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Special Issue "Development and Utilization of Yeast Resources"

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A special issue of Journal of Fungi (ISSN 2309-608X).

Deadline for manuscript submissions: 30 June 2023 | Viewed by 4595

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Prof. Dr. Xin-Qing Zhao

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Guest Editor

School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
Interests: yeast; synthetic biology; metabolic engineering; biofuels; organic acids; genome mining
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Qi-Ming Wang

E-Mail Website
Guest Editor

School of Life Sciences, Hebei University, Baoding 071002, China
Interests: yeast systematics & phylogenomic; evolutionary & population genetics; systems & synthetic biology; fungal evolution

Special Issue Information

Dear Colleagues,

Yeasts are simple and single cellular fungi that are widely distributed and have been widely used in various traditional industries. Yeasts are also being investigated as microbial cell factories in novel applications in medicine, agriculture, and biorefinery of lignocellulosic biomass. Among various yeasts, budding yeast is efficient to ferment sugars into alcohol, and has been used in the production of wine, beer, beverage and biofuels. In recent years, non-conventional yeasts, such as Yarrowia lipolytica, Kluyveromyces marxianus, Komagataella phaffii (also known as Pichia pastoris) have emerged as attracting cell factories to produce organic acids, natural products from plants, vaccines and antibodies. The development of yeast strains benefits not only their applications but also the discovery of novel mechanisms that provide a basis for studying other more complicated eukaryotic systems, including human being. In the past few years, great progress has been made in the characterization of novel yeast species or strains, metabolic engineering and genome editing of yeasts, as well as exploration of both wild yeasts and engineered yeast strains in various applications. In this special issue, we would like to present valuable latest findings in the development and utilization of yeast resources. Both dedicated review and research articles are welcome for the special issue. We welcome articles related but not limited to the following contents:

Yeast diversity and its potential in industrial applications;
Advanced technologies for the development of yeast strains;
Metabolic engineering of yeast strains for bioproduction;
Synthetic biology and artificial intelligence of yeast host.

We wish that this special issue contributes to summarizing the latest progress in the related fields, which would promote the utilization of yeast resources for efficient biological manufacturing.

Prof. Dr. Xin-Qing Zhao
Prof. Dr. Qi-Ming Wang
Guest Editors

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. Journal of Fungi 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 2200 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

Yeast
diversity
metabolic engineering
gene editing
synthetic biology
cell factory
artificial intelligence
lignocellulosic biomass
biofuels
biorefinery

Published Papers (5 papers)

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Research

Open AccessArticle

Metabolic Engineering of Saccharomyces cerevisiae for Efficient Retinol Synthesis

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J. Fungi 2023, 9(5), 512; https://doi.org/10.3390/jof9050512 - 26 Apr 2023

Viewed by 660

Abstract

Retinol, the main active form of vitamin A, plays a role in maintaining vision, immune function, growth, and development. It also inhibits tumor growth and alleviates anemia. Here, we developed a Saccharomyces cerevisiae strain capable of high retinol production. Firstly, the de novo synthesis pathway of retinol was constructed in S. cerevisiae to realize the production of retinol. Second, through modular optimization of the metabolic network of retinol, the retinol titer was increased from 3.6 to 153.6 mg/L. Then, we used transporter engineering to regulate and promote the accumulation of the intracellular precursor retinal to improve retinol production. Subsequently, we screened and semi-rationally designed the key enzyme retinol dehydrogenase to further increase the retinol titer to 387.4 mg/L. Lastly, we performed two-phase extraction fermentation using olive oil to obtain a final shaking flask retinol titer of 1.2 g/L, the highest titer reported at the shake flask level. This study laid the foundation for the industrial production of retinol. Full article

(This article belongs to the Special Issue Development and Utilization of Yeast Resources)

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Open AccessArticle

Metabolic Engineering of Pichia pastoris for the Production of Triacetic Acid Lactone

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J. Fungi 2023, 9(4), 494; https://doi.org/10.3390/jof9040494 - 20 Apr 2023

Cited by 1 | Viewed by 631

Abstract

Triacetic acid lactone (TAL) is a promising renewable platform polyketide with broad biotechnological applications. In this study, we constructed an engineered Pichia pastoris strain for the production of TAL. We first introduced a heterologous TAL biosynthetic pathway by integrating the 2-pyrone synthase encoding gene from Gerbera hybrida (Gh2PS). We then removed the rate-limiting step of TAL synthesis by introducing the posttranslational regulation-free acetyl-CoA carboxylase mutant encoding gene from S. cerevisiae (ScACC1*) and increasing the copy number of Gh2PS. Finally, to enhance intracellular acetyl-CoA supply, we focused on the introduction of the phosphoketolase/phosphotransacetylase pathway (PK pathway). To direct more carbon flux towards the PK pathway for acetyl-CoA generation, we combined it with a heterologous xylose utilization pathway or endogenous methanol utilization pathway. The combination of the PK pathway with the xylose utilization pathway resulted in the production of 825.6 mg/L TAL in minimal medium with xylose as the sole carbon source, with a TAL yield of 0.041 g/g xylose. This is the first report on TAL biosynthesis in P. pastoris and its direct synthesis from methanol. The present study suggests potential applications in improving the intracellular pool of acetyl-CoA and provides a basis for the construction of efficient cell factories for the production of acetyl-CoA derived compounds. Full article

