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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (15 June 2023) | Viewed by 26747

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Dr. María-Isabel González-Siso

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Guest Editor

Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain
Interests: yeasts; functional metagenomics; thermophiles; thermozymes; protein engineering
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Dr. Manuel Becerra

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Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain
Interests: yeasts; functional metagenomics; thermophiles and thermozymes; structure and function of proteins; protein engineering
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Yeasts are eukaryotic unicellular microorganisms of the fungi kingdom that have served mankind since ancient times. The most studied yeast hitherto is Saccharomyces cerevisiae, whose genome was the first eukaryotic genome to be fully sequenced, pioneering the development of genetic engineering and gene editing tools. It has been used as a simple model for research on metabolism, physiology, gene regulation, diseases, etc. At the same time, it has been the main protagonist of the biotechnological industry, providing recombinant proteins, biofuels, and several other bioproducts. Other yeast species, which have been called non-conventional, have been gaining prominence in the scientific world due to their differential characteristics compared to S. cerevisiae, such as their utilization of a wider variety of carbon sources, including waste materials, different respiro-fermentative metabolism processes, different glycosylation patterns of recombinant proteins, etc.

The aim of this Special Issue is to provide a multidisciplinary space to share valuable information about recent research (basic and applied) on yeasts and on using yeasts as tools, from their genome to their proteins (native and recombinant), and as other bioproducts. Research on S. cerevisiae and non-conventional yeasts is welcome, as are articles about the history of yeast research.

As Guest Editors of the Special Issue, we invite you to submit research articles, review articles, and short communications related to recent advances in yeast research.

Dr. María-Isabel González-Siso
Dr. Manuel Becerra
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. Microorganisms 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 2700 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
eukaryote model
biotechnology
recombinant protein
bioproduction
protein engineering

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Yeasts Biochemistry and Biotechnology, 2nd Edition in Microorganisms (3 articles)

Published Papers (11 papers)

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Editorial

Jump to: Research, Review

2 pages, 172 KiB

Open AccessEditorial

Editorial for Special Issue “Yeasts Biochemistry and Biotechnology”

by María-Isabel González-Siso and Manuel Becerra

Microorganisms 2024, 12(3), 534; https://doi.org/10.3390/microorganisms12030534 - 7 Mar 2024

Viewed by 949

Abstract

Yeasts, both Saccharomyces and non-conventional strains, are currently the focus of active research due to their impressive applications in biotechnological bioprocesses, such as being hosts to produce recombinant proteins or main actors of the fermentation industries [...] Full article

(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology)

Research

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22 pages, 4605 KiB

Open AccessArticle

Study of a First Approach to the Controlled Fermentation for Lambic Beer Production

by Vanesa Postigo, Margarita García and Teresa Arroyo

Microorganisms 2023, 11(7), 1681; https://doi.org/10.3390/microorganisms11071681 - 28 Jun 2023

Cited by 3 | Viewed by 2123

Abstract

Non-Saccharomyces yeasts represent a great source of biodiversity for the production of new beer styles, since they can be used in different industrial areas, as pure culture starters, in co-fermentation with Saccharomyces, and in spontaneous fermentation (lambic and gueuze production, with the main contribution of Brettanomyces yeast). The fermentation process of lambic beer is characterized by different phases with a characteristic predominance of different microorganisms in each of them. As it is a spontaneous process, fermentation usually lasts from 10 months to 3 years. In this work, an attempt was made to perform a fermentation similar to the one that occurred in this process with lactic bacteria, Saccharomyces yeast and Brettanomyces yeast, but controlling their inoculation and therefore decreasing the time necessary for their action. For this purpose, after the first screening in 100 mL where eight Brettanomyces yeast strains from D.O. “Ribeira Sacra” (Galicia) were tested, one Brettanomyces bruxellensis strain was finally selected (B6) for fermentation in 1 L together with commercial strains of Saccharomyces cerevisiae S-04 yeast and Lactobacillus brevis lactic acid bacteria in different sequences. The combinations that showed the best fermentative capacity were tested in 14 L. Volatile compounds, lactic acid, acetic acid, colour, bitterness, residual sugars, ethanol, melatonin and antioxidant capacity were analysed at different maturation times of 1, 2, 6 and 12 months. Beers inoculated with Brettanomyces yeast independently of the other microorganisms showed pronounced aromas characteristic of the Brettanomyces yeast. Maturation after 12 months showed balanced beers with “Brett” aromas, as well as an increase in the antioxidant capacity of the beers. Full article

