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Hu M, Ge J, Jiang Y, Sun X, Guo D, Gu Y. Advances and perspectives in genetic expression and operation for the oleaginous yeast Yarrowia lipolytica. Synth Syst Biotechnol 2024; 9:618-626. [PMID: 38784195 PMCID: PMC11109602 DOI: 10.1016/j.synbio.2024.05.003] [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: 01/14/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
The utilization of industrial biomanufacturing has emerged as a viable and sustainable alternative to fossil-based resources for producing functional chemicals. Moreover, advancements in synthetic biology have created new opportunities for the development of innovative cell factories. Notably, Yarrowia lipolytica, an oleaginous yeast that is generally regarded as safe, possesses several advantageous characteristics, including the ability to utilize inexpensive renewable carbon sources, well-established genetic backgrounds, and mature genetic manipulation methods. Consequently, there is increasing interest in manipulating the metabolism of this yeast to enhance its potential as a biomanufacturing platform. Here, we reviewed the latest developments in genetic expression strategies and manipulation tools related to Y. lipolytica, particularly focusing on gene expression, chromosomal operation, CRISPR-based tool, and dynamic biosensors. The purpose of this review is to serve as a valuable reference for those interested in the development of a Y. lipolytica microbial factory.
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Affiliation(s)
- Mengchen Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jianyue Ge
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yaru Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Dongshen Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
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Li DX, Guo Q, Yang YX, Jiang SJ, Ji XJ, Ye C, Wang YT, Shi TQ. Recent Advances and Multiple Strategies of Monoterpenoid Overproduction in Saccharomyces cerevisiae and Yarrowia lipolytica. ACS Synth Biol 2024; 13:1647-1662. [PMID: 38860708 DOI: 10.1021/acssynbio.4c00297] [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: 06/12/2024]
Abstract
Monoterpenoids are an important subclass of terpenoids that play important roles in the energy, cosmetics, pharmaceuticals, and fragrances fields. With the development of biotechnology, microbial synthesis of monoterpenoids has received great attention. Yeasts such Saccharomyces cerevisiae and Yarrowia lipolytica are emerging as potential hosts for monoterpenoids production because of unique advantages including rapid growth cycles, mature gene editing tools, and clear genetic background. Recently, advancements in metabolic engineering and fermentation engineering have significantly enhanced the accumulation of monoterpenoids in cell factories. First, this review introduces the biosynthetic pathway of monoterpenoids and comprehensively summarizes the latest production strategies, which encompass enhancing precursor flux, modulating the expression of rate-limited enzymes, suppressing competitive pathway flux, mitigating cytotoxicity, optimizing substrate utilization, and refining the fermentation process. Subsequently, this review introduces four representative monoterpenoids. Finally, we outline the future prospects for efficient construction cell factories tailored for the production of monoterpenoids and other terpenoids.
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Affiliation(s)
- Dong-Xun Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Yu-Xin Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Shun-Jie Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, 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
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
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Xu M, Yang N, Pan J, Hua Q, Li CX, Xu JH. Remodeling the Homologous Recombination Mechanism of Yarrowia lipolytica for High-Level Biosynthesis of Squalene. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:9984-9993. [PMID: 38635942 DOI: 10.1021/acs.jafc.4c01779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Squalene is a high-value antioxidant with many commercial applications. The use of microbial cell factories to produce squalene as an alternative to plant and animal extracts could meet increasing market demand. Yarrowia lipolytica is an excellent host for squalene production due to its high levels of acetyl-CoA and a hydrophobic environment. However, the need for precise and complicated gene editing has hindered the industrialization of this strain. Herein, the rapid construction of a strain with high squalene production was achieved by enhancing the homologous recombination efficiency in Y. lipolytica. First, remodeling of the homologous recombination efficiency resulted in a 10-fold increase in the homologous recombination rate. Next, the whole mevalonate pathway was integrated into the chromosome to enhance squalene production. Then, a higher level of squalene accumulation was achieved by increasing the level of acetyl coenzyme A and regulating the downstream steroid synthesis pathway. Finally, the squalene production reached 35 g/L after optimizing the fermentation conditions and performing a fed-batch culture in a 5 L jar fermenter. This is the highest squalene production ever reported to date by de novo biosynthesis without adding any inhibitors, paving a new path toward the industrial production of squalene and its downstream products.
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Affiliation(s)
- Man Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Nan Yang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jiang Pan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Chun-Xiu Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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Guo Q, Peng QQ, Li YW, Yan F, Wang YT, Ye C, Shi TQ. Advances in the metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica for the production of β-carotene. Crit Rev Biotechnol 2024; 44:337-351. [PMID: 36779332 DOI: 10.1080/07388551.2023.2166809] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/20/2022] [Accepted: 12/08/2022] [Indexed: 02/14/2023]
Abstract
β-Carotene is one kind of the most important carotenoids. The major functions of β-carotene include the antioxidant and anti-cardiovascular properties, which make it a growing market. Recently, the use of metabolic engineering to construct microbial cell factories to synthesize β-carotene has become the latest model for its industrial production. Among these cell factories, yeasts including Saccharomyces cerevisiae and Yarrowia lipolytica have attracted the most attention because of the: security, mature genetic manipulation tools, high flux toward carotenoids using the native mevalonate pathway and robustness for large-scale fermentation. In this review, the latest strategies for β-carotene biosynthesis, including protein engineering, promoters engineering and morphological engineering are summarized in detail. Finally, perspectives for future engineering approaches are proposed to improve β-carotene production.
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Affiliation(s)
- Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Qian-Qian Peng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ya-Wen Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Fang Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
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5
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Bejenari M, Spedtsberg EML, Mathiesen J, Jeppesen AC, Cernat L, Toussaint A, Apostol C, Stoianov V, Pedersen TB, Nielsen MR, Sørensen JL. First-class - biosynthesis of 6-MSA and bostrycoidin type I polyketides in Yarrowia lipolytica. FRONTIERS IN FUNGAL BIOLOGY 2024; 5:1327777. [PMID: 38586602 PMCID: PMC10995274 DOI: 10.3389/ffunb.2024.1327777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/09/2024] [Indexed: 04/09/2024]
Abstract
Fungal polyketides are a large group of secondary metabolites, valuable due to their diverse spectrum of pharmacological activities. Polyketide biosynthesis in filamentous fungi presents some challenges: small yield and low-purity titers. To tackle these issues, we switched to the yeast Yarrowia lipolytica, an easily cultivable heterologous host. As an oleaginous yeast, Y. lipolytica displays a high flux of acetyl- and malonyl-CoA precursors used in lipid synthesis. Likewise, acetyl- and malonyl-CoA are the building blocks of many natural polyketides, and we explored the possibility of redirecting this flux toward polyketide production. Despite its promising prospect, Y. lipolytica has so far only been used for heterologous expression of simple type III polyketide synthases (PKSs) from plants. Therefore, we decided to evaluate the potential of Y. lipolytica by targeting the more complex fungal polyketides synthesized by type I PKSs. We employed a CRISPR-Cas9-mediated genome editing method to achieve markerless gene integration of the genes responsible for bostrycoidin biosynthesis in Fusarium solani (fsr1, fsr2, and fsr3) and 6-methylsalicylic acid (6-MSA) biosynthesis in Aspergillus hancockii (6MSAS). Moreover, we attempted titer optimization through metabolic engineering by overexpressing two enzymes, TGL4 and AOX2, involved in lipid β-oxidation, but we did not observe an effect on polyketide production. With maximum titers of 403 mg/L 6-MSA and 35 mg/L bostrycoidin, the latter being substantially higher than our previous results in Saccharomyces cerevisiae (2.2 mg/L), this work demonstrates the potential of Y. lipolytica as a platform for heterologous production of complex fungal polyketides.
