Yeast Biotechnology 6.0

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

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 21586

Special Issue Editor


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Guest Editor
Structural Biology Brussels Lab, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
Interests: yeast biotechnology; cell immobilization; beer brewing biochemistry and fermentation; mini- and microbioreactors; Saccharomyces cerevisiae; Candida; yeast space biology (bioreactors for microgravity research); yeast adhesins; yeast systems biology; glycobiology; nanobiotechnology; atomic force microscopy; protein crystallization; yeast protein structural biology
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Special Issue Information

Dear Colleagues,

Yeasts are truly fascinating microorganisms. Due to their diverse and dynamic activities, they have been used to produce many interesting products, such as beer, wine, bread, biofuels and biopharmaceuticals. Saccharomyces cerevisiae (bakers’ yeast) is likely the most human-exploited yeast species. Saccharomyces is a popular choice for industrial applications, although its use in beer production dates back to at least the sixth millennium BC. Bakers’ yeast represents a cornerstone of modern biotechnology, enabling the development of efficient production processes for antibiotics, biopharmaceuticals, technical enzymes and ethanol and biofuels.

Today, diverse yeast species are explored for industrial applications, such as, e.g., the Saccharomyces species, Pichia pastoris and other Pichia species, Kluyveromyces marxianus, Hansenula polymorpha, Yarrowia lipolytica, Candida species, Phaffia rhodozyma, wild yeasts for beer brewing and winemaking and others with proven potential.

This Special Issue, “Yeast Biotechnology 6.0”, is a continuation of the “Yeast Biotechnology” series in Fermentation (published by MDPI). This instalment will compile the current state-of-the-art research and technology in the area of “yeast biotechnology” and highlight prominent current research directions for hot topics, such as recently developed techniques for characterizing yeast and their physiology (including omics and nanobiotechnology techniques), methods for adapting industrial strains (including metabolic, synthetic and evolutionary engineering) and the use of yeasts as microbial cell factories to produce biopharmaceuticals, enzymes, alcohols, organic acids, flavours and fine chemicals, as well as advances in yeast fermentation technology and industrial fermentation processes.

Topics of interest include, but are not limited to:

Yeast characterization and analysis
Brewing yeasts (including wild yeasts), wine yeasts and baker’s yeasts.
Evolution and variation in industrial yeast genomes.
Yeast systems biology: genomics, proteomics, fluxomics, metabolomics and omics integration.
Yeast nanobiotechnology (nano analysis techniques, construction of nanostructures, etc.).

Yeast strain engineering
Yeast metabolic engineering: production of biofuels, secondary metabolites, commodity chemicals, proteins, biopharmaceuticals and material precursors.
Yeast synthetic biology: yeasts as cell factories, tools for controlling enzyme expression levels, strategies for regulating spatial localization of enzymes in yeast, regulatory networks and biomolecular logic gates.
Strain improvement via evolutionary engineering.

Fermentation technology
Industrial bioreactors.
Mini- and microbioreactors: single-cell analysis, high-throughput screening and microfluidic bioreactors.
Process intensification: high-density fermentations, high-gravity fermentation.
Fermentative stress adaptation.

Industrial fermentation processes
Production of food (bread, etc.) and beverages (beer, wine, cider, etc.).
Production of baker’s yeast.
Production of biofuels (bioethanol, 1-butanol, biodiesel, jetfuels), commodity chemicals, pharmaceuticals, material precursors and secondary metabolites.

Prof. Dr. Ronnie Willaert
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 2600 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.

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Published Papers (11 papers)

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Editorial

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5 pages, 199 KiB  
Editorial
Yeast Biotechnology 6.0
by Ronnie G. Willaert
Fermentation 2024, 10(3), 172; https://doi.org/10.3390/fermentation10030172 - 19 Mar 2024
Viewed by 676
Abstract
This Special Issue continues the “Yeast Biotechnology” Special Issue series of the MDPI journal Fermentation [...] Full article
(This article belongs to the Special Issue Yeast Biotechnology 6.0)

