: A systematic review from a biotechnology perspective. J Adv Res 2022; 46:31-47. [PMID: 35753652 PMCID: PMC10105081 DOI: 10.1016/j.jare.2022.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/31/2022] [Accepted: 06/20/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Lycopene is a natural red compound with potent antioxidant activity that can be utilized both as pigment and as a raw material in functional food, and so possesses good commercial prospects. The biosynthetic pathway has already been documented, which provides the foundation for lycopene production using biotechnology. AIM OF REVIEW Although lycopene production has begun to take shape, there is still an urgent need to alleviate the yield of lycopene. Progress in this area can provide useful reference for metabolic engineering of lycopene production utilizing multiple approaches. Key scientific concepts of review Using conventional microbial fermentation approaches, biotechnologists have enhanced the yield of lycopene by selecting suitable host strains, utilizing various additives, and optimizing culture conditions. With the development of modern biotechnology, genetic engineering, protein engineering, and metabolic engineering have been applied for lycopene production. Extraction from natural plants is the main way for lycopene production at present. Based on the molecular mechanism of lycopene accumulation, the production of lycopene by plant bioreactor through genetic engineering has a good prospect. Here we summarized common strategies for optimizing lycopene production engineering from a biotechnology perspective, which are mainly carried out by microbial cultivation. We reviewed the challenges and limitations of this approach, summarized the critical aspects, and provided suggestions with the aim of potential future breakthroughs for lycopene production in plants.
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12
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Casas A, Bultelle M, Motraghi C, Kitney R. PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies. ACS Synth Biol 2022; 11:1272-1291. [PMID: 35261238 PMCID: PMC8938949 DOI: 10.1021/acssynbio.1c00562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We present here a
newly developed workflow—which we have
called PASIV—designed to provide a solution to a practical
problem with design of experiments (DoE) methodology: i.e., what can
be done if the scoping phase of the DoE cycle is severely hampered
by burden and toxicity issues (caused by either the metabolite or
an intermediary), making it unreliable or impossible to proceed to
the screening phase? PASIV—standing for pooled approach, screening,
identification, and visualization—was designed so the (viable)
region of interest can be made to appear through an interplay between
biology and software. This was achieved by combining multiplex construction
in a pooled approach (one-pot reaction) with a viability assay and
with a range of bioinformatics tools (including a novel construct
matching tool). PASIV was tested on the exemplar of the lycopene pathway—under
stressful constitutive expression—yielding a region of interest
with comparatively stronger producers.
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Affiliation(s)
- Alexis Casas
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| | - Matthieu Bultelle
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| | - Charles Motraghi
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| | - Richard Kitney
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
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13
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Baisya D, Ramesh A, Schwartz C, Lonardi S, Wheeldon I. Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica. Nat Commun 2022; 13:922. [PMID: 35177617 PMCID: PMC8854577 DOI: 10.1038/s41467-022-28540-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli, use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica. A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide's ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.
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Affiliation(s)
- Dipankar Baisya
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
| | - Adithya Ramesh
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Cory Schwartz
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
- iBio Inc., San Diego, CA, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA.
- Integrative Institute for Genome Biology, University of California, Riverside, CA, 92521, USA.
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
- Integrative Institute for Genome Biology, University of California, Riverside, CA, 92521, USA.
- Center for Industrial Biotechnology, University of California, Riverside, CA, 92521, USA.
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14
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Seo SO, Jin YS. Next-Generation Genetic and Fermentation Technologies for Safe and Sustainable Production of Food Ingredients: Colors and Flavorings. Annu Rev Food Sci Technol 2022; 13:463-488. [DOI: 10.1146/annurev-food-052720-012228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A growing human population is a significant issue in food security owing to the limited land and resources available for agricultural food production. To solve these problems, sustainable food manufacturing processes and the development of alternative foods and ingredients are needed. Metabolic engineering and synthetic biology can help solve the food security issue and satisfy the demand for alternative food production. Bioproduction of food ingredients by microbial fermentation is a promising method to replace current manufacturing processes, such as extraction from natural materials and chemical synthesis, with more ecofriendly and sustainable operations. This review highlights successful examples of bioproduction for food additives by engineered microorganisms, with an emphasis on colorants and flavors that are extensively used in the food industry. Recent strain engineering developments and fermentation strategies for producing selected food colorants and flavors are introduced with discussions on the current status and future perspectives. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Seung-Oh Seo
- Department of Food Science and Nutrition, Catholic University of Korea, Bucheon, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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15
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Zhao Y, Zhu K, Li J, Zhao Y, Li S, Zhang C, Xiao D, Yu A. High-efficiency production of bisabolene from waste cooking oil by metabolically engineered Yarrowia lipolytica. Microb Biotechnol 2021; 14:2497-2513. [PMID: 33605546 PMCID: PMC8601197 DOI: 10.1111/1751-7915.13768] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 12/13/2022] Open
Abstract
The natural plant product bisabolene serves as a precursor for the production of a wide range of industrially relevant chemicals. However, the low abundance of bisabolene in plants renders its isolation from plant sources non-economically viable. Therefore, creation of microbial cell factories for bisabolene production supported by synthetic biology and metabolic engineering strategies presents a more competitive and environmentally sustainable method for industrial production of bisabolene. In this proof-of-principle study, for the first time, we engineered the oleaginous yeast Yarrowia lipolytica to produce α-bisabolene, β-bisabolene and γ-bisabolene through heterologous expression of the α-bisabolene synthase from Abies grandis, the β-bisabolene synthase gene from Zingiber officinale and the γ-bisabolene synthase gene from Helianthus annuus respectively. Subsequently, two metabolic engineering approaches, including overexpression of the endogenous mevalonate pathway genes and introduction of heterologous multidrug efflux transporters, were employed in order to improve bisabolene production. Furthermore, the fermentation conditions were optimized to maximize bisabolene production by the engineered Y. lipolytica strains from glucose. Finally, we explored the potential of the engineered Y. lipolytica strains for bisabolene production from the waste cooking oil. To our knowledge, this is the first report of bisabolene production in Y. lipolytica using metabolic engineering strategies. These findings provide valuable insights into the engineering of Y. lipolytica for a higher-level production of bisabolene and its utilization in converting waste cooking oil into various industrially valuable products.
