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Genomics of Yeast
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Genomics of Yeast

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 4282

Special Issue Editors

Dr. Chang-Hui Shen

E-Mail Website
Guest Editor
Biology Department, College of Staten Island, City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314, USA
Interests: mechanism of transcriptional activation; chromatin structure; programmed cell death; biofuel production; epigenetics
Dr. Milena Georgieva

E-Mail Website1 Website2
Co-Guest Editor
Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Roumen Tsanev”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
Interests: cellular ageing; molecular biology and genetics; epigenetics; nuclear structure and function; chromatin; linker histones; yeast genetics; cancer biology; genotoxicology; nanotoxicology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent development in genomic studies using the model organism Saccharomyces cerevisiae has provided great insights into the effect of genetic materials on cell functions and responses. For example, by systematically addressing the phenotypes of specific genetic interventions along a given set of conditions, functional genomics provides a comprehensive and integrated view of the processes that affect yeast physiology in response to the conditions. Furthermore, the development and application of chemical genomic assays using Saccharomyces cerevisiae has provided effective methods to identify the mechanism of action of known drugs and novel small molecules in vivo. These assays identify drug target candidates, genes involved in buffering drug target pathways, and also help to define the general cellular response to small molecules. As such, the yeast Saccharomyces cerevisiae has served as an important model system for genomic studies. In this Special Issue, we welcome all areas of genomic studies using Saccharomyces cerevisiae as the model system to examine basic, translational, and clinical insights with particular interest in chromatin studies.

Dr. Chang-Hui Shen
Dr. Milena Georgieva
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 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.

Keywords

  • saccharomyces cerevisiae
  • genomics epigenetics
  • functional genomics
  • comparative genomics
  • genomic assay chromatin
  • high-throughput screening
  • model organism ageing

Published Papers (2 papers)

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Research

24 pages, 2780 KiB  
Article
Yeast Chromatin Mutants Reveal Altered mtDNA Copy Number and Impaired Mitochondrial Membrane Potential
by Dessislava Staneva, Bela Vasileva, Petar Podlesniy, George Miloshev and Milena Georgieva
J. Fungi 2023, 9(3), 329; https://doi.org/10.3390/jof9030329 - 07 Mar 2023
Cited by 3 | Viewed by 2168
Abstract
Mitochondria are multifunctional, dynamic organelles important for stress response, cell longevity, ageing and death. Although the mitochondrion has its genome, nuclear-encoded proteins are essential in regulating mitochondria biogenesis, morphology, dynamics and function. Moreover, chromatin structure and epigenetic mechanisms govern the accessibility to DNA [...] Read more.
Mitochondria are multifunctional, dynamic organelles important for stress response, cell longevity, ageing and death. Although the mitochondrion has its genome, nuclear-encoded proteins are essential in regulating mitochondria biogenesis, morphology, dynamics and function. Moreover, chromatin structure and epigenetic mechanisms govern the accessibility to DNA and control gene transcription, indirectly influencing nucleo-mitochondrial communications. Thus, they exert crucial functions in maintaining proper chromatin structure, cell morphology, gene expression, stress resistance and ageing. Here, we present our studies on the mtDNA copy number in Saccharomyces cerevisiae chromatin mutants and investigate the mitochondrial membrane potential throughout their lifespan. The mutants are arp4 (with a point mutation in the ARP4 gene, coding for actin-related protein 4—Arp4p), hho1Δ (lacking the HHO1 gene, coding for the linker histone H1), and the double mutant arp4 hho1Δ cells with the two mutations. Our findings showed that the three chromatin mutants acquired strain-specific changes in the mtDNA copy number. Furthermore, we detected the disrupted mitochondrial membrane potential in their chronological lifespan. In addition, the expression of nuclear genes responsible for regulating mitochondria biogenesis and turnover was changed. The most pronounced were the alterations found in the double mutant arp4 hho1Δ strain, which appeared as the only petite colony-forming mutant, unable to grow on respiratory substrates and with partial depletion of the mitochondrial genome. The results suggest that in the studied chromatin mutants, hho1Δ, arp4 and arp4 hho1Δ, the nucleus-mitochondria communication was disrupted, leading to impaired mitochondrial function and premature ageing phenotype in these mutants, especially in the double mutant. Full article
(This article belongs to the Special Issue Genomics of Yeast)
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19 pages, 3145 KiB  
Article
Renewing Lost Genetic Variability with a Classical Yeast Genetics Approach
by Ameya Pankaj Gupte, Debora Casagrande Pierantoni, Angela Conti, Leonardo Donati, Marina Basaglia, Sergio Casella, Lorenzo Favaro, Laura Corte and Gianluigi Cardinali
J. Fungi 2023, 9(2), 264; https://doi.org/10.3390/jof9020264 - 16 Feb 2023
Viewed by 1464
Abstract
Due to their long domestication time course, many industrial Saccharomyces cerevisiae strains are adopted in numerous processes mostly for historical reasons instead of scientific and technological needs. As such, there is still significant room for improvement for industrial yeast strains relying on yeast [...] Read more.
Due to their long domestication time course, many industrial Saccharomyces cerevisiae strains are adopted in numerous processes mostly for historical reasons instead of scientific and technological needs. As such, there is still significant room for improvement for industrial yeast strains relying on yeast biodiversity. This paper strives to regenerate biodiversity with the innovative application of classic genetic methods to already available yeast strains. Extensive sporulation was indeed applied to three different yeast strains, specifically selected for their different origins as well as backgrounds, with the aim of clarifying how new variability was generated. A novel and easy method to obtain mono-spore colonies was specifically developed, and, to reveal the extent of the generated variability, no selection after sporulation was introduced. The obtained progenies were then tested for their growth in defined mediums with high stressor levels. A considerable and strain-specific increase in both phenotypic and metabolomic variability was assessed, and a few mono-spore colonies were found to be of great interest for their future exploitation in selected industrial processes. Full article
(This article belongs to the Special Issue Genomics of Yeast)
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