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Zhu Y, Liu J, Sun L, Liu M, Qi Q, Hou J. Development of genetic markers in Yarrowia lipolytica. Appl Microbiol Biotechnol 2024; 108:14. [PMID: 38170308 DOI: 10.1007/s00253-023-12835-3] [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: 04/04/2023] [Revised: 10/28/2023] [Accepted: 11/04/2023] [Indexed: 01/05/2024]
Abstract
The oleaginous yeast Yarrowia lipolytica represents a potential microbial cell factory for the recombinant production of various valuable products. Currently, the commonly used selection markers for transformation in Y. lipolytica are limited, and successive genetic manipulations are often restricted by the number of available selection markers. In our study, we developed a dominant marker, dsdA, which encodes a D-serine deaminase for genetic manipulation in Y. lipolytica. In Y. lipolytica, this marker confers the ability to use D-serine as a nitrogen source. In addition, the selection conditions of several infrequently used dominant markers including bleoR (zeocin resistance), kanMX (G418 resistance), and guaB (mycophenolic acid resistance) were also analyzed. Our results demonstrated that these selection markers can be used for the genetic manipulation of Y. lipolytica and their selection conditions were different for various strains. Ultimately, the selection markers tested here will be useful to expand the genetic toolbox of Y. lipolytica. KEY POINTS: • The dsdA from Escherichia coli was developed as a dominant marker. • The applicability of several resistance markers in Y. lipolytica was determined. • We introduced the Cre/mutant lox system for marker recycling.
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Affiliation(s)
- Yamin Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, People's Republic of China
| | - Jianhui Liu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, People's Republic of China
| | - Lingxuan Sun
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, People's Republic of China
| | - Mengmeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, People's Republic of China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, People's Republic of China.
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Hu M, Ge J, Jiang Y, Sun X, Guo D, Gu Y. Advances and perspectives in genetic expression and operation for the oleaginous yeast Yarrowia lipolytica. Synth Syst Biotechnol 2024; 9:618-626. [PMID: 38784195 PMCID: PMC11109602 DOI: 10.1016/j.synbio.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
The utilization of industrial biomanufacturing has emerged as a viable and sustainable alternative to fossil-based resources for producing functional chemicals. Moreover, advancements in synthetic biology have created new opportunities for the development of innovative cell factories. Notably, Yarrowia lipolytica, an oleaginous yeast that is generally regarded as safe, possesses several advantageous characteristics, including the ability to utilize inexpensive renewable carbon sources, well-established genetic backgrounds, and mature genetic manipulation methods. Consequently, there is increasing interest in manipulating the metabolism of this yeast to enhance its potential as a biomanufacturing platform. Here, we reviewed the latest developments in genetic expression strategies and manipulation tools related to Y. lipolytica, particularly focusing on gene expression, chromosomal operation, CRISPR-based tool, and dynamic biosensors. The purpose of this review is to serve as a valuable reference for those interested in the development of a Y. lipolytica microbial factory.
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Affiliation(s)
- Mengchen Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jianyue Ge
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yaru Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Dongshen Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
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3
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Gorczyca M, Korpys-Woźniak P, Celińska E. An Interplay between Transcription Factors and Recombinant Protein Synthesis in Yarrowia lipolytica at Transcriptional and Functional Levels-The Global View. Int J Mol Sci 2024; 25:9450. [PMID: 39273402 PMCID: PMC11395014 DOI: 10.3390/ijms25179450] [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: 07/31/2024] [Revised: 08/26/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024] Open
Abstract
Transcriptional regulatory networks (TRNs) associated with recombinant protein (rProt) synthesis in Yarrowia lipolytica are still under-described. Yet, it is foreseen that skillful manipulation with TRNs would enable global fine-tuning of the host strain's metabolism towards a high-level-producing phenotype. Our previous studies investigated the transcriptomes of Y. lipolytica strains overproducing biochemically different rProts and the functional impact of transcription factors (TFs) overexpression (OE) on rProt synthesis capacity in this species. Hence, much knowledge has been accumulated and deposited in public repositories. In this study, we combined both biological datasets and enriched them with further experimental data to investigate an interplay between TFs and rProts synthesis in Y. lipolytica at transcriptional and functional levels. Technically, the RNAseq datasets were extracted and re-analyzed for the TFs' expression profiles. Of the 140 TFs in Y. lipolytica, 87 TF-encoding genes were significantly deregulated in at least one of the strains. The expression profiles were juxtaposed against the rProt amounts from 125 strains co-overexpressing TF and rProt. In addition, several strains bearing knock-outs (KOs) in the TF loci were analyzed to get more insight into their actual involvement in rProt synthesis. Different profiles of the TFs' transcriptional deregulation and the impact of their OE or KO on rProts synthesis were observed, and new engineering targets were pointed.
