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Duan Y, Chen L, Ma L, Amin FR, Zhai Y, Chen G, Li D. From lignocellulosic biomass to single cell oil for sustainable biomanufacturing: Current advances and prospects. Biotechnol Adv 2024:108460. [PMID: 39383979 DOI: 10.1016/j.biotechadv.2024.108460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 09/12/2024] [Accepted: 09/29/2024] [Indexed: 10/11/2024]
Abstract
As global temperatures rise and arid climates intensify, the reserves of Earth's resources and the future development of humankind are under unprecedented pressure. Traditional methods of food production are increasingly inadequate in meeting the demands of human life while remaining environmentally sustainable and resource-efficient. Consequently, the sustainable supply of lipids is expected to become a pivotal area for future food development. Lignocellulose biomass (LB), as the most abundant and cost-effective renewable resource, has garnered significant attention from researchers worldwide. Thus, bioprocessing based on LB is appearing as a sustainable model for mitigating the depletion of energy reserves and reducing carbon footprints. Currently, the transformation of LB primarily focuses on producing biofuels, such as bioethanol, biobutanol, and biodiesel, to address the energy crisis. However, there are limited reports on the production of single-cell oil (SCO) from LB. This review, therefore, provides a comprehensive summary of the research progress in lignocellulosic pretreatment. Subsequently, it describes how the capability for lignocellulosic use can be conferred to cells through genetic engineering. Additionally, the current status of saccharification and fermentation of LB is outlined. The article also highlights the advances in synthetic biology aimed at driving the development of oil-producing microorganism (OPM), including genetic transformation, chassis modification, and metabolic pathway optimization. Finally, the limitations currently faced in SCO production from straw are discussed, and future directions for achieving high SCO yields from various perspectives are proposed. This review aims to provide a valuable reference for the industrial application of green SCO production.
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Affiliation(s)
- Yu Duan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Limei Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Longxue Ma
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Farrukh Raza Amin
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yida Zhai
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China.
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, 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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3
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Zhou Y, Huang X, Hu T, Chen S, Wang Y, Shi X, Yin M, Li R, Wang J, Jia X. Genome-Wide Analysis of Glycerol-3-Phosphate Acyltransferase (GPAT) Family in Perilla frutescens and Functional Characterization of PfGPAT9 Crucial for Biosynthesis of Storage Oils Rich in High-Value Lipids. Int J Mol Sci 2023; 24:15106. [PMID: 37894786 PMCID: PMC10606570 DOI: 10.3390/ijms242015106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the first step in triacylglycerol (TAG) biosynthesis. However, GPAT members and their functions remain poorly understood in Perilla frutescens, a special edible-medicinal plant with its seed oil rich in polyunsaturated fatty acids (mostly α-linolenic acid, ALA). Here, 14 PfGPATs were identified from the P. frutescens genome and classified into three distinct groups according to their phylogenetic relationships. These 14 PfGPAT genes were distributed unevenly across 11 chromosomes. PfGPAT members within the same subfamily had highly conserved gene structures and four signature functional domains, despite considerable variations detected in these conserved motifs between groups. RNA-seq and RT-qPCR combined with dynamic analysis of oil and FA profiles during seed development indicated that PfGPAT9 may play a crucial role in the biosynthesis and accumulation of seed oil and PUFAs. Ex vivo enzymatic assay using the yeast expression system evidenced that PfGPAT9 had a strong GPAT enzyme activity crucial for TAG assembly and also a high substrate preference for oleic acid (OA, C18:1) and ALA (C18:3). Heterogeneous expression of PfGPAT9 significantly increased total oil and UFA (mostly C18:1 and C18:3) levels in both the seeds and leaves of the transgenic tobacco plants. Moreover, these transgenic tobacco lines exhibited no significant negative effect on other agronomic traits, including plant growth and seed germination rate, as well as other morphological and developmental properties. Collectively, our findings provide important insights into understanding PfGPAT functions, demonstrating that PfGPAT9 is the desirable target in metabolic engineering for increasing storage oil enriched with valuable FA profiles in oilseed crops.
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Affiliation(s)
- Yali Zhou
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Xusheng Huang
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Ting Hu
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Shuwei Chen
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Yao Wang
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Xianfei Shi
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Miao Yin
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Runzhi Li
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Jiping Wang
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
| | - Xiaoyun Jia
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Jinzhong 030801, China; (Y.Z.); (Y.W.); (X.J.)
- College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, China
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Matthews CJ, Patrick WM. An enzyme-centric approach for constructing an amperometric l-malate biosensor with a long and programmable linear range. Protein Sci 2023; 32:e4743. [PMID: 37515423 PMCID: PMC10451018 DOI: 10.1002/pro.4743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
l-Malate is a key flavor enhancer and acidulant in the food and beverage industry, particularly winemaking. Enzyme-based amperometric biosensors offer convenience for monitoring its concentration. However, only a small number of off-the-shelf malate-oxidizing enzymes have been used in previous devices. These typically have linear ranges poorly suited for the l-malate concentrations found in fruit processing and winemaking, making it necessary to use precisely diluted samples. Here, we describe a pipeline of database-mining, gene synthesis, recombinant expression, and spectrophotometric assays to characterize previously untested enzymes for their suitability in biosensors. The pipeline yielded a bespoke biocatalyst-the Ascaris suum malic enzyme carrying mutation R181Q [AsME(R181Q)]. Our first prototype with AsME(R181Q) had an ultra-wide linear range of 50-200 mM l-malate, corresponding to concentrations found in undiluted fruit juices (including grape). Changing the dication from Mg2+ to Mn2+ increased sensitivity five-fold and adding citrate (100 mM) increased it another six-fold, albeit decreasing the linear range to 1-10 mM. To our knowledge, this is the first time an l-malate biosensor with a tuneable combination of sensitivity and linear range has been described. The sensor response was also tested in the presence of various molecules abundant in juices and wines, with ascorbate shown to be a potent interferent. Interference was mitigated by the addition of ascorbate oxidase, allowing for differential measurements on an undiluted, untreated wine sample that corresponded well with commercial l-malate testing kits. Overall, this work demonstrates the power of an enzyme-centric approach for designing electrochemical biosensors with improved operational parameters and novel functionality.
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Affiliation(s)
- Christopher J. Matthews
- Centre for Biodiscovery, School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Wayne M. Patrick
- Centre for Biodiscovery, School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
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5
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Gu X, Huang L, Lian J. Biomanufacturing of γ-linolenic acid-enriched galactosyldiacylglycerols: Challenges in microalgae and potential in oleaginous yeasts. Synth Syst Biotechnol 2023; 8:469-478. [PMID: 37692201 PMCID: PMC10485790 DOI: 10.1016/j.synbio.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 09/12/2023] Open
Abstract
γ-Linolenic acid-enriched galactosyldiacylglycerols (GDGs-GLA), as the natural form of γ-linolenic acid in microalgae, have a range of functional activities, including anti-inflammatory, antioxidant, and anti-allergic properties. The low abundance of microalgae and the structural stereoselectivity complexity impede microalgae extraction or chemical synthesis, resulting in a lack of supply of GDGs-GLA with a growing demand. At present, there is a growing interest in engineering oleaginous yeasts for mass production of GDGs-GLA based on their ability to utilize a variety of hydrophobic substrates and a high metabolic flux toward fatty acid and lipid (triacylglycerol, TAG) production. Here, we first introduce the GDGs-GLA biosynthetic pathway in microalgae and challenges in the engineering of the native host. Subsequently, we describe in detail the applications of oleaginous yeasts with Yarrowia lipolytica as the representative for GDGs-GLA biosynthesis, including the development of synthetic biology parts, gene editing tools, and metabolic engineering of lipid biosynthesis. Finally, we discuss the development trend of GDGs-GLA biosynthesis in Y. lipolytica.
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Affiliation(s)
- Xiaosong Gu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
- Zhejiang Key Laboratory of Smart Biomaterials, Zhejiang University, Hangzhou, 310027, China
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Bi H, Xu C, Bao Y, Zhang C, Wang K, Zhang Y, Wang M, Chen B, Fang Y, Tan T. Enhancing precursor supply and modulating metabolism to achieve high-level production of β-farnesene in Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2023; 382:129171. [PMID: 37196740 DOI: 10.1016/j.biortech.2023.129171] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
β-Farnesene is a sesquiterpene commonly found in essential oils of plants, with applications spanning from agricultural pest control and biofuels to industrial chemicals. The use of renewable substrates in microbial cell factories offers a sustainable approach to β-farnesene biosynthesis. In this study, malic enzyme from Mucor circinelloides was examined for NADPH regeneration, concomitant with the augmentation of cytosolic acetyl-CoA supply by expressing ATP-citrate lyase from Mus musculus and manipulating the citrate pathway via AMP deaminase and isocitrate dehydrogenase. Carbon flux was modulated through the elimination of native 6-phosphofructokinase, while the incorporation of an exogenous non-oxidative glycolysis pathway served to bridge the pentose phosphate pathway with the mevalonate pathway. The resulting orthogonal precursor supply pathway facilitated β-farnesene production, reaching 810 mg/L in shake-flask fermentation. Employing optimal fermentation conditions and feeding strategy, a titer of 28.9 g/L of β-farnesene was attained in a 2 L bioreactor.
