Trends in Yeast Biochemistry and Biotechnology

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

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 25028

Special Issue Editors


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Guest Editor
Laboratory of Natural Science, Faculty of Economics, Toyo University, Hakusan Bunkyo-ku, Tokyo 112-8606, Japan
Interests: S. cerevisiae; C. albicans; vaccines; proteomics; inflammation; cell surface; yeast biotechnology; fermentation
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Guest Editor
Office of Society-Academia Collaboration for Innovation (SACI), Kyoto University, Yoshidahonmachi, Sakyo-ku, Kyoto 606-8501, Japan
Interests: cell surface engineering; yeast engineering; yeast genome editing; yeast organelle engineering; yeast cell whole catalyst
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

At present, yeasts are indispensable microorganisms for studies in biochemistry and biotechnology. Yeasts are important microorganisms not only as a eukaryote model in basic biology, but also as a powerful producer of recombinant proteins and physiologically active compounds in the pharmaceutical industry. Furthermore, basic and applied research using yeasts are connected to each other, and the significance of knowledge exchange between both research fields is receiving attention. To open a door to future yeast biochemistry and biotechnology, we hope that researchers using yeasts in their studies will submit a research paper or review article to this Special Issue.

Dr. Seiji Shibasaki
Dr. Mitsuyoshi Ueda
Guest Editors

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Published Papers (10 papers)