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Affiliation(s)
- Yakun Zhao
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyCollege of BiotechnologyTianjin University of Science and TechnologyNo. 29 the 13th Street TEDATianjin300457China
| | - Kun Zhu
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyCollege of BiotechnologyTianjin University of Science and TechnologyNo. 29 the 13th Street TEDATianjin300457China
| | - Jian Li
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyCollege of BiotechnologyTianjin University of Science and TechnologyNo. 29 the 13th Street TEDATianjin300457China
| | - Yu Zhao
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyCollege of BiotechnologyTianjin University of Science and TechnologyNo. 29 the 13th Street TEDATianjin300457China
| | - Shenglong Li
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyCollege of BiotechnologyTianjin University of Science and TechnologyNo. 29 the 13th Street TEDATianjin300457China
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyCollege of BiotechnologyTianjin University of Science and TechnologyNo. 29 the 13th Street TEDATianjin300457China
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyCollege of BiotechnologyTianjin University of Science and TechnologyNo. 29 the 13th Street TEDATianjin300457China
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and SafetyKey Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyCollege of BiotechnologyTianjin University of Science and TechnologyNo. 29 the 13th Street TEDATianjin300457China
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16
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Soong YHV, Zhao L, Liu N, Yu P, Lopez C, Olson A, Wong HW, Shao Z, Xie D. Microbial synthesis of wax esters. Metab Eng 2021; 67:428-442. [PMID: 34391890 DOI: 10.1016/j.ymben.2021.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/27/2021] [Accepted: 08/10/2021] [Indexed: 01/10/2023]
Abstract
Microbial synthesis of wax esters (WE) from low-cost renewable and sustainable feedstocks is a promising path to achieve cost-effectiveness in biomanufacturing. WE are industrially high-value molecules, which are widely used for applications in chemical, pharmaceutical, and food industries. Since the natural WE resources are limited, the WE production mostly rely on chemical synthesis from rather expensive starting materials, and therefore solution are sought from development of efficient microbial cell factories. Here we report to engineer the yeast Yarrowia lipolytica and bacterium Escherichia coli to produce WE at the highest level up to date. First, the key genes encoding fatty acyl-CoA reductases and wax ester synthase from different sources were investigated, and the expression system for two different Y. lipolytica hosts were compared and optimized for enhanced WE production and the strain stability. To improve the metabolic pathway efficiency, different carbon sources including glucose, free fatty acid, soybean oil, and waste cooking oil (WCO) were compared, and the corresponding pathway engineering strategies were optimized. It was found that using a lipid substrate such as WCO to replace glucose led to a 60-fold increase in WE production. The engineered yeast was able to produce 7.6 g/L WE with a yield of 0.31 (g/g) from WCO within 120 h and the produced WE contributed to 57% of the yeast DCW. After that, E. coli BL21(DE3), with a faster growth rate than the yeast, was engineered to significantly improve the WE production rate. Optimization of the expression system and the substrate feeding strategies led to production of 3.7-4.0 g/L WE within 40 h in a 1-L bioreactor. The predominant intracellular WE produced by both Y. lipolytica and E. coli in the presence of hydrophobic substrates as sole carbon sources were C36, C34 and C32, in an order of decreasing abundance and with a large proportion being unsaturated. This work paved the way for the biomanufacturing of WE at a large scale.
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Affiliation(s)
- Ya-Hue Valerie Soong
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Le Zhao
- Department of Chemical and Biological Engineering, NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50011, USA
| | - Na Liu
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Peng Yu
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Carmen Lopez
- Department of Chemical and Biological Engineering, NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50011, USA
| | - Andrew Olson
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Hsi-Wu Wong
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50011, USA.
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA.
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17
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Abstract
With the discovery of Western blotting as first described by Towbin et al. in 1979, the transfer and visualization of electrophoretically separated proteins on membranes has become the de facto method for the qualitative and quantitative detection of proteins of interest. In this method, proteins are resolved by electrophoresis on a polyacrylamide gel, followed by a transfer of the separated proteins onto a nitrocellulose or polyvinyl difluoride (PVDF) membrane. Once immobilized on these membranes, the protein of interest can be detected and visualized by exploiting antigen-antibody interactions. However, not all proteins are amenable to easy detection by Western blotting. Integral membrane proteins are a class of proteins that are attached to a biological membrane through a series of transmembrane segments that span the width of the membrane. Due to the inherent hydrophobicity of these proteins and their tendency to aggregate, the characterization and detection of these proteins can be challenging. In this methods chapter, we present a protocol for the easy detection and quantification of these proteins in the industrially important oleaginous yeast Yarrowia lipolytica. The first protocol describes a Western blotting procedure to quantify soluble cytosolic proteins of interest in Yarrowia lipolytica from its total cell lysate. The second protocol describes modifications to the first that are done to enhance detection and quantification of membrane-bound proteins in Yarrowia lipolytica from its total cell lysate, without the need for isolating the membrane-bound proteins, for use in Western blotting. The immunoblotting strategies described here should serve as an efficient and simple guide to quantify both cytosolic and the intractable membrane-bound proteins in Yarrowia lipolytica.
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18
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Zhang G, Wang H, Zhang Z, Verstrepen KJ, Wang Q, Dai Z. Metabolic engineering of Yarrowia lipolytica for terpenoids production: advances and perspectives. Crit Rev Biotechnol 2021; 42:618-633. [PMID: 34325575 DOI: 10.1080/07388551.2021.1947183] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Terpenoids are a large family of natural products with diversified structures and functions that are widely used in the food, pharmaceutical, cosmetic, and agricultural fields. However, the traditional methods of terpenoids production such as plant extraction and chemical synthesis are inefficient due to the complex processes, high energy consumption, and low yields. With progress in metabolic engineering and synthetic biology, microbial cell factories provide an interesting alternative for the sustainable production of terpenoids. The non-conventional yeast, Yarrowia lipolytica, is a promising host for terpenoid biosynthesis due to its inherent mevalonate pathway, high fluxes of acetyl-CoA and NADPH, and the naturally hydrophobic microenvironment. In this review, we highlight progress in the engineering of Y. lipolytica as terpenoid biomanufacturing factories, describing the different terpenoid biosynthetic pathways and summarizing various metabolic engineering strategies, including progress in genetic manipulation, dynamic regulation, organelle engineering, and terpene synthase variants.
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Affiliation(s)
- Ge Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,TIB-VIB Joint Center of Synthetic Biology, National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Huan Wang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - Ze Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - Kevin J Verstrepen
- TIB-VIB Joint Center of Synthetic Biology, National Center of Technology Innovation for Synthetic Biology, Tianjin, China.,VIB-KU Leuven Center for Microbiology and KU Leuven Laboratory for Genetics and Genomics, Department M2S, Leuven, Belgium
| | - Qinhong Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,TIB-VIB Joint Center of Synthetic Biology, National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zongjie Dai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,TIB-VIB Joint Center of Synthetic Biology, National Center of Technology Innovation for Synthetic Biology, Tianjin, China
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19
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Shi T, Li Y, Zhu L, Tong Y, Yang J, Fang Y, Wang M, Zhang J, Jiang Y, Yang S. Engineering the oleaginous yeast Yarrowia lipolytica for β-farnesene overproduction. Biotechnol J 2021; 16:e2100097. [PMID: 33938153 DOI: 10.1002/biot.202100097] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/25/2021] [Accepted: 04/28/2021] [Indexed: 11/10/2022]
Abstract
β-farnesene is a sesquiterpenoid with various industrial applications which is now commercially produced by a Saccharomyces cerevisiae strain obtained by random mutagenesis and genetic engineering. We rationally designed a genetically defined Yarrowia lipolytica through recovery of L-leucine biosynthetic route, gene dosage optimization of β-farnesene synthase and disruption of the competition pathway. The resulting β-farnesene titer was improved from 8 to 345 mg L-1 . Finally, the strategy for decreasing the lipid accumulation by individually and iteratively knocking out four acyltransferases encoding genes was adopted. The result displayed that β-farnesene titer in the engineered strain CIBT6304 in which acyltransferases (DGA1 and DGA2) were deleted increased by 45% and reached 539 mg L-1 (88 mg g-1 DCW). Using fed-batch fermentation, CIBT6304 could produce the highest β-farnesene titer (22.8 g L-1 ) among the genetically defined strains. This study will provide the foundation of engineering Y. lipolytica to produce other terpenoids more cost-efficiently.
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Affiliation(s)
- Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Yawen Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Li Zhu
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai, China
| | - Yangyang Tong
- Key Laboratory of Synthetic Biology, CAS Center for Excellence of Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence of Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yunming Fang
- The College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Meng Wang
- The College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Jieze Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Yu Jiang
- Shanghai Taoyusheng Biotechnology Co., Ltd, Shanghai, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence of Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou, China
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20
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Wang RQ, Chen G, Chen SN, Zhu HL, Xiong WN, Xu M, Jian SP. Metabolic changes of Neurospora crassa in the presence of oleic acid for promoting lycopene production. J Biosci Bioeng 2021; 132:148-153. [PMID: 33994113 DOI: 10.1016/j.jbiosc.2021.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/30/2021] [Accepted: 04/14/2021] [Indexed: 11/16/2022]
Abstract
Neurospora crassa has been generally recognized as a safe organism and possesses a remarkable ability to produce yellow-to-orange carotenoids. The present work mainly explored the potential mechanism of exogenous oleic acid on promoting lycopene production in N. crassa. Carbon flux was conducively channelized into the mevalonate metabolic pathway to synthesize more lycopene, associating with the increased levels of acetyl-CoA, NADPH and factors related to the mevalonate pathway. Additionally, exogenous oleic acid boosted the intracellular triacylglycerol production through de novo and ex novo fatty acid synthesis pathways, which contributed to improving the accumulation of lycopene via lipid bodies. Further, the regulated fatty acid profile also enhanced the storage capacity of lipid bodies. Consequently, this study provided an effective strategy to enhance the lycopene production in N. crassa by adding oleic acid to the culture medium and elucidated an extraordinary insight into the potential mechanism.