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Affiliation(s)
- Haoran Bi
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Chenchen Xu
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Yufei Bao
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Changwei Zhang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Kai Wang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Yang Zhang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Meng Wang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China.
| | - Biqiang Chen
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Yunming Fang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Tianwei Tan
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China.
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Theodosiou E. Engineering Strategies for Efficient Bioconversion of Glycerol to Value-Added Products by Yarrowia lipolytica. Catalysts 2023. [DOI: 10.3390/catal13040657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Yarrowia lipolytica has been a valuable biotechnological workhorse for the production of commercially important biochemicals for over 70 years. The knowledge gained so far on the native biosynthetic pathways, as well as the availability of numerous systems and synthetic biology tools, enabled not only the regulation and the redesign of the existing metabolic pathways, but also the introduction of novel synthetic ones; further consolidating the position of the yeast in industrial biotechnology. However, for the development of competitive and sustainable biotechnological production processes, bioengineering should be reinforced by bioprocess optimization strategies. Although there are many published reviews on the bioconversion of various carbon sources to value-added products by Yarrowia lipolytica, fewer works have focused on reviewing up-to-date strain, medium, and process engineering strategies with an aim to emphasize the significance of integrated engineering approaches. The ultimate goal of this work is to summarize the necessary knowledge and inspire novel routes to manipulate at a systems level the yeast biosynthetic machineries by combining strain and bioprocess engineering. Due to the increasing surplus of biodiesel-derived waste glycerol and the favored glycerol-utilization metabolic pathways of Y. lipolytica over other carbon sources, the present review focuses on pure and crude glycerol-based biomanufacturing.
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Using oils and fats to replace sugars as feedstocks for biomanufacturing: Challenges and opportunities for the yeast Yarrowia lipolytica. Biotechnol Adv 2023; 65:108128. [PMID: 36921878 DOI: 10.1016/j.biotechadv.2023.108128] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023]
Abstract
More than 200 million tons of plant oils and animal fats are produced annually worldwide from oil, crops, and the rendered animal fat industry. Triacylglycerol, an abundant energy-dense compound, is the major form of lipid in oils and fats. While oils or fats are very important raw materials and functional ingredients for food or related products, a significant portion is currently diverted to or recovered as waste. To significantly increase the value of waste oils or fats and expand their applications with a minimal environmental footprint, microbial biomanufacturing is presented as an effective strategy for adding value. Though both bacteria and yeast can be engineered to use oils or fats as the biomanufacturing feedstocks, the yeast Yarrowia lipolytica is presented as one of the most attractive platforms. Y. lipolytica is oleaginous, generally regarded as safe, demonstrated as a promising industrial producer, and has unique capabilities for efficient catabolism and bioconversion of lipid substrates. This review summarizes the major challenges and opportunities for Y. lipolytica as a new biomanufacturing platform for the production of value-added products from oils and fats. This review also discusses relevant cellular and metabolic engineering strategies such as fatty acid transport, fatty acid catabolism and bioconversion, redox balances and energy yield, cell morphology and stress response, and bioreaction engineering. Finally, this review highlights specific product classes including long-chain diacids, wax esters, terpenes, and carotenoids with unique synthesis opportunities from oils and fats in Y. lipolytica.
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Transcriptomic Analysis Revealed the Differences in Lipid Accumulation between Spores and Mycelia of Mucor circinelloides WJ11 under Solid–State Fermentation. FERMENTATION 2022. [DOI: 10.3390/fermentation8120667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The oleaginous fungus Mucor circinelloides has been studied for microbial oil production. Solid–state fermentation may be more suitable for lipid production than submerged fermentation due to its special filamentous structure and lower fermentation costs. M. circinelloides WJ11 under solid–state fermentation indicated that the total fatty acid content of mycelia was significantly higher than that of spores (15.0 and 10.4% in mycelia and spores after 192 h, respectively), while the biomass of the fungal mycelia was lower than that of the spores, reaching 78.2 and 86.9 mg/g, respectively. Transcriptomic studies showed that a total of 9069 genes were differentially expressed between spores and mycelia during solid–state fermentation, of which 4748 were up-regulated and 4321 were down-regulated. Among them, triglyceride-related synthases in M. circinelloides were significantly up-regulated in the mycelia. The mRNA expression level of ATP: citrate lyase was obviously increased to provide more acetyl-CoA for fatty acid synthesis in mycelia, moreover, the metabolism of leucine and isoleucine can also produce more acetyl-CoA for lipid accumulation in M. circinelloides. For NADPH supply, the expression of the pentose phosphate pathway was significantly up-regulated in mycelia, while NADP+-dependent malic enzyme was also increased by 9.5-fold under solid–state fermentation. Compared with gene expression in spores, the autophagy pathway was clearly up-regulated in mycelia to prove that autophagy was related to lipid accumulation in M. circinelloides.
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Han L, Zhai Y, Wang Y, Shi X, Xu Y, Gao S, Zhang M, Luo J, Zhang Q. Diacylglycerol Acyltransferase 3(DGAT3) Is Responsible for the Biosynthesis of Unsaturated Fatty Acids in Vegetative Organs of Paeonia rockii. Int J Mol Sci 2022; 23:ijms232214390. [PMID: 36430868 PMCID: PMC9692848 DOI: 10.3390/ijms232214390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
'Diacylglycerol acyltransferase (DGAT)' acts as a key rate-limiting enzyme that catalyzes the final step of the de novo biosynthesis of triacylglycerol (TAG). The study was to characterize the function of the DGAT3 gene in Paeonia rockii, which is known for its accumulation of high levels of unsaturated fatty acids (UFAs). We identified a DGAT3 gene which encodes a soluble protein that is located within the chloroplasts of P. rockii. Functional complementarity experiments in yeast demonstrated that PrDGAT3 restored TAG synthesis. Linoleic acid (LA, C18:2) and α-linolenic acid (ALA, C18:3) are essential unsaturated fatty acids that cannot be synthesized by the human body. Through the yeast lipotoxicity test, we found that the yeast cell density was largely increased by adding exogenous LA and, especially, ALA to the yeast medium. Further ectopic transient overexpression in Nicotiana benthamiana leaf tissue and stable overexpression in Arabidopsis thaliana indicated that PrDGAT3 significantly enhanced the accumulation of the TAG and UFAs. In contrast, we observed a significant decrease in the total fatty acid content and in several major fatty acids in PrDGAT3-silenced tree peony leaves. Overall, PrDGAT3 is important in catalyzing TAG synthesis, with a substrate preference for UFAs, especially LA and ALA. These results suggest that PrDGAT3 may have practical applications in improving plant lipid nutrition and increasing oil production in plants.
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Affiliation(s)
- Longyan Han
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Xianyang 712100, China
- Oil Peony Engineering Technology, Research Center of National Forestry Administration, Yangling, Xianyang 712100, China
| | - Yuhui Zhai
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Xianyang 712100, China
- Oil Peony Engineering Technology, Research Center of National Forestry Administration, Yangling, Xianyang 712100, China
| | - Yumeng Wang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Xianyang 712100, China
- Oil Peony Engineering Technology, Research Center of National Forestry Administration, Yangling, Xianyang 712100, China
| | - Xiangrui Shi
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Xianyang 712100, China
- Oil Peony Engineering Technology, Research Center of National Forestry Administration, Yangling, Xianyang 712100, China
| | - Yanfeng Xu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Xianyang 712100, China
- Oil Peony Engineering Technology, Research Center of National Forestry Administration, Yangling, Xianyang 712100, China
| | - Shuguang Gao
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Xianyang 712100, China
- Oil Peony Engineering Technology, Research Center of National Forestry Administration, Yangling, Xianyang 712100, China
| | - Man Zhang
- National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing 100010, China
| | - Jianrang Luo
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Xianyang 712100, China
- Oil Peony Engineering Technology, Research Center of National Forestry Administration, Yangling, Xianyang 712100, China
| | - Qingyu Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Xianyang 712100, China
- Oil Peony Engineering Technology, Research Center of National Forestry Administration, Yangling, Xianyang 712100, China
- Correspondence: ; Tel.: +86-29-8708-2878; Fax: +86-29-8708-0269
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11
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Mota MN, Múgica P, Sá-Correia I. Exploring Yeast Diversity to Produce Lipid-Based Biofuels from Agro-Forestry and Industrial Organic Residues. J Fungi (Basel) 2022; 8:687. [PMID: 35887443 PMCID: PMC9315891 DOI: 10.3390/jof8070687] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. However, sustainable, and economically viable bioprocesses require yeast strains exhibiting: (i) high tolerance to multiple bioprocess-related stresses, including the various chemical inhibitors present in hydrolysates from lignocellulosic biomass and residues; (ii) the ability to efficiently consume all the major carbon sources present; (iii) the capacity to produce lipids with adequate composition in high yields. More than 160 non-conventional (non-Saccharomyces) yeast species are described as oleaginous, but only a smaller group are relatively well characterised, including Lipomyces starkeyi, Yarrowia lipolytica, Rhodotorula toruloides, Rhodotorula glutinis, Cutaneotrichosporonoleaginosus and Cutaneotrichosporon cutaneum. This article provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. This is essential knowledge to better understand and guide the rational improvement of yeast performance either by genetic manipulation or by exploring yeast physiology and optimal process conditions. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are provided.