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Affiliation(s)
- Mihaela Bejenari
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Eva Mie Lang Spedtsberg
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
- Department of Energy, Aalborg University, Esbjerg, Denmark
| | - Julie Mathiesen
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | | | - Lucia Cernat
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Aouregane Toussaint
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire Végétale, CEA, CNRS, INRA, IRIG-LPCV, Grenoble, France
| | - Cristina Apostol
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Victor Stoianov
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | | | - Mikkel Rank Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
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Liu H, Huang X, Liu Y, Jing X, Ning Y, Xu P, Deng L, Wang F. Efficient Production of Triacetic Acid Lactone from Lignocellulose Hydrolysate by Metabolically Engineered Yarrowia lipolytica. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18909-18918. [PMID: 37999448 DOI: 10.1021/acs.jafc.3c06528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Lignocellulose is a promising renewable feedstock for the bioproduction of high-value biochemicals. The poorly expressed xylose catabolic pathway was the bottleneck in the efficient utilization of the lignocellulose feedstock in yeast. Herein, multiple genetic and process engineering strategies were explored to debottleneck the conversion of xylose to the platform chemical triacetic acid lactone (TAL) in Yarrowia lipolytica. We identified that xylose assimilation generating more cofactor NADPH was favorable for the TAL synthesis. pH control improved the expression of acetyl-CoA carboxylase and generated more precursor malonyl-CoA. Combined with the suppression of the lipid synthesis pathway, 5.03 and 4.18 g/L TAL were produced from pure xylose and xylose-rich wheat straw hydrolysate, respectively. Our work removed the bottleneck of the xylose assimilation pathway and effectively upgraded wheat straw hydrolysate to TAL, which enabled us to build a sustainable oleaginous yeast cell factory to cost-efficiently produce green chemicals from low-cost lignocellulose by Y. lipolytica.
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Affiliation(s)
- Huan Liu
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolan Huang
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yangming Liu
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinyun Jing
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuchen Ning
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China
| | - Li Deng
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Fang Wang
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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Agrawal A, Yang Z, Blenner M. Engineering Yarrowia lipolytica for the biosynthesis of geraniol. Metab Eng Commun 2023; 17:e00228. [PMID: 38029016 PMCID: PMC10652127 DOI: 10.1016/j.mec.2023.e00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Geraniol is a monoterpene with wide applications in the food, cosmetics, and pharmaceutical industries. Microbial production has largely used model organisms lacking favorable properties for monoterpene production. In this work, we produced geraniol in metabolically engineered Yarrowia lipolytica. First, two plant-derived geraniol synthases (GES) from Catharanthus roseus (Cr) and Valeriana officinalis (Vo) were tested based on previous reports of activity. Both wild type and truncated mutants of GES (without signal peptide targeting chloroplast) were examined by co-expressing with MVA pathway enzymes tHMG1 and IDI1. Truncated CrGES (tCrGES) produced the most geraniol and thus was used for further experimentation. The initial strain was obtained by overexpression of the truncated HMG1, IDI and tCrGES. The acetyl-CoA precursor pool was enhanced by overexpressing mevalonate pathway genes such as ERG10, HMGS or MVK, PMK. The final strain overexpressing 3 copies of tCrGES and single copies of ERG10, HMGS, tHMG1, IDI produced approximately 1 g/L in shake-flask fermentation. This is the first demonstration of geraniol production in Yarrowia lipolytica and the highest de novo titer reported to date in yeast.
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Affiliation(s)
- Ayushi Agrawal
- Department of Chemical and Biomolecular Engineering, 590 Avenue 1743, University of Delaware, Newark, DE, 19713, USA
| | - Zhiliang Yang
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634, USA
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, 590 Avenue 1743, University of Delaware, Newark, DE, 19713, USA
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634, USA
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8
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Jovanovic Gasovic S, Dietrich D, Gläser L, Cao P, Kohlstedt M, Wittmann C. Multi-omics view of recombinant Yarrowia lipolytica: Enhanced ketogenic amino acid catabolism increases polyketide-synthase-driven docosahexaenoic production to high selectivity at the gram scale. Metab Eng 2023; 80:45-65. [PMID: 37683719 DOI: 10.1016/j.ymben.2023.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
DHA is a marine PUFA of commercial value, given its multiple health benefits. The worldwide emerging shortage in DHA supply has increased interest in microbial cell factories that can provide the compound de novo. In this regard, the present work aimed to improve DHA production in the oleaginous yeast strain Y. lipolytica Af4, which synthetized the PUFA via a heterologous myxobacterial polyketide synthase (PKS)-like gene cluster. As starting point, we used transcriptomics, metabolomics, and 13C-based metabolic pathway profiling to study the cellular dynamics of Y. lipolytica Af4. The shift from the growth to the stationary DHA-production phase was associated with fundamental changes in carbon core metabolism, including a strong upregulation of the PUFA gene cluster, as well as an increase in citrate and fatty acid degradation. At the same time, the intracellular levels of the two DHA precursors acetyl-CoA and malonyl-CoA dropped by up to 98% into the picomolar range. Interestingly, the degradation pathways for the ketogenic amino acids l-lysine, l-leucine, and l-isoleucine were transcriptionally activated, presumably to provide extra acetyl-CoA. Supplementation with small amounts of these amino acids at the beginning of the DHA production phase beneficially increased the intracellular CoA-ester pools and boosted the DHA titer by almost 40%. Isotopic 13C-tracer studies revealed that the supplements were efficiently directed toward intracellular CoA-esters and DHA. Hereby, l-lysine was found to be most efficient, as it enabled long-term activation, due to storage within the vacuole and continuous breakdown. The novel strategy enabled DHA production in Y. lipolytica at the gram scale for the first time. DHA was produced at a high selectivity (27% of total fatty acids) and free of the structurally similar PUFA DPA, which facilitates purification for high-value medical applications that require API-grade DHA. The assembled multi-omics picture of the central metabolism of Y. lipolytica provides valuable insights into this important yeast. Beyond our work, the enhanced catabolism of ketogenic amino acids seems promising for the overproduction of other compounds in Y. lipolytica, whose synthesis is limited by the availability of CoA ester precursors.
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Affiliation(s)
| | - Demian Dietrich
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Peng Cao
- Institute of Systems Biotechnology, Saarland University, Germany
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Matsuoka Y, Fujie N, Nakano M, Koshiba A, Kondo A, Tanaka T. Triacetic acid lactone production using 2-pyrone synthase expressing Yarrowia lipolytica via targeted gene deletion. J Biosci Bioeng 2023; 136:320-326. [PMID: 37574415 DOI: 10.1016/j.jbiosc.2023.07.006] [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: 03/14/2023] [Revised: 07/11/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023]
Abstract
An environmentally sustainable world can be realized by using microorganisms to produce value-added materials from renewable biomass. Triacetic acid lactone (TAL) is a high-value-added compound that is used as a precursor of various organic compounds such as food additives and pharmaceuticals. In this study, we used metabolic engineering to produce TAL from glucose using an oleaginous yeast Yarrowia lipolytica. We first introduced TAL-producing gene 2-pyrone synthase into Y. lipolytica, which enabled TAL production. Next, we increased TAL production by engineering acetyl-CoA and malonyl-CoA biosynthesis pathways by redirecting carbon flux to glycolysis. Finally, we optimized the carbon and nitrogen ratios in the medium, culminating in the production of 4078 mg/L TAL. The strategy presented in this study had the potential to improve the titer and yield of polyketide biosynthesis.
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Affiliation(s)
- Yuta Matsuoka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Naofumi Fujie
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Mariko Nakano
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Ayumi Koshiba
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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10
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Zhang P, Wei W, Shang Y, Ye BC. Metabolic engineering of Yarrowia lipolytica for high-level production of scutellarin. BIORESOURCE TECHNOLOGY 2023:129421. [PMID: 37392967 DOI: 10.1016/j.biortech.2023.129421] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
Scutellarin drugs have been recognized as a key item in the national development of essential clinical emergency drugs for treating cardiovascular and cerebrovascular diseases; therefore, the market demand for scutellarin is growing rapidly. Microbial synthesis based on synthetic biology is a promising method for industrial production of scutellarin. In this study, the highest reported scutellarin titer in the shake flask of 703.01 ± 4.83 mg/L was achieved in Yarrowia lipolytica through the systematic metabolic engineering modifications, including screening for the optimal flavone-6-hydroxylase-cytochrome P450 reductase combination SbF6H-ATR2 to enhance P450 enzyme activity, increasing the copy numbers of rate-limiting enzyme genes, overexpressing ZWF1 and GND1 to increase NADPH supply, enhancing the supply of p-coumaric acid and uridine diphosphate glucose, and introducing the heterologous gene VHb to enhance oxygen supply. This study has significant implications for the industrial production of scutellarin and other valuable flavonoids in green economies.
