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Yeast: Molecular and Cell Biology

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 19507

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Dr. Galina Zhouravleva

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Guest Editor

Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
Interests: yeasts as a model organism; yeast genome and its stability; DNA replication and repair; cell cycle and its regulation; transcription; translation and posttranslational modification; signal transduction; mitochondria; synthetic biology; yeast biotechnology; biomedicines
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Special Issue Information

Dear Colleagues,

The yeast Saccharomyces cerevisiae is a popular model organism widely used in genetic and biochemical studies. The advantage of heterothallic yeast is the ability to stably exist both in the haploid and diploid state. This makes it possible not only to carry out traditional genetic analysis but also to study such specific aspects of the eukaryotic cell as the regulation of the cell cycle and meiosis. Yeast turned out to be a very convenient object for genetic engineering, allowing the introduction of exogenous DNA both on plasmids and through integration into the genome. A feature of yeast is the predominance of homologous recombination during such integration.

The genome of the yeast Saccharomyces cerevisiae was the first eukaryotic genome to be sequenced. Numerous yeast databases make it easy to find up-to-date information; one such popular database is https://www.yeastgenome.org/.

Yeasts are widely used to analyze the genes of other eukaryotic organisms, as well as to study genes associated with human diseases. It was in yeast that a two-hybrid system was developed to characterize and search for various protein–protein interactions. Yeast is one of the popular organisms for the production of heterologous proteins in biotechnology. Many plasmids and yeast strains are commercially available including sets of different deletion strains.

The main aim of this Special Issue is to highlight the advantages of yeast as a model organism. The can be in the form of a review, mini-review, original research article, or short communication.

Dr. Galina Zhouravleva
Guest Editor

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Keywords

yeasts as a model organism
yeast genome and its stability
DNA replication and repair
cell cycle and its regulation
transcription
translation and posttranslational modification
signal transduction
mitochondria
synthetic biology
yeast biotechnology
biomedicines

Published Papers (12 papers)

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Research

Jump to: Review

13 pages, 4166 KiB

Open AccessArticle

The Aβ42 Peptide and IAPP Physically Interact in a Yeast-Based Assay

by Daniel V. Kachkin, Veronika V. Lashkul, Natalia A. Gorsheneva, Sergey A. Fedotov, Maria S. Rubel, Yury O. Chernoff and Aleksandr A. Rubel

Int. J. Mol. Sci. 2023, 24(18), 14122; https://doi.org/10.3390/ijms241814122 - 15 Sep 2023

Cited by 1 | Viewed by 1086

Abstract

Numerous studies have demonstrated that people with type 2 diabetes mellitus (associated with IAPP peptide aggregation) show an increased incidence of Alzheimer’s disease (associated with Aβ aggregation), but the mechanism responsible for this correlation is presently unknown. Here, we applied a yeast-based model to study the interactions of IAPP with PrP (associated with TSEs) and with the Aβ42 peptide. We demonstrated that fluorescently tagged IAPP forms detergent-resistant aggregates in yeast cells. Using the FRET approach, we showed that IAPP and Aβ aggregates co-localize and physically interact in yeast cells. We also showed that this interaction is specific and that there is no interaction between IAPP and PrP in the yeast system. Our data confirmed a direct physical interaction between IAPP and Aβ42 aggregates in a living cell. Based on these findings, we hypothesize that this interaction may play a crucial role in seeding Aβ42 aggregation in T2DM patients, thereby promoting the development of AD. Full article

(This article belongs to the Special Issue Yeast: Molecular and Cell Biology)

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22 pages, 3259 KiB

Open AccessArticle

Detection of Primary DNA Lesions by Transient Changes in Mating Behavior in Yeast Saccharomyces cerevisiae Using the Alpha-Test

by Anna S. Zhuk, Anna A. Shiriaeva, Yulia V. Andreychuk, Olga V. Kochenova, Elena R. Tarakhovskaya, Vladimir M. Bure, Youri I. Pavlov, Sergey G. Inge-Vechtomov and Elena I. Stepchenkova

Int. J. Mol. Sci. 2023, 24(15), 12163; https://doi.org/10.3390/ijms241512163 - 29 Jul 2023