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Affiliation(s)
- Marta N. Mota
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
| | - Paula Múgica
- BIOREF—Collaborative Laboratory for Biorefineries, Rua da Amieira, Apartado 1089, São Mamede de Infesta, 4465-901 Matosinhos, Portugal
| | - Isabel Sá-Correia
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
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12
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Cui J, Chen H, Tang X, Zhang H, Chen YQ, Chen W. Characterization and Molecular Mechanism of a Novel Cytochrome b5 Reductase with NAD(P)H Specificity from Mortierella alpina. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5186-5196. [PMID: 35416034 DOI: 10.1021/acs.jafc.1c08108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The electron-transfer capabilities of cytochrome b5 reductase (Cyt b5R) and NADPH supply have been shown to be critical factors in microbial fatty acid synthesis. Unfortunately, Cyt b5R substrate specificity is limited to the coenzyme NADH. In this study, we discovered that a novel Cyt b5R from Mortierella alpina (MaCytb5RII) displays affinity for NADPH and NADH. The enzymatic characteristics of high-purity MaCytb5RII were determined with the Km,NADPH and Km,NADH being 0.42 and 0.07 mM, respectively. MaCytb5RII shows high specific activity at 4 °C and pH 9.0. We anchored the residues that interacted with the coenzymes using the homology models of MaCytb5Rs docking NAD(P)H and FAD. The enzyme activity analysis of the purified mutants MaCytb5RII[S230N], MaCytb5RII[Y242F], and MaCytb5RII[S272A] revealed that Ser230 is essential for MaCytb5RII to have dual NAD(P)H dependence, whereas Tyr242 influences MaCytb5RII's NADPH affinity and Ala272 greatly decreases MaCytb5RII's NADH affinity.
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Affiliation(s)
- Jie Cui
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, P. R. China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, P. R. China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, P. R. China
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27127, United States
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, P. R. China
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13
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Liu Y, Wang Z, Cui Z, Qi Q, Hou J. Progress and perspectives for microbial production of farnesene. BIORESOURCE TECHNOLOGY 2022; 347:126682. [PMID: 35007732 DOI: 10.1016/j.biortech.2022.126682] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Farnesene is increasingly used in industry, agriculture, and other fields due to its unique and excellent properties, necessitating its efficient synthesis. Microbial synthesis is an ideal farnesene production method. Recently, researchers have used several strategies to optimize the production performance of microorganisms. This review summarized these strategies, including regulation of farnesene synthesis pathways, and proposed some emerging tools and methods in stain engineering. Meanwhile, new farnesene biosynthetic pathways and effective farnesene production from cheap or waste substrates were emphatically introduced. Finally, future farnesene biosynthesis challenges were discussed.
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Affiliation(s)
- Yinghang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Zhaoxuan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
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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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15
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Chang L, Lu H, Chen H, Tang X, Zhao J, Zhang H, Chen YQ, Chen W. Lipid metabolism research in oleaginous fungus Mortierella alpina: Current progress and future prospects. Biotechnol Adv 2021; 54:107794. [PMID: 34245810 DOI: 10.1016/j.biotechadv.2021.107794] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 06/11/2021] [Accepted: 07/04/2021] [Indexed: 12/19/2022]
Abstract
The oleaginous fungus Mortierella alpina has distinct advantages in long-chain PUFAs production, and it is the only source for dietary arachidonic acid (ARA) certificated by FDA and European Commission. This review provides an overall introduction to M. alpina, including its major research methods, key factors governing lipid biosynthesis, metabolic engineering and omics studies. Currently, the research interests in M. alpina focus on improving lipid yield and fatty acid desaturation degree by enhancing fatty acid precursors and the reducing power NADPH, and genetic manipulation on PUFAs synthetic pathways is carried to optimise fatty acid composition. Besides, multi-omics studies have been applied to elucidate the global regulatory mechanism of lipogenesis in M. alpina. However, research challenges towards achieving a lipid cell factory lie in strain breeding and cost control due to the coenocytic mycelium, long fermentation period and insufficient conversion rate from carbon to lipid. We also proposed future research goals based on a multilevel regulating strategy: obtaining ideal chassis by directional evolution and high-throughput screening; rewiring central carbon metabolism and inhibiting competitive pathways by multi-gene manipulation system to enhance carbon to lipid conversion rate; optimisation of protein function based on post-translational modification; application of dynamic fermentation strategies suitable for different fermentation phases. By reviewing the comprehensive research progress of this oleaginous fungus, we aim to further comprehend the fungal lipid metabolism and provide reference information and guidelines for the exploration of microbial oils from the perspectives of fundamental research to industrial application.
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Affiliation(s)
- Lulu Chang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Hengqian Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China; Wuxi Translational Medicine Research Center, Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, Jiangsu 214122, PR China; Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
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16
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Jia YL, Wang LR, Zhang ZX, Gu Y, Sun XM. Recent advances in biotechnological production of polyunsaturated fatty acids by Yarrowia lipolytica. Crit Rev Food Sci Nutr 2021; 62:8920-8934. [PMID: 34120537 DOI: 10.1080/10408398.2021.1937041] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Owing to the important physiological functions, polyunsaturated fatty acids (PUFAs) play a vital role in protecting human health, such as preventing cancer, cardiovascular disease, and diabetes. Specifically, Yarrowia lipolytica has been identified as the most popular non-conventional oleaginous yeast, which can accumulate the abundant intracellular lipids, indicating that has great potential as an industrial host for production of PUFAs. Notably, some novel engineering strategies have been applied to endow and improve the abilities of Y. lipolytica to synthesize PUFAs, including construction and optimization of PUFAs biosynthetic pathways, improvement of preucrsors acetyl-coA and NADPH supply, inhibition of competing pathways, knockout of β-oxidation pathways, regulation of oxidative stress defense pathways, and regulation of genes involved in upstream lipid metabolism. Besides, some bypass approaches, such as strain mating, evolutionary engineering, and computational model based on omics, also have been proposed to improve the performance of engineering strains. Generally, in this review, we summarized the recent advances in engineering strategies and bypass approaches for improving PUFAs production by Y. lipolytica. In addition, we further summarized the latest efforts of CRISPR/Cas genome editing technology in Y. lipolytica, which is aimed to provide its potential applications in PUFAs production.
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Affiliation(s)
- Yu-Lei Jia
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ling-Ru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Zi-Xu Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
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17
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Chattopadhyay A, Maiti MK. Lipid production by oleaginous yeasts. ADVANCES IN APPLIED MICROBIOLOGY 2021; 116:1-98. [PMID: 34353502 DOI: 10.1016/bs.aambs.2021.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Microbial lipid production has been studied extensively for years; however, lipid metabolic engineering in many of the extraordinarily high lipid-accumulating yeasts was impeded by inadequate understanding of the metabolic pathways including regulatory mechanisms defining their oleaginicity and the limited genetic tools available. The aim of this review is to highlight the prominent oleaginous yeast genera, emphasizing their oleaginous characteristics, in conjunction with diverse other features such as cheap carbon source utilization, withstanding the effect of inhibitory compounds, commercially favorable fatty acid composition-all supporting their future development as economically viable lipid feedstock. The unique aspects of metabolism attributing to their oleaginicity are accentuated in the pretext of outlining the various strategies successfully implemented to improve the production of lipid and lipid-derived metabolites. A large number of in silico data generated on the lipid accumulation in certain oleaginous yeasts have been carefully curated, as suggestive evidences in line with the exceptional oleaginicity of these organisms. The different genetic elements developed in these yeasts to execute such strategies have been scrupulously inspected, underlining the major types of newly-found and synthetically constructed promoters, transcription terminators, and selection markers. Additionally, there is a plethora of advanced genetic toolboxes and techniques described, which have been successfully used in oleaginous yeasts in the recent years, promoting homologous recombination, genome editing, DNA assembly, and transformation at remarkable efficiencies. They can accelerate and effectively guide the rational designing of system-wide metabolic engineering approaches pinpointing the key targets for developing industrially suitable yeast strains.