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Affiliation(s)
- Ping Zhang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wenping Wei
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Yanzhe Shang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
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11
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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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12
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Zhu J, Gu Y, Yan Y, Ma J, Sun X, Xu P. Knocking out central metabolism genes to identify new targets and alternating substrates to improve lipid synthesis in Y. lipolytica. Front Bioeng Biotechnol 2023; 11:1098116. [PMID: 36714010 PMCID: PMC9880266 DOI: 10.3389/fbioe.2023.1098116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Introduction: Systematic gene knockout studies may offer us novel insights on cell metabolism and physiology. Specifically, the lipid accumulation mechanism at the molecular or cellular level is yet to be determined in the oleaginous yeast Y. lipolytica. Methods: Herein, we established ten engineered strains with the knockout of important genes involving in central carbon metabolism, NADPH generation, and fatty acid biosynthetic pathways. Results: Our result showed that NADPH sources for lipogenesis include the OxPP pathway, POM cycle, and a trans-mitochondrial isocitrate-α-oxoglutarate NADPH shuttle in Y. lipolytica. Moreover, we found that knockout of mitochondrial NAD+ isocitrate dehydrogenase IDH2 and overexpression of cytosolic NADP+ isocitrate dehydrogenase IDP2 could facilitate lipid synthesis. Besides, we also demonstrated that acetate is a more favorable carbon source for lipid synthesis when glycolysis step is impaired, indicating the evolutionary robustness of Y. lipolytica. Discussion: This systematic investigation of gene deletions and overexpression across various lipogenic pathways would help us better understand lipogenesis and engineer yeast factories to upgrade the lipid biomanufacturing platform.
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Affiliation(s)
- Jiang Zhu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China,Department of Chemical, Biochemical and Environmental Engineering, University of MD, Baltimore County, Baltimore, MD, United States,*Correspondence: Yang Gu, ; Peng Xu,
| | - Yijing Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Jingbo Ma
- Department of Chemical, Biochemical and Environmental Engineering, University of MD, Baltimore County, Baltimore, MD, United States,College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, Anhui, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of MD, Baltimore County, Baltimore, MD, United States,Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong, China,The Wolfson Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel,*Correspondence: Yang Gu, ; Peng Xu,
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13
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Marsafari M, Azi F, Dou S, Xu P. Modular co-culture engineering of Yarrowia lipolytica for amorphadiene biosynthesis. Microb Cell Fact 2022; 21:279. [PMID: 36587216 PMCID: PMC9805133 DOI: 10.1186/s12934-022-02010-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 12/23/2022] [Indexed: 01/02/2023] Open
Abstract
Amorphadiene is the precursor to synthesize the antimalarial drug artemisinin. The production of amorphadiene and artemisinin from metabolically engineered microbes may provide an alternate to plant secondary metabolite extraction. Microbial consortia can offer division of labor, and microbial co-culture system can be leveraged to achieve cost-efficient production of natural products. Using a co-culture system of Y. lipolytica Po1f and Po1g strains, subcellular localization of ADS gene (encoding amorphadiene synthase) into the endoplasmic reticulum, co-utilization of mixed carbon source, and enlargement of the endoplasmic reticulum (ER) surface area, we were able to significantly improve amorphadiene production in this work. Using Po1g/PPtM and Po1f/AaADSERx3/iGFMPDU strains and co-utilization of 5 µM sodium acetate with 20 g/L glucose in YPD media, amorphadiene titer were increased to 65.094 mg/L. The enlargement of the ER surface area caused by the deletion of the PAH1 gene provided more subcellular ER space for the action of the ADS-tagged gene. It further increased the amorphadiene production to 71.74 mg/L. The results demonstrated that the importance of the spatial localization of critical enzymes, and manipulating metabolic flux in the co-culture of Y. lipolytica can be efficient over a single culture for the bioproduction of isoprenoid-related secondary metabolites in a modular manner.
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Affiliation(s)
- Monireh Marsafari
- grid.266673.00000 0001 2177 1144Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD 21250 USA
| | - Fidelis Azi
- grid.499254.70000 0004 7668 8980Department of Chemical Engineering, Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion (MATEC), Guangdong Technion – Israel Institute of Technology, Shantou, 515063 Guangdong China
| | - Shaohua Dou
- grid.440706.10000 0001 0175 8217College of Life and Health, Dalian University, Dalian, 116622 Liaoning China ,Liaoning Marine Microorganism Engineering and Technology Research Center, Dalian, 116622 Liaoning China
| | - Peng Xu
- grid.266673.00000 0001 2177 1144Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD 21250 USA ,grid.499254.70000 0004 7668 8980Department of Chemical Engineering, Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion (MATEC), Guangdong Technion – Israel Institute of Technology, Shantou, 515063 Guangdong China
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14
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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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15
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Characterization of the endogenous promoters in Yarrowia lipolytica for the biomanufacturing applications. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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16
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Cai Y, Chen H, Tang X, Zhao J, Zhang H, Chen YQ, Chen W. The relationship between amino acid and lipid metabolism in oleaginous eukaryotic microorganism. Appl Microbiol Biotechnol 2022; 106:3405-3417. [PMID: 35503470 DOI: 10.1007/s00253-022-11931-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022]
Abstract
Amino acids are the building blocks of protein, promoting the balance between growth and lipid synthesis. However, the accumulation of microbial lipids involves multiple pathways, which requires the analysis of the global cellular metabolic network in which amino acid metabolism is involved. This review illustrates the dependence patterns of intracellular amino acids and lipids of oleaginous eukaryotic microorganisms in different environments and points out the contribution of amino acid metabolic precursors to the de novo synthesis of fatty acids. We emphasized the key role of amino acid metabolism in lipid remodeling and autophagy behavior and highlighted the regulatory effects of amino acids and their secondary metabolites as signal factors for microbial lipid synthesis. The application prospects of omics technology and genetic engineering technology in the field of microbial lipids are described. KEY POINTS: • Overview of microbial lipid synthesis mediated by amino acid metabolism • Insight into metabolic mechanisms founding multiple regulatory networks is provided • Description of microbial lipid homeostasis mediated by amino acid excitation signal.
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Affiliation(s)
- Yibo Cai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China. .,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China. .,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China.
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China.,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, 214122, People's Republic of China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 5: , 27127, USA
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China
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17
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Zhang Y, Pang J, Liu S, Nie K, Deng L, Wang F, Liu J. Harnessing transcription factor Mga2 and fatty acid elongases to overproduce palmitoleic acid in Saccharomyces cerevisiae. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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Screening novel genes by a comprehensive strategy to construct multiple stress-tolerant industrial Saccharomyces cerevisiae with prominent bioethanol production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:11. [PMID: 35418148 PMCID: PMC8783499 DOI: 10.1186/s13068-022-02109-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/09/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Strong multiple stress-tolerance is a desirable characteristic for Saccharomyces cerevisiae when different feedstocks are used for economical industrial ethanol production. Random mutagenesis or genome shuffling has been applied for improving multiple stress-tolerance, however, these techniques are generally time-consuming and labor cost-intensive and their molecular mechanisms are unclear. Genetic engineering, as an efficient technology, is poorly applied to construct multiple stress-tolerant industrial S. cerevisiae due to lack of clear genetic targets. Therefore, constructing multiple stress-tolerant industrial S. cerevisiae is challenging. In this study, some target genes were mined by comparative transcriptomics analysis and applied for the construction of multiple stress-tolerant industrial S. cerevisiae strains with prominent bioethanol production. RESULTS Twenty-eight shared differentially expressed genes (DEGs) were identified by comparative analysis of the transcriptomes of a multiple stress-tolerant strain E-158 and its original strain KF-7 under five stress conditions (high ethanol, high temperature, high glucose, high salt, etc.). Six of the shared DEGs which may have strong relationship with multiple stresses, including functional genes (ASP3, ENA5), genes of unknown function (YOL162W, YOR012W), and transcription factors (Crz1p, Tos8p), were selected by a comprehensive strategy from multiple aspects. Through genetic editing based on the CRISPR/Case9 technology, it was demonstrated that expression regulation of each of these six DEGs improved the multiple stress-tolerance and ethanol production of strain KF-7. In particular, the overexpression of ENA5 significantly enhanced the multiple stress-tolerance of not only KF-7 but also E-158. The resulting engineered strain, E-158-ENA5, achieved higher accumulation of ethanol. The ethanol concentrations were 101.67% and 27.31% higher than those of the E-158 when YPD media and industrial feedstocks (straw, molasses, cassava) were fermented, respectively, under stress conditions. CONCLUSION Six genes that could be used as the gene targets to improve multiple stress-tolerance and ethanol production capacities of S. cerevisiae were identified for the first time. Compared to the other five DEGs, ENA5 has a more vital function in regulating the multiple stress-tolerance of S. cerevisiae. These findings provide novel insights into the efficient construction of multiple stress-tolerant industrial S. cerevisiae suitable for the fermentation of different raw materials.