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Affiliation(s)
- Maria Gorczyca
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-637 Poznan, Poland
| | - Paulina Korpys-Woźniak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-637 Poznan, Poland
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-637 Poznan, Poland
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Yuzbashev TV, Yuzbasheva EY, Melkina OE, Patel D, Bubnov D, Dietz H, Ledesma-Amaro R. A DNA assembly toolkit to unlock the CRISPR/Cas9 potential for metabolic engineering. Commun Biol 2023; 6:858. [PMID: 37596335 PMCID: PMC10439232 DOI: 10.1038/s42003-023-05202-5] [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: 03/26/2023] [Accepted: 08/01/2023] [Indexed: 08/20/2023] Open
Abstract
CRISPR/Cas9-based technologies are revolutionising the way we engineer microbial cells. One of the key advantages of CRISPR in strain design is that it enables chromosomal integration of marker-free DNA, eliminating laborious and often inefficient marker recovery procedures. Despite the benefits, assembling CRISPR/Cas9 editing systems is still not a straightforward process, which may prevent its use and applications. In this work, we have identified some of the main limitations of current Cas9 toolkits and designed improvements with the goal of making CRISPR technologies easier to access and implement. These include 1) A system to quickly switch between marker-free and marker-based integration constructs using both a Cre-expressing and standard Escherichia coli strains, 2) the ability to redirect multigene integration cassettes into alternative genomic loci via Golden Gate-based exchange of homology arms, 3) a rapid, simple in-vivo method to assembly guide RNA sequences via recombineering between Cas9-helper plasmids and single oligonucleotides. We combine these methodologies with well-established technologies into a comprehensive toolkit for efficient metabolic engineering using CRISPR/Cas9. As a proof of concept, we developed the YaliCraft toolkit for Yarrowia lipolytica, which is composed of a basic set of 147 plasmids and 7 modules with different purposes. We used the toolkit to generate and characterize a library of 137 promoters and to build a de novo strain synthetizing 373.8 mg/L homogentisic acid.
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Affiliation(s)
- Tigran V Yuzbashev
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
- Plant Sciences and the Bioeconomy, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK.
| | | | - Olga E Melkina
- NRC 'Kurchatov Institute'-GosNIIgenetika, Kurchatov Genomic Centre, 1-st Dorozhny Pr., 1, Moscow, 117545, Russia
| | - Davina Patel
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Dmitrii Bubnov
- NRC 'Kurchatov Institute'-GosNIIgenetika, Kurchatov Genomic Centre, 1-st Dorozhny Pr., 1, Moscow, 117545, Russia
| | - Heiko Dietz
- Kaesler Research Institute, Kaesler Nutrition GmbH, Fischkai 1, 27572, Bremerhaven, Germany
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Messina E, de Souza CP, Cappella C, Barile SN, Scarcia P, Pisano I, Palmieri L, Nicaud JM, Agrimi G. Genetic inactivation of the Carnitine/Acetyl-Carnitine mitochondrial carrier of Yarrowia lipolytica leads to enhanced odd-chain fatty acid production. Microb Cell Fact 2023; 22:128. [PMID: 37443049 DOI: 10.1186/s12934-023-02137-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Mitochondrial carriers (MCs) can deeply affect the intracellular flux distribution of metabolic pathways. The manipulation of their expression level, to redirect the flux toward the production of a molecule of interest, is an attractive target for the metabolic engineering of eukaryotic microorganisms. The non-conventional yeast Yarrowia lipolytica is able to use a wide range of substrates. As oleaginous yeast, it directs most of the acetyl-CoA therefrom generated towards the synthesis of lipids, which occurs in the cytoplasm. Among them, the odd-chain fatty acids (OCFAs) are promising microbial-based compounds with several applications in the medical, cosmetic, chemical and agricultural industries. RESULTS In this study, we have identified the MC involved in the Carnitine/Acetyl-Carnitine shuttle in Y. lipolytica, YlCrc1. The Y. lipolytica Ylcrc1 knock-out strain failed to grow on ethanol, acetate and oleic acid, demonstrating the fundamental role of this MC in the transport of acetyl-CoA from peroxisomes and cytoplasm into mitochondria. A metabolic engineering strategy involving the deletion of YlCRC1, and the recombinant expression of propionyl-CoA transferase from Ralstonia eutropha (RePCT), improved propionate utilization and its conversion into OCFAs. These genetic modifications and a lipogenic medium supplemented with glucose and propionate as the sole carbon sources, led to enhanced accumulation of OCFAs in Y. lipolytica. CONCLUSIONS The Carnitine/Acetyl-Carnitine shuttle of Y. lipolytica involving YlCrc1, is the sole pathway for transporting peroxisomal or cytosolic acetyl-CoA to mitochondria. Manipulation of this carrier can be a promising target for metabolic engineering approaches involving cytosolic acetyl-CoA, as demonstrated by the effect of YlCRC1 deletion on OCFAs synthesis.
