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Yarrowia lipolytica: A Beneficial Yeast as a Biofactory for Biotechnological...
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Yarrowia lipolytica: A Beneficial Yeast as a Biofactory for Biotechnological Applications: 2nd Edition

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 12805

Special Issue Editor

Dr. Bartłomiej Zieniuk

E-Mail Website
Guest Editor
Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, Warsaw, Poland
Interests: lipase-catalyzed ester synthesis; lipophilization; enzymatic (trans)esterification; whole-cell modification of phenolic compounds; microbiology; yarrowia lipolytica; lipases biosynthesis; antimicrobial and antioxidant activities of phenolic compounds; microbial enzymes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Yeasts were used for fermentation processes long before their various properties were discovered and described. Among at least 1500 recognized yeast species, in addition to the most well-known baker’s yeasts, e.g., Saccharomyces cerevisiae, other yeasts also stand out, often characterized by their unique features and capabilities.

Yarrowia lipolytica is one of the most studied “non-conventional” yeast species. The high secretory capacity and the capability of biosynthesis of many important secondary metabolites affect the growing scientific interest and biotechnological importance of this yeast. Y. lipolytica is considered to be non-pathogenic, and additionally, some commercial-scale processes with its participation have been granted GRAS (generally recognized as safe) status by the US Food and Drug Administration (FDA). The major advantages of using Y. lipolytica are its ability to grow and consume of a wide range of substrates, such as alkanes, fatty acids, fats, and oils, as well as some waste substrates, namely, crude glycerol, waste cooking oils, sewage sludge, or olive mill wastewater, with simultaneous biosynthesis of varied metabolites.

This Special Issue will compile the current state-of-the-art research on Y. lipolytica and shed light on the current research directions with the use of this yeast. Potential topics include but are not limited to the following:

- Metabolic engineering of Y. lipolytica;
- The biosynthesis of secondary metabolites, namely enzymes, e.g., lipases or proteases, as well as organic acids, sugar alcohols, flavors, and aromas;
- Whole-cell catalysis;
- Lipid biosynthesis and accumulation;
- Utilization of agri-food waste.

Dr. Bartłomiej Zieniuk
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Fermentation is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • yarrowia lipolytica
  • secondary metabolites
  • single-cell oils (SCO)
  • lipid accumulation
  • single-cell proteins (SCP)
  • enzymes biosynthesis
  • lipases production
  • metabolic engineering
  • organic acids synthesis
  • agri-food waste upgradation
  • whole-cell catalysis
  • biosynthesis of metal nanoparticles
  • bioreactor processes

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Related Special Issues

Published Papers (6 papers)