Cited by 2 | Viewed by 1059

Abstract

Spontaneous or induced DNA lesions can result in stable gene mutations and chromosomal aberrations due to their inaccurate repair, ultimately resulting in phenotype changes. Some DNA lesions per se may interfere with transcription, leading to temporary phenocopies of mutations. The direct impact of primary DNA lesions on phenotype before their removal by repair is not well understood. To address this question, we used the alpha-test, which allows for detecting various genetic events leading to temporary or hereditary changes in mating type α→a in heterothallic strains of yeast Saccharomyces cerevisiae. Here, we compared yeast strains carrying mutations in DNA repair genes, mismatch repair (pms1), base excision repair (ogg1), and homologous recombination repair (rad52), as well as mutagens causing specific DNA lesions (UV light and camptothecin). We found that double-strand breaks and UV-induced lesions have a stronger effect on the phenotype than mismatches and 8-oxoguanine. Moreover, the loss of the entire chromosome III leads to an immediate mating type switch α→a and does not prevent hybridization. We also evaluated the ability of primary DNA lesions to persist through the cell cycle by assessing the frequency of UV-induced inherited and non-inherited genetic changes in asynchronous cultures of a wild-type (wt) strain and in a cdc28-4 mutant arrested in the G1 phase. Our findings suggest that the phenotypic manifestation of primary DNA lesions depends on their type and the stage of the cell cycle in which it occurred. Full article

(This article belongs to the Special Issue Yeast: Molecular and Cell Biology)

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13 pages, 2325 KiB

Open AccessArticle

The N-Terminal Region of the BcWCL1 Photoreceptor Is Necessary for Self-Dimerization and Transcriptional Activation upon Light Stimulation in Yeast

by Matías Guerrero, Carlos Ruiz, Andrés Romero, Luka Robeson, Diego Ruiz and Francisco Salinas

Int. J. Mol. Sci. 2023, 24(15), 11874; https://doi.org/10.3390/ijms241511874 - 25 Jul 2023

Viewed by 1048

Abstract

The BcWCL1 protein is a blue-light photoreceptor from the fungus Botrytis cinerea. This protein has a central role in B. cinerea circadian regulation and is an ortholog to WC-1 from Neurospora crassa. The BcWCL1 and WC-1 proteins have similar protein domains, including a LOV (Light Oxygen Voltage) domain for light sensing, two PAS (Per Arnt Sim) domains for protein–protein interaction, and a DNA binding domain from the GATA family. Recently, the blue-light response of BcWCL1 was demonstrated in a version without PAS domains (BcWCL1^PAS∆). Here, we demonstrated that BcWCL1^PAS∆ is capable of self-dimerization through its N-terminal region upon blue-light stimulation. Interestingly, we observed that BcWCL1^PAS∆ enables transcriptional activation as a single component in yeast. By using chimeric transcription factors and the luciferase reporter gene, we assessed the transcriptional activity of different fragments of the N-terminal and C-terminal regions of BcWCL1^PAS∆, identifying a functional transcriptional activation domain (AD) in the N-terminal region that belongs to the 9aaTAD family. Finally, we determined that the transcriptional activation levels of BcWCL1^PAS∆ AD are comparable to those obtained with commonly used ADs in eukaryotic cells (Gal4 and p65). In conclusion, the BcWCL1^PAS∆ protein self-dimerized and activated transcription in a blue-light-dependent fashion, opening future applications of this photoreceptor in yeast optogenetics. Full article

(This article belongs to the Special Issue Yeast: Molecular and Cell Biology)

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15 pages, 4025 KiB

Open AccessArticle

A New Role for Yeast Cells in Health and Nutrition: Antioxidant Power Assessment

by Thomas Gosselin-Monplaisir, Adilya Dagkesamanskaya, Mylène Rigal, Aurélie Floch, Christophe Furger and Hélène Martin-Yken

Int. J. Mol. Sci. 2023, 24(14), 11800; https://doi.org/10.3390/ijms241411800 - 22 Jul 2023