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19
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Yang W, Shah AM, Dong S, Sun C, Zhang H, Mohamed H, Gao X, Fan H, Song Y. Tricarboxylate Citrate Transporter of an Oleaginous Fungus Mucor circinelloides WJ11: From Function to Structure and Role in Lipid Production. Front Nutr 2021; 8:802231. [PMID: 34957193 PMCID: PMC8696028 DOI: 10.3389/fnut.2021.802231] [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: 10/26/2021] [Accepted: 11/15/2021] [Indexed: 11/30/2022] Open
Abstract
The citrate transporter protein (CTP) plays an important role in citrate efflux from the mitochondrial matrix to cytosol that has great importance in oleaginous fungi. The cytoplasmic citrate produced after citrate efflux serves as the primary carbon source for the triacylglycerol and cholesterol biosynthetic pathways. Because of the CTP's importance, our laboratory has extensively studied its structure/function relationships in Mucor circinelloides to comprehend its molecular mechanism. In the present study, the tricarboxylate citrate transporter (Tct) of M. circinelloides WJ11 has been cloned, overexpressed, purified, kinetically, and structurally characterized. The Tct protein of WJ11 was expressed in Escherichia coli, isolated, and functionally reconstituted in a liposomal system for kinetic studies. Our results showed that Tct has a high affinity for citrate with Km 0.018 mM. Furthermore, the tct overexpression and knockout plasmids were created and transformed into M. circinelloides WJ11. The mitochondria of the tct-overexpressing transformant of M. circinelloides WJ11 showed a 49% increase in citrate efflux, whereas the mitochondria of the tct-knockout transformant showed a 39% decrease in citrate efflux compared to the mitochondria of wild-type WJ11. To elucidate the structure-function relationship of this biologically important transporter a 3D model of the mitochondrial Tct protein was constructed using homology modeling. The overall structure of the protein is V-shaped and its 3D structure is dimeric. The transport stability of the structure was also assessed by molecular dynamics simulation studies. The activity domain was identified to form hydrogen bond and stacking interaction with citrate and malate upon docking. Tricarboxylate citrate transporter has shown high binding energy of −4.87 kcal/mol to citric acid, while −3.80 kcal/mol to malic acid. This is the first report of unraveling the structural characteristics of WJ11 mitochondrial Tct protein and understanding the approach of the transporting toward its substrate. In conclusion, the present findings support our efforts to combine functional and structural data to better understand the Tct of M. circinelloides at the molecular level and its role in lipid accumulation.
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Affiliation(s)
- Wu Yang
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
| | - Aabid Manzoor Shah
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
| | - Shiqi Dong
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Caili Sun
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
| | - Huaiyuan Zhang
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
| | - Hassan Mohamed
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China.,Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut, Egypt
| | - Xiuzhen Gao
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
| | - Huirong Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
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20
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Zeng L, Bi Y, Guo P, Bi Y, Wang T, Dong L, Wang F, Chen L, Zhang W. Metabolic Analysis of Schizochytrium Mutants With High DHA Content Achieved With ARTP Mutagenesis Combined With Iodoacetic Acid and Dehydroepiandrosterone Screening. Front Bioeng Biotechnol 2021; 9:738052. [PMID: 34869256 PMCID: PMC8637758 DOI: 10.3389/fbioe.2021.738052] [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: 07/08/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
High DHA production cost caused by low DHA titer and productivity of the current Schizochytrium strains is a bottleneck for its application in competition with traditional fish-oil based approach. In this study, atmospheric and room-temperature plasma with iodoacetic acid and dehydroepiandrosterone screening led to three mutants, 6–8, 6–16 and 6–23 all with increased growth and DHA accumulations. A LC/MS metabolomic analysis revealed the increased metabolism in PPP and EMP as well as the decreased TCA cycle might be relevant to the increased growth and DHA biosynthesis in the mutants. Finally, the mutant 6–23, which achieved the highest growth and DHA accumulation among all mutants, was evaluated in a 5 L fermentor. The results showed that the DHA concentration and productivity in mutant 6–23 were 41.4 g/L and 430.7 mg/L/h in fermentation for 96 h, respectively, which is the highest reported so far in literature. The study provides a novel strain improvement strategy for DHA-producing Schizochytrium.
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Affiliation(s)
- Lei Zeng
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Yanqi Bi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Pengfei Guo
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Yali Bi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Tiantian Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Liang Dong
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Fangzhong Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
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21
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Bowman EK, Wagner JM, Yuan SF, Deaner M, Palmer CM, D'Oelsnitz S, Cordova L, Li X, Craig FF, Alper HS. Sorting for secreted molecule production using a biosensor-in-microdroplet approach. Proc Natl Acad Sci U S A 2021; 118:e2106818118. [PMID: 34475218 PMCID: PMC8433520 DOI: 10.1073/pnas.2106818118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022] Open
Abstract
Sorting large libraries of cells for improved small molecule secretion is throughput limited. Here, we combine producer/secretor cell libraries with whole-cell biosensors using a microfluidic-based screening workflow. This approach enables a mix-and-match capability using off-the-shelf biosensors through either coencapsulation or pico-injection. We demonstrate the cell type and library agnostic nature of this workflow by utilizing single-guide RNA, transposon, and ethyl-methyl sulfonate mutagenesis libraries across three distinct microbes (Escherichia coli, Saccharomyces cerevisiae, and Yarrowia lipolytica), biosensors from two organisms (E. coli and S. cerevisiae), and three products (triacetic acid lactone, naringenin, and L-DOPA) to identify targets improving production/secretion.
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Affiliation(s)
- Emily K Bowman
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712
| | - James M Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Shuo-Fu Yuan
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712
| | - Matthew Deaner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Claire M Palmer
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712
| | - Simon D'Oelsnitz
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712
| | - Lauren Cordova
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Xin Li
- Sphere Fluidics Limited, Cambridge CB21 6GP, United Kingdom
| | - Frank F Craig
- Sphere Fluidics Limited, Cambridge CB21 6GP, United Kingdom
| | - Hal S Alper
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712;
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
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22
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Exploring Proteomes of Robust Yarrowia lipolytica Isolates Cultivated in Biomass Hydrolysate Reveals Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation. mSystems 2021; 6:e0044321. [PMID: 34342539 PMCID: PMC8407480 DOI: 10.1128/msystems.00443-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yarrowia lipolytica is an oleaginous yeast exhibiting robust phenotypes beneficial for industrial biotechnology. The phenotypic diversity found within the undomesticated Y. lipolytica clade from various origins illuminates desirable phenotypic traits not found in the conventional laboratory strain CBS7504 (or W29), which include xylose utilization, lipid accumulation, and growth on undetoxified biomass hydrolysates. Currently, the related phenotypes of lipid accumulation and degradation when metabolizing nonpreferred sugars (e.g., xylose) associated with biomass hydrolysates are poorly understood, making it difficult to control and engineer in Y. lipolytica. To fill this knowledge gap, we analyzed the genetic diversity of five undomesticated Y. lipolytica strains and identified singleton genes and genes exclusively shared by strains exhibiting desirable phenotypes. Strain characterizations from controlled bioreactor cultures revealed that the undomesticated strain YB420 used xylose to support cell growth and maintained high lipid levels, while the conventional strain CBS7504 degraded cell biomass and lipids when xylose was the sole remaining carbon source. From proteomic analysis, we identified carbohydrate transporters, xylose metabolic enzymes, and pentose phosphate pathway proteins stimulated during the xylose uptake stage for both strains. Furthermore, we distinguished proteins involved in lipid metabolism (e.g., lipase, NADPH generation, lipid regulators, and β-oxidation) activated by YB420 (lipid maintenance phenotype) or CBS7504 (lipid degradation phenotype) when xylose was the sole remaining carbon source. Overall, the results relate genetic diversity of undomesticated Y. lipolytica strains to complex phenotypes of superior growth, sugar utilization, lipid accumulation, and degradation in biomass hydrolysates. IMPORTANCE Yarrowia lipolytica is an important industrial oleaginous yeast due to its robust phenotypes for effective conversion of inhibitory lignocellulosic biomass hydrolysates into neutral lipids. While lipid accumulation has been well characterized in this organism, its interconnected lipid degradation phenotype is poorly understood during fermentation of biomass hydrolysates. Our investigation into the genetic diversity of undomesticated Y. lipolytica strains, coupled with detailed strain characterization and proteomic analysis, revealed metabolic processes and regulatory elements conferring desirable phenotypes for growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates by these natural variants. This study provides a better understanding of the robust metabolism of Y. lipolytica and suggests potential metabolic engineering strategies to enhance its performance.