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Research

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26 pages, 3714 KiB  
Article
Evaluating the Performance of Yarrowia lipolytica 2.2ab in Solid-State Fermentation under Bench-Scale Conditions in a Packed-Tray Bioreactor
by Alejandro Barrios-Nolasco, Carlos Omar Castillo-Araiza, Sergio Huerta-Ochoa, María Isabel Reyes-Arreozola, José Juan Buenrostro-Figueroa and Lilia Arely Prado-Barragán
Fermentation 2024, 10(7), 344; https://doi.org/10.3390/fermentation10070344 - 29 Jun 2024
Cited by 3 | Viewed by 1041
Abstract
Solid-State Fermentation (SSF) offers a valuable process for converting agri-food by-products (AFBP) into high-value metabolites, with Yarrowia lipolytica 2.2ab (Yl2.2ab) showing significant potential under laboratory-scale controlled conditions; however, its assessment in larger-scale bioreactor scenarios is needed. This work evaluates Yl2.2ab’s [...] Read more.
Solid-State Fermentation (SSF) offers a valuable process for converting agri-food by-products (AFBP) into high-value metabolites, with Yarrowia lipolytica 2.2ab (Yl2.2ab) showing significant potential under laboratory-scale controlled conditions; however, its assessment in larger-scale bioreactor scenarios is needed. This work evaluates Yl2.2ab’s performance in a bench-scale custom-designed packed-tray bioreactor. Key features of this bioreactor design include a short packing length, a wall-cooling system, and forced aeration, enhancing hydrodynamics and heat and mass transfer within the tray. Preliminary studies under both abiotic and biotic conditions assessed Yl2.2ab’s adaptability to extreme temperature variations. The results indicated effective oxygen transport but poor heat transfer within the tray bed, with Yl2.2ab leading to a maximum growth rate of 28.15 mgx gssdb−1 h−1 and maximum production of proteases of 40.10 U gssdb−1 h−1, even when temperatures at the packed-tray outlet were around 49 °C. Hybrid-based modeling, incorporating Computational Fluid Dynamics (CFD) and Pseudo-Continuous Simulations (PCSs), elucidated that the forced-aeration system successfully maintained necessary oxygen levels in the bed. However, the low thermal conductivity of AFBP posed challenges for heat transfer. The bioreactor design presents promising avenues for scaling up SSF to valorize AFBP using Yl2.2ab’s extremophilic capabilities. Full article
(This article belongs to the Special Issue Yarrowia lipolytica: A Beneficial Yeast as a Biofactory for Biotechnological Applications: 2nd Edition)
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14 pages, 2857 KiB  
Article
Biodepolymerization of Polyamide Fibers Using Yarrowia lipolytica as Whole-Cell Biocatalyst
by Adriano Carniel, Nathália Ferreira dos Santos, Filipe Smith Buarque, Absai da Conceição Gomes, Luiz Silvino Chinelatto Junior, Luiz Alexandre Sacorague, Maria Alice Zarur Coelho and Aline M. Castro
Fermentation 2024, 10(5), 239; https://doi.org/10.3390/fermentation10050239 - 30 Apr 2024
Viewed by 1620
Abstract
Polyamide is a thermoplastic polymer widely used for several applications, including cables in offshore oil and gas operations. Due to its growing annual production worldwide, this poorly biodegradable material has been a source of pollution. Given this scenario, the need has arisen to [...] Read more.
Polyamide is a thermoplastic polymer widely used for several applications, including cables in offshore oil and gas operations. Due to its growing annual production worldwide, this poorly biodegradable material has been a source of pollution. Given this scenario, the need has arisen to develop environmentally friendly techniques to degrade this waste, and biotechnology has emerged as a possible solution to mitigate this problem. This study aimed to investigate the potential of Yarrowia lipolytica to biodepolymerize polyamide fibers (PAF). Microbial cultures were grown in shaken flasks containing different concentrations of PAF (0.5 and 2 g·L−1) and in a bioreactor with and without pH adjustment. PAF mass loss was up to 16.8%, achieved after 96 h of cultivation in a bioreactor without pH adjustment. Additionally, NMR analyses revealed that the amorphous regions of PAF, which are more susceptible to depolymerization, were reduced by 6% during cultivation. These preliminary results indicate the biotechnological potential of Y. lipolytica to depolymerize PAF. Full article
(This article belongs to the Special Issue Yarrowia lipolytica: A Beneficial Yeast as a Biofactory for Biotechnological Applications: 2nd Edition)
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16 pages, 2577 KiB  
Article
Polyhydroxybutyrate (PHB) Biosynthesis by an Engineered Yarrowia lipolytica Strain Using Co-Substrate Strategy
by Masoud Tourang, Xiaochao Xiong, Sara Sarkhosh and Shulin Chen
Fermentation 2023, 9(12), 1003; https://doi.org/10.3390/fermentation9121003 - 29 Nov 2023
Cited by 2 | Viewed by 2581
Abstract
High production cost is one of the major factors that limit the market growth of polyhydroxyalkanoates (PHAs) as a biopolymer. Improving PHA synthesis performance and utilizing low-grade feedstocks are two logical strategies for reducing costs. As an oleaginous yeast, Y. lipolytica has a [...] Read more.
High production cost is one of the major factors that limit the market growth of polyhydroxyalkanoates (PHAs) as a biopolymer. Improving PHA synthesis performance and utilizing low-grade feedstocks are two logical strategies for reducing costs. As an oleaginous yeast, Y. lipolytica has a high carbon flux through acetyl-CoA (the main PHB precursor), which makes it a desired cell factory for PHB biosynthesis. In the current study, two different metabolic pathways (NBC and ABC) were introduced into Y. lipolytica PO1f for synthesizing PHB. Compared to the ABC pathway, the NBC pathway, which includes NphT7 to redirect the lipogenesis pathway and catalyze acetoacetyl-CoA synthesis in a more energy-favored reaction, led to PHB accumulation of up to 11% of cell dry weight (CDW), whereas the ABC pathway resulted in non-detectable accumulations of PHB. Further modifications of the strain with the NBC pathway through peroxisomal compartmentalization and gene dose overexpression reached 41% PHB of CDW and a growth rate of 0.227 h−1. A low growth rate was observed with acetate as the sole source of carbon and energy or glucose as the sole substrate at high concentrations. Using a co-substrate strategy helped overcoming the inhibitory and toxic effects of both substrates. Cultivating the engineered strain in the optimal co-substrate condition predicted by response surface methodology (RSM) led to 83.4 g/L of biomass concentration and 31.7 g/L of PHB. These results offer insight into a more cost-effective production of PHB with engineered Y. lipolytica. Full article
(This article belongs to the Special Issue Yarrowia lipolytica: A Beneficial Yeast as a Biofactory for Biotechnological Applications: 2nd Edition)
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14 pages, 1818 KiB  
Article
Valorization of Macauba (Acromia aculeata) for Integrated Production of Lipase by Yarrowia lipolytica and Biodiesel Esters
by Filipe Smith Buarque, Marcelle A. Farias, Júlio Cesar Soares Sales, Adriano Carniel, Bernardo Dias Ribeiro, Verônica Regina de Oliveira Lopes, Aline Machado Castro and Maria Alice Zarur Coelho
Fermentation 2023, 9(12), 992; https://doi.org/10.3390/fermentation9120992 - 21 Nov 2023
Cited by 4 | Viewed by 1479
Abstract
Enzymatic biodiesel production is a potential eco-friendly alternative to the conventional chemical route which requires extensive study to reduce the costs associated with the application of commercial enzymes. Thus, this study aimed to develop a bioprocess using residues from macauba (Acrocomia aculeata [...] Read more.
Enzymatic biodiesel production is a potential eco-friendly alternative to the conventional chemical route which requires extensive study to reduce the costs associated with the application of commercial enzymes. Thus, this study aimed to develop a bioprocess using residues from macauba (Acrocomia aculeata) as raw material for lipase production in solid-state fermentation (SSF) by Yarrowia lipolytica. Then, the product obtained was used as a biocatalyst for the conversion (hydrolysis/esterification) of macauba acidic oil to biodiesel esters. Firstly, different SSF parameters (inoculum concentration, initial moisture content, and carbon and nitrogen levels) were investigated in a factorial design approach, using the cake from macauba fruit. Afterwards, moisture and urea concentration were shown to be statistically significant variables for lipase production. Lipase productnivities were 12.6 ± 0.6 U g−1 h−1 (at 24 h) for macauba fruit cake and 11.6 ± 1 U g−1 h−1 (at 20 h) for macauba pulp and peel cake. The solid enzymatic preparation (biocatalyst) showed optimized values at pH 6–7 at 37 °C, remaining stable (>70% retention) for 90 days at room temperature. Finally, enzymatic hydrolysis of the acidic oil from macauba reached 96% conversion (72 h) to fatty acids, and esterification of fatty acids reached 72% (biodiesel yield of 67%). The bioprocess described is a promising alternative for an integral and self-sufficient valorization of the macauba products. Full article
(This article belongs to the Special Issue Yarrowia lipolytica: A Beneficial Yeast as a Biofactory for Biotechnological Applications: 2nd Edition)
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16 pages, 2119 KiB  
Article
Solid State and Semi-Solid Fermentations of Olive and Sunflower Cakes with Yarrowia lipolytica: Impact of Biological and Physical Pretreatments
by Ana Rita Costa, Helena Fernandes, José Manuel Salgado and Isabel Belo
Fermentation 2023, 9(8), 734; https://doi.org/10.3390/fermentation9080734 - 6 Aug 2023
Cited by 3 | Viewed by 2254
Abstract
Lignocellulosic biomass is a promising feedstock for added value compound production in biotechnological processes such as solid-state fermentation (SSF). Although these solid materials can be directly used as substrates in fermentations in a solid state, a pretreatment is often required, especially if the [...] Read more.
Lignocellulosic biomass is a promising feedstock for added value compound production in biotechnological processes such as solid-state fermentation (SSF). Although these solid materials can be directly used as substrates in fermentations in a solid state, a pretreatment is often required, especially if the microorganism selected is unable to produce lignocellulosic enzymes. In the present work, several pretreatment strategies were applied to a 50% (w/w) mixture of olive and sunflower cakes before SSF for lipase production by the oleaginous yeast Yarrowia lipolytica W29. Co-culture strategies with Y. lipolytica and Aspergillus niger did not improve lipase production by the oleaginous yeast. Biological pretreatment with a fungal enzymatic extract led to a significant increase in sugar availability in the substrate mixture after a short incubation period, improving yeast growth. Microwave and ultrasound were the physical pretreatments selected and microwave irradiation proved to be the best method, resulting in 44% and 17% increases in yeast growth and lipase production, respectively, compared to the untreated mixture. An improvement in lipase activity was also observed after ultrasonic treatment in semi-solid fermentations, leading to a 2-fold increase in this enzyme activity compared to the control. The utilization of pretreatments before SSF with Y. lipolytica can increase sugars availability and result in structural changes in the solid substrate, which can improve the bioprocesses’ productivity. Full article
(This article belongs to the Special Issue Yarrowia lipolytica: A Beneficial Yeast as a Biofactory for Biotechnological Applications: 2nd Edition)
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Review