Research

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11 pages, 3678 KiB  
Communication
Candida albicans Adhesion Measured by Optical Nanomotion Detection
by Maria I. Villalba, Salomé LeibundGut-Landmann, Marie-Elisabeth Bougnoux, Christophe d’Enfert, Ronnie G. Willaert and Sandor Kasas
Fermentation 2023, 9(11), 991; https://doi.org/10.3390/fermentation9110991 - 20 Nov 2023
Cited by 1 | Viewed by 1209
Abstract
Cellular adhesion plays an important role in numerous fundamental physiological and pathological processes. Its measurement is relatively complex, requires sophisticated equipment, and, in most cases, cannot be carried out without breaking the links between the studied cell and its target. In this contribution, [...] Read more.
Cellular adhesion plays an important role in numerous fundamental physiological and pathological processes. Its measurement is relatively complex, requires sophisticated equipment, and, in most cases, cannot be carried out without breaking the links between the studied cell and its target. In this contribution, we propose a novel, nanomotion-based, technique that overcomes these drawbacks. The applied force is generated by the studied cell itself (nanomotion), whereas cellular movements are detected by traditional optical microscopy and dedicated software. The measurement is non-destructive, single-cell sensitive, and permits following the evolution of the adhesion as a function of time. We applied the technique on different strains of the fungal pathogen Candida albicans on a fibronectin-coated surface. We demonstrated that this novel approach can significantly simplify, accelerate, and make more affordable living cells–substrate adhesion measurements. Full article
(This article belongs to the Special Issue Yeast Biotechnology 6.0)
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15 pages, 2147 KiB  
Article
Exploring the Potential of Non-Conventional Yeasts in Wine Fermentation with a Focus on Saccharomycopsis fermentans
by Madina Akan, Andreas Gudiksen, Yasemin Baran, Heike Semmler, Silvia Brezina, Stefanie Fritsch, Doris Rauhut and Jürgen Wendland
Fermentation 2023, 9(9), 786; https://doi.org/10.3390/fermentation9090786 - 25 Aug 2023
Cited by 1 | Viewed by 943
Abstract
Despite the increasing number of publications on non-conventional yeasts (NCYs), many areas in this field remain poorly understood, making the examination of these strains important for determining their potential in wine fermentations. The amino acid metabolic pathways involved, particularly the catabolic Ehrlich pathway [...] Read more.
Despite the increasing number of publications on non-conventional yeasts (NCYs), many areas in this field remain poorly understood, making the examination of these strains important for determining their potential in wine fermentations. The amino acid metabolic pathways involved, particularly the catabolic Ehrlich pathway but also anabolic pathways such as the leucine biosynthesis pathway, are crucial for producing high-value aroma compounds that contribute to the final flavour of wine. We examined the potential use of Saccharomycopsis fermentans in wine fermentations. We selected mutant strains resistant to the toxic compound trifluoro-leucine (TFL), verified mutations in the SfLEU4 gene, and characterized the ability of the resulting strains to contribute to fermentation bouquets. Resistance to TFL relieves feedback inhibition in the leucine biosynthesis pathway and resulted in increased leucine biosynthesis. Concomitantly, the S. fermentans TFL-resistant mutants generated increased amounts of isoamyl alcohol and isovalerate during wine fermentation. Selection of TFL-resistant strains thus provides a generally applicable strategy for the improvement in NCYs and their utilization in co-fermentation processes for different grape must varieties. Full article
(This article belongs to the Special Issue Yeast Biotechnology 6.0)
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20 pages, 2521 KiB  
Article
Development of a Cost-Effective Process for the Heterologous Production of SARS-CoV-2 Spike Receptor Binding Domain Using Pichia pastoris in Stirred-Tank Bioreactor
by Diego G. Noseda, Cecilia D’Alessio, Javier Santos, Tommy Idrovo-Hidalgo, Florencia Pignataro, Diana E. Wetzler, Hernán Gentili, Alejandro D. Nadra, Ernesto Roman, Carlos Paván and Lucas A. M. Ruberto
Fermentation 2023, 9(6), 497; https://doi.org/10.3390/fermentation9060497 - 23 May 2023
Cited by 3 | Viewed by 1645
Abstract
SARS-CoV-2 was identified as the pathogenic agent causing the COVID-19 pandemic. Among the proteins codified by this virus, the Spike protein is one of the most-external and -exposed. A fragment of the Spike protein, named the receptor binding domain (RBD), interacts with the [...] Read more.