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23
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A Multiphase Multiobjective Dynamic Genome-Scale Model Shows Different Redox Balancing among Yeast Species of the Saccharomyces Genus in Fermentation. mSystems 2021; 6:e0026021. [PMID: 34342535 PMCID: PMC8407324 DOI: 10.1128/msystems.00260-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeasts constitute over 1,500 species with great potential for biotechnology. Still, the yeast Saccharomyces cerevisiae dominates industrial applications, and many alternative physiological capabilities of lesser-known yeasts are not being fully exploited. While comparative genomics receives substantial attention, little is known about yeasts’ metabolic specificity in batch cultures. Here, we propose a multiphase multiobjective dynamic genome-scale model of yeast batch cultures that describes the uptake of carbon and nitrogen sources and the production of primary and secondary metabolites. The model integrates a specific metabolic reconstruction, based on the consensus Yeast8, and a kinetic model describing the time-varying culture environment. In addition, we proposed a multiphase multiobjective flux balance analysis to compute the dynamics of intracellular fluxes. We then compared the metabolism of S. cerevisiae and Saccharomyces uvarum strains in a rich medium fermentation. The model successfully explained the experimental data and brought novel insights into how cryotolerant strains achieve redox balance. The proposed model (along with the corresponding code) provides a comprehensive picture of the main steps occurring inside the cell during batch cultures and offers a systematic approach to prospect or metabolically engineering novel yeast cell factories. IMPORTANCE Nonconventional yeast species hold the promise to provide novel metabolic routes to produce industrially relevant compounds and tolerate specific stressors, such as cold temperatures. This work validated the first multiphase multiobjective genome-scale dynamic model to describe carbon and nitrogen metabolism throughout batch fermentation. To test and illustrate its performance, we considered the comparative metabolism of three yeast strains of the Saccharomyces genus in rich medium fermentation. The study revealed that cryotolerant Saccharomyces species might use the γ-aminobutyric acid (GABA) shunt and the production of reducing equivalents as alternative routes to achieve redox balance, a novel biological insight worth being explored further. The proposed model (along with the provided code) can be applied to a wide range of batch processes started with different yeast species and media, offering a systematic and rational approach to prospect nonconventional yeast species metabolism and engineering novel cell factories.
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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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Tong Y, Zhou J, Zhang L, Xu P. A Golden-Gate Based Cloning Toolkit to Build Violacein Pathway Libraries in Yarrowia lipolytica. ACS Synth Biol 2021; 10:115-124. [PMID: 33399465 PMCID: PMC7812646 DOI: 10.1021/acssynbio.0c00469] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
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Violacein is a naturally
occurring anticancer therapeutic compound
with deep purple color. In this work, we harnessed the modular and
combinatorial feature of a Golden Gate assembly method to construct
a library of violacein producing strains in the oleaginous yeast Yarrowia lipolytica, where each gene in the violacein pathway
was controlled by three different promoters with varying transcriptional
strength. After optimizing the linker sequence and the Golden Gate
reaction, we achieved high transformation efficiency and obtained
a panel of representative Y. lipolytica recombinant
strains. By evaluating the gene expression profile of 21 yeast strains,
we obtained three colorful compounds in the violacein pathway: green
(proviolacein), purple (violacein), and pink (deoxyviolacein). Our
results indicated that strong expression of VioB, VioC, and VioD favors violacein production
with minimal byproduct deoxyvioalcein in Y. lipolytica, and high deoxyviolacein production was found strongly associated
with the weak expression of VioD. By further optimizing
the carbon to nitrogen ratio and cultivation pH, the maximum violacein
reached 70.04 mg/L with 5.28 mg/L of deoxyviolacein in shake flasks.
Taken together, the development of Golden Gate cloning protocols to
build combinatorial pathway libraries, and the optimization of culture
conditions set a new stage for accessing the violacein pathway intermediates
and engineering violacein production in Y. lipolytica. This work further expands the toolbox to engineering Y.
lipolytica as an industrially relevant host for plant or
marine natural product biosynthesis.
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Affiliation(s)
- Yingjia Tong
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Jingwen Zhou
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Liang Zhang
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Peng Xu
- Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
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Liu H, Wang F, Deng L, Xu P. Genetic and bioprocess engineering to improve squalene production in Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2020; 317:123991. [PMID: 32805480 PMCID: PMC7561614 DOI: 10.1016/j.biortech.2020.123991] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 05/23/2023]
Abstract
Squalene is the precursor for triterpene-based natural products and steroids-based drugs. It has been widely used as pharmaceutical intermediates and personal care products. The aim of this work is to test the feasibility of engineering Yarrowia lipolytica as a potential host for squalene production. The bottleneck of the pathway was removed by overexpressing native HMG-CoA (3-hydroxy-3-methylglutaryl-CoA) reductase. With the recycling of NADPH from the mannitol cycle, the engineered strain produced about 180.3 mg/L and 188.2 mg/L squalene from glucose or acetate minimal media. By optimizing the C/N ratio, controlling the media pH and mitigating acetyl-CoA flux competition from lipogenesis, the engineered strain produced 502.7 mg/L squalene, a 28-fold increase over the parental strain (17.2 mg/L). This work may serve as a baseline to harness Y. lipolytica as an oleaginous cell factory for sustainable production of squalene or terpenoids-based chemicals and natural products.
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Affiliation(s)
- Huan Liu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD 21250, China; College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Fang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Li Deng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD 21250, China.
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Aburatani S, Ishiya K, Itoh T, Hayashi T, Taniguchi T, Takaku H. Inference of Regulatory System for TAG Biosynthesis in Lipomyces starkeyi. Bioengineering (Basel) 2020; 7:bioengineering7040148. [PMID: 33227954 PMCID: PMC7711605 DOI: 10.3390/bioengineering7040148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/14/2020] [Accepted: 11/18/2020] [Indexed: 12/23/2022] Open
Abstract
Improving the bioproduction ability of efficient host microorganisms is a central aim in bioengineering. To control biosynthesis in living cells, the regulatory system of the whole biosynthetic pathway should be clearly understood. In this study, we applied our network modeling method to infer the regulatory system for triacylglyceride (TAG) biosynthesis in Lipomyces starkeyi, using factor analyses and structural equation modeling to construct a regulatory network model. By factor analysis, we classified 89 TAG biosynthesis-related genes into nine groups, which were considered different regulatory sub-systems. We constructed two different types of regulatory models. One is the regulatory model for oil productivity, and the other is the whole regulatory model for TAG biosynthesis. From the inferred oil productivity regulatory model, the well characterized genes DGA1 and ACL1 were detected as regulatory factors. Furthermore, we also found unknown feedback controls in oil productivity regulation. These regulation models suggest that the regulatory factor induction targets should be selected carefully. Within the whole regulatory model of TAG biosynthesis, some genes were detected as not related to TAG biosynthesis regulation. Using network modeling, we reveal that the regulatory system is helpful for the new era of bioengineering.