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30 pages, 8540 KiB  
Review
Yarrowia lipolytica Yeast: A Treasure Trove of Enzymes for Biocatalytic Applications—A Review
by Bartłomiej Zieniuk, Karina Jasińska, Katarzyna Wierzchowska, Şuheda Uğur and Agata Fabiszewska
Fermentation 2024, 10(5), 263; https://doi.org/10.3390/fermentation10050263 - 18 May 2024
Cited by 1 | Viewed by 2985
Abstract
Yarrowia lipolytica is a robust yeast species that has gained significant attention as a biofactory for various biotechnological applications and undoubtedly can be referred to as a hidden treasure trove due to boasting a diverse array of enzymes with wide-ranging applications in multiple [...] Read more.
Yarrowia lipolytica is a robust yeast species that has gained significant attention as a biofactory for various biotechnological applications and undoubtedly can be referred to as a hidden treasure trove due to boasting a diverse array of enzymes with wide-ranging applications in multiple industries, including biofuel production, food processing, biotechnology, and pharmaceuticals. As the biotechnology field continues to expand, Y. lipolytica is poised to play a pivotal role in developing eco-friendly and economically viable bioprocesses. Its versatility and potential for large-scale production make it a promising candidate for sustainably addressing various societal and industrial needs. The current review article aimed to highlight the diverse enzymatic capabilities of Y. lipolytica and provide a detailed analysis of its relevance in biocatalysis, including the use of whole-cell catalysts and isolated enzymes. The review focused on wild-type yeast strains and their species-dependant properties and selected relevant examples of Y. lipolytica used as a host organism for overexpressing some enzymes. Furthermore, the application of Y. lipolytica’s potential in enantiomers resolution, lipids processing, and biodiesel synthesis, as well as the synthesis of polymers or esterification of different substrates for upgrading biologically active compounds, was discussed. Full article
(This article belongs to the Special Issue Yarrowia lipolytica: A Beneficial Yeast as a Biofactory for Biotechnological Applications: 2nd Edition)
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