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Affiliation(s)
- Rui-Qi Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Qingshanhu District, Nanchang, 330047 Jiangxi, China
| | - Gang Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Qingshanhu District, Nanchang, 330047 Jiangxi, China.
| | - Sun-Ni Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Qingshanhu District, Nanchang, 330047 Jiangxi, China
| | - Hong-Lin Zhu
- State Key Laboratory of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Qingshanhu District, Nanchang, 330047 Jiangxi, China
| | - Wen-Neng Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Qingshanhu District, Nanchang, 330047 Jiangxi, China
| | - Mao Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Qingshanhu District, Nanchang, 330047 Jiangxi, China
| | - Su-Ping Jian
- State Key Laboratory of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Qingshanhu District, Nanchang, 330047 Jiangxi, China
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21
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Liu L, Qu YL, Dong GR, Wang J, Hu CY, Meng YH. Elevated β-Carotene Production Using Codon-Adapted CarRA&B and Metabolic Balance in Engineered Yarrowia lipolytica. Front Microbiol 2021; 12:627150. [PMID: 33746920 PMCID: PMC7970187 DOI: 10.3389/fmicb.2021.627150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/22/2021] [Indexed: 11/13/2022] Open
Abstract
β-carotene is a precursor of vitamin A and has multiple physiological functions. Producing β-carotene by microbial fermentation has attracted much attention to consumers' preference for natural products. This study focused on improving β-carotene production by constructing codon-adapted genes and minimizing intermediate accumulation. The codon-adapted CarRA and CarB genes from the industrial strain of Blakeslea trispora were integrated into the genome of the Yarrowia lipolytica to construct YL-C0, the baseline strain for producing β-carotene. Thereafter, the β-carotene biosynthetic pathway's metabolic balance was accurately regulated to reduce the intermediates' accumulation. Notably, the β-carotene content increased by 21 times to reach 12.5 dry cell weight (DCW) mg/g when minimizing HMG-CoA and FPP accumulation. Further, we improved the expression levels of the CarRA and CarB genes to minimize the accumulation of phytoene and lycopene. Total production of β-carotene of 1.7 g/L and 21.6 mg/g DCW was achieved. These results reveal that the rate-limiting enzymes CarRA and CarB of B. trispora exhibited higher catalytic activity than the same enzymes from other microorganisms. Promoting metabolic balance by minimizing the accumulation of intermediates is a very effective strategy for increasing β-carotene. The β-carotene-producing strain constructed in this study has established the foundation for its potential use in industrial production. These successful engineering strategies also provide a foundation for large-scale production of other terpenoids.
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Affiliation(s)
- Liang Liu
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Yu Ling Qu
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Gui Ru Dong
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Jing Wang
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Ching Yuan Hu
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China.,Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Yong Hong Meng
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
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22
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Li ZJ, Wang YZ, Wang LR, Shi TQ, Sun XM, Huang H. Advanced Strategies for the Synthesis of Terpenoids in Yarrowia lipolytica. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2367-2381. [PMID: 33595318 DOI: 10.1021/acs.jafc.1c00350] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Terpenoids are an important class of secondary metabolites that play an important role in food, agriculture, and other fields. Microorganisms are rapidly emerging as a promising source for the production of terpenoids. As an oleaginous yeast, Yarrowia lipolytica contains a high lipid content which indicates that it must produce high amounts of acetyl-CoA, a necessary precursor for the biosynthesis of terpenoids. Y. lipolytica has a complete eukaryotic mevalonic acid (MVA) pathway but it has not yet seen commercial use due to its low productivity. Several metabolic engineering strategies have been developed to improve the terpenoids production of Y. lipolytica, including developing the orthogonal pathway for terpenoid synthesis, increasing the catalytic efficiency of terpenoids synthases, enhancing the supply of acetyl-CoA and NADPH, expressing rate-limiting genes, and modifying the branched pathway. Moreover, most of the acetyl-CoA is used to produce lipid, so it is an effective strategy to strike a balance of precursor distribution by rewiring the lipid biosynthesis pathway. Lastly, the latest developed non-homologous end-joining strategy for improving terpenoid production is introduced. This review summarizes the status and metabolic engineering strategies of terpenoids biosynthesis in Y. lipolytica and proposes new insights to move the field forward.
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Affiliation(s)
- Zi-Jia Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Yu-Zhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Ling-Ru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, People's Republic of China
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23
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Jing Y, Guo F, Zhang S, Dong W, Zhou J, Xin F, Zhang W, Jiang M. Recent Advances on Biological Synthesis of Lycopene by Using Industrial Yeast. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.0c05228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yiwen Jing
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Shangjie Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, P. R. China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, P. R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, P. R. China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, P. R. China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, P. R. China
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24
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Pathway engineering of Saccharomyces cerevisiae for efficient lycopene production. Bioprocess Biosyst Eng 2021; 44:1033-1047. [PMID: 33486569 DOI: 10.1007/s00449-020-02503-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/25/2020] [Indexed: 10/22/2022]
Abstract
To construct a Saccharomyces cerevisiae strain for efficient lycopene production, we used a pathway engineering strategy based on expression modules comprising fusion proteins and a strong constitutive promoter. The two recombinant plasmids pEBI encoding the fusion genes with an inducible promoter, as well as pIETB with a constitutive promoter and terminator were introduced into S. cerevisiae YPH499 and BY4741 to obtain the four recombinant strains ypEBI, ypIETB, byEBI and byIETB. The lycopene production and the transcription levels of key genes were higher in the BY4741 chassis than in YPH499. Accordingly, the content of total and unsaturated fatty acids was also higher in BY4741, which also exhibited a decrease of glucose, increase of trehalose, increase of metabolite in citrate cycle, and low levels of amino acids. These changes rerouted metabolic fluxes toward lycopene synthesis, indicating that the BY4741 chassis was more suitable for lycopene synthesis. The lycopene content of bpIETB in SG-Leu medium supplemented with 100 mg/L of linolenic acid reached 10.12 mg/g dry cell weight (DCW), which was 85.7% higher than without the addition of unsaturated fatty acids. The constitutive promoter expression strategy employed in this study achieved efficient lycopene synthesis in S. cerevisiae, and the strain bpIETB was obtained a suitable chassis host for lycopene production, which provides a basis for further optimization of lycopene production in artificial synthetic cells and a reference for the multi-enzyme synthesis of other similar complex terpenoids.