(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology)

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15 pages, 2894 KiB

Open AccessArticle

Identification and Construction of Strong Promoters in Yarrowia lipolytica Suitable for Glycerol-Based Bioprocesses

by Ioannis Georgiadis, Christina Tsiligkaki, Victoria Patavou, Maria Orfanidou, Antiopi Tsoureki, Aggeliki Andreadelli, Eleni Theodosiou and Antonios M. Makris

Microorganisms 2023, 11(5), 1152; https://doi.org/10.3390/microorganisms11051152 - 28 Apr 2023

Cited by 3 | Viewed by 3119

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. Full article

(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology)

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25 pages, 2186 KiB

Open AccessArticle

Conversion of Mixed Waste Food Substrates by Carotenogenic Yeasts of Rhodotorula sp. Genus

by Martin Szotkowski, Žaneta Plhalová, Pavlína Sniegoňová, Jiří Holub, Oleg Chujanov, Dominika Špačková, Jana Blažková and Ivana Márová

Microorganisms 2023, 11(4), 1013; https://doi.org/10.3390/microorganisms11041013 - 13 Apr 2023

Cited by 3 | Viewed by 1686

Abstract

The consequence of the massive increase in population in recent years is the enormous production of mainly industrial waste. The effort to minimize these waste products is, therefore, no longer sufficient. Biotechnologists, therefore, started looking for ways to not only reuse these waste products, but also to valorise them. This work focuses on the biotechnological use and processing of waste oils/fats and waste glycerol by carotenogenic yeasts of the genus Rhodotorula and Sporidiobolus. The results of this work show that the selected yeast strains are able to process waste glycerol as well as some oils and fats in a circular economy model and, moreover, are resistant to potential antimicrobial compounds present in the medium. The best-growing strains, Rhodotorula toruloides CCY 062-002-004 and Rhodotorula kratochvilovae CCY 020-002-026, were selected for fed-batch cultivation in a laboratory bioreactor in a medium containing a mixture of coffee oil and waste glycerol. The results show that both strains were able to produce more than 18 g of biomass per litre of media with a high content of carotenoids (10.757 ± 1.007 mg/g of CDW in R. kratochvilovae and 10.514 ± 1.520 mg/g of CDW in R. toruloides, respectively). The overall results prove that combining different waste substrates is a promising option for producing yeast biomass enriched with carotenoids, lipids, and beta-glucans. Full article

(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology)

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11 pages, 772 KiB

Open AccessArticle

Physico-Chemical Characterization of an Exocellular Sugars Tolerant Β-Glucosidase from Grape Metschnikowia pulcherrima Isolates

by José Juan Mateo

Microorganisms 2023, 11(4), 964; https://doi.org/10.3390/microorganisms11040964 - 7 Apr 2023

Cited by 5 | Viewed by 1520

Abstract

A broad variety of microorganisms with useful characteristics in the field of biotechnology live on the surface of grapes; one of these microorganisms is Metschnikowia pulcherrima. This yeast secretes a β-glucosidase that can be used in fermentative processes to liberate aromatic compounds. In this work, the synthesis of an exocellular β-glucosidase has been demonstrated and the optimal conditions to maximize the enzyme’s effectiveness were determined. There was a maximum enzymatic activity at 28 °C and pH 4.5. Furthermore, the enzyme presents a great glucose and fructose tolerance, and to a lesser extent, ethanol tolerance. In addition, its activity was stimulated by calcium ions and low concentrations of ethanol and methanol. The impact of terpene content in wine was also determined. Because of these characteristics, β-glucosidase is a good candidate for use in enology. Full article

(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology)

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15 pages, 1302 KiB

Open AccessArticle

Effect of Methionine on Gene Expression in Komagataella phaffii Cells

by Tatiana Ianshina, Anton Sidorin, Kristina Petrova, Maria Shubert, Anastasiya Makeeva, Elena Sambuk, Anastasiya Govdi, Andrey Rumyantsev and Marina Padkina

Microorganisms 2023, 11(4), 877; https://doi.org/10.3390/microorganisms11040877 - 29 Mar 2023