SARS-CoV-2 was identified as the pathogenic agent causing the COVID-19 pandemic. Among the proteins codified by this virus, the Spike protein is one of the most-external and -exposed. A fragment of the Spike protein, named the receptor binding domain (RBD), interacts with the ACE2 receptors of human cells, allowing the entrance of the viruses. RBD has been proposed as an interesting protein for the development of diagnosis tools, treatment, and prevention of the disease. In this work, a method for recombinant RBD production using Pichia pastoris as a cell factory in a stirred-tank bioreactor (SRTB) up to 7 L was developed. Using a basal saline medium with glycerol, methanol, and compressed air in a four-stage procedure, around 500 mg/L of the raw RBD produced by yeasts (yRBD) and 206 mg/L of purified (>95%) RBD were obtained. Thereby, the proposed method represents a feasible, simple, scalable, and inexpensive procedure for the obtention of RBD for diagnosis kits and vaccines’ formulation. Full article
(This article belongs to the Special Issue Yeast Biotechnology 6.0)
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27 pages, 12405 KiB  
Article
Single-Cell Optical Nanomotion of Candida albicans in Microwells for Rapid Antifungal Susceptibility Testing
by Vjera Radonicic, Charlotte Yvanoff, Maria Ines Villalba, Bart Devreese, Sandor Kasas and Ronnie G. Willaert
Fermentation 2023, 9(4), 365; https://doi.org/10.3390/fermentation9040365 - 07 Apr 2023
Cited by 4 | Viewed by 1899
Abstract
Candida albicans is an emerging multidrug-resistant opportunistic pathogen representing an important source of invasive disease in humans and generating high healthcare costs worldwide. The development of a rapid and simple antifungal susceptibility test (AFST) could limit the spread of this disease, increase the [...] Read more.
Candida albicans is an emerging multidrug-resistant opportunistic pathogen representing an important source of invasive disease in humans and generating high healthcare costs worldwide. The development of a rapid and simple antifungal susceptibility test (AFST) could limit the spread of this disease, increase the efficiency of treatment, and lower the risk of developing resistant strains. We developed a microfluidic chip containing an array of microwells that were designed to trap the cells and perform rapid antifungal susceptibility tests using optical nanomotion detection (ONMD). Yeast cell entrapment in a microwell allows for a very rapid exchange of growth medium with the antifungal, which enables performing single-cell ONMD measurements on the same cell before and after antifungal treatment. The exposure to a low concentration of the antifungal caspofungin or flucanozole induced a significant decrease in the nanomotion signal, demonstrating the high sensitivity of this technique. We used this chip to quantify the real-time response of individual C. albicans cells to the antifungal treatment in as fast as 10 min. This simple and label-free technique could be further developed into a simple-to-use device that allows the performance of fast AFST as part of a routine hospital procedure in developed and also eventually developing world countries. Full article
(This article belongs to the Special Issue Yeast Biotechnology 6.0)
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22 pages, 2230 KiB  
Article
Assessment of Starters of Lactic Acid Bacteria and Killer Yeasts: Selected Strains in Lab-Scale Fermentations of Table Olives (Olea europaea L.) cv. Leccino
by Grazia Federica Bencresciuto, Claudio Mandalà, Carmela Anna Migliori, Giovanna Cortellino, Maristella Vanoli and Laura Bardi
Fermentation 2023, 9(2), 182; https://doi.org/10.3390/fermentation9020182 - 17 Feb 2023
Cited by 6 | Viewed by 1896
Abstract
Olives debittering, organoleptic quality and safety can be improved with yeasts and lactic acid bacteria (LABs) selected strain starters, that allow for better fermentation control with respect to natural fermentation. Two selected killer yeasts (Wickerhamomyces anomalus and Saccharomyces cerevisiae) and Lactobacillus [...] Read more.
Olives debittering, organoleptic quality and safety can be improved with yeasts and lactic acid bacteria (LABs) selected strain starters, that allow for better fermentation control with respect to natural fermentation. Two selected killer yeasts (Wickerhamomyces anomalus and Saccharomyces cerevisiae) and Lactobacillus plantarum strains were tested for olive (cv. Leccino) fermentation to compare different starter combinations and strategies; the aim was to assess their potential in avoiding pretreatments and the use of excessive salt in the brines and preservatives. Lactobacilli, yeasts, molds, Enterobacteriaceae and total aerobic bacteria were detected, as well as pH, soluble sugars, alcohols, organic acids, phenolic compounds, and rheological properties of olives. Sugars were rapidly consumed in the brines and olives; the pH dropped quickly, then rose until neutrality after six months. The oleuropein final levels in olives were unaffected by the treatments. The use of starters did not improve the LABs’ growth nor prevent the growth of Enterobacteriaceae and molds. The growth of undesirable microorganisms could have been induced by the availability of selective carbon source such as mannitol, whose concentration in olive trees rise under drought stress. The possible role of climate change on the quality and safety of fermented foods should be furtherly investigated. The improvement of olives’ nutraceutical value can be induced by yeasts and LABs starters due to the higher production of hydroxytyrosol. Full article