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Ramesh A, Wheeldon I. Guide RNA Design for Genome-Wide CRISPR Screens in Yarrowia lipolytica. Methods Mol Biol 2021; 2307:123-137. [PMID: 33847986 DOI: 10.1007/978-1-0716-1414-3_8] [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: 01/05/2024]
Abstract
Genome-wide functional genomic screens are essential to determining the genetic underpinning of a biological process. Novel and powerful tools for perturbing gene function, with the help of genetic and epigenetic information, have made it possible to systematically investigate the contribution of every gene to evolved and engineered phenotypes. Functional genomics and screening for enhanced phenotypes become ever more important when dealing with nonconventional hosts. Non-model organisms are valuable to metabolic engineering as they present a range of desirable phenotypes and can help in avoiding complex and intensive engineering of less suitable hosts that do not possess the desired phenotype(s). Domestication of such hosts however requires a suite of synthetic biology tools that allow for targeted genome engineering, regulation of gene expression, and genome-wide mutational screens. The widespread adoption of CRISPR-Cas9 and CRISPR-Cpf1 based systems has allowed for such screens in many organisms. Key considerations in any genome-wide CRISPR screen are the design of a set of unique guide RNAs targeting the required set of genes in the genome and the design of nontargeting guide RNAs that function as appropriate negative controls for the experiment. In this methods chapter, we present protocols for the design of guides for a CRISPR screen, targeting every gene in the genome of the industrially relevant oleaginous yeast Yarrowia lipolytica. The first set of protocols describes the algorithm for the design of genome targeting and nontargeting guides for a genome-wide CRISPR-Cpf1 screen. The second set of protocols describes modifications to the first for the design of guides for a CRISPR-Cas9 screen. The strategies described here should serve as an efficient guide to design a library of gRNAs for most genome-wide CRISPR screens.
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Affiliation(s)
- Adithya Ramesh
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, USA.
- Center for Industrial Biotechnology, Bourns College of Engineering, University of California Riverside, Riverside, CA, USA.
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Misa J, Schwartz C. CRISPR Interference and Activation to Modulate Transcription in Yarrowia lipolytica. Methods Mol Biol 2021; 2307:95-109. [PMID: 33847984 DOI: 10.1007/978-1-0716-1414-3_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent developments in RNA-guided nuclease technologies have advanced the engineering of a wide range of organisms, including the nonconventional yeast Yarrowia lipolytica. Y. lipolytica has been the focus of a range of synthetic biology and metabolic engineering studies due to its high capacity to synthesize and accumulate intracellular lipids. The CRISPR-Cas9 system from Streptococcus pyogenes has been successfully adapted and used for genome editing in Y. lipolytica. However, as engineered strains are moved closer to industrialization, the need for finer control of transcription is still present. To overcome this challenge, we have developed CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) systems to allow modulating the transcription of endogenous genes. We begin this protocol chapter by describing how to use the CRISPRi system to repress expression of any gene in Y. lipolytica. A second method describes how to use the CRISPRa system to increase expression of native Y. lipolytica genes. Finally, we describe how CRISPRi or CRISPRa vectors can be combined to enable multiplexed activation or repression of more than one gene. The implementation of CRISPRi and CRISPRa systems improves our ability to control gene expression in Y. lipolytica and promises to enable more advanced synthetic biology and metabolic engineering studies in this host.
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Affiliation(s)
- Joshua Misa
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, USA
| | - Cory Schwartz
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, USA.
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Li M, Xia Q, Zhang H, Zhang R, Yang J. Metabolic Engineering of Different Microbial Hosts for Lycopene Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14104-14122. [PMID: 33207118 DOI: 10.1021/acs.jafc.0c06020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As a result of the extensive use of lycopene in a variety of fields, especially the dietary supplement and health food industries, the production of lycopene has attracted considerable interest. Lycopene can be obtained through extraction from vegetables and chemical synthesis. Alternatively, the microbial production of lycopene has been extensively researched in recent years. Various types of microbial hosts have been evaluated for their potential to accumulate a high level of lycopene. Metabolic engineering of the hosts and optimization of culture conditions are performed to enhance lycopene production. After years of research, great progress has been made in lycopene production. In this review, strategies used to improve lycopene production in different microbial hosts and the advantages and disadvantages of each microbial host are summarized. In addition, future perspectives of lycopene production in different microbial hosts are discussed.
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Affiliation(s)
- Meijie Li
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changchen Road, Qingdao, Shandong 266109, People's Republic of China
| | - Qingqing Xia
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changchen Road, Qingdao, Shandong 266109, People's Republic of China
| | - Haibo Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 135 Songling Road, Qingdao, Shandong 266101, People's Republic of China
| | - Rubing Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 135 Songling Road, Qingdao, Shandong 266101, People's Republic of China
| | - Jianming Yang
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changchen Road, Qingdao, Shandong 266109, People's Republic of China
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Li L, Liu Z, Jiang H, Mao X. Biotechnological production of lycopene by microorganisms. Appl Microbiol Biotechnol 2020; 104:10307-10324. [PMID: 33097966 DOI: 10.1007/s00253-020-10967-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/13/2020] [Accepted: 10/18/2020] [Indexed: 12/16/2022]
Abstract
Lycopene is a dark red carotenoid belonging to C40 terpenoids and is widely found in a variety of plants, especially ripe red fruits and vegetables. Lycopene has been shown to reduce the risk of prostate cancer, other cancers, and cardiovascular disease. It is one of the most widely used carotenoids in the healthcare product market. Currently, commercially available lycopene is mainly extracted from tomatoes. However, production of lycopene from plants is costly and environmentally unfriendly. To date, there have been many reports on the biosynthesis of lycopene by microorganisms, providing another route for lycopene production. This review discusses the lycopene biosynthetic pathway and natural and engineered lycopene-accumulating microorganisms, as well as their production of lycopene. The effects of different metabolic engineering strategies on lycopene accumulation are also considered. Furthermore, this work presents perspectives concerning the microbial production of lycopene, especially trends to construct microbial cell factories for lycopene production. KEY POINTS: • Recent achievements in the lycopene biosynthesis in microorganisms. • Review of lycopene biosynthetic metabolism engineering strategy. • Discuss the current challenges and prospects of using microorganisms to produce lycopene.
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Affiliation(s)
- Lei Li
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Zhen Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.
| | - Hong Jiang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Gu Y, Ma J, Zhu Y, Ding X, Xu P. Engineering Yarrowia lipolytica as a Chassis for De Novo Synthesis of Five Aromatic-Derived Natural Products and Chemicals. ACS Synth Biol 2020; 9:2096-2106. [PMID: 32650638 PMCID: PMC7445739 DOI: 10.1021/acssynbio.0c00185] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Yarrowia
lipolytica is a novel microbial chassis
to upgrade renewable low-cost carbon feedstocks to high-value commodity
chemicals and natural products. In this work, we systematically characterized
and removed the rate-limiting steps of the shikimate pathway and achieved de novo synthesis of five aromatic chemicals in Y. lipolytica. We determined that eliminating amino
acids formation and engineering feedback-insensitive DAHP synthases
are critical steps to mitigate precursor competition and relieve the
feedback regulation of the shikimate pathway. Further overexpression
of heterologous phosphoketolase and deletion of pyruvate kinase provided
a sustained metabolic driving force that channels E4P (erythrose 4-phosphate)
and PEP (phosphoenolpyruvate) precursors through the shikimate pathway.
Precursor competing pathways and byproduct formation pathways were
also blocked by inactivating chromosomal genes. To demonstrate the
utility of our engineered chassis strain, three natural products,
2-phenylethanol (2-PE), p-coumaric acid, and violacein,
which were derived from phenylalanine, tyrosine, and tryptophan, respectively,
were chosen to test the chassis performance. We obtained 2426.22 ±
48.33 mg/L of 2-PE, 593.53 ± 28.75 mg/L of p-coumaric acid, 12.67 ± 2.23 mg/L of resveratrol, 366.30 ±
28.99 mg/L of violacein, and 55.12 ± 2.81 mg/L of deoxyviolacein
from glucose in a shake flask. The 2-PE production represents a 286-fold
increase over the initial strain (8.48 ± 0.50 mg/L). Specifically,
we obtained the highest 2-PE, violacein, and deoxyviolacein titer
ever reported from the de novo shikimate pathway
in yeast. These results set up a new stage of engineering Y. lipolytica as a sustainable biorefinery chassis
strain for de novo synthesis of aromatic compounds
with economic values.
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Affiliation(s)
- Yang Gu
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jingbo Ma
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Yonglian Zhu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xinyu Ding
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Peng Xu
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
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Arnesen JA, Kildegaard KR, Cernuda Pastor M, Jayachandran S, Kristensen M, Borodina I. Yarrowia lipolytica Strains Engineered for the Production of Terpenoids. Front Bioeng Biotechnol 2020; 8:945. [PMID: 32923433 PMCID: PMC7456906 DOI: 10.3389/fbioe.2020.00945] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022] Open
Abstract
Terpenoids are a diverse group of over 55,000 compounds with potential applications as advanced fuels, bulk and fine chemicals, pharmaceutical ingredients, agricultural chemicals, etc. To facilitate their bio-based production, there is a need for plug-and-play hosts, capable of high-level production of different terpenoids. Here we engineer Yarrowia lipolytica platform strains for the overproduction of mono-, sesqui-, di-, tri-, and tetraterpenoids. The monoterpene platform strain was evaluated by expressing Perilla frutescens limonene synthase, which resulted in limonene titer of 35.9 mg/L and was 100-fold higher than when the same enzyme was expressed in the strain without mevalonate pathway improvement. Expression of Callitropsis nootkatensis valencene synthase in the sesquiterpene platform strain resulted in 113.9 mg/L valencene, an 8.4-fold increase over the control strain. Platform strains for production of squalene, complex triterpenes, or diterpenes and carotenoids were also constructed and resulted in the production of 402.4 mg/L squalene, 22 mg/L 2,3-oxidosqualene, or 164 mg/L β-carotene, respectively. The presented terpenoid platform strains can facilitate the evaluation of terpenoid biosynthetic pathways and are a convenient starting point for constructing efficient cell factories for the production of various terpenoids. The platform strains and exemplary terpenoid strains can be obtained from Euroscarf.
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Affiliation(s)
- Jonathan Asmund Arnesen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Marc Cernuda Pastor
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sidharth Jayachandran
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mette Kristensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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Synthetic biology, systems biology, and metabolic engineering of Yarrowia lipolytica toward a sustainable biorefinery platform. J Ind Microbiol Biotechnol 2020; 47:845-862. [PMID: 32623653 DOI: 10.1007/s10295-020-02290-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/25/2020] [Indexed: 01/24/2023]
Abstract
Yarrowia lipolytica is an oleaginous yeast that has been substantially engineered for production of oleochemicals and drop-in transportation fuels. The unique acetyl-CoA/malonyl-CoA supply mode along with the versatile carbon-utilization pathways makes this yeast a superior host to upgrade low-value carbons into high-value secondary metabolites and fatty acid-based chemicals. The expanded synthetic biology toolkits enabled us to explore a large portfolio of specialized metabolism beyond fatty acids and lipid-based chemicals. In this review, we will summarize the recent advances in genetic, omics, and computational tool development that enables us to streamline the genetic or genomic modification for Y. lipolytica. We will also summarize various metabolic engineering strategies to harness the endogenous acetyl-CoA/malonyl-CoA/HMG-CoA pathway for production of complex oleochemicals, polyols, terpenes, polyketides, and commodity chemicals. We envision that Y. lipolytica will be an excellent microbial chassis to expand nature's biosynthetic capacity to produce plant secondary metabolites, industrially relevant oleochemicals, agrochemicals, commodity, and specialty chemicals and empower us to build a sustainable biorefinery platform that contributes to the prosperity of a bio-based economy in the future.
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Li N, Han Z, O'Donnell TJ, Kurasaki R, Kajihara L, Williams PG, Tang Y, Su WW. Production and excretion of astaxanthin by engineered Yarrowia lipolytica using plant oil as both the carbon source and the biocompatible extractant. Appl Microbiol Biotechnol 2020; 104:6977-6989. [PMID: 32601736 DOI: 10.1007/s00253-020-10753-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 11/27/2022]
Abstract
This study aimed to develop a bioprocess using plant oil as the carbon source for lipid-assimilating yeast to produce high-value astaxanthin. Using high-oleic safflower oil as a model, efficient cell growth and astaxanthin production by the engineered Yarrowia lipolytica strain ST7403 was demonstrated, and a considerable portion of astaxanthin was found excreted into the spent oil. Astaxanthin was the predominant carotenoid in the extracellular oil phase that allowed facile in situ recovery of astaxanthin without cell lysis. Autoclaving the safflower oil medium elevated the peroxide level but it declined quickly during fermentation (reduced by 84% by day 3) and did not inhibit cell growth or astaxanthin production. In a 1.5-L fed-batch bioreactor culture with a YnB-based medium containing 20% safflower oil, and with the feeding of casamino acids, astaxanthin production reached 54 mg/L (53% excreted) in 28 days. Further improvement in astaxanthin titer and productivity was achieved by restoring leucine biosynthesis in the host, and running fed-batch fermentation using a high carbon-to-nitrogen ratio yeast extract/peptone medium containing 70% safflower oil, with feeding of additional yeast extract/peptone, to attain 167 mg/L astaxanthin (48% excreted) in 9.5 days of culture. These findings facilitate industrial microbial biorefinery development that utilizes renewable lipids as feedstocks to not only produce high-value products but also effectively extract and recover the products, including non-native ones.Key Points• Yarrowia lipolytica can use plant oil as a C-source for astaxanthin production.• Astaxanthin is excreted and accumulated in the extracellular oil phase.• Astaxanthin is the predominant carotenoid in the extracellular oil phase.• Plant oil serves as a biocompatible solvent for in situ astaxanthin extraction. Graphical abstract.
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Affiliation(s)
- Ningyang Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.,Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science & Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Zhenlin Han
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Timothy J O'Donnell
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Ryan Kurasaki
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Lexie Kajihara
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Philip G Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Yinjie Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St Louis, St. Louis, MO, 63130, USA
| | - Wei Wen Su
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.
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Qiang S, Wang J, Xiong XC, Qu YL, Liu L, Hu CY, Meng YH. Promoting the Synthesis of Precursor Substances by Overexpressing Hexokinase (Hxk) and Hydroxymethylglutaryl-CoA Synthase (Erg13) to Elevate β-Carotene Production in Engineered Yarrowia lipolytica. Front Microbiol 2020; 11:1346. [PMID: 32636824 PMCID: PMC7316989 DOI: 10.3389/fmicb.2020.01346] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/26/2020] [Indexed: 11/23/2022] Open
Abstract
As a valuable carotenoid, β-carotene is commercially used in food, cosmetics, animal feeds, and other industries. Metabolic engineering of microorganisms has been widely explored to improve the production of β-carotene. Compared with the traditional genetic modifications mainly focused on the pathways of mevalonate (MVA) and β-carotene biosynthesis, this study aims to increase the β-carotene production through promoting the synthesis of precursor substances by overexpressing hexokinase and hydroxymethylglutaryl-CoA synthase in an engineered Yarrowia lipolytica. In this study, we investigated the effect of the unique hexokinase gene (Hxk) overexpression on β-carotene accumulation and glucose consumption. The Hxk gene was introduced into a β-carotene producing strain Y.L-1 to generate strain Y.L-2, and this increased the β-carotene content by 98%. Overexpression of the Hxk gene led to increasing in hexokinase activity (329% higher), glucose-6-phosphate content (92% higher), and improvement of the transcriptional level of Hxk (315% higher) compared to the control Y.L-1 strain. Moreover, Hxk overexpression accelerated the utilization rate of glucose. The gene erg13 encoding hydroxymethylglutaryl-CoA synthase was also overexpressed to increase the precursor supply for β-carotene biosynthesis. Recombinant Y.L-4 harboring two copies of erg13 produced 8.41 mg/g dry cell weight (DCW) of β-carotene, which was 259% higher than Y.L-1. The β-carotene content of 9.56 mg/g DCW was achieved in strain Y.L-6 by integrating erg13 into the chromosome and Hxk overexpression. The 3-Hydroxy-3-Methylglutaryl-CoA content in the cells was increased by overexpressing two copies of the erg13 gene. Finally, the titer of β-carotene reached 2.4 g/L using a 50 L bioreactor by the engineered strain, and the fermentation cycle was shortened from 144 to 120 h. Overall, overexpression of Hxk and erg13 could improve β-carotene production and successfully overcoming the bottleneck of precursor generation to support a more efficient pathway for the production of the target product. Our results revealed a novel strategy to engineer the pathway of β-carotene synthesis.