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Affiliation(s)
- Atrayee Chattopadhyay
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Mrinal K Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India.
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Genome Sequence Analysis of the Oleaginous Yeast, Rhodotorula diobovata, and Comparison of the Carotenogenic and Oleaginous Pathway Genes and Gene Products with Other Oleaginous Yeasts. J Fungi (Basel) 2021; 7:jof7040320. [PMID: 33924147 PMCID: PMC8074367 DOI: 10.3390/jof7040320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/18/2022] Open
Abstract
Rhodotorula diobovata is an oleaginous and carotenogenic yeast, useful for diverse biotechnological applications. To understand the molecular basis of its potential applications, the genome was sequenced using the Illumina MiSeq and Ion Torrent platforms, assembled by AbySS, and annotated using the JGI annotation pipeline. The genome size, 21.1 MB, was similar to that of the biotechnological “workhorse”, R. toruloides. Comparative analyses of the R. diobovata genome sequence with those of other Rhodotorula species, Yarrowia lipolytica, Phaffia rhodozyma, Lipomyces starkeyi, and Sporidiobolus salmonicolor, were conducted, with emphasis on the carotenoid and neutral lipid biosynthesis pathways. Amino acid sequence alignments of key enzymes in the lipid biosynthesis pathway revealed why the activity of malic enzyme and ATP-citrate lyase may be ambiguous in Y. lipolytica and L. starkeyi. Phylogenetic analysis showed a close relationship between R. diobovata and R. graminis WP1. Dot-plot analysis of the coding sequences of the genes crtYB and ME1 corroborated sequence homologies between sequences from R. diobovata and R. graminis. There was, however, nonsequential alignment between crtYB CDS sequences from R. diobovata and those from X. dendrorhous. This research presents the first genome analysis of R. diobovata with a focus on its biotechnological potential as a lipid and carotenoid producer.
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19
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Fakankun I, Spicer V, Levin DB. Proteomic analyses of the oleaginous and carotenogenic yeast Rhodotorula diobovata across growth phases under nitrogen- and oxygen-limited conditions. J Biotechnol 2021; 332:11-19. [PMID: 33781863 DOI: 10.1016/j.jbiotec.2021.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Carotenoids and triacylglycerols from yeasts are important bioproducts that can be utilized for the nutraceutical and biodiesel industries respectively. Rhodotorula diobovata is capable of producing these bioproducts under varied culture conditions. These productions have been linked to the early stationary growth phase and their levels only start to decline at the late stationary phase when carbon becomes limiting. While nitrogen-limitation influences the onset of lipogenesis, continuous synthesis and accumulation of neutral lipids (triacylglycerides) may be dependent on other culture conditions such as aeration. Proteomic analyses were conducted to enhance our understanding of changes in gene product expression under culture conditions with nitrogen-limitation, coupled with insufficient aeration, and revealed a correlation between the upregulation of proteins in the lipolysis pathways and the reduced synthesis of fatty acids at the early stationary phase. Upregulation of glycolytic pathway enzymes suggested that glucose was quickly converted into pyruvate and then acetyl-CoA. However, acetyl-CoA flux favoured carotenoids biosynthesis over fatty acid synthesis, as cells transitioned into the stationary phase. This work provides insights into how culture conditions influence gene product expression levels, pathway utilization, and end-product synthesis patterns.
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Affiliation(s)
- Irene Fakankun
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, R3E 3P4, Canada.
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
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Chattopadhyay A, Mitra M, Maiti MK. Recent advances in lipid metabolic engineering of oleaginous yeasts. Biotechnol Adv 2021; 53:107722. [PMID: 33631187 DOI: 10.1016/j.biotechadv.2021.107722] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 01/12/2023]
Abstract
With the increasing demand to develop a renewable and sustainable biolipid feedstock, several species of non-conventional oleaginous yeasts are being explored. Apart from the platform oleaginous yeast Yarrowia lipolytica, the understanding of metabolic pathway and, therefore, exploiting the engineering prospects of most of the oleaginous species are still in infancy. However, in the past few years, enormous efforts have been invested in Rhodotorula, Rhodosporidium, Lipomyces, Trichosporon, and Candida genera of yeasts among others, with the rapid advancement of engineering strategies, significant improvement in genetic tools and techniques, generation of extensive bioinformatics and omics data. In this review, we have collated these recent progresses to make a detailed and insightful summary of the major developments in metabolic engineering of the prominent oleaginous yeast species. Such a comprehensive overview would be a useful resource for future strain improvement and metabolic engineering studies for enhanced production of lipid and lipid-derived chemicals in oleaginous yeasts.
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Affiliation(s)
- Atrayee Chattopadhyay
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Mohor Mitra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Mrinal K Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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21
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Gao H, Gao Y, Zhang F, Liu B, Ji C, Xue J, Yuan L, Li R. Functional characterization of an novel acyl-CoA:diacylglycerol acyltransferase 3-3 (CsDGAT3-3) gene from Camelina sativa. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110752. [PMID: 33487340 DOI: 10.1016/j.plantsci.2020.110752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/06/2020] [Accepted: 11/06/2020] [Indexed: 06/12/2023]
Abstract
Diacylglycerol acyltransferases (DGAT) catalyze the final committed step of de novo biosynthesis of triacylglycerol (TAG) in plant seeds. This study was to functionally characterize DGAT3 genes in Camelina sativa, an important oil crops accumulating high levels of unsaturated fatty acids (UFAs) in seeds. Three camelina DGAT3 genes (CsDGAT3-1, CsDGAT3-2 and CsDGAT3-3) were identified, and the encoded proteins were predicted to be cytosolic-soluble proteins present as a homodimer containing the 2Fe-2S domain. They had divergent expression patterns in various tissues, suggesting that they may function in tissue-specific manner with CsDGAT3-1 in roots, CsDGAT3-2 in flowers and young seedlings, and CsDGAT3-3 in developing seeds. Functional complementation assay in yeast demonstrated that CsDGAT3-3 restored TAG synthesis. TAG content and UFAs, particularly eicosenoic acid (EA, 20:1n-9) were largely increased by adding exogenous UFAs in the yeast medium. Further heterogeneously transient expression in N. benthamiana leaves and seed-specific expression in tobacco seeds indicated that CsDGAT3-3 significantly enhanced oil and UFA accumulation with much higher level of EA. Overall, CsDGAT3-3 exhibited a strong abilty catalyzing TAG synthesis and high substrate preference for UFAs, especially for 20:1n-9. The present data provide new insights for further understanding oil biosynthesis mechanism in camelina seeds, indicating that CsDGAT3-3 may have practical applications for increasing both oil yield and quality.
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Affiliation(s)
- Huiling Gao
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Yu Gao
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Fei Zhang
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Baoling Liu
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Chunli Ji
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Jinai Xue
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Taigu, Shanxi, China.
| | - Lixia Yuan
- College of Biological Science and Technology, Jinzhong University, Jinzhong, Shanxi, China.
| | - Runzhi Li
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Taigu, Shanxi, China.
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Enzyme-based amperometric biosensors for malic acid - A review. Anal Chim Acta 2021; 1156:338218. [PMID: 33781460 DOI: 10.1016/j.aca.2021.338218] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/18/2022]
Abstract
Malic acid is a key flavour component of many fruits and vegetables. There is significant interest in technologies for monitoring its concentration, particularly in winemaking. In this review we systematically and comprehensively chart progress in the development of enzyme-based amperometric biosensors for malic acid. We summarise the components and analytical parameters of malic acid sensors that have been reported over the past four decades, discussing their merits and pitfalls in terms of accuracy, sensitivity, linear range, response time and stability. We discuss how advances in electrode materials, electron mediators and the use of coupled enzymes have improved sensitivity and minimised interference, but also uncover a trade-off between sensitivity and linear range. A particular focus of our review is the three types of malate oxidoreductase enzyme that have been used in malic acid biosensors. We describe their different properties and conclude that identifying and/or engineering superior alternatives will be a key future direction for improving the commercial utility of malic acid biosensors.