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Affiliation(s)
- Eugenia Messina
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy
- Université Paris-Saclay, INRAE, Micalis Institute, Jouy-en-Josas, 78350, AgroParisTech, France
| | - Camilla Pires de Souza
- Université Paris-Saclay, INRAE, Micalis Institute, Jouy-en-Josas, 78350, AgroParisTech, France
| | - Claudia Cappella
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy
| | - Simona Nicole Barile
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy
| | - Pasquale Scarcia
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy
| | - Isabella Pisano
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy
| | - Luigi Palmieri
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy
- Bioenergetics and Molecular Biotechnologies (IBIOM), CNR Institute of Biomembranes, Campus Universitario, via Orabona 4, Bari, 70125, Italy
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, Micalis Institute, Jouy-en-Josas, 78350, AgroParisTech, France.
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Campus Universitario, via Orabona 4, Bari, 70125, Italy.
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Gorczyca M, Nicaud JM, Celińska E. Transcription factors enhancing synthesis of recombinant proteins and resistance to stress in Yarrowia lipolytica. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12607-z. [PMID: 37318637 DOI: 10.1007/s00253-023-12607-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023]
Abstract
Resistance to environmental stress and synthesis of recombinant proteins (r-Prots) are both complex, strongly interconnected biological traits relying on orchestrated contribution of multiple genes. This, in turn, makes their engineering a challenging task. One of the possible strategies is to modify the operation of transcription factors (TFs) associated with these complex traits. The aim of this study was to examine the potential implications of selected five TFs (HSF1-YALI0E13948g, GZF1-YALI0D20482g, CRF1-YALI0B08206g, SKN7-YALI0D14520g, and YAP-like-YALI0D07744g) in stress resistance and/or r-Prot synthesis in Yarrowia lipolytica. The selected TFs were over-expressed or deleted (OE/KO) in a host strain synthesizing a reporter r-Prot. The strains were subjected to phenotype screening under different environmental conditions (pH, oxygen availability, temperature, and osmolality), and the obtained data processing was assisted by mathematical modeling. The results demonstrated that growth and the r-Prot yields under specific conditions can be significantly increased or decreased due to the TFs' engineering. Environmental factors "awakening" individual TFs were indicated, and their contribution was mathematically described. For example, OE of Yap-like TF was proven to alleviate growth retardation under high pH, while Gzf1 and Hsf1 were shown to serve as universal enhancers of r-Prot production in Y. lipolytica. On the other hand, KO of SKN7 and HSF1 disabled growth under hyperosmotic stress. This research demonstrates the usefulness of the TFs engineering approach in the manipulation of complex traits and evidences newly identified functions of the studied TFs. KEY POINTS: • Function and implication in complex traits of 5 TFs in Y. lipolytica were studied. • Gzf1 and Hsf1 are the universal r-Prots synthesis enhancers in Y. lipolytica. • Yap-like TF's activity is pH-dependent; Skn7 and Hsf1 act in osmostress response.
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Affiliation(s)
- Maria Gorczyca
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 60-637, Poznań, Poland
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 60-637, Poznań, Poland.