Viewed by 1160

Abstract

As the use of antioxidant compounds in the domains of health, nutrition and well-being is exponentially rising, there is an urgent need to quantify antioxidant power quickly and easily, ideally within living cells. We developed an Anti Oxidant Power in Yeast (AOPY) assay which allows for the quantitative measurement of the Reactive Oxygen Species (ROS) and free-radical scavenging effects of various molecules in a high-throughput compatible format. Key parameters for Saccharomyces cerevisiae were investigated, and the optimal values were determined for each of them. The cell density in the reaction mixture was fixed at 0.6; the concentration of the fluorescent biosensor (TO) was found to be optimal at 64 µM, and the strongest response was observed for exponentially growing cells. Our optimized procedure allows accurate quantification of the antioxidant effect in yeast of well-known antioxidant molecules: resveratrol, epigallocatechin gallate, quercetin and astaxanthin added in the culture medium. Moreover, using a genetically engineered carotenoid-producing yeast strain, we realized the proof of concept of the usefulness of this new assay to measure the amount of β-carotene directly inside living cells, without the need for cell lysis and purification. Full article

(This article belongs to the Special Issue Yeast: Molecular and Cell Biology)

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18 pages, 7593 KiB

Open AccessArticle

Development of Terminator–Promoter Bifunctional Elements for Application in Saccharomyces cerevisiae Pathway Engineering

by Xiaoxia Ni, Zhengyang Liu, Jintang Guo and Genlin Zhang

Int. J. Mol. Sci. 2023, 24(12), 9870; https://doi.org/10.3390/ijms24129870 - 07 Jun 2023

Viewed by 1436

Abstract

The construction of a genetic circuit requires the substitution and redesign of different promoters and terminators. The assembly efficiency of exogenous pathways will also decrease significantly when the number of regulatory elements and genes is increased. We speculated that a novel bifunctional element with promoter and terminator functions could be created via the fusion of a termination signal with a promoter sequence. In this study, the elements from a Saccharomyces cerevisiae promoter and terminator were employed to design a synthetic bifunctional element. The promoter strength of the synthetic element is apparently regulated through a spacer sequence and an upstream activating sequence (UAS) with a ~5-fold increase, and the terminator strength could be finely regulated by the efficiency element, with a ~5-fold increase. Furthermore, the use of a TATA box-like sequence resulted in the adequate execution of both functions of the TATA box and the efficiency element. By regulating the TATA box-like sequence, UAS, and spacer sequence, the strengths of the promoter-like and terminator-like bifunctional elements were optimally fine-tuned with ~8-fold and ~7-fold increases, respectively. The application of bifunctional elements in the lycopene biosynthetic pathway showed an improved pathway assembly efficiency and higher lycopene yield. The designed bifunctional elements effectively simplified pathway construction and can serve as a useful toolbox for yeast synthetic biology. Full article

(This article belongs to the Special Issue Yeast: Molecular and Cell Biology)

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12 pages, 1877 KiB

Open AccessArticle

Polymorphism of Saccharomyces cerevisiae Strains in DNA Metabolism Genes

by Anna S. Zhuk, Artem G. Lada and Youri I. Pavlov

Int. J. Mol. Sci. 2023, 24(9), 7795; https://doi.org/10.3390/ijms24097795 - 25 Apr 2023

Viewed by 1479

Abstract

Baker’s yeast, S. cerevisiae, is an excellent model organism exploited for molecular genetic studies of the mechanisms of genome stability in eukaryotes. Genetic peculiarities of commonly used yeast strains impact the processes of DNA replication, repair, and recombination (RRR). We compared the genomic DNA sequence variation of the five strains that are intensively used for RRR studies. We used yeast next-generation sequencing data to detect the extent and significance of variation in 183 RRR genes. We present a detailed analysis of the differences that were found even in closely related strains. Polymorphisms of common yeast strains should be considered when interpreting the outcomes of genome stability studies, especially in cases of discrepancies between laboratories describing the same phenomena. Full article

(This article belongs to the Special Issue Yeast: Molecular and Cell Biology)

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11 pages, 2160 KiB

Open AccessArticle

The GEM-GECO Calcium Indicator Is Useable in Ogataea parapolymorpha Yeast, but Aggravates Effects of Increased Cytosolic Calcium Levels

by Maria V. Kulakova, Azamat V. Karginov, Alexander I. Alexandrov and Michael O. Agaphonov

Int. J. Mol. Sci. 2022, 23(17), 10004; https://doi.org/10.3390/ijms231710004 - 02 Sep 2022

