Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
4.9
4.7
Journals
JoF
Special Issues
Yeast Genetics 2022
share announcement

Yeast Genetics 2022

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 (28 February 2023) | Viewed by 8950

Special Issue Editors

Dr. Ivan-Kresimir Svetec

E-Mail Website
Guest Editor
Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
Interests: yeast molecular genetics; genetic recombination; DNA repair; genome stability
Special Issues, Collections and Topics in MDPI journals
Dr. Marina Svetec Miklenić

E-Mail Website
Guest Editor
Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
Interests: yeast molecular genetics; genetic recombination; DNA repair; non-conventional yeasts

Special Issue Information

Dear Colleagues,

The yeast Saccharomyces cerevisiae, along with being a crucial industrial microorganism, also represents a model organism for the investigation of the majority of biological processes in eukaryotes. This conventional yeast was the first eukariote to be successfully transformed with exogenous DNA. Due to efficient homologous recombination between transforming DNA and its genome, it is easy to precisely genetically modify this yeast, allowing the construction of both biotechnologically relevant strains and strains for application in scientific research. On the other hand, there is a huge number of uncharacterized or poorly characterized nonconventional yeasts, many of which are known to have certain advantages over conventional yeasts, such as efficient use of alternative carbon sources, higher resistance to growth and fermentation inhibitors, production of interesting metabolites, etc. However, for a great majority of these nonconventional yeasts, the construction of desired strains is not yet a routine procedure because the molecular tools needed for precise modification of their genome have not been developed yet. Therefore, this Special Issue focuses on research on the genetics of conventional and nonconventional yeast, as well as development of molecular tools for targeted modification of yeasts and genomes and construction of potentially biotechnologically relevant yeast strains.

Dr. Ivan-Krešimir Svetec
Dr. Marina Svetec Miklenić
Guest Editor

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
  • conventional yeasts
  • nonconventional yeasts
  • genetics
  • genome stability
  • genetic recombination
  • DNA repair
  • gene expression
  • strain construction
  • genetic transformation
  • targeted genetic modification

Related Special Issue

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Other

16 pages, 4135 KiB  
Article
Disruption of the Schizosaccharomyces japonicus lig4 Disturbs Several Cellular Processes and Leads to a Pleiotropic Phenotype
by Lajos Acs-Szabo, Laszlo Attila Papp, Szonja Takacs and Ida Miklos
J. Fungi 2023, 9(5), 550; https://doi.org/10.3390/jof9050550 - 10 May 2023
Viewed by 1345
Abstract
Gene targeting is a commonly used method to reveal the function of genes. Although it is an attractive tool for molecular studies, it can frequently be a challenge because its efficiency can be low and it requires the screening of a large number [...] Read more.
Gene targeting is a commonly used method to reveal the function of genes. Although it is an attractive tool for molecular studies, it can frequently be a challenge because its efficiency can be low and it requires the screening of a large number of transformants. Generally, these problems originate from the elevated level of ectopic integration caused by non-homologous DNA end joining (NHEJ). To eliminate this problem, NHEJ-related genes are frequently deleted or disrupted. Although these manipulations can improve gene targeting, the phenotype of the mutant strains raised the question of whether mutations have side effects. The aim of this study was to disrupt the lig4 gene in the dimorphic fission yeast, S. japonicus, and investigate the phenotypic changes of the mutant strain. The mutant cells have shown various phenotypic changes, such as increased sporulation on complete medium, decreased hyphal growth, faster chronological aging, and higher sensitivity to heat shock, UV light, and caffeine. In addition, higher flocculation capacity has been observed, especially at lower sugar concentrations. These changes were supported by transcriptional profiling. Many genes belonging to metabolic and transport processes, cell division, or signaling had altered mRNA levels compared to the control strain. Although the disruption improved the gene targeting, we assume that the lig4 inactivation can cause unexpected physiological side effects, and we have to be very careful with the manipulations of the NHEJ-related genes. To reveal the exact mechanisms behind these changes, further investigations are required. Full article
(This article belongs to the Special Issue Yeast Genetics 2022)
►▼ Show Figures