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Liu H, Song Y, Fan X, Wang C, Lu X, Tian Y. Yarrowia lipolytica as an Oleaginous Platform for the Production of Value-Added Fatty Acid-Based Bioproducts. Front Microbiol 2021; 11:608662. [PMID: 33469452 PMCID: PMC7813756 DOI: 10.3389/fmicb.2020.608662] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/26/2020] [Indexed: 01/14/2023] Open
Abstract
The microbial fermentation process has been used as an alternative pathway to the production of value-added natural products. Of the microorganisms, Yarrowia lipolytica, as an oleaginous platform, is able to produce fatty acid-derived biofuels and biochemicals. Nowadays, there are growing progresses on the production of value-added fatty acid-based bioproducts in Y. lipolytica. However, there are fewer reviews performing the metabolic engineering strategies and summarizing the current production of fatty acid-based bioproducts in Y. lipolytica. To this end, we briefly provide the fatty acid metabolism, including fatty acid biosynthesis, transportation, and degradation. Then, we introduce the various metabolic engineering strategies for increasing bioproduct accumulation in Y. lipolytica. Further, the advanced progress in the production of fatty acid-based bioproducts by Y. lipolytica, including nutraceuticals, biofuels, and biochemicals, is summarized. This review will provide attractive thoughts for researchers working in the field of Y. lipolytica.
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Affiliation(s)
- Huhu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yulan Song
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Xiao Fan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Chong Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Xiangyang Lu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yun Tian
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
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Park YK, Nicaud JM. Metabolic Engineering for Unusual Lipid Production in Yarrowia lipolytica. Microorganisms 2020; 8:E1937. [PMID: 33291339 PMCID: PMC7762315 DOI: 10.3390/microorganisms8121937] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
Using microorganisms as lipid-production factories holds promise as an alternative method for generating petroleum-based chemicals. The non-conventional yeast Yarrowia lipolytica is an excellent microbial chassis; for example, it can accumulate high levels of lipids and use a broad range of substrates. Furthermore, it is a species for which an array of efficient genetic engineering tools is available. To date, extensive work has been done to metabolically engineer Y. lipolytica to produce usual and unusual lipids. Unusual lipids are scarce in nature but have several useful applications. As a result, they are increasingly becoming the targets of metabolic engineering. Unusual lipids have distinct structures; they can be generated by engineering endogenous lipid synthesis or by introducing heterologous enzymes to alter the functional groups of fatty acids. In this review, we describe current metabolic engineering strategies for improving lipid production and highlight recent researches on unusual lipid production in Y. lipolytica.
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Affiliation(s)
- Young-Kyoung Park
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 78352 Jouy-en-Josas, France;
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Lignocellulosic Biomass as a Substrate for Oleaginous Microorganisms: A Review. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10217698] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Microorganisms capable of accumulating lipids in high percentages, known as oleaginous microorganisms, have been widely studied as an alternative for producing oleochemicals and biofuels. Microbial lipid, so-called Single Cell Oil (SCO), production depends on several growth parameters, including the nature of the carbon substrate, which must be efficiently taken up and converted into storage lipid. On the other hand, substrates considered for large scale applications must be abundant and of low acquisition cost. Among others, lignocellulosic biomass is a promising renewable substrate containing high percentages of assimilable sugars (hexoses and pentoses). However, it is also highly recalcitrant, and therefore it requires specific pretreatments in order to release its assimilable components. The main drawback of lignocellulose pretreatment is the generation of several by-products that can inhibit the microbial metabolism. In this review, we discuss the main aspects related to the cultivation of oleaginous microorganisms using lignocellulosic biomass as substrate, hoping to contribute to the development of a sustainable process for SCO production in the near future.
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Wang J, Ledesma-Amaro R, Wei Y, Ji B, Ji XJ. Metabolic engineering for increased lipid accumulation in Yarrowia lipolytica - A Review. BIORESOURCE TECHNOLOGY 2020; 313:123707. [PMID: 32595069 DOI: 10.1016/j.biortech.2020.123707] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Current energy security and climate change policies encourage the development and utilization of bioenergy. Oleaginous yeasts provide a particularly attractive platform for the sustainable production of biofuels and industrial chemicals due to their ability to accumulate high amounts of lipids. In particular, microbial lipids in the form of triacylglycerides (TAGs) produced from renewable feedstocks have attracted considerable attention because they can be directly used in the production of biodiesel and oleochemicals analogous to petrochemicals. As an oleaginous yeast that is generally regarded as safe, Yarrowia lipolytica has been extensively studied, with large amounts of data on its lipid metabolism, genetic tools, and genome sequencing and annotation. In this review, we highlight the newest strategies for increasing lipid accumulation using metabolic engineering and summarize the research advances on the overaccumulation of lipids in Y. lipolytica. Finally, perspectives for future engineering approaches are proposed.
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Affiliation(s)
- Jinpeng Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Key Laboratory of State Ministry of Education, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, People's Republic of China
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China.
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Xia Y, Zhang YT, Sun JY, Huang H, Zhao Q, Ren LJ. Strategies for enhancing eicosapentaenoic acid production: From fermentation to metabolic engineering. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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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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Kamineni A, Shaw J. Engineering triacylglycerol production from sugars in oleaginous yeasts. Curr Opin Biotechnol 2020; 62:239-247. [DOI: 10.1016/j.copbio.2019.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/10/2019] [Accepted: 12/22/2019] [Indexed: 02/06/2023]
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Yan FX, Dong GR, Qiang S, Niu YJ, Hu CY, Meng YH. Overexpression of △12, △15-Desaturases for Enhanced Lipids Synthesis in Yarrowia lipolytica. Front Microbiol 2020; 11:289. [PMID: 32158438 PMCID: PMC7051990 DOI: 10.3389/fmicb.2020.00289] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
Microbial oil triacylglycerol (TAG) from the renewable feedstock attract much attention. The oleaginous yeast Yarrowia lipolytica has become the most studied for lipid biosynthesis. Fatty acid desaturases catalyze the introduction of a double bond into fatty-acid hydrocarbon chains to produce unsaturated fatty acids. Desaturases are known to enhance lipid accumulation. In this study, we have achieved a significant increase in lipid production and increase the unsaturated fatty acids content in Y. lipolytica. By comparing the expression of the native genes of △-9 stearoyl-CoA desaturase (SCD) and △12 desaturase (△12D), and an exogenous △15 desaturase (△15D) from flax in the strain with deleted peroxisomal biogenesis factor 10 (PEX10) and overexpressed diacylglyceride acyl-transferase (DGA1), we found that the strain with overexpressed △15 desaturase accumulated 30.7% lipid. Simultaneously, we explored the effect of two copies of desaturase genes (12D-SCD, 15D-SCD, 12D-15D) on lipid production, and found co-expression of △12D and △15D accumulated 42.6% lipid. The lipid content was further increased by 56.3% through the deletion of the multifunctional enzyme (MFE1) and the overexpression of acetyl-CoA carboxylase (ACC1). Finally, the lipid productivity of 50 g/L and maximal lipid content of 77.8% DCW are obtained using a 5-L stirred-tank bioreactor during the stationary phase in the engineered YL-10. Our result demonstrated that the △12 and △15 desaturases play an important role in lipid production in Y. lipolytica and provides an effective strategy for biodiesel development.
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Affiliation(s)
- Feng Xin Yan
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, China
| | - Gui Ru Dong
- Shaanxi Engineering Laboratory for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Shan Qiang
- Shaanxi Engineering Laboratory for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China.,Xi'an Healthful Biotechnology Co., Ltd., Xi'an, China
| | - Yong Jie Niu
- Xi'an Healthful Biotechnology Co., Ltd., Xi'an, China
| | - Ching Yuan Hu
- Shaanxi Engineering Laboratory for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China.,Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Yong Hong Meng
- Shaanxi Engineering Laboratory for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
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Chen M, Gao X, Yang W, Sun C, Yang J, Zhang H, Song Y. Discovery and characterization of a stable lipase with preference toward long-chain fatty acids. Biotechnol Lett 2019; 42:171-180. [DOI: 10.1007/s10529-019-02765-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/14/2019] [Indexed: 11/30/2022]
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Llamas M, Magdalena JA, González-Fernández C, Tomás-Pejó E. Volatile fatty acids as novel building blocks for oil-based chemistry via oleaginous yeast fermentation. Biotechnol Bioeng 2019; 117:238-250. [PMID: 31544974 DOI: 10.1002/bit.27180] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/20/2019] [Accepted: 09/16/2019] [Indexed: 02/06/2023]
Abstract
Microbial oils are proposed as a suitable alternative to petroleum-based chemistry in terms of environmental preservation. These oils have traditionally been studied using sugar-based feedstock, which implies high costs, substrate limitation, and high contamination risks. In this sense, low-cost carbon sources such as volatile fatty acids (VFAs) are envisaged as promising building blocks for lipid biosynthesis to produce oil-based bioproducts. VFAs can be generated from a wide variety of organic wastes through anaerobic digestion and further converted into lipids by oleaginous yeasts (OYs) in a fermentation process. These microorganisms can accumulate in the form of lipid bodies, lipids of up to 60% wt/wt of their biomass. In this context, OY is a promising biotechnological tool for biofuel and bioproduct generation using low-cost VFA media as substrates. This review covers recent advances in microbial oil production from VFAs. Production of VFAs via anaerobic digestion processes and the involved metabolic pathways are reviewed. The main challenges as well as recent approaches for lipid overproduction are also discussed.