Cited by 2 | Viewed by 1772

Abstract

Ca²⁺ is a ubiquitous second messenger, which allows eukaryotic cells to respond to external stimuli. The use of genetically encoded Ca²⁺ indicators allows real-time monitoring of cytosolic Ca²⁺ levels to study such responses. Here we explored the possibility of using the ratiometric Ca²⁺ indicator GEM-GECO for monitoring cytosolic Ca²⁺ concentration ([Ca²⁺]_cyt) in the yeast Ogataea parapolymorpha. High-level production of GEM-GECO led to a severe growth defect in cells lacking the vacuolar Ca²⁺ ATPase Pmc1, which is involved in [Ca²⁺]_cyt control, and prompted a phenotype resembling that of Pmc1 deficiency, in a strain with wild-type PMC1. This was likely due to the presence of the calmodulin domain in GEM-GECO. In contrast to previous studies of genetically-encoded calcium indicators in neuronal cells, our results suggest that physiological effects of GEM-GECO expression in yeast cells are due not to Ca²⁺ depletion, but to excessive Ca²⁺ signaling. Despite these drawbacks, study of fluorescence in individual cells revealed switching of GEM-GECO from the Ca²⁺-free to Ca²⁺-bound state minutes after external addition of CaCl₂. This was followed by gradual return of GEM-GECO to a Ca²⁺-free-state that was impaired in the pmc1-Δ mutant. These results demonstrate GEM-GECO usability for [Ca²⁺]_cyt monitoring in budding yeast. Full article

(This article belongs to the Special Issue Yeast: Molecular and Cell Biology)

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Review

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33 pages, 3361 KiB

Open AccessReview

Practical Approaches for the Yeast Saccharomyces cerevisiae Genome Modification

by Elena I. Stepchenkova, Sergey P. Zadorsky, Andrey R. Shumega and Anna Y. Aksenova

Int. J. Mol. Sci. 2023, 24(15), 11960; https://doi.org/10.3390/ijms241511960 - 26 Jul 2023

Cited by 3 | Viewed by 3211

Abstract

The yeast S. cerevisiae is a unique genetic object for which a wide range of relatively simple, inexpensive, and non-time-consuming methods have been developed that allow the performing of a wide variety of genome modifications. Among the latter, one can mention point mutations, disruptions and deletions of particular genes and regions of chromosomes, insertion of cassettes for the expression of heterologous genes, targeted chromosomal rearrangements such as translocations and inversions, directed changes in the karyotype (loss or duplication of particular chromosomes, changes in the level of ploidy), mating-type changes, etc. Classical yeast genome manipulations have been advanced with CRISPR/Cas9 technology in recent years that allow for the generation of multiple simultaneous changes in the yeast genome. In this review we discuss practical applications of both the classical yeast genome modification methods as well as CRISPR/Cas9 technology. In addition, we review methods for ploidy changes, including aneuploid generation, methods for mating type switching and directed DSB. Combined with a description of useful selective markers and transformation techniques, this work represents a nearly complete guide to yeast genome modification. Full article

(This article belongs to the Special Issue Yeast: Molecular and Cell Biology)

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16 pages, 446 KiB

Open AccessReview

How Big Is the Yeast Prion Universe?

by Galina A. Zhouravleva, Stanislav A. Bondarev and Nina P. Trubitsina

Int. J. Mol. Sci. 2023, 24(14), 11651; https://doi.org/10.3390/ijms241411651 - 19 Jul 2023

Cited by 2 | Viewed by 1208

Abstract

The number of yeast prions and prion-like proteins described since 1994 has grown from two to nearly twenty. If in the early years most scientists working with the classic mammalian prion, PrP^Sc, were skeptical about the possibility of using the term prion to refer to yeast cytoplasmic elements with unusual properties, it is now clear that prion-like phenomena are widespread and that yeast can serve as a convenient model for studying them. Here we give a brief overview of the yeast prions discovered so far and focus our attention to the various approaches used to identify them. The prospects for the discovery of new yeast prions are also discussed. Full article

(This article belongs to the Special Issue Yeast: Molecular and Cell Biology)

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23 pages, 954 KiB

Open AccessReview

Alzheimer’s Disease: Significant Benefit from the Yeast-Based Models

by Khoren K. Epremyan, Dmitry V. Mamaev and Renata A. Zvyagilskaya

Int. J. Mol. Sci. 2023, 24(12), 9791; https://doi.org/10.3390/ijms24129791 - 06 Jun 2023