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Liu S, Sun Y, Wei T, Gong D, Wang Q, Zhan Z, Song J. Engineering 3-Hydroxypropionic Acid Production from Glucose in Yarrowia lipolytica through Malonyl-CoA Pathway. J Fungi (Basel) 2023; 9:jof9050573. [PMID: 37233284 DOI: 10.3390/jof9050573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
3-Hydroxypropionic acid (3-HP) is an important intermediate compound in the chemical industry. Green and environmentally friendly microbial synthesis methods are becoming increasingly popular in a range of industries. Compared to other chassis cells, Yarrowia lipolytica possesses advantages, such as high tolerance to organic acid and a sufficient precursor required to synthesize 3-HP. In this study, gene manipulations, including the overexpression of genes MCR-NCa, MCR-CCa, GAPNSm, ACC1 and ACSSeL641P and knocking out bypass genes MLS1 and CIT2, leading to the glyoxylate cycle, were performed to construct a recombinant strain. Based on this, the degradation pathway of 3-HP in Y. lipolytica was discovered, and relevant genes MMSDH and HPDH were knocked out. To our knowledge, this study is the first to produce 3-HP in Y. lipolytica. The yield of 3-HP in recombinant strain Po1f-NC-14 in shake flask fermentation reached 1.128 g·L-1, and the yield in fed-batch fermentation reached 16.23 g·L-1. These results are highly competitive compared to other yeast chassis cells. This study creates the foundation for the production of 3-HP in Y. lipolytica and also provides a reference for further research in the future.
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Affiliation(s)
- Shiyu Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
| | - Yao Sun
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
| | - Tianhui Wei
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
| | - Dianliang Gong
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
| | - Qi Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
| | - Zhe Zhan
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
| | - Jinzhu Song
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
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Liang P, Cao M, Li J, Wang Q, Dai Z. Expanding sugar alcohol industry: Microbial production of sugar alcohols and associated chemocatalytic derivatives. Biotechnol Adv 2023; 64:108105. [PMID: 36736865 DOI: 10.1016/j.biotechadv.2023.108105] [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: 08/27/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023]
Abstract
Sugar alcohols are polyols that are widely employed in the production of chemicals, pharmaceuticals, and food products. Chemical synthesis of polyols, however, is complex and necessitates the use of hazardous compounds. Therefore, the use of microbes to produce polyols has been proposed as an alternative to traditional synthesis strategies. Many biotechnological approaches have been described to enhancing sugar alcohols production and microbe-mediated sugar alcohol production has the potential to benefit from the availability of inexpensive substrate inputs. Among of them, microbe-mediated erythritol production has been implemented in an industrial scale, but microbial growth and substrate conversion rates are often limited by harsh environmental conditions. In this review, we focused on xylitol, mannitol, sorbitol, and erythritol, the four representative sugar alcohols. The main metabolic engineering strategies, such as regulation of key genes and cofactor balancing, for improving the production of these sugar alcohols were reviewed. The feasible strategies to enhance the stress tolerance of chassis cells, especially thermotolerance, were also summarized. Different low-cost substrates like glycerol, molasses, cellulose hydrolysate, and CO2 employed for producing these sugar alcohols were presented. Given the value of polyols as precursor platform chemicals that can be leveraged to produce a diverse array of chemical products, we not only discuss the challenges encountered in the above parts, but also envisioned the development of their derivatives for broadening the application of sugar alcohols.
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Affiliation(s)
- Peixin Liang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Mingfeng Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jing Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.
| | - Zongjie Dai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.
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Georgiadis I, Tsiligkaki C, Patavou V, Orfanidou M, Tsoureki A, Andreadelli A, Theodosiou E, Makris AM. Identification and Construction of Strong Promoters in Yarrowia lipolytica Suitable for Glycerol-Based Bioprocesses. Microorganisms 2023; 11:1152. [PMID: 37317126 DOI: 10.3390/microorganisms11051152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 06/16/2023] Open
Abstract
Yarrowia lipolytica is a non-pathogenic aerobic yeast with numerous industrial biotechnology applications. The organism grows in a wide variety of media, industrial byproducts, and wastes. A need exists for molecular tools to improve heterologous protein expression and pathway reconstitution. In an effort to identify strong native promoters in glycerol-based media, six highly expressed genes were mined from public data, analyzed, and validated. The promoters from the three most highly expressed (H3, ACBP, and TMAL) were cloned upstream of the reporter mCherry in episomal and integrative vectors. Fluorescence was quantified by flow cytometry and promoter strength was benchmarked with known strong promoters (pFBA1in, pEXP1, and pTEF1in) in cells growing in glucose, glycerol, and synthetic glycerol media. The results show that pH3 > pTMAL > pACBP are very strong promoters, with pH3 exceeding all other tested promoters. Hybrid promoters were also constructed, linking the Upstream Activating Sequence 1B (UAS1B8) with H3(260) or TMAL(250) minimal promoters, and compared to the UAS1B8-TEF1(136) promoter. The new hybrid promoters exhibited far superior strength. The novel promoters were utilized to overexpress the lipase LIP2, achieving very high secretion levels. In conclusion, our research identified and characterized several strong Y. lipolytica promoters that expand the capacity to engineer Yarrowia strains and valorize industrial byproducts.