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Research

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14 pages, 2873 KiB  
Article
Targeted Mutations Produce Divergent Characteristics in Pedigreed Sake Yeast Strains
by Norapat Klinkaewboonwong, Shinsuke Ohnuki, Tomoya Chadani, Ikuhisa Nishida, Yuto Ushiyama, Saki Tomiyama, Atsuko Isogai, Tetsuya Goshima, Farzan Ghanegolmohammadi, Tomoyuki Nishi, Katsuhiko Kitamoto, Takeshi Akao, Dai Hirata and Yoshikazu Ohya
Microorganisms 2023, 11(5), 1274; https://doi.org/10.3390/microorganisms11051274 - 12 May 2023
Cited by 4 | Viewed by 1441
Abstract
Modification of the genetic background and, in some cases, the introduction of targeted mutations can play a critical role in producing trait characteristics during the breeding of crops, livestock, and microorganisms. However, the question of how similar trait characteristics emerge when the same [...] Read more.
Modification of the genetic background and, in some cases, the introduction of targeted mutations can play a critical role in producing trait characteristics during the breeding of crops, livestock, and microorganisms. However, the question of how similar trait characteristics emerge when the same target mutation is introduced into different genetic backgrounds is unclear. In a previous study, we performed genome editing of AWA1, CAR1, MDE1, and FAS2 on the standard sake yeast strain Kyokai No. 7 to breed a sake yeast with multiple excellent brewing characteristics. By introducing the same targeted mutations into other pedigreed sake yeast strains, such as Kyokai strains No. 6, No. 9, and No. 10, we were able to create sake yeasts with the same excellent brewing characteristics. However, we found that other components of sake made by the genome-edited yeast strains did not change in the exact same way. For example, amino acid and isobutanol contents differed among the strain backgrounds. We also showed that changes in yeast cell morphology induced by the targeted mutations also differed depending on the strain backgrounds. The number of commonly changed morphological parameters was limited. Thus, divergent characteristics were produced by the targeted mutations in pedigreed sake yeast strains, suggesting a breeding strategy to generate a variety of sake yeasts with excellent brewing characteristics. Full article
(This article belongs to the Special Issue Trends in Yeast Biochemistry and Biotechnology)
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18 pages, 2429 KiB  
Article
Ubiquitin-Conjugating Enzymes Ubc1 and Ubc4 Mediate the Turnover of Hap4, a Master Regulator of Mitochondrial Biogenesis in Saccharomyces cerevisiae
by Denise Capps, Arielle Hunter, Mengying Chiang, Tammy Pracheil and Zhengchang Liu
Microorganisms 2022, 10(12), 2370; https://doi.org/10.3390/microorganisms10122370 - 30 Nov 2022
Cited by 3 | Viewed by 1716
Abstract
Mitochondrial biogenesis is tightly regulated in response to extracellular and intracellular signals, thereby adapting yeast cells to changes in their environment. The Hap2/3/4/5 complex is a master transcriptional regulator of mitochondrial biogenesis in yeast. Hap4 is the regulatory subunit of the complex and [...] Read more.
Mitochondrial biogenesis is tightly regulated in response to extracellular and intracellular signals, thereby adapting yeast cells to changes in their environment. The Hap2/3/4/5 complex is a master transcriptional regulator of mitochondrial biogenesis in yeast. Hap4 is the regulatory subunit of the complex and exhibits increased expression when the Hap2/3/4/5 complex is activated. In cells grown under glucose derepression conditions, both the HAP4 transcript level and Hap4 protein level are increased. As part of an inter-organellar signaling mechanism coordinating gene expression between the mitochondrial and nuclear genomes, the activity of the Hap2/3/4/5 complex is reduced in respiratory-deficient cells, such as ρ0 cells lacking mitochondrial DNA, as a result of reduced Hap4 protein levels. However, the underlying mechanism is unclear. Here, we show that reduced HAP4 expression in ρ0 cells is mediated through both transcriptional and post-transcriptional mechanisms. We show that loss of mitochondrial DNA increases the turnover of Hap4, which requires the 26S proteasome and ubiquitin-conjugating enzymes Ubc1 and Ubc4. Stabilization of Hap4 in the ubc1 ubc4 double mutant leads to increased expression of Hap2/3/4/5-target genes. Our results indicate that mitochondrial biogenesis in yeast is regulated by the functional state of mitochondria partly through ubiquitin/proteasome-dependent turnover of Hap4. Full article
(This article belongs to the Special Issue Trends in Yeast Biochemistry and Biotechnology)
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12 pages, 2103 KiB  
Article
Isolation and Characterization of Basidiomycetous Yeasts Capable of Producing Phytase under Oligotrophic Conditions
by Akino Kurosawa, Ryo Nishioka, Nobuhiro Aburai and Katsuhiko Fujii
Microorganisms 2022, 10(11), 2182; https://doi.org/10.3390/microorganisms10112182 - 3 Nov 2022
Cited by 1 | Viewed by 1343
Abstract
Phytic acid is an organic phosphorus source naturally produced by plants as phosphorus stock and can be an alternative to rock phosphate, which is a dwindling resource globally. However, phytic acid is insoluble, owing to its binding to divalent metals and is, thus, [...] Read more.