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Affiliation(s)
- Shan Qiang
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, Shaanxi Normal University, Xi'an, China.,National Research & Development Center of Apple Processing Technology, Shaanxi Normal University, Xi'an, China.,College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China.,Xi'an Healthful Biotechnology Co., Ltd., Xi'an, China
| | - Jing Wang
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, Shaanxi Normal University, Xi'an, China.,National Research & Development Center of Apple Processing Technology, Shaanxi Normal University, Xi'an, China.,College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Xiao Chao Xiong
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
| | - Yu Ling Qu
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, Shaanxi Normal University, Xi'an, China.,National Research & Development Center of Apple Processing Technology, Shaanxi Normal University, Xi'an, China.,College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Liang Liu
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, Shaanxi Normal University, Xi'an, China.,National Research & Development Center of Apple Processing Technology, Shaanxi Normal University, Xi'an, China.,College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Ching Yuan Hu
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, Shaanxi Normal University, Xi'an, China.,National Research & Development Center of Apple Processing Technology, Shaanxi Normal University, Xi'an, China.,College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China.,Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Yong Hong Meng
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, Shaanxi Normal University, Xi'an, China.,National Research & Development Center of Apple Processing Technology, Shaanxi Normal University, Xi'an, China.,College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
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34
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Microbial astaxanthin biosynthesis: recent achievements, challenges, and commercialization outlook. Appl Microbiol Biotechnol 2020; 104:5725-5737. [DOI: 10.1007/s00253-020-10648-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/15/2020] [Accepted: 04/26/2020] [Indexed: 12/15/2022]
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35
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Ramesh A, Ong T, Garcia JA, Adams J, Wheeldon I. Guide RNA Engineering Enables Dual Purpose CRISPR-Cpf1 for Simultaneous Gene Editing and Gene Regulation in Yarrowia lipolytica. ACS Synth Biol 2020; 9:967-971. [PMID: 32208677 DOI: 10.1021/acssynbio.9b00498] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Yarrowia lipolytica has fast become a biotechnologically significant yeast for its ability to accumulate lipids to high levels. While there exists a suite of synthetic biology tools for genetic engineering in this yeast, there is a need for multipurposed tools for rapid strain generation. Here, we describe a dual purpose CRISPR-Cpf1 system that is capable of simultaneous gene disruption and gene regulation. Truncating guide RNA spacer length to 16 nt inhibited nuclease activity but not binding to the target loci, enabling gene activation and repression with Cpf1-fused transcriptional regulators. Gene repression was demonstrated using a Cpf1-Mxi1 fusion achieving a 7-fold reduction in mRNA, while CRISPR-activation with Cpf1-VPR increased hrGFP expression by 10-fold. High efficiency disruptions were achieved with gRNAs 23-25 bp in length, and efficiency and repression levels were maintained with multiplexed expression of truncated and full-length gRNAs. The developed CRISPR-Cpf1 system should prove useful in metabolic engineering, genome wide screening, and functional genomics studies.
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Affiliation(s)
- Adithya Ramesh
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Thomas Ong
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Jaime A Garcia
- Department of Physics and Environmental Science, St. Mary's University, San Antonio, Texas 78228, United States
| | - Jessica Adams
- Molecular and Cell Biology Department, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
- Center for Industrial Biotechnology, Bourns College of Engineering, University of California Riverside, Riverside, California 92521, United States
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36
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Metabolic engineering of β-carotene biosynthesis in Yarrowia lipolytica. Biotechnol Lett 2020; 42:945-956. [DOI: 10.1007/s10529-020-02844-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/19/2020] [Indexed: 12/20/2022]
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37
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Usmani Z, Sharma M, Sudheer S, Gupta VK, Bhat R. Engineered Microbes for Pigment Production Using Waste Biomass. Curr Genomics 2020; 21:80-95. [PMID: 32655303 PMCID: PMC7324876 DOI: 10.2174/1389202921999200330152007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/08/2020] [Accepted: 03/16/2020] [Indexed: 12/17/2022] Open
Abstract
Agri-food waste biomass is the most abundant organic waste and has high valorisation potential for sustainable bioproducts development. These wastes are not only recyclable in nature but are also rich sources of bioactive carbohydrates, peptides, pigments, polyphenols, vitamins, natural antioxidants, etc. Bioconversion of agri-food waste to value-added products is very important towards zero waste and circular economy concepts. To reduce the environmental burden, food researchers are seeking strategies to utilize this waste for microbial pigments production and further biotechnological exploitation in functional foods or value-added products. Microbes are valuable sources for a range of bioactive molecules, including microbial pigments production through fermentation and/or utilisation of waste. Here, we have reviewed some of the recent advancements made in important bioengineering technologies to develop engineered microbial systems for enhanced pigments production using agri-food wastes biomass/by-products as substrates in a sustainable way.
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Affiliation(s)
| | - Minaxi Sharma
- Address correspondence to these authors at the ERA Chair for Food (By-) Products Valorization Technologies- VALORTECH, Estonian University of Life Sciences, Kreutzwaldi 56/5, 51006, Tartu, Estonia; Tel/Fax: +372 7313927; E-mails: ;, ;
| | | | | | - Rajeev Bhat
- Address correspondence to these authors at the ERA Chair for Food (By-) Products Valorization Technologies- VALORTECH, Estonian University of Life Sciences, Kreutzwaldi 56/5, 51006, Tartu, Estonia; Tel/Fax: +372 7313927; E-mails: ;, ;
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38
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Czajka JJ, Kambhampati S, Tang YJ, Wang Y, Allen DK. Application of Stable Isotope Tracing to Elucidate Metabolic Dynamics During Yarrowia lipolytica α-Ionone Fermentation. iScience 2020; 23:100854. [PMID: 32058965 PMCID: PMC7005465 DOI: 10.1016/j.isci.2020.100854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 12/19/2019] [Accepted: 01/15/2020] [Indexed: 11/15/2022] Open
Abstract
Targeted metabolite analysis in combination with 13C-tracing is a convenient strategy to determine pathway activity in biological systems; however, metabolite analysis is limited by challenges in separating and detecting pathway intermediates with current chromatographic methods. Here, a hydrophilic interaction chromatography tandem mass spectrometry approach was developed for improved metabolite separation, isotopologue analysis, and quantification. The physiological responses of a Yarrowia lipolytica strain engineered to produce ∼400 mg/L α-ionone and temporal changes in metabolism were quantified (e.g., mevalonate secretion, then uptake) indicating bottleneck shifts in the engineered pathway over the course of fermentation. Dynamic labeling results indicated limited tricarboxylic acid cycle label incorporation and, combined with a measurable ATP shortage during the high ionone production phase, suggested that electron transport and oxidative phosphorylation may limit energy supply and strain performance. The results provide insights into terpenoid pathway metabolic dynamics of non-model yeasts and offer guidelines for sensor development and modular engineering. A HILIC method is demonstrated for efficient separation of 57 cellular metabolites Production of α-ionone was ∼400 mg/L in bench-top bioreactors Engineered Y. lipolytica secreted then consumed mevalonate during fermentation Oxidative phosphorylation may limit performance in high-cell-density fermentations
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Affiliation(s)
- Jeffrey J Czajka
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA
| | | | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA.
| | - Yechun Wang
- Arch Innotek, LLC, 4320 Forest Park Avenue, St Louis, MO, USA.
| | - Doug K Allen
- Donald Danforth Plant Science Center, St. Louis, MO, USA; United States Department of Agriculture, Agricultural Research Service, St. Louis, MO, USA.