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Affiliation(s)
- Ioannis Georgiadis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Christina Tsiligkaki
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Victoria Patavou
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Maria Orfanidou
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
- Department of Chemical Engineering, School of Engineering, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Antiopi Tsoureki
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
| | - Aggeliki Andreadelli
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
| | - Eleni Theodosiou
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
| | - Antonios M Makris
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
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10
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Yuzbashev T, Yuzbasheva E, Melkina O, Patel D, Bubnov D, Dietz H, Ledesma-Amaro R. A DNA assembly toolkit to unlock the CRISPR/Cas9 potential for metabolic engineering. RESEARCH SQUARE 2023:rs.3.rs-2738543. [PMID: 37066237 PMCID: PMC10104256 DOI: 10.21203/rs.3.rs-2738543/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
CRISPR/Cas9-based technologies are revolutionising the way we engineer microbial cells. One of the key advantages of CRISPR in strain design is that it enables chromosomal integration of marker-free DNA, eliminating laborious and often inefficient marker recovery procedures. Despite the benefits, assembling CRISPR/Cas9 editing systems is still not a straightforward process, which may prevent its use and applications. In this work, we have identified some of the main limitations of current Cas9 toolkits and designed improvements with the goal of making CRISPR technologies easier to access and implement. These include 1) A system to quickly switch between marker-free and marker-based integration constructs using both a Cre-expressing and standard Escherichia coli strains, 2) the ability to redirect multigene integration cassettes into alternative genomic loci via Golden Gate-based exchange of homology arms, 3) a rapid, simple in-vivo method to assembly guide RNA sequences via recombineering between Cas9-helper plasmids and single oligonucleotides. We combine these methodologies with well-established technologies into a comprehensive toolkit for efficient metabolic engineering using CRISPR/Cas9. As a proof of concept, we generated and characterized a library of 137 promoters and built a de novo Yarrowia lipolytica strain synthetizing 373.8 mg/L homogentisic acid.
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11
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Cao L, Li J, Yang Z, Hu X, Wang P. A review of synthetic biology tools in Yarrowia lipolytica. World J Microbiol Biotechnol 2023; 39:129. [PMID: 36944859 DOI: 10.1007/s11274-023-03557-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/24/2023] [Indexed: 03/23/2023]
Abstract
Yarrowia lipolytica is a non-conventional oleaginous yeast with great potential for industrial production. Y. lipolytica has a high propensity for flux through tricarboxylic acid cycle intermediates. Therefore, this host is currently being developed as a workhorse, and is rapidly emerging in biotechnology fields, especially for industrial chemical production, whole-cell bioconversion, and the treatment and recycling of industrial waste. In recent studies, Y. lipolytica has been rewritten and introduced with non-native metabolites of certain compounds of interest owing to the advancement in synthetic biology tools. In this review, we collate recent progress to present a detailed and insightful summary of the major developments in synthetic biology tools and techniques for Y. lipolytica, including promoters, terminators, selection markers, autonomously replicating sequences, DNA assembly techniques, genome editing techniques, and subcellular organelle engineering. This comprehensive overview would be a useful resource for future genetic engineering studies to improve the yield of desired metabolic products in Y. lipolytica.
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Affiliation(s)
- Linshan Cao
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Jiajie Li
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Zihan Yang
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Xiao Hu
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Pengchao Wang
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China.
- Northeast Forestry University, No. 26 Hexing Road, Harbin, 150000, People's Republic of China.
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12
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Watcharawipas A, Runguphan W. Red yeasts and their carotenogenic enzymes for microbial carotenoid production. FEMS Yeast Res 2023; 23:6895548. [PMID: 36513367 DOI: 10.1093/femsyr/foac063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Carotenoids are C40 isoprene-based compounds with significant commercial interests that harbor diverse bioactivities. Prominent examples of carotenoids are beta-carotene, a precursor to vitamin A essential for proper eye health, and lycopene and astaxanthin, powerful antioxidants implicated in preventing cancers and atherosclerosis. Due to their benefits to human health, the market value for carotenoids is rapidly increasing and is projected to reach USD 1.7 billion by 2025. However, their production now relies on chemical synthesis and extraction from plants that pose risks to food management and numerous biological safety issues. Thus, carotenoid production from microbes is considered a promising strategy for achieving a healthy society with more sustainability. Red yeast is a heterogeneous group of basidiomycetous fungi capable of producing carotenoids. It is a critical source of microbial carotenoids from low-cost substrates. Carotenogenic enzymes from red yeasts have also been highly efficient, invaluable biological resources for biotechnological applications. In this minireview, we focus on red yeast as a promising source for microbial carotenoids, strain engineering strategies for improving carotenoid production in red yeasts, and potential applications of carotenogenic enzymes from red yeasts in conventional and nonconventional yeasts.
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Affiliation(s)
- Akaraphol Watcharawipas
- Department of Microbiology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
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13
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Bird J, Marles-Wright J, Giachino A. A User's Guide to Golden Gate Cloning Methods and Standards. ACS Synth Biol 2022; 11:3551-3563. [PMID: 36322003 PMCID: PMC9680027 DOI: 10.1021/acssynbio.2c00355] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Indexed: 11/06/2022]
Abstract
The continual demand for specialized molecular cloning techniques that suit a broad range of applications has driven the development of many different cloning strategies. One method that has gained significant traction is Golden Gate assembly, which achieves hierarchical assembly of DNA parts by utilizing Type IIS restriction enzymes to produce user-specified sticky ends on cut DNA fragments. This technique has been modularized and standardized, and includes different subfamilies of methods, the most widely adopted of which are the MoClo and Golden Braid standards. Moreover, specialized toolboxes tailored to specific applications or organisms are also available. Still, the quantity and range of assembly methods can constitute a barrier to adoption for new users, and even experienced scientists might find it difficult to discern which tools are best suited toward their goals. In this review, we provide a beginner-friendly guide to Golden Gate assembly, compare the different available standards, and detail the specific features and quirks of commonly used toolboxes. We also provide an update on the state-of-the-art in Golden Gate technology, discussing recent advances and challenges to inform existing users and promote standard practices.
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Affiliation(s)
- Jasmine
E. Bird
- School
of Computing, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Jon Marles-Wright
- Biosciences
Institute, Faculty of Medical Sciences, Newcastle University, Newcastle
upon Tyne, NE2 4HH, United
Kingdom
| | - Andrea Giachino
- Biosciences
Institute, Faculty of Medical Sciences, Newcastle University, Newcastle
upon Tyne, NE2 4HH, United
Kingdom
- School
of Science, Engineering & Environment, University of Salford, Salford, M5 4NT, United Kingdom
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14
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Onésime D, Vidal L, Thomas S, Henry C, Martin V, André G, Kubiak P, Minard P, Celinska E, Nicaud JM. A unique, newly discovered four-member protein family involved in extracellular fatty acid binding in Yarrowia lipolytica. Microb Cell Fact 2022; 21:200. [PMID: 36182920 PMCID: PMC9526294 DOI: 10.1186/s12934-022-01925-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yarrowia lipolytica, a nonconventional oleaginous yeast species, has attracted attention due to its high lipid degradation and accumulation capacities. Y. lipolytica is used as a chassis for the production of usual and unusual lipids and lipid derivatives. While the genes involved in the intracellular transport and activation of fatty acids in different cellular compartments have been characterized, no genes involved in fatty acid transport from the extracellular medium into the cell have been identified thus far. In this study, we identified secreted proteins involved in extracellular fatty acid binding. RESULTS Recent analysis of the Y. lipolytica secretome led to the identification of a multigene family that encodes four secreted proteins, preliminarily named UP1 to UP4. These proteins were efficiently overexpressed individually in wild-type and multideletant strain (Q4: Δup1Δup2Δup3Δup4) backgrounds. Phenotypic analysis demonstrated the involvement of these proteins in the binding of extracellular fatty acids. Additionally, gene deletion and overexpression prevented and promoted sensitivity to octanoic acid (C8) toxicity, respectively. The results suggested binding is dependent on aliphatic chain length and fatty acid concentration. 3D structure modeling supports the proteins' role in fatty acid assimilation at the molecular level. CONCLUSIONS We discovered a family of extracellular-fatty-acid-binding proteins in Y. lipolytica and have proposed to name its members eFbp1 to eFbp4. The exact mode of eFbps action remains to be deciphered individually and synergistically; nevertheless, it is expected that the proteins will have applications in lipid biotechnology, such as improving fatty acid production and/or bioconversion.