Cited by 3 | Viewed by 1933

Abstract

Komagataella phaffii yeast plays a prominent role in modern biotechnology as a recombinant protein producer. For efficient use of this yeast, it is essential to study the effects of different media components on its growth and gene expression. We investigated the effect of methionine on gene expression in K. phaffii cells using RNA-seq analysis. Several gene groups exhibited altered expression when K. phaffii cells were cultured in a medium with methanol and methionine, compared to a medium without this amino acid. Methionine primarily affects the expression of genes involved in its biosynthesis, fatty acid metabolism, and methanol utilization. The AOX1 gene promoter, which is widely used for heterologous expression in K. phaffii, is downregulated in methionine-containing media. Despite great progress in the development of K. phaffii strain engineering techniques, a sensitive adjustment of cultivation conditions is required to achieve a high yield of the target product. The revealed effect of methionine on K. phaffii gene expression is important for optimizing media recipes and cultivation strategies aimed at maximizing the efficiency of recombinant product synthesis. Full article

(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology)

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14 pages, 2298 KiB

Open AccessArticle

Loss of a Functional Mitochondrial Pyruvate Carrier in Komagataella phaffii Does Not Improve Lactic Acid Production from Glycerol in Aerobic Cultivation

by Ana Caroline de Oliveira Junqueira, Nadielle Tamires Moreira Melo, Nádia Skorupa Parachin and Hugo Costa Paes

Microorganisms 2023, 11(2), 483; https://doi.org/10.3390/microorganisms11020483 - 15 Feb 2023

Cited by 1 | Viewed by 1623

Abstract

Cytosolic pyruvate is an essential metabolite in lactic acid production during microbial fermentation. However, under aerobiosis, pyruvate is transported to the mitochondrial matrix by the mitochondrial pyruvate carrier (MPC) and oxidized in cell respiration. Previous reports using Saccharomyces cerevisiae or Aspergillus oryzae have shown that the production of pyruvate-derived chemicals is improved by deleting the MPC1 gene. A previous lactate-producing K. phaffii strain engineered by our group was used as a host for the deletion of the MPC1 gene. In addition, the expression of a bacterial hemoglobin gene under the alcohol dehydrogenase 2 promoter from Scheffersomyces stipitis, known to work as a hypoxia sensor, was used to evaluate whether aeration would supply enough oxygen to meet the metabolic needs during lactic acid production. However, unlike S. cerevisiae and A. oryzae, the deletion of Mpc1 had no significant impact on lactic acid production but negatively affected cell growth in K. phaffii strains. Furthermore, the relative quantification of the VHb gene revealed that the expression of hemoglobin was detected even in aerobic cultivation, which indicates that the demand for oxygen in the bioreactor could result in functional hypoxia. Overall, the results add to our previously published ones and show that blocking cell respiration using hypoxia is more suitable than deleting Mpc for producing lactic acid in K. phaffii. Full article

(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology)

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16 pages, 2295 KiB

Open AccessArticle

Exploiting Non-Conventional Yeasts for Low-Alcohol Beer Production

by João Simões, Eduardo Coelho, Paulo Magalhães, Tiago Brandão, Pedro Rodrigues, José António Teixeira and Lucília Domingues

Microorganisms 2023, 11(2), 316; https://doi.org/10.3390/microorganisms11020316 - 26 Jan 2023

Cited by 12 | Viewed by 3578

Abstract

Non-Saccharomyces yeasts represent a very appealing alternative to producing beers with zero or low ethanol content. The current study explores the potential of seven non-Saccharomyces yeasts to produce low-alcohol or non-alcoholic beer, in addition to engineered/selected Saccharomyces yeasts for low-alcohol production. The yeasts were first screened for their sugar consumption and ethanol production profiles, leading to the selection of strains with absent or inefficient maltose consumption and consequently with low-to-null ethanol production. The selected yeasts were then used in larger-scale fermentations for volatile and sensory evaluation. Overall, the yeasts produced beers with ethanol concentrations below 1.2% in which fusel alcohols and esters were also detected, making them eligible to produce low-alcohol beers. Among the lager beers produced in this study, beers produced using Saccharomyces yeast demonstrated a higher acceptance by taster panelists. This study demonstrates the suitability of non-conventional yeasts for producing low-alcohol or non-alcoholic beers and opens perspectives for the development of non-conventional beers. Full article

(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology)