(This article belongs to the Special Issue Yeast Biotechnology 6.0)
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13 pages, 3636 KiB  
Article
Effects of Diamond Nanoparticles Immobilisation on the Surface of Yeast Cells: A Phenomenological Study
by Yuri Dekhtyar, Dagnis Abols, Liga Avotina, Anita Stoppel, Sascha Balakin, Galina Khroustalyova, Joerg Opitz, Hermanis Sorokins, Natalia Beshchasna, Patricija Tamane and Alexander Rapoport
Fermentation 2023, 9(2), 162; https://doi.org/10.3390/fermentation9020162 - 10 Feb 2023
Cited by 1 | Viewed by 1557
Abstract
An interesting development of biotechnology has linked microbial cell immobilisation with nanoparticles. The main task of our research was to reveal the possible influences of differently electrically charged diamond nanoparticles upon physiological characteristics of the yeast Saccharomyces cerevisiae. It was revealed that [...] Read more.
An interesting development of biotechnology has linked microbial cell immobilisation with nanoparticles. The main task of our research was to reveal the possible influences of differently electrically charged diamond nanoparticles upon physiological characteristics of the yeast Saccharomyces cerevisiae. It was revealed that the adverse impact of these nanoparticles can manifest not only against prokaryotes, but also against eukaryotic yeast cells. However, the obtained results also indicate that it is possible to reduce and, most likely, completely eliminate the dangerous effects of nanoparticles to cells by using special physical approaches. Comparison of non-arylated and arylated nanoparticles showed that in terms of changes in the physiological activity of cells, which are important to biotechnology and biomedicine, the selection of certain nanoparticles (non-arylated or arylated) may be necessary in each specific case, depending on the purpose of their use. Full article
(This article belongs to the Special Issue Yeast Biotechnology 6.0)
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14 pages, 1235 KiB  
Article
Application of Immobilized Yeasts for Improved Production of Sparkling Wines
by Encarnación Fernández-Fernández, José Manuel Rodríguez-Nogales, Josefina Vila-Crespo and Elena Falqué-López
Fermentation 2022, 8(10), 559; https://doi.org/10.3390/fermentation8100559 - 20 Oct 2022
Cited by 2 | Viewed by 2000
Abstract
Verdejo sparkling wines from two consecutive vintages were elaborated following the “champenoise” method. The second fermentation was developed with the same free or immobilized Saccharomyces cerevisiae bayanus yeast strain, carrying out four batch replicates each year. The sparkling wines were analyzed after 9 [...] Read more.
Verdejo sparkling wines from two consecutive vintages were elaborated following the “champenoise” method. The second fermentation was developed with the same free or immobilized Saccharomyces cerevisiae bayanus yeast strain, carrying out four batch replicates each year. The sparkling wines were analyzed after 9 months of aging, showing no significant differences among the two typologies in the enological parameters (pH, total acidity, volatile acidity, reducing sugars, and alcoholic strength), the effervescence, or the spectrophotometric measurements. The free amino nitrogen content was significantly higher in the sparkling wines obtained from immobilized yeasts, nevertheless, the levels of neutral polysaccharides and total proteins were lower. No significant differences in the volatile composition were found, except for only two volatile compounds (isobutyric acid and benzyl alcohol); however, these two substances were present at levels below their respective olfactory thresholds. The sensory analysis by consumers showed identical preferences for both types of sparkling wines, except for the color acceptability. The descriptive analysis by a tasting panel revealed that sensorial differences between both sparkling wines were only found for the smell of dough. Therefore, the use of immobilized yeasts for the second fermentation of sparkling wines can reduce and simplify some enological practices such as the procedure of riddling and disgorging, with no impact on the so-mentioned quality parameters. Full article
(This article belongs to the Special Issue Yeast Biotechnology 6.0)
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Review

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16 pages, 750 KiB  
Review
Biocontainment Techniques and Applications for Yeast Biotechnology
by Guilherme Pavão, Isabela Sfalcin and Diego Bonatto
Fermentation 2023, 9(4), 341; https://doi.org/10.3390/fermentation9040341 - 29 Mar 2023
Cited by 2 | Viewed by 2291
Abstract
Biocontainment techniques for genetically modified yeasts (GMYs) are pivotal due to the importance of these organisms for biotechnological processes and also due to the design of new yeast strains by using synthetic biology tools and technologies. Due to the large genetic modifications that [...] Read more.
Biocontainment techniques for genetically modified yeasts (GMYs) are pivotal due to the importance of these organisms for biotechnological processes and also due to the design of new yeast strains by using synthetic biology tools and technologies. Due to the large genetic modifications that many yeast strains display, it is highly desirable to avoid the leakage of GMY cells into natural environments and, consequently, the spread of synthetic genes and circuits by horizontal or vertical gene transfer mechanisms within the microorganisms. Moreover, it is also desirable to avoid patented yeast gene technologies spreading outside the production facility. In this review, the different biocontainment technologies currently available for GMYs were evaluated. Interestingly, uniplex-type biocontainment approaches (UTBAs), which rely on nutrient auxotrophies induced by gene mutation or deletion or the expression of the simple kill switches apparatus, are still the major biocontainment approaches in use with GMY. While bacteria such as Escherichia coli account for advanced biocontainment technologies based on synthetic biology and multiplex-type biocontainment approaches (MTBAs), GMYs are distant from this scenario due to many reasons. Thus, a comparison of different UTBAs and MTBAs applied for GMY and genetically engineered microorganisms (GEMs) was made, indicating the major advances of biocontainment techniques for GMYs. Full article
(This article belongs to the Special Issue Yeast Biotechnology 6.0)
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16 pages, 1684 KiB  
Review
Nonconventional Yeasts Engineered Using the CRISPR-Cas System as Emerging Microbial Cell Factories
by Jongbeom Park, In Jung Kim and Soo Rin Kim
Fermentation 2022, 8(11), 656; https://doi.org/10.3390/fermentation8110656 - 19 Nov 2022
Cited by 5 | Viewed by 2420
Abstract
Because the petroleum-based chemical synthesis of industrial products causes serious environmental and societal issues, biotechnological production using microorganisms is an alternative approach to achieve a more sustainable economy. In particular, the yeast Saccharomyces cerevisiae is widely used as a microbial cell factory to [...] Read more.
Because the petroleum-based chemical synthesis of industrial products causes serious environmental and societal issues, biotechnological production using microorganisms is an alternative approach to achieve a more sustainable economy. In particular, the yeast Saccharomyces cerevisiae is widely used as a microbial cell factory to produce biofuels and valuable biomaterials. However, product profiles are often restricted due to the Crabtree-positive nature of S. cerevisiae, and ethanol production from lignocellulose is possibly enhanced by developing alternative stress-resistant microbial platforms. With desirable metabolic pathways and regulation in addition to strong resistance to diverse stress factors, nonconventional yeasts (NCY) may be considered an alternative microbial platform for industrial uses. Irrespective of their high industrial value, the lack of genetic information and useful gene editing tools makes it challenging to develop metabolic engineering-guided scaled-up applications using yeasts. The recently developed clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system is a powerful gene editing tool for NCYs. This review describes the current status of and recent advances in promising NCYs in terms of industrial and biotechnological applications, highlighting CRISPR-Cas9 system-based metabolic engineering strategies. This will serve as a basis for the development of novel yeast applications. Full article
(This article belongs to the Special Issue Yeast Biotechnology 6.0)
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37 pages, 2430 KiB  
Review
Advances in Komagataella phaffii Engineering for the Production of Renewable Chemicals and Proteins
by Clara Vida Galrão Corrêa Carneiro, Luana Assis Serra, Thályta Fraga Pacheco, Letícia Maria Mallmann Ferreira, Lívia Teixeira Duarte Brandão, Mariana Nogueira de Moura Freitas, Débora Trichez and João Ricardo Moreira de Almeida
Fermentation 2022, 8(11), 575; https://doi.org/10.3390/fermentation8110575 - 24 Oct 2022
Cited by 11 | Viewed by 3420
Abstract
The need for a more sustainable society has prompted the development of bio-based processes to produce fuels, chemicals, and materials in substitution for fossil-based ones. In this context, microorganisms have been employed to convert renewable carbon sources into various products. The methylotrophic yeast [...] Read more.
The need for a more sustainable society has prompted the development of bio-based processes to produce fuels, chemicals, and materials in substitution for fossil-based ones. In this context, microorganisms have been employed to convert renewable carbon sources into various products. The methylotrophic yeast Komagataella phaffii has been extensively used in the production of heterologous proteins. More recently, it has been explored as a host organism to produce various chemicals through new metabolic engineering and synthetic biology tools. This review first summarizes Komagataella taxonomy and diversity and then highlights the recent approaches in cell engineering to produce renewable chemicals and proteins. Finally, strategies to optimize and develop new fermentative processes using K. phaffii as a cell factory are presented and discussed. The yeast K. phaffii shows an outstanding performance for renewable chemicals and protein production due to its ability to metabolize different carbon sources and the availability of engineering tools. Indeed, it has been employed in producing alcohols, carboxylic acids, proteins, and other compounds using different carbon sources, including glycerol, glucose, xylose, methanol, and even CO2. Full article
(This article belongs to the Special Issue Yeast Biotechnology 6.0)
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