Figure 1

13 pages, 1880 KiB  
Article
A Correlation between 3′-UTR of OXA1 Gene and Yeast Mitochondrial Translation
by Maryam Hajikarimlou, Mohsen Hooshyar, Noor Sunba, Nazila Nazemof, Mohamed Taha Moutaoufik, Sadhena Phanse, Kamaledin B. Said, Mohan Babu, Martin Holcik, Bahram Samanfar, Myron Smith and Ashkan Golshani
J. Fungi 2023, 9(4), 445; https://doi.org/10.3390/jof9040445 - 05 Apr 2023
Viewed by 1589
Abstract
Mitochondria possess their own DNA (mtDNA) and are capable of carrying out their transcription and translation. Although protein synthesis can take place in mitochondria, the majority of the proteins in mitochondria have nuclear origin. 3′ and 5′ untranslated regions of mRNAs (3′-UTR and [...] Read more.
Mitochondria possess their own DNA (mtDNA) and are capable of carrying out their transcription and translation. Although protein synthesis can take place in mitochondria, the majority of the proteins in mitochondria have nuclear origin. 3′ and 5′ untranslated regions of mRNAs (3′-UTR and 5′-UTR, respectively) are thought to play key roles in directing and regulating the activity of mitochondria mRNAs. Here we investigate the association between the presence of 3′-UTR from OXA1 gene on a prokaryotic reporter mRNA and mitochondrial translation in yeast. OXA1 is a nuclear gene that codes for mitochondrial inner membrane insertion protein and its 3′-UTR is shown to direct its mRNA toward mitochondria. It is not clear, however, if this mRNA may also be translated by mitochondria. In the current study, using a β-galactosidase reporter gene, we provide genetic evidence for a correlation between the presence of 3′-UTR of OXA1 on an mRNA and mitochondrial translation in yeast. Full article
(This article belongs to the Special Issue Yeast Genetics 2022)
►▼ Show Figures

Figure 1

23 pages, 11957 KiB  
Article
Whole Genome Sequencing Analysis of Effects of CRISPR/Cas9 in Komagataella phaffii: A Budding Yeast in Distress
by Veronika Schusterbauer, Jasmin E. Fischer, Sarah Gangl, Lisa Schenzle, Claudia Rinnofner, Martina Geier, Christian Sailer, Anton Glieder and Gerhard G. Thallinger
J. Fungi 2022, 8(10), 992; https://doi.org/10.3390/jof8100992 - 21 Sep 2022
Cited by 4 | Viewed by 2384
Abstract
The industrially important non-conventional yeast Komagataella phaffii suffers from low rates of homologous recombination, making site specific genetic engineering tedious. Therefore, genome editing using CRISPR/Cas represents a simple and efficient alternative. To characterize on- and off-target mutations caused by CRISPR/Cas9 followed by non-homologous [...] Read more.
The industrially important non-conventional yeast Komagataella phaffii suffers from low rates of homologous recombination, making site specific genetic engineering tedious. Therefore, genome editing using CRISPR/Cas represents a simple and efficient alternative. To characterize on- and off-target mutations caused by CRISPR/Cas9 followed by non-homologous end joining repair, we chose a diverse set of CRISPR/Cas targets and conducted whole genome sequencing on 146 CRISPR/Cas9 engineered single colonies. We compared the outcomes of single target CRISPR transformations to double target experiments. Furthermore, we examined the extent of possible large deletions by targeting a large genomic region, which is likely to be non-essential. The analysis of on-target mutations showed an unexpectedly high number of large deletions and chromosomal rearrangements at the CRISPR target loci. We also observed an increase of on-target structural variants in double target experiments as compared to single target experiments. Targeting of two loci within a putatively non-essential region led to a truncation of chromosome 3 at the target locus in multiple cases, causing the deletion of 20 genes and several ribosomal DNA repeats. The identified de novo off-target mutations were rare and randomly distributed, with no apparent connection to unspecific CRISPR/Cas9 off-target binding sites. Full article
(This article belongs to the Special Issue Yeast Genetics 2022)
►▼ Show Figures