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Affiliation(s)
- Djamila Onésime
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Léa Vidal
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Stéphane Thomas
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Céline Henry
- Plateforme d'Analyse Protéomique Paris Sud-Ouest (PAPPSO), INRAE, MICALIS Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Véronique Martin
- INRAE, MaIAGE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Gwenaëlle André
- INRAE, MaIAGE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Piotr Kubiak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Philippe Minard
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Ewelina Celinska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Jean-Marc Nicaud
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,INRAE-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Micalis Institute, Domaine de Vilvert, 78352, Jouy-en-Josas, France.
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15
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Jach ME, Malm A. Yarrowia lipolytica as an Alternative and Valuable Source of Nutritional and Bioactive Compounds for Humans. Molecules 2022; 27:2300. [PMID: 35408699 PMCID: PMC9000428 DOI: 10.3390/molecules27072300] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 12/04/2022] Open
Abstract
Yarrowia lipolytica, an oleagineous species of yeast, is a carrier of various important nutrients. The biomass of this yeast is an extensive source of protein, exogenous amino acids, bioavailable essenctial trace minerals, and lipid compounds as mainly unsaturated fatty acids. The biomass also contains B vitamins, including vitamin B12, and many other bioactive components. Therefore, Y. lipolytica biomass can be used in food supplements for humans as safe and nutritional additives for maintaining the homeostasis of the organism, including for vegans and vegetarians, athletes, people after recovery, and people at risk of B vitamin deficiencies.
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Affiliation(s)
- Monika Elżbieta Jach
- Department of Molecular Biology, The John Paul II Catholic University of Lublin, Konstantynów Street 1I, 20-708 Lublin, Poland
| | - Anna Malm
- Department of Pharmaceutical Microbiology, Medical University of Lublin, Chodźki Street 1, 20-093 Lublin, Poland;
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16
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Jagtap SS, Bedekar AA, Singh V, Jin YS, Rao CV. Metabolic engineering of the oleaginous yeast Yarrowia lipolytica PO1f for production of erythritol from glycerol. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:188. [PMID: 34563235 PMCID: PMC8466642 DOI: 10.1186/s13068-021-02039-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/11/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Sugar alcohols are widely used as low-calorie sweeteners in the food and pharmaceutical industries. They can also be transformed into platform chemicals. Yarrowia lipolytica, an oleaginous yeast, is a promising host for producing many sugar alcohols. In this work, we tested whether heterologous expression of a recently identified sugar alcohol phosphatase (PYP) from Saccharomyces cerevisiae would increase sugar alcohol production in Y. lipolytica. RESULTS Y. lipolytica was found natively to produce erythritol, mannitol, and arabitol during growth on glucose, fructose, mannose, and glycerol. Osmotic stress is known to increase sugar alcohol production, and was found to significantly increase erythritol production during growth on glycerol. To better understand erythritol production from glycerol, since it was the most promising sugar alcohol, we measured the expression of key genes and intracellular metabolites. Osmotic stress increased the expression of several key genes in the glycerol catabolic pathway and the pentose phosphate pathway. Analysis of intracellular metabolites revealed that amino acids, sugar alcohols, and polyamines are produced at higher levels in response to osmotic stress. Heterologous overexpression of the sugar alcohol phosphatase increased erythritol production and glycerol utilization in Y. lipolytica. We further increased erythritol production by increasing the expression of native glycerol kinase (GK), and transketolase (TKL). This strain was able to produce 27.5 ± 0.7 g/L erythritol from glycerol during batch growth and 58.8 ± 1.68 g/L erythritol during fed-batch growth in shake-flasks experiments. In addition, the glycerol utilization was increased by 2.5-fold. We were also able to demonstrate that this strain efficiently produces erythritol from crude glycerol, a major byproduct of the biodiesel production. CONCLUSIONS We demonstrated the application of a promising enzyme for increasing erythritol production in Y. lipolytica. We were further able to boost production by combining the expression of this enzyme with other approaches known to increase erythritol production in Y. lipolytica. This suggest that this new enzyme provides an orthogonal route for boosting production and can be stacked with existing designs known to increase sugar alcohol production in yeast such as Y. lipolytica. Collectively, this work establishes a new route for increasing sugar alcohol production and further develops Y. lipolytica as a promising host for erythritol production from cheap substrates such as glycerol.
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Affiliation(s)
- Sujit Sadashiv Jagtap
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ashwini Ashok Bedekar
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Vijay Singh
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yong-Su Jin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Food Science and Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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17
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Gottardi D, Siroli L, Vannini L, Patrignani F, Lanciotti R. Recovery and valorization of agri-food wastes and by-products using the non-conventional yeast Yarrowia lipolytica. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.06.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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18
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Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement. J Fungi (Basel) 2021; 7:jof7070548. [PMID: 34356927 PMCID: PMC8307478 DOI: 10.3390/jof7070548] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild-type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade.
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19
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Wang Y, Li Q, Tian P, Tan T. Charting the landscape of RNA polymerases to unleash their potential in strain improvement. Biotechnol Adv 2021; 54:107792. [PMID: 34216775 DOI: 10.1016/j.biotechadv.2021.107792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/28/2021] [Accepted: 06/26/2021] [Indexed: 11/19/2022]
Abstract
One major mission of microbial cell factory is overproduction of desired chemicals. To this end, it is necessary to orchestrate enzymes that affect metabolic fluxes. However, only modification of a small number of enzymes in most cases cannot maximize desired metabolites, and global regulation is required. Of myriad enzymes influencing global regulation, RNA polymerase (RNAP) may be the most versatile enzyme in biological realm because it not only serves as the workhorse of central dogma but also participates in a plethora of biochemical events. In fact, recent years have witnessed extensive exploitation of RNAPs for phenotypic engineering. While a few impressive reviews showcase the structures and functionalities of RNAPs, this review not only summarizes the state-of-the-art advance in the structures of RNAPs but also points out their enormous potentials in metabolic engineering and synthetic biology. This review aims to provide valuable insights for strain improvement.
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Affiliation(s)
- Ye Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Qingyang Li
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, PR China
| | - Pingfang Tian
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China.
| | - Tianwei Tan
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
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20
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A Yarrowia lipolytica Strain Engineered for Pyomelanin Production. Microorganisms 2021; 9:microorganisms9040838. [PMID: 33920006 PMCID: PMC8071058 DOI: 10.3390/microorganisms9040838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 11/20/2022] Open
Abstract
The yeast Yarrowia lipolytica naturally produces pyomelanin. This pigment accumulates in the extracellular environment following the autoxidation and polymerization of homogentisic acid, a metabolite derived from aromatic amino acids. In this study, we used a chassis strain optimized to produce aromatic amino acids for the de novo overproduction of pyomelanin. The gene 4HPPD, which encodes an enzyme involved in homogentisic acid synthesis (4-hydroxyphenylpyruvic acid dioxygenase), was characterized and overexpressed in the chassis strain with up to three copies, leading to pyomelanin yields of 4.5 g/L. Homogentisic acid is derived from tyrosine. When engineered strains were grown in a phenylalanine-supplemented medium, pyomelanin production increased, revealing that the yeast could convert phenylalanine to tyrosine, or that the homogentisic acid pathway is strongly induced by phenylalanine.
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21
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Liu H, Wang F, Deng L, Xu P. Genetic and bioprocess engineering to improve squalene production in Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2020; 317:123991. [PMID: 32805480 PMCID: PMC7561614 DOI: 10.1016/j.biortech.2020.123991] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 05/23/2023]
Abstract
Squalene is the precursor for triterpene-based natural products and steroids-based drugs. It has been widely used as pharmaceutical intermediates and personal care products. The aim of this work is to test the feasibility of engineering Yarrowia lipolytica as a potential host for squalene production. The bottleneck of the pathway was removed by overexpressing native HMG-CoA (3-hydroxy-3-methylglutaryl-CoA) reductase. With the recycling of NADPH from the mannitol cycle, the engineered strain produced about 180.3 mg/L and 188.2 mg/L squalene from glucose or acetate minimal media. By optimizing the C/N ratio, controlling the media pH and mitigating acetyl-CoA flux competition from lipogenesis, the engineered strain produced 502.7 mg/L squalene, a 28-fold increase over the parental strain (17.2 mg/L). This work may serve as a baseline to harness Y. lipolytica as an oleaginous cell factory for sustainable production of squalene or terpenoids-based chemicals and natural products.
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Affiliation(s)
- Huan Liu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD 21250, China; College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Fang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Li Deng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD 21250, China.
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