Phytic acid is an organic phosphorus source naturally produced by plants as phosphorus stock and can be an alternative to rock phosphate, which is a dwindling resource globally. However, phytic acid is insoluble, owing to its binding to divalent metals and is, thus, not readily bioavailable for plants and monogastric livestock. Therefore, the enzyme phytase is indispensable for hydrolyzing phytic acid to liberate free phosphates for nutritional availability, making the screening of novel phytase-producing microbes an attractive research focus to agriculture and animal feed industries. In the present study, a soil-extract-based culture medium was supplemented with phytic acid as the sole phosphorus source and oligotrophic phytase-producing strains, which had not been previously studied, were isolated. Four fungal strains with phytic acid, assimilation activities were isolated. They were found to produce phytase in the culture supernatants and phylogenetic analysis identified three strains as basidiomycetous yeasts (Saitozyma, Leucosporidium, and Malassezia) and one strain as an ascomycetous fungus (Chaetocapnodium). The optimal pH for phytase activity of the strains was 6.0–7.0, suggesting that they are suitable for industrial applications as feed supplements or fertilizer additives for farmland. Full article
(This article belongs to the Special Issue Trends in Yeast Biochemistry and Biotechnology)
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7 pages, 1990 KiB  
Communication
Construction of HGF-Displaying Yeast by Cell Surface Engineering
by Seiji Shibasaki, Yuki Nakatani, Kazuaki Taketani, Miki Karasaki, Kiyoshi Matsui, Mitsuyoshi Ueda and Tsuyoshi Iwasaki
Microorganisms 2022, 10(7), 1373; https://doi.org/10.3390/microorganisms10071373 - 7 Jul 2022
Viewed by 1814
Abstract
Hepatocyte growth factor (HGF) has been investigated as a regulator for immune reactions caused by transplantation and autoimmune diseases and other biological functions. Previous studies demonstrated that cDNA-encoding HGF administration could inhibit acute graft-versus-host disease (GVHD) after treatment via hematopoietic stem cell transplantation. [...] Read more.
Hepatocyte growth factor (HGF) has been investigated as a regulator for immune reactions caused by transplantation and autoimmune diseases and other biological functions. Previous studies demonstrated that cDNA-encoding HGF administration could inhibit acute graft-versus-host disease (GVHD) after treatment via hematopoietic stem cell transplantation. This study aimed to show the preparation of HGF protein on yeast cell surfaces to develop a tool for the oral administration of HGF to a GVHD mouse model. In this study, full-length HGF and the heavy chain of HGF were genetically fused with α-agglutinin and were successfully displayed on the yeast cell surface. This study suggested that yeast cell surface display engineering could provide a novel administration route for HGF. Full article
(This article belongs to the Special Issue Trends in Yeast Biochemistry and Biotechnology)
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14 pages, 2182 KiB  
Article
UME6 Is Involved in the Suppression of Basal Transcription of ABC Transporters and Drug Resistance in the ρ+ Cells of Saccharomyces cerevisiae
by Yoichi Yamada
Microorganisms 2022, 10(3), 601; https://doi.org/10.3390/microorganisms10030601 - 10 Mar 2022
Cited by 2 | Viewed by 2280
Abstract
In Saccharomycescerevisiae, the Rpd3L complex contains a histone deacetylase, Rpd3, and the DNA binding proteins, Ume6 and Ash1, and acts as a transcriptional repressor or activator. We previously showed that RPD3 and UME6 are required for the activation of PDR5, [...] Read more.
In Saccharomycescerevisiae, the Rpd3L complex contains a histone deacetylase, Rpd3, and the DNA binding proteins, Ume6 and Ash1, and acts as a transcriptional repressor or activator. We previously showed that RPD3 and UME6 are required for the activation of PDR5, which encodes a major efflux pump, and pleiotropic drug resistance (PDR) in ρ0/− cells, which lack mitochondrial DNA. However, there are inconsistent reports regarding whether RPD3 and UME6 are required for Pdr5-mediated PDR in ρ+ cells with mitochondrial DNA. Since PDR5 expression or PDR in the ρ+ cells of the rpd3Δ and ume6Δ mutants have primarily been examined using fermentable media, mixed cultures of ρ+ and ρ0/− cells could be used. Therefore, we examined whether RPD3 and UME6 are required for basal and drug-induced PDR5 transcription and PDR in ρ+ cells using fermentable and nonfermentable media. UME6 suppresses the basal transcription levels of the ABC transporters, including PDR5, and drug resistance in ρ+ cells independent of the carbon source used in the growth medium. In contrast, RPD3 is required for drug resistance but did not interfere with the basal PDR5 mRNA levels. UME6 is also required for the cycloheximide-induced transcription of PDR5 in nonfermentable media but not in fermentable media. Full article
(This article belongs to the Special Issue Trends in Yeast Biochemistry and Biotechnology)
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Review