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Affiliation(s)
- Mercedes Llamas
- Biotechnological Processes Unit, IMDEA Energy, Móstoles, Spain
| | | | | | - Elia Tomás-Pejó
- Biotechnological Processes Unit, IMDEA Energy, Móstoles, Spain
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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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Arhar S, Natter K. Common aspects in the engineering of yeasts for fatty acid- and isoprene-based products. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:158513. [PMID: 31465888 DOI: 10.1016/j.bbalip.2019.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/26/2019] [Accepted: 08/20/2019] [Indexed: 11/18/2022]
Abstract
The biosynthetic pathways for most lipophilic metabolites share several common principles. These substances are built almost exclusively from acetyl-CoA as the donor for the carbon scaffold and NADPH is required for the reductive steps during biosynthesis. Due to their hydrophobicity, the end products are sequestered into the same cellular compartment, the lipid droplet. In this review, we will summarize the efforts in the metabolic engineering of yeasts for the production of two major hydrophobic substance classes, fatty acid-based lipids and isoprenoids, with regard to these common aspects. We will compare and discuss the results of genetic engineering strategies to construct strains with enhanced synthesis of the precursor acetyl-CoA and with modified redox metabolism for improved NADPH supply. We will also discuss the role of the lipid droplet in the storage of the hydrophobic product and review the strategies to either optimize this organelle for higher capacity or to achieve excretion of the product into the medium.
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Affiliation(s)
- Simon Arhar
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria.
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Hünnefeld M, Persicke M, Kalinowski J, Frunzke J. The MarR-Type Regulator MalR Is Involved in Stress-Responsive Cell Envelope Remodeling in Corynebacterium glutamicum. Front Microbiol 2019; 10:1039. [PMID: 31164873 PMCID: PMC6536590 DOI: 10.3389/fmicb.2019.01039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/25/2019] [Indexed: 12/03/2022] Open
Abstract
It is the enormous adaptive capacity of microorganisms, which is key to their competitive success in nature, but also challenges antibiotic treatment of human diseases. To deal with a diverse set of stresses, bacteria are able to reprogram gene expression using a wide variety of transcription factors. Here, we focused on the MarR-type regulator MalR conserved in the Corynebacterineae, including the prominent pathogens Corynebacterium diphtheriae and Mycobacterium tuberculosis. In several corynebacterial species, the malR gene forms an operon with a gene encoding a universal stress protein (uspA). Chromatin affinity purification and sequencing (ChAP-Seq) analysis revealed that MalR binds more than 60 target promoters in the C. glutamicum genome as well as in the large cryptic prophage CGP3. Overproduction of MalR caused severe growth defects and an elongated cell morphology. ChAP-Seq data combined with a global transcriptome analysis of the malR overexpression strain emphasized a central role of MalR in cell envelope remodeling in response to environmental stresses. For example, prominent MalR targets are involved in peptidoglycan biosynthesis and synthesis of branched-chain fatty acids. Phenotypic microarrays suggested an altered sensitivity of a ΔmalR mutant toward several β-lactam antibiotics. Furthermore, we revealed MalR as a repressor of several prophage genes, suggesting that MalR may be involved in the control of stress-responsive induction of the large CGP3 element. In conclusion, our results emphasize MalR as a regulator involved in stress-responsive remodeling of the cell envelope of C. glutamicum and suggest a link between cell envelope stress and the control of phage gene expression.
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Affiliation(s)
- Max Hünnefeld
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Marcus Persicke
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
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Understanding lipogenesis by dynamically profiling transcriptional activity of lipogenic promoters in Yarrowia lipolytica. Appl Microbiol Biotechnol 2019; 103:3167-3179. [PMID: 30734122 DOI: 10.1007/s00253-019-09664-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/07/2019] [Accepted: 01/22/2019] [Indexed: 10/27/2022]
Abstract
Lipogenesis is a complicated process involving global transcriptional reprogramming of lipogenic pathways. It is commonly believed that nitrogen starvation triggers a metabolic shift that reroutes carbon flux from Krebs cycles to lipogenesis. In this study, we systematically surveyed and dynamically profiled the transcriptional activity of 22 lipogenic promoters aiming to delineate a picture how nitrogen starvation regulates lipogenesis in Y. lipolytica. These lipogenic promoters drive the expression of critical pathways that are responsible for the generation of reducing equivalents (NADPH), carbon backbones (acetyl-CoA, malonyl-CoA, DHAP, etc.), synthesis and degradation of fatty acids. Specifically, our investigated promoters span across an array of metabolic pathways, including glycolysis, Krebs cycle, pentose phosphate pathway, mannitol cycle, glutamine-GABA cycle, fatty acid and lipid synthesis, glyoxylate, β-oxidation, and POM (pyruvate-oxaloacetate-malate) cycle. Our work provides evidences that mannitol cycle, glutamine-GABA cycle and amino acid degradation, pyruvate oxidation, and acetate assimilation pathways are lipogenesis-related steps involved in generating cytosolic NADPH and acetyl-CoA precursors. This systematic investigation and dynamic profiling of lipogenic promoters may help us better understand lipogenesis, facilitate the formulation of structure-based kinetic models, as well as develop efficient cell factories for fuels and chemical production in oleaginous species.
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Hernández MA, Alvarez HM. Increasing lipid production using an NADP +-dependent malic enzyme from Rhodococcus jostii. MICROBIOLOGY-SGM 2018; 165:4-14. [PMID: 30372408 DOI: 10.1099/mic.0.000736] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The occurrence of NADP+-dependent malic enzymes (NADP+-MEs) in several Rhodococcus strains was analysed. The NADP+-ME number in Rhodococcus genomes seemed to be a strain-dependent property. Total NADP+-ME activity increased by 1.8- and 2.6-fold in the oleaginous Rhodococcus jostii RHA1 and Rhodococcus opacus PD630 strains during cultivation under nitrogen-limiting conditions. Total NADP+-ME activity inhibition by sesamol resulted in a significant decrease of the cellular biomass and lipid production in oleaginous rhodococci. A non-redundant ME coded by the RHA1_RS44255 gene located in a megaplasmid (pRHL3) of R. jostii RHA1 was characterized and its heterologous expression in Escherichia coli resulted in a twofold increase in ME activity in an NADP+-dependent manner. The overexpression of RHA1_RS44255 in RHA1 and PD630 strains grown on glucose promoted an increase in total NADP+-ME activity and an up to 1.9-foldincrease in total fatty acid production without sacrificing cellular biomass. On the other hand, its expression in Rhodococcus fascians F7 grown on glycerol resulted in a 1.3-1.4-foldincrease in total fatty acid content. The results of this study confirmed the contribution of NADP+-MEs to TAG accumulation in oleaginous rhodococci and the utility of these enzymes as an alternative approach to increase bacterial oil production from different carbon sources.