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17 pages, 4124 KiB

Open AccessArticle

Functional Characterization of Saccharomyces cerevisiae P5C Reductase, the Enzyme at the Converging Point of Proline and Arginine Metabolism

by Giuseppe Forlani, Giuseppe Sabbioni and Milosz Ruszkowski

Microorganisms 2022, 10(10), 2077; https://doi.org/10.3390/microorganisms10102077 - 20 Oct 2022

Cited by 2 | Viewed by 2038

Abstract

The enzyme that, in Saccharomyces cerevisiae, catalyzes the last step in both proline synthesis and arginine catabolism, δ¹-pyrroline-5-carboxylate (P5C) reductase, was purified to near homogeneity and characterized thoroughly. Retention patterns upon gel permeation chromatography were consistent with a homodecameric composition of the holomer. High lability of the purified preparations and stabilization by reducing compounds suggested susceptibility to reactive-oxygen-species-mediated damage. Both NADH and NADPH were used as the electron donor, the latter resulting in a 3-fold higher V_max. However, a higher affinity toward NADH was evident, and the NADPH-dependent activity was inhibited by NAD⁺, proline, arginine, and a variety of anions. With proline and arginine, the inhibition was of the competitive type with respect to the specific substrate, and of the uncompetitive- or mixed-type with respect to NADPH, respectively. The results suggest that, contrary to the enzyme from higher plants, yeast P5C reductase may preferentially use NADH in vivo. An in silico analysis was also performed to investigate the structural basis of such enzyme features. Superposition of the protein model with the experimental structure of P5C reductase from Medicago truncatula allowed us to hypothesize on the possible allosteric sites for arginine and anion binding, and the cysteine pairs that may be involved in disulfide formation. Full article

(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology)

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Review

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14 pages, 432 KiB

Open AccessReview

The Life of Saccharomyces and Non-Saccharomyces Yeasts in Drinking Wine

by Sergi Maicas and José Juan Mateo

Microorganisms 2023, 11(5), 1178; https://doi.org/10.3390/microorganisms11051178 - 30 Apr 2023

Cited by 18 | Viewed by 3990

Abstract

Drinking wine is a processed beverage that offers high nutritional and health benefits. It is produced from grape must, which undergoes fermentation by yeasts (and sometimes lactic acid bacteria) to create a product that is highly appreciated by consumers worldwide. However, if only one type of yeast, specifically Saccharomyces cerevisiae, was used in the fermentation process, the resulting wine would lack aroma and flavor and may be rejected by consumers. To produce wine with a desirable taste and aroma, non-Saccharomyces yeasts are necessary. These yeasts contribute volatile aromatic compounds that significantly impact the wine’s final taste. They promote the release of primary aromatic compounds through a sequential hydrolysis mechanism involving several glycosidases unique to these yeasts. This review will discuss the unique characteristics of these yeasts (Schizosaccharomyces pombe, Pichia kluyveri, Torulaspora delbrueckii, Wickerhamomyces anomalus, Metschnikowia pulcherrima, Hanseniaspora vineae, Lachancea thermotolerans, Candida stellata, and others) and their impact on wine fermentations and co-fermentations. Their existence and the metabolites they produce enhance the complexity of wine flavor, resulting in a more enjoyable drinking experience. Full article

(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology)

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18 pages, 1599 KiB

Open AccessReview

Thanksgiving to Yeast, the HMGB Proteins History from Yeast to Cancer

by Mónica Lamas-Maceiras, Ángel Vizoso-Vázquez, Aida Barreiro-Alonso, María Cámara-Quílez and María Esperanza Cerdán

Microorganisms 2023, 11(4), 993; https://doi.org/10.3390/microorganisms11040993 - 11 Apr 2023

Cited by 1 | Viewed by 2458

Abstract

Yeasts have been a part of human life since ancient times in the fermentation of many natural products used for food. In addition, in the 20th century, they became powerful tools to elucidate the functions of eukaryotic cells as soon as the techniques of molecular biology developed. Our molecular understandings of metabolism, cellular transport, DNA repair, gene expression and regulation, and the cell division cycle have all been obtained through biochemistry and genetic analysis using different yeasts. In this review, we summarize the role that yeasts have had in biological discoveries, the use of yeasts as biological tools, as well as past and on-going research projects on HMGB proteins along the way from yeast to cancer. Full article

(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology)

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