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39
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HamediRad M, Chao R, Weisberg S, Lian J, Sinha S, Zhao H. Towards a fully automated algorithm driven platform for biosystems design. Nat Commun 2019; 10:5150. [PMID: 31723141 PMCID: PMC6853954 DOI: 10.1038/s41467-019-13189-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 10/24/2019] [Indexed: 12/16/2022] Open
Abstract
Large-scale data acquisition and analysis are often required in the successful implementation of the design, build, test, and learn (DBTL) cycle in biosystems design. However, it has long been hindered by experimental cost, variability, biases, and missed insights from traditional analysis methods. Here, we report the application of an integrated robotic system coupled with machine learning algorithms to fully automate the DBTL process for biosystems design. As proof of concept, we have demonstrated its capacity by optimizing the lycopene biosynthetic pathway. This fully-automated robotic platform, BioAutomata, evaluates less than 1% of possible variants while outperforming random screening by 77%. A paired predictive model and Bayesian algorithm select experiments which are performed by Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB). BioAutomata excels with black-box optimization problems, where experiments are expensive and noisy and the success of the experiment is not dependent on extensive prior knowledge of biological mechanisms. Existing efforts have been focused on one of the elements in the automation of the design, build, test, and learn (DBTL) cycle for biosystems design. Here, the authors integrate a robotic system with machine learning algorithms to fully automate the DBTL cycle and apply it in optimizing the lycopene biosynthetic pathway.
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Affiliation(s)
- Mohammad HamediRad
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,LifeFoundry Inc., 60 Hazelwood Dr., Champaign, IL, 61820, USA
| | - Ran Chao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,LifeFoundry Inc., 60 Hazelwood Dr., Champaign, IL, 61820, USA
| | - Scott Weisberg
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jiazhang Lian
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China
| | - Saurabh Sinha
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Departments of Chemistry and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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40
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Bruder S, Melcher FA, Zoll T, Hackenschmidt S, Kabisch J. Evaluation of a
Yarrowia lipolytica
Strain Collection for Its Lipid and Carotenoid Production Capabilities. EUR J LIPID SCI TECH 2019. [DOI: 10.1002/ejlt.201900172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stefan Bruder
- Computer‐Aided Synthetic Biology TU Darmstadt Schnittspahnstr. 12 64287 Darmstadt Germany
| | - Felix Arthur Melcher
- Computer‐Aided Synthetic Biology TU Darmstadt Schnittspahnstr. 12 64287 Darmstadt Germany
| | - Thomas Zoll
- Computer‐Aided Synthetic Biology TU Darmstadt Schnittspahnstr. 12 64287 Darmstadt Germany
| | - Silke Hackenschmidt
- Computer‐Aided Synthetic Biology TU Darmstadt Schnittspahnstr. 12 64287 Darmstadt Germany
| | - Johannes Kabisch
- Computer‐Aided Synthetic Biology TU Darmstadt Schnittspahnstr. 12 64287 Darmstadt Germany
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41
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Egermeier M, Sauer M, Marx H. Golden Gate-based metabolic engineering strategy for wild-type strains of Yarrowia lipolytica. FEMS Microbiol Lett 2019; 366:5304171. [PMID: 30698703 DOI: 10.1093/femsle/fnz022] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/27/2019] [Indexed: 12/14/2022] Open
Abstract
The yeast Yarrowia lipolytica represents a future microbial cell factory for numerous applications in a bio-based economy. Outstanding feature of this yeast is the metabolic flexibility in utilising various substrates (sugars, fatty acids, glycerol, etc.). The potential of wild-type isolates of Y. lipolytica to convert glycerol into various value-added compounds is attracting attention of academia and industry. However, the already established tools for efficient engineering of the metabolism of Y. lipolytica are often dependent on genetic features like auxotrophic markers. With the present work we want to introduce a new set of vectors for metabolic engineering strategies, including CRISPR/Cas9 technology. The system is based on GoldenMOCS, a recently established rapid Golden Gate cloning strategy applicable in multiple organisms. We could show that our new GoldenMOCS plasmids are suitable for the extrachromosomal overexpression of the gene glycerol kinase (GUT1) in wild-type isolates of Y. lipolytica resulting in enhanced conversion of glycerol to erythritol and citric acid. Moreover, a GoldenMOCS plasmid for CRISPR/Cas9 mediated genome editing has been designed, which facilitates single gene knock-outs with efficiencies between 6% and 25% in strains with genetic wild-type background.
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Affiliation(s)
- Michael Egermeier
- CD-Laboratory for Biotechnology of Glycerol, Muthgasse 18, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Michael Sauer
- CD-Laboratory for Biotechnology of Glycerol, Muthgasse 18, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Hans Marx
- CD-Laboratory for Biotechnology of Glycerol, Muthgasse 18, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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42
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Shiferaw Terefe N, Augustin MA. Fermentation for tailoring the technological and health related functionality of food products. Crit Rev Food Sci Nutr 2019; 60:2887-2913. [PMID: 31583891 DOI: 10.1080/10408398.2019.1666250] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fermented foods are experiencing a resurgence due to the consumers' growing interest in foods that are natural and health promoting. Microbial fermentation is a biotechnological process which transforms food raw materials into palatable, nutritious and healthy food products. Fermentation imparts unique aroma, flavor and texture to food, improves digestibility, degrades anti-nutritional factors, toxins and allergens, converts phytochemicals such as polyphenols into more bioactive and bioavailable forms, and enriches the nutritional quality of food. Fermentation also modifies the physical functional properties of food materials, rendering them differentiated ingredients for use in formulated foods. The science of fermentation and the technological and health functionality of fermented foods is reviewed considering the growing interest worldwide in fermented foods and beverages and the huge potential of the technology for reducing food loss and improving nutritional food security.
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43
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Arhar S, Natter K. Common aspects in the engineering of yeasts for fatty acid- and isoprene-based products. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:158513. [PMID: 31465888 DOI: 10.1016/j.bbalip.2019.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/26/2019] [Accepted: 08/20/2019] [Indexed: 11/18/2022]
Abstract
The biosynthetic pathways for most lipophilic metabolites share several common principles. These substances are built almost exclusively from acetyl-CoA as the donor for the carbon scaffold and NADPH is required for the reductive steps during biosynthesis. Due to their hydrophobicity, the end products are sequestered into the same cellular compartment, the lipid droplet. In this review, we will summarize the efforts in the metabolic engineering of yeasts for the production of two major hydrophobic substance classes, fatty acid-based lipids and isoprenoids, with regard to these common aspects. We will compare and discuss the results of genetic engineering strategies to construct strains with enhanced synthesis of the precursor acetyl-CoA and with modified redox metabolism for improved NADPH supply. We will also discuss the role of the lipid droplet in the storage of the hydrophobic product and review the strategies to either optimize this organelle for higher capacity or to achieve excretion of the product into the medium.
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Affiliation(s)
- Simon Arhar
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria.
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44
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Moser S, Pichler H. Identifying and engineering the ideal microbial terpenoid production host. Appl Microbiol Biotechnol 2019; 103:5501-5516. [PMID: 31129740 PMCID: PMC6597603 DOI: 10.1007/s00253-019-09892-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022]
Abstract
More than 70,000 different terpenoid structures are known so far; many of them offer highly interesting applications as pharmaceuticals, flavors and fragrances, or biofuels. Extraction of these compounds from their natural sources or chemical synthesis is-in many cases-technically challenging with low or moderate yields while wasting valuable resources. Microbial production of terpenoids offers a sustainable and environment-friendly alternative starting from simple carbon sources and, frequently, safeguards high product specificity. Here, we provide an overview on employing recombinant bacteria and yeasts for heterologous de novo production of terpenoids. Currently, Escherichia coli and Saccharomyces cerevisiae are the two best-established production hosts for terpenoids. An increasing number of studies have been successful in engineering alternative microorganisms for terpenoid biosynthesis, which we intend to highlight in this review. Moreover, we discuss the specific engineering challenges as well as recent advances for microbial production of different classes of terpenoids. Rationalizing the current stages of development for different terpenoid production hosts as well as future prospects shall provide a valuable decision basis for the selection and engineering of the cell factory(ies) for industrial production of terpenoid target molecules.