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Affiliation(s)
- Martín A Hernández
- Facultad de Ciencias Naturales, Instituto de Biociencias de la Patagonia, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de la Patagonia San Juan Bosco, Ruta Provincial no. 1, Km 4-Ciudad Universitaria, 9000 Comodoro Rivadavia, Chubut, Argentina
| | - Héctor M Alvarez
- Facultad de Ciencias Naturales, Instituto de Biociencias de la Patagonia, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de la Patagonia San Juan Bosco, Ruta Provincial no. 1, Km 4-Ciudad Universitaria, 9000 Comodoro Rivadavia, Chubut, Argentina
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Maruyama Y, Toya Y, Kurokawa H, Fukano Y, Sato A, Umemura H, Yamada K, Iwasaki H, Tobori N, Shimizu H. Characterization of oil-producing yeast Lipomyces starkeyi on glycerol carbon source based on metabolomics and 13C-labeling. Appl Microbiol Biotechnol 2018; 102:8909-8920. [PMID: 30097695 DOI: 10.1007/s00253-018-9261-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/30/2018] [Accepted: 07/19/2018] [Indexed: 11/27/2022]
Abstract
Lipomyces starkeyi is an oil-producing yeast that can produce triacylglycerol (TAG) from glycerol as a carbon source. The TAG was mainly produced after nitrogen depletion alongside reduced cell proliferation. To obtain clues for enhancing the TAG production, cell metabolism during the TAG-producing phase was characterized by metabolomics with 13C labeling. The turnover analysis showed that the time constants of intermediates from glycerol to pyruvate (Pyr) were large, whereas those of tricarboxylic acid (TCA) cycle intermediates were much smaller than that of Pyr. Surprisingly, the time constants of intermediates in gluconeogenesis and the pentose phosphate (PP) pathway were large, suggesting that a large amount of the uptaken glycerol was metabolized via the PP pathway. To synthesize fatty acids that make up TAG from acetyl-CoA (AcCoA), 14 molecules of nicotinamide adenine dinucleotide phosphate (NADPH) per C16 fatty acid molecule are required. Because the oxidative PP pathway generates NADPH, this pathway would contribute to supply NADPH for fatty acid synthesis. To confirm that the oxidative PP pathway can supply the NADPH required for TAG production, flux analysis was conducted based on the measured specific rates and mass balances. Flux analysis revealed that the NADPH necessary for TAG production was supplied by metabolizing 48.2% of the uptaken glycerol through gluconeogenesis and the PP pathway. This result was consistent with the result of the 13C-labeling experiment. Furthermore, comparison of the actual flux distribution with the ideal flux distribution for TAG production suggested that it is necessary to flow more dihydroxyacetonephosphate (DHAP) through gluconeogenesis to improve TAG yield.
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Affiliation(s)
- Yuki Maruyama
- Analytical Technology Research Center, Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan.
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Kurokawa
- Functional Materials Science Research Laboratories, Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Yuka Fukano
- Functional Materials Science Research Laboratories, Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Atsushi Sato
- Analytical Technology Research Center, Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Hiroyasu Umemura
- Analytical Technology Research Center, Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Kaoru Yamada
- Analytical Technology Research Center, Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Hideaki Iwasaki
- Analytical Technology Research Center, Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Norio Tobori
- Functional Materials Science Research Laboratories, Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Abdel-Mawgoud AM, Markham KA, Palmer CM, Liu N, Stephanopoulos G, Alper HS. Metabolic engineering in the host Yarrowia lipolytica. Metab Eng 2018; 50:192-208. [PMID: 30056205 DOI: 10.1016/j.ymben.2018.07.016] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022]
Abstract
The nonconventional, oleaginous yeast, Yarrowia lipolytica is rapidly emerging as a valuable host for the production of a variety of both lipid and nonlipid chemical products. While the unique genetics of this organism pose some challenges, many new metabolic engineering tools have emerged to facilitate improved genetic manipulation in this host. This review establishes a case for Y. lipolytica as a premier metabolic engineering host based on innate metabolic capacity, emerging synthetic tools, and engineering examples. The metabolism underlying the lipid accumulation phenotype of this yeast as well as high flux through acyl-CoA precursors and the TCA cycle provide a favorable metabolic environment for expression of relevant heterologous pathways. These properties allow Y. lipolytica to be successfully engineered for the production of both native and nonnative lipid, organic acid, sugar and acetyl-CoA derived products. Finally, this host has unique metabolic pathways enabling growth on a wide range of carbon sources, including waste products. The expansion of carbon sources, together with the improvement of tools as highlighted here, have allowed this nonconventional organism to act as a cellular factory for valuable chemicals and fuels.
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Affiliation(s)
- Ahmad M Abdel-Mawgoud
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Kelly A Markham
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States
| | - Claire M Palmer
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States
| | - Nian Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States.
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Li S, Li L, Xiong X, Ji X, Wei Y, Lin L, Zhang Q. A novel malic enzyme gene, Mime2, from Mortierella isabellina M6-22 contributes to lipid accumulation. Biotechnol Lett 2018; 40:1109-1118. [PMID: 29777513 DOI: 10.1007/s10529-018-2560-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/27/2018] [Indexed: 11/28/2022]
Abstract
OBJECTIVE This study was aimed at cloning and characterizing a novel malic enzyme (ME) gene of Mortierella isabellina M6-22 and identifying its relation with lipid accumulation. METHODS Mime2 was cloned from strain M6-22. Plasmid pET32aMIME2 was constructed to express ME of MIME2 in Escherichia coli BL21. After purification, the optimal pH and temperature of MIME2, as well as Km and Vmax for NADP+ were determined. The effects of EDTA or metal ions (Mn2+, Mg2+, Co2+, Cu2+, Ca2+, or Zn2+) on the enzymatic activity of MIME2 were evaluated. Besides, plasmid pRHMIME2 was created to express MIME2 in Rhodosporidium kratochvilovae YM25235, and its cell lipid content was measured by the acid-heating method. The optimal pH and temperature of MIME2 are 5.8 and 30 °C, respectively. RESULTS The act ivity of MIME2 was significantly increased by Mg2+, Ca2+, or Mn2+ at 0.5 mM but inhibited by Cu2+ or Zn2+ (p < 0.05). The optimal enzymatic activity of MIME2 is 177.46 U/mg, and the Km and Vmax for NADP+ are 0.703 mM and 156.25 μg/min, respectively. Besides, Mime2 transformation significantly increased the cell lipid content in strain YM25235 (3.15 ± 0.24 vs. 2.17 ± 0.31 g/L, p < 0.01). CONCLUSIONS The novel ME gene Mime2 isolated from strain M6-22 contributes to lipid accumulation in strain YM25235.
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Affiliation(s)
- Shan Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan, China
| | - Lingyan Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan, China
| | - Xiangfeng Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan, China
| | - Xiuling Ji
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan, China
| | - Lianbing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan, China.
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41
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Critical steps in carbon metabolism affecting lipid accumulation and their regulation in oleaginous microorganisms. Appl Microbiol Biotechnol 2018; 102:2509-2523. [DOI: 10.1007/s00253-018-8813-z] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 12/11/2022]
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Zeng SY, Liu HH, Shi TQ, Song P, Ren LJ, Huang H, Ji XJ. Recent Advances in Metabolic Engineering ofYarrowia lipolyticafor Lipid Overproduction. EUR J LIPID SCI TECH 2018. [DOI: 10.1002/ejlt.201700352] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Si-Yu Zeng
- College of Biotechnology and Pharmaceutical Engineering; Nanjing Tech University; No. 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Hu-Hu Liu
- College of Biotechnology and Pharmaceutical Engineering; Nanjing Tech University; No. 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Tian-Qiong Shi
- College of Biotechnology and Pharmaceutical Engineering; Nanjing Tech University; No. 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Ping Song
- College of Biotechnology and Pharmaceutical Engineering; Nanjing Tech University; No. 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Lu-Jing Ren
- College of Biotechnology and Pharmaceutical Engineering; Nanjing Tech University; No. 30 South Puzhu Road Nanjing 211816 P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM); No.5 Xinmofan Road Nanjing 210009 P. R. China
| | - He Huang
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM); No.5 Xinmofan Road Nanjing 210009 P. R. China
- School of Pharmaceutical Sciences; Nanjing Tech University; No.30 South Puzhu Road Nanjing 211816 P. R. of China
- State Key Laboratory of Materials-Oriented Chemical Engineering; Nanjing Tech University; No.5 Xinmofan Road Nanjing 210009 P. R. China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering; Nanjing Tech University; No. 30 South Puzhu Road Nanjing 211816 P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM); No.5 Xinmofan Road Nanjing 210009 P. R. China
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Zhang L, Zhang H, Song Y. Identification and Characterization of Diacylglycerol Acyltransferase from Oleaginous Fungus Mucor circinelloides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:674-681. [PMID: 29260551 DOI: 10.1021/acs.jafc.7b04295] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT) is a pivotal regulator of triacylglycerol (TAG) synthesis. The oleaginous fungus Mucor circinelloides has four putative DGATs: McDGAT1A, McDGAT1B, McDGAT2A, and McDGAT2B, classified into the DGAT1 and DGAT2 subfamilies, respectively. To identify and characterize DGATs in M. circinelloides, these four genes were expressed in Saccharomyces cerevisiae H1246 (TAG-deficient quadruple mutant), individually. TAG biosynthesis was restored only by the expression of McDGAT2B, and TAG content was significantly higher in the mutants with McDGAT2B expression than in a S. cerevisiae mutant with endogenous DGA1 expression. McDGAT2B prefers saturated fatty acids to monounsaturated fatty acids and has an obvious preference for C18:3 (ω-6) according to the results of substrate preference experiments. Furthermore, only the mRNA expression pattern of McDGAT2B correlated with TAG biosynthesis during a fermentation process. Our experiments strongly indicate that McDGAT2B is crucial for TAG accumulation, suggesting that it may be an essential target for metabolic engineering aimed at increasing lipid content of M. circinelloides.