(This article belongs to the Special Issue Development and Utilization of Yeast Resources)

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Open AccessArticle

Proposal of Four New Aureobasidium Species for Exopolysaccharide Production

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J. Fungi 2023, 9(4), 447; https://doi.org/10.3390/jof9040447 - 06 Apr 2023

Viewed by 884

Abstract

In this study, 99 strains of Aureobasidium species were isolated from various samples collected from different locations in China, among which 14 isolates showed different morphological characteristics to other strains identified as known Aureobasidium species. Based on morphological characteristics, those 14 strains were classified into four groups, represented by stains of KCL139, MDSC−10, XZY411−4, and MQL9−100, respectively. Molecular analysis of the internal transcriptional spacer (ITS) and part of the large ribosome subunit (D1/D2 domains) indicated that those four groups represent four new species in the Aureobasidium. Therefore, the names Aureobasidium insectorum sp. nov., A. planticola sp. nov., A. motuoense sp. nov., and A. intercalariosporum sp. nov. are proposed for KCL139, MDSC−10, XZY411−4, and MQL9−100, respectively. We also found that there were differences in the yield of exopolysaccharides (EPS) among and within species, indicating strain-related exopolysaccharide-producing diversity. Full article

(This article belongs to the Special Issue Development and Utilization of Yeast Resources)

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Open AccessArticle

Improving Methanol Utilization by Reducing Alcohol Oxidase Activity and Adding Co-Substrate of Sodium Citrate in Pichia pastoris

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J. Fungi 2023, 9(4), 422; https://doi.org/10.3390/jof9040422 - 29 Mar 2023

Viewed by 883

Abstract

Methanol, which produced in large quantities from low-quality coal and the hydrogenation of CO₂, is a potentially renewable one-carbon (C1) feedstock for biomanufacturing. The methylotrophic yeast Pichia pastoris is an ideal host for methanol biotransformation given its natural capacity as a methanol assimilation system. However, the utilization efficiency of methanol for biochemical production is limited by the toxicity of formaldehyde. Therefore, reducing the toxicity of formaldehyde to cells remains a challenge to the engineering design of a methanol metabolism. Based on genome-scale metabolic models (GSMM) calculations, we speculated that reducing alcohol oxidase (AOX) activity would re-construct the carbon metabolic flow and promote balance between the assimilation and dissimilation of formaldehyde metabolism processes, thereby increasing the biomass formation of P. pastoris. According to experimental verification, we proved that the accumulation of intracellular formaldehyde can be decreased by reducing AOX activity. The reduced formaldehyde formation upregulated methanol dissimilation and assimilation and the central carbon metabolism, which provided more energy for the cells to grow, ultimately leading to an increased conversion of methanol to biomass, as evidenced by phenotypic and transcriptome analysis. Significantly, the methanol conversion rate of AOX-attenuated strain PC110-AOX1-464 reached 0.364 g DCW/g, representing a 14% increase compared to the control strain PC110. In addition, we also proved that adding a co-substrate of sodium citrate could further improve the conversion of methanol to biomass in the AOX-attenuated strain. It was found that the methanol conversion rate of the PC110-AOX1-464 strain with the addition of 6 g/L sodium citrate reached 0.442 g DCW/g, representing 20% and 39% increases compared to AOX-attenuated strain PC110-AOX1-464 and control strain PC110 without sodium citrate addition, respectively. The study described here provides insight into the molecular mechanism of efficient methanol utilization by regulating AOX. Reducing AOX activity and adding sodium citrate as a co-substrate are potential engineering strategies to regulate the production of chemicals from methanol in P. pastoris. Full article

(This article belongs to the Special Issue Development and Utilization of Yeast Resources)

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Open AccessArticle

Engineering Flocculation for Improved Tolerance and Production of d-Lactic Acid in Pichia pastoris

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J. Fungi 2023, 9(4), 409; https://doi.org/10.3390/jof9040409 - 27 Mar 2023

Viewed by 833

Abstract

d-lactic acid, a chiral organic acid, can enhance the thermal stability of polylactic acid plastics. Microorganisms such as the yeast Pichia pastoris, which lack the natural ability to produce or accumulate high amounts of d-lactic acid, have been metabolically engineered to produce it in high titers. However, tolerance to d-lactic acid remains a challenge. In this study, we demonstrate that cell flocculation improves tolerance to d-lactic acid and increases d-lactic acid production in Pichia pastoris. By incorporating a flocculation gene from Saccharomyces cerevisiae (ScFLO1) into P. pastoris KM71, we created a strain (KM71-ScFlo1) that demonstrated up to a 1.6-fold improvement in specific growth rate at high d-lactic acid concentrations. Furthermore, integrating a d-lactate dehydrogenase gene from Leuconostoc pseudomesenteroides (LpDLDH) into KM71-ScFlo1 resulted in an engineered strain (KM71-ScFlo1-LpDLDH) that could produce d-lactic acid at a titer of 5.12 ± 0.35 g/L in 48 h, a 2.6-fold improvement over the control strain lacking ScFLO1 expression. Transcriptomics analysis of this strain provided insights into the mechanism of increased tolerance to d-lactic acid, including the upregulations of genes involved in lactate transport and iron metabolism. Overall, our work represents an advancement in the efficient microbial production of d-lactic acid by manipulating yeast flocculation. Full article

(This article belongs to the Special Issue Development and Utilization of Yeast Resources)

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