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Affiliation(s)
- Sandra Moser
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010, Graz, Austria
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, Petersgasse 14/2, 8010, Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010, Graz, Austria.
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, Petersgasse 14/2, 8010, Graz, Austria.
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45
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Schwartz C, Cheng JF, Evans R, Schwartz CA, Wagner JM, Anglin S, Beitz A, Pan W, Lonardi S, Blenner M, Alper HS, Yoshikuni Y, Wheeldon I. Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica. Metab Eng 2019; 55:102-110. [PMID: 31216436 DOI: 10.1016/j.ymben.2019.06.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/06/2019] [Accepted: 06/14/2019] [Indexed: 12/26/2022]
Abstract
Genome-wide mutational screens are central to understanding the genetic underpinnings of evolved and engineered phenotypes. The widespread adoption of CRISPR-Cas9 genome editing has enabled such screens in many organisms, but identifying functional sgRNAs still remains a challenge. Here, we developed a methodology to quantify the cutting efficiency of each sgRNA in a genome-scale library, and in doing so improve screens in the biotechnologically important yeast Yarrowia lipolytica. Screening in the presence and absence of native DNA repair enabled high-throughput quantification of sgRNA function leading to the identification of high efficiency sgRNAs that cover 94% of genes. Library validation enhanced the classification of essential genes by identifying inactive guides that create false negatives and mask the effects of successful disruptions. Quantification of guide effectiveness also creates a dataset from which determinants of CRISPR-Cas9 can be identified. Finally, application of the library identified novel mutations for metabolic engineering of high lipid accumulation.
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Affiliation(s)
- Cory Schwartz
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Robert Evans
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Christopher A Schwartz
- Department of Civil and Mechanical Engineering, United States Military Academy, West Point, NY, 10996, USA
| | - James M Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - Scott Anglin
- Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Adam Beitz
- Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Weihua Pan
- Computer Science and Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Computer Science and Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Mark Blenner
- Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, 78712, USA
| | - Yasuo Yoshikuni
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA.
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46
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Ma YR, Wang KF, Wang WJ, Ding Y, Shi TQ, Huang H, Ji XJ. Advances in the metabolic engineering of Yarrowia lipolytica for the production of terpenoids. BIORESOURCE TECHNOLOGY 2019; 281:449-456. [PMID: 30846235 DOI: 10.1016/j.biortech.2019.02.116] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/24/2019] [Accepted: 02/26/2019] [Indexed: 05/02/2023]
Abstract
Terpenoids are a large class of natural compounds based on the C5 isoprene unit, with many biological effects such activity against cancer and allergies, while some also have an agreeable aroma. Consequently, they have received extensive attention in the food, pharmaceutical and cosmetic fields. With the identification and analysis of the underlying natural product synthesis pathways, current microbial-based metabolic engineering approaches have yielded new strategies for the production of highly valuable terpenoids. Yarrowia lipolytica is a non-conventional oleaginous yeast that is rapidly emerging as a valuable host for the production of terpenoids due to its own endogenous mevalonate pathway and high oil production capacity. This review aims to summarize the status and strategies of metabolic engineering for the heterologous synthesis of terpenoids in Y. lipolytica in recent years and proposes new methods aiming towards further improvement of terpenoid production.
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Affiliation(s)
- Yi-Rong Ma
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Kai-Feng Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Wei-Jian Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Ying Ding
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Tian-Qiong Shi
- 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 Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, No. 5 Xinmofan Road, Nanjing 210009, 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; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China.
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47
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Liu D, Liu H, Qi H, Guo XJ, Jia B, Zhang JL, Yuan YJ. Constructing Yeast Chimeric Pathways To Boost Lipophilic Terpene Synthesis. ACS Synth Biol 2019; 8:724-733. [PMID: 30779549 DOI: 10.1021/acssynbio.8b00360] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Synthetic chimeric biological system offers opportunities to illuminate principles of designing life, and a primary step is constructing synthetic chimeric pathways. Here, we constructed yeast chimeric pathways by transferring the genes from Saccharomyces cerevisiae pathways into another budding yeast Yarrowia lipolytica for in vivo assembly. We efficiently diversified gene option, combination, localization order, and copy number as expected. Convergence of two yeast pathways, especially mevalonic acid (MVA) pathways, remarkably enhanced synthesis of a lipophilic terpene, lycopene. In the selected champion strain with 50-fold of enhanced lycopene production, the chimeric MVA pathway gathered three S. cerevisiae genes with particular copies and locations. Amazingly, therein we discovered distinct transcriptional up-regulation of three significant pathways correlated with acetyl-CoA supply and tuning of cellular lipid amounts and composition. Modulating these pathways further improved lycopene production to 150-fold, a final 259 mg/L (approximately 80 mg/g DCW). We primarily showed the capacity of boosting the synthesis of lipophilic products with yeast chimeric pathways.
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Affiliation(s)
- Duo Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Hong Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Hao Qi
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Xue-Jiao Guo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Bin Jia
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Jin-Lai Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Ying-Jin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
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48
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Wang C, Zhao S, Shao X, Park JB, Jeong SH, Park HJ, Kwak WJ, Wei G, Kim SW. Challenges and tackles in metabolic engineering for microbial production of carotenoids. Microb Cell Fact 2019; 18:55. [PMID: 30885243 PMCID: PMC6421696 DOI: 10.1186/s12934-019-1105-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/08/2019] [Indexed: 02/07/2023] Open
Abstract
Naturally occurring carotenoids have been isolated and used as colorants, antioxidants, nutrients, etc. in many fields. There is an ever-growing demand for carotenoids production. To comfort this, microbial production of carotenoids is an attractive alternative to current extraction from natural sources. This review summarizes the biosynthetic pathway of carotenoids and progresses in metabolic engineering of various microorganisms for carotenoid production. The advances in synthetic pathway and systems biology lead to many versatile engineering tools available to manipulate microorganisms. In this context, challenges and possible directions are also discussed to provide an insight of microbial engineering for improved production of carotenoids in the future.
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Affiliation(s)
- Chonglong Wang
- School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123, People's Republic of China.
| | - Shuli Zhao
- School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123, People's Republic of China
| | - Xixi Shao
- School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123, People's Republic of China
| | - Ji-Bin Park
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Seong-Hee Jeong
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Hyo-Jin Park
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Won-Ju Kwak
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Gongyuan Wei
- School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123, People's Republic of China
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Wurtzel ET. Changing Form and Function through Carotenoids and Synthetic Biology. PLANT PHYSIOLOGY 2019; 179:830-843. [PMID: 30361256 PMCID: PMC6393808 DOI: 10.1104/pp.18.01122] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/06/2018] [Indexed: 05/06/2023]
Abstract
The diverse structures and multifaceted roles of carotenoids make these colorful pigments attractive targets for synthetic biology.
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Affiliation(s)
- Eleanore T Wurtzel
- Department of Biological Sciences, Lehman College, The City University of New York, Bronx, New York 10468
- The Graduate School and University Center-CUNY, New York, New York 10016-4309
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Multicopy integrants of crt genes and co-expression of AMP deaminase improve lycopene production in Yarrowia lipolytica. J Biotechnol 2019; 289:46-54. [DOI: 10.1016/j.jbiotec.2018.11.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 11/13/2018] [Accepted: 11/13/2018] [Indexed: 01/26/2023]
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