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Affiliation(s)
- Luning Zhang
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology , Zibo, 255049 Shandong, People's Republic of China
- Shanghai Lida Polytechnic Institute , Shanghai 201609, People's Republic of China
| | - Huaiyuan Zhang
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology , Zibo, 255049 Shandong, People's Republic of China
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology , Zibo, 255049 Shandong, People's Republic of China
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Xie D. Integrating Cellular and Bioprocess Engineering in the Non-Conventional Yeast Yarrowia lipolytica for Biodiesel Production: A Review. Front Bioeng Biotechnol 2017; 5:65. [PMID: 29090211 PMCID: PMC5650997 DOI: 10.3389/fbioe.2017.00065] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/02/2017] [Indexed: 12/14/2022] Open
Abstract
As one of the major biofuels to replace fossil fuel, biodiesel has now attracted more and more attention due to its advantages in higher energy density and overall less greenhouse gas generation. Biodiesel (fatty acid alkyl esters) is produced by chemically or enzymatically catalyzed transesterification of lipids from microbial cells, microalgae, oil crops, or animal fats. Currently, plant oils or waste cooking oils/fats remain the major source for biodiesel production via enzymatic route, but the production capacity is limited either by the uncertain supplement of plant oils or by the low or inconsistent quality of waste oils/fats. In the past decades, significant progresses have been made on synthesis of microalgae oils directly from CO2via a photosynthesis process, but the production cost from any current technologies is still too high to be commercialized due to microalgae’s slow growth rate on CO2, inefficiency in photo-bioreactors, lack of efficient contamination control methods, and high cost in downstream recovery. At the same time, many oleaginous microorganisms have been studied to produce lipids via the fatty acid synthesis pathway under aerobic fermentation conditions, among them one of the most studied is the non-conventional yeast, Yarrowia lipolytica, which is able to produce fatty acids at very high titer, rate, and yield from various economical substrates. This review summarizes the recent research progresses in both cellular and bioprocess engineering in Y. lipolytica to produce lipids at a low cost that may lead to commercial-scale biodiesel production. Specific technologies include the strain engineering for using various substrates, metabolic engineering in high-yield lipid synthesis, cell morphology study for efficient substrate uptake and product formation, free fatty acid formation and secretion for improved downstream recovery, and fermentation engineering for higher productivities and less operating cost. To further improve the economics of the microbial oil-based biodiesel, production of lipid-related or -derived high-value products are also discussed.
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Affiliation(s)
- Dongming Xie
- Massachusetts Biomanufacturing Center, Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, United States
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45
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Yuzbasheva EY, Mostova EB, Andreeva NI, Yuzbashev TV, Laptev IA, Sobolevskaya TI, Sineoky SP. Co-expression of glucose-6-phosphate dehydrogenase and acyl-CoA binding protein enhances lipid accumulation in the yeast Yarrowia lipolytica. N Biotechnol 2017; 39:18-21. [DOI: 10.1016/j.nbt.2017.05.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/08/2017] [Accepted: 03/28/2017] [Indexed: 10/19/2022]
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46
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Qiao K, Wasylenko TM, Zhou K, Xu P, Stephanopoulos G. Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism. Nat Biotechnol 2017; 35:173-177. [DOI: 10.1038/nbt.3763] [Citation(s) in RCA: 280] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 12/08/2016] [Indexed: 01/12/2023]
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47
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Tan KWM, Lee YK. The dilemma for lipid productivity in green microalgae: importance of substrate provision in improving oil yield without sacrificing growth. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:255. [PMID: 27895709 PMCID: PMC5120525 DOI: 10.1186/s13068-016-0671-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/16/2016] [Indexed: 05/02/2023]
Abstract
Rising oil prices and concerns over climate change have resulted in more emphasis on research into renewable biofuels from microalgae. Unlike plants, green microalgae have higher biomass productivity, will not compete with food and agriculture, and do not require fertile land for cultivation. However, microalgae biofuels currently suffer from high capital and operating costs due to low yields and costly extraction methods. Microalgae grown under optimal conditions produce large amounts of biomass but with low neutral lipid content, while microalgae grown in nutrient starvation accumulate high levels of neutral lipids but are slow growing. Producing lipids while maintaining high growth rates is vital for biofuel production because high biomass productivity increases yield per harvest volume while high lipid content decreases the cost of extraction per unit product. Therefore, there is a need for metabolic engineering of microalgae to constitutively produce high amounts of lipids without sacrificing growth. Substrate availability is a rate-limiting step in balancing growth and fatty acid (FA) production because both biomass and FA synthesis pathways compete for the same substrates, namely acetyl-CoA and NADPH. In this review, we discuss the efforts made for improving biofuel production in plants and microorganisms, the challenges faced in achieving lipid productivity, and the important role of precursor supply for FA synthesis. The main focus is placed on the enzymes which catalyzed the reactions supplying acetyl-CoA and NADPH.
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Affiliation(s)
- Kenneth Wei Min Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545 Singapore
| | - Yuan Kun Lee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545 Singapore
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Park BG, Kim M, Kim J, Yoo H, Kim BG. Systems biology for understanding and engineering of heterotrophic oleaginous microorganisms. Biotechnol J 2016; 12. [DOI: 10.1002/biot.201600104] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Beom Gi Park
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute; Seoul National University; Seoul Republic of Korea
| | - Minsuk Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute; Seoul National University; Seoul Republic of Korea
| | - Joonwon Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute; Seoul National University; Seoul Republic of Korea
| | - Heewang Yoo
- Interdisciplinary Program for Biochemical Engineering and Biotechnology; Seoul National University; Seoul Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute; Seoul National University; Seoul Republic of Korea
- Interdisciplinary Program for Biochemical Engineering and Biotechnology; Seoul National University; Seoul Republic of Korea
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Liu N, Qiao K, Stephanopoulos G. 13C Metabolic Flux Analysis of acetate conversion to lipids by Yarrowia lipolytica. Metab Eng 2016; 38:86-97. [DOI: 10.1016/j.ymben.2016.06.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/17/2016] [Accepted: 06/20/2016] [Indexed: 12/18/2022]
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Ochsenreither K, Glück C, Stressler T, Fischer L, Syldatk C. Production Strategies and Applications of Microbial Single Cell Oils. Front Microbiol 2016; 7:1539. [PMID: 27761130 PMCID: PMC5050229 DOI: 10.3389/fmicb.2016.01539] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/14/2016] [Indexed: 11/16/2022] Open
Abstract
Polyunsaturated fatty acids (PUFAs) of the ω-3 and ω-6 class (e.g., α-linolenic acid, linoleic acid) are essential for maintaining biofunctions in mammalians like humans. Due to the fact that humans cannot synthesize these essential fatty acids, they must be taken up from different food sources. Classical sources for these fatty acids are porcine liver and fish oil. However, microbial lipids or single cell oils, produced by oleaginous microorganisms such as algae, fungi and bacteria, are a promising source as well. These single cell oils can be used for many valuable chemicals with applications not only for nutrition but also for fuels and are therefore an ideal basis for a bio-based economy. A crucial point for the establishment of microbial lipids utilization is the cost-effective production and purification of fuels or products of higher value. The fermentative production can be realized by submerged (SmF) or solid state fermentation (SSF). The yield and the composition of the obtained microbial lipids depend on the type of fermentation and the particular conditions (e.g., medium, pH-value, temperature, aeration, nitrogen source). From an economical point of view, waste or by-product streams can be used as cheap and renewable carbon and nitrogen sources. In general, downstream processing costs are one of the major obstacles to be solved for full economic efficiency of microbial lipids. For the extraction of lipids from microbial biomass cell disruption is most important, because efficiency of cell disruption directly influences subsequent downstream operations and overall extraction efficiencies. A multitude of cell disruption and lipid extraction methods are available, conventional as well as newly emerging methods, which will be described and discussed in terms of large scale applicability, their potential in a modern biorefinery and their influence on product quality. Furthermore, an overview is given about applications of microbial lipids or derived fatty acids with emphasis on food applications.
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Affiliation(s)
- Katrin Ochsenreither
- Technical Biology, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of TechnologyKarlsruhe, Germany
| | - Claudia Glück
- Biotechnology and Enzyme Science, Institute of Food Science and Biotechnology, University of HohenheimStuttgart, Germany
| | - Timo Stressler
- Biotechnology and Enzyme Science, Institute of Food Science and Biotechnology, University of HohenheimStuttgart, Germany
| | - Lutz Fischer
- Biotechnology and Enzyme Science, Institute of Food Science and Biotechnology, University of HohenheimStuttgart, Germany
| | - Christoph Syldatk
- Technical Biology, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of TechnologyKarlsruhe, Germany
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