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15 pages, 552 KiB  
Review
Yeast-Based Screening of Anti-Viral Molecules
by Vartika Srivastava, Ravinder Kumar and Aijaz Ahmad
Microorganisms 2024, 12(3), 578; https://doi.org/10.3390/microorganisms12030578 - 14 Mar 2024
Viewed by 1691
Abstract
Viruses are minuscule infectious agents that reproduce exclusively within the living cells of an organism and are present in almost every ecosystem. Their continuous interaction with humans poses a significant threat to the survival and well-being of everyone. Apart from the common cold [...] Read more.
Viruses are minuscule infectious agents that reproduce exclusively within the living cells of an organism and are present in almost every ecosystem. Their continuous interaction with humans poses a significant threat to the survival and well-being of everyone. Apart from the common cold or seasonal influenza, viruses are also responsible for several important diseases such as polio, rabies, smallpox, and most recently COVID-19. Besides the loss of life and long-term health-related issues, clinical viral infections have significant economic and social impacts. Viral enzymes, especially proteases which are essential for viral multiplication, represent attractive drug targets. As a result, screening of viral protease inhibitors has gained a lot of interest in the development of anti-viral drugs. Despite the availability of anti-viral therapeutics, there is a clear need to develop novel curative agents that can be used against a given virus or group of related viruses. This review highlights the importance of yeasts as an in vivo model for screening viral enzyme inhibitors. We also discuss the advantages of yeast-based screening platforms over traditional assays. Therefore, in the present article, we discuss why yeast is emerging as a model of choice for in vivo screening of anti-viral molecules and why yeast-based screening will become more relevant in the future for screening anti-viral and other molecules of clinical importance. Full article
(This article belongs to the Special Issue Trends in Yeast Biochemistry and Biotechnology)
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19 pages, 1856 KiB  
Review
Utilization of Macroalgae for the Production of Bioactive Compounds and Bioprocesses Using Microbial Biotechnology
by Seiji Shibasaki and Mitsuyoshi Ueda
Microorganisms 2023, 11(6), 1499; https://doi.org/10.3390/microorganisms11061499 - 5 Jun 2023
Cited by 3 | Viewed by 1824
Abstract
To achieve sustainable development, alternative resources should replace conventional resources such as fossil fuels. In marine ecosystems, many macroalgae grow faster than terrestrial plants. Macroalgae are roughly classified as green, red, or brown algae based on their photosynthetic pigments. Brown algae are considered [...] Read more.
To achieve sustainable development, alternative resources should replace conventional resources such as fossil fuels. In marine ecosystems, many macroalgae grow faster than terrestrial plants. Macroalgae are roughly classified as green, red, or brown algae based on their photosynthetic pigments. Brown algae are considered to be a source of physiologically active substances such as polyphenols. Furthermore, some macroalgae can capture approximately 10 times more carbon dioxide from the atmosphere than terrestrial plants. Therefore, they have immense potential for use in the environment. Recently, macroalgae have emerged as a biomass feedstock for bioethanol production owing to their low lignin content and applicability to biorefinery processes. Herein, we provided an overview of the bioconversion of macroalgae into bioactive substances and biofuels using microbial biotechnology, including engineered yeast designed using molecular display technology. Full article
(This article belongs to the Special Issue Trends in Yeast Biochemistry and Biotechnology)
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19 pages, 3878 KiB  
Review
Overcoming the Limitations of CRISPR-Cas9 Systems in Saccharomyces cerevisiae: Off-Target Effects, Epigenome, and Mitochondrial Editing
by Genki Sato and Kouichi Kuroda
Microorganisms 2023, 11(4), 1040; https://doi.org/10.3390/microorganisms11041040 - 16 Apr 2023
Cited by 1 | Viewed by 4708
Abstract
Modification of the genome of the yeast Saccharomyces cerevisiae has great potential for application in biological research and biotechnological advancements, and the CRISPR-Cas9 system has been increasingly employed for these purposes. The CRISPR-Cas9 system enables the precise and simultaneous modification of any genomic [...] Read more.