Figure 1

15 pages, 2555 KiB  
Article
Cryptococcus neoformans Prp8 Intein: An In Vivo Target-Based Drug Screening System in Saccharomyces cerevisiae to Identify Protein Splicing Inhibitors and Explore Its Dynamics
by José Alex Lourenço Fernandes, Matheus da Silva Zatti, Thales Domingos Arantes, Maria Fernanda Bezerra de Souza, Mariana Marchi Santoni, Danuza Rossi, Cleslei Fernando Zanelli, Xiang-Qin Liu, Eduardo Bagagli and Raquel Cordeiro Theodoro
J. Fungi 2022, 8(8), 846; https://doi.org/10.3390/jof8080846 - 12 Aug 2022
Viewed by 1631
Abstract
Inteins are genetic mobile elements that are inserted within protein-coding genes, which are usually housekeeping genes. They are transcribed and translated along with the host gene, then catalyze their own splicing out of the host protein, which assumes its functional conformation thereafter. As [...] Read more.
Inteins are genetic mobile elements that are inserted within protein-coding genes, which are usually housekeeping genes. They are transcribed and translated along with the host gene, then catalyze their own splicing out of the host protein, which assumes its functional conformation thereafter. As Prp8 inteins are found in several important fungal pathogens and are absent in mammals, they are considered potential therapeutic targets since inhibiting their splicing would selectively block the maturation of fungal proteins. We developed a target-based drug screening system to evaluate the splicing of Prp8 intein from the yeast pathogen Cryptococcus neoformans (CnePrp8i) using Saccharomyces cerevisiae Ura3 as a non-native host protein. In our heterologous system, intein splicing preserved the full functionality of Ura3. To validate the system for drug screening, we examined cisplatin, which has been described as an intein splicing inhibitor. By using our system, new potential protein splicing inhibitors may be identified and used, in the future, as a new class of drugs for mycosis treatment. Our system also greatly facilitates the visualization of CnePrp8i splicing dynamics in vivo. Full article
(This article belongs to the Special Issue Yeast Genetics 2022)
►▼ Show Figures

Figure 1

Other

Jump to: Research

10 pages, 2326 KiB  
Brief Report
Histone Abundance Quantification via Flow Cytometry of Htb2-GFP Allows Easy Monitoring of Cell Cycle Perturbations in Living Yeast Cells, Comparable to Standard DNA Staining
by Maria V. Kulakova, Eslam S. M. O. Ghazy, Fedor Ryabov, Yaroslav M. Stanishevskiy, Michael O. Agaphonov and Alexander I. Alexandrov
J. Fungi 2023, 9(10), 1033; https://doi.org/10.3390/jof9101033 - 20 Oct 2023
Viewed by 1015
Abstract
Assaying changes in the amount of DNA in single cells is a well-established method for studying the effects of various perturbations on the cell cycle. A drawback of this method is the need for a fixation procedure that does not allow for in [...] Read more.
Assaying changes in the amount of DNA in single cells is a well-established method for studying the effects of various perturbations on the cell cycle. A drawback of this method is the need for a fixation procedure that does not allow for in vivo study nor simultaneous monitoring of additional parameters such as fluorescence of tagged proteins or genetically encoded indicators. In this work, we report on a method of Histone Abundance Quantification (HAQ) of live yeast harboring a GFP-tagged histone, Htb2. We show that it provides data highly congruent with DNA levels, both in Saccharomyces cerevisiae and Ogataea polymorpha yeasts. The protocol for the DNA content assay was also optimized to be suitable for both Ogataea and Saccharomyces yeasts. Using the HAQ approach, we demonstrate the expected effects on the cell cycle progression for several compounds and conditions and show usability in conjunction with additional fluorophores. Thus, our data provide a simple approach that can be utilized in a wide range of studies where the effects of various stimuli on the cell cycle need to be monitored directly in living cells. Full article
(This article belongs to the Special Issue Yeast Genetics 2022)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop