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Li J, Rong L, Zhao Y, Li S, Zhang C, Xiao D, Foo JL, Yu A. Next-generation metabolic engineering of non-conventional microbial cell factories for carboxylic acid platform chemicals. Biotechnol Adv 2020; 43:107605. [DOI: 10.1016/j.biotechadv.2020.107605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/30/2020] [Accepted: 07/27/2020] [Indexed: 01/21/2023]
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52
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Chroumpi T, Mäkelä MR, de Vries RP. Engineering of primary carbon metabolism in filamentous fungi. Biotechnol Adv 2020; 43:107551. [DOI: 10.1016/j.biotechadv.2020.107551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 10/24/2022]
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53
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Muhammad A, Feng X, Rasool A, Sun W, Li C. Production of plant natural products through engineered Yarrowia lipolytica. Biotechnol Adv 2020; 43:107555. [DOI: 10.1016/j.biotechadv.2020.107555] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/13/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022]
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54
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Wang R, Sun J, Lassabliere B, Yu B, Liu SQ. Fermentation characteristics of four non-Saccharomyces yeasts in green tea slurry. Food Microbiol 2020; 92:103609. [PMID: 32950144 DOI: 10.1016/j.fm.2020.103609] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/20/2020] [Accepted: 07/25/2020] [Indexed: 01/19/2023]
Abstract
The fermentation characteristics of non-Saccharomyces yeasts (Pichia kluyveri FrootZen, Torulaspora delbrueckii Prelude, Williopsis saturnus var. mrakii NCYC2251 and Torulaspora delbrueckii Biodiva) were evaluated in green tea slurry fermentation. Each yeast showed different fermentation performances: strains Prelude and Biodiva utilized sucrose faster than the other two yeasts; strain NCYC2251 was the only species that metabolized xylose. Strain FrootZen increased the caffeine content significantly and strain Prelude showed the opposite trend, both at a statistical level, while theanine contents in four samples were relatively stable. Biodiva and FrootZen significantly improved polyphenols content and the oxygen radical absorbance capacity of fermented teas. Some endogenous volatiles such as ketones, lactones and aldehydes decreased to lower or undetected levels, but one of the key tea aroma compounds methyl salicylate increased by 34-fold and 100-fold in P. kluyveri and W. saturnus samples respectively. Therefore, green tea fermentation by appropriate non-Saccharomyces yeasts can enhance its antioxidant capacity and alter the aroma compound profile.
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Affiliation(s)
- Rui Wang
- Department of Food Science & Technology, National University of Singapore, Science Drive 3, Singapore, 117543, Singapore
| | - Jingcan Sun
- Mane SEA PTE LTD, Biopolis Drive 3, 138623, Singapore
| | | | - Bin Yu
- Mane SEA PTE LTD, Biopolis Drive 3, 138623, Singapore
| | - Shao Quan Liu
- Department of Food Science & Technology, National University of Singapore, Science Drive 3, Singapore, 117543, Singapore; National University of Singapore (Suzhou) Research Institute, No. 377 Linquan Street, Suzhou Industrial Park, Suzhou, Jiangsu, 215123, China.
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55
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Gu Y, Ma J, Zhu Y, Ding X, Xu P. Engineering Yarrowia lipolytica as a Chassis for De Novo Synthesis of Five Aromatic-Derived Natural Products and Chemicals. ACS Synth Biol 2020; 9:2096-2106. [PMID: 32650638 PMCID: PMC7445739 DOI: 10.1021/acssynbio.0c00185] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Yarrowia
lipolytica is a novel microbial chassis
to upgrade renewable low-cost carbon feedstocks to high-value commodity
chemicals and natural products. In this work, we systematically characterized
and removed the rate-limiting steps of the shikimate pathway and achieved de novo synthesis of five aromatic chemicals in Y. lipolytica. We determined that eliminating amino
acids formation and engineering feedback-insensitive DAHP synthases
are critical steps to mitigate precursor competition and relieve the
feedback regulation of the shikimate pathway. Further overexpression
of heterologous phosphoketolase and deletion of pyruvate kinase provided
a sustained metabolic driving force that channels E4P (erythrose 4-phosphate)
and PEP (phosphoenolpyruvate) precursors through the shikimate pathway.
Precursor competing pathways and byproduct formation pathways were
also blocked by inactivating chromosomal genes. To demonstrate the
utility of our engineered chassis strain, three natural products,
2-phenylethanol (2-PE), p-coumaric acid, and violacein,
which were derived from phenylalanine, tyrosine, and tryptophan, respectively,
were chosen to test the chassis performance. We obtained 2426.22 ±
48.33 mg/L of 2-PE, 593.53 ± 28.75 mg/L of p-coumaric acid, 12.67 ± 2.23 mg/L of resveratrol, 366.30 ±
28.99 mg/L of violacein, and 55.12 ± 2.81 mg/L of deoxyviolacein
from glucose in a shake flask. The 2-PE production represents a 286-fold
increase over the initial strain (8.48 ± 0.50 mg/L). Specifically,
we obtained the highest 2-PE, violacein, and deoxyviolacein titer
ever reported from the de novo shikimate pathway
in yeast. These results set up a new stage of engineering Y. lipolytica as a sustainable biorefinery chassis
strain for de novo synthesis of aromatic compounds
with economic values.
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Affiliation(s)
- Yang Gu
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jingbo Ma
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Yonglian Zhu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xinyu Ding
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Peng Xu
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
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56
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Xiong X, Chen S. Expanding Toolbox for Genes Expression of Yarrowia lipolytica to Include Novel Inducible, Repressible, and Hybrid Promoters. ACS Synth Biol 2020; 9:2208-2213. [PMID: 32584553 DOI: 10.1021/acssynbio.0c00243] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Promoters are critical tools to precisely control gene expression for both synthetic biology and metabolic engineering. Although Yarrowia lipolytica has demonstrated many industrially relevant advantages, promoter discovery efforts on this non-conventional yeast are limited due to the challenge in finding suitable inducible and repressible promoters. Six copper-inducible promoters and five repressible promoters were isolated in this work. Especially, Cu2+-repressible promoters showed relatively high activity under non-repressing conditions compared with a constitutive promoter, but the strength could be almost fully repressed by a supplement of a low content of Cu2+. The six Cu2+-inducible promoters were engineered to improve their dynamic regulation range with a tandem upstream activation sequence. An engineered promoter was successfully used to construct a more productive pathway for production of a novel bioproduct, wax ester, than that used for both Cu2+-inducible promoter and constitutive promoter. This study provides effective tools applicable to fine-tune the gene expression in this microbial host.
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Affiliation(s)
- Xiaochao Xiong
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Shulin Chen
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington 99164, United States
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57
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Ghogare R, Chen S, Xiong X. Metabolic Engineering of Oleaginous Yeast Yarrowia lipolytica for Overproduction of Fatty Acids. Front Microbiol 2020; 11:1717. [PMID: 32849364 PMCID: PMC7418586 DOI: 10.3389/fmicb.2020.01717] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/30/2020] [Indexed: 01/24/2023] Open
Abstract
The oleaginous yeast Yarrowia lipolytica has attracted much attention due to its ability to utilize a wide range of substrates to accumulate high lipid content and its flexibility for genetic manipulation. In this study, intracellular lipid metabolism in Y. lipolytica was tailored to produce fatty acid, a renewable oleochemical and precursor for production of advanced biofuels. Two main strategies, including blocking activation and peroxisomal uptake of fatty acids and elimination of biosynthesis of lipids, were employed to reduce fatty acid consumption by the native pathways in Y. lipolytica. Both genetic modifications improved fatty acid production. However, disruption of the genes responsible for assembly of nonpolar lipid molecules including triacylglycerols (TAGs) and steryl esters resulted in the deleterious effects on the cell growth. The gene tesA encoding thioesterase from Escherichia coli was expressed in the strain with disrupted faa genes encoding fatty acyl-CoA synthetases and pxa1 encoding peroxisomal acyl-CoA transporter, and the titer of fatty acids resulted in 2.3 g/L in shake flask culture, representing 11-fold improvement compared with the parent strain. Expressing the native genes encoding acetyl-CoA carboxylase (ACC) and hexokinase also increased fatty acid production, although the improvement was not as significant as that with tesA expression. Saturated fatty acids including palmitic acid (C16:0) and stearic acid (C18:0) increased remarkably in the fatty acid composition of the recombinant bearing tesA compared with the parent strain. The recombinant expressing tesA gene resulted in high lipid content, indicating the great fatty acid producing potential of Y. lipolytica. The results highlight the achievement of fatty acid overproduction without adverse effect on growth of the strain. Results of this study provided insight into the relationship between fatty acid and lipid metabolism in Y. lipolytica, confirming the avenue to reprogram lipid metabolism of this host for overproduction of renewable fatty acids.
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Affiliation(s)
- Rishikesh Ghogare
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
| | - Shulin Chen
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
| | - Xiaochao Xiong
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
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58
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An artificial chromosome ylAC enables efficient assembly of multiple genes in Yarrowia lipolytica for biomanufacturing. Commun Biol 2020; 3:199. [PMID: 32350406 PMCID: PMC7190667 DOI: 10.1038/s42003-020-0936-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/07/2020] [Indexed: 12/18/2022] Open
Abstract
The efficient use of the yeast Yarrowia lipolytica as a cell factory is hampered by the lack of powerful genetic engineering tools dedicated for the assembly of large DNA fragments and the robust expression of multiple genes. Here we describe the design and construction of artificial chromosomes (ylAC) that allow easy and efficient assembly of genes and chromosomal elements. We show that metabolic pathways can be rapidly constructed by various assembly of multiple genes in vivo into a complete, independent and linear supplementary chromosome with a yield over 90%. Additionally, our results reveal that ylAC can be genetically maintained over multiple generations either under selective conditions or, without selective pressure, using an essential gene as the selection marker. Overall, the ylACs reported herein are game-changing technology for Y. lipolytica, opening myriad possibilities, including enzyme screening, genome studies and the use of this yeast as a previous unutilized bio-manufacturing platform. Zhong-peng Guo et al. develop artificial chromosomes (ylAC) that allow easy and efficient assembly of multiple genes in Yarrowia lipolytica, a yeast strain commonly used for synthetic biology. ylAC provides an improved bio-manufacturing platform that is potentially useful for food, pharmaceutical, and environmental industries.
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59
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Fickers P, Cheng H, Sze Ki Lin C. Sugar Alcohols and Organic Acids Synthesis in Yarrowia lipolytica: Where Are We? Microorganisms 2020; 8:E574. [PMID: 32326622 PMCID: PMC7232202 DOI: 10.3390/microorganisms8040574] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 01/01/2023] Open
Abstract
Sugar alcohols and organic acids that derive from the metabolism of certain microorganisms have a panoply of applications in agro-food, chemical and pharmaceutical industries. The main challenge in their production is to reach a productivity threshold that allow the process to be profitable. This relies on the construction of efficient cell factories by metabolic engineering and on the development of low-cost production processes by using industrial wastes or cheap and widely available raw materials as feedstock. The non-conventional yeast Yarrowia lipolytica has emerged recently as a potential producer of such metabolites owing its low nutritive requirements, its ability to grow at high cell densities in a bioreactor and ease of genome edition. This review will focus on current knowledge on the synthesis of the most important sugar alcohols and organic acids in Y. lipolytica.
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Affiliation(s)
- Patrick Fickers
- Microbial Process and Interactions, TERRA Teaching and Research Centre, University of Liege—Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Hairong Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong;
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60
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Metabolic engineering for the production of dicarboxylic acids and diamines. Metab Eng 2020; 58:2-16. [DOI: 10.1016/j.ymben.2019.03.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 11/18/2022]
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61
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Ong KL, Fickers P, Lin CSK. Enhancing succinic acid productivity in the yeast Yarrowia lipolytica with improved glycerol uptake rate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 702:134911. [PMID: 31733546 DOI: 10.1016/j.scitotenv.2019.134911] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 05/22/2023]
Abstract
Development of cost effective and highly efficient process for bio-based succinic acid (SA) production is a main concern for industry. The metabolically engineered Y. lipolytica strain PGC01003 was successfully used for SA production with high titre. However, this strain possesses as main drawback with a low growth rate when glycerol is used as a feedstock. Herein, gene GUT1, encoding glycerol kinase, was overexpressed in strain PGC01003 with the aim to improve glycerol uptake capacity. In the resulting strain RIY420, glycerol uptake was 13.5% higher than for the parental strain. GUT1 gene overexpression also positively influences SA production. In batch bioreactor, SA titre, yield and productivity were 32%, 39% and 143% higher, respectively, than for the parental strain PGC01003. Using a glycerol feeding strategy, SA titre, yield and productivity were further improved by 11%, 5% and 10%, respectively. Moreover, the process duration to yield the highest concentration of SA in the culture supernatant was reduced by 9%. This demonstrated the contribution of metabolically engineered strain RIY420 to lower SA process cost and increase the efficiency of bio-based SA production.
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Affiliation(s)
- Khai Lun Ong
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, Av. De la Faculté, 2B, 5030 Gembloux, Belgium
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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62
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Rigaki A, Webb C, Theodoropoulos C. Double substrate limitation model for the bio-based production of succinic acid from glycerol. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107391] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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63
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Li G, Huang D, Sui X, Li S, Huang B, Zhang X, Wu H, Deng Y. Advances in microbial production of medium-chain dicarboxylic acids for nylon materials. REACT CHEM ENG 2020. [DOI: 10.1039/c9re00338j] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Medium-chain dicarboxylic acids (MDCAs) are widely used in the production of nylon materials, and among which, succinic, glutaric, adipic, pimelic, suberic, azelaic and sebacic acids are particularly important for that purpose.
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Affiliation(s)
- Guohui Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Dixuan Huang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Xue Sui
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Shiyun Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Bing Huang
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
| | - Xiaojuan Zhang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF)
- Jiangnan University
- Wuxi
- China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology
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64
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Prabhu AA, Ledesma-Amaro R, Lin CSK, Coulon F, Thakur VK, Kumar V. Bioproduction of succinic acid from xylose by engineered Yarrowia lipolytica without pH control. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:113. [PMID: 32607128 PMCID: PMC7321536 DOI: 10.1186/s13068-020-01747-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/05/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Xylose is the most prevalent sugar available in hemicellulose fraction of lignocellulosic biomass (LCB) and of great interest for the green economy. Unfortunately, most of the cell factories cannot inherently metabolize xylose as sole carbon source. Yarrowia lipolytica is a non-conventional yeast that produces industrially important metabolites. The yeast is able to metabolize a large variety of substrates including both hydrophilic and hydrophobic carbon sources. However, Y. lipolytica lacks effective metabolic pathway for xylose uptake and only scarce information is available on utilization of xylose. For the economica feasibility of LCB-based biorefineries, effective utilization of both pentose and hexose sugars is obligatory. RESULTS In the present study, succinic acid (SA) production from xylose by Y. lipolytica was examined. To this end, Y. lipolytica PSA02004 strain was engineered by overexpressing pentose pathway cassette comprising xylose reductase (XR), xylitol dehydrogenase (XDH) and xylulose kinase (XK) gene. The recombinant strain exhibited a robust growth on xylose as sole carbon source and produced substantial amount of SA. The inhibition of cell growth and SA formation was observed above 60 g/L xylose concentration. The batch cultivation of the recombinant strain in a bioreactor resulted in a maximum biomass concentration of 7.3 g/L and SA titer of 11.2 g/L with the yield of 0.19 g/g. Similar results in terms of cell growth and SA production were obtained with xylose-rich hydrolysate derived from sugarcane bagasse. The fed-batch fermentation yielded biomass concentration of 11.8 g/L (OD600: 56.1) and SA titer of 22.3 g/L with a gradual decrease in pH below 4.0. Acetic acid was obtained as a main by-product in all the fermentations. CONCLUSION The recombinant strain displayed potential for bioconversion of xylose to SA. Further, this study provided a new insight on conversion of lignocellulosic biomass into value-added products. To the best of our knowledge, this is the first study on SA production by Y. lipolytica using xylose as a sole carbon source.
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Affiliation(s)
- Ashish A. Prabhu
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ UK
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL UK
| | - Vijay Kumar Thakur
- Biorefining and Advanced Materials Research Centre, Scotland’s Rural College (SRUC), Edinburgh, UK
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL UK
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Babaei M, Rueksomtawin Kildegaard K, Niaei A, Hosseini M, Ebrahimi S, Sudarsan S, Angelidaki I, Borodina I. Engineering Oleaginous Yeast as the Host for Fermentative Succinic Acid Production From Glucose. Front Bioeng Biotechnol 2019; 7:361. [PMID: 31828067 PMCID: PMC6892388 DOI: 10.3389/fbioe.2019.00361] [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: 09/15/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022] Open
Abstract
Oleaginous yeast Yarrowia lipolytica is a prospective host for production of succinic acid. The interruption of tricarboxylic acid cycle through succinate dehydrogenase gene (SDH) deletion was reported to result in strains incapable of glucose utilization and this ability had to be restored by chemical mutation or long adaptive laboratory evolution. In this study, a succinate producing strain of Y. lipolytica was engineered by truncating the promoter of SDH1 gene, which resulted in 77% reduction in SDH activity but did not impair the ability of the strain to grow on glucose. The flux toward succinic acid was further improved by overexpressing the genes in the glyoxylate pathway and the oxidative TCA branch, and expressing phosphoenolpyruvate carboxykinase from Actinobacillus succinogenes. A short adaptation on glucose reduced the lag phase of the strain and increased its tolerance to high glucose concentrations. The resulting strain produced 7.8 ± 0.0 g/L succinic acid with a yield of 0.105 g/g glucose in shake flasks without pH control, while mannitol (11.8 ± 0.8 g/L) was the main by-product. Further investigations showed that mannitol accumulation was caused by low pH stress and buffering the fermentation medium eliminated mannitol formation. In a fed-batch bioreactor in mineral medium at pH 5, at which point according to Ka values of succinic acid, the major fraction of product was in acidic form rather than dissociated form, the strain produced 35.3 ± 1.5 g/L succinic acid with 0.26 ± 0.00 g/g glucose yield.
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Affiliation(s)
- Mahsa Babaei
- Department of Chemical & Petroleum Engineering, University of Tabriz, Tabriz, Iran
| | | | - Aligholi Niaei
- Department of Chemical & Petroleum Engineering, University of Tabriz, Tabriz, Iran
| | - Maryam Hosseini
- Department of Chemical Engineering, Faculty of Engineering, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Sirous Ebrahimi
- Biotechnology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, Tabriz, Iran
| | - Suresh Sudarsan
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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66
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CRISPR-Cas12a/Cpf1-assisted precise, efficient and multiplexed genome-editing in Yarrowia lipolytica. Metab Eng Commun 2019; 10:e00112. [PMID: 31867213 PMCID: PMC6906711 DOI: 10.1016/j.mec.2019.e00112] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/03/2019] [Accepted: 11/14/2019] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 has been widely adopted as the basic toolkit for precise genome-editing and engineering in various organisms. Alternative to Cas9, Cas12 or Cpf1 uses a simple crRNA as a guide and expands the protospacer adjacent motif (PAM) sequence to TTTN. This unique PAM sequence of Cpf1 may significantly increase the on-target editing efficiency due to lower chance of Cpf1 misreading the PAMs on a high GC genome. To demonstrate the utility of CRISPR-Cpf1, we have optimized the CRISPR-Cpf1 system and achieved high-editing efficiency for two counter-selectable markers in the industrially-relevant oleaginous yeast Yarrowia lipolytica: arginine permease (93% for CAN1) and orotidine 5′-phosphate decarboxylase (~96% for URA3). Both mutations were validated by indel mutation sequencing. For the first time, we further expanded this toolkit to edit three sulfur house-keeping genetic markers (40%–75% for MET2, MET6 and MET25), which confers yeast distinct colony color changes due to the formation of PbS (lead sulfide) precipitates. Different from Cas9, we demonstrated that the crRNA transcribed from a standard type II RNA promoter was sufficient to guide Cpf1 endonuclease activity. Furthermore, modification of the crRNA with 3′ polyUs facilitates the faster maturation and folding of crRNA and improve the genome editing efficiency. We also achieved multiplexed genome editing, and the editing efficiency reached 75%–83% for duplex genomic targets (CAN1-URA3 and CAN1-MET25) and 41.7% for triplex genomic targets (CAN1-URA3-MET25). Taken together, this work expands the genome-editing toolbox for oleaginous yeast species and may accelerate our ability to engineer oleaginous yeast for both biotechnological and biomedical applications. Cpf1 expands the PAM to TTTN and increases the on-target editing efficiency. CRISPR-Cpf1 is optimized to edit genetic markers CAN1, URA3, MET2, MET6 and MET25. A type II RNA promoter was sufficient to guide Cpf1 endonuclease activity. CrRNA modified with 3′ polyUs improves the on-target genome editing efficiency. Duplex genome-editing reaches 75%–83% and triplex editing reaches 42% in Y. lipolytica.
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67
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Lv Y, Marsafari M, Koffas M, Zhou J, Xu P. Optimizing Oleaginous Yeast Cell Factories for Flavonoids and Hydroxylated Flavonoids Biosynthesis. ACS Synth Biol 2019; 8:2514-2523. [PMID: 31622552 DOI: 10.1021/acssynbio.9b00193] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plants possess myriads of secondary metabolites with a broad spectrum of health-promoting benefits. To date, plant extraction is still the primary route to produce high-value natural products which inherently suffers from economics and scalability issues. Heterologous expression of plant biosynthetic gene clusters in microbial host is considered as a feasible approach to overcoming these limitations. Oleaginous yeast produces a large amount of lipid bodies, the abundant membrane structure and the lipophilic environment provide the ideal environment for the regioselectivity and stereoselectivity of many plant-derived P450 enzymes. In this work, we used modular method to construct, characterize, and optimize the flavonoid pathways in Yarrowia lipolytica. We also evaluated various precursor biosynthetic routes and unleashed the metabolic potential of Y. lipolytica to produce flavonoids and hydroxylated flavonoids. Specifically, we have identified that chalcone synthase (CHS) and cytochrome P450 reductases (CPR) were the bottlenecks of hydroxylated flavonoid production. We determined the optimal gene copy number of CHS and CPR to be 5 and 2, respectively. We further removed precursor pathway limitations by expressing genes associated with chorismate and malonyl-CoA supply. With pH and carbon-nitrogen ratio (C/N) optimization, our engineered strain produced 252.4 mg/L naringenin, 134.2 mg/L eriodictyol, and 110.5 mg/L taxifolin from glucose in shake flasks. Flavonoid and its hydroxylated derivatives are most prominently known as antioxidant and antiaging agents. These findings demonstrate our ability to harness the oleaginous yeast as the microbial workhorse to expand nature's biosynthetic potential, enabling us to bridge the gap between drug discovery and natural product manufacturing.
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Affiliation(s)
- Yongkun Lv
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Monireh Marsafari
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
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68
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Bae S, Park BG, Kim B, Hahn J. Multiplex Gene Disruption by Targeted Base Editing ofYarrowia lipolyticaGenome Using Cytidine Deaminase Combined with the CRISPR/Cas9 System. Biotechnol J 2019; 15:e1900238. [DOI: 10.1002/biot.201900238] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/18/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Sang‐Jeong Bae
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| | - Beom Gi Park
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| | - Byung‐Gee Kim
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| | - Ji‐Sook Hahn
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
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69
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Zhang W, Yang Q, Wu M, Liu H, Zhou J, Dong W, Ma J, Jiang M, Xin F. Metabolic Regulation of Organic Acid Biosynthesis in Actinobacillus succinogenes. Front Bioeng Biotechnol 2019; 7:216. [PMID: 31620431 PMCID: PMC6759810 DOI: 10.3389/fbioe.2019.00216] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/27/2019] [Indexed: 11/13/2022] Open
Abstract
Actinobacillus succinogenes is one of the most promising strains for succinic acid production; however, the lack of efficient genetic tools for strain modification development hinders its further application. In this study, a markerless knockout method for A. succinogenes using in-frame deletion was first developed. The resulting ΔpflA (encode pyruvate formate lyase 1-activating protein) strain displayed distinctive organic acid synthesis capacity under different cultivation modes. Additional acetate accumulation was observed in the ΔpflA strain relative to that of the wild type under aerobic conditions, indicating that acetate biosynthetic pathway was activated. Importantly, pyruvate was completely converted to lactate under anaerobic fermentation. The transcription analysis and enzyme assay revealed that the expression level and specific activity of lactate dehydrogenase (LDH) were significantly increased. In addition, the mRNA expression level of ldh was nearly increased 85-fold compared to that of the wild-type strain during aerobic-anaerobic dual-phase fermentation, resulting in 43.05 g/L lactate. These results demonstrate that pflA plays an important role in the regulation of C3 flux distribution. The deletion of pflA leads to the improvement of acetic acid production under aerobic conditions and activates lactic acid biosynthesis under anaerobic conditions. This study will help elaborate the mechanism governing organic acid biosynthesis in A. succinogenes.
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Affiliation(s)
- Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, China
| | - Qiao Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Min Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Haojie Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, China
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Li X, Zhang M, Luo J, Zhang S, Yang X, Igalavithana AD, Ok YS, Tsang DC, Lin CSK. Efficient succinic acid production using a biochar-treated textile waste hydrolysate in an in situ fibrous bed bioreactor. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107249] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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71
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Wang J, Liu F, Su T, Chang Y, Guo Q, Wang Q, Liang Q, Qi Q. The phage T4 DNA ligase in vivo improves the survival-coupled bacterial mutagenesis. Microb Cell Fact 2019; 18:107. [PMID: 31196093 PMCID: PMC6567493 DOI: 10.1186/s12934-019-1160-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/09/2019] [Indexed: 01/09/2023] Open
Abstract
Background Microbial mutagenesis is an important avenue to acquire microbial strains with desirable traits for industry application. However, mutagens either chemical or physical used often leads narrow library pool due to high lethal rate. The T4 DNA ligase is one of the most widely utilized enzymes in modern molecular biology. Its contribution to repair chromosomal DNA damages, therefore cell survival during mutagenesis will be discussed. Results Expression of T4 DNA ligase in vivo could substantially increase cell survival to ionizing radiation in multiple species. A T4 mediated survival-coupled mutagenesis approach was proposed. When polyhydroxybutyrate (PHB)-producing E. coli with T4 DNA ligase expressed in vivo was subjected to ionizing radiation, mutants with improved PHB production were acquired quickly owing to a large viable mutant library generated. Draft genome sequence analysis showed that the mutants obtained possess not only single nucleotide variation (SNV) but also DNA fragment deletion, indicating that T4 DNA ligase in vivo may contribute to the repair of DNA double strand breaks. Conclusions Expression of T4 DNA ligase in vivo could notably enhance microbial survival to excess chromosomal damages caused by various mutagens. Potential application of T4 DNA ligase in microbial mutagenesis was explored by mutating and screening PHB producing E. coli XLPHB strain. When applied to atmospheric and room temperature plasma (ARTP) microbial mutagenesis, large survival pool was obtained. Mutants available for subsequent screening for desirable features. The use of T4 DNA ligase we were able to quickly improve the PHB production by generating a larger viable mutants pool. This method is a universal strategy can be employed in wide range of bacteria. It indicated that traditional random mutagenesis became more powerful in combine with modern genetic molecular biology and has exciting prospect. Electronic supplementary material The online version of this article (10.1186/s12934-019-1160-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junshu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Fapeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Yizhao Chang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Qi Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.,National Glycoengineering Center, Shandong University, Qingdao, 266237, China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China. .,CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 2566101, China.
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72
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Recent advancements in fungal-derived fuel and chemical production and commercialization. Curr Opin Biotechnol 2019; 57:1-9. [DOI: 10.1016/j.copbio.2018.08.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/15/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
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73
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Ding Y, Wang KF, Wang WJ, Ma YR, Shi TQ, Huang H, Ji XJ. Increasing the homologous recombination efficiency of eukaryotic microorganisms for enhanced genome engineering. Appl Microbiol Biotechnol 2019; 103:4313-4324. [DOI: 10.1007/s00253-019-09802-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/28/2022]
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74
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Chromosome engineering of the TCA cycle in Halomonas bluephagenesis for production of copolymers of 3-hydroxybutyrate and 3-hydroxyvalerate (PHBV). Metab Eng 2019; 54:69-82. [PMID: 30914380 DOI: 10.1016/j.ymben.2019.03.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/12/2019] [Accepted: 03/16/2019] [Indexed: 01/08/2023]
Abstract
Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is a promising biopolyester with good mechanical properties and biodegradability. Large-scale production of PHBV is still hindered by the high production cost. CRISPR/Cas9 method was used to engineer the TCA cycle in Halomonas bluephagenesis on its chromosome for production of PHBV from glucose as a sole carbon source. Two TCA cycle related genes sdhE and icl encoding succinate dehydrogenase assembly factor 2 and isocitrate lysase were deleted, respectively, in H. bluephagenesis TD08AB containing PHBV synthesis genes on the chromosome, to channel more flux to increase the 3-hydroxyvalerate (3HV) ratio of PHBV. Due to a poor growth behavior of the mutant strains, H. bluephagenesis TY194 equipped with a medium strength Pporin-194 promoter was selected for further studies. The sdhE and/or icl mutant strains of H. bluephagenesis TY194 were constructed to show enhanced cell growth, PHBV synthesis and 3HV molar ratio. Gluconate was used to activate ED pathway and thus TCA cycle to increase 3HV content. H. bluephagenesis TY194 (ΔsdhEΔicl) was found to synthesize 17mol% 3HV in PHBV. Supported by the synergetic function of phosphoenolpyruvate carboxylase and Vitreoscilla hemoglobin encoded by genes ppc and vgb inserted into the chromosome of H. bluephagenesis TY194 (ΔsdhE) serving to enhance TCA cycle activity, a series of strains were generated that could produce PHBV containing 3-18mol% 3HV using glucose as a sole carbon source. Shake flask studies showed that H. bluephagenesis TY194 (ΔsdhE, G7::Pporin-ppc) produced 6.3 g/L cell dry weight (CDW), 65% PHBV in CDW and 25mol% 3HV in PHBV when grown in glucose and gluconate. 25mol% 3HV was the highest reported via chromosomal expression system. PHBV copolymers with different 3HV molar ratios were extracted and characterized. Next-generation industrial biotechnology (NGIB) based on recombinant H. bluephagenesis grown under unsterile and continuous conditions, allows production of P(3HB-0∼25mol% 3HV) in a convenient way with reduced production complexity and cost.
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75
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Rakicka M, Wolniak J, Lazar Z, Rymowicz W. Production of high titer of citric acid from inulin. BMC Biotechnol 2019; 19:11. [PMID: 30744615 PMCID: PMC6371587 DOI: 10.1186/s12896-019-0503-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/31/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Citric acid is considered as the most economically feasible product of microbiological production, therefore studies on cheap and renewable raw materials for its production are highly desirable. In this study citric acid was synthesized by genetically engineered strains of Yarrowia lipolytica from widely available, renewable polysaccharide - inulin. Hydrolysis of inulin by the Y. lipolytica strains was established by expressing the inulinase gene (INU1 gene; GenBank: X57202.1) with its native secretion signal sequence was amplified from genomic DNA from Kluyveromyces marxianus CBS6432. To ensure the maximum citric acid titer, the optimal cultivation strategy-repeated-batch culture was applied. RESULTS The strain Y. lipolytica AWG7 INU 8 secreted more than 200 g dm- 3 of citric acid during repeated-batch culture on inulin, with a productivity of 0.51 g dm- 3 h- 1 and a yield of 0.85 g g- 1. CONCLUSIONS The citric acid titer obtained in the proposed process is the highest value reported in the literature for Yarrowia yeast. The obtained results suggest that citric acid production from inulin by engineered Y. lipolytica may be a very promising technology for industrial citric acid production.
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Affiliation(s)
- Magdalena Rakicka
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, 37 Chełmońskiego St, 51-630 Wroclaw, Poland
| | - Jakub Wolniak
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, 37 Chełmońskiego St, 51-630 Wroclaw, Poland
| | - Zbigniew Lazar
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, 37 Chełmońskiego St, 51-630 Wroclaw, Poland
| | - Waldemar Rymowicz
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, 37 Chełmońskiego St, 51-630 Wroclaw, Poland
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Zhao C, Cui Z, Zhao X, Zhang J, Zhang L, Tian Y, Qi Q, Liu J. Enhanced itaconic acid production in Yarrowia lipolytica via heterologous expression of a mitochondrial transporter MTT. Appl Microbiol Biotechnol 2019; 103:2181-2192. [DOI: 10.1007/s00253-019-09627-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/14/2018] [Accepted: 12/23/2018] [Indexed: 12/25/2022]
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77
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Wong L, Holdridge B, Engel J, Xu P. Genetic Tools for Streamlined and Accelerated Pathway Engineering in Yarrowia lipolytica. Methods Mol Biol 2019; 1927:155-177. [PMID: 30788791 DOI: 10.1007/978-1-4939-9142-6_11] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Yarrowia lipolytica is an industrial oleaginous yeast that has many attractive physiological and metabolic characteristics for various biotechnological applications. Although it has a long history of industrial applications, the number of genetic tools available to effectively and efficiently engineer Y. lipolytica still falls behind the vast number of tools available for common organisms such as Escherichia coli and Saccharomyces cerevisiae. In this protocol, we have developed a complete and versatile genetic toolkit tailored for facile genetic manipulation in Y. lipolytica. We created a versatile DNA assembly platform YaliBrick, which can streamline the cloning of large multigene pathways with reused genetic parts. We established a sensitive luciferase reporter assay to characterize a set of 12 native promoters. In addition, we used YaliBrick to generate different gene configurations in multigene constructs. The five-gene biosynthetic pathway of the anticancer, antimicrobial pigment violacein was rapidly assembled in 1 week to demonstrate the simplicity and effectiveness of integrating pathway-balancing strategies with our YaliBrick vectors. In the end, we incorporated CRISPR-Cas9 into our YaliBrick vectors and achieved indel mutation and frameshift gene deletion at the CAN1 (arginine permease) genomic loci of Yarrowia lipolytica. The reported protocol provides a standard procedure to streamline and accelerate metabolic pathway engineering in Yarrowia lipolytica.
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Affiliation(s)
- Lynn Wong
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Benjamin Holdridge
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Jake Engel
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA.
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Cui Z, Jiang X, Zheng H, Qi Q, Hou J. Homology‐independent genome integration enables rapid library construction for enzyme expression and pathway optimization inYarrowia lipolytica. Biotechnol Bioeng 2018; 116:354-363. [DOI: 10.1002/bit.26863] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong UniversityQingdao China
| | - Xin Jiang
- State Key Laboratory of Microbial Technology, Shandong UniversityQingdao China
| | - Huihui Zheng
- State Key Laboratory of Microbial Technology, Shandong UniversityQingdao China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong UniversityQingdao China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong UniversityQingdao China
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Liebal UW, Blank LM, Ebert BE. CO 2 to succinic acid - Estimating the potential of biocatalytic routes. Metab Eng Commun 2018; 7:e00075. [PMID: 30197864 PMCID: PMC6127376 DOI: 10.1016/j.mec.2018.e00075] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/07/2018] [Accepted: 06/25/2018] [Indexed: 11/26/2022] Open
Abstract
Microbial carbon dioxide assimilation and conversion to chemical platform molecules has the potential to be developed as economic, sustainable processes. The carbon dioxide assimilation can proceed by a variety of natural pathways and recently even synthetic CO2 fixation routes have been designed. Early assessment of the performance of the different carbon fixation alternatives within biotechnological processes is desirable to evaluate their potential. Here we applied stoichiometric metabolic modeling based on physiological and process data to evaluate different process variants for the conversion of C1 carbon compounds to the industrial relevant platform chemical succinic acid. We computationally analyzed the performance of cyanobacteria, acetogens, methylotrophs, and synthetic CO2 fixation pathways in Saccharomyces cerevisiae in terms of production rates, product yields, and the optimization potential. This analysis provided insight into the economic feasibility and allowed to estimate the future industrial applicability by estimating overall production costs. With reported, or estimated data of engineered or wild type strains, none of the simulated microbial succinate production processes showed a performance allowing competitive production. The main limiting factors were identified as gas and photon transfer and metabolic activities whereas metabolic network structure was not restricting. In simulations with optimized parameters most process alternatives reached economically interesting values, hence, represent promising alternatives to sugar-based fermentations.
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Affiliation(s)
| | - Lars M. Blank
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
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Yu Q, Cui Z, Zheng Y, Huo H, Meng L, Xu J, Gao C. Exploring succinic acid production by engineered Yarrowia lipolytica strains using glucose at low pH. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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81
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Zhang W, Song M, Yang Q, Dai Z, Zhang S, Xin F, Dong W, Ma J, Jiang M. Current advance in bioconversion of methanol to chemicals. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:260. [PMID: 30258494 PMCID: PMC6151904 DOI: 10.1186/s13068-018-1265-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/19/2018] [Indexed: 05/25/2023]
Abstract
Methanol has become an attractive substrate for biotechnological applications due to its abundance and low-price. Chemicals production from methanol could alleviate the environmental concerns, costs, and foreign dependency associated with the use of petroleum feedstock. Recently, a growing fraction of research has focused on metabolites production using methanol as sole carbon and energy source or as co-substrate with carbohydrates by native or synthetic methylotrophs. In this review, we summarized the recent significant progress in native and synthetic methylotrophs and their application for methanol bioconversion into various products. Moreover, strategies for improvement of methanol metabolism and new perspectives on the generation of desired products from methanol were also discussed, which will benefit for the development of a methanol-based economy.
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Affiliation(s)
- Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Pukou District Nanjing, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Meng Song
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Pukou District Nanjing, Nanjing, 211816 People’s Republic of China
| | - Qiao Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Pukou District Nanjing, Nanjing, 211816 People’s Republic of China
| | - Zhongxue Dai
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Pukou District Nanjing, Nanjing, 211816 People’s Republic of China
| | - Shangjie Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Pukou District Nanjing, Nanjing, 211816 People’s Republic of China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Pukou District Nanjing, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Pukou District Nanjing, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Pukou District Nanjing, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Pukou District Nanjing, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
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Succinic acid production using a glycerol-based medium by an engineered strain of Yarrowia lipolytica: Statistical optimization and preliminary economic feasibility study. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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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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85
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Markham KA, Alper HS. Synthetic Biology Expands the Industrial Potential of Yarrowia lipolytica. Trends Biotechnol 2018; 36:1085-1095. [PMID: 29880228 DOI: 10.1016/j.tibtech.2018.05.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 10/14/2022]
Abstract
The oleaginous yeast Yarrowia lipolytica is quickly emerging as the most popular non-conventional (i.e., non-model organism) yeast in the bioproduction field. With a high propensity for flux through tricarboxylic acid (TCA) cycle intermediates and biological precursors such as acetyl-CoA and malonyl-CoA, this host is especially well suited to meet our industrial chemical production needs. Recent progress in synthetic biology tool development has greatly enhanced our ability to rewire this organism, with advances in genetic component design, CRISPR technologies, and modular cloning strategies. In this review we investigate recent developments in metabolic engineering and describe how the new tools being developed help to realize the full industrial potential of this host. Finally, we conclude with our vision of the developments that will be necessary to enhance future engineering efforts.
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Affiliation(s)
- Kelly A Markham
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Austin, TX 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA.
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86
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Yun EJ, Lee J, Kim DH, Kim J, Kim S, Jin YS, Kim KH. Metabolomic elucidation of the effects of media and carbon sources on fatty acid production by Yarrowia lipolytica. J Biotechnol 2018; 272-273:7-13. [PMID: 29499237 DOI: 10.1016/j.jbiotec.2018.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/16/2018] [Accepted: 02/27/2018] [Indexed: 12/17/2022]
Abstract
Lipid production by oleaginous Yarrowia lipolytica depends highly on culture environments, such as carbon sources, carbon/nitrogen (C/N) ratios, types of media, and cellular growth phases. In this study, the effects of media and carbon sources on lipid and metabolite production were investigated by profiling fatty acids and intracellular metabolites of Y. lipolytica grown in various media. The highest total fatty acid yield 114.04 ± 6.23 mg/g dry cell weight was achieved by Y. lipolytica grown in minimal medium with glycerol (SCG) in the exponential phase. The high lipid production by Y. lipolytica in SCG was presumed to be due to the higher C/N ratio in SCG than in the complex media. Moreover, glycerol promoted lipid production better than glucose in both complex and minimal media because glycerol can easily incorporate into the core of triglycerides. Metabolite profiling revealed that levels of long-chain fatty acids, such as stearic acid, palmitic acid, and arachidic acid, increased in SCG medium. Meanwhile, in complex media supplemented with either glucose or glycerol, levels of amino acids, such as cysteine, methionine, and glycine, highly increased. This metabolomic approach could be applied to modulate the global metabolic network of Y. lipolytica for producing lipids and other valuable products.
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Affiliation(s)
- Eun Ju Yun
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - James Lee
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Do Hyoung Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Sooah Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, South Korea.
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87
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Li C, Gao S, Li X, Yang X, Lin CSK. Efficient metabolic evolution of engineered Yarrowia lipolytica for succinic acid production using a glucose-based medium in an in situ fibrous bioreactor under low-pH condition. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:236. [PMID: 30181775 PMCID: PMC6116362 DOI: 10.1186/s13068-018-1233-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/22/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Alkali used for pH control during fermentation and acidification for downstream recovery of succinic acid (SA) are the two largest cost contributors for bio-based SA production. To promote the commercialization process of fermentative SA, the development of industrially important microorganisms that can tolerate low pH has emerged as a crucial issue. RESULTS In this study, an in situ fibrous bed bioreactor (isFBB) was employed for the metabolic evolution for selection of Y. lipolytica strain that can produce SA at low pH using glucose-based medium. An evolved strain named Y. lipolytica PSA3.0 that could produce SA with a titer of 19.3 g/L, productivity of 0.52 g/L/h, and yield of 0.29 g/g at pH 3.0 from YPD was achieved. The enzyme activity analysis demonstrated that the pathway from pyruvate to acetate was partially blocked in Y. lipolytica PSA3.0 after the evolution, which is beneficial to cell growth and SA production at low pH. When free-cell batch fermentations were performed using the parent and evolved strains separately, the evolved strain PSA3.0 produced 18.4 g/L SA with a yield of 0.23 g/g at pH 3.0. Although these values were lower than that obtained by the parent strain PSA02004 at its optimal pH 6.0, which were 25.2 g/L and 0.31 g/g, respectively, they were 4.8 and 4.6 times higher than that achieved by PSA02004 at pH 3.0. By fed-batch fermentation, the resultant SA titer of 76.8 g/L was obtained, which is the highest value that ever achieved from glucose-based medium at low pH, to date. When using mixed food waste (MFW) hydrolysate as substrate, 18.9 g/L SA was produced with an SA yield of 0.38 g/g, which demonstrates the feasibility of using low-cost glucose-based hydrolysate for SA production by Y. lipolytica in a low-pH environment. CONCLUSIONS This study presents an effective and efficient strategy for the evolution of Y. lipolytica for SA production under low-pH condition for the first time. The isFBB was demonstrated to improve the metabolic evolution efficiency of Y. lipolytica to the acidic condition. Moreover, the acetate accumulation was found to be the major reason for the inhibition of SA production at low pH by Y. lipolytica, which suggested the direction for further metabolic modification of the strain for improved SA production. Furthermore, the evolved strain Y. lipolytica PSA3.0 was demonstrated to utilize glucose-rich hydrolysate from MFW for fermentative SA production at low pH. Similarly, Y. lipolytica PSA3.0 is expected to utilize the glucose-rich hydrolysate generated from other carbohydrate-rich waste streams for SA production. This study paves the way for the commercialization of bio-based SA and contributes to the sustainable development of a green economy.
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Affiliation(s)
- Chong Li
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
- Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 Guangdong People’s Republic of China
| | - Shi Gao
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Xiaotong Li
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 People’s Republic of China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
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88
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Bae JH, Kim HJ, Kim MJ, Sung BH, Jeon JH, Kim HS, Jin YS, Kweon DH, Sohn JH. Direct fermentation of Jerusalem artichoke tuber powder for production of l -lactic acid and d -lactic acid by metabolically engineered Kluyveromyces marxianus. J Biotechnol 2018; 266:27-33. [DOI: 10.1016/j.jbiotec.2017.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 09/22/2017] [Accepted: 12/01/2017] [Indexed: 10/18/2022]
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Wong L, Engel J, Jin E, Holdridge B, Xu P. YaliBricks, a versatile genetic toolkit for streamlined and rapid pathway engineering in Yarrowia lipolytica. Metab Eng Commun 2017; 5:68-77. [PMID: 29188186 PMCID: PMC5699529 DOI: 10.1016/j.meteno.2017.09.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 11/16/2022] Open
Abstract
Effective metabolic engineering of microorganisms relies on balanced expression of both heterologous and endogenous genes to channel metabolic flux towards products of interest while achieving reasonable biomass buildup. To facilitate combinatorial pathway engineering and facile genetic operation, we engineered a set of modular cloning vectors compatible with BioBrick standards, called YaliBricks, to allow for rapid assembly of multigene pathways with customized genetic control elements (promoters, intronic sequences and terminators) in the oleaginous yeast Yarrowia lipolytica. We established a sensitive luciferase reporter and characterized a set of 12 native promoters to expand the oleaginous yeast genetic toolbox for transcriptional fine-tuning. We harnessed the intron alternative splicing mechanism and explored three unique gene configurations that allow us to encode genetic structural variations into metabolic function. We elucidated the role of how these genetic structural variations affect gene expression. To demonstrate the simplicity and effectiveness of streamlined genetic operations, we assembled the 12 kb five-gene violacein biosynthetic pathway in one week. We also expanded this set of vectors to accommodate self-cleavage ribozymes and efficiently deliver guide RNA (gRNA) for targeted genome-editing with a codon-optimized CRISPR-Cas9 nuclease. Taken together, the tools built in this study provide a standard procedure to streamline and accelerate metabolic pathway engineering and genetic circuits construction in Yarrowia lipolytica.
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Affiliation(s)
- Lynn Wong
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Jake Engel
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Erqing Jin
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
- Department of Food Science and Engineering, Jinan University, 601 West Huangpu Road, Guangzhou 510632, China
| | - Benjamin Holdridge
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
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90
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Shi S, Zhao H. Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals. Front Microbiol 2017; 8:2185. [PMID: 29167664 PMCID: PMC5682390 DOI: 10.3389/fmicb.2017.02185] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 10/25/2017] [Indexed: 01/23/2023] Open
Abstract
Oleaginous yeasts have been increasingly explored for production of chemicals and fuels via metabolic engineering. Particularly, there is a growing interest in using oleaginous yeasts for the synthesis of lipid-related products due to their high lipogenesis capability, robustness, and ability to utilize a variety of substrates. Most of the metabolic engineering studies in oleaginous yeasts focused on Yarrowia that already has plenty of genetic engineering tools. However, recent advances in systems biology and synthetic biology have provided new strategies and tools to engineer those oleaginous yeasts that have naturally high lipid accumulation but lack genetic tools, such as Rhodosporidium, Trichosporon, and Lipomyces. This review highlights recent accomplishments in metabolic engineering of oleaginous yeasts and recent advances in the development of genetic engineering tools in oleaginous yeasts within the last 3 years.
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Affiliation(s)
- Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore, Singapore
| | - Huimin Zhao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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