Cited by 2 | Viewed by 1708

Abstract

Alzheimer’s disease (AD) is an age-related, multifaceted neurological disorder associated with accumulation of aggregated proteins (amyloid Aβ and hyperphosphorylated tau), loss of synapses and neurons, and alterations in microglia. AD was recognized by the World Health Organization as a global public health priority. The pursuit of a better understanding of AD forced researchers to pay attention to well-defined single-celled yeasts. Yeasts, despite obvious limitations in application to neuroscience, show high preservation of basic biological processes with all eukaryotic organisms and offer great advantages over other disease models due to the simplicity, high growth rates on low-cost substrates, relatively simple genetic manipulations, the large knowledge base and data collections, and availability of an unprecedented amount of genomic and proteomic toolboxes and high-throughput screening techniques, inaccessible to higher organisms. Research reviewed above clearly indicates that yeast models, together with other, more simple eukaryotic models including animal models, C. elegans and Drosophila, significantly contributed to understanding Aβ and tau biology. These models allowed high throughput screening of factors and drugs that interfere with Aβ oligomerization, aggregation and toxicity, and tau hyperphosphorylation. In the future, yeast models will remain relevant, with a focus on creating novel high throughput systems to facilitate the identification of the earliest AD biomarkers among different cellular networks in order to achieve the main goal—to develop new promising therapeutic strategies to treat or prevent the disease. Full article

(This article belongs to the Special Issue Yeast: Molecular and Cell Biology)

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33 pages, 4072 KiB

Open AccessReview

Impact of Saccharomyces cerevisiae on the Field of Single-Molecule Biophysics

by David A. Ball, Binta Jalloh and Tatiana S. Karpova

Int. J. Mol. Sci. 2022, 23(24), 15895; https://doi.org/10.3390/ijms232415895 - 14 Dec 2022

Cited by 1 | Viewed by 1639

Abstract

Cellular functions depend on the dynamic assembly of protein regulator complexes at specific cellular locations. Single Molecule Tracking (SMT) is a method of choice for the biochemical characterization of protein dynamics in vitro and in vivo. SMT follows individual molecules in live cells and provides direct information about their behavior. SMT was successfully applied to mammalian models. However, mammalian cells provide a complex environment where protein mobility depends on numerous factors that are difficult to control experimentally. Therefore, yeast cells, which are unicellular and well-studied with a small and completely sequenced genome, provide an attractive alternative for SMT. The simplicity of organization, ease of genetic manipulation, and tolerance to gene fusions all make yeast a great model for quantifying the kinetics of major enzymes, membrane proteins, and nuclear and cellular bodies. However, very few researchers apply SMT techniques to yeast. Our goal is to promote SMT in yeast to a wider research community. Our review serves a dual purpose. We explain how SMT is conducted in yeast cells, and we discuss the latest insights from yeast SMT while putting them in perspective with SMT of higher eukaryotes. Full article

(This article belongs to the Special Issue Yeast: Molecular and Cell Biology)

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15 pages, 907 KiB

Open AccessReview

The Anaphase-Promoting Complex/Cyclosome Is a Cellular Ageing Regulator

by Xiangdong Hu, Xuejiao Jin, Xiuling Cao and Beidong Liu

Int. J. Mol. Sci. 2022, 23(23), 15327; https://doi.org/10.3390/ijms232315327 - 05 Dec 2022

Cited by 2 | Viewed by 1737

Abstract

The anaphase-promoting complex/cyclosome (APC/C) is a complicated cellular component that plays significant roles in regulating the cell cycle process of eukaryotic organisms. The spatiotemporal regulation mechanisms of APC/C in distinct cell cycle transitions are no longer mysterious, and the components of this protein complex are gradually identified and characterized. Given the close relationship between the cell cycle and lifespan, it is urgent to understand the roles of APC/C in lifespan regulation, but this field still seems to have not been systematically summarized. Furthermore, although several reviews have reported the roles of APC/C in cancer, there are still gaps in the summary of its roles in other age-related diseases. In this review, we propose that the APC/C is a novel cellular ageing regulator based on its indispensable role in the regulation of lifespan and its involvement in age-associated diseases. This work provides an extensive review of aspects related to the underlying mechanisms of APC/C in lifespan regulation and how it participates in age-associated diseases. More comprehensive recognition and understanding of the relationship between APC/C and ageing and age-related diseases will increase the development of targeted strategies for human health. Full article

(This article belongs to the Special Issue Yeast: Molecular and Cell Biology)

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