Modification of the genome of the yeast Saccharomyces cerevisiae has great potential for application in biological research and biotechnological advancements, and the CRISPR-Cas9 system has been increasingly employed for these purposes. The CRISPR-Cas9 system enables the precise and simultaneous modification of any genomic region of the yeast to a desired sequence by altering only a 20-nucleotide sequence within the guide RNA expression constructs. However, the conventional CRISPR-Cas9 system has several limitations. In this review, we describe the methods that were developed to overcome these limitations using yeast cells. We focus on three types of developments: reducing the frequency of unintended editing to both non-target and target sequences in the genome, inducing desired changes in the epigenetic state of the target region, and challenging the expansion of the CRISPR-Cas9 system to edit genomes within intracellular organelles such as mitochondria. These developments using yeast cells to overcome the limitations of the CRISPR-Cas9 system are a key factor driving the advancement of the field of genome editing. Full article
(This article belongs to the Special Issue Trends in Yeast Biochemistry and Biotechnology)
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18 pages, 2634 KiB  
Review
Progress of Molecular Display Technology Using Saccharomyces cerevisiae to Achieve Sustainable Development Goals
by Seiji Shibasaki and Mitsuyoshi Ueda
Microorganisms 2023, 11(1), 125; https://doi.org/10.3390/microorganisms11010125 - 3 Jan 2023
Cited by 4 | Viewed by 3348
Abstract
In the long history of microorganism use, yeasts have been developed as hosts for producing biologically active compounds or for conventional fermentation. Since the introduction of genetic engineering, recombinant proteins have been designed and produced using yeast or bacterial cells. Yeasts have the [...] Read more.
In the long history of microorganism use, yeasts have been developed as hosts for producing biologically active compounds or for conventional fermentation. Since the introduction of genetic engineering, recombinant proteins have been designed and produced using yeast or bacterial cells. Yeasts have the unique property of expressing genes derived from both prokaryotes and eukaryotes. Saccharomyces cerevisiae is one of the well-studied yeasts in genetic engineering. Recently, molecular display technology, which involves a protein-producing system on the yeast cell surface, has been established. Using this technology, designed proteins can be displayed on the cell surface, and novel abilities are endowed to the host yeast strain. This review summarizes various molecular yeast display technologies and their principles and applications. Moreover, S. cerevisiae laboratory strains generated using molecular display technology for sustainable development are described. Each application of a molecular displayed yeast cell is also associated with the corresponding Sustainable Development Goals of the United Nations. Full article
(This article belongs to the Special Issue Trends in Yeast Biochemistry and Biotechnology)
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12 pages, 1852 KiB  
Review
Condensate Formation by Metabolic Enzymes in Saccharomyces cerevisiae
by Natsuko Miura
Microorganisms 2022, 10(2), 232; https://doi.org/10.3390/microorganisms10020232 - 21 Jan 2022
Cited by 4 | Viewed by 3449
Abstract
Condensate formation by a group of metabolic enzymes in the cell is an efficient way of regulating cell metabolism through the formation of “membrane-less organelles.” Because of the use of green fluorescent protein (GFP) for investigating protein localization, various enzymes were found to [...] Read more.
Condensate formation by a group of metabolic enzymes in the cell is an efficient way of regulating cell metabolism through the formation of “membrane-less organelles.” Because of the use of green fluorescent protein (GFP) for investigating protein localization, various enzymes were found to form condensates or filaments in living Saccharomyces cerevisiae, mammalian cells, and in other organisms, thereby regulating cell metabolism in the certain status of the cells. Among different environmental stresses, hypoxia triggers the spatial reorganization of many proteins, including more than 20 metabolic enzymes, to form numerous condensates, including “Glycolytic body (G-body)” and “Purinosome.” These individual condensates are collectively named “Metabolic Enzymes Transiently Assembling (META) body”. This review overviews condensate or filament formation by metabolic enzymes in S. cerevisiae, focusing on the META body, and recent reports in elucidating regulatory machinery of META body formation. Full article
(This article belongs to the Special Issue Trends in Yeast Biochemistry and Biotechnology)
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