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Affiliation(s)
- Sachiyo Aburatani
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 305-8568, Japan
- Correspondence: (S.A.); (H.T.); Tel.: +81-3-3599-8712 (S.A.); +81-250-25-5119 (H.T.)
| | - Koji Ishiya
- BPRI, National Institute of Advance Industrial Science and Technology (AIST), Sapporo 062-8517, Japan;
| | - Toshikazu Itoh
- Mitsubishi Research Institute, Inc., Chiyoda District, Tokyo 100-8141, Japan; (T.I.); (T.H.); (T.T.)
| | - Toshihiro Hayashi
- Mitsubishi Research Institute, Inc., Chiyoda District, Tokyo 100-8141, Japan; (T.I.); (T.H.); (T.T.)
| | - Takeaki Taniguchi
- Mitsubishi Research Institute, Inc., Chiyoda District, Tokyo 100-8141, Japan; (T.I.); (T.H.); (T.T.)
| | - Hiroaki Takaku
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603, Japan
- Correspondence: (S.A.); (H.T.); Tel.: +81-3-3599-8712 (S.A.); +81-250-25-5119 (H.T.)
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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
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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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Xiong X, Chen S. Expanding Toolbox for Genes Expression of Yarrowia lipolytica to Include Novel Inducible, Repressible, and Hybrid Promoters. ACS Synth Biol 2020; 9:2208-2213. [PMID: 32584553 DOI: 10.1021/acssynbio.0c00243] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Promoters are critical tools to precisely control gene expression for both synthetic biology and metabolic engineering. Although Yarrowia lipolytica has demonstrated many industrially relevant advantages, promoter discovery efforts on this non-conventional yeast are limited due to the challenge in finding suitable inducible and repressible promoters. Six copper-inducible promoters and five repressible promoters were isolated in this work. Especially, Cu2+-repressible promoters showed relatively high activity under non-repressing conditions compared with a constitutive promoter, but the strength could be almost fully repressed by a supplement of a low content of Cu2+. The six Cu2+-inducible promoters were engineered to improve their dynamic regulation range with a tandem upstream activation sequence. An engineered promoter was successfully used to construct a more productive pathway for production of a novel bioproduct, wax ester, than that used for both Cu2+-inducible promoter and constitutive promoter. This study provides effective tools applicable to fine-tune the gene expression in this microbial host.
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Affiliation(s)
- Xiaochao Xiong
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Shulin Chen
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington 99164, United States
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Li JX, Xu J, Ruan JC, Meng HM, Su H, Han XF, Lu M, Li FL, Wang SA. Disrupting a phospholipase A 2 gene increasing lipid accumulation in the oleaginous yeast Yarrowia lipolytica. J Appl Microbiol 2020; 130:100-108. [PMID: 32648664 DOI: 10.1111/jam.14779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/26/2020] [Accepted: 07/04/2020] [Indexed: 02/05/2023]
Abstract
AIMS Phospholipase A2 (PLA2 ) is a diverse superfamily that hydrolyzes fatty acyl ester bonds at the sn-2 position of phospholipids. The correlation between phospholipid metabolism and the anabolism of neutral lipids remains unclear in yeasts. This study aims to explore the effects of PLA2 on lipid accumulation in the oleaginous yeast Yarrowia lipolytica. METHODS AND RESULTS This study identified an actively expressed phospholipase A2 gene (PLA2-3, YAIL0_E16060g) in Y. lipolytica by quantitative PCR analysis. The gene PLA2-3 was disrupted in the strain po1gΔKu70 by homologous recombination and in the strain po1g-G3 by a CRISPR-Cas9 system, which caused an increase in stress sensitivity while the cell growth was not altered under fermentative conditions. Lipid production was performed in both flasks and bioreactors. The results showed that the lipid titre and lipid content were improved over 25% and 8-30%, respectively, in PLA2-3 disrupted strains compared to the controls. CONCLUSIONS Disruption of the phospholipase PLA2-3 gene could effectively improve lipid production in Y. lipolytica. SIGNIFICANCE AND IMPACT OF THE STUDY This study presented a strategy on improving the lipid production of oleaginous yeasts and a similar strategy might be used in other oleaginous microbes.
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Affiliation(s)
- J X Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - J Xu
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Department of Environmental Science and Engineering, Qingdao University, Qingdao, Shandong, China
| | - J C Ruan
- Zhejiang Zhenyuan Share Co., Ltd, Hangzhou, China
| | - H M Meng
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - H Su
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - X F Han
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - M Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - F L Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - S A Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
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Ghogare R, Chen S, Xiong X. Metabolic Engineering of Oleaginous Yeast Yarrowia lipolytica for Overproduction of Fatty Acids. Front Microbiol 2020; 11:1717. [PMID: 32849364 PMCID: PMC7418586 DOI: 10.3389/fmicb.2020.01717] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/30/2020] [Indexed: 01/24/2023] Open
Abstract
The oleaginous yeast Yarrowia lipolytica has attracted much attention due to its ability to utilize a wide range of substrates to accumulate high lipid content and its flexibility for genetic manipulation. In this study, intracellular lipid metabolism in Y. lipolytica was tailored to produce fatty acid, a renewable oleochemical and precursor for production of advanced biofuels. Two main strategies, including blocking activation and peroxisomal uptake of fatty acids and elimination of biosynthesis of lipids, were employed to reduce fatty acid consumption by the native pathways in Y. lipolytica. Both genetic modifications improved fatty acid production. However, disruption of the genes responsible for assembly of nonpolar lipid molecules including triacylglycerols (TAGs) and steryl esters resulted in the deleterious effects on the cell growth. The gene tesA encoding thioesterase from Escherichia coli was expressed in the strain with disrupted faa genes encoding fatty acyl-CoA synthetases and pxa1 encoding peroxisomal acyl-CoA transporter, and the titer of fatty acids resulted in 2.3 g/L in shake flask culture, representing 11-fold improvement compared with the parent strain. Expressing the native genes encoding acetyl-CoA carboxylase (ACC) and hexokinase also increased fatty acid production, although the improvement was not as significant as that with tesA expression. Saturated fatty acids including palmitic acid (C16:0) and stearic acid (C18:0) increased remarkably in the fatty acid composition of the recombinant bearing tesA compared with the parent strain. The recombinant expressing tesA gene resulted in high lipid content, indicating the great fatty acid producing potential of Y. lipolytica. The results highlight the achievement of fatty acid overproduction without adverse effect on growth of the strain. Results of this study provided insight into the relationship between fatty acid and lipid metabolism in Y. lipolytica, confirming the avenue to reprogram lipid metabolism of this host for overproduction of renewable fatty acids.
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Affiliation(s)
- Rishikesh Ghogare
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
| | - Shulin Chen
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
| | - Xiaochao Xiong
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
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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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Worland AM, Czajka JJ, Xing Y, Harper WF, Moore A, Xiao Z, Han Z, Wang Y, Su WW, Tang YJ. Analysis of Yarrowia lipolytica growth, catabolism, and terpenoid biosynthesis during utilization of lipid-derived feedstock. Metab Eng Commun 2020; 11:e00130. [PMID: 32577396 PMCID: PMC7300164 DOI: 10.1016/j.mec.2020.e00130] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/29/2020] [Accepted: 05/02/2020] [Indexed: 12/26/2022] Open
Abstract
This study employs biomass growth analyses and 13C-isotope tracing to investigate lipid feedstock utilization by Yarrowia lipolytica. Compared to glucose, oil-feedstock in the minimal medium increases the yeast's biomass yields and cell sizes, but decreases its protein content (<20% of total biomass) and enzyme abundances for product synthesis. Labeling results indicate a segregated metabolic network (the glycolysis vs. the TCA cycle) during co-catabolism of sugars (glucose or glycerol) with fatty acid substrates, which facilitates resource allocations for biosynthesis without catabolite repressions. This study has also examined the performance of a β-carotene producing strain in different growth mediums. Canola oil-containing yeast-peptone (YP) has resulted in the best β-carotene titer (121 ± 13 mg/L), two-fold higher than the glucose based YP medium. These results highlight the potential of Y. lipolytica for the valorization of waste-derived lipid feedstock. 13C tracing was used to track Y. lipolytica metabolism of lipid-based feedstock. Y. lipolytica has a segregated flux network for lipid and sugar co-utilizations. Lipid feedstock and nitrogen sources affect cell morphology and optical density. Lipid feedstock benefits both Y. lipolytica growth and carotenoid biosynthesis.
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Affiliation(s)
- Alyssa M Worland
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Jeffrey J Czajka
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Yun Xing
- Department of Systems Engineering and Management, Air Force Institute of Technology, Wright-Patterson AFB, OH, 45433, USA
| | - Willie F Harper
- Department of Systems Engineering and Management, Air Force Institute of Technology, Wright-Patterson AFB, OH, 45433, USA
| | - Aryiana Moore
- Department of Environmental Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Zhengyang Xiao
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Zhenlin Han
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Yechun Wang
- Arch Innotek, LLC, 400 Farmington Ave, Farmington, CT, 06032, USA
| | - Wei Wen Su
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
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Diao J, Song X, Guo T, Wang F, Chen L, Zhang W. Cellular engineering strategies toward sustainable omega-3 long chain polyunsaturated fatty acids production: State of the art and perspectives. Biotechnol Adv 2020; 40:107497. [DOI: 10.1016/j.biotechadv.2019.107497] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 12/28/2022]
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35
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Worland AM, Czajka JJ, Li Y, Wang Y, Tang YJ, Su WW. Biosynthesis of terpene compounds using the non-model yeast Yarrowia lipolytica: grand challenges and a few perspectives. Curr Opin Biotechnol 2020; 64:134-140. [PMID: 32299032 DOI: 10.1016/j.copbio.2020.02.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/24/2020] [Accepted: 02/25/2020] [Indexed: 12/17/2022]
Abstract
Yarrowia lipolytica has emerged as an important non-model host for terpene production. However, three main challenges remain in industrial production using this yeast. First, considerable knowledge gaps exist in metabolic flux across multiple compartments, cofactor generation, and catabolism of non-sugar carbon sources. Second, many enzymatic steps in the complex-terpene synthesis pathway can pose rate-limitations, causing accumulation of toxic intermediates and increased metabolic burdens. Third, metabolic shifts, morphological changes, and genetic mutations are poorly characterized under industrial fermentation conditions. To overcome these challenges, systems metabolic analysis, protein engineering, novel pathway engineering, model-guided strain design, and fermentation optimization have been attempted with some successes. Further developments that address these challenges are needed to advance the Yarrowia lipolytica platform for industrial-scale production of high-value terpenes, including those with highly complex structures such as anticancer molecules withanolides and insecticidal limonoids.
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Affiliation(s)
- Alyssa M Worland
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO 63130, United States
| | - Jeffrey J Czajka
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO 63130, United States
| | - Yanran Li
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, United States
| | - Yechun Wang
- Arch Innotek, LLC, 4320 Forest Park Ave, St. Louis, MO 63108, United States
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO 63130, United States
| | - Wei Wen Su
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, United States.
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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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Marsafari M, Xu P. Debottlenecking mevalonate pathway for antimalarial drug precursor amorphadiene biosynthesis in Yarrowia lipolytica. Metab Eng Commun 2020; 10:e00121. [PMID: 31956504 PMCID: PMC6957783 DOI: 10.1016/j.mec.2019.e00121] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/13/2019] [Accepted: 12/31/2019] [Indexed: 11/17/2022] Open
Abstract
World Health Organization reports that half of the population in developing countries are at risk of malaria infection. Artemisinin, the most potent anti-malaria drug, is a sesquiterpene endoperoxide extracted from the plant Artemisia annua. Due to scalability and economics issues, plant extraction or chemical synthesis could not provide a sustainable route for large-scale manufacturing of artemisinin. The price of artemisinin has been fluctuating from 200$/Kg to 1100$/Kg, due to geopolitical and climate factors. Microbial fermentation was considered as a promising method to stabilize the artemisinin supply chain. Yarrowia lipolytica, is an oleaginous yeast with proven capacity to produce large quantity of lipids and oleochemicals. In this report, the lipogenic acetyl-CoA pathways and the endogenous mevalonate pathway of Y. lipolytica were harnessed for amorphadiene production. Gene overexpression indicate that HMG-CoA and acetyl-CoA supply are two limiting bottlenecks for amorphadiene production. We have identified the optimal HMG-CoA reductase and determined the optimal gene copy number for the precursor pathways. Amorphadiene production was improved further by either inhibiting fatty acids synthase or activating the fatty acid degradation pathway. With co-expression of mevalonate kinase (encoded by Erg12), a push-and-pull strategy enabled the engineered strain to produce 171.5 mg/L of amorphadiene in shake flasks. These results demonstrate that balancing carbon flux and manipulation of precursor competing pathways are key factors to improve amorphadiene biosynthesis in oleaginous yeast; and Y. lipolytica is a promising microbial host to expand nature’s biosynthetic capacity, allowing us to quickly access antimalarial drug precursors. Endogenous acetyl-CoA and mevalonate pathway were harnessed for amorphadiene synthesis. Expression of native untruncated HMG-CoA reductase (HMG1) removes rate-limiting steps. Balancing ADS, HMG1 and MVK activity effectively pull FPP flux toward amorphadiene. Activation of fatty acid degradation pushes carbon flux toward HMG-CoA pathways. A push-and-pull strategy boosts amorphadiene production to 171.5 mg/L in shake flasks.
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Affiliation(s)
- Monireh Marsafari
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
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CRISPR-Cas12a/Cpf1-assisted precise, efficient and multiplexed genome-editing in Yarrowia lipolytica. Metab Eng Commun 2019; 10:e00112. [PMID: 31867213 PMCID: PMC6906711 DOI: 10.1016/j.mec.2019.e00112] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/03/2019] [Accepted: 11/14/2019] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 has been widely adopted as the basic toolkit for precise genome-editing and engineering in various organisms. Alternative to Cas9, Cas12 or Cpf1 uses a simple crRNA as a guide and expands the protospacer adjacent motif (PAM) sequence to TTTN. This unique PAM sequence of Cpf1 may significantly increase the on-target editing efficiency due to lower chance of Cpf1 misreading the PAMs on a high GC genome. To demonstrate the utility of CRISPR-Cpf1, we have optimized the CRISPR-Cpf1 system and achieved high-editing efficiency for two counter-selectable markers in the industrially-relevant oleaginous yeast Yarrowia lipolytica: arginine permease (93% for CAN1) and orotidine 5′-phosphate decarboxylase (~96% for URA3). Both mutations were validated by indel mutation sequencing. For the first time, we further expanded this toolkit to edit three sulfur house-keeping genetic markers (40%–75% for MET2, MET6 and MET25), which confers yeast distinct colony color changes due to the formation of PbS (lead sulfide) precipitates. Different from Cas9, we demonstrated that the crRNA transcribed from a standard type II RNA promoter was sufficient to guide Cpf1 endonuclease activity. Furthermore, modification of the crRNA with 3′ polyUs facilitates the faster maturation and folding of crRNA and improve the genome editing efficiency. We also achieved multiplexed genome editing, and the editing efficiency reached 75%–83% for duplex genomic targets (CAN1-URA3 and CAN1-MET25) and 41.7% for triplex genomic targets (CAN1-URA3-MET25). Taken together, this work expands the genome-editing toolbox for oleaginous yeast species and may accelerate our ability to engineer oleaginous yeast for both biotechnological and biomedical applications. Cpf1 expands the PAM to TTTN and increases the on-target editing efficiency. CRISPR-Cpf1 is optimized to edit genetic markers CAN1, URA3, MET2, MET6 and MET25. A type II RNA promoter was sufficient to guide Cpf1 endonuclease activity. CrRNA modified with 3′ polyUs improves the on-target genome editing efficiency. Duplex genome-editing reaches 75%–83% and triplex editing reaches 42% in Y. lipolytica.
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Lv Y, Marsafari M, Koffas M, Zhou J, Xu P. Optimizing Oleaginous Yeast Cell Factories for Flavonoids and Hydroxylated Flavonoids Biosynthesis. ACS Synth Biol 2019; 8:2514-2523. [PMID: 31622552 DOI: 10.1021/acssynbio.9b00193] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plants possess myriads of secondary metabolites with a broad spectrum of health-promoting benefits. To date, plant extraction is still the primary route to produce high-value natural products which inherently suffers from economics and scalability issues. Heterologous expression of plant biosynthetic gene clusters in microbial host is considered as a feasible approach to overcoming these limitations. Oleaginous yeast produces a large amount of lipid bodies, the abundant membrane structure and the lipophilic environment provide the ideal environment for the regioselectivity and stereoselectivity of many plant-derived P450 enzymes. In this work, we used modular method to construct, characterize, and optimize the flavonoid pathways in Yarrowia lipolytica. We also evaluated various precursor biosynthetic routes and unleashed the metabolic potential of Y. lipolytica to produce flavonoids and hydroxylated flavonoids. Specifically, we have identified that chalcone synthase (CHS) and cytochrome P450 reductases (CPR) were the bottlenecks of hydroxylated flavonoid production. We determined the optimal gene copy number of CHS and CPR to be 5 and 2, respectively. We further removed precursor pathway limitations by expressing genes associated with chorismate and malonyl-CoA supply. With pH and carbon-nitrogen ratio (C/N) optimization, our engineered strain produced 252.4 mg/L naringenin, 134.2 mg/L eriodictyol, and 110.5 mg/L taxifolin from glucose in shake flasks. Flavonoid and its hydroxylated derivatives are most prominently known as antioxidant and antiaging agents. These findings demonstrate our ability to harness the oleaginous yeast as the microbial workhorse to expand nature's biosynthetic potential, enabling us to bridge the gap between drug discovery and natural product manufacturing.
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Affiliation(s)
- Yongkun Lv
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- National Engineering Laboratory for Cereal Fermentation Technology, 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
| | - Monireh Marsafari
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, 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
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
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Yang K, Qiao Y, Li F, Xu Y, Yan Y, Madzak C, Yan J. Subcellular engineering of lipase dependent pathways directed towards lipid related organelles for highly effectively compartmentalized biosynthesis of triacylglycerol derived products in Yarrowia lipolytica. Metab Eng 2019; 55:231-238. [DOI: 10.1016/j.ymben.2019.08.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/11/2019] [Accepted: 08/02/2019] [Indexed: 11/25/2022]
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Liu H, Marsafari M, Wang F, Deng L, Xu P. Engineering acetyl-CoA metabolic shortcut for eco-friendly production of polyketides triacetic acid lactone in Yarrowia lipolytica. Metab Eng 2019; 56:60-68. [PMID: 31470116 DOI: 10.1016/j.ymben.2019.08.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/08/2019] [Accepted: 08/22/2019] [Indexed: 12/25/2022]
Abstract
Acetyl-CoA is the central metabolic node connecting glycolysis, Krebs cycle and fatty acids synthase. Plant-derived polyketides, are assembled from acetyl-CoA and malonyl-CoA, represent a large family of biological compounds with diversified bioactivity. Harnessing microbial bioconversion is considered as a feasible approach to large-scale production of polyketides from renewable feedstocks. Most of the current polyketide production platform relied on the lengthy glycolytic steps to provide acetyl-CoA, which inherently suffers from complex regulation with metabolically-costly cofactor/ATP requirements. Using the simplest polyketide triacetic acid lactone (TAL) as a testbed molecule, we demonstrate that acetate uptake pathway in oleaginous yeast (Yarrowia lipolytica) could function as an acetyl-CoA shortcut to achieve metabolic optimality in producing polyketides. We identified the metabolic bottlenecks to rewire acetate utilization for efficient TAL production in Y. lipolytica, including generation of the driving force for acetyl-CoA, malonyl-CoA and NADPH. The engineered strain, with the overexpression of endogenous acetyl-CoA carboxylase (ACC1), malic enzyme (MAE1) and a bacteria-derived cytosolic pyruvate dehydrogenase (PDH), affords robust TAL production with titer up to 4.76 g/L from industrial glacier acetic acid in shake flasks, representing 8.5-times improvement over the parental strain. The acetate-to-TAL conversion ratio (0.149 g/g) reaches 31.9% of the theoretical maximum yield. The carbon flux through this acetyl-CoA metabolic shortcut exceeds the carbon flux afforded by the native glycolytic pathways. Potentially, acetic acid could be manufactured in large-quantity at low-cost from Syngas fermentation or heterogenous catalysis (methanol carbonylation). This alternative carbon sources present a metabolic advantage over glucose to unleash intrinsic pathway limitations and achieve high carbon conversion efficiency and cost-efficiency. This work also highlights that low-cost acetic acid could be sustainably upgraded to high-value polyketides by oleaginous yeast species in an eco-friendly and cost-efficient manner.
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Affiliation(s)
- Huan Liu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA; College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Monireh Marsafari
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA; Department of Agronomy and Plant Breeding, University of Guilan, Rasht, Islamic Republic of Iran
| | - Fang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Li Deng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA.
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Stress tolerance phenotype of industrial yeast: industrial cases, cellular changes, and improvement strategies. Appl Microbiol Biotechnol 2019; 103:6449-6462. [DOI: 10.1007/s00253-019-09993-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/17/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
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Wang F, Bi Y, Diao J, Lv M, Cui J, Chen L, Zhang W. Metabolic engineering to enhance biosynthesis of both docosahexaenoic acid and odd-chain fatty acids in Schizochytrium sp. S31. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:141. [PMID: 31182976 PMCID: PMC6555965 DOI: 10.1186/s13068-019-1484-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/03/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Docosahexaenoic acid (DHA, C22:6) and odd-chain fatty acids (OCFAs, C15:0 and C17:0) have attracted great interest, since they have been widely used in food and therapeutic industries, as well as chemical industry, such as biodiesel production and improvement. The oil-producing heterotrophic microalgae Schizochytrium sp. 31 is one of main DHA-producing strains. Recently, it was found that Schizochytrium can also synthesize OCFAs; however, contents and titers of DHA and OCFAs in Schizochytrium are still low, which limit its practical application. RESULTS In this study, we found that acetyl-CoA carboxylase suffered from a feedback inhibition by C16-CoA in Schizochytrium, and relief of the inhibition resulted in improved both lipid content and the ratio of OCFAs in total fatty acids. Based on this finding, a novel strategy for elevating both DHA and OCFAs contents was established. First, the total lipid accumulation was increased by overexpressing a malic enzyme from Crypthecodinium cohnii to elevate NADPH supply. Second, the inhibition effect on acetyl-CoA carboxylase was relieved by overexpressing a codon-optimized ELO3 gene from Mortierella alpina, which encodes an elongase enzyme responsible for converting C16 into C18 fatty acids. After the above two-step engineering, contents of DHA and OCFAs were increased by 1.39- and 3.30-fold, reaching a level of 26.70 and 25.08% of dry cell weight, respectively, which are the highest contents reported so far for Schizochytrium. The titers of DHA and OCFAs were elevated by 1.08- and 2.57-fold, reaching a level of 3.54 and 3.32 g/L, respectively. Notably, the OCFAs titer achieved was 2.66-fold higher than the highest reported in Escherichia coli (1.25 g/L), implying potential value for industry application. To reveal the potential metabolic mechanism for the enhanced biosynthesis of both DHA and OCFAs, LC-MS metabolomic analysis was employed and the results showed that the pentose phosphate pathway and the glycolysis pathway were strengthened and intracellular propionyl-CoA concentration were also significantly increased in the engineered Schizochytrium, suggesting an increased supply of NADPH, acetyl-CoA, and propionyl-CoA for DHA and OCFAs accumulation. CONCLUSIONS The discovery provides a new source of OCFAs production, and proposes a new strategy to improve contents and titers of both DHA and OCFAs in Schizochytrium. These will be valuable for improving commercial potential of Schizochytrium and guiding the engineering strategy in other fatty acids producing heterotrophic microalga.
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Affiliation(s)
- Fangzhong Wang
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, People’s Republic of China
| | - Yali Bi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, 300350 People’s Republic of China
| | - Jinjin Diao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, 300350 People’s Republic of China
| | - Mingming Lv
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, 300350 People’s Republic of China
| | - Jinyu Cui
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, 300350 People’s Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, 300350 People’s Republic of China
| | - Weiwen Zhang
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, People’s Republic of China
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, 300350 